Paper2.bib

@incollection{Altieri2014a,
  ids = {Altieri2014},
  title = {Foundation {{Species}} in {{Marine Ecosystems}}},
  booktitle = {Marine {{Community Ecology}} and {{Conservation}}},
  author = {Altieri, A. H. and {van de Koppel}, J.},
  editor = {Bertness, M. D. and Bruno, J. F. and Silliman, B. R. and Stachowicz, J. J.},
  year = {2014},
  pages = {37--56},
  publisher = {{Sinauer Associates, Inc.}},
  address = {{Sunderland, MA}},
  isbn = {978-1-60535-228-2}
}

@article{Anderson1992,
  title = {Diversity of Eukaryotic Algae},
  author = {Anderson, R. A.},
  year = {1992},
  journal = {Biodiversity and Conservation},
  volume = {1},
  pages = {267--292}
}

@article{Archer2017,
  ids = {archer2017a},
  title = {Abiotic Conditions Drive Significant Variability in Nutrient Processing by a Common {{Caribbean}} Sponge, {{{\emph{Ircinia}}}}{\emph{ Felix}}},
  author = {Archer, Stephanie K. and Stevens, Julia L. and Rossi, Ryann E. and Matterson, Kenan O. and Layman, Craig A.},
  year = {2017},
  month = jul,
  journal = {Limnology and Oceanography},
  volume = {62},
  number = {4},
  pages = {1783--1793},
  issn = {0024-3590, 1939-5590},
  doi = {10.1002/lno.10533},
  abstract = {Coral reefs typically occur in oligotrophic waters, where tight recycling of energy and nutrients is essential in order to support their high productivity. Sponges are efficient filter feeders that host diverse and abundant microbial communities that often contain members capable of carrying out complex nutrient transformations. Consequently, sponges often act as significant sources of bioavailable forms of nitrogen and phosphorus while acting as sinks for dissolved organic carbon (DOC). However, little attention has focused on variability of nutrient release by sponges and no studies have reported how abiotic conditions may impact sponge-driven changes in nutrient concentrations. Here, we show that a common Caribbean sponge, Ircinia felix, is capable of being both a source and a sink for DOC, ammonium, nitrate/nitrite (NO2x ), and phosphate (PO432). Additionally, we show that abiotic conditions, particularly ambient nutrient availability, seem to explain a significant amount of the variability (R2 range from 0.40 to 0.65). Interestingly, as ambient nutrient concentrations increased, I. felix transitioned from acting as a source to serving as a sink for all nutrient forms measured. We also found I. felix-associated bacteria exhibit a significantly higher abundance of predicted nitrogen metabolism, carbon fixation, and photosynthetic genes relative to ambient water and sediment. These results suggest that sponges play an important and dynamic role in biogeochemical cycling on reefs, particularly as human activities alter natural nutrient dynamics in coastal systems.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\33V6NC6F\\Archer et al. - 2017 - Abiotic conditions drive significant variability i.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\WMHR4DA4\\Archeretal_2017.pdf}
}

@article{Archer2021a,
  ids = {Archer2021},
  title = {Sponges Facilitate Primary Producers in a {{Bahamas}} Seagrass System},
  author = {Archer, Stephanie K. and English, Philina A. and Campanino, Finella M. and Layman, Craig A.},
  year = {2021},
  month = oct,
  journal = {Marine Biology},
  volume = {168},
  number = {11},
  pages = {162},
  issn = {1432-1793},
  doi = {10.1007/s00227-021-03977-x},
  abstract = {Seagrass beds are important coastal ecosystems worldwide that are shaped by facilitative interactions. Consequently, it is important to identify which taxa facilitate seagrasses. In other ecosystems, sponges contribute to the maintenance of diverse and productive systems through their facilitation of foundation species (e.g., mangroves) and the retention and recycling of energy and nutrients. Sponges are common in tropical and subtropical seagrass beds, yet we know little about how their presence impacts these communities. Here, we examine the impact of the sponge Ircinia felix on primary producers in a Thalassia testudinum dominated seagrass bed using a long-term field experiment in The Bahamas. We transplanted live sponges into the center of 5\,\texttimes\,5~m plots and monitored the response of seagrasses and macroalgae. Sponge presence increased seagrass nutrient content and growth, as well as the abundance of macroalgae and non-dominant seagrass species (Syringodium filiforme and Halodule wrightii). These changes were not seen in the control (unmanipulated) or structure (where we placed a polypropylene sponge replica) plots. We conclude that I. felix facilitates seagrass bed primary producers in oligotrophic systems, likely due to nutrients supplied by the sponge. Our study shows that sponges can have a positive influence on seagrass bed foundation species. Since recent theoretical work emphasizes the potential for facilitative interactions involving foundation species to be destabilized in the face of anthropogenic change, further work, is needed to understand how this facilitation impacts the stability of seagrass beds in areas where human activities have increased ambient nutrient levels.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\BAEZI864\\Archer et al. - 2021 - Sponges facilitate primary producers in a Bahamas .pdf;C\:\\Users\\sarcher\\Zotero\\storage\\NAWSCSYM\\Archer et al. - 2021 - Sponges facilitate primary producers in a Bahamas .pdf}
}

@article{Arrivillaga1999,
  title = {Comparison of {{Fishes}} and {{Macroinvertebrates}} on Seagrass and Bare-Sand Sites on {{Guatemala}}'s {{Atlantic}} Coast},
  author = {Arrivillaga, Alejandro and Baltz, Donald M.},
  year = {1999},
  journal = {Bulletin of Marine Science},
  volume = {65},
  number = {2},
  pages = {301--319},
  abstract = {We describe the diversity and abundance of fishes and macroinvertebrates inhabiting sandy, shallow water seagrass and adjacent bare-sand sites near Bah\'ia La Graciosa, on the Atlantic coast of Guatemala, to assess the relative importance of turtle grass (Thalassia testudinum) meadows as nurseries. Twenty-six samples (13 on each strata) were collected with a cylindrical drop sampler (1.18 m2) during 14\textendash 17 December 1993. Microhabitat data, including mean depth, water temperature, turbidity, mid-water column velocity, distance to the shore, substrate percent sand content, salinity, dissolved oxygen concentration, and percent of the bottom covered by seagrass were recorded. Means for seagrass coverage, biomass, and leaf surface area index were 79.6\%, 44.2 g dry wt m-2, and 1.1 m2 m-2, respectively, on seagrass sites. Total crustacean and fish abundances were significantly higher (P {$<$} 0.01) by a factor of seven and 20 times, respectively, on seagrasses than on bare-sand sites, but no significant differences (P {$>$} 0.05) were detected for gastropods. The species diversity and evenness of fishes and crustaceans were both also significantly higher (P {$<$} 0.01) in seagrass samples. Seagrass fishes included 19 species and were numerically dominated by juvenile Haemulon steindachnery. The only fish present in bare-sand sites was Dactiloscopus poeyi, which was second in overall abundance. Other abundant seagrass fishes were Nicholsina usta and Halichoeres pictus. The most abundant crustacean species was the hermit crab, Pagurus critinicornis, followed by the longtail grass shrimp, Periclimenes longicaudatus, and the marsh grass shrimp, Palemonetes vulgaris. The dominant gastropod species was Nassarius polygonatus, followed by Nerita virginica and Jaspidella jaspidea. The size of seagrass fishes ranged from 12 to 69 mm standard length, and the majority (83\%) were early juveniles, supporting the hypothesis of seagrasses as an important nursery for fishes.}
}

@article{Barry2021,
  title = {Variation in {{Seagrass-Associated Macroinvertebrate Communities Along}} the {{Gulf Coast}} of {{Peninsular Florida}}: {{An Exploration}} of {{Patterns}} and {{Ecological Consequences}}},
  shorttitle = {Variation in {{Seagrass-Associated Macroinvertebrate Communities Along}} the {{Gulf Coast}} of {{Peninsular Florida}}},
  author = {Barry, Savanna C. and Hyman, A. Challen and Jacoby, Charles A. and Reynolds, Laura K. and Kowalewski, Michal and Frazer, Thomas K.},
  year = {2021},
  journal = {Frontiers in Marine Science},
  volume = {8},
  issn = {2296-7745},
  abstract = {Seagrasses form vast meadows of structurally complex habitat that support faunal communities with greater numbers of species and individuals than nearby unstructured habitats. The Gulf coast of peninsular Florida represents a natural laboratory ideally suited to the study of processes that shape seagrass-associated invertebrate and fish communities within meadows of a single species of seagrass, Thalassia testudinum. This suitability arises from a pronounced structural and chemical gradient that exists over ecologically relevant spatial and temporal scales, as revealed by extensive monitoring of water quality and seagrass. We hypothesized that seagrass-associated invertebrate communities would vary across five estuarine systems spread along a spatial gradient in phosphorus concentration, an important driver of seagrass and phytoplankton growth in this region. The quantitative results based on data acquired at 25 stations (75 samples, 52,086 specimens, and 161 taxa) indicated that each of the five estuarine systems were distinct with regard to species composition and differences among systems were driven by abundant or relatively common species. In addition, we found evidence to indicate food webs in seagrass meadows along this gradient may differ, especially in the relative dominance of algal grazers and predatory invertebrates. These changes in species composition and trophic roles could be driven by phosphorus directly, through increases in rates of primary production with higher concentrations of phosphorus, or indirectly, through nutrient-mediated changes in the physical structure of the seagrass canopy. Our results suggest that differences in the habitat created by T. testudinum under differing phosphorus supplies lead to ecologically significant shifts in macroinvertebrate communities.},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\RWQ9JSWN\\Barry et al. - 2021 - Variation in Seagrass-Associated Macroinvertebrate.pdf}
}

@article{Beazley2013,
  title = {Deep-Sea Sponge Grounds Enhance Diversity and Abundance of Epibenthic Megafauna in the {{Northwest Atlantic}}},
  author = {Beazley, Lindsay I. and Kenchington, Ellen L. and Murillo, Francisco Javier and Sacau, Mar{\'i}a del Mar},
  year = {2013},
  month = nov,
  journal = {ICES Journal of Marine Science},
  volume = {70},
  number = {7},
  pages = {1471--1490},
  issn = {1054-3139},
  doi = {10.1093/icesjms/fst124},
  abstract = {Beazley, L. I., Kenchington E. L., Murillo, F. J., and Sacau, M. 2013. Deep-sea sponge grounds enhance diversity and abundance of epibenthic megafauna in the Northwest Atlantic. \textendash{} ICES Journal of Marine Science, 70: .The influence of structure-forming deep-water sponge grounds on the composition, diversity, and abundance of the local epibenthic megafaunal community of the Flemish Pass area, Northwest Atlantic was statistically assessed. These habitats are considered vulnerable marine ecosystems and, therefore, warrant conservation measures to protect them from bottom fishing activities. The epibenthic megafauna were quantified from four photographic transects, three of which were located on the western slope of the Flemish Cap with an overall depth range of 444\textendash 940 m, and the fourth in the southern Flemish Pass between 1328 and 1411 m. We observed a diverse megafaunal community dominated by large numbers of ophiuroids and sponges. On the slope of the Flemish Cap, sponge grounds were dominated by axinellid and polymastid sponges, while the deeper sponge ground in the southern Flemish Pass was formed mainly by geodiids and Asconema sp. The presence of structure-forming sponges was associated with a higher biodiversity and abundance of associated megafauna compared with non-sponge habitat. The composition of megafauna significantly differed between sponge grounds and non-sponge grounds and also between different sponge morphologies. Surface chlorophyll a and near-bottom salinity were important environmental determinants in generalized linear models of megafaunal species richness and abundance.},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\CHPRN6JZ\\Beazley et al. - 2013 - Deep-sea sponge grounds enhance diversity and abun.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\WHDMX5QG\\610631.html}
}

@article{Bell1986,
  title = {Importance of Local Changes in Leaf Height and Density to Fish and Decapods Associated with Seagrasses},
  author = {Bell, Johann D. and Westoby, Mark},
  year = {1986},
  month = dec,
  journal = {Journal of Experimental Marine Biology and Ecology},
  volume = {104},
  number = {1},
  pages = {249--274},
  issn = {0022-0981},
  doi = {10.1016/0022-0981(86)90109-7},
  abstract = {The height and density of seagrass leaves were manipulated to about one-third normal levels to test whether associated fish and decapods were affected. The experiments tested for effects of height, density and their interaction, and were run separately in single beds of Zostera capricorni Aschers, and Posidoniaaustralis Hook f. to determine if effects were consistent for each seagrass. Abundances of individual species were often affected significantly by the manipulations. In Zostera, abundances of six species decreased when leaves were shortened, whereas abundances of three species increased, and seven species decreased, when leaves were thinned. In Posidonia, abundances of four species decreased when leaves were shortened, while abundances of two species increased and five decreased when leaves were thinned. Significant height \texttimes{} density interactions did not occur for any of the 13 species analysed from Zostera, but did occur for two of the 12 species from Posidonia. Several species, in both seagrasses, did not respond to the manipulations. Of the six species that were analysed in both seagrasses, four responded in the same way to height and density, and a fifth species responded consistently to height. There were significant effects on the number of individuals in feeding guilds. However, effects on guilds masked (opposite) effects, and the lack of effects, for component species, and showed little consistency between Zostera and Posidonia. This was also true for effects on the total number of individuals. The data do not support an existing model predicting responses of species richness and abundance to changes in physical complexity of seagrasses.},
  langid = {english},
  keywords = {Feeding guilds,Field experiments,Habitat complexity,Organization of communities},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\T48RQTF2\\Bell and Westoby - 1986 - Importance of local changes in leaf height and den.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\SP7KVE7R\\0022098186901097.html}
}

@article{Bell2008a,
  title = {The Functional Roles of Marine Sponges},
  author = {Bell, J. J.},
  year = {2008},
  month = sep,
  journal = {Estuarine Coastal and Shelf Science},
  volume = {79},
  number = {3},
  pages = {341--353},
  issn = {0272-7714},
  doi = {10.1016/j.ecss.2008.05.002},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\SRM6QBS7\\bell2008.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\XVWHCYE8\\Bell_2008_The functional roles of marine sponges.pdf}
}

@article{Brook1977,
  title = {Trophic {{Relationships}} in a {{Seagrass Community}} ({{Thalassia}} Testudinum), in {{Card Sound}}, {{Florida}}. {{Fish Diets}} in {{Relation}} to {{Macrobenthic}} and {{Cryptic Faunal Abundance}}},
  author = {Brook, Iver M.},
  year = {1977},
  month = may,
  journal = {Transactions of the American Fisheries Society},
  volume = {106},
  number = {3},
  pages = {219--229},
  publisher = {{Taylor \& Francis}},
  issn = {0002-8487},
  doi = {10.1577/1548-8659(1977)106<219:TRIASC>2.0.CO;2},
  abstract = {Seagrass communities are a major feature of shallow marine areas throughout the world. The marine spermatophyte Thalassia testudinum is the dominant seagrass in southeast Florida and the Florida Gulf coast. The trophic interaction between the fishes and the macrobenthic and cryptic fauna found in the area was examined. Based on digestive tract analysis, the principal interaction between the primary consumers of the study area and the higher trophic level predators was via the polychaetes and peracaridean crustaceans. The mollusks which contributed significantly to the benthic biomass were not a preferred food for the animals frequenting the study site. The maximum mollusk biomass in any benthic and cryptic sample was 2.31 g dry/m2. It was felt that the predator population was limited by the small stock of polychaetes and peracaridean crustaceans which had a maximum biomass in any one sample equivalent to 1.74 g dry/m2. The majority of the fishes captured were foragers over a wide area. The main residents were the syngnathids and the gold-spotted killifish, Floridichthys carpio.},
  annotation = {\_eprint: https://doi.org/10.1577/1548-8659(1977)106{$<$}219:TRIASC{$>$}2.0.CO;2},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\7336D5E3\\1548-8659(1977)106219TRIASC2.0.html}
}

@article{Brooks2017a,
  ids = {Brooks2017},
  title = {{{glmmTMB}} Balances Speed and Flexibility among Packages for Zero-Inflated Generalized Linear Mixed Modeling},
  author = {Brooks, Mollie E. and Kristensen, Kasper and {van Benthem}, Koen J. and Magnusson, Arni and Berg, Casper W. and Nielsen, Anders and Skaug, Hans J. and Maechler, Martin and Bolker, Benjamin M.},
  year = {2017},
  journal = {The R Journal},
  volume = {9},
  number = {2},
  pages = {378--400},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\66AL5288\\Brooks et al. - 2017 - glmmTMB Balances Speed and Flexibility Among Packa.pdf}
}

@incollection{Bruno2001a,
  ids = {Bruno2001},
  title = {Habitat Modification and Facilitation in Benthic Marine Communities},
  booktitle = {Marine {{Community Ecology}}},
  author = {Bruno, J. F. and Bertness, M. D.},
  editor = {Bertness, M.D.},
  year = {2001},
  pages = {201--218},
  publisher = {{Sinauer}}
}

@article{Butler1995,
  title = {Cascading Disturbances in {{Florida}} Bay, {{USA}}: {{Cyanobacteria}} Blooms, Sponge Mortality, and Implications for Juvenile Spiny Lobsters {{Panulirus}} Argus},
  author = {Butler, M. J. and Hunt, J. H. and Herrnkind, W. F. and Childress, M. J. and Bertelsen, R. and Sharp, W. and Matthews, T. and Field, J. M. and Marshall, H. G.},
  year = {1995},
  month = dec,
  journal = {Marine Ecology Progress Series},
  volume = {129},
  number = {1-3},
  pages = {119--125},
  issn = {0171-8630},
  doi = {10.3354/meps129119},
  abstract = {Florida Bay, the shallow lagoon separating mainland Florida and the Florida Keys, USA, is experiencing an unprecedented series of ecological disturbances. In 1991, following reports of other ecosystem perturbations, we observed widespread and persistent blooms of cyanobacteria that coincided with the decimation of sponge communities over hundreds of square kilometers. Juvenile Caribbean spiny lobsters Panulirus argus, among other animals, rely on sponges for shelter; the impact of sponge loss on the abundance of lobsters and their use of shelter, in particular, has been dramatic. The loss of sponges on 27 experimental sites in hard bottom habitat in central Florida Bay resulted in the redistribution of juvenile lobsters among the remaining shelters, an influx of lobsters into sites where artificial shelters were present, and a decline in lobster abundances on sites without artificial shelters. Diver surveys of sponge damage at additional sites in central Florida Bay confirmed that the sponge die-off was widespread and its occurrence coincided with areas that had been exposed to the cyanobacteria bloom. This cascade of disturbances has dramatically altered the community structure of affected hard bottom areas and demonstrates the coupled dynamics of this shallow marine ecosystem.},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\JPD9U3GE\\butleretal1995.pdf}
}

@article{Butler2016a,
  ids = {Butler2016},
  title = {Underwater Soundscapes in Near-Shore Tropical Habitats and the Effects of Environmental Degradation and Habitat Restoration},
  author = {Butler, Jack and Stanley, Jenni A and Butler, Mark J},
  year = {2016},
  journal = {Journal of Experimental Marine Biology and Ecology},
  volume = {479},
  pages = {89--96},
  issn = {0022-0981},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\6EU2IBJG\\Butleretal2016.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\KZSZK4TK\\Butleretal2016.pdf}
}

@article{Byers2006,
  title = {Using Ecosystem Engineers to Restore Ecological Systems},
  author = {Byers, James E. and Cuddington, Kim and Jones, Clive G. and Talley, Theresa S. and Hastings, Alan and Lambrinos, John G. and Crooks, Jeffrey A. and Wilson, William G.},
  year = {2006},
  journal = {Trends in Ecology \& Evolution},
  volume = {21},
  number = {9},
  pages = {493--500},
  issn = {0169-5347},
  doi = {10.1016/j.tree.2006.06.002},
  abstract = {Ecosystem engineers affect other organisms by creating, modifying, maintaining or destroying habitats. Despite widespread recognition of these often important effects, the ecosystem engineering concept has yet to be widely used in ecological applications. Here, we present a conceptual framework that shows how consideration of ecosystem engineers can be used to assess the likelihood of restoration of a system to a desired state, the type of changes necessary for successful restoration and how restoration efforts can be most effectively partitioned between direct human intervention and natural ecosystem engineers.}
}

@article{Carman2016,
  title = {Distribution and Diversity of Tunicates Utilizing Eelgrass as Substrate in the Western {{North Atlantic}} between 39\textdegree{} and 47\textdegree{} North Latitude ({{New Jersey}} to {{Newfoundland}})},
  author = {Carman, Mary R. and Colarusso, Philip D. and Nelson, Eric P. and Grunden, David W. and Wong, Melisa C. and McKenzie, Cynthia and Matheson, Kyle and Davidson, Jeff and Fox, Sophia and Neckles, Hilary A. and Bayley, Holly and Schott, Stephen and Dijkstra, Jennifer A. and {Stewart-Clark}, Sarah},
  year = {2016},
  month = mar,
  journal = {Management of Biological Invasions},
  volume = {7},
  number = {1},
  pages = {51--57},
  publisher = {{Regional Euro-Asian Biological Invasions Centre}},
  address = {{Almer\'ia, Finland}},
  abstract = {Seagrass meadows are ecologically important habitats that are declining globally at an accelerating rate due to natural and anthropogenic stressors. Their decline is a serious concern as this habitat provides many ecosystem services. Eelgrass (Zostera marina) is the dominant seagrass species in the western North Atlantic. It has recently been established that invasive tunicate species possibly threaten the health of eelgrass beds. Colonization of eelgrass leaves by tunicates can inhibit eelgrass growth and may cause shoot mortality. To document the distribution and diversity of tunicate species that attach to eelgrass in the western North Atlantic, we surveyed twenty-one eelgrass sites from New Jersey to Newfoundland. Eight species of tunicates were found to be colonizing eelgrass, of which 6 are considered invasive. Botrylloides violaceus and Botryllus schlosseri were most commonly attached to eelgrass, with B. schlosseri having the largest latitudinal range of any species. Tunicate faunas attached to eelgrass were less diverse north of Gloucester, Massachusetts, where individual survey sites exhibited two species at most and only 4 of the 8 species observed in this study. Percent tunicate cover on eelgrass tended to fall within the 1\textendash 25 range, with occasional coverage up to {$>$}75\textendash 100. Density of eelgrass was highly variable among sites, ranging from {$<$}1 to 820 shoots/m{$^2$}. The solitary tunicate Ciona intestinalis was only found on eelgrass at the highest latitude sampled, in Newfoundland, where it is a new invader. The tunicates observed in this study, both solitary and colonial, are viable when attached to eelgrass and pose a potential threat to overgrow and weaken seagrass shoots and reduce the sustainability of seagrass meadows.},
  chapter = {Research articles},
  copyright = {\textcopyright{} 2016. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the associated terms available at https://www.reabic.net/journals/mbi/About.aspx},
  langid = {english},
  keywords = {Biology,Botryllus schlosseri,Colonization,Latitude,Shoots,Species,Tunicata},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\U28XJQZU\\Carman et al. - 2016 - Distribution and diversity of tunicates utilizing .pdf}
}

@article{Cervigon1966,
  title = {Los {{Peces Marinos}} de {{Venezuela}}},
  author = {Cervigon, M. F.},
  year = {1966},
  journal = {Caracas: Fundacion la salle de Ciencias Naturales},
  volume = {I \& II}
}

@article{CocheretdelaMoriniere2003,
  title = {Diet Shifts of {{Caribbean}} Grunts ({{Haemulidae}}) and Snappers ({{Lutjanidae}}) and the Relation with Nursery-to-Coral Reef Migrations},
  author = {{Cocheret de la Morini{\`e}re}, E. and Pollux, B. J. A. and Nagelkerken, I. and {van der Velde}, G.},
  year = {2003},
  month = aug,
  journal = {Estuarine, Coastal and Shelf Science},
  volume = {57},
  number = {5},
  pages = {1079--1089},
  issn = {0272-7714},
  doi = {10.1016/S0272-7714(03)00011-8},
  abstract = {The spatial size distribution of grunts and snappers have previously indicated the separation of juveniles in nursery habitats from the adults on the coral reef. This implies life cycle migrations from nursery habitats (such as seagrass beds and mangroves) to the coral reef. If diet shifts are related to such migrations, then the diets of these fish must change before or around the fish size at which such migrations take place. A wide size range of juveniles of two grunt species (Haemulon sciurus and Haemulon flavolineatum) and of two snapper species (Lutjanus apodus and Ocyurus chrysurus) were caught in seagrass beds and mangroves, and their gut contents identified and quantified. Regression analysis between fish size and dietary importance of small crustaceans showed a negative relationship in all four species. Positive relations were found for H. sciurus, L. apodus and O. chrysurus between fish length and the dietary importance of decapods, and for L. apodusand O. chrysurus between fish length and prey fish importance. Critical changes in the fish diets with fish size were examined by application of a Canonical Correspondence Analysis (CCA). The CCA yielded three clusters of size-classes of fishes with similar diets, and application of a Mantel test showed that each of these clusters had significantly different diets, and that each cluster diet was significantly specialised. The size at which a fish species `switched' from one cluster to another was compared with size-at-maturity data and with the typical size at which these species migrate from the nursery habitats to the coral reef. H. sciurus and H. flavolineatum may be prompted to migrate from the nursery habitats to coral reef habitats because of dietary changes, or because of the development of the gonads. For L. apodus and O. chrysurus, a dietary changeover forms a more likely explanation for nursery-to-reef migrations than does sexual maturation because these species reach maturity at sizes much larger than the maximum size of individuals found in nursery habitats. Although other factors may theoretically initiate or promote the migration patterns, the results of this study indicate that ontogenetic dietary changes may crucially influence the nursery-to-coral reef migrations of these reef fish species.},
  langid = {english},
  keywords = {diet shifts,nursery habitats,nursery-to-reef migration},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\WZ653QX3\\Cocheret de la Morinière et al. - 2003 - Diet shifts of Caribbean grunts (Haemulidae) and s.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\EMR9MDRD\\S0272771403000118.html}
}

@article{Coleman2002,
  title = {Overexploiting Marine Ecosystem Engineers: Potential Consequences for Biodiversity},
  author = {Coleman, Felicia C. and Williams, Susan L.},
  year = {2002},
  journal = {Trends in Ecology \& Evolution},
  volume = {17},
  number = {1},
  pages = {40--44},
  doi = {10.1016/S0169-5347(01)02330-8},
  abstract = {Overfishing is a major environmental problem in the oceans. In addition to the direct loss of the exploited species, the very act of fishing, particularly with mobile bottom gear, destroys habitat and ultimately results in the loss of biodiversity. Furthermore, overfishing can create trophic cascades in marine communities that cause similar declines in species richness. These effects are compounded by indirect effects on habitat that occur through removal of ecological or ecosystem engineers. Mass removal of species that restructure the architecture of habitat and thus increase its complexity or influence the biogeochemistry of sediments could have devastating effects on local biodiversity and important water\textendash sediment processes. The possible overexploitation of engineering species requires more attention because the consequences extend beyond their own decline to affect the rest of the ecosystem. This is particularly problematic in the deep ocean, where oil and gas exploration and fishing pressure are likely to increase.}
}

@article{D.Bell1986,
  title = {Variation in Seagrass Height and Density over a Wide Spatial Scale: {{Effects}} on Common Fish and Decapods},
  shorttitle = {Variation in Seagrass Height and Density over a Wide Spatial Scale},
  author = {D. Bell, Johann and Westoby, Mark},
  year = {1986},
  month = dec,
  journal = {Journal of Experimental Marine Biology and Ecology},
  volume = {104},
  number = {1},
  pages = {275--295},
  issn = {0022-0981},
  doi = {10.1016/0022-0981(86)90110-3},
  abstract = {This study examines whether relationships between abundances of fishes and decapods and the leaf height and density of seagrass determined from small scale field experiments within a seagrass bed were also evident at a wider spatial scale, i.e. among beds within a bay. Separate comparisons were made for common species of fishes and decapods associated with the seagrasses Zostera capricorni Aschers, and Posidonia australis Hook f. Of the 23 significant responses by species to leaf height or density in the small scale experimental study, 15 were not repeated at the wider scale. Abundances of species with inconsistent responses at the two scales were not correlated meaningfully with other major environmental variables such as sediment size, area of seagrass bed or distance from the ocean. We reconcile the high incidence of effects of leaf height and density within beds, and their scarcity among beds, with a model of how postlarvae settle into, and move within, seagrass beds. The model holds that (1) larvae of fishes and decapods are distributed patchily when ready to settle, (2) larvae do not discriminate among beds when they settle, and (3) individuals do not leave a bed soon after settling but do redistribute within the bed to select microsites favouring survival.},
  langid = {english},
  keywords = {Decapods,Fishes,Habitat complexity,Larval settlement,Stochastic recruitment},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\N9WLJYJ8\\D. Bell and Westoby - 1986 - Variation in seagrass height and density over a wi.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\VIFWVE3L\\0022098186901103.html}
}

@article{Dayton1972,
  title = {Toward an Understanding of Community Resilience and the Potential Effects of Enrichments to the Benthos at {{McMurdo Sound}}, {{Antarctica}}},
  author = {Dayton, Paul K.},
  year = {1972},
  journal = {Proceedings of the Colloquium on Conservation Problems in Antarctica},
  pages = {81--95},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\ITA9RW3E\\Dayton72_Understanding.pdf}
}

@article{Demers2016,
  title = {Under the Radar: {{Sessile}} Epifaunal Invertebrates in the Seagrass {{{\emph{Posidonia}}}}{\emph{ Australis}}},
  shorttitle = {Under the Radar},
  author = {Demers, Marie-Claire A. and Knott, Nathan A. and Davis, Andrew R.},
  year = {2016},
  month = mar,
  journal = {Journal of the Marine Biological Association of the United Kingdom},
  volume = {96},
  number = {2},
  pages = {363--377},
  issn = {0025-3154, 1469-7769},
  doi = {10.1017/S0025315415000612},
  abstract = {Despite the current global decline in seagrass, sessile epifaunal invertebrates inhabiting seagrass ecosystems, particularly sponges and ascidians, have been poorly studied due to their taxonomic complexity. Understanding patterns of distribution of sessile epifaunal communities in seagrass meadows is an important precursor to determining the processes driving their distribution and species interactions. This study (1) identified the sponge and ascidian assemblage associated with Posidonia australis meadows and (2) determined distributional patterns of these invertebrates at a hierarchy of spatial scales in Jervis Bay, Australia. We used a fully nested design with transects distributed in the seagrass (10s m apart), two sites (100s m apart), and six locations (km apart). Within these transects, we recorded the abundance, volume, diversity and substratum used for attachment by sponges and ascidians. We encountered 20 sponge species and eight ascidian species; they were sporadically distributed in the seagrass meadows with high variability among the transects, sites and locations. A few sponge and ascidian species dominated the assemblage and were widespread across the largest spatial scale sampled. The remaining species were mostly rare and sparsely distributed. Sponges attached to a variety of substrata but most notably shells, P. australis and polychaete tubes. No obligate seagrass species were recorded although three species predominantly used P. australis as a substratum. These sponge species relying heavily on seagrass for their attachment are likely prone to disturbances impacting their host habitat. Examining the response of sessile epifauna to the degradation of their seagrass habitat remains a key challenge for the future.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\7CAQGRZK\\Demers et al. - 2016 - Under the radar Sessile epifaunal invertebrates i.pdf}
}

@article{Diaz1997,
  title = {Sponge-Mediated Nitrification in Tropical Benthic Communities},
  author = {Diaz, M. C. and Ward, B. B.},
  year = {1997},
  journal = {Marine Ecology Progress Series},
  volume = {156},
  pages = {97--107},
  issn = {0171-8630},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\IB7JYU35\\DiazandWard1997.pdf}
}

@article{Diaz2005a,
  title = {Common Sponges from Shallow Marine Habitats from {{Bocas}} Del {{Toro}} Region, {{Panama}}},
  author = {Diaz, M. C.},
  year = {2005},
  journal = {Caribbean Journal of Science},
  volume = {41},
  number = {3},
  pages = {465--475},
  issn = {0008-6452},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\KNB9IS4H\\Diaz2005.pdf}
}

@article{Duffy1996,
  title = {Eusociality in a Coral-Reef Shrimp},
  author = {Duffy, J.Emmett},
  year = {1996},
  month = jun,
  journal = {Nature},
  volume = {381},
  number = {6582},
  pages = {512--514},
  issn = {0028-0836, 1476-4687},
  doi = {10.1038/381512a0},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\5SS42AGV\\Duffy - 1996 - Eusociality in a coral-reef shrimp.pdf}
}

@article{Duffy2006,
  ids = {duffy2006a},
  title = {Biodiversity and the Functioning of Seagrass Ecosystems},
  author = {Duffy, Je},
  year = {2006},
  month = apr,
  journal = {Marine Ecology Progress Series},
  volume = {311},
  pages = {233--250},
  issn = {0171-8630, 1616-1599},
  doi = {10.3354/meps311233},
  abstract = {Biodiversity at multiple levels \textemdash{} genotypes within species, species within functional groups, habitats within a landscape \textemdash{} enhances productivity, resource use, and stability of seagrass ecosystems. Several themes emerge from a review of the mostly indirect evidence and the few experiments that explicitly manipulated diversity in seagrass systems. First, because many seagrass communities are dominated by 1 or a few plant species, genetic and phenotypic diversity within such foundation species has important influences on ecosystem productivity and stability. Second, in seagrass beds and many other aquatic systems, consumer control is strong, extinction is biased toward large body size and high trophic levels, and thus human impacts are often mediated by interactions of changing `vertical diversity' (food chain length) with changing `horizontal diversity' (heterogeneity within trophic levels). Third, the openness of marine systems means that ecosystem structure and processes often depend on interactions among habitats within a landscape (landscape diversity). There is clear evidence from seagrass systems that advection of resources and active movement of consumers among adjacent habitats influence nutrient fluxes, trophic transfer, fishery production, and species diversity. Future investigations of biodiversity effects on processes within seagrass and other aquatic ecosystems would benefit from broadening the concept of biodiversity to encompass the hierarchy of genetic through landscape diversity, focusing on links between diversity and trophic interactions, and on links between regional diversity, local diversity, and ecosystem processes. Maintaining biodiversity and biocomplexity of seagrass and other coastal ecosystems has important conservation and management implications.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\8DAPHCKT\\Duffy2006.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\QGU8XWET\\Duffy - 2006 - Biodiversity and the functioning of seagrass ecosy.pdf}
}

@article{Edgar1992,
  title = {The Influence of Seagrass Structure on the Distribution and Abundance of Mobile Epifauna: Pattern and Process in a {{Western Australian Amphibolis}} Bed},
  shorttitle = {The Influence of Seagrass Structure on the Distribution and Abundance of Mobile Epifauna},
  author = {Edgar, Graham J. and Robertson, Alistar I.},
  year = {1992},
  month = sep,
  journal = {Journal of Experimental Marine Biology and Ecology},
  volume = {160},
  number = {1},
  pages = {13--31},
  issn = {0022-0981},
  doi = {10.1016/0022-0981(92)90107-L},
  abstract = {Patches within a mixed bed of the seagrasses Amphibolis antarctica and Amphibolis griffithii were manipulated in three ways: by the removal of epiphytes, by the removal of leaves, and by altering seagrass density. 1 month after the manipulation, large differences remained between the faunas inhabiting the variously treated patches. Leaf removal and epiphyte removal decreased total abundances by 64 and 31\%, respectively, with the majority of the common species being negatively affected by one or the other of these treatments but not both. Three species significantly increased in abundance in the leaf removal treatment and were not affected by the removal of epiphytes. The fauna inhabiting Amphibolis beds therefore can be subdivided into relatively independent leaf-associated and epiphyte-associated assemblages, with a small additional assemblage of animals, possibly associated with plant stems, which was negatively affected by the presence of leaves. Four species of mollusc required both epiphyte and leaf habitats, thus providing some overlap between the two major assemblages. When seagrass plant density was reduced by half, major changes in the three faunal assemblages occurred which were almost identical to those caused by the leaf removal manipulation. The faunal densities (g-1 seagrass) of all species negatively affected by leaf removal decreased in reduced density reduction treatment while the densities of species in the epiphyte-associated assemblage showed no significant differences when compared with control patches. Species which increased in abundance in the leaf removal treatment were more abundant in the reduced density seagrass patches than in the control patches. Field experiments carried out subsequent to the seagrass manipulation experiment showed that a change in the leaf-associated faunal assemblage similar to that identified in the seagrass density reduction treatment occurred in {$<$}4 d when seagrass plants were placed in the open, and that the settlement rates of animals onto isolated seagrass plants were generally similar to the settlement rates amongst dense Amphibolis. Caging experiments further showed that a reduction in faunal densities occurred on seagrass plants in the open even when plants were enclosed in 10-mm mesh cages, hence predation by fish or decapod predators was unlikely to be the proximate cause for the faunal decline on open seagrasses. Epifauna associated with seagrass leaves at our shallow Seven Mile Beach site appear to actively select dense seagrass habitats, possibly because of evolutionary selection to minimize predation or to avoid high levels of solar radiation.},
  langid = {english},
  keywords = {Epifauna,Epiphyte,Habitat selection,Predator,Seagrass,Western Australia},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\64KJHTXF\\Edgar and Robertson - 1992 - The influence of seagrass structure on the distrib.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\RX8X6WM8\\002209819290107L.html}
}

@article{Eggleston1998,
  title = {Ontogenetic {{Diet Shifts}} in {{Nassau Grouper}}: {{Trophic Linkages}} and {{Predatory Impact}}},
  author = {Eggleston, David B and Grover, Jill J and Lipcius, Romuald N},
  year = {1998},
  journal = {BULLETIN OF MARINE SCIENCE},
  volume = {63},
  number = {1},
  pages = {16},
  abstract = {Understanding which fauna and flora from seagrass beds serve as primary food for reef-based commuters is critical in defining trophic linkages between shallow-water habitats of tropical oceanic regions. Although numerous studies have documented the relative importance of crustaceans in the diet of reef fishes associated with tropical seagrass meadows, it is unknown if trophic importance corresponds to a significant effect on prey distribution and abundance patterns. We quantified size-specific diet of juvenile Nassau grouper (Epinephelus striatus) inhabiting natural and artificial patch reefs, and manipulated the density of artificial patch reefs (0, 8, and 16 patch reefs per ha) to examine the predatory impact of patch reef associates on nocturnally foraging crabs. Stomach content analysis indicated an ontogenetic shift in diet, where small grouper ({$<$}20 cm TL) consumed mainly brachyuran crabs and other small crustaceans, and large grouper ({$>$}30 cm TL) consumed primarily fish. Mid-size fish (20.0\textendash 29.9 cm TL) were transitional in diet, with crustaceans occurring more frequently than fish. Diet was least diverse for large fish, and nearly identical for mid-size and small fish. Similar numbers of prey taxa were ingested in natural and artificial patch reefs. Before patch reefs were deployed in the field, nighttime band censuses revealed a mean density of 3 crabs per 240 m2 (ranges = 0\textendash 8 crabs/transect) in nearby seagrass beds. After patch reefs were deployed, crab densities dropped by one-half to 43-fold in sites with patch reefs compared to control sites (0 patch reefs). There was a negative and significant relationship between grouper density (no. ha-1) and crab density (no. 240 m-2) at all sites and locations combined. These results suggest that patch reef associated predators have a significant predatory impact on nocturnally foraging crabs in adjacent seagrass meadows, and highlight an important trophic link between tropical patch reef and seagrass habitats.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\RHGGSXQS\\Eggleston et al. - 1998 - Ontogenetic Diet Shifts in Nassau Grouper Trophic.pdf}
}

@article{Ferrari2018,
  title = {Habitat Structural Complexity Metrics Improve Predictions of Fish Abundance and Distribution},
  author = {Ferrari, Renata and Malcolm, Hamish A. and Byrne, Maria and Friedman, Ariell and Williams, Stefan B. and Schultz, Arthur and Jordan, Alan R. and Figueira, Will F.},
  year = {2018},
  journal = {Ecography},
  volume = {41},
  number = {7},
  pages = {1077--1091},
  issn = {1600-0587},
  doi = {10.1111/ecog.02580},
  abstract = {Habitat structural complexity influences biotic diversity and abundance, but its influence on marine ecosystems has not been widely addressed. Recent advances in computer vision and robotics allow quantification of structural complexity at higher-resolutions than previously achieved. This provides an important opportunity to determine the ecological role of habitat structural complexity in marine ecosystems. We used high-resolution three-dimensional (3D) maps to test multiple structural complexity metrics, depth and benthic biota as surrogates of fish assemblages across hundreds of meters on subtropical reefs. Non-parametric multivariate statistics were used to determine the relationship between these surrogates and the entire fish assemblage. Fish were divided into functional groups, which were used to further investigate the relationship between surrogates and fish abundance using generalized linear models. Fish community composition and abundance were strongly related to habitat complexity metrics, benthic biota and depth. Surface rugosity and its variance had a significant positive influence on the abundance of piscivores and sediment infauna predators, and a negative effect on the abundance of predators, herbivores, planktivores and cleaners. Final models for fish functional groups explained up to 68\% of the variance. The best metrics to explain the variance in fish abundance were benthic biota (25 {$\pm$}7.5\% of variance explained, mean {$\pm$} SE) and complexity metrics (16 {$\pm$}6.6\%, mean {$\pm$} SE). Our results show that high-resolution 3D maps and derived metrics can predict a large percentage of variance in fish abundance and potentially serve as useful surrogates of fish abundance across all functional groups in spatially dynamic reefs.},
  langid = {english},
  annotation = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ecog.02580},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\N6RPB9KB\\Ferrari et al. - 2018 - Habitat structural complexity metrics improve pred.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\RDDP4MZX\\ecog.html}
}

@article{Folmer2012,
  ids = {folmer2012a},
  title = {Seagrass\textendash{{Sediment Feedback}}: {{An Exploration Using}} a {{Non-recursive Structural Equation Model}}},
  shorttitle = {Seagrass\textendash{{Sediment Feedback}}},
  author = {Folmer, Eelke O. and {van der Geest}, Matthijs and Jansen, Erik and Olff, Han and Michael Anderson, T. and Piersma, Theunis and {van Gils}, Jan A.},
  year = {2012},
  month = dec,
  journal = {Ecosystems},
  volume = {15},
  number = {8},
  pages = {1380--1393},
  issn = {1432-9840, 1435-0629},
  doi = {10.1007/s10021-012-9591-6},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\FNLWBTG4\\Folmer et al. - 2012 - Seagrass–Sediment Feedback An Exploration Using a.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\HJNJSWBX\\Folmaretal2012.pdf}
}

@article{Fonseca1992,
  ids = {fonseca1992a},
  title = {A Preliminary Evaluation of Wave Attenuation by Four Species of Seagrass},
  author = {Fonseca, Mark S. and Cahalan, Jennifer A.},
  year = {1992},
  month = dec,
  journal = {Estuarine, Coastal and Shelf Science},
  volume = {35},
  number = {6},
  pages = {565--576},
  issn = {02727714},
  doi = {10.1016/S0272-7714(05)80039-3},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\CBIMZSLM\\Fonseca and Cahalan - 1992 - A preliminary evaluation of wave attenuation by fo.pdf}
}

@article{Fuchs2013,
  title = {Effects of Habitat Complexity on Invertebrate Biodiversity},
  author = {Fuchs, Travis},
  year = {2013},
  month = jan,
  journal = {Immediate Science Ecology},
  volume = {2},
  doi = {10.7332/ise2013.2.1.dsc}
}

@article{Goreau1963,
  title = {Calcium Carbonate Deposition by Coralline Algae and Corals in Relation to Their Roles as Reef-builders},
  author = {Goreau, Thomas F.},
  year = {1963},
  journal = {Annals of the New York Academy of Sciences}
}

@article{Gratwicke2005,
  title = {The Relationship between Fish Species Richness, Abundance and Habitat Complexity in a Range of Shallow Tropical Marine Habitats},
  author = {Gratwicke, B. and Speight, M. R.},
  year = {2005},
  journal = {Journal of Fish Biology},
  volume = {66},
  number = {3},
  eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.0022-1112.2005.00629.x},
  pages = {650--667},
  doi = {10.1111/j.0022-1112.2005.00629.x},
  abstract = {A simple habitat assessment score (HAS) was designed to assess habitat complexity across several different shallow tropical marine habitats including sandy patches, algal beds, seagrass beds and reefs. It measured rugosity, variety of growth forms, height, refuge size categories, percentage live cover and percentage hard substratum. Multiple regression models using HAS variables as predictors accounted for 71 and 22\% of the variation in observed species richness and total fish abundance respectively. The two most important predictors of observed species richness were rugosity and variety of growth forms, while height was the most important predictor of total fish abundance. The HAS method worked consistently across a variety of habitat types and the complexity map closely mirrored the map of observed species richness, reflecting the patchy habitat mosaic of shallow tropical marine areas. Stations at the mouth of an enclosed lagoon, however, had a higher number of species than might have been expected judging from the habitat complexity scores. It is possible that this was linked to the preferential settling of pelagic fish larvae in this area as tidal water exchanges between the bay and the reef were funnelled through one small gap. This study highlights the need for fish biodiversity studies to take habitat complexity into account.},
  keywords = {British Virgin Islands,environmental impact,fish diversity,habitat structure,rapid assessment}
}

@phdthesis{Greene2008,
  type = {{{MSc Thesis}}},
  title = {Invertebrate Endofauna Associated with Sponge and Octocoral Epifauna at {{Gray}}'s {{Reef National Marine Sanctuary}} off the Coast of {{Georgia}}},
  author = {Greene, Anna Kjellin},
  year = {2008},
  school = {College of Charleston},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\5HHIRPYN\\Greene.pdf}
}

@misc{Hallett2020,
  title = {Codyn: {{Community Dynamics Metrics}}},
  author = {Hallett, L and Avolio, M and Carroll, I and Jones, S and MacDonald, A and Flynn, D and Slaughter, P and Ripplinger, J and Collins, S and Gries, C and Jones, M},
  year = {2020}
}

@article{Harris2021,
  title = {Benthic Community Composition of Temperate Mesophotic Ecosystems ({{TMEs}}) in {{New Zealand}}: Sponge Domination and Contribution to Habitat Complexity},
  shorttitle = {Benthic Community Composition of Temperate Mesophotic Ecosystems ({{TMEs}}) in {{New Zealand}}},
  author = {Harris, B and Davy, Sk and Bell, Jj},
  year = {2021},
  month = aug,
  journal = {Marine Ecology Progress Series},
  volume = {671},
  pages = {21--43},
  issn = {0171-8630, 1616-1599},
  doi = {10.3354/meps13758},
  abstract = {Temperate mesophotic ecosystems (TMEs) typically occur between 30 and 150 m depth and support rich benthic communities. However, despite their widespread distribution and ecological importance, TMEs are one of the most poorly studied marine ecosystems globally. We measured changes in the benthic community composition of rocky reefs through the infralittoral and mesophotic zone from 5 to 120 m at 6 locations across New Zealand (the Poor Knights Islands, the inner, mid-, and outer regions of the Fiordland Marine Area [FMA], and the North and South Taranaki Bights) which we considered as potential shallow-water TME surrogates due to these sites having environmental conditions and biological communities similar to deeper-water communities. Benthic community data were analysed from videos and photographs collected using SCUBA ({$<$} 30 m) and a remotely operated vehicle (ROV) ({$>$} 30 m). We found significant changes in community composition with depth at all locations, suggesting that TMEs provide habitats different from those in shallower water. We consistently found that TME benthic communities were dominated by sponges, but their abundance varied significantly with depth at 3 out of 4 locations, while the morphological composition of these assemblages changed with depth at all locations. Given their particularly high abundance and morphological complexity, we suggest that sponge assemblages make an important contribution to habitat complexity in benthic TME communities.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\ULNVMZ8B\\Harris et al. - 2021 - Benthic community composition of temperate mesopho.pdf}
}

@manual{Hartig2020,
  type = {Manual},
  title = {{{DHARMa}}: {{Residual}} Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models},
  author = {Hartig, Florian},
  year = {2020}
}

@article{Healey2004,
  title = {Journal of {{Experimental Marine Biology}} and {{Ecology Seagrass}} Bed Patchiness: Effects on Epifaunal Communities in {{San Diego Bay}}, {{USA}}},
  author = {Healey, Danielle and Hovel, Kevin A.},
  year = {2004},
  journal = {Journal of Experimental Marine Biology and Ecology},
  volume = {313},
  number = {1},
  pages = {155--174},
  doi = {10.1016/j.jembe.2004.08.002},
  abstract = {Seagrass habitat structure influences epifaunal density, diversity, community composition and survival, but covariation of structural elements at multiple scales (e.g., shoot density or biomass per unit area, patch size, and patch configuration) can confound studies attempting to correlate habitat structure with ecological patterns and processes. In this study, we standardized simulated seagrass shoot density and bed area among artificial seagrass beds in San Diego Bay, California, USA to evaluate the singular effect of seagrass bed configuration (``patchiness'') on the density and diversity of seagrass epifauna. Artificial seagrass beds all were 1 m2, but were composed of a single large patch (``continuous'' treatment), four smaller patches (``patchy'' treatment), or 16 very small patches (``very patchy'' treatment). We allowed epifauna to colonize beds for 1 month, and then sampled beds monthly over the next 3 months. Effects of seagrass bed patchiness on total epifaunal density and species-specific densities were highly variable among sampling dates, and there was no general trend for the effects of fragmentation on epifaunal densities to be positive or negative. Epifaunal diversity (measured as Simpson's index of diversity) was highest in very patchy or patchy beds on two out of the three sampling dates. Very patchy beds exhibited the highest dissimilarity in community composition in the first two sampling periods (August and September), but patchy beds exhibited the highest dissimilarity in the third sampling period (October). Our results indicate that seagrass patch configuration affects patterns of epifaunal density, diversity, and community composition in the absence of covarying bed area or structural complexity, and that patchy seagrass beds may be no less valuable as a habitat than are continuous seagrass beds. The spatial pattern employed when harvesting or planting seagrass may influence epifaunal habitat use and should be a key consideration in restoration plans.}
}

@article{Heck1977,
  title = {Habitat {{Complexity}} and {{Invertebrate Species Richness}} and {{Abundance}} in {{Tropical Seagrass Meadows}}},
  author = {Heck, Kenneth L. and Wetstone, Gregory S.},
  year = {1977},
  month = jun,
  journal = {Journal of Biogeography},
  volume = {4},
  number = {2},
  pages = {135--142},
  issn = {03050270},
  doi = {10.2307/3038158},
  abstract = {Two potentialmeasuresof habitatcomplexityp, lant species numberand abovegrounpdlantbiomassa,reconsideredinrelationto thespecies richnessand abundanceof motilemacroinvertebraitneshabitintgropicalseagrass(Thalassiatestudinum(Konig)) meadows.Plantspeciesnumberwas not significantlryelatedto eitherinvertebratsepeciesnumberor abundanceand therefordeoes not appearto adequatelyrepresenhtabitatcomplexityforthe invertebratsepeciesbeingconsideredH. owever,abovegroundplantbiomassis significantlcyorrelatedwithbothinvertebratsepeciesnumberand abundance and appearsto be a reasonablemeasureofhabitatcomplexityforthesespecies. A considerationof severalalternativexplanationsfortheseresultssuggests thatthesignificanctorrelationbetweenabovegrounpdlantbiomassandinvertebratespeciesnumberprobablyresultfs romtheadditionofcryptiscpecieswhich inhabitprotectedhabitatsthatareformedamongthefoliosebrancheosfcertain plant specieswhen theyare verydense.The significanatbovegroundplant biomass-invertebraatbeundancecorrelatioins mostlikelydueto theprotection frompredatortshatthickvegetationprovidesb,utmayalsobe partlya resultof thegreaterplantsurfaceareathatis availableforhabitationinheavilyvegetated areas.Theresultosfthisfirststeptowardquantifyinrgelationshipams ongplants and animalsin seagrassmeadowsclearlyindicatethatexperimentsatl udiesare neededto differentiactoenclusivelyamongthecompetingexplanationws hich seekto explaincommunitoyrganizatioinnseagrasms eadows.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\YA3KJADD\\Heck and Wetstone - 1977 - Habitat Complexity and Invertebrate Species Richne.pdf}
}

@article{Heck1980,
  title = {Seagrass Habitats: The Roles of Habitat Complexity, Competition and Predation in Structuring Associated Fish and Motile Macroinvertebrate Assemblages},
  author = {Heck, KL and Orth, RJ and Kennedy, V},
  year = {1980},
  journal = {Estuarine Perspectives. Academic Press, New York, USA}
}

@article{Heck2003,
  ids = {heck2003},
  title = {Critical Evaluation of the Nursery Role Hypothesis for Seagrass Meadows},
  author = {Heck, Kl and Hays, G and Orth, Rj},
  year = {2003},
  journal = {Marine Ecology Progress Series},
  volume = {253},
  pages = {123--136},
  issn = {0171-8630, 1616-1599},
  doi = {10.3354/meps253123},
  abstract = {The vast majority of published papers concerning seagrass meadows contain statements to the effect that seagrass beds serve as important nurseries for many species. We reviewed more than 200 papers that were relevant to the nursery role hypothesis. We used both vote counting and meta-analytic techniques to evaluate whether the body of previous studies that report seagrass meadows to be nursery grounds actually contain data that support this proposition. We restricted our analyses to papers that compared seagrass beds to other habitats, and examined data on a variety of well-studied species concerning their density, growth, survival and migration to adult habitat. Within this group of papers, we considered potential factors that could influence the nursery function (e.g. location, or laboratory vs field studies). We also evaluated case histories of well-documented largescale seagrass losses on the nursery function. Major results were consistent with the expectations that abundance, growth and survival were greater in seagrass than in unstructured habitats. Abundance data also suggested that seagrass beds in the Northern Hemisphere might be more important as nursery areas than those in the Southern Hemisphere. Surprisingly, few significant differences existed in abundance, growth or survival when seagrass meadows were compared to other structured habitats, such as oyster or cobble reefs, or macroalgal beds. Nor were there decreases in harvests of commercially important species that could clearly be attributed to significant seagrass declines in 3 wellstudied areas. However, there were decreased abundances of juveniles of commercially important species in these areas, suggesting a strong link between seagrass abundance and those of juvenile finfish and shellfish. One important implication of these results is that structure per se, rather than the type of structure, appears to be an important determinant of nursery value. Clearly, more rigorous studies that test all aspects of the nursery role hypothesis are clearly needed for seagrass meadows as well as other structured habitats. The results of such studies will allow better decisions to be made concerning the conservation and restoration of marine habitats.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\T6PMXCRR\\Heck Hay et al. - 2003 - Critical evaluation of the nursery role hypothesis.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\TPAPA7P8\\Heck et al 2003.pdf}
}

@article{Hemminga1991,
  type = {Journal {{Article}}},
  ids = {hemminga1991a},
  title = {The Balance of Nutrient Losses and Gains in Seagrass Meadows},
  author = {Hemminga, MA and Harrison, PG and Van Lent, F.},
  year = {1991},
  journal = {Marine Ecology Progress Series},
  volume = {71},
  pages = {85--96},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\4GMT46CR\\Heminga1991.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\636MGT2Z\\Heminga1991.pdf}
}

@article{Henkel2011,
  title = {Host Specialization of an Obligate Sponge-Dwelling Brittlestar},
  author = {Henkel, Timothy P and Pawlik, Joseph R},
  year = {2011},
  journal = {Aquatic Biology},
  volume = {12},
  number = {1},
  pages = {37--46},
  issn = {1864-7782},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\FNG8DVIG\\Henkel.pdf}
}

@article{Hori2009,
  ids = {Hori2009a},
  title = {High Seagrass Diversity and Canopy-Height Increase Associated Fish Diversity and Abundance},
  author = {Hori, Masakazu and Suzuki, Takao and Monthum, Yaowaluk and Srisombat, Tippamas and Tanaka, Yoshiyuki and Nakaoka, Masahiro and Mukai, Hiroshi},
  year = {2009},
  journal = {Marine Biology},
  volume = {156},
  pages = {1147--1458},
  doi = {10.1007/s00227-009-1184-3},
  abstract = {Seagrass species function as typical foundation species that uniWes most ecosystem processes. This ecosystem role depends largely on the morphological characteristics and structural complexity of seagrass beds, including their ecological importance for Wsh species. This study examined relationships between seagrass bed characteristics and associated Wsh communities in mixed seagrass beds. Correspondence analysis (CA) and canonical correlation analysis (CCoA) were performed to estimate relationships for individual seagrass bed characteristics. The CCoA results revealed that species richness and threedimensional structure of seagrass had great eVect on the biomass and richness of the associated Wsh community. The CA results revealed that the relative importance of seagrass bed characteristics diVered among Wsh functional groups including Wshes appearing on the surface of, inside, and on the bottom of seagrass beds. The Wshes found on the surface of the beds preferred beds with low seagrass biomass and high three-dimensional structure, those inside the beds preferred beds with high seagrass biomass and high three-dimensional structure, and those on the bottom of the beds preferred locations with low seagrass biomass and low three-dimensional structure. The results of this study provide compelling evidence that seagrass beds with high species diversity and high three-dimensional structure, but intermediate biomass, may provide the great beneWt to the associated Wsh community. Such niche complementarity among Wshes may be a process facilitated by seagrass diversity for secondary production as an ecosystem functioning.},
  keywords = {Nearshore Ecosystem,Oyster Reef,Seagrass Biomass,Seagrass Meadow,Seagrass Species},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\WBWPWVUT\\Hori et al. - 2009 - High seagrass diversity and canopy-height increase.pdf}
}

@article{Huang2017,
  title = {Mean-Parametrized {{Conway}}\textendash{{Maxwell}}\textendash{{Poisson}} Regression Models for Dispersed Counts},
  author = {Huang, Alan},
  year = {2017},
  month = dec,
  journal = {Statistical Modelling},
  volume = {17},
  number = {6},
  pages = {359--380},
  publisher = {{SAGE Publications India}},
  issn = {1471-082X},
  doi = {10.1177/1471082X17697749},
  abstract = {Conway\textendash Maxwell\textendash Poisson (CMP) distributions are flexible generalizations of the Poisson distribution for modelling overdispersed or underdispersed counts. The main hindrance to their wider use in practice seems to be the inability to directly model the mean of counts, making them not compatible with nor comparable to competing count regression models, such as the log-linear Poisson, negative-binomial or generalized Poisson regression models. This note illustrates how CMP distributions can be parametrized via the mean, so that simpler and more easily interpretable mean-models can be used, such as a log-linear model. Other link functions are also available, of course. In addition to establishing attractive theoretical and asymptotic properties of the proposed model, its good finite-sample performance is exhibited through various examples and a simulation study based on real datasets. Moreover, the MATLAB routine to fit the model to data is demonstrated to be up to an order of magnitude faster than the current software to fit standard CMP models, and over two orders of magnitude faster than the recently proposed hyper-Poisson model.},
  langid = {english},
  keywords = {Conway–Maxwell–Poisson distribution,Count data,generalized linear model,overdispersion,underdispersion},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\E2PQCSYE\\Huang - 2017 - Mean-parametrized Conway–Maxwell–Poisson regressio.pdf}
}

@article{Ismet2020,
  title = {Associative-Mesofauna Abundance and Its Correlation with Sponges Antibacterial Activity in Seagrass Ecosystem},
  author = {Ismet, M. S. and Bengen, D. G. and Setianingsih, W. A. and Yudhani, B. A. and Natih, N. M. N.},
  year = {2020},
  month = jan,
  journal = {IOP Conference Series: Earth and Environmental Science},
  volume = {404},
  number = {1},
  pages = {012007},
  publisher = {{IOP Publishing}},
  issn = {1755-1315},
  doi = {10.1088/1755-1315/404/1/012007},
  abstract = {Sponge is one of the benthic organisms that could be found in seagrass ecosystem. Sponge is also could harbor various organisms within its tissue, as a biogenic habitat for those associative organisms. This interaction could benefit from enhancing marine biodiversity in the seagrass ecosystem. Aims of this research were study the abundance of associative mesofauna and its correlation with the sponges antibacterial activity. Sponges samples were preserved in 70\% ethyl alcohol (0.5-1 cm3 thickness) and observed under stereomicroscope, to find the associative mesofauna. Meanwhile fresh tissue samples were tested against several pathogenic bacteria in antibacterial assay. Associative mesofauna that was found in 14 of 23 seagrass sponge species, belong to Ophiuridae, Mollusca, Gastropoda, Arthropoda, Polychaeta, and Oligochaeta groups. Mollusca and Polychaeta were highly correlated with most of the sponge species (8 of 14), based on statistical correspondence analysis (CA). Antibacterial assay on sponge tissue showed that only 6 of 14 sponge species has activity against several pathogenic bacteria. Statistical analysis (CA) showed that Mollusca and Polychaeta also have high correlation with the antibacterial activity. This suspected that sponges defense mechanism strategy against pathogenic bacterial infections, could influence the preference of associative mesofauna inhabiting seagrass sponges.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\T3RD52JB\\Ismet et al. - 2020 - Associative-mesofauna abundance and its correlatio.pdf}
}

@article{James1994,
  title = {The Effects of Habitat Complexity and Light Intensity on Ambush Predation within a Simulated Seagrass Habitat},
  author = {James, Pamala L. and Heck Jr, Kenneth L.},
  year = {1994},
  journal = {Journal of Experimental Marine Biology and Ecology},
  volume = {176},
  pages = {187--200},
  doi = {10.1016/0022-0981(94)90184-8},
  abstract = {Laboratory studies were used to evaluate the effects of varying structural complexity (at densities of 0, 747, 1494, 2250 and 3032 blades/m' artificial seagrass) and light intensity (0. 1.67, 76.28 pEin/m''/sec) on the foraging behavior and success rate of an ambush predator, the lined seahorse (Hippocampus erectus Perry). In the presence of artificial seagrass, seahorses used ``sit and wait'' foraging behavior, but in the absence of structure, seahorses actively pursued prey. Even the highest seagrass densities did not significantly reduce seahorse captures of their shrimp [Hippo\&e zostericola (Smith)] prey, in contrast to the reduced capture rates often reported for actively foraging fish predators in dense vegetation. However, capture rates were significantly reduced at low light levels, even though seahorses were able to capture small numbers of shrimp in 0 light treatments. We conclude that variation in structural complexity appears to have little effect on the foraging success of this visual ``sit and wait'' predator, while variation in light level produces significant shifts in capture rates.}
}

@article{Jones1994,
  title = {Organisms as Ecosystem Engineers},
  author = {Jones, Clive G and Lawton, John H and Shachak, Moshe},
  year = {1994},
  journal = {Oikos},
  volume = {69},
  number = {3},
  pages = {373--386},
  issn = {0030-1299},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\U9YLZSSX\\Jones_et_al_1994_Organisms_as_Oikos_69_373-386.pdf}
}

@article{Jones2021a,
  ids = {Jones2021},
  title = {Seagrass {{Structural Traits Drive Fish Assemblages}} in {{Small-Scale Fisheries}}},
  author = {Jones, Benjamin L. and Nordlund, Lina M. and Unsworth, Richard K. F. and Jiddawi, Narriman S. and Ekl{\"o}f, Johan S.},
  year = {2021},
  month = apr,
  journal = {Frontiers in Marine Science},
  volume = {8},
  pages = {640528},
  issn = {2296-7745},
  doi = {10.3389/fmars.2021.640528},
  abstract = {Seagrasses \textendash{} a group of foundation species in coastal ecosystems \textendash{} provide key habitat for diverse and abundant faunal assemblages and support numerous ecosystem functions and services. However, whether the habitat role of seagrasses is influenced by seagrass diversity, by dominant species or both, remains unclear. To that end, we sought to investigate the specific seagrass characteristics (e.g., species diversity, seagrass traits) that influence tropical fish assemblages, and place this in the context of small-scale fishery use. We surveyed seagrass variables at 55 plots, nested within 12 sites around Zanzibar (Tanzania) in the Western Indian Ocean, and used Baited Remote Underwater Video (BRUV) systems to assess fish assemblages across plots. Using linear mixed models, we reveal that seagrass structural complexity and depth were the best predictors of fish abundance, with higher abundance occurring in deeper meadows or meadows with high canopy, leaf length and number of leaves per shoot. Moreover, an interaction between seagrass cover and land-use was the best predictor of fish species richness, where sites closer to human impacts were less affected by cover than sites with lower human impact. Overall, models with seagrass species richness or functional diversity as predictors poorly explained fish assemblages. Fish taxa that were important for small-scale fishery sectors (e.g., emperors, snappers, rabbitfish, and parrotfish) were primarily driven by seagrass structural complexity. Our results provide a unique analysis of the relationship between seagrass habitat and its associated fish assemblages in that we show that seagrass species diversity had little effect on seagrass fish assemblages, which instead appear driven by specific seagrass traits and seagrass cover. If conserving high value species that support adjacent fisheries is the priority for protecting seagrass meadows, then seagrass areas should be chosen with high cover and structural complexity that are in deeper waters. Any conservation measures also need to balance the needs of fishers that use the resources supported by seagrasses.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\7LXYVL9B\\Jones et al. - 2021 - Seagrass Structural Traits Drive Fish Assemblages .pdf}
}

@article{Legendre2001,
  title = {Ecologically Meaningful Transformations for Ordination of Species Data},
  author = {Legendre, Pierre and Gallagher, Eugene D.},
  year = {2001},
  month = oct,
  journal = {Oecologia},
  volume = {129},
  number = {2},
  pages = {271--280},
  publisher = {{Springer Berlin Heidelberg}},
  issn = {1432-1939},
  doi = {10.1007/s004420100716},
  abstract = {This paper examines how to obtain species biplots in unconstrained or constrained ordination without resorting to the Euclidean distance [used in principal-component analysis (PCA) and redundancy analysis (RDA)] or the chi-square distance [preserved in correspondence analysis (CA) and canonical correspondence analysis (CCA)] which are not always appropriate for the analysis of community composition data. To achieve this goal, transformations are proposed for species data tables. They allow ecologists to use ordination methods such as PCA and RDA, which are Euclidean-based, for the analysis of community data, while circumventing the problems associated with the Euclidean distance, and avoiding CA and CCA which present problems of their own in some cases. This allows the use of the original (transformed) species data in RDA carried out to test for relationships with explanatory variables (i.e. environmental variables, or factors of a multifactorial analysis-of-variance model); ecologists can then draw biplots displaying the relationships of the species to the explanatory variables. Another application allows the use of species data in other methods of multivariate data analysis which optimize a least-squares loss function; an example is K-means partitioning.},
  copyright = {2001 Springer-Verlag},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\DFM34QHZ\\Legendre and Gallagher - 2001 - Ecologically meaningful transformations for ordina.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\HD2TK9HE\\10.html}
}

@article{Lillis2014,
  ids = {lillis2014a},
  title = {Soundscape Variation from a Larval Perspective: The Case for Habitat-Associated Sound as a Settlement Cue for Weakly Swimming Estuarine Larvae},
  shorttitle = {Soundscape Variation from a Larval Perspective},
  author = {Lillis, A and Eggleston, Db and Bohnenstiehl, Dr},
  year = {2014},
  month = aug,
  journal = {Marine Ecology Progress Series},
  volume = {509},
  pages = {57--70},
  issn = {0171-8630, 1616-1599},
  doi = {10.3354/meps10917},
  abstract = {Settlement is a critical phase in the life history of most benthic marine organisms and has important implications for their survival and reproductive success, and ultimately for population and community dynamics. Larval encounter with settlement habitats is likely facilitated through the use of habitat-specific physical and chemical cues, but the scales over which particular habitat-related environmental cues may operate are rarely measured. In Pamlico Sound, North Carolina, USA we used passively drifting acoustic recorders to measure the variation in habitat-related underwater sound, a potential broad-scale settlement cue, at spatiotemporal scales relevant to dispersing bivalve larvae in the estuary. Sound levels increased by up to 30 dB during passage over oyster reefs compared to off-reef soft bottom areas, and sound level fluctuations in the 2000 to 23 000 Hz frequency range closely corresponded to the presence of oyster reef patches below drifters, indicating that sound characteristics could reliably provide a signal of benthic habitat type to planktonic larvae. Using these soundscape measurements and the known descent capabilities of oyster larvae, we demonstrate with a conceptual model that response to habitat-related sound cues is a feasible mechanism for enhanced larval encounter with settlement substrate.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\AMYZH4IV\\Lillisetal2014.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\F2PV8EPA\\Lillis et al. - 2014 - Soundscape variation from a larval perspective th.pdf}
}

@article{Loh2014,
  title = {Chemical Defenses and Resource Trade-Offs Structure Sponge Communities on {{Caribbean}} Coral Reefs},
  author = {Loh, T and Pawlik, Joseph R.},
  year = {2014},
  journal = {Proceedings of the National Academy of Sciences},
  volume = {111},
  pages = {4151--4156},
  doi = {10.1073/pnas.1321626111}
}

@article{Maldonado2017,
  title = {Sponge {{Grounds}} as {{Key Marine Habitats}}: {{A Synthetic Review}} of {{Types}}, {{Structure}}, {{Functional Roles}}, and {{Conservation Concerns}}},
  shorttitle = {Sponge {{Grounds}} as {{Key Marine Habitats}}},
  author = {Maldonado, Manuel and Aguilar, Ricardo and Bannister, Raymond J. and Bell, James J. and Conway, Kim W. and Dayton, Paul K. and D{\'i}az, Cristina and Gutt, Julian and Kelly, Michelle and Kenchington, Ellen L. R. and Leys, Sally P. and Pomponi, S. A. and Rapp, H. T. and R{\"u}tzler, Klaus and Tendal, Ole S. and Vacelet, Jean and Young, Craig M.},
  year = {2017},
  publisher = {{Springer}},
  doi = {10.1007/978-3-319-17001-5_24-1},
  abstract = {This chapter reviews the major known monospecific and multispecific sponge  aggregations in the world's oceans. They are shown to occur from the intertidal to  abyssal depths, in tropical, temperate, and high latitudes and sometimes to create spectacular formations, such as glass sponge reefs, lithistid reef-like fields, and  carnivorous sponge grounds. Sponge aggregations are recognized as singular  vulnerable habitats that deserve special research attention and legal protection.  However, this review reveals that there is only a poor and fragmentary understanding  of the main biological, environmental, and geochemical factors that  favor and maintain these systems, including the food supply, which is fundamental  knowledge. There is also a particular lack of information regarding  reproductive biology, growth rates, life spans, and the main factors causing  mortality, all crucial drivers for understanding population and community  dynamics and for developing conservation strategies. The sponge aggregations  have been shown to increase the structural complexity of the habitats, attracting  a larger variety of organisms and locally enhancing biodiversity. From the very  few cases in which sponge biomass and sponge physiology have been reliably  approached jointly, phenomenal fluxes of matter and energy have been inferred.  Through their benthic-pelagic coupling, some of the densest sponge aggregations  have a significant local or regional impact on major biogeochemical cycles  and food webs. Physical damage and habitat destruction derived from  man-driven activities along with epidemic diseases facilitated by global environmental  alterations emerge as major threats to the future of the sponge  aggregations.},
  copyright = {closedAccess},
  langid = {english},
  annotation = {Accepted: 2018-10-29T08:32:16Z},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\9NCRAU6N\\Maldonado et al. - 2017 - Sponge Grounds as Key Marine Habitats A Synthetic.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\3PVB8MA6\\171671.html}
}

@article{Mann2007,
  title = {On the Attraction of Larval Fishes to Reef Sounds},
  author = {Mann, Da and Casper, Bm and Boyle, Ks and Tricas, Tc},
  year = {2007},
  month = may,
  journal = {Marine Ecology Progress Series},
  volume = {338},
  pages = {307--310},
  issn = {0171-8630, 1616-1599},
  doi = {10.3354/meps338307},
  abstract = {Several recent studies have shown that some larval fishes will approach underwater speakers that broadcast reef noise, leading to the hypothesis that larval fishes use acoustic cues to locate reefs for settlement. The purpose of the present study was to examine existing hearing data of fishes in relation to ambient sound levels around reefs to estimate the distance over which reef fish might detect reefs sounds, and to highlight how future data should be collected to answer this important question. The few available measurements of larval fish hearing indicate that they have poor acoustic sensitivity relative to sound levels found around reefs. The apparent poor sensitivity of larval fishes to sound pressure suggests that particle motion, the back and forth motion of water that is associated with acoustic pressure, is the principal stimulus for larval fish hearing. To estimate the maximum distance of orientation to reefs, the acoustic particle velocity of reef sound was calculated from measurements of the acoustic pressure on and away from shore, assuming conditions of a planar propagating wave. Based on these calculations, we propose that larval fishes in acoustically unbounded habitats most probably cannot detect the ambient noise of particle motion at distances {$>$}1 km. To better understand the distances over which larval fishes can detect sounds from reefs, more studies on larval fish hearing and reef noise are needed. Larval fish hearing measurements need to independently distinguish sensitivities to particle motion and acoustic pressure. Likewise, independent measurements of particle motion around reefs are required.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\SWPA72IK\\Mann et al. - 2007 - On the attraction of larval fishes to reef sounds.pdf}
}

@article{Martin1992,
  title = {Harmoth\"oe Hyalonemae {{SF}}. {{NOV}}. (Polychaeta, Polynoidae), an Exclusive Inhabitant of Different Atlanto-Mediterranean Species of Hyalonema (Porifera, Hexactinellida)},
  author = {Martin, D. and Rosell, D. and {M. J. Uriz}},
  year = {1992},
  journal = {Ophelia},
  volume = {35},
  number = {3},
  pages = {169--185},
  doi = {10.1080/00785326.1992.10429925},
  abstract = {Abstract A new polynoid species, Harmoth\"oe liyalonemae, living as an inquiline inside the atrial cavities of deep-water hexactinellid sponges of the genus Hyalonema - viz. H. thomsoni, H. infundibulum, H. lusitanicum and H. toxeras - is fully described and illustrated. It is characterized by the notched, bill-shaped tips of neurosetae, smooth cephalic sensory organs and cirri, and smooth margined elytra with a patch of papillae near the reniform indentation. The species shows sexual dimorphism and the morphology of the polychaetes changes slightly when comparing specimens from Mediterranean hosts to those of Atlantic hosts. Some trends of the association between the polychaete and the sponge have been studied on a dense population of Mediterranean H. thomsoni (including 171 of the total 176 hexactinellid specimens examined). 88.3\% of the sponges were infested by the polychaete, with 52.3\% of them harbouring a male and female together. The absence of correlation between sponge size and polychaete size, together with their particular distributions in size-classes (normal unimodal in sponges, and bimodal in polychaetes), suggest that the life-history of the polychaete population is independent of the host, with sponge life being notably longer than inquiline life.}
}

@misc{Mazerolle2020,
  title = {{{AICcmodavg}}: {{Model}} Selection and Multimodel   Inference Based on ({{Q}}){{AIC}}(c)},
  author = {Mazerolle, Marc J.},
  year = {2020}
}

@article{McClay1983,
  title = {Dispersal and Use of Sponges and Ascidians as Camouflage by {{Cryptodromia}} Hilgendorfi ({{Brachyura}}: {{Dromiacea}})},
  author = {McClay, C. L.},
  year = {1983},
  month = sep,
  journal = {Marine Biology},
  volume = {76},
  number = {1},
  pages = {17--32},
  issn = {1432-1793},
  doi = {10.1007/BF00393051},
  abstract = {From May 1977 to February 1979, the use of sponges and ascidians by Cryptodromia hilgendorfi was studied in Moreton Bay, Queensland, Australia. The aim was to investigate patterns of seasonal use, cap making behaviour, cap turnover, the effect of intraspecific interactions on cap life and the effect of movement of crabs between hosts on background matching. C. hilgendorfi uses 12 (of 16 available) species of sponge and 3 species of ascidians to construct caps, which are carried by the crabs using their last two pairs of legs. Cap area increases non-linearly with crab size, and caps are normally two to three times as large as the crabs. Cap making behaviour is described. It occurs during intermoult periods, with females making most of their caps at night. Caps decrease in size with time, but conceal the crabs which commonly occupy exposed sites on sponges. Cap life is independent of crab size, differs between different cap species and is influenced by the presence of other crabs who can dislodge caps through aggressive behaviour. Caps are made from the sponge Suberites carnosus more often than from other available sponges. S. carnosus caps also decay less rapidly than caps made from other sponges. Use of sponge and ascidian species varies seasonally, with Halichondria sp. and S. carnosus being used in all months. C. hilgendorfi exhibits a preference for certain sponges. The majority of crabs carried caps which matched their host sponge or ascidian, but mis-matches varied seasonally with a winter peak following the breeding season. Young C. hilgendorfi settle only on S. carnosus sponges and disperse from this host to other species in the environment. Males and females differ in their rate of discovery of new hosts. Males, despite their greater mobility, find new hosts slower than females. It is hypothesized that males occupy ``home ranges'' which females do not. Crabs frequently move between sponges, mostly at night. Sponges and ascidian species grow in intimate association with each other, and sponge crabs act a selective asexual propagation mechanism. Depending upon the nature of the interactions between sponge and ascidian species (co-operative or competitive) and whether competitive hierarchies or networks are involved, the sponge crabs may have either stabilizing or destabilizing effects on the sponge community.}
}

@book{McCune2002,
  title = {Analysis of Ecological Communities},
  author = {McCune, Bruce and Grace, James B. and Urban, Dean L.},
  year = {2002},
  volume = {28},
  abstract = {Analysis of Ecological Communities is a book by Bruce McCune, James B. Grace, and Dean L. Urban on methods for analyzing multivariate data in community ecology, published by MjM Software Design, 2002. Bruce McCune is a professor of Department of Botany \& Plant Pathology at Oregon State University, co-author of PC-ORD software, and author of several lichen books. Analysis of Ecological Communities offers a rationale and guidance for selecting appropriate, effective, analytical methods in community ecology. The book is suitable as a textbook and reference book on methods for multivariate analysis of ecological communities and their environments. The book covers distance measures, data transformation, outlier analysis, ordination, cluster analysis, PCA, RA, CA, DCA, NMS, CCA, Bray-Curtis, MRPP, Mantel test, discriminant analysis, twinspan, classification and regression trees, structural equation modeling, and more. It also includes brief treatments of community sampling and diversity measures. The 304 page book is richly illustrated. It provides many examples from the literature and demonstrations of basic principles with simulated and real data sets.}
}

@misc{Meszaros2021,
  title = {'{{Dead Zone}}' {{In Gulf Of Mexico Is Larger Than Average For}} 2021},
  author = {Meszaros, Jessica},
  year = {2021},
  month = aug,
  journal = {WUSF Public Media},
  abstract = {Scientists say the area of little-to-no oxygen is about the size of Lake Ontario and Lake Erie put together.},
  chapter = {Environment},
  howpublished = {https://wusfnews.wusf.usf.edu/environment/2021-08-04/gulf-dead-zone-is-larger-than-average},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\56K2JTZB\\gulf-dead-zone-is-larger-than-average.html}
}

@article{Meyer1983,
  ids = {meyer1983a},
  title = {Fish {{Schools}}: {{An Asset}} to {{Corals}}},
  author = {Meyer, Judy L. and Schultz, Eric T. and Helfman, Gene S.},
  year = {1983},
  journal = {Science, New Series},
  volume = {220},
  number = {4601},
  pages = {1047--1049},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\K2LN9TF4\\Meyer et al. - 1983 - Fish Schools An Asset to Corals.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\X3Z3DR3F\\meyerschultzandhelfman.pdf}
}

@article{Nagelkerken2008,
  title = {Interlinkage between {{Caribbean}} Coral Reefs and Seagrass Beds through Feeding Migrations by Grunts ({{Haemulidae}}) Depends on Habitat Accessibility},
  author = {Nagelkerken, I. and Bothwell, J. and Nemeth, R. S. and Pitt, J. M. and van der Velde, G.},
  year = {2008},
  month = sep,
  journal = {Marine Ecology Progress Series},
  volume = {368},
  pages = {155--164},
  issn = {0171-8630, 1616-1599},
  doi = {10.3354/meps07528},
  abstract = {Tropical marine habitats are often energetically linked through feeding migrations by fish. A widely accepted assumption is that species of Haemulidae (grunts) undertake nocturnal feeding migrations from coral reefs to seagrass beds. This has been based on studies investigating migrations between small patch reefs and surrounding seagrass beds located in lagoons. Due to the size and location of these patch reefs, we argue that this does not represent migration from coral reef to seagrass ecosystems, and a literature search shows limited proof for such migration. We hypothesised that the spatial arrangement of these habitats in the seascape may have profound effects on the degree to which such migrations occur. Haemulon flavolineatum caught from seagrass beds located in semi-enclosed embayments, and thus isolated to a high degree from adjacent reefs, showed a diet and stable isotope signature of muscle tissue that differed from those collected from the coral reef. In contrast, fishes from open seagrass systems without restricted access from the reef showed the same stable isotope signature as those collected from the coral reef, suggesting feeding from the same habitat, viz. the seagrass beds. Additional visual census data showed that semi-enclosed seagrass beds did not have elevated densities of large-sized fish at night, which would be expected if large individuals from the reef migrated to the seagrass beds to feed. The data thus show that interlinkages between coastal ecosystems, such as coral reefs and seagrass beds, by fishes may strongly depend on the spatial arrangement of habitats within the seascape.},
  langid = {english},
  keywords = {Coral reef,Diet analysis,Feeding migrations,Habitat linkages,Haemulon flavolineatum,Seagrass,Stable isotopes},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\YH8TK96U\\Nagelkerken et al. - 2008 - Interlinkage between Caribbean coral reefs and sea.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\W367U7ZT\\p155-164.html}
}

@article{Nakamura2012,
  title = {Variability in Nursery Function of Tropical Seagrass Beds during Fish Ontogeny: Timing of Ontogenetic Habitat Shift},
  author = {Nakamura, Yohei and Hirota, Keisuke and Shibuno, Takuro and Watanabe, Yoshiro},
  year = {2012},
  month = jun,
  journal = {Marine Biology},
  volume = {159},
  number = {6},
  pages = {1305--1315},
  issn = {1432-1793},
  doi = {10.1007/s00227-012-1911-z},
  abstract = {Seagrass beds are often considered to be important nurseries for coral reef fish, yet the effectiveness of these nursery functions (refuge and food availability) at different juvenile stages is poorly understood. To understand how the demands of juvenile fish on seagrass nursery functions determines the timing of ontogenetic habitat shifts from seagrass beds to coral reefs, we conducted visual transect survey and field tethering and caging experiments on three different sizes of the coral reef fish Pacific yellowtail emperor (Lethrinus atkinsoni) during its juvenile tenure in seagrass beds at Ishigaki Island, southern Japan. The study showed that although the number of individual L. atkinsoni juveniles decreased by {$>$}90~\% during their stay in the seagrass nursery, the shelter and/or food availability functions of the nursery, at least for a juvenile size of approximately 5~cm total length (TL), provided the best survival and growth option. The timing of ontogenetic migration to coral reefs of larger fish ({$>$}8~cm TL) was attributed to foraging efficiency for larger food items in different habitats. Overall, the function of the seagrass bed nursery changed with juvenile body size, with marginally higher survival and significantly greater growth rates during early juvenile stages in seagrass beds compared to coral reefs. This would contribute to the enhancement in the number of individuals eventually recruited to adult populations.}
}

@misc{Oksanen2020,
  title = {Vegan: {{Community Ecology Package}}},
  author = {Oksanen, Jari and Blanchet, F. Guillaume and Friendly, Michael and Kindt, Roeland and Legendre, Pierre and McGlinn, Dan and Minchin, Peter R. and O'Hara, R. B. and Simpson, Gavin L. and Solymos, Peter and Stevens, M. Henry H. and Szoecs, Eduard and Wagner, Helene},
  year = {2020}
}

@article{Orth1984,
  ids = {orth1984,orth1984a,orthFaunalCommunitiesSeagrass1984a},
  title = {Faunal {{Communities}} in {{Seagrass Beds}}: {{A Review}} of the {{Influence}} of {{Plant Structure}} and {{Prey Characteristics}} on {{Predator}}: {{Prey Relationships}}},
  shorttitle = {Faunal {{Communities}} in {{Seagrass Beds}}},
  author = {Orth, Robert J. and Heck, Kenneth L. and {van Montfrans}, Jacques},
  year = {1984},
  month = dec,
  journal = {Estuaries},
  volume = {7},
  number = {4},
  pages = {339},
  issn = {01608347},
  doi = {10.2307/1351618},
  abstract = {When compared with nearby unvegetated areas, seagrass meadows contain a dense and strikingly rich assemblage of vertebrates and invertebrates. Most recent literature has focused on evaluating the role of predation in structuring seagrass faunal communities; however, habitat complexity, abundance of food and sediment stability may also be important. This paper summarizes studies relating predator-prey relationships to different features of the seagrass system. This review suggests that the abundance of many species, both epifauna and infauna, is positively correlated with two distinct aspects of plant morphology: 1) the root-rhizome mat, and 2) the plant canopy. A scheme was developed that defines the conditions under which any particular species will be abundant or rare in a seagrass assemblage. This scheme is based on prey and predator characteristics (e.g., epifaunal vs. infaunal, tube-dweller vs. nontube dweller, burrowers vs. nonburrowers, and large vs. small as adult) and on characteristics of the seagrasses (e.g., leaf morphology, shoot density, shoot biomass, structural complexity of the meadow, and root-rhizome density and standing crop).},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\5FNKB8XE\\Orth et al. - 1984 - Faunal Communities in Seagrass Beds A Review of t.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\EXXPGUGW\\Orthetal.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\R8UJH68B\\Orthetal1984.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\TATLKXFN\\Orth et al. - 1984 - Faunal Communities in Seagrass Beds A Review of t.pdf}
}

@article{Orth2006,
  title = {A Global Crisis for Seagrass Ecosystems},
  author = {Orth, R. J. and Carruthers, T. J. B. and Dennison, W. C. and Duarte, C. M. and Fourqurean, J. W. and Heck, K. L. and Hughes, A. R. and Kendrick, G. A. and Kenworthy, W. J. and Olyarnik, S. and Short, F. T. and Waycott, M. and Williams, S. L.},
  year = {2006},
  month = dec,
  journal = {Bioscience},
  volume = {56},
  number = {12},
  pages = {987--996},
  issn = {0006-3568},
  doi = {10.1641/0006-3568(2006)56[987:agcfse]2.0.co;2},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\GHJBHAS3\\orthetal.pdf}
}

@article{Pearse1950,
  title = {Notes on the Inhabitants of Certain Sponges at {{Bimini}}},
  author = {Pearse, A. S.},
  year = {1950},
  journal = {Ecology},
  volume = {31},
  number = {1},
  pages = {149--151},
  issn = {00129658},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\ZHCNH2HQ\\Pearse1950.pdf}
}

@article{Peters2015,
  title = {Comparison of Fish Assemblages in Restored and Natural Mangrove Habitats along an Urban Shoreline},
  author = {Peters, Joseph R and Yeager, Lauren A and Layman, Craig A},
  year = {2015},
  journal = {Bulletin of Marine Science},
  volume = {91},
  number = {2},
  pages = {125--139},
  issn = {0007-4977},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\F6SJDTMK\\Peters-BMS-paper.pdf}
}

@article{Pita2018,
  title = {The Sponge Holobiont in a Changing Ocean: From Microbes to Ecosystems},
  author = {Pita, L. and Rix, L. and Franke, A. and Hentschel, U.},
  year = {2018},
  journal = {Microbiome},
  volume = {6},
  doi = {10.1186/s40168-018-0428-1},
  abstract = {The recognition that all macroorganisms live in symbiotic association with microbial communities has opened up a new field in biology. Animals, plants, and algae are now considered holobionts, complex ecosystems consisting of the host, the microbiota, and the interactions among them. Accordingly, ecological concepts can be applied to understand the host-derived and microbial processes that govern the dynamics of the interactive networks within the holobiont. In marine systems, holobionts are further integrated into larger and more complex communities and ecosystems, a concept referred to as ``nested ecosystems.'' In this review, we discuss the concept of holobionts as dynamic ecosystems that interact at multiple scales and respond to environmental change. We focus on the symbiosis of sponges with their microbial communities\textemdash a symbiosis that has resulted in one of the most diverse and complex holobionts in the marine environment. In recent years, the field of sponge microbiology has remarkably advanced in terms of curated databases, standardized protocols, and information on the functions of the microbiota. Like a Russian doll, these microbial processes are translated into sponge holobiont functions that impact the surrounding ecosystem. For example, the sponge-associated microbial metabolisms, fueled by the high filtering capacity of the sponge host, substantially affect the biogeochemical cycling of key nutrients like carbon, nitrogen, and phosphorous. Since sponge holobionts are increasingly threatened by anthropogenic stressors that jeopardize the stability of the holobiont ecosystem, we discuss the link between environmental perturbations, dysbiosis, and sponge diseases. Experimental studies suggest that the microbial community composition is tightly linked to holobiont health, but whether dysbiosis is a cause or a consequence of holobiont collapse remains unresolved. Moreover, the potential role of the microbiome in mediating the capacity for holobionts to acclimate and adapt to environmental change is unknown. Future studies should aim to identify the mechanisms underlying holobiont dynamics at multiple scales, from the microbiome to the ecosystem, and develop management strategies to preserve the key functions provided by the sponge holobiont in our present and future oceans.}
}

@article{Radford2007,
  title = {Directional {{Swimming Behavior}} by {{Five Species}} of {{Crab Postlarvae}} in {{Response}} to {{Reef Sound}}},
  author = {Radford, Craig and Jeffs, Andrew and Montgomery, John},
  year = {2007},
  journal = {Bulletin of Marine Science},
  volume = {80},
  number = {2},
  pages = {369--378},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\UWDJTR8G\\Directional swimming behavior by five species of crab postlarvae in response to reef sound.pdf}
}

@article{Randall1968,
  title = {Sponge-Feeding Fishes of the {{West Indies}}},
  author = {Randall, J.E. and Hartman, W.D.},
  year = {1968},
  journal = {Marine Biology},
  volume = {1},
  pages = {216--225},
  doi = {10.1007/BF00347115},
  abstract = {In an analysis of the stomach contents of 212 species of West Indian reef and inshore fishes, sponge remains were found in 21 species. In eleven of these, sponges comprised 6\% or more of the stomach contents; it is assumed that these fishes feed intentionally on sponges. Sponges comprise over 95\% of the food of angelfishes of the genus Holacanthus, over 70\% of the food of species of the related genus Pomacanthus, and more than 85\% of the food of the filefish, Cantherhines macrocerus. Lesser quantities of sponges are ingested by the remaining fish species. Fishes that feed on sponges belong to highly specialized teleost families, suggesting that this habit has evolved in geologically late time. The small number of fish species that concentrate on sponges as food suggests that the defensive characters of sponges\textemdash mineralized sclerites, noxious chemical substances, and tough fibrous components\textemdash are highly effective in discouraging predation. The two sponges most frequently eaten by fishes have a low percentage of siliceous spicules relative to organic matter, but among the 20 next most frequently consumed species no striking correlation occurs with respect to spicule content. Color and form of the sponge show no special correlation with frequency of occurrence in fish stomachs. Three species of fishes appear to concentrate on one species of sponge, but in these cases over 60\% of the food taken consists of a variety of other organisms. Those fishes, more than half of whose diet consists of sponges, tend to sample a wide variety of species. No strong evidence is provided by our data that fish predation is a significant factor in limiting sponge distribution in the West Indian region.}
}

@misc{RCoreTeam2021,
  title = {R: {{A}} Language and Environment for Statistical Computing.},
  author = {{R Core Team}},
  year = {2021},
  address = {{Vienna, Austria}},
  howpublished = {R Foundation for Statistical Computing}
}

@article{Ribeiro2003,
  title = {Macrofauna Associated to {{Mycale}} Microsigmatosa ({{Porifera}}, {{Demospongiae}}) in {{Rio}} de {{Janeiro State}}, {{SE}} Brazil},
  author = {Ribeiro, S. M. and Omena, E. P. and Muricy, G.},
  year = {2003},
  month = aug,
  journal = {Estuarine Coastal and Shelf Science},
  volume = {57},
  number = {5-6},
  pages = {951--959},
  issn = {0272-7714},
  doi = {10.1016/s0272-7714(02)00425-0},
  abstract = {The macrofauna (endo- and epi-biotic) associated to the sponge Mycale (Carmia) microsigniatosa Arndt, 1927 was studied at three sites in Rio de Janeiro State, Brazil (Arraial do Cabo, Niteroi, and Rio de Janeiro). A total of 2235 individuals (over I mm long) of 75 invertebrate species were found associated to 19 specimens of the sponge. The most abundant and diverse taxa were the crustaceans (83\%, 31 spp.), polychetes (10\%, 18 spp.), and molluscs (3.7\%, 15 spp.). Cnidarians, platyhelminthes, ascidians, echinoderms, pycnogonids, bryozoans, and sponges were also represented. Amphipod crustaceans were the dominant group, comprising 61\% of all individuals collected. Species richness and abundance of associated fauna were highly correlated with sponge volume, but diversity and evenness were not. The site of collection influenced the species composition of the fauna associated to M. microsigniatosa but did not change significantly its diversity, abundance, richness, and dominance patterns of higher taxa. Pregnant females and juvenile stages of 29\% of the species associated, including crustaceans, molluscs, echinoderms, and pycnogonids were frequently found inside ill. microsigmatosa. Although many of these organisms do occur and reproduce in other habitats outside the sponge as well, M. microsigmatosa is also important for their reproduction and survivorship, thus contributing for the maintenance of biodiversity in Southwestern Atlantic sublittoral rocky shores. (C) 2003 Elsevier Ltd. All rights reserved.},
  langid = {english},
  keywords = {AMPHIPODA,associated fauna,CABO,CRUSTACEA,ecology,ECOLOGY,EPIFAUNA,FAUNA,LEUCOTHOE-SPINICARPA,MARINE SPONGES,Mycale,NORTH AEGEAN SEA,poecilosclerida,sponge,SW Atlantic,WASHINGTON},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\ZN642MZE\\Ribeiro (03) Macrofauna associated to Mycale microsigmatosa.pdf}
}

@article{Schielzeth2010,
  title = {Simple Means to Improve the Interpretability of Regression Coefficients: {{{\emph{Interpretation}}}}{\emph{ of Regression Coefficients}}},
  shorttitle = {Simple Means to Improve the Interpretability of Regression Coefficients},
  author = {Schielzeth, Holger},
  year = {2010},
  month = jun,
  journal = {Methods in Ecology and Evolution},
  volume = {1},
  number = {2},
  pages = {103--113},
  issn = {2041210X},
  doi = {10.1111/j.2041-210X.2010.00012.x},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\VAID7X5C\\Schielzeth - 2010 - Simple means to improve the interpretability of re.pdf}
}

@article{Smulders2022,
  title = {Fish Grazing Enhanced by Nutrient Enrichment May Limit Invasive Seagrass Expansion},
  author = {Smulders, Fee O. H. and Becker, S. Tatiana and Campbell, Justin E. and Bakker, Elisabeth S. and Bo{\"a}sson, Mickey J. and Bouwmeester, Mark M. and Vonk, J. Arie and Christianen, Marjolijn J. A.},
  year = {2022},
  month = jan,
  journal = {Aquatic Botany},
  volume = {176},
  pages = {103464},
  issn = {0304-3770},
  doi = {10.1016/j.aquabot.2021.103464},
  abstract = {The success of invasive macrophytes can depend on local nutrient availability and consumer pressure, which may interact. We therefore experimentally investigated the interacting effects of nutrient (nitrogen and phosphorus) addition, the exclusion of large herbivorous fishes and mimicked grazing on the expansion rates of the invasive seagrass Halophila stipulacea. The experiments were established on Bonaire and Aruba, two islands in the southern Caribbean, which differ in fish community structure. We observed that multiple Caribbean fish species feed on H. stipulacea. At both study sites, nutrient enrichment decreased invasive leaf carbon:nitrogen ratios. However only on Bonaire, where herbivore fish abundance was 7 times higher and diversity was 4.5 times higher, did nutrient enrichment result in a significant reduction of H. stipulacea expansion into native Thalassia testudinum meadows. This effect was likely due to increased herbivory on nutrient enriched seagrass leaves, as we found that excluding large herbivorous fish (e.g. parrotfish) doubled invasive expansion rates in bare patches on Bonaire. On Aruba, H. stipulacea expansion rates were higher overall, which coincided with lower abundances and diversity of native fishes, and were limited by mimicked fish grazing. We suggest that top-down control by the native fish community may counteract eutrophication effects by increased grazing pressure on nutrient-rich invasive seagrass leaves. We conclude that diverse and abundant herbivore communities likely play an important role in limiting invasion success and their conservation and restoration may serve as a tool to slow down seagrass invasions.},
  langid = {english},
  keywords = {Biotic resistance,Fertilization,Invasive species,Plant-herbivore interactions},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\6A29K3AA\\Smulders et al. - 2022 - Fish grazing enhanced by nutrient enrichment may l.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\MCNK8L8F\\S0304377021001133.html}
}

@article{Southwell2008,
  title = {In Situ Fluxes of Dissolved Inorganic Nitrogen from the Sponge Community on {{Conch Reef}}, {{Key Largo}}, {{Florida}}},
  author = {Southwell, M. W. and Weisz, J. B. and Martens, C. S. and Lindquist, N.},
  year = {2008},
  month = may,
  journal = {Limnology and Oceanography},
  volume = {53},
  number = {3},
  pages = {986--996},
  issn = {0024-3590},
  abstract = {We measured ammonium and nitrate plus nitrite fluxes from 14 common sponge species on a Florida Keys reef (Conch Reef) using a combination of incubation experiments and an in situ method that requires no manipulation of the sponge. On a 600- m(2) section of Conch Reef, species-specific biomass for all nonencrusting sponges was measured. The biomass data combined with species-specific dissolved inorganic nitrogen ( DIN) flux rates yielded the benthic DIN flux from 14 species, and allowed us to extrapolate these data to the total nonencrusting sponge community. The species for which we measured DIN fluxes represented 85\% of the nonencrusting sponge biomass in the study area and released a combined 480 +/- 93 mu mol m(-2) h(-1) of nitrate plus nitrite, and 57 +/- 73 mu mol m(-2) h(-1) of ammonium. Approximately 73\% of the measured DIN flux was produced by Xestospongia muta, a massive barrel sponge. Of the 14 species studied, 10 hosted active nitrifying communities, and 8 hosted photosynthetic microbial associates. However, the presence of these microbial communities had no apparent effect on the magnitude of the total DIN flux. We estimate that the DIN flux for the entire nonencrusting sponge community is 640 +/- 130 mu mol m(-2) h(-1).},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\2XVI7BSN\\Southwell.pdf}
}

@article{Southwell2008a,
  title = {Nitrification Controls on Fluxes and Isotopic Composition of Nitrate from {{Florida Keys}} Sponges},
  author = {Southwell, M. W. and Popp, B. N. and Martens, C. S.},
  year = {2008},
  month = jan,
  journal = {Marine Chemistry},
  volume = {108},
  number = {1-2},
  pages = {96--108},
  issn = {0304-4203},
  doi = {10.1016/j.marchem.2007.10.005},
  abstract = {We performed a combination of field and laboratory experiments designed to investigate sponge-hosted microbial nitrification processes, plus a survey of the prevalence of nitrification among sponge species at patch and outer reefs, Florida Keys, USA. Results from dissolved inorganic nitrogen (DIN) measurements, chemical inhibition, and N-15 isotope tracer experiments with Caribbean sponges show that 9 of 12 species tested hosted nitrification. Of the species in our study that are reported to host internal microbial populations, all but one has been found to host this process. Nitrification occurred with an apparent N isotopic fractionation factor of 11 +/- 2.6 parts per thousand (standard error) and was inhibited by nitrapyrin. Both of these characteristics are consistent with bacterially mediated ammonium oxidation; however, ammonium oxidation by crenarchaeota is also possible. The isotopic composition of nitrate expelled from sponges in situ had lower delta N-15 values than nitrate from the ambient water column, suggesting active utilization of the nitrate product after it is released. The frequency of the association between nitrifying microbial communities and sponges that harbor large microbial communities suggests that nitrification is an integral part of the metabolic function of many sponge species. Given the abundance of these species on Conch Reef and the magnitude of their nitrification rates, the majority of benthic nitrification on the Florida Keys outer reef tract probably occurs in sponges. Sponge population size and composition could therefore strongly influence the concentration and speciation of DIN in the reef water column, and possibly other ecosystems where sponges are abundant. (C) 2007 Elsevier B.V. All rights reserved.},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\QU9V7QJ5\\Southwell_et_al_2008.pdf}
}

@article{Taylor2007,
  title = {Sponge-{{Associated Microorganisms}}: {{Evolution}}, {{Ecology}}, and {{Biotechnological Potential}}},
  author = {Taylor, Michael W. and Radax, Regina and Steger, Doris and Wagner, Michael},
  year = {2007},
  journal = {Microbiology and Molecular Biology Reviews},
  volume = {71},
  number = {2},
  pages = {295--347},
  doi = {10.1128/MMBR.00040-06},
  annotation = {\_eprint: https://journals.asm.org/doi/pdf/10.1128/MMBR.00040-06}
}

@article{Tin2021,
  title = {Species Biodiversity and Distribution of Seagrass Beds in Several Coastal Areas of Central {{Vietnam}}},
  author = {Tin, Hoang C. and Phung, Bui T. and Hieu, Duong V.},
  year = {2021},
  month = jan,
  journal = {Regional Studies in Marine Science},
  volume = {41},
  pages = {101531},
  issn = {2352-4855},
  doi = {10.1016/j.rsma.2020.101531},
  abstract = {Seagrasses provide habitat and abundant food supplies for numerous marine species and seagrass ecosystems play a vital role in protecting the coast from erosion. There were numerous seagrass studies in Vietnam, however, while these studies provide information on specific studied places, there is a lack of comparison between studies for providing a broad picture of the overall seagrass ecosystem along the coast of Central Vietnam. Hence, this study of species diversity and distribution of seagrasses along the coast of Central Vietnam was conducted to provide comparative data, which is highly valuable for the proper exploitation, management, and sustainable development of seagrass resources in Central Vietnam. This study identified eight species of seagrass belonging to two families\textemdash Hydrocharitaceae and Cymodoceaceae\textemdash in the waters around several islands in Central Vietnam. Among them Halophila beccarii in the Cua Dai estuary was listed in the Red List of Threatened Species by the International Union for Conservation of Nature (IUCN) (2017)\textemdash at risk of global extinction. The results revealed that the seagrass beds in several coastal areas of Central Vietnam have diminished over time with respect to the number of species and their distribution with causes attributed to anthropogenic activities. The seagrass canopy coverage ranged from 5 to 100\% (57~{$\pm~$}36.20\%) near several coastal islands of Central Vietnam. The majority of seagrass is distributed in both intertidal and subtidal zones Our findings suggest that water quality and important sedimentary processes vital to ecosystem health need to be assessed throughout the coastal region.},
  langid = {english},
  keywords = {Distribution,Seagrass ecosystem,Species biodiversity,The coast of central Vietnam},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\H6H6LRTQ\\S2352485520306599.html}
}

@article{Vermeij2010,
  title = {Coral {{Larvae Move}} toward {{Reef Sounds}}},
  author = {Vermeij, Mark J. A. and Marhaver, Kristen L. and Huijbers, Chantal M. and Nagelkerken, Ivan and Simpson, Stephen D.},
  year = {2010},
  month = may,
  journal = {PLOS ONE},
  volume = {5},
  number = {5},
  pages = {e10660},
  publisher = {{Public Library of Science}},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0010660},
  abstract = {Free-swimming larvae of tropical corals go through a critical life-phase when they return from the open ocean to select a suitable settlement substrate. During the planktonic phase of their life cycle, the behaviours of small coral larvae ({$<$}1 mm) that influence settlement success are difficult to observe in situ and are therefore largely unknown. Here, we show that coral larvae respond to acoustic cues that may facilitate detection of habitat from large distances and from upcurrent of preferred settlement locations. Using in situ choice chambers, we found that settling coral larvae were attracted to reef sounds, produced mainly by fish and crustaceans, which we broadcast underwater using loudspeakers. Our discovery that coral larvae can detect and respond to sound is the first description of an auditory response in the invertebrate phylum Cnidaria, which includes jellyfish, anemones, and hydroids as well as corals. If, like settlement-stage reef fish and crustaceans, coral larvae use reef noise as a cue for orientation, the alleviation of noise pollution in the marine environment may gain further urgency.},
  langid = {english},
  keywords = {Acoustics,Coral reefs,Invertebrates,Larvae,Marine environments,Marine fish,Oceans,Sound pressure},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\SWTMILXM\\Vermeij et al. - 2010 - Coral Larvae Move toward Reef Sounds.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\YA2W5FVU\\article.html}
}

@article{Vicente1980,
  title = {Thalassia as a Food Source: {{Importance}} and Potential in the Marine and Terrestrial Environments},
  author = {Vicente, V. P. and {Arroyo-Aguil{\'u}}, J. A. and Rivera, J. A.},
  year = {1980},
  month = jan,
  journal = {The Journal of Agriculture of the University of Puerto Rico},
  volume = {64},
  number = {1},
  pages = {107--120},
  doi = {10.46429/jaupr.v64i1.10252},
  annotation = {Abstract note: The chemical composition of \&lt;em\&gt;Thalassia\&lt;/em\&gt; leaves is described. Of the leaf-dry matter, 40.6\% consists of soluble nutrients: crude protein, lipids, soluble carbohydrates and ash. Crude protein content was 17\% (R = 15.8-18.1\%). Essential nutritive minerals were found in considerable quantities: calcium, 1.32\% (R = 1.21-1.47\%); phosphorus, .21\% (R = .19-.23\%); potassium, 3.0\% (R = 2.47\%-3.30\%) and magnesium, 1.26\% (R = 1.09\%-1.38\%). The cell wall or neutral-detergent fiber fraction was 59.4\% (R = 46.1-64.6\%), of which 19.1\% consisted of hemicellulose. The lignin content varied from 22.9\% (KMnO\&lt;sub\&gt;4\&lt;/sub\&gt;) to 9.1\% (H\&lt;sub\&gt;2\&lt;/sub\&gt;SO\&lt;sub\&gt;4\&lt;/sub\&gt;) depending on whether KMnO\&lt;sub\&gt;4 \&lt;/sub\&gt;or H\&lt;sub\&gt;2\&lt;/sub\&gt;SO\&lt;sub\&gt;4 \&lt;/sub\&gt;was used as an oxidizing agent. The importance of \&lt;em\&gt;Thalassia\&lt;/em\&gt; leaves as a food source for the seagrass community is described by five major food chains hereby proposed: the large herbivore, the fish herbivore, the gastropod herbivore, the urchin herbivore and the detrital food chains. The potential value of \&lt;em\&gt;Thalassia\&lt;/em\&gt; as a food source for domestic animals is evaluated on the basis of comparison with forage crops.}
}

@article{Waycott2009,
  title = {Accelerating Loss of Seagrasses across the Globe Threatens Coastal Ecosystems},
  author = {Waycott, Michelle and Duarte, Carlos M. and Carruthers, Tim J. B. and Orth, Robert J. and Dennison, William C. and Olyarnik, Suzanne and Calladine, Ainsley and Fourqurean, James W. and Heck, Jr., Kenneth L. and Hughes, A. Randall and Kendrick, Gary A. and Kenworthy, W. Judson and Short, Frederick T. and Williams, Susan L.},
  year = {2009},
  month = jul,
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  volume = {106},
  number = {30},
  pages = {12377--12381},
  issn = {0027-8424},
  doi = {10.1073/pnas.0905620106},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\PPZYF4UY\\Waycottetal2009.pdf}
}

@article{Webster1998,
  title = {Effect of {{Shoot Density}} on the {{Infaunal Macro-invertebrate Community}} within {{aZostera marinaSeagrass Bed}}},
  author = {Webster, P. J. and Rowden, A. A. and Attrill, M. J.},
  year = {1998},
  month = sep,
  journal = {Estuarine, Coastal and Shelf Science},
  volume = {47},
  number = {3},
  pages = {351--357},
  issn = {0272-7714},
  doi = {10.1006/ecss.1998.0358},
  abstract = {A seagrass (Zostera marina) bed in south-west United Kingdom was mapped using SCUBA in July 1996. Within the bed, three seagrass density ranges (shoots m-2) were sampled, low (1\textendash 50), medium (51\textendash 100) and high ({$>$}100), to assess infaunal macro-invertebrate community structure. At each of the sites seagrass and sediment parameters were measured (shoot density, number of leaves per shoot, root-rhizome biomass, median grain size, sorting coefficient, silt fraction). As seagrass density increased, a corresponding increase in infaunal diversity was observed, multivariate analysis indicating that there were significant differences in community structure between the shoot density ranges sampled. The main factors explaining community structure were above-ground parameters (leaf number per shoot, shoot density), whilst sediment and root-rhizome measures were apparently unimportant in structuring the infaunal community. The influence of increased seagrass structural complexity on the infauna is possibly indirect (e.g. increased detrital deposition, reduced predator efficiency), however, the direct influence of root-rhizome complexity requires further investigation.},
  langid = {english},
  keywords = {community structure,English Channel,infauna,macro-invertebrate,seagrass,shoot density},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\FCTEYPUE\\S0272771498903584.html}
}

@article{Weisz2008,
  title = {Do Associated Microbial Abundances Impact Marine Demosponge Pumping Rates and Tissue Densities?},
  author = {Weisz, J. B. and Lindquist, N. and Martens, C. S.},
  year = {2008},
  month = mar,
  journal = {Oecologia},
  volume = {155},
  number = {2},
  pages = {367--376},
  issn = {0029-8549},
  doi = {10.1007/s00442-007-0910-0},
  abstract = {The evolution of marine demosponges has led to two basic life strategies: one involving close associations with large and diverse communities of microorganisms, termed high microbial abundance (HMA) species, and one that is essentially devoid of associated microorganisms, termed low microbial abundance (LMA) species. This dichotomy has previously been suggested to correlate with morphological differences, with HMA species having a denser mesohyl and a more complex aquiferous systems composed of longer and narrower water canals that should necessitate slower seawater filtration rates. We measured mesohyl density for a variety of HMA and LMA sponges in the Florida Keys, and seawater pumping rates for a select group of these sponges using an in situ dye technique. HMA sponges were substantially denser than LMA species, and had per unit volume pumping rates 52-94\% slower than the LMA sponges. These density and pumping rate differences suggest that evolutionary differences between HMA and LMA species may have resulted in profound morphological and physiological differences between the two groups. The LMA sponge body plan moves large quantities of water through their porous tissues allowing them to rapidly acquire the small particulate organic matter (POM) that supplies the majority of their nutritional needs. In contrast, the HMA sponge body plan is suited to host large and tightly packed communities of microorganisms and has an aquiferous system that increases contact time between seawater and the sponge/microbial consortium that feeds on POM, dissolved organic matter and the raw inorganic materials for chemolithotrophic sponge symbionts. The two evolutionary patterns represent different, but equally successful patterns and illustrate how associated microorganisms can potentially have substantial effects on host evolution.},
  langid = {english},
  keywords = {aquiferous systems,bacteria,baikal littoral-zone,current-induced flow,ecology,evolution,filtration,food,halichondria-panicea,mutualism,natural diet,reef sponges,sponge,symbiosis},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\6W37Y7HD\\weiszetal2008.pdf}
}

@misc{Wong,
  title = {\textcopyright{} 2012 {{The Author}}(s). {{Journal}} Compilation \textcopyright{} 2012 {{REABIC Open Access}}},
  author = {Wong, Melisa C. and Vercaemer, B{\'e}n{\'e}dikte},
  abstract = {Effects of invasive colonial tunicates and a native sponge on the growth, survival, and light attenuation of eelgrass (Zostera marina)},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\IJZZFMRR\\Wong and Vercaemer - © 2012 The Author(s). Journal compilation © 2012 R.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\TL8AXUH8\\download.html}
}

@article{Wulff1984,
  title = {Sponge-Mediated Coral Reef Growth and Rejuvenation},
  author = {Wulff, Janie L.},
  year = {1984},
  month = nov,
  journal = {Coral Reefs},
  volume = {3},
  number = {3},
  pages = {157--163},
  issn = {1432-0975},
  doi = {10.1007/BF00301960},
  abstract = {Sponges mediate consolidation of Porites furcata rubble on shallow Caribbean reefs by quickly adhering to rubble and stabilizing it until carbonate secreting organisms can grow and consolidate it to the reef. Experimental investigations demonstrate that the entire cycle from (1) temporary binding of rubble by sponges, through (2) rubble consolidation by encrusting coralline algae, to (3) colonization of consolidated rubble by corals, can be completed within 10 months. Bound rubble both adds to vertical reef growth and also provides stable substrata for colonization by corals. Corals that colonize stabilized rubble are damaged less and survive better than on unstable rubble. Rubble that is not temporarily stabilized by sponges does not become bound to the reef, because continuous movement disturbs the consolidation process, and does not provide suitable substrata for settlement and growth of corals. Sponge-mediated consolidation of rubble may increase rates of reef growth and enhance reef recovery after damage. This new role for sponges in reef growth is not obvious from examination of the internal fabric of a reef frame. Spongemediated consolidation may help to explain geographic and temporal differences in growth and morphology among shallow reefs of ramose corals.}
}

@article{Wulff1997,
  title = {Mutualisms among Species of Coral Reef Sponges},
  author = {Wulff, J. L.},
  year = {1997},
  month = jan,
  journal = {Ecology},
  volume = {78},
  number = {1},
  pages = {146--159},
  issn = {0012-9658},
  doi = {10.1890/0012-9658(1997)078[0146:masocr]2.0.co;2},
  abstract = {Intimate associations among individuals of three common species of Caribbean coral reef sponges can be mutually beneficial. Both growth rate and survival are enhanced when heterospecific sponges adhere to each other, as demonstrated by experiments in which sponges of the same size and genotype were grown (1) in intimate association with conspecific vs. heterospecific sponges, (2) alone vs. in intimate association with conspecific sponges, and (3) alone on the primary substratum vs. attached to an intact branch of a conspecific or heterospecific sponge. Natural development and long-term dynamics of these associations were observed in unmanipulated individuals and also modelled by an experiment in which branches were exchanged between neighboring sponges. The three species studied (lotrochota birotulata, Amphimedon rubens, and Aplysina fulva) share an erect branching growth form but differ in tissue and skeletal characteristics sufficiently that they are in different orders of the Class Demospongiae. Reflecting these differences, the species are demonstrated to differ from each other in their susceptibility to a variety of environmental hazards, including predation by angelfishes and trunkfishes, predation by starfish, smothering by sediment, breakage by storm waves, pulverization by storm waves, toppling by storm waves, fragment mortality, and pathogens. Although the mechanisms by which growth rate is enhanced by adhering to a heterospecific sponge are unknown, these sponges appear to be able to decrease their loss rate by adhering tightly to sponges of species that differ from them in chemistry, tissue density, and skeletal construction, thereby increasing survival of hazards to which they would succumb when growing alone.},
  langid = {english},
  keywords = {ABUNDANCE,ASSOCIATIONS,COMPETITION,coral reefs,diffuse mutualism,direct mutualism,FACILITATION,facultative mutualism,GROWTH,MARSH PLANTS,POPULATIONS,PORIFERA,PRODUCTIVITY,sponge extensibility,sponge strength,SURVIVAL},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\47I9RPCE\\wulffmutualism.pdf}
}

@article{Wulff1997a,
  title = {Parrotfish Predation on Cryptic Sponges of {{Caribbean}} Coral Reefs},
  author = {Wulff, J. L.},
  year = {1997},
  month = jul,
  journal = {Marine Biology},
  volume = {129},
  number = {1},
  pages = {41--52},
  issn = {0025-3162},
  abstract = {Some sponge species that live in crevices in the reef frame appear to be restricted to their cryptic habitat by predation. When cryptic sponges were excavated, on Guigalotupo reef. San Bias, Panama, exposing them to potential predators, they were eaten by fishes that are generally considered to be herbivores, primarily parrot-fishes of the genus Sparisoma: S. aurofrenatum (Cuvier \& Valenciennes), S. viride (Bonnaterre), and S. aurofrenatum (Bloch \& Schneider). Of the 9150 bites observed to be taken by these species during paired (i.e., with sponges versus without sponges) trials conducted in defined feeding areas during 1986, 1987, and 1988, 72\% (i.e. 6581 bites) were on cryptic sponges, even though these were only offered during half of the total observation time and never constituted more than 7\% of the cover of the feeding observation areas. Individual parrotfish returned over and over to take bites of the exposed cryptic sponges until they were entirely consumed. They vigorously chased each other away from the sponges, but exhibited no such defense of their usual algal foods. A total of 18 sponge species were tested. Of the cryptic and semi-cryptic sponge species tested, only one of six was rejected by the parrotfish. Two of these six sponge species were consistently consumed entirely, and two were consumed entirely whenever their surfaces were sliced off with a razor blade, demonstrating that these sponges concentrate defenses against predators in their surfaces. One semi-cryptic species and one semi-exposed species were fed upon, but not entirely consumed. By contrast, 11 of 12 of the exposed and semi-exposed species were rejected. Cryptic sponges grew out of their cavities in the reef only when protected by seasonally thick mats of macroalgae or by cages that excluded fish.},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\4TPSB3JC\\wulff3.pdf}
}

@article{Wulff2000,
  title = {Sponge Predators May Determine Differences in Sponge Fauna between Two Sets of Mangrove Cays. {{Belize Barrier Reef}}.},
  author = {Wulff, J.},
  year = {2000},
  journal = {Atoll Res Bull},
  volume = {477},
  pages = {251--263},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\8HINHZV5\\Wulff2000.pdf}
}

@article{Wulff2006,
  title = {Ecological Interactions of Marine Sponges},
  author = {Wulff, J. L.},
  year = {2006},
  month = feb,
  journal = {Canadian Journal of Zoology-Revue Canadienne De Zoologie},
  volume = {84},
  number = {2},
  pages = {146--166},
  issn = {0008-4301},
  doi = {10.1139/z06-019},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\6CSTFPM8\\Wulff2006.pdf}
}

@article{Wulff2008,
  title = {Collaboration among Sponge Species Increases Sponge Diversity and Abundance in a Seagrass Meadow},
  author = {Wulff, J. L.},
  year = {2008},
  month = jun,
  journal = {Marine Ecology-an Evolutionary Perspective},
  volume = {29},
  number = {2},
  pages = {193--204},
  issn = {0173-9565},
  doi = {10.1111/j.1439-0485.2008.00224.x},
  abstract = {Caribbean sponge species typical of coral reefs are generally inhibited from living in seagrass meadows by their vulnerability to predation by the large starfish Oreaster reticulatus (Linnaeus 1758). Although readily consumed by Oreaster, the conspicuous coral reef sponge species Lissodendoryx colombiensis Zea \& van Soest, 1986 has expanded its habitat distribution to include a seagrass (Thalassia testudinum Banks ex Konig, 1805) meadow in Belize, where individuals grow to volumes of nearly 7 l. By simple observation, L. colombiensis appears to be an inferior competitor in this system, because portions of many individuals are overgrown by seagrass sponge species. However, experimentally clustering seagrass sponges around L. colombiensis individuals deterred starfish from feeding on them, suggesting an advantage to being overgrown. Sizes of individual L. colombiensis can fluctuate widely over short time intervals, reflecting both a relatively fast growth rate and the high rate at which starfish consume this species. At the population level these fluctuations are not evident, as losses of L. colombiensis due to Oreaster are balanced by a combination of efficient recruitment, rapid regeneration and growth, and protection of portions of many individuals by the overgrowth of seagrass sponge species that are unpalatable to Oreaster. In turn, the seagrass sponges acquire stable perches on L. colombiensis individuals in this sediment-dominated habitat. Community ecology theory relating to diversity patterns in sessile organisms has focused on competition between space-requiring neighbors as the underlying process that inevitably decreases diversity unless curtailed. Sponges, with their propensity for engaging in beneficial interactions with neighbors, demand expansion of the theory to acknowledge how collaboration can increase abundance and species diversity within a community.},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\SP9NXY84\\wulff.pdf}
}

@article{Yeager2011,
  title = {Effects of Habitat Heterogeneity at Multiple Spatial Scales on Fish Community Assembly},
  author = {Yeager, L. A. and Layman, C. A. and Allgeier, J. E.},
  year = {2011},
  month = sep,
  journal = {Oecologia},
  volume = {167},
  number = {1},
  pages = {157--168},
  issn = {0029-8549},
  doi = {10.1007/s00442-011-1959-3},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\3QW9TASA\\yeageretal2011.pdf}
}

@article{Yeager2012,
  ids = {yeager2012a},
  title = {Effects of Seascape Context on Condition, Abundance, and Secondary Production of a Coral Reef Fish, {{Haemulon}} Plumierii},
  author = {Yeager, La and Acevedo, Cl and Layman, Ca},
  year = {2012},
  month = aug,
  journal = {Marine Ecology Progress Series},
  volume = {462},
  pages = {231--240},
  issn = {0171-8630, 1616-1599},
  doi = {10.3354/meps09855},
  abstract = {Variation in seascape composition has the potential to impact habitat quality for fishes, and characteristics of the surrounding seascape have been correlated with abundance of organisms in many systems. Less studied is how seascape context may affect other aspects of habitat quality including growth, condition, or production of focal species. Juvenile white grunts Haemulon plumierii are known to rest on patch reefs during the day and move into seagrass habitat at night to feed, linking multiple habitats through these daily foraging migrations. We created artificial reefs across a gradient of seagrass cover and determined how juvenile white grunt condition, growth, abundance, and secondary production were related to seagrass cover within the seascape. White grunt abundance was positively correlated with the cover of seagrass within the seascape, while condition (relative condition factor, Kn) and growth rate (measured using the ratio of RNA to DNA) did not vary among reefs within different seascapes. Secondary production of white grunts was found to be highest on reefs in seascapes with more seagrass. Our results are consistent with the hypothesis that increased food resources associated with higher seagrass cover contribute to increased grunt production. Differences in habitat quality among reefs in different seascapes were manifest at the population (abundance) and ecosystem function (secondary production) levels and not at the individual level (individual growth rate or condition factor). These results highlight the importance of considering multiple levels of individual and population responses in assessments of habitat quality, and add evidence that seascape composition should be considered in spatially explicit management strategies.},
  langid = {english},
  file = {C\:\\Users\\sarcher\\Zotero\\storage\\6DCJAD7N\\Yeager et al. - 2012 - Effects of seascape context on condition, abundanc.pdf;C\:\\Users\\sarcher\\Zotero\\storage\\VCRWERNU\\yeageretal2012.pdf}
}