Determining the Extent and Characterizing Coral Reef Habitats of the Northern Latitudes of the Florida Reef Tract (Martin County)

Climate change has recently been implicated in poleward shifts of many tropical species including corals; thus attention focused on higher-latitude coral communities is warranted to investigate possible range expansions and ecosystem shifts due to global warming. As the northern extension of the Florida Reef Tract (FRT), the third-largest barrier reef ecosystem in the world, southeast Florida (25–27° N latitude) is a prime region to study such effects. Most of the shallow-water FRT benthic habitats have been mapped, however minimal data and limited knowledge exist about the coral reef communities of its northernmost reaches off Martin County. First benthic habitat mapping was conducted using newly acquired high resolution LIDAR bathymetry and aerial photography where possible to map the spatial extent of coral reef habitats. Quantitative data were collected to characterize benthic cover and stony coral demographics and a comprehensive accuracy assessment was performed. The data were then analyzed in a habitat biogeography context to determine if a new coral reef ecosystem region designation was warranted. Of the 374 km² seafloor mapped, 95.2% was Sand, 4.1% was Coral Reef and Colonized Pavement, and 0.7% was Other Delineations. Map accuracy assessment yielded an overall accuracy of 94.9% once adjusted for known map marginal proportions. Cluster analysis of cross-shelf habitat type and widths indicated that the benthic habitats were different than those further south and warranted designation of a new coral reef ecosystem region. Unlike the FRT further south, coral communities were dominated by cold-water tolerant species and LIDAR morphology indicated no evidence of historic reef growth during warmer climates. Present-day hydrographic conditions may be inhibiting poleward expansion of coral communities along Florida. This study provides new information on the benthic community composition of the northern FRT, serving as a baseline for future community shift and range expansion investigations.     

Coral Reef Community Composition in the Context of Disturbance History on the Great Barrier Reef,Australia

Much research on coral reefs has documented differential declines in coral and associated organisms. In order to contextualise this general degradation, research on community composition is necessary in the context of varied disturbance histories and the biological processes and physical features thought to retard or promote recovery. We conducted a spatial assessment of coral reef communities across five reefs of the central Great Barrier Reef, Australia, with known disturbance histories, and assessed patterns of coral cover and community composition related to a range of other variables thought to be important for reef dynamics. Two of the reefs had not been extensively disturbed for at least 15 years prior to the surveys. Three of the reefs had been severely impacted by crown-of-thorns starfish outbreaks and coral bleaching approximately a decade before the surveys, from which only one of them was showing signs of recovery based on independent surveys. We incorporated wave exposure (sheltered and exposed) and reef zone (slope, crest and flat) into our design, providing a comprehensive assessment of the spatial patterns in community composition on these reefs. Categorising corals into life history groupings, we document major coral community differences in the unrecovered reefs, compared to the composition and covers found on the undisturbed reefs. The recovered reef, despite having similar coral cover, had a different community composition from the undisturbed reefs, which may indicate slow successional processes, or a different natural community dominance pattern due to hydrology and other oceanographic factors. The variables that best correlated with patterns in the coral community among sites included the density of juvenile corals, herbivore fish biomass, fish species richness and the cover of macroalgae. Given increasing impacts to the Great Barrier Reef, efforts to mitigate local stressors will be imperative to encouraging coral communities to persist into the future.     

Geomorphology and community structure of Middle Reef, central Great Barrier Reef, Australia: an inner-shelf turbid zone reef subject to episodic mortality events

Middle Reef is an inshore turbid zone reef located 4 km offshore from Townsville, Queensland, Australia. The reef consists of four current-aligned, interconnected reef patches that have reached sea level and formed reef flats. It is regularly exposed to high turbidity (up to 50 mg l⁻¹) generated by wave-driven sediment resuspension or by episodic flood plumes. Middle Reef has a high mean hard coral cover (>39%), relatively low mean macro-algal cover (<15%) and a coral community comprising at least 81 hard coral species. Cluster analysis differentiated six benthic communities which were mapped onto the geomorphological structure of the reef to reveal a spatially patchy community mosaic that reflects hydrodynamic and sediment redistribution processes. Coral cover data collected annually from windward slope transects since 1993 show that coral cover has increased over the last ~15 years despite a history of episodic mortality events. Although episodic mortality may be interpreted as an indication of marginality, over decadal timescales, Middle Reef has recovered rapidly following mortality events and is clearly a resilient coral reef.     

Recovery without resilience: persistent disturbance and long-term shifts in the structure of fish and coral communities at Tiahura Reef, Moorea

Disturbances have a critical effect on the structure of natural communities. In this study long-term changes were examined in the reef community at Tiahura Reef, on the northern coast of Moorea, which had been subject to many and varied disturbances over the last 25 years. Tiahura Reef was subject to an outbreak of crown-of-thorns starfish (Acanthaster planci) in 1980–1981, causing significant declines in the abundance of scleractinian corals and butterflyfishes. By 2003, the abundance of corals and butterflyfishes had returned to former levels, but despite this apparent recovery, the species composition of coral communities and butterflyfish assemblages was very different from those recorded in 1979. Ongoing disturbances (including further outbreaks of crown-of-thorns starfish, cyclones, and coral bleaching events) appear to have prevented recovery of many important coral species (notably, Acropora spp.), which has had subsequent effects on the community structure of coral-feeding butterflyfishes. This study shows that recurrent disturbances may have persistent effects on the structure and dynamics of natural communities.     

Patterns in the structural typology of benthic communities on two coral reefs of the central Great Barrier Reef

The morphological life-forms, that is to say, physiognomic-structural attributes, of two coral reef communities were used in a numerical analysis to determine the power of these attributes in recovering the underlying community structure. We used 17 attributes from the benthic communities at 6 reef slope sites on each of a midshelf and off-shore reef of the central Great Barrier Reef. These reefs had been previously well studied by traditional species-level means for several major taxonomic groups such as corals, fish and soft corals. Our multivariate analyses were able to recover broad patterns of between-reef affinity and discrete within-reef zonation patterns similar to those found in earlier studies, and in broad accord with the prevailing model of reef community structure, but with far greater efficacy. But perhaps more importantly, by placing all the benthos within the same context for the first time, our analyses were able to recover new patterns of community structure independent of the ones described earlier. This suggests that single-model explantations for the complex phenomena of coral reefs are likely to be inadequate.     

Great Barrier Reef butterflyfish community structure: the role of shelf position and benthic community type

The extent to which fish communities are structured by spatial variability in coral reef habitats versus stochastic processes (such as larval supply) is very important in predicting responses to sustained and ongoing habitat degradation. In this study, butterflyfish and benthic communities were surveyed annually over 15 years on 47 reefs (spanning 12° of latitude) of the Great Barrier Reef (GBR). Spatial autocorrelation in the structure of butterflyfish communities versus key differences in reef habitats was investigated to assess the extent to which the structure of these fish communities is influenced by habitat conditions. Benthic communities on each of the 47 reefs were broadly categorised as either: 1. Poritidae/Alcyoniidae, 2. mixed taxa, 3. soft coral or 4. Acropora-dominated habitats. These habitat types most reflected increases in water clarity and wave exposure, moving across the GBR shelf from coastal to outer-shelf environments. In turn, each habitat type also supported very distinct butterflyfish communities. Hard coral feeders were always the dominant butterflyfish species in each community type. However, the numerically dominant species changed according to habitat type, representing spatial replacement of species across the shelf. This study reveals clear and consistent differences in the structure of fish communities among reefs associated with marked differences in habitat structure.     

Controls on coral-ground development along the northern Mesoamerican Reef tract

Coral-grounds are reef communities that colonize rocky substratum but do not form framework or three-dimensional reef structures. To investigate why, we used video transects and underwater photography to determine the composition, structure and status of a coral-ground community located on the edge of a rocky terrace in front of a tourist park, Xcaret, in the northern Mesoamerican Reef tract, Mexico. The community has a relatively low coral, gorgonian and sponge cover (<10%) and high algal cover (>40%). We recorded 23 species of Scleractinia, 14 species of Gorgonacea and 30 species of Porifera. The coral community is diverse but lacks large coral colonies, being dominated instead by small, sediment-tolerant, and brooding species. In these small colonies, the abundance of potentially lethal interactions and partial mortality is high but decreases when colonies are larger than 40 cm. Such characteristics are consistent with an environment control whereby storm waves periodically remove larger colonies and elevate sediment flux. The community only survives these storm conditions due to its slope-break location, which ensures lack of burial and continued local recruitment. A comparison with similar coral-ground communities in adjacent areas suggests that the narrow width of the rock terrace hinders sediment stabilization, thereby ensuring that communities cannot escape bottom effects and develop into three-dimensional reef structures on geological time scales.     

Retention of phytoplankton and planktonic microbes on coral reefs within the Great Barrier Reef,Australia

Concentrations of phytoplankton (coccoid cychobacteria and total chlorophyll) and planktonic microrial communities (heterotropic bacteria, nanoflagellates and ciliates) were lower over leeward reef flats than over open water or reef faces, around Davies Reef and Myrmidon Reef in the central Great Barrier Reef, Australia. Concentrations of cyanobacteria, which accounted for approximately 15–50% of the carbon biomass of phytoplankton in open water, decreased from the reef face towards the leeward reef flat. Concentrations of ciliates were consistently lower at the leeward reef flat than at the reef face. For Davies Reef, the retention rates of phytoplankton and planktonic microbial communities were estimated to reach 253 gC d^-1 per 1 m strip of the reef or about 0.09 gC m^-2 d^-1. This value is virtually equal to estimates of net community production (0.1 gC m^-2 d^-1). This allocthonous organic subsidy may help maintain spositive carbon balance on both Davies and Myrmidon Reefs on the Great Barrier Reef.     

Additive Diversity Partitioning of Fish in a Caribbean Coral Reef Undergoing Shift Transition

Shift transitions in dominance on coral reefs from hard coral cover to fleshy macroalgae are having negative effects on Caribbean coral reef communities. Data on spatiotemporal changes in biodiversity during these modifications are important for decision support for coral reef biodiversity protection. The main objective of this study is to detect the spatiotemporal patterns of coral reef fish diversity during this transition using additive diversity-partitioning analysis. We examined α, β and γ fish diversity from 2000 to 2010, during which time a shift transition occurred at Mahahual Reef, located in Quintana Roo, Mexico. Data on coral reef fish and benthic communities were obtained from 12 transects per geomorphological unit (GU) in two GUs (reef slope and terrace) over six years (2000, 2005, 2006, 2007, 2008, 2010). Spatial analysis within and between the GUs indicated that the γ-diversity was primarily related to higher β-diversity. Throughout the six study years, there were losses of α, β and γ-diversity associated spatially with the shallow (reef slope) and deeper (reef terrace) GUs and temporally with the transition in cover from mound corals to fleshy macroalgae and boulder corals. Despite a drastic reduction in the number of species over time, β-diversity continues to be the highest component of γ-diversity. The shift transition had a negative effect on α, β and γ-diversity, primarily by impacting rare species, leading a group of small and less vulnerable fish species to become common and an important group of rare species to become locally extinct. The maintenance of fish heterogeneity (β-diversity) over time may imply the abetment of vulnerability in the face of local and global changes.     

Long-term coral community records from Lugger Shoal on the terrigenous inner-shelf of the central Great Barrier Reef,Australia

Long-term (millennial timescale) records of coral community structure can be developed from the analysis of corals preserved in radiometrically dated reef cores. Here, we present such a record (based on six cores) from Lugger Shoal, a turbid zone, nearshore reef on the inner-shelf of the central Great Barrier Reef. Lugger Shoal initiated growth ~800 cal yBP. It is constructed of large in situ Porites bommies, between which a framework of coral rubble (dominated by Acropora pulchra, Montipora mollis, Galaxea fascicularis and Cyphastrea serailia) has accumulated. Reef accretion occurred under conditions of net long-term fine-grained, terrigenous sediment accumulation, and with a coral community dominated throughout by a consistent, but low diversity, suite of coral taxa. This dataset supports recent suggestions that nearshore coral communities that establish themselves under conditions that are already close to the thresholds for coral survival may be resilient to water quality deteriorations associated with human activities.     

Sponge distribution across Davies Reef,Great Barrier Reef,relative to location,depth, and water movement

Sponge populations were surveyed at different depths in three zones of Davies Reef, a large platform reef of the central Great Barrier Reef. Depth is the major discriminatory factor as few sponges are found within the first 10 m depth and maximal populations occur between 15 m and 30 m on fore-reef, lagoon and back-reef slopes. Reef location is another major factor, with the lagoon containing a significantly different sponge population to either the fore-reef or the back-reef slopes. Physical factors are considered to be the major influences behind these patterns. Physical turbulence is strongest within the first 10 m and apparently limits sponge growth within these shallow zones. Insufficient photosynthetic radiation limits the growth of the sponge population below 30 m depth as many of the species are phototrophic with a dependence on cyanobacterial symbionts for nutrition. Sponge populations on the outer (fore- and back-) reef slopes are comparable with each other but different from those on lagoon slopes where currents are reduced and fine sediment loads are higher. The largest populations occur on the back-reef slope where currents are stronger and there are possibly higher concentrations of organic nutrients originating from the more productive shallow parts of the reef. While there are correlations between sponge populations and environmental parameters, data are insufficient to enable more definitive conclusions to be drawn. Most sponge species are distributed widely over the reef, however, some are restricted to a few habitats and, hence, may be used to characterize those habitats.     

An all-taxon microbial inventory of the Moorea coral reef ecosystem

The Moorea Coral Reef Long Term Ecological Research (LTER) Site (17.50°S, 149.83°W) comprises the fringe of coral reefs and lagoons surrounding the volcanic island of Moorea in the Society Islands of French Polynesia. As part of our Microbial Inventory Research Across Diverse Aquatic LTERS biodiversity inventory project, we characterized microbial community composition across all three domains of life using amplicon pyrosequencing of the V6 (bacterial and archaeal) and V9 (eukaryotic) hypervariable regions of small-subunit ribosomal RNA genes. Our survey spanned eight locations along a 130-km transect from the reef lagoon to the open ocean to examine changes in communities along inshore to offshore gradients. Our results illustrate consistent community differentiation between inshore and offshore ecosystems across all three domains, with greater richness in all domains in the reef-associated habitats. Bacterial communities were more homogenous among open ocean sites spanning >100 km than among inshore sites separated by <1 km, whereas eukaryotic communities varied more offshore than inshore, and archaea showed more equal levels of dissimilarity among subhabitats. We identified signature communities representative of specific geographic and geochemical milieu, and characterized co-occurrence patterns of specific microbial taxa within the inshore ecosystem including several bacterial groups that persist in geographical niches across time. Bacterial and archaeal communities were dominated by few abundant taxa but spatial patterning was consistent through time and space in both rare and abundant communities. This is the first in-depth inventory analysis of biogeographic variation of all three microbial domains within a coral reef ecosystem.     

Latitudinal variation in coral communities in eastern Australia: a qualitative biophysical model of factors regulating coral reefs

The processes underlying the distributional limits of both corals and coral reefs can be elucidated by examining coral communities at high latitudes. Coral-dominated communities in eastern Australia cover a latitudinal range of >2,500 km, from the northern Great Barrier Reef (11°S) to South West Rocks (31.5°S). Patterns of coral species richness from 11 locations showed a clear separation between the Great Barrier Reef and subtropical sites, with a further abrupt change at around 31°S. Differences in community structure between the Great Barrier Reef and more southern sites were mainly attributable to higher cover of massive corals, branching Acropora, dead coral and coralline algae on the Great Barrier Reef, and higher cover of macroalgae and bare rock at more southern sites. The absence of some major reef-building taxa (i.e., staghorn Acropora and massive Porites) from most subtropical sites coincided with the loss of reef accretion capacity. Despite high cover of hard corals in communities at up to 31°S, only Lord Howe Island contained areas of reef accretion south of the Great Barrier Reef. Factors that have been hypothesized to account for latitudinal changes in coral community structure include water temperature, aragonite saturation, light availability, currents and larval dispersal, competition between corals and other biota including macroalgae, reduced coral growth rates, and failure of coral reproduction or recruitment. These factors do not operate independently of each other, and they interact in complex ways.     

Patterns in the distribution of fish communities across the Central Great Barrier Reef

Summary Changes in the structure of fish communities along a transect from the Australian mainland to the Coral Sea, in the Central region of the Great Barrier Reef, were examined. Visual censuses of fish were made on the outer reef slopes (0 to 13 m deep) of two inshore reefs, approximately 10 km offshore, three reefs on the mid-shelf, 50 km offshore, three reefs on the outer shelf, 100 km offshore, and three reefs in the Coral Sea approximately 200 km offshore. The Pomacentridae, Chaetodontidae, Acanthuridae and Scaridae were examined in detail—the Labridac, Siganidae and the lutjanid genus Caesio in less detail. Major changes in the composition of fish communities occurred along the transect (Fig. 3). There were differences in the composition of assemblages among replicate censuses within individual reefs and also differences between reefs at the same location on the transect but these differences were small compared to those among locations. The nature of the distribution of species across the transect differed between families (Figs. 4–6). Pomacentrid and chaetodontid species were significantly more restricted in distribution than acanthurids, scarids or labrids.     

Strong but opposing β-diversity–stability relationships in coral reef fish communities

The ‘diversity–stability hypothesis’, in which higher species diversity within biological communities buffers the risk of ecological collapse, is now generally accepted. However, empirical evidence for a relationship between β-diversity (spatial turnover in community structure) and temporal stability in community structure remains equivocal, despite important implications for theoretical ecology and conservation biology. Here, we report strong β-diversity–stability relationships across a broad sample of fish taxa on Australia''s Great Barrier Reef. These relationships were robust to random sampling error and spatial and environmental factors, such as latitude, reef size and isolation. While β-diversity was positively associated with temporal stability at the community level, the relationship was negative for some taxa, for example surgeonfishes (Acanthuridae), one of the most abundant reef fish families. This demonstrates that the β-diversity–stability relationship should not be indiscriminately assumed for all taxa, but that a species’ risk of extirpation in response to disturbance is likely to be taxon specific and trait based. By combining predictions of spatial and temporal turnover across the study area with observations in marine-protected areas, we conclude that protection alone does not necessarily confer temporal stability and that taxon-specific considerations will improve the outcome of conservation efforts.     

Retention of Habitat Complexity Minimizes Disassembly of Reef Fish Communities following Disturbance: A Large-Scale Natural Experiment

High biodiversity ecosystems are commonly associated with complex habitats. Coral reefs are highly diverse ecosystems, but are under increasing pressure from numerous stressors, many of which reduce live coral cover and habitat complexity with concomitant effects on other organisms such as reef fishes. While previous studies have highlighted the importance of habitat complexity in structuring reef fish communities, they employed gradient or meta-analyses which lacked a controlled experimental design over broad spatial scales to explicitly separate the influence of live coral cover from overall habitat complexity. Here a natural experiment using a long term (20 year), spatially extensive (∼115,000 kms²) dataset from the Great Barrier Reef revealed the fundamental importance of overall habitat complexity for reef fishes. Reductions of both live coral cover and habitat complexity had substantial impacts on fish communities compared to relatively minor impacts after major reductions in coral cover but not habitat complexity. Where habitat complexity was substantially reduced, species abundances broadly declined and a far greater number of fish species were locally extirpated, including economically important fishes. This resulted in decreased species richness and a loss of diversity within functional groups. Our results suggest that the retention of habitat complexity following disturbances can ameliorate the impacts of coral declines on reef fishes, so preserving their capacity to perform important functional roles essential to reef resilience. These results add to a growing body of evidence about the importance of habitat complexity for reef fishes, and represent the first large-scale examination of this question on the Great Barrier Reef.     

南沙群岛渚碧礁大型底栖动物群落特征

利用2002年5月12日至5月21日在南沙群岛渚碧礁用轻潜水(SCUBA)方法于该礁盘不同位置设立的4个定量取样站采集的调查资料,采用IRI指数、ABC曲线方法和大型多元统计分析软件PRIMER对渚碧礁大型底栖动物进行等级聚类分析(CLUSTER)和非度量MDS标序,研究群落结构格局以及用Shannon-Wiener指数、物种丰富度指数和物种均匀度指数分析物种多样性和群落种类组成的相似程度,对渚碧礁大型底栖动物的群落结构进行了初步研究。结果表明:调查获得渚碧礁调查站大型底栖动物总种数314种,平均栖息密度为357.94个/m2,平均生物量为64.85g/m2;群落中主要的重要种或优势种为粗糙毛壳蟹(Pilodius scabriculus)和鼓虾(Alpheus spp.),但IRI指数相对较低;群落结构聚类分析和MDS标序表明,4个取样站的群落结构非常相似,Bray-Curtis相似性系数达到80%以上。     

Variability in Microbial Community Composition and Function Between Different Niches Within a Coral Reef

To explore how microbial community composition and function varies within a coral reef ecosystem, we performed metagenomic sequencing of seawater from four niches across Heron Island Reef, within the Great Barrier Reef. Metagenomes were sequenced from seawater samples associated with (1) the surface of the coral species Acropora palifera, (2) the surface of the coral species Acropora aspera, (3) the sandy substrate within the reef lagoon and (4) open water, outside of the reef crest. Microbial composition and metabolic function differed substantially between the four niches. The taxonomic profile showed a clear shift from an oligotroph-dominated community (e.g. SAR11, Prochlorococcus, Synechococcus) in the open water and sandy substrate niches, to a community characterised by an increased frequency of copiotrophic bacteria (e.g. Vibrio, Pseudoalteromonas, Alteromonas) in the coral seawater niches. The metabolic potential of the four microbial assemblages also displayed significant differences, with the open water and sandy substrate niches dominated by genes associated with core house-keeping processes such as amino acid, carbohydrate and protein metabolism as well as DNA and RNA synthesis and metabolism. In contrast, the coral surface seawater metagenomes had an enhanced frequency of genes associated with dynamic processes including motility and chemotaxis, regulation and cell signalling. These findings demonstrate that the composition and function of microbial communities are highly variable between niches within coral reef ecosystems and that coral reefs host heterogeneous microbial communities that are likely shaped by habitat structure, presence of animal hosts and local biogeochemical conditions.     

The dynamics of benthic microbial communities at Davies Reef,central Great Barrier Reef

The dynamics of benthic microbial communities were examined within different functional zones (reef crest, reef flat, lagoon) of Davies Reef, central Great Barrier Reef, in winter. Bacterial numbers did not change significantly across the reef with a mean abundance of 1.3 (±0.6) x 10⁹ cells g^-1 DW of sediment. Bacterial production, measured as thymidine incorporation into DNA, ranged from 1.2 (±0.2) to 11.6 (±1.5) mg C m^-2h^-1 across the reef and was significantly lower in a reef crest basin than in the other zones. Bacterial growth rates () across the reef (0.05 to 0.33 g^-1) correlated only with sediment organic carbon and nitrogen. Protozoan and meiofaunal densities varied by an order of magnitude across the reef and correlated with one or more sediment variables but not with bacterial numbers or growth rates. Nutrient flux rates were similar to those found at other reefs in the central and southern Great Barrier Reef and are significantly lower than rates measured in temperate sand communities. In the front lagoon, bioturbation and feeding acitivity by thalassinid shrimps (Callianassa spp.) negatively influenced microbial and meiofaunal communities with a net import of organic matter necessary to support the estimated rates of bacterial productivity. In lagoonal areas not colonized by shrimps, primary productivity (400–1100 mg C m^-2d^-1) from algal mats was sufficient to support bacterial growth. It is suggested that deposit-feeding macrobenthos such as thalassinid crustaceans play a major role in the tructuring and functioning of lower trophic groups (bacteria, microalgae, protozoa, meiofauna) in coral reef sedments, particularly in laggons.     

Influence of an Oyster Reef on Development of the Microbial Heterotrophic Community of an Estuarine Biofilm

We characterized microbial biofilm communities developed over two very closely located but distinct benthic habitats in the Pensacola Bay estuary using two complementary cultivation-independent molecular techniques. Biofilms were grown for 7 days on glass slides held in racks 10 to 15 cm over an oyster reef and an adjacent muddy sand bottom. Total biomass and optical densities of dried biofilms showed dramatic differences for oyster reef versus non-oyster reef biofilms. This study assessed whether the observed spatial variation was reflected in the heterotrophic prokaryotic species composition. Genomic biofilm DNA from both locations was isolated and served as a template to amplify 16S rRNA genes with universal eubacterial primers. Fluorescently labeled PCR products were analyzed by terminal restriction fragment length polymorphism, creating a genetic fingerprint of the composition of the microbial communities. Unlabeled PCR products were cloned in order to construct a clone library of 16S rRNA genes. Amplified ribosomal DNA restriction analysis was used to screen and define ribotypes. Partial sequences from unique ribotypes were compared with existing database entries to identify species and to construct phylogenetic trees representative of community structures. A pronounced difference in species richness and evenness was observed at the two sites. The biofilm community structure from the oyster reef setting had greater evenness and species richness than the one from the muddy sand bottom. The vast majority of the bacteria in the oyster reef biofilm were related to members of the γ- and δ-subdivisions of Proteobacteria, the Cytophaga-Flavobacterium -Bacteroides cluster, and the phyla Planctomyces and Holophaga-Acidobacterium. The same groups were also present in the biofilm harvested at the muddy sand bottom, with the difference that nearly half of the community consisted of representatives of the Planctomyces phylum. Total species richness was estimated to be 417 for the oyster reef and 60 for the muddy sand bottom, with 10.5% of the total unique species identified being shared between habitats. The results suggest dramatic differences in habitat-specific microbial diversity that have implications for overall microbial diversity within estuaries.