Spatial scales of bacterial diversity in cold-water coral reef ecosystems

Background

Cold-water coral reef ecosystems are recognized as biodiversity hotspots in the deep sea, but insights into their associated bacterial communities are still limited. Deciphering principle patterns of bacterial community variation over multiple spatial scales may however prove critical for a better understanding of factors contributing to cold-water coral reef stability and functioning.

Methodology/Principal Findings

Bacterial community structure, as determined by Automated Ribosomal Intergenic Spacer Analysis (ARISA), was investigated with respect to (i) microbial habitat type and (ii) coral species and color, as well as the three spatial components (iii) geomorphologic reef zoning, (iv) reef boundary, and (v) reef location. Communities revealed fundamental differences between coral-generated (branch surface, mucus) and ambient microbial habitats (seawater, sediments). This habitat specificity appeared pivotal for determining bacterial community shifts over all other study levels investigated. Coral-derived surfaces showed species-specific patterns, differing significantly between Lophelia pertusa and Madrepora oculata, but not between L. pertusa color types. Within the reef center, no community distinction corresponded to geomorphologic reef zoning for both coral-generated and ambient microbial habitats. Beyond the reef center, however, bacterial communities varied considerably from local to regional scales, with marked shifts toward the reef periphery as well as between different in- and offshore reef sites, suggesting significant biogeographic imprinting but weak microbe-host specificity.

Conclusions/Significance

This study presents the first multi-scale survey of bacterial diversity in cold-water coral reefs, spanning a total of five observational levels including three spatial scales. It demonstrates that bacterial communities in cold-water coral reefs are structured by multiple factors acting at different spatial scales, which has fundamental implications for the monitoring of microbial diversity and function in those ecosystems.     

Composition of Archaea in Seawater,Sediment, and Sponges in the Kepulauan Seribu Reef System,Indonesia

Coral reefs are among the most diverse and productive ecosystems in the world. Most research has, however, focused on eukaryotes such as corals and fishes. Recently, there has been increasing interest in the composition of prokaryotes, particularly those inhabiting corals and sponges, but these have mainly focused on bacteria. There have been very few studies of coral reef Archaea, despite the fact that Archaea have been shown to play crucial roles in nutrient dynamics, including nitrification and methanogenesis, of oligotrophic environments such as coral reefs. Here, we present the first study to assess Archaea in four different coral reef biotopes (seawater, sediment, and two sponge species, Stylissa massa and Xestospongia testudinaria). The archaeal community of both sponge species and sediment was dominated by Crenarchaeota, while the seawater community was dominated by Euryarchaeota. The biotope explained more than 72 % of the variation in archaeal composition. The number of operational taxonomic units (OTUs) was highest in sediment and seawater biotopes and substantially lower in both sponge hosts. No “sponge-specific” archaeal OTUs were found, i.e., OTUs found in both sponge species but absent from nonhost biotopes. Despite both sponge species hosting phylogenetically distinct microbial assemblages, there were only minor differences in Kyoto Encyclopedia of Genes and Genomes (KEGG) functional pathways. In contrast, most functional pathways differed significantly between microbiomes from sponges and nonhost biotopes including all energy metabolic pathways. With the exception of the methane and nitrogen metabolic pathway, all energy metabolic pathways were enriched in sponges when compared to nonhost biotopes.     

Impact of Virioplankton on Archaeal and Bacterial Community Richness as Assessed in Seawater Batch Cultures

During cruises in the tropical Atlantic Ocean (January to February 2000) and the southern North Sea (December 2000), experiments were conducted to monitor the impact of virioplankton on archaeal and bacterial community richness. Prokaryotic cells equivalent to 10 to 100% of the in situ abundance were inoculated into virus-free seawater, and viruses equivalent to 35 to 360% of the in situ abundance were added. Batch cultures with microwave-inactivated viruses and without viruses served as controls. The apparent richness of archaeal and bacterial communities was determined by terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR-amplified 16S rRNA gene fragments. Although the estimated richness of the prokaryotic communities generally was greatly reduced within the first 24 h of incubation due to confinement, the effects of virus amendment were detected at the level of individual operational taxonomic units (OTUs) in the T-RFLP patterns of both groups, Archaea and Bacteria. One group of OTUs was detected in the control samples but was absent from the virus-treated samples. This negative response of OTUs to virus amendment probably was caused by viral lysis. Additionally, we found OTUs not responding to the amendments, and several OTUs exhibited variable responses to the addition of inactive or active viruses. Therefore, we conclude that individual members of pelagic archaeal and bacterial communities can be differently affected by the presence of virioplankton.     

Crustose coralline algal species host distinct bacterial assemblages on their surfaces

Crustose coralline algae (CCA) are important components of many marine ecosystems. They aid in reef accretion and stabilization, create habitat for other organisms, contribute to carbon sequestration and are important settlement substrata for a number of marine invertebrates. Despite their ecological importance, little is known about the bacterial communities associated with CCA or whether differences in bacterial assemblages may have ecological implications. This study examined the bacterial communities on four different species of CCA collected in Belize using bacterial tag-encoded FLX amplicon pyrosequencing of the V1–V3 region of the 16S rDNA. CCA were dominated by Alphaproteobacteria, Gammaproteobacteria and Actinomycetes. At the operational taxonomic unit (OTU) level, each CCA species had a unique bacterial community that was significantly different from all other CCA species. Hydrolithon boergesenii and Titanoderma prototypum, CCA species that facilitate larval settlement in multiple corals, had higher abundances of OTUs related to bacteria that inhibit the growth and/or biofilm formation of coral pathogens. Fewer coral larvae settle on the surfaces of Paragoniolithon solubile and Porolithon pachydermum. These CCA species had higher abundances of OTUs related to known coral pathogens and cyanobacteria. Coral larvae may be able to use the observed differences in bacterial community composition on CCA species to assess the suitability of these substrata for settlement and selectively settle on CCA species that contain beneficial bacteria.     

Distribution and Diversity of Archaeal Ammonia Monooxygenase Genes Associated with Corals

Corals are known to harbor diverse microbial communities of Bacteria and Archaea, yet the ecological role of these microorganisms remains largely unknown. Here we report putative ammonia monooxygenase subunit A (amoA) genes of archaeal origin associated with corals. Multiple DNA samples drawn from nine coral species and four different reef locations were PCR screened for archaeal and bacterial amoA genes, and archaeal amoA gene sequences were obtained from five different species of coral collected in Bocas del Toro, Panama. The 210 coral-associated archaeal amoA sequences recovered in this study were broadly distributed phylogenetically, with most only distantly related to previously reported sequences from coastal/estuarine sediments and oceanic water columns. In contrast, the bacterial amoA gene could not be amplified from any of these samples. These results offer further evidence for the widespread presence of the archaeal amoA gene in marine ecosystems, including coral reefs.     

Bacterial and archaeal communities inhabiting mussels,sediment and water in Indonesian anchialine lakes

Anchialine lakes are a globally rare and unique ecosystem consisting of saline lakes surrounded by land and isolated from the surrounding marine environment. These lakes host a unique flora and fauna including numerous endemic species. Relatively few studies have, however, studied the prokaryote communities present in these lakes and compared them with the surrounding ‘open water’ marine environment. In the present study, we used a 16S rRNA gene barcoded pyrosequencing approach to examine prokaryote (Bacteria and Archaea) composition in three distinct biotopes (sediment, water and the mussel Brachidontes sp.) inhabiting four habitats, namely, three marine lakes and the surrounding marine environment of Berau, Indonesia. Biotope and habitat proved significant predictors of variation in bacterial and archaeal composition and higher taxon abundance. Most bacterial sequences belonged to OTUs assigned to the Proteobacteria. Compared to sediment and water, mussels had relatively high abundances of the classes Mollicutes and Epsilonproteobacteria. Most archaeal sequences, in turn, belonged to OTUs assigned to the Crenarchaeota with the relative abundance of crenarchaeotes highest in mussel samples. For both Bacteria and Archaea, the main variation in composition was between water samples on the one hand and sediment and mussel samples on the other. Sediment and mussels also shared much more OTUs than either shared with water. Abundant bacterial OTUs in mussels were related to organisms previously obtained from corals, oysters and the deepsea mussel Bathymodiolus manusensis. Abundant archaeal OTUs in mussels, in contrast, were closely related to organisms previously obtained from sediment.     

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.     

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.     

Diversities of coral-associated bacteria differ with location, but not species, for three acroporid corals on the Great Barrier Reef

Patterns in the diversity of bacterial communities associated with three species of Acropora ( Acropora millepora, Acropora tenuis and Acropora valida ) were compared at two locations (Magnetic Island and Orpheus Island) on the Great Barrier Reef to better understand the nature and specificity of coral–microbial symbioses. Three culture-independent techniques demonstrated consistent bacterial communities among replicate samples of each coral species, confirming that corals associate with specific microbiota. Profiles were also conserved among all three species of Acropora within each location, suggesting that closely related corals of the same genus harbor similar bacterial types. Bacterial community profiles of A. millepora at Orpheus Island were consistent in samples collected throughout the year, indicating a stable community despite temporal changes. However, DGGE and T-RFLP profiles differed on corals from different reefs. Nonmetric multidimensional scaling of T-RFLP profiles showed that samples grouped according to location rather than coral species. Although similar sequences were retrieved from clone libraries of corals at both Magnetic and Orpheus Island, differences in the relative dominant bacterial ribotypes within the libraries drive bacterial community structure at different geographical locations. These results indicate certain bacterial groups associated specifically with corals, but the dominant bacterial genera differ between geographically-spaced corals.     

Impact of virioplankton on archaeal and bacterial community richness as assessed in seawater batch cultures

During cruises in the tropical Atlantic Ocean (January to February 2000) and the southern North Sea (December 2000), experiments were conducted to monitor the impact of virioplankton on archaeal and bacterial community richness. Prokaryotic cells equivalent to 10 to 100% of the in situ abundance were inoculated into virus-free seawater, and viruses equivalent to 35 to 360% of the in situ abundance were added. Batch cultures with microwave-inactivated viruses and without viruses served as controls. The apparent richness of archaeal and bacterial communities was determined by terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR-amplified 16S rRNA gene fragments. Although the estimated richness of the prokaryotic communities generally was greatly reduced within the first 24 h of incubation due to confinement, the effects of virus amendment were detected at the level of individual operational taxonomic units (OTUs) in the T-RFLP patterns of both groups, Archaea and BACTERIA: One group of OTUs was detected in the control samples but was absent from the virus-treated samples. This negative response of OTUs to virus amendment probably was caused by viral lysis. Additionally, we found OTUs not responding to the amendments, and several OTUs exhibited variable responses to the addition of inactive or active viruses. Therefore, we conclude that individual members of pelagic archaeal and bacterial communities can be differently affected by the presence of virioplankton.     

Effect of substrate type on bacterial community composition in biofilms from the Great Barrier Reef

Natural and anthropogenic impacts such as terrestrial runoff, influence the water quality along the coast of the Great Barrier Reef (GBR) and may in turn affect coral reef communities. Associated bacterial biofilms respond rapidly to environmental conditions and are potential bioindicators for changes in water quality. As a prerequisite to study the effects of water quality on biofilm communities, appropriate biofilm substrates for deployment in the field must be developed and evaluated. This study investigates the effect of different settlement substrates (i.e. glass slides, ceramic tiles, coral skeletons and reef sediments) on bacterial biofilm communities grown in situ for 48 days at two locations in the Whitsunday Island Group (Central GBR) during two sampling times. Bacterial communities associated with the biofilms were analysed using terminal restriction fragment length polymorphism (T-RFLP) and clone library analyses of 16S rRNA genes. Findings revealed that substrate type had little influence on bacterial community composition. Of particular relevance, glass slides and coral skeletons exhibited very similar communities during both sampling times, suggesting the suitability of standardized glass slides for long-term biofilm indicator studies in tropical coral reef ecosystems.     

Mariana Forearc Serpentinite Mud Volcanoes Harbor Novel Communities of Extremophilic Archaea

Extremophilic archaeal communities living in serpentinized muds influenced by pH 12.5 deep-slab derived fluids were detected and their richness and relatedness assessed from across seven serpentinite mud volcanoes located along the Mariana forearc. In addition, samples from two near surface core sections (Holes D and E) at ODP Site 1200 from South Chamorro were subjected to SSU rDNA clone library and phylogenetic analysis resulting in the discovery of several novel operational taxonomic units (OTUs). Five dominant OTUs of Archaea from Hole 1200D and six dominant OTUs of Archaea from Hole 1200E were determined by groups having three or more clones. Terminal-restriction fragment length polymorphism (T-RFLP) analysis revealed all of the dominant OTUs were detected within both clone libraries. Cluster analysis of the T-RFLP data revealed archaeal community structures from sites on Big Blue and Blue Moon to be analogous to the South Chamorro Hole 1200E site. These unique archaeal community fingerprints resulted from an abundance of potential methane-oxidizing and sulfate-reducing phylotypes. This study used deep-sea sediment coring techniques across seven different mud volcanoes along the entire Mariana forearc system. The discovery and detection of both novel Euryarchaeota and Marine Benthic Group B Crenarcheaota phylotypes could be efficacious archaeal indicator populations involved with anaerobic methane oxidation (AMO) and sulfate reduction fueled by deep subsurface serpentinization reactions.     

Corals form characteristic associations with symbiotic nitrogen-fixing bacteria

The complex symbiotic relationship between corals and their dinoflagellate partner Symbiodinium is believed to be sustained through close associations with mutualistic bacterial communities, though little is known about coral associations with bacterial groups able to fix nitrogen (diazotrophs). In this study, we investigated the diversity of diazotrophic bacterial communities associated with three common coral species (Acropora millepora, Acropora muricata, and Pocillopora damicormis) from three midshelf locations of the Great Barrier Reef (GBR) by profiling the conserved subunit of the nifH gene, which encodes the dinitrogenase iron protein. Comparisons of diazotrophic community diversity among coral tissue and mucus microenvironments and the surrounding seawater revealed that corals harbor diverse nifH phylotypes that differ between tissue and mucus microhabitats. Coral mucus nifH sequences displayed high heterogeneity, and many bacterial groups overlapped with those found in seawater. Moreover, coral mucus diazotrophs were specific neither to coral species nor to reef location, reflecting the ephemeral nature of coral mucus. In contrast, the dominant diazotrophic bacteria in tissue samples differed among coral species, with differences remaining consistent at all three reefs, indicating that coral-diazotroph associations are species specific. Notably, dominant diazotrophs for all coral species were closely related to the bacterial group rhizobia, which represented 71% of the total sequences retrieved from tissue samples. The species specificity of coral-diazotroph associations further supports the coral holobiont model that bacterial groups associated with corals are conserved. Our results suggest that, as in terrestrial plants, rhizobia have developed a mutualistic relationship with corals and may contribute fixed nitrogen to Symbiodinium.     

The putative functional ecology and distribution of archaeal communities in sponges,sediment and seawater in a coral reef environment

Archaea play crucial roles in a number of key ecological processes including nitrification and methanogenesis. Although several studies have been conducted on these organisms, the roles and dynamics of coral reef archaeal communities are still poorly understood, particularly in host and nonhost biotopes and in high (HMA) and low microbial abundance (LMA) sponges. Here, archaeal communities detected in six distinct biotopes, namely, sediment, seawater and four different sponge species Stylissa carteri, Stylissa massa, Xestospongia testudinaria and Hyrtios erectus from the Spermonde Archipelago, SW Sulawesi, Indonesia were investigated using 454‐pyrosequencing of 16S rRNA genes (OTU cut‐off 97%). Archaeal communities from sediment and sponges were dominated by Crenarchaeota, while the seawater community was dominated by Euryarchaeota. The biotope explained almost 75% of the variation in archaeal composition, with clear separation between microbial assemblages from sediment, X. testudinaria and H. erectus (HMA). In contrast, samples from seawater and both Stylissa species (LMA) showed considerable overlap in the ordination and, furthermore, shared most abundant OTUs with the exception of a single dominant OTU specifically enriched in both Stylissa species. Predicted functional gene content in archaeal assemblages also revealed significant differences among biotopes. Different ammonia assimilation strategies were exhibited by the archaeal communities: X. testudinaria, H. erectus and sediment archaeal communities were enriched for glutamate dehydrogenase with mixed specificity (NAD(P)⁺) pathways, while archaeal planktonic communities were enriched for specific glutamate dehydrogenase (NADP⁺) and glutamate synthase pathways. Archaeal communities in Stylissa had intermediate levels of enrichment. Our results indicate that archaeal communities in different biotopes have distinct ecophysiological roles.     

Pleistocene reef environments, constituent grains, and coral community structure: Curaçao, Netherlands Antilles

We investigated the degree to which component grains vary with depositional environment in sediments from three reef habitats from the Pleistocene (125?ka) Hato Unit of the Lower Terrace, Curaçao, Netherlands Antilles: windward reef crest, windward back reef, and leeward reef crest. The windward reef crest sediment is the most distinctive, dominated by fragments of encrusting and branching coralline red algae, coral fragments and the encrusting foraminiferan Carpenteria sp. Windward back reef and leeward reef crest sediments are more similar compositionally, only showing significant differences in relative abundance of coral fragments and Homotrema rubrum. Although lacking high taxonomic resolution and subject to modification by transport, relative abundance of constituent grain types offers a way of assessing ancient skeletal reef community composition, and one which is not limited to a single taxonomic group. The strong correlation between grain type and environment we found in the Pleistocene of Curaçao suggests that constituent grain analysis may be an effective tool in delineating Pleistocene Caribbean reef environments. However, it will not be a sufficient indicator where communities vary significantly within reef environments or where evolutionary and/or biogeographical processes lead to different relationships between community composition and reef environment. Detailed interpretation of geological, biological, and physical characteristics of the Pleistocene reefs of Curaçao reveals that the abundance of the single coral species, Acropora palmata, is not a good predictor of the ecological structure of the ancient reef coral communities. This coral was the predominant species in two of the three reef habitats (windward and leeward reef crest), but the taxonomic composition (based on species relative abundance data) of the reef coral communities was substantially different in these two environments. We conclude that qualitative estimates of coral distribution patterns (presence of a key coral species or the use of a distinctive coral skeletal architecture), when used as a component in a multi-component analysis of ancient reef environments, probably introduces minimal circular reasoning into quantitative paleoecological studies of reef coral community structure.     

Relative Importance of Coral Cover,Habitat Complexity and Diversity in Determining the Structure of Reef Fish Communities

The structure of coral reef habitat has a pronounced influence on the diversity, composition and abundance of reef-associated fishes. However, the particular features of the habitat that are most critical are not always known. Coral habitats can vary in many characteristics, notably live coral cover, topographic complexity and coral diversity, but the relative effects of these habitat characteristics are often not distinguished. Here, we investigate the strength of the relationships between these habitat features and local fish diversity, abundance and community structure in the lagoon of Lizard Island, Great Barrier Reef. In a spatial comparison using sixty-six 2m² quadrats, fish species richness, total abundance and community structure were examined in relation to a wide range of habitat variables, including topographic complexity, habitat diversity, coral diversity, coral species richness, hard coral cover, branching coral cover and the cover of corymbose corals. Fish species richness and total abundance were strongly associated with coral species richness and cover, but only weakly associated with topographic complexity. Regression tree analysis showed that coral species richness accounted for most of the variation in fish species richness (63.6%), while hard coral cover explained more variation in total fish abundance (17.4%), than any other variable. In contrast, topographic complexity accounted for little spatial variation in reef fish assemblages. In degrading coral reef environments, the potential effects of loss of coral cover and topographic complexity are often emphasized, but these findings suggest that reduced coral biodiversity may ultimately have an equal, or greater, impact on reef-associated fish communities.     

Down under the tunic: bacterial biodiversity hotspots and widespread ammonia-oxidizing archaea in coral reef ascidians

Ascidians are ecologically important components of marine ecosystems yet the ascidian microbiota remains largely unexplored beyond a few model species. We used 16S rRNA gene tag pyrosequencing to provide a comprehensive characterization of microbial symbionts in the tunic of 42 Great Barrier Reef ascidian samples representing 25 species. Results revealed high bacterial biodiversity (3 217 unique operational taxonomic units (OTU_0.03) from 19 described and 14 candidate phyla) and the widespread occurrence of ammonia-oxidizing Thaumarchaeota in coral reef ascidians (24 of 25 host species). The ascidian microbiota was clearly differentiated from seawater microbial communities and included symbiont lineages shared with other invertebrate hosts as well as unique, ascidian-specific phylotypes. Several rare seawater microbes were markedly enriched (200–700 fold) in the ascidian tunic, suggesting that the rare biosphere of seawater may act as a conduit for horizontal symbiont transfer. However, most OTUs (71%) were rare and specific to single hosts and a significant correlation between host relatedness and symbiont community similarity was detected, indicating a high degree of host-specificity and potential role of vertical transmission in structuring these communities. We hypothesize that the complex ascidian microbiota revealed herein is maintained by the dynamic microenvironments within the ascidian tunic, offering optimal conditions for different metabolic pathways such as ample chemical substrate (ammonia-rich host waste) and physical habitat (high oxygen, low irradiance) for nitrification. Thus, ascidian hosts provide unique and fertile niches for diverse microorganisms and may represent an important and previously unrecognized habitat for nitrite/nitrate regeneration in coral reef ecosystems.     

Drivers of bacterial diversity dynamics in permeable carbonate and silicate coral reef sands from the Red Sea

Permeable sediments and associated microbial communities play a fundamental role in nutrient recycling within coral reef ecosystems by ensuring high levels of primary production in oligotrophic environments. A previous study on organic matter degradation within biogenic carbonate and terrigenous silicate reef sands in the Red Sea suggested that observed sand-specific differences in microbial activity could be caused by variations in microbial biomass and diversity. Here, we tested this hypothesis by comparing bacterial abundance and community structure in both sand types, and by further exploring the structuring effects of time (season) and space (sediment depth, in/out-reef). Changes in bacterial community structure, as determined via automated ribosomal intergenic spacer analysis (ARISA), were primarily driven by sand mineralogy at specific seasons, sediment depths and reef locations. By coupling ARISA with 16S-ITS rRNA sequencing, we detected significant community shifts already at the bacterial class level, with Proteobacteria (Gamma-, Delta-, Alpha-) and Actinobacteria being prominent members of the highly diverse communities. Overall, our findings suggest that reef sand-associated bacterial communities vary substantially with sand type. Especially in synergy with environmental variation over time and space, mineralogical differences seem to play a central role in maintaining high levels of bacterial community heterogeneity. The local co-occurrence of carbonate and silicate sands may thus significantly increase the availability of microbial niches within a single coral reef ecosystem.     

Biogeography and Host Fidelity of Bacterial Communities in Ircinia spp. from the Bahamas

Research on sponge microbial assemblages has revealed different trends in the geographic variability and specificity of bacterial symbionts. Here, we combined replicated terminal-restriction fragment length polymorphism (T-RFLP) and clone library analyses of 16S rRNA gene sequences to investigate the biogeographic and host-specific structure of bacterial communities in two congeneric and sympatric sponges: Ircinia strobilina, two color morphs of Ircinia felix and ambient seawater. Samples were collected from five islands of the Bahamas separated by 80 to 400 km. T-RFLP profiles revealed significant differences in bacterial community structure among sponge hosts and ambient bacterioplankton. Pairwise statistical comparisons of clone libraries confirmed the specificity of the bacterial assemblages to each host species and differentiated symbiont communities between color morphs of I. felix. Overall, differences in bacterial communities within each host species and morph were unrelated to location. Our results show a high degree of symbiont fidelity to host sponge across a spatial scale of up to 400 km, suggesting that host-specific rather than biogeographic factors play a primary role in structuring and maintaining sponge–bacteria relationships in Ircinia species from the Bahamas.     

Habitat-specific environmental conditions primarily control the microbiomes of the coral Seriatopora hystrix

Reef-building corals form complex relationships with a range of microorganisms including bacteria, archaea, fungi and the unicellular microalgae of the genus Symbiodinium, which together form the coral holobiont. These symbionts are known to have both beneficial and deleterious effects on their coral host, but little is known about what the governing factors of these relationships are, or the interactions that exist between the different members of the holobiont and their environment. Here we used 16S ribosomal RNA gene amplicon sequencing to investigate how archaeal and bacterial communities associated with the widespread scleractinian coral Seriatopora hystrix are influenced by extrinsic (reef habitat and geographic location) and intrinsic (host genotype and Symbiodinium subclade) factors. Bacteria dominate the microbiome of S. hystrix, with members of the Alphaproteobacteria, Gammaproteobacteria and Bacteriodetes being the most predominant in all samples. The richness and evenness of these communities varied between reef habitats, but there was no significant difference between distinct coral host lineages or corals hosting distinct Symbiodinium subclades. The coral microbiomes correlated to reef habitat (depth) and geographic location, with a negative correlation between Alpha- and Gammaproteobacteria, driven by the key members of both groups (Rhodobacteraceae and Hahellaceae, respectively), which showed significant differences between location and depth. This study suggests that the control of microbial communities associated with the scleractinian coral S. hystrix is driven primarily by external environmental conditions rather than by those directly associated with the coral holobiont.