Effects of age and composition of field-produced biofilms on oyster larval setting

Lack of success in restoring the native Eastern oyster, Crassostrea virginica, to Chesapeake Bay has been linked to the low occurrence of oyster larval setting in tributaries to the Bay. Among the many potential factors that could affect efforts to produce oysters through aquaculture or supplementation of shell beds is substratum condition. The present study examined larval setting on field-produced biofilms from Little Wicomico River (Virginia, USA) to assess whether bacterial community structure (examined by terminal restriction fragment length polymorphism, T-RFLP) or other characteristics of contemporary biofilms in this tributary (biofilm age and mass, algal abundance, and percentage organic matter) inhibited setting of larval oysters. The structure of the natural and heterogenous bacterial community in the biofilms and the success of oyster set were correlated, suggesting that specific microbial species may play a role in oyster setting. Larval set increased with biofilm age and mass, suggesting that established field-produced biofilms have no inhibitory effect. In contrast, the percentage of organic matter was negatively correlated with oyster set, whereas chlorophyll a concentration had no observed effect. The study expands prior knowledge by providing a more realistic timeframe for biofilm development (weeks as opposed to days), recounting effects of biofilms that are more representative of the natural dynamic and disturbance processes that would be expected to occur on submerged structures, and by incorporating seasonal and spatial variation. An important negative effect observed during the study period was heavy predation by Stylochus ellipticus on newly set oysters. Overall, the results of this study, which is the first assessment of the effects of biofilms produced naturally within a Chesapeake Bay tributary, suggest that the absence of large numbers of oysters in Little Wicomico River is not related to microbes or other specific characteristics of biofilms that develop on suitable setting substrata, but rather to heavy predation of newly set larvae.     

Abundance and community composition of ammonia-oxidizing archaea and bacteria in two different zones of Lake Taihu

The abundance and community composition of ammonia-oxidizing archaea and ammonia-oxidizing bacteria in the surface sediments of 2 different zones (Meiliang Bay and Eastern Lake Taihu) of Lake Taihu were investigated using real-time quantitative polymerase chain reaction and clone libraries. The amoA gene copy numbers in the surface sediment of Meiliang Bay ranged from 4.91?× 10(5) to 8.65?× 10(6) copies/g dry sediment for the archaeal amoA gene and from 3.74?× 10(4) to 3.86?× 10(5) copies/g dry sediment for the bacterial amoA gene, which were significantly higher than those of Eastern Lake Taihu (P?< 0.05). Concentrations of ammonia (NH(4)(+)), total nitrogen, organic matter, and pH of the sediments exhibited significantly negative correlations with the abundance of ammonia-oxidizing archaea or ammonia-oxidizing bacteria (P?< 0.05 or P?< 0.01, respectively). The potential nitrification rates show remarkable correlations with the copy numbers of the archaeal amoA gene. Diversity of the archaeal amoA gene in Eastern Lake Taihu was significantly higher than that of Meiliang Bay, whereas the bacterial amoA gene diversity was comparable for the 2 lake zones. The data obtained in this study would be useful to elucidate the role of ammonia-oxidizing archaea and ammonia-oxidizing bacteria in the nitrogen cycle of freshwater ecosystems.     

青藏高原淡水湖普莫雍错和盐水湖阿翁错湖底沉积物中细菌群落的垂直分布

【目的】湖泊沉积物中存储着大量独特的微生物,这些微生物在湖泊生态系统生物地球化学循环中扮演着非常重要的角色。然而,很少有研究报道微生物群落在湖泊沉积物中的垂直分布。本文比较研究青藏高原淡水湖普莫雍错和盐水湖阿翁错沉积物在不同深度下细菌的丰度和群落结构。【方法】利用定量PCR(q PCR)和变性梯度凝胶电泳(DGGE)技术分别测定细菌群落的丰度与群落结构。【结果】定量PCR结果显示,湖泊沉积物中细菌丰度均随深度增加而降低,盐水湖阿翁错和淡水湖普莫雍错的细菌丰度分别从1011数量级降到108数量级,从1012数量级降到1010数量级。在相对应的沉积物层,淡水湖沉积物的细菌丰度比盐水湖高1-2个数量级。变性梯度凝胶电泳(DGGE)指纹图谱的分析表明,淡水湖沉积物细菌群落的DGGE条带数(丰富度)显著高于盐水湖(P=0.014);淡水与盐水湖泊沉积物细菌群落结构明显不同,同时在同一湖泊沉积物中上层(0-6 cm)和下层(7-20 cm)细菌群落结构也呈明显分异。系统发育分析表明,盐水湖阿翁错沉积物特有菌门为Gamma-变形菌、拟杆菌门、蓝细菌和栖热菌门,而淡水湖普莫雍错沉积物中特有菌门为Delta-和Beta-变形菌、酸杆菌和绿弯菌门。【结论】青藏高原淡水与盐水湖泊沉积物细菌丰度与群落结构具有明显的差异;同时,细菌群落结构在沉积物的不同深度也表现出差异。这些结果可为进一步阐明青藏高原湖泊生态系统中微生物对气候环境变化的响应提供科学依据。     

Evaluating Intertidal Oyster Reef Development in South Carolina Using Associated Faunal Indicators

Eastern oyster (Crassostrea virginica) habitat is increasingly being restored for the ecosystem services it provides rather than solely as a fishery resource. Community‐based projects with the goal of ecological restoration have successfully constructed oyster reefs; however, the habitat benefits of these restoration efforts are usually not assessed or reported. In this study, we examined oyster habitat development at five community‐based oyster restoration sites in South Carolina using oyster population parameters, resident fauna densities, and sedimentation (percent sediment coverage) as assessment metrics. All sites included multiple‐aged reefs (1–3 years old) at the time of the fall 2004 sampling. Resident crabs and mussels were abundant at all five sites and crab assemblages were related to the size structure of the oyster microhabitat. Scorched mussel (Brachidontes exustus) abundances were most frequently correlated with oyster and other resident species abundances. Associations among oysters and resident crabs and mussels were not evident when analyses were conducted with higher level taxonomic groupings (e.g., total number of crabs, mussels, or oysters), indicating that species‐level identifications improve our understanding of interactions among reef inhabitants and oyster populations. Community‐based restoration sites in South Carolina provide habitat for mussels and resident crabs, in some cases in the absence of dense populations of relatively large oysters. Monitoring programs that neglect species‐level identifications and counts of mussels and crabs may underestimate the successful habitat provision that can arise independent of large, dense oyster assemblages.     

Geographic distance and pH drive bacterial distribution in alkaline lake sediments across Tibetan Plateau

Continent-scale biogeography has been extensively studied in soils and marine systems, but little is known about biogeographical patterns in non-marine sediments. We used barcode pyrosequencing to quantify the effects of local geochemical properties and geographic distance for bacterial community structure and membership, using sediment samples from 15 lakes on the Tibetan Plateau (4-1670?km apart). Bacterial communities were surprisingly diverse, and distinct from soil communities. Four of 26 phyla detected were dominant: Proteobacteria, Bacteroidetes, Firmicutes and Actinobacteria, albeit 20.2% of sequences were unclassified at the phylum level. As previously observed in acidic soil, pH was the dominant factor influencing alkaline sediment community structure, phylotype richness and phylogenetic diversity. In contrast, archaeal communities were less affected by pH. More geographically distant sites had more dissimilar communities (r?=?0.443, P?=?0.030). Variance partitioning analysis showed that geographic distance (historical contingencies) contributed more to bacterial community variation (12.2%) than any other factor, although the environmental factors explained more variance when combined (28.9%). Together, our results show that pH is the best predictor of bacterial community structure in alkaline sediments, and confirm that both geographic distance and chemical factors govern bacterial biogeography in lake sediments.     

In situ study of the effect of oyster biomass on benthic metabolic exchange rates

Oxygen consumption and dissolved nitrogen fluxes at the water-sediment interface of an oyster-bed were measured in situ using transparent enclosures inserted on undisturbed sediment. Experiments were performed in summer, under dark and light conditions, with various densities of the oyster Crassostrea gigas (0–150 animals m ^{– 2}). The influence of oyster biomass on oxygen and ammonia exchange rates was similar in both lighting conditions. Oxygen consumption increased with increasing biomass, though not at the level of prediction for the highest biomasses, suggesting a depressed respiration rate. Ammonia release never matched the rates predicted by adding sediment efflux to oyster excretion, when biomass exceeded 100 g DW m ^{– 2}. The coupling between oxygen consumption and ammonia release (O : N ratio) was thus influenced by oyster biomass. Stabilization of nitrogen release was related to enhanced nitrification in the presence of oyster and/or sediment uptake of ammonia against the molecular gradient. Urea release was erratic but appeared uninfluenced by oyster biomass. Fluxes of oxygen and of each nitrogen compound displayed thus a specific response to modifications of the oyster biomass. Both the organisms and the sediment are involved in regulation processes of metabolic exchange rates at the water-sediment interface.     

Molecular analysis of the bacterial communities in the live Pacific oyster (Crassostrea gigas) and the influence of postharvest temperature on its structure

Aims: To evaluate the effect of postharvest temperature on bacterial communities in live Pacific oysters (Crassostrea gigas) using nonculture‐based methods. Methods and Results: Live oysters were compared before and after storage at 4, 6, 15, 20 and 30°C using terminal restriction fragment length polymorphism (T‐RFLP). Bacterial communities in freshly harvested (control) vs stored oysters were significantly different. Changes in bacterial communities at 4, 15 and 30°C observed by T‐RFLP were further investigated by clone library analysis. Members of the Proteobacteria predominated (43·0–57·0% of clones) in control oysters, while storage altered the bacterial profile. At 4°C, Psychrilyobacter spp. (phylum Fusobacteria) predominated (43·8% of clones), while at 15 and 30°C, members of the phylum Bacteroidetes represented 63·0 and 60·2% of clones, respectively. High microbial diversity in oysters was observed, with at least 73 different genera‐related clones among all samples. Conclusions: Changes in the overall bacterial community of Pacific oysters were influenced by storage temperature and would likely not be detected by standard culture‐based methods currently used to assess oyster quality. Certain dominant genera, such as Psychrilyobacter, Polynucleobacter and a bacterial group related to Alkaliflexus, should be further studied as possible indicators for postharvest temperature control. Significance and Impact of the Study: This work is the first report describing the effect of different storage temperatures on bacterial diversity in postharvest live Pacific oysters using molecular‐based methods.     

Dynamics of Seawater Bacterial Communities in a Shellfish Hatchery

Bacterial disease is a significant issue for larviculture of several species of shellfish, including oysters. One source of bacteria is the seawater used throughout the hatchery. In this study carried out at a commercial oyster hatchery in Tasmania, Australia, the diversity of the bacterial community and its relationship with larval production outcomes were studied over a 2-year period using terminal restriction fragment length polymorphism and tag-encoded pyrosequencing. The bacterial communities were very diverse, dominated by the Alphaproteobacteria, Gammaproteobacteria, Flavobacteria and Cyanobacteria. The communities were highly variable on scales of days, weeks and seasons. The difference between the intake seawater and treated clean seawater used in the hatchery was smaller than the observed temporal differences in the seawater throughout the year. No clear correlation was observed between production outcomes and the overall bacterial community structure. However, one group of Cyanobacterial sequences was more abundant when mass mortality events occurred than when healthy spat were produced although they were always present.     

A Vibrio splendidus strain is associated with summer mortality of juvenile oysters Crassostrea gigas in the Bay of Morlaix (North Brittany, France).

Juvenile oysters Crassostrea gigas cultured in the Bay of Morlaix (France) have suffered unexplained summer mortalities for over a decade. In the present study, we tested the hypothesis that a bacterial pathogen could be responsible for this phenomenon. A first attempt failed to isolate a bacterial pathogen from moribund or weak oysters. Only non-pathogenic, probably opportunistic, bacteria were isolated. As an alternative approach, we focused on oysters presenting reduced stress-response capacities (determined by circulating noradrenaline measurements), a characteristic of juvenile oysters entering an early phase of the disease. Cultures of bacterial isolates on TCBS plates revealed that a Vibrio strain was present in diseased oysters and scarce or absent in healthy oysters. Experimental infections indicated that this Vibrio can cause mortalities of juvenile oysters when injected at concentrations ranging from 10(4) to 10(8) CFU oyster(-1). Similarly to the summer mortality disease, the Vibrio isolate caused higher mortalities at higher temperatures; apparently, it could not be transmitted horizontally, it did not affect adult oysters and it induced stress-response dysfunctions in juvenile oysters. Phenotypic and genotypic characterizations identified the pathogen as Vibrio splendidus. Taken together, the present results satisfy Koch's postulate and suggest that this bacterial strain is probably responsible for the juvenile oyster summer mortalities in the Bay of Morlaix.     

Evidence for colonization and destruction of hinge ligaments in cultured juvenile Pacific oysters (Crassostrea gigas) by cytophaga-like bacteria.

Several strains of cytophaga-like gliding bacteria (CLB) were isolated as numerically dominant or codominant components of bacterial populations associated with proteinaceous hinge ligaments of cultured juvenile Pacific oysters, Crassostrea gigas. These bacteria were morphologically similar to long, flexible bacilli occurring within degenerative lesions in oyster hinge ligaments. Among bacteria isolated from hinge ligaments, only CLB strains were capable of sustained growth with hinge ligament matrix as the sole source of organic carbon and nitrogen. In vitro incubation of cuboidal portions of ligament resilium with ligament CLB resulted in bacterial proliferation on the surfaces and penetration deep into ligament matrices. Bacterial proliferation was accompanied by loss of resilium structural and mechanical integrity, including complete liquefaction, at incubation temperatures between 10 and 20 degrees C. The morphological, distributional, and degradative characteristics of CLB isolated from oyster hinge ligaments provide compelling, albeit indirect, evidence that CLB are the agents of a degenerative disease affecting juvenile cultured oysters. The motility, metabolic, and hydrolytic characteristics of hinge ligament CLB and the low moles percent G + C values (32.4 to 32.9) determined for three representative strains indicate that they are marine Cytophaga spp.     

Evidence for colonization and destruction of hinge ligaments in cultured juvenile Pacific oysters (Crassostrea gigas) by cytophaga-like bacteria

Several strains of cytophaga-like gliding bacteria (CLB) were isolated as numerically dominant or codominant components of bacterial populations associated with proteinaceous hinge ligaments of cultured juvenile Pacific oysters, Crassostrea gigas. These bacteria were morphologically similar to long, flexible bacilli occurring within degenerative lesions in oyster hinge ligaments. Among bacteria isolated from hinge ligaments, only CLB strains were capable of sustained growth with hinge ligament matrix as the sole source of organic carbon and nitrogen. In vitro incubation of cuboidal portions of ligament resilium with ligament CLB resulted in bacterial proliferation on the surfaces and penetration deep into ligament matrices. Bacterial proliferation was accompanied by loss of resilium structural and mechanical integrity, including complete liquefaction, at incubation temperatures between 10 and 20 degrees C. The morphological, distributional, and degradative characteristics of CLB isolated from oyster hinge ligaments provide compelling, albeit indirect, evidence that CLB are the agents of a degenerative disease affecting juvenile cultured oysters. The motility, metabolic, and hydrolytic characteristics of hinge ligament CLB and the low moles percent G + C values (32.4 to 32.9) determined for three representative strains indicate that they are marine Cytophaga spp.     

Effect of copper exposure on bacterial community structure and function in the sediments of Jiaozhou Bay,China

Microcosms were setup to investigate the possible impact of copper exposure on bacterial community structure and function in sediments of Jiaozhou Bay, China, by culture-independent microbial ecological techniques and community-level physiological profiling. Bacterial 16S rDNA libraries indicated that proportion of the bacteria in phyla Chloroflexi and Acidobacteria decreased, but that of Gammaproteobacteria and Planctomycetes slightly increased in copper-treated sediment. Denaturing gradient gel profiles showed that bacterial communities in control and copper exposed sediments developed into different directions, while the copper exposure did not change the pattern of ammonia oxidizing bacterial community. Microbial community-level physiological profiling revealed an obvious response to copper dosage. The copper pollution caused an acute decrease of carbon utilizing ability as well as bacterial functional diversity; the number of culturable heterotrophic bacteria was reduced by 90 %. This study demonstrated that high copper input would obviously reduce culturable bacterial counts and seriously impact bacterial community function in marine sediments.     

Temporal and spatial variations of aquatic environmental characteristics and sediment bacterial community in five regions of Lake Taihu

Sediment bacterial community and their relation with environmental factors were investigated in the five different trophic status lake regions sediment, Meiliang Bay, Wuli Lake, Gonghu Bay, Western Lake Taihu and Xukou Bay in a large, shallow, eutrophic freshwater lake (Lake Taihu, China). Water and surface sediment samples were collected at 35 sampling sites in January 2014 (winter) and July 2015 (summer). The physicochemical characterization showed that there were obvious changes in the trophic status and eutrophic index of five lake regions, which was mainly due to the difference of organic matter source. Based on the analysis of aquatic environmental characteristics, the organic nitrogen or nitrate nitrogen was the main storing form in the overlying water of five lake regions. In addition, nitrate nitrogen in pore water was lower than in overlying water, while ammonia nitrogen in pore water was higher than in overlying water. According to the DGGE profiles, temporal and spatial variations of bacterial community were apparent. Bacterial diversity was higher in summer than in winter and increased with the decrease in the lake region trophic status. The dendrogram of the bacterial community similarities revealed that samples were almost all grouped into two defined clusters (summer and winter), which indicated that season rather than region was the dominant factor. Canonical correspondence analysis demonstrated that ammonia nitrogen and nitrate–nitrite nitrogen in the sediment and pore water, organic matter and temperature significantly influenced the sediment bacterial community in the five lake regions.     

Return of the native facilitated by the invasive? Population composition,substrate preferences and epibenthic species richness of a recently discovered shellfish reef with native European flat oysters (Ostrea edulis) in the North Sea

After being ecologically extinct for almost a century, the discovery of a shellfish reef with native European flat oysters (Ostrea edulis) in the Dutch coastal area of the North Sea by the authors of this study called for an extensive survey to better understand some of the key requirements for the return of the native oyster in coastal waters. We assessed habitat conditions, its potential for increasing biodiversity, and the role of substrate provision by other bivalves such as the invasive alien Pacific oyster (Crassostrea gigas). Using underwater visual census, O. edulis size-frequency distributions and attachment substrate was investigated, as well as the composition of the epibenthic community and substrata types inside quadrats that were distributed across the reef. This reef was found to be composed of native European flat oysters, invasive alien Pacific oysters and blue mussels (Mytilus edulis), alternated with sandy patches. The O. edulis population (6.8?±?0.6 oysters m^?2) consisted of individuals of different size classes. In quadrats with native and non-native oysters the number of epibenthic species was 60% higher compared to adjacent sand patches within the reef. Notably, our results showed that the native oyster predominantly used shell (fragments) of the invasive Pacific oyster as settlement substrate (81% of individuals). Our results optimistically show that conditions for native oyster restoration can be suitable at a local scale in the coastal North Sea area and suggest that the return of native oysters may be facilitated by novel substrate provided by invasive oysters at sites where their distribution overlap.     

Bacterial 16S rRNA Gene Analysis Revealed That Bacteria Related to Arcobacter spp. Constitute an Abundant and Common Component of the Oyster Microbiota (Tiostrea chilensis)

To explore the bacterial microbiota in Chilean oyster (Tiostrea chilensis), a molecular approach that permits detection of different bacteria, independently of their capacity to grow in culture media, was used. Bacterial diversity was assessed by analysis of both the 16S rDNA and the 16S-23S intergenic region, obtained by PCR amplifications of DNA extracted from depurated oysters. RFLP of the PCR amplified 16S rDNA showed a prevailing pattern in most of the individuals analyzed, indicating that a few bacterial species were relatively abundant and common in oysters. Cloning and sequencing of the 16S rDNA with the prevailing RFLP pattern indicated that this rRNA was most closely related to Arcobacter spp. However, analysis by the size of the amplified 16S-23S rRNA intergenic regions revealed not Arcobacter spp. but Staphylococcus spp. related bacteria as a major and common component in oyster. These different results may be caused by the absence of target for one of the primers employed for amplification of the intergenic region. Neither of the two bacteria species found in large abundance was recovered after culturing under aerobic, anaerobic, or microaerophilic conditions. This result, however, is expected because the number of bacteria recovered after cultivation was less than 0.01% of the total. All together, these observations suggest that Arcobacter-related strains are probably abundant and common in the Chilean oyster bacterial microbiota.     

Bacterial abundance and aerobic microbial activity across natural and oyster aquaculture habitats during summer conditions in a northeastern Pacific estuary

We measured sediment properties and the abundance and aerobic metabolism of microbes in Willapa Bay, Washington, USA, to test the response of sediment microbes to oyster aquaculture. Sites spanned the estuary gradient (practical salinity units ranged from 24 to 30 under seasonally low river flows) and six different low-intertidal habitat types: eelgrass (Zostera marina), unstructured tideflat, oyster hummocks (reefs of Crassostrea gigas), longline oyster aquaculture, hand-picked on-bottom oyster aquaculture, and dredged on-bottom oyster aquaculture. Aerobic metabolism was assessed by sole-source carbon use (SSCU) of 31 carbon sources on Biolog plates. Sediments generally became siltier and more organically enriched into the estuary, but no consistent differences in sediment properties occurred across habitat types. Bacterial cell density tracked organic content. Across the estuary gradient, overall aerobic SSCU increased less steeply than bacterial cell density, possibly as anaerobic metabolism became more important. Across habitats, aerobic SSCU differed significantly in both overall metabolism and diversity of carbon sources. Aerobic metabolism was generally lower for sediment microbes from intertidal on-bottom oyster aquaculture than from eelgrass. Humans indirectly alter microbial activity through biogenic habitats created during aquaculture, but, as has been shown for bivalves more generally, these changes were relatively small, particularly in comparison to sediment changes along estuarine gradients.     

Community structure of methanogenic archaea and methane production associated with compost-treated tropical rice-field soil

The diversity and density of methanogenic archaea and methane production were investigated ex situ at different growth stages of rice plant cultivated in compost-treated tropical rice fields. The qPCR analysis revealed variation in methanogens population from 3.40?×?10(6) to 1.11?×?10(7) copies?g(-1) dws, in the year 2009 and 4.37?×?10(6) to 1.36?×?10(7) copies?g(-1) dws in the year 2010. Apart from methanogens, a large number of bacterial (9.60?×?10(9) -1.44?×?10(10) copies?g(-1) dws) and archaeal (7.13?×?10(7) -3.02?×?10(8) copies?g(-1) dws) communities were also associated with methanogenesis. Methanogen population size varied in the order: flowering > ripening > tillering > postharvest > preplantation stage. The RFLP-based 16S rRNA gene-targeted phylogenetic analysis showed that clones were closely related to diverse group of methanogens comprising members of Methanomicrobiaceae, Methanosarcinaceae, Methanosaetaceae and RC I. Laboratory incubation studies revealed higher amount of cumulative CH(4) at the flowering stage. The integration of methanogenic community structure and CH(4) production potential of soil resulted in a better understanding of the dynamics of CH(4) production in organically treated rice-field soil. The hypothesis that the stages of plant development influence the methanogenic community structure leading to temporal variation in the CH(4) production has been successfully tested.     

PLFA Analyses of Microbial Communities Associated with PAH-Contaminated Riverbank Sediment

Sediment contaminated with polycyclic aromatic hydrocarbons (PAHs) is widely distributed in aquatic ecosystems. The microbial community structure of riverbank PAH-contaminated sediments was investigated using phospholipid-derived fatty acid (PLFA) analysis. Surface and subsurface riverbank sediment was collected from a highly contaminated site and from an uncontaminated site along the Mahoning River, OH. PAH concentrations, physical sediment characteristics, and other microbial community parameters (biomass as phospholipid phosphate (PLP) and activity) were also measured. PAHs were detected in all samples but were only quantifiable in the contaminated (250?μg/g?g(-1)) subsurface sediment. Subsurface samples from both locations showed very similar PLP values and distribution of PLFAs, with 27-37?% of the microbial community structure being composed of sulfate reducing and other anaerobic bacteria. Principal components analysis indicated no correlation between PAH contamination and PLFA diversity. Although PLP and phospholipid fatty acid measurements of bacterial communities did not reflect the environmental differences among sites, the highly PAH-contaminated sediment showed the highest measured microbial activity (reduction of 1,200?nmol?INT?g(-1)?h(-1)), likely from a population adapted to environmental pollutants, rates that are much higher than measured in many uncontaminated soil and sediment systems. These data warrant further investigation into community structure at the genetic level and indicate potential for bioremediation by indigenous microbes.     

Ribosomal tag pyrosequencing of DNA and RNA from benthic coral reef microbiota: community spatial structure, rare members and nitrogen-cycling guilds

Ribosomal tag libraries based on DNA and RNA in coral reef sediment from Hawaii show the microbial community to be dominated by the bacterial phyla Proteobacteria, Firmicutes and Actinobacteria, the archaeal order Nitrosopumilales and the uncultivated divisions Marine Group III (Euryarchaeota) and Marine Benthic Group C (Crenarchaeota). Operational taxonomic units (OTUs) number in the high thousands, and richness varies with site, presence or absence of porewater sulfide (sediment depth), and nucleotide pool. Rank abundance curves of DNA-based libraries, but not RNA-based libraries, possess a tail of low abundance taxa, supporting the existence of an inactive 'rare' biosphere. While bacterial libraries from two oxic samples differ markedly, those from two anoxic (sulfidic) samples are similar. The four dominant bacterial OTUs are members of genera that include pathogens, but are found in marine environments, and include facultative anaerobes, i.e. dissimilatory nitrate reducers and denitrifiers. This may explain their abundance in both oxic and anoxic samples. A numerous archaeon is closely related to the lithoautotrophic ammonia oxidizer Nitrosopumilus maritimus. Known bacterial ammonia oxidizers are essentially absent, but bacterial nitrite oxidizers are abundant. Although other studies of this reef found evidence for anaerobic ammonia oxidizers, primer bias rendered that clade invisible to this study.     

Analysis of Stomach and Gut Microbiomes of the Eastern Oyster (Crassostrea virginica) from Coastal Louisiana,USA

We used high throughput pyrosequencing to characterize stomach and gut content microbiomes of Crassostrea virginica, the Easter oyster, obtained from two sites, one in Barataria Bay (Hackberry Bay) and the other in Terrebonne Bay (Lake Caillou), Louisiana, USA. Stomach microbiomes in oysters from Hackberry Bay were overwhelmingly dominated by Mollicutes most closely related to Mycoplasma; a more rich community dominated by Planctomyctes occurred in Lake Caillou oyster stomachs. Gut communities for oysters from both sites differed from stomach communities, and harbored a relatively diverse assemblage of phylotypes. Phylotypes most closely related to Shewanella and a Chloroflexi strain dominated the Lake Caillou and Hackberry Bay gut microbiota, respectively. While many members of the stomach and gut microbiomes appeared to be transients or opportunists, a putative core microbiome was identified based on phylotypes that occurred in all stomach or gut samples only. The putative core stomach microbiome comprised 5 OTUs in 3 phyla, while the putative core gut microbiome contained 44 OTUs in 12 phyla. These results collectively revealed novel microbial communities within the oyster digestive system, the functions of the oyster microbiome are largely unknown. A comparison of microbiomes from Louisiana oysters with bacterial communities reported for other marine invertebrates and fish indicated that molluscan microbiomes were more similar to each other than to microbiomes of polychaetes, decapods and fish.