Marine Benthic Group B Research Articles

Microbial community structure of soils in Bamenwan mangrove wetland

Microbial community diversity and composition are important for the maintenance of mangrove ecosystem. Bacterial and archaeal community composition of the Bamenwan Mangrove Wetland soil in Hainan, China, was determined using pyrosequencing technique. Bacterial community composition presented differences among the five soil samples. Rhizobiales with higher abundance were observed in inner mangrove forest samples, while Desulfobacterales were in the seaward edge samples, and Frankiales, Gaiellales and Rhodospirillales in the landedge sample. For archaea, Crenarchaeota and Euryarchaeota dominated in five samples, but the proportion in each samples were different. Dominant archaeal community composition at the order level was similar in the seaward edge samples. The dominant archaeal clusters in the two inner mangrove forest samples were different, with Soil Crenarchaeotic Group (SCG) and Halobacteriales in sample inside of Bruguiera sexangula forest and SCG, Methanosarcinales and Marine Benthic Group B (MBGB) in sample inside of Xylocarpus mekongensis forest. The dominant archaeal clusters in land sample were unique, with Terrestrial Group and South African Gold Mine Group 1. The metabolic pathways including metabolism, genetic information processing, environmental information processing, cellular processes, organismal systems and human diseases were all detected for bacterial and archaeal functional profiles, but metabolic potentials among five samples were different.

Geochemical and microbial characters of sediment from the gas hydrate area in the Taixinan Basin, South China Sea

The Taixinan Basin is one of the most potential gas hydrate bearing areas in the South China Sea and abundant gas hydrates have been discovered during expedition in 2013. In this study, geochemical and microbial methods are combinedly used to characterize the sediments from a shallow piston Core DH_CL_11 (gas hydrate free) and a gas hydrate-bearing drilling Core GMGS2-16 in this basin. Geochemical analyses indicate that anaerobic oxidation of methane (AOM) which is speculated to be linked to the ongoing gas hydrate dissociation is taking place in Core DH_CL_11 at deep. For Core GMGS2-16, AOM related to past episodes of methane seepage are suggested to dominate during its diagenetic process; while the relatively enriched δ 18O bulk-sediment values indicate that methane involved in AOM might be released from the “episodic dissociation” of gas hydrate. Microbial analyses indicate that the predominant phyla in the bacterial communities are Firmicutes and Proteobacteria (Gammaproteobacteria and Epsilonproteobacteria), while the dominant taxa in the archaeal communities are Marine_Benthic_Group_B (MBGB), Halobacteria, Thermoplasmata, Methanobacteria, Methanomicrobia, Group C3 and MCG. Under parallel experimental operations, comparable dominant members (Firmicutes and MBGB) are found in the piston Core DH_CL_11 and the near surface layer of the long drilling Core GMGS2-16. Moreover, these members have been found predominant in other known gas hydrate bearing cores, and the dominant of MBGB has even been found significantly related to gas hydrate occurrence. Therefore, a high possibility for the existing of gas hydrate underlying Core DH_CL_11 is inferred, which is consistent with the geochemical analyses. In all, combined geochemical and microbiological analyses are more informative in characterizing sediments from gas hydrate-associated areas in the South China Sea.

Contribution of thermogenic organic matter to the formation of biogenic gas hydrate: Evidence from geochemical and microbial characteristics of hydrate-containing sediments in the Taixinan Basin, South China Sea

High-saturation (40–100%), microbial gas hydrates have been acquired by expedition GMGS2 from the Taixinan Basin. In this study, geochemical and microbial features of hydrate-containing sediments from the drilling cores (GMGS2-09 and GMGS2-16) were characterized to explore their relationships with gas hydrate formation. Results showed that the average TOC content of GMGS2-09 and GMGS2-16 were 0.45% and 0.63%, respectively. They could meet the threshold for in situ gas hydrate formation, but were not available for the formation of high-saturation gas hydrates. The dominant members of Bacteria at the class taxonomic level were Alphaproteobacteria, Bacilli, Bacteroidia, Epsilonproteobacteria and Gammaproteobacteria, and those in Archaea were Marine_Benthic_Group_B (MBGB), Miscellaneous_Crenarchaeotic_Group (MCG), Group C3, Methanomicrobia and Methanobacteria. Indicators of microbes associated with thermogenic organic matter were measured. These include: (1) most of the dominant microbes had been found dominant in other gas hydrates bearing sediments, mud volcanos as well as oil/coal deposits; (2) hydrogenotrophic methanogens and an oilfield-origin thermophilic, methylotrophic methanogen were found dominant the methanogen community; (3) hydrocarbon-assimilating bacteria and other hyperthermophiles were frequently detected. Therefore, thermogenic signatures were inferred existed in the sediments. This deduction is consistent with the interpretation from the seismic reflection profiles. Owing to the inconsistency between low TOC content and gas hydrates with high saturation, secondary microbial methane generated from the bioconversion of thermogenic organic matters (oil or coal) was speculated to serve as enhanced gas flux for the formation of high-saturation gas hydrates. A preliminary formation model of high-saturation biogenic gas hydrates was proposed, in which diagenesis processes, tectonic movements and microbial activities were all emphasized regarding to their contribution to gas hydrates formation. In short, this research helps explain how microbial act and what kind of organic matter they use in forming biogenic gas hydrates with high saturations.

Microbial Community Structure Associated with Biogeochemical Processes in the Sulfate–Methane Transition Zone (SMTZ) of Gas-hydrate-bearing Sediment of the Ulleung Basin, East Sea

ABSTRACTWe investigated the biogeochemical constituents, microbial communities and functional genes (mcr and dsr) associated with anaerobic methane oxidation and sulfate reduction, and metabolic activities by sulfate reduction in the sulfate–methane transition zone (SMTZ) of gas-hydrate-bearing sediment of the Ulleung Basin in the East Sea. Maxima in the sulfate reduction rate (12.6 nmol cm−3 d−1), CO concentration (83 μM), and gene abundances of dsrA (9.1 × 106 copies cm−3) and mcrA (11.6 × 106 copies cm−3) occurred in the SMTZ. The peaks of CO consistently found in the SMTZ suggested that CO is an intermediate metabolic product related to methane oxidation. Candidate division JS1, the predominant bacterial group that comprised 59.0–63.7% of the 16S rRNA gene sequences, was recognized as an important organic carbon oxidizer. Both Marine Benthic Group D (MBGD) and Marine Benthic Group B (MBGB), which constituted 40.8–52.9 and 10.3–43.9% of the 16S rRNA gene sequences, respectively, were the dominant archaeal groups. Analysis of functional gene diversity revealed that anaerobic methanotroph-1-related phylotypes appeared to be the major CH4 oxidizer, whereas Firmicutes-like group was a predominant sulfate reducer in the 0.8 mbsf in SMTZ with low SO42− concentration. Overall results indicated that JS1 and two archaeal groups (MBGB and MBGD) seem to play a significant role in carbon and elements cycles in the gas-hydrate-bearing subsurface sediment of the Ulleung Basin.

Changes in microbial communities associated with gas hydrates in subseafloor sediments from the Nankai Trough.

Little is known about the microbial distribution patterns in subseafloor sediments. This study examines microbial diversity and activities in sediments of the Nankai Trough, where biogenic gas hydrates are deposited. Illumina sequencing of 16S rRNA genes revealed that the prokaryotic community structure is correlated with hydrate occurrence and depth but not with the sedimentary facies. The bacterial phyla 'Atribacteria' lineage JS1 and Chloroflexi dominated in all samples, whereas lower taxonomic units of Chloroflexi accounted for community variation related to hydrate saturation. In archaeal communities, 'Bathyarchaeota' was significantly abundant in the hydrate-containing samples, whereas Marine Benthic Group-B dominated in the upper sediments without hydrates. mcrA gene sequences assigned to deeply branching groups and ANME-1 were detected only in hydrate-containing samples. A predominance of hydrogenotrophic methanogens, Methanomicrobiales and Methanobacteriales, over acetoclastic methanogens was found throughout the depth. Incubation tests on hydrate-containing samples with a stable isotope tracer showed anaerobic methane oxidation activities under both low- and seawater-like salinity conditions. These results indicate that the distribution patterns of microorganisms involved in carbon cycling changed with gas hydrate occurrence, possibly because of the previous hydrate dissociation followed by pore water salinity decrease in situ, as previously proposed by a geochemical study at the study site.

Vertical distribution of archaeal communities in cold seep sediments from the jiulong methane reef area in the south China sea

Jiulong methane reef, a large cold seep area on the continental slope of the South China Sea (SCS), was characterized by chemosynthetic fauna, bacterial mats, methane-derived carbonate structures, and a shallow depth of sulfate-methane transition zone (SMTZ) in gravity cores. To characterize the microbial diversity and variation in correlation to methane venting in the cold seep area, the archaeal community in sediments of the gravity Core CL11 was analyzed, using the Illumina MiSeq sequencing system. A total of 96,917 valid sequences were obtained and classified into 275 OTUs. Taxonomic analysis showed that all the archaeal sequences belonged to the phyla of Crenarchaeota (69.41%) and Eurarchaeota (25.26%). Vertical distribution of the archaeal communities showed that the Marine Benthic Group B (MBG-B) was the predominant group (58.92%) in the topmost sediment of the core, while percentages of the South African Gold Mine Euryarchaeotal Group (SAGMEG) sequences increased with depth. Our findings indicate that the archaeal community in the cold seep of Jiulong Methane Reef is unique and provides us new insights into the archaeal community composition of the cold seep area.

Biogeography of Planktonic and Benthic Archaeal Communities in a Subtropical Eutrophic Estuary of China.

Mounting evidence suggests that Archaea are widespread and abundant in aquatic and terrestrial habitats and play fundamental roles in global biogeochemical cycles, yet the pattern and its ecological drivers of biogeographic distribution of archaeal community in estuarine ecosystem are still not well understood. Here, we investigated planktonic and benthic archaeal communities in the human-impacted Jiulong River estuary (JRE), southern China by using real-time PCR (RT-PCR) and Illumina 16S ribosomal RNA (rRNA) amplicon sequencing. RT-PCR analysis indicated that Archaea accounted for an average of 0.79 and 5.31% of prokaryotic biomass in water and sediment samples of the JRE, respectively. The diversity of planktonic archaeal community decreased gradually from the river runoff to seawater, whereas that of benthic community did not show the similar pattern. The results of taxonomic assignments indicated that Thaumarchaeota (Nitrosopumilus and Cenarchaeum), Methanocorpusculum, and Methanospirillum were significantly more abundant in planktonic than benthic communities, whereas the relative abundances of Miscellaneous Crenarchaeotic Group, Marine Benthic Group-B/-D, anaerobic methane-oxidizingArchaea -1/-2D, and South Africa Gold Mine Euryarchaeotic Group 1 were higher in sediments than in surface waters. Moreover, planktonic archaeal community composition varied significantly at broad and finer-scale taxonomic levels along the salinity gradient. Multivariate statistical analyses revealed that salinity is the main factor structuring the JRE planktonic but not benthic archaeal community at both total community and population level. SourceTrakcer analysis indicated that river might be a major source of archaea in the freshwater zone of the JRE. Overall, this study advances our understanding of the biogeographic patterns and its ecological drivers of estuarine archaeal communities.

Microbial community structures of methane hydrate-bearing sediments in the Ulleung Basin, East Sea of Korea

Microbial communities of a methane hydrate-bearing deep sediment cores, collect from Site UBGH2-10 from the Ulleung-Basin (East Sea of Korea), were characterized by phylogenetic analysis on the basis of 16S rRNA gene cloning. Quantification of key functional genes related to sulfate reduction (dsrA) and methanogenesis (mcrA) and that of bacteria and archaea were conducted using molecular approaches. On the basis of geochemical data, four subsections were selected to compare the microbial diversity relative to the presence of methane hydrate. Marine benthic group B (MBGB) and candidate division JS1 (JS1) were the dominant taxa in the archaeal and bacterial libraries, respectively, throughout the core, except in the deep layer. Interestingly, ANME-1b members and mcrA were detected only in sulfate methane transition zone (SMTZ). However, the proportions of sulfate-reducing Deltaproteobacteria clones and dsrA copy numbers differed (i.e., a very low proportion of clones but a sufficiently high dsrA copy number relative to bacteria). These results suggests that anaerobic oxidation of methane may occur mainly in SMTZ of Ulleung Basin sediment, where it is performed by ANME-1b via an unidentified oxidization process.

Microbial distributions detected by an oligonucleotide microarray across geochemical zones associated with methane in marine sediments from the Ulleung Basin

The biogeochemical processes that occur in marine sediments on continental margins are complex; however, from one perspective they can be considered with respect to three geochemical zones based on the presence and form of methane: sulfate–methane transition (SMTZ), gas hydrate stability zone (GHSZ), and free gas zone (FGZ). These geochemical zones may harbor distinct microbial communities that are important in biogeochemical carbon cycles. The objective of this study was to describe the microbial communities in sediments from the SMTZ, GHSZ, and FGZ using molecular ecology methods (i.e. PhyloChip microarray analysis and terminal restriction fragment length polymorphism (T-RFLP)) and examining the results in the context of non-biological parameters in the sediments. Non-metric multidimensional scaling and multi-response permutation procedures were used to determine whether microbial community compositions were significantly different in the three geochemical zones and to correlate samples with abiotic characteristics of the sediments. This analysis indicated that microbial communities from all three zones were distinct from one another and that variables such as sulfate concentration, hydrate saturation of the nearest gas hydrate layer, and depth (or unmeasured variables associated with depth e.g. temperature, pressure) were correlated to differences between the three zones. The archaeal anaerobic methanotrophs typically attributed to performing anaerobic oxidation of methane were not detected in the SMTZ; however, the marine benthic group-B, which is often found in SMTZ, was detected. Within the GHSZ, samples that were typically closer to layers that contained higher hydrate saturation had indicator sequences related to Vibrio-type taxa. These results suggest that the biogeographic patterns of microbial communities in marine sediments are distinct based on geochemical zones defined by methane.

Influence of Deglaciation on Microbial Communities in Marine Sediments Off the Coast of Svalbard, Arctic Circle

Increases in global temperatures have been shown to enhance glacier melting in the Arctic region. Here, we have evaluated the effects of meltwater runoff on the microbial communities of coastal marine sediment located along a transect of Temelfjorden, in Svalbard. As close to the glacier front, the sediment properties were clearly influenced by deglaciation. Denaturing gradient gel electrophoresis profiles showed that the sediment microbial communities of the stations of glacier front (stations 188-178) were distinguishable from that of outer fjord region (station 176). Canonical correspondence analysis indicated that total carbon and calcium carbonate in sediment and chlorophyll a in bottom water were key factors driving the change of microbial communities. Analysis of 16S rRNA gene clone libraries suggested that microbial diversity was higher within the glacier-proximal zone (station 188) directly affected by the runoffs than in the outer fjord region. While the crenarchaeotal group I.1a dominated at station 176 (62%), Marine Benthic Group-B and other Crenarchaeota groups were proportionally abundant. With regard to the bacterial community, alpha-Proteobacteria and Flavobacteria lineages prevailed (60%) at station 188, whereas delta-Proteobacteria (largely sulfate-reducers) predominated (32%) at station 176. Considering no clone sequences related to sulfate-reducers, station 188 may be more oxic compared to station 176. The distance-wise compositional variation in the microbial communities is attributable to their adaptations to the sediment environments which are differentially affected by melting glaciers.

Diversity of Achaea Communities in Deep Sea Sediments from the Sulu Sea

To study the archaeal diversity of deep-sea sediments in the tropical Western Pacific,we investigated the archaeal community structure in six sediments subsamples along the MD3059 sediment core collected during the IMAGES ⅪⅤ cruise with 16S rDNA analysis. A total of 543 archaeal 16S rDNA clones were examined and a total of 137 OTUs were obtained. Phylogenetic results showed that the archaeal diversity in the collected samples was very diverse,and the obtained OTUs were grouped into Crenarchaeota and Euryarchaeota,with the former dominated by Miscellaneous Crenarchaeotic Group ( MCG,54% of total archaeal clones) and the latter dominated by Marine Benthic Group D ( MBG-D) ,South African Gold Mine Euryarchaeotic Group ( SAGMEG) and Marine Benthic Group B ( MBG-B). These data have important implications for our understanding of archaeal community in deep-sea sediments of the tropical Western Pacific.

Investigation of archaeal and bacterial diversity in fermented seafood using barcoded pyrosequencing

Little is known about the archaeal diversity of fermented seafood; most of the earlier studies of fermented food have focused on lactic acid bacteria (LAB) in the fermentation process. In this study, the archaeal and bacterial diversity in seven kinds of fermented seafood were culture-independently examined using barcoded pyrosequencing and PCR-denaturing gradient gel electrophoresis (DGGE) methods. The multiplex barcoded pyrosequencing was performed in a single run, with multiple samples tagged uniquely by multiplex identifiers, using different primers for Archaea or Bacteria. Because PCR-DGGE analysis is a conventional molecular ecological approach, this analysis was also performed on the same samples and the results were compared with the results of the barcoded pyrosequencing analysis. A total of 13 372 sequences were retrieved from 15 898 pyrosequencing reads and were analyzed to evaluate the diversity of the archaeal and bacterial populations in seafood. The most predominant types of archaea and bacteria identified in the samples included extremely halophilic archaea related to the family Halobacteriaceae; various uncultured mesophilic Crenarchaeota, including Crenarchaeota Group I.1 (CG I.1a and CG I.1b), Marine Benthic Group B (MBG-B), and Miscellaneous Crenarchaeotic Group (MCG); and LAB affiliated with genus Lactobacillus and Weissella. Interestingly, numerous uncultured mesophilic Crenarchaeota groups were as ubiquitous in the fermented seafood as in terrestrial and aquatic niches; the existence of these Crenarchaeota groups has not been reported in any fermented food. These results indicate that the archaeal populations in the fermented seafood analyzed are diverse and include the halophilic and mesophilic groups, and that barcoded pyrosequencing is a promising and cost-effective method for analyzing microbial diversity compared with conventional approaches.

Archaeal Methane Cycling Communities Associated with Gassy Subsurface Sediments of Marennes-Oléron Bay (France)

In Marennes-Oléron Bay, a macro-tidal bay located on the French Atlantic coast, kilometer-scale acoustic turbidity reveals an accumulation of free gas in the sediment. Large concentrations of organic matter and rapid sedimentation rates provide ideal settings for biogenic methane cycling. We integrate seismic, sedimentologic, biogeochemical and molecular genetic approaches to determine whether microbial methane cycling is involved in this process. Here we show that the acoustic turbidity upper boundary matched with X-ray facies displaying fissures with the highest methane concentrations, demonstrating the existence of methane bubbles in the sediment. 16S rRNA and mcrA gene clone libraries were dominated by sequences affiliated to the three known ANME lineages and to putative methanogens. Sequences related to the marine benthic group B (MBG-B) and miscellaneous crenarchaeotal group (MCG) were also detected. However, the highest methane concentration facies was the only section where active Archaea were detected, using reverse-transcribed rRNA, indicating that these communities were involved either directly or indirectly in the methane cycling process. Moreover, three metabolically active novel uncultivated lineages, related to putative methane cycling Archaea, could be specifically associated to these methane bearing sediments. As methane cycling Archaea are commonly retrieved from deep subseafloor and methane seep sediment, the study of coastal gassy sediments, could therefore help to define the biogeochemical habitats of deep biosphere communities.

Stratified Communities of Active Archaea in Deep Marine Subsurface Sediments

Archaeal 16S rRNA was extracted from samples of deep marine subsurface sediments from Peru Margin site 1227, Ocean Drilling Program leg 201. The amounts of archaeal 16S rRNA in each extract were quantified by serial dilution and reverse transcription (RT)-PCR. The results indicated a 1,000-fold variation in rRNA content with depth in the sediment, with the highest concentrations found near the sediment surface and in the sulfate-methane transition zone (SMTZ). The phylogenetic composition of the active archaeal population revealed by cloning and sequencing of RT-PCR products changed with depth. Several phylotypes affiliated with marine benthic group B (MBGB) dominated clone libraries from the upper part of the SMTZ and were detected only in this layer. Members of the miscellaneous crenarchaeotal group (MCG) dominated clone libraries from the other layers. These results demonstrate that archaeal communities change in activity and community composition over short distances in geochemically distinct zones of deep subseafloor sediments and that these changes are traceable in the rRNA pool. It was shown for the first time that members of both the MCG and MBGB Archaea are more active in the SMTZ than in layers above and below. This indicates that they benefit either directly or indirectly from the anaerobic oxidation of methane. They also appear to be ecophysiologically flexible, as they have been retrieved from a wide range of marine sediments of various geochemical properties.