Bacterial dominance in subseafloor sediments characterized by methane hydrates

Methane seepage intensity distinguish microbial communities in sediments at the Mid-Okinawa Trough

Shallow methane/sulfate transition zones in cold seeps are hotspots to study microbially mediated geochemical cycles due to high methane fluxes. However, our knowledge about the microbial communities in remote seafloor cold seep ecosystems with different methane seepage intensity is still sparse due to the challenge for sampling and visual observations. In this work, three remotely operated vehicle (ROV) video-guided push sediment cores were sampled from cold seep fields with different methane seepage intensity (low-intensity seepage, R5-C1; moderate-intensity seepage, R6-C2; high-intensity seepage, R6-C3) at the western slope of Mid-Okinawa Trough (Mid-OT) and subjected to high throughput sequencing of 16S rRNA genes for bacteria and archaea. Vesicomyid clams and white microbial mats are visible by video at R6-C3 with methane bubbles. The high relative abundances of anaerobic methanotrophic archaea (ANME-1, -2, and -3), δ-Proteobacteriacea and Campylobacteria in R6-C3 indicated that the processes of anaerobic methane oxidation (AOM), sulfate reduction and sulfur oxidation might occur in this active seeping site. In contrast, Bathyarchaeia, Nitrosopumilales, Sphingomonadales, and Burkholderiales were enriched in bubble-free sites, which commonly involved in the degradation of organic compounds. Principal coordinate analysis showed that both bacterial and archaeal communities were clustered according to sampling sites, also indicating the impact of methane seepage intensity on microbial communities. The co-occurrence network analysis revealed that microbes at the site with high methane fluxes mainly cooperated with each other to sustain the ecosystems, whereas competition enhanced at sites with low methane fluxes. Detection of thermophiles Thermoanaerobaculia and Hydrothermarchaeota may indicate microbial transmission from nearby hydrothermal vents, suggesting potential interactions between cold seepage and hydrothermal vent ecosystems. These results expand our knowledge about the composition and distribution of bacteria and archaea with different methane seepage intensity in cold seep field at the Mid-OT, contributing to the ongoing efforts in understanding carbon cycling in the cold seep ecosystems.

Microbial communities associated with thermogenic gas hydrate-bearing marine sediments in Qiongdongnan Basin, South China Sea

Biogenic and thermogenic gas are two major contributors to gas hydrate formation. Methane hydrates from both origins may have critical impacts on the ecological properties of marine sediments. However, research on microbial diversity in thermogenic hydrate-containing sediments is limited. This study examined the prokaryotic diversity and distributions along a sediment core with a vertical distribution of thermogenic gas hydrates with different occurrences obtained from the Qiongdongnan Basin by Illumina sequencing of 16S rRNA genes as well as molecular and geochemical techniques. Here, we show that gas hydrate occurrence has substantial impacts on both microbial diversity and community composition. Compared to the hydrate-free zone, distinct microbiomes with significantly higher abundance and lower diversity were observed within the gas hydrate-containing layers. Gammaproteobacteria and Actinobacterota dominated the bacterial taxa in all collected samples, while archaeal communities shifted sharply along the vertical profile of sediment layers. A notable stratified distribution of anaerobic methanotrophs shaped by both geophysical and geochemical parameters was also determined. In addition, the hydrate-free zone hosted a large number of rare taxa that might perform a fermentative breakdown of proteins in the deep biosphere and probably respond to the hydrate formation.

Cultivation and biogeochemical analyses reveal insights into methanogenesis in deep subseafloor sediment at a biogenic gas hydrate site

Gas hydrates deposited in subseafloor sediments are considered to primarily consist of biogenic methane. However, little evidence for the occurrence of living methanogens in subseafloor sediments has been provided. This study investigated viable methanogen diversity, population, physiology and potential activity in hydrate-bearing sediments (1–307 m below the seafloor) from the eastern Nankai Trough. Radiotracer experiments, the quantification of coenzyme F430 and molecular sequencing analysis indicated the occurrence of potential methanogenic activity and living methanogens in the sediments and the predominance of hydrogenotrophic methanogens followed by methylotrophic methanogens. Ten isolates and nine representative culture clones of hydrogenotrophic, methylotrophic and acetoclastic methanogens were obtained from the batch incubation of sediments and accounted for 0.5–76% of the total methanogenic sequences directly recovered from each sediment. The hydrogenotrophic methanogen isolates of Methanocalculus and Methanoculleus that dominated the sediment methanogen communities produced methane at temperatures from 4 to 55 °C, with an abrupt decline in the methane production rate at temperatures above 40 °C, which is consistent with the depth profiles of potential methanogenic activity in the Nankai Trough sediments in this and previous studies. Our results reveal the previously overlooked phylogenetic and metabolic diversity of living methanogens, including methylotrophic methanogenesis.

Evidence in the Japan Sea of microdolomite mineralization within gas hydrate microbiomes

Over the past 15 years, massive gas hydrate deposits have been studied extensively in Joetsu Basin, Japan Sea, where they are associated primarily with active gas chimney structures. Our research documents the discovery of spheroidal microdolomite aggregates found in association with other impurities inside of these massive gas hydrates. The microdolomites are often conjoined and show dark internal cores occasionally hosting saline fluid inclusions. Bacteroidetes sp. are concentrated on the inner rims of microdolomite grains, where they degrade complex petroleum-macromolecules present as an impurity within yellow methane hydrate. These oils show increasing biodegradation with depth which is consistent with the microbial activity of Bacteroidetes. Further investigation of these microdolomites and their contents can potentially yield insight into the dynamics and microbial ecology of other hydrate localities. If microdolomites are indeed found to be ubiquitous in both present and fossil hydrate settings, the materials preserved within may provide valuable insights into an unusual microhabitat which could have once fostered ancient life.

Gas hydrates in sustainable chemistry

This review includes the current state of the art understanding and advances in technical developments about various fields of gas hydrates, which are combined with expert perspectives and analyses.

Influence of 16S rRNA Hypervariable Region on Estimates of Bacterial Diversity and Community Composition in Seawater and Marine Sediment

To assess the influence of 16S ribosomal RNA (rRNA) tag choice on estimates of microbial diversity and/or community composition in seawater and marine sediment, we examined bacterial diversity and community composition from a site in the Central North Atlantic and a site in the Equatorial Pacific. For each site, we analyzed samples from four zones in the water column, a seafloor sediment sample, and two subseafloor sediment horizons (with stratigraphic ages of 1.5 and 5.5 million years old). We amplified both the V4 and V6 hypervariable regions of the 16S rRNA gene and clustered the sequences into operational taxonomic units (OTUs) of 97% similarity to analyze for diversity and community composition. OTU richness is much higher with the V6 tag than with the V4 tag, and subsequently OTU-level community composition is quite different between the two tags. Vertical patterns of relative diversity are broadly the same for both tags, with maximum taxonomic richness in seafloor sediment and lowest richness in subseafloor sediment at both geographic locations. Genetic dissimilarity between sample locations is also broadly the same for both tags. Community composition is very similar for both tags at the class level, but very different at the level of 97% similar OTUs. Class-level diversity and community composition of water-column samples are very similar at each water depth between the Atlantic and Pacific. However, sediment communities differ greatly from the Atlantic site to the Pacific site. Finally, for relative patterns of diversity and class-level community composition, deep sequencing and shallow sequencing provide similar results.

Microbial Selection and Survival in Subseafloor Sediment

Many studies have examined relationships of microorganisms to geochemical zones in subseafloor sediment. However, responses to selective pressure and patterns of community succession with sediment depth have rarely been examined. Here we use 16S rDNA sequencing to examine the succession of microbial communities at sites in the Indian Ocean and the Bering Sea. The sediment ranges in depth from 0.16 to 332 m below seafloor and in age from 660 to 1,300,000 years. The majority of subseafloor taxonomic diversity is present in the shallowest depth sampled. The best predictor of sequence presence or absence in the oldest sediment is relative abundance in the near-seafloor sediment. This relationship suggests that perseverance of specific taxa into deep, old sediment is primarily controlled by the taxonomic abundance that existed when the sediment was near the seafloor. The operational taxonomic units that dominate at depth comprise a subset of the local seafloor community at each site, rather than a grown-in group of geographically widespread subseafloor specialists. At both sites, most taxa classified as abundant decrease in relative frequency with increasing sediment depth and age. Comparison of community composition to cell counts at the Bering Sea site indicates that the rise of the few dominant taxa in the deep subseafloor community does not require net replication, but might simply result from lower mortality relative to competing taxa on the long timescale of community burial.

Microbial Diversity in Sub-Seafloor Sediments from the Costa Rica Margin

The exploration of the deep biosphere continues to reveal a great diversity of microorganisms, many of which remain poorly understood. This study provides a first look at the microbial community composition of the Costa Rica Margin sub-seafloor from two sites on the upper plate of the subduction zone, between the Cocos and Caribbean plates. Despite being in close geographical proximity, with similar lithologies, both sites show distinctions in the relative abundance of the archaeal domain and major microbial phyla, assessed using a pair of universal primers and supported by the sequencing of six metagenomes. Elusimicrobia, Chloroflexi, Aerophobetes, Actinobacteria, Lokiarchaeota, and Atribacteria were dominant phyla at Site 1378, and Bathyarchaeota, Chloroflexi, Hadesarchaeota, Aerophobetes, Elusimicrobia, and Lokiarchaeota were dominant at Site 1379. Correlations of microbial taxa with geochemistry were examined and notable relationships were seen with ammonia, sulfate, and depth. With deep sediments, there is always a concern that drilling technologies impact analyses due to contamination of the sediments via drilling fluid. Here, we use analysis of the drilling fluid in conjunction with the sediment analysis, to assess the level of contamination and remove any problematic sequences. In the majority of samples, we find the level of drilling fluid contamination, negligible.

Microbial diversity of two cold seep systems in gas hydrate-bearing sediments in the South China Sea

Cold seep is a unique habitat for microorganisms in deep marine sediments, and microbial communities and biogeochemical processes are still poorly understood, especially in relation to hydrate-bearing geo-systems. In this study, two cold seep systems were sampled and microbial diversity was studied at Site GMGS2-08 in the northern part of the South China Sea (SCS) during the GMGS2 gas hydrate expedition. The current cold seep system was composed of a sulfate methane transition zone (SMTZ) and an upper gas hydrate zone (UGHZ). The buried cold seep system was composed of an authigenic carbonate zone (ACZ) and a lower gas hydrate zone (LGHZ). These drill core samples provided an excellent opportunity for analyzing the microbial abundance and diversity based on quantitative polymerase chain reaction (qPCR) and high-throughput 16S rRNA gene sequencing. Compared to previous studies, the high relative abundance of ANME-1b, a clade of anaerobic methanotrophic archaea (ANME), may perform anaerobic oxidation of methane (AOM) in collaboration with ANME-2c and Desulfobacteraceae in the SMTZ, and the high relative abundances of Hadesarchaea, ANME-1b archaea and Aerophobetes bacteria were found in the gas hydrate zone (GHZ) at Site GMGS2-08. ANME-1b, detected in the GHZ, might mainly mediate the AOM process, and the process might occur in a wide depth range within the LGHZ. Moreover, bacterial communities were significantly different between the GHZ and non-GHZ sediments. In the ACZ, archaeal communities were different between the two samples from the upper and the lower layers, while bacterial communities shared similarities. Overall, this new record of cold seep microbial diversity at Site GMGS2-08 showed the complexity of the interaction between biogeochemical reactions and environmental conditions.

Crustal fluid and ash alteration impacts on the biosphere of Shikoku Basin sediments, Nankai Trough, Japan

We present data from sediment cores collected from IODP Site C0012 in the Shikoku Basin. Our site lies at the Nankai Trough, just prior to subduction of the 19 Ma Philippine Sea plate. Our data indicate that the sedimentary package is undergoing multiple routes of electron transport and that these differing pathways for oxidant supply generate a complex array of metabolic routes and microbial communities involved in carbon cycling. Numerical simulations matched to pore water data document that Ca(2+) and Cl(1-) are largely supplied via diffusion from a high-salinity (44.5 psu) basement fluid, which supports the presence of halophile Archean communities within the deep sedimentary package that are not observed in shallow sediments. Sulfate supply from basement supports anaerobic oxidation of methane (AOM) at a rate of ~0.2 pmol cm(-3) day(-1) at ~400 mbsf. We also note the disappearance of δ-Proteobacteria at 434 mbsf, coincident with the maximum in methane concentration, and their reappearance at 463 mbsf, coinciding with the observed deeper increase in sulfate concentration toward the basement. We did not, however, find ANME representatives in any of the samples analyzed (from 340 to 463 mbsf). The lack of ANME may be due to an overshadowing effect from the more dominant archaeal phylotypes or may indicate involvement of unknown groups of archaea in AOM (i.e., unclassified Euryarchaeota). In addition to the supply of sulfate from a basement aquifer, the deep biosphere at this site is also influenced by an elevated supply of reactive iron (up to 143 μmol g(-1)) and manganese (up to 20 μmol g(-1)). The effect of these metal oxides on the sulfur cycle is inferred from an accompanying sulfur isotope fractionation much smaller than expected from traditional sulfate-reducing pathways. The detection of the manganese- and iron-reducer γ-Proteobacteria Alteromonas at 367 mbsf is consistent with these geochemical inferences.

Seasonal patterns in microbial communities inhabiting the hot springs of Tengchong, Yunnan Province, China

Studies focusing on seasonal dynamics of microbial communities in terrestrial and marine environments are common; however, little is known about seasonal dynamics in high-temperature environments. Thus, our objective was to document the seasonal dynamics of both the physicochemical conditions and the microbial communities inhabiting hot springs in Tengchong County, Yunnan Province, China. The PhyloChip microarray detected 4882 operational taxonomic units (OTUs) within 79 bacterial phylum-level groups and 113 OTUs within 20 archaeal phylum-level groups, which are additional 54 bacterial phyla and 11 archaeal phyla to those that were previously described using pyrosequencing. Monsoon samples (June 2011) showed increased concentrations of potassium, total organic carbon, ammonium, calcium, sodium and total nitrogen, and decreased ferrous iron relative to the dry season (January 2011). At the same time, the highly ordered microbial communities present in January gave way to poorly ordered communities in June, characterized by higher richness of Bacteria, including microbes related to mesophiles. These seasonal changes in geochemistry and community structure are likely due to high rainfall influx during the monsoon season and indicate that seasonal dynamics occurs in high-temperature environments experiencing significant changes in seasonal recharge. Thus, geothermal environments are not isolated from the surrounding environment and seasonality affects microbial ecology.

Richness and diversity of bacteria in the Nansha carbonate platform (Core MD05-2896), South China Sea

We explored the bacterial diversity and vertical distribution along a sediment core (MD05-2896) from the coral reefs of the Nansha carbonate platform in the South China Sea. Bacterial diversity is determined by 16S rRNA molecular survey from twelve subsamples A, obtained via cloning, sequencing and phylogenetic analyses. We estimated the species richness by parametric and nonparametric models, which identified 326 ± 40 (SE) bacteria species. The dominant bacterial groups included Planctomycetes, Deltaproteobacteria, and candidate division OP3, which constituting 23.7, 10.4, and 9.5 % of bacterial 16S rRNAclone libraries, respectively. The observed stratification of bacterial communities was correlated with C/N ratio. This study improves our understanding of the species-environment relationship in the sub-sea floor sediment.

Assessment of Microbial Richness in Pelagic Sediment of Andaman Sea by Bacterial Tag Encoded FLX Titanium Amplicon Pyrosequencing (bTEFAP)

Microbial diversity of 1,000 m deep pelagic sediment from off Coast of Andaman Sea was analyzed by a culture independent technique, bacterial tag encoded FLX titanium amplicon pyrosequencing. The hypervariable region of small subunit ribosomal rRNA gene covering V6-V9, was amplified from the metagenomic DNA and sequenced. We obtained 19,271 reads, of which 18,206 high quality sequences were subjected to diversity analysis. A total of 305 operational taxonomic units (OTUs) were obtained corresponding to the members of firmicutes, proteobacteria, plantomycetes, actinobacteria, chloroflexi, bacteroidetes, and verucomicrobium. Firmicutes was the predominant phylum, which was largely represented with the family bacillaceae. More than 44 % of sequence reads could not be classified up to the species level and more than 14 % of the reads could not be assigned to any genus. Thus, the data indicates the possibility for the presence of uncultivable or unidentified novel bacterial species. In addition, the community structure identified in this study significantly differs with other reports from marine sediments.