Deep-sea Surface Sediments Research Articles

Distribution Characteristics of Nitrogen-Cycling Microorganisms in Deep-Sea Surface Sediments of Western South China Sea.

Nitrogen-cycling processes in the deep sea remain understudied. This study investigates the distribution of nitrogen-cycling microbial communities in the deep-sea surface sediments of the western South China Sea, using metagenomic sequencing and real-time fluorescent quantitative PCR techniques to analyze their composition and abundance, and the effects of 11 environmental parameters, including NH4+-N, NO3--N, NO2--N, PO43--P, total nitrogen (TN), total organic carbon (TOC), C/N ratio, pH, electrical conductivity (EC), SO42-, and Cl-. The phylum- and species-level microbial community compositions show that five sites can be grouped as a major cluster, with sites S1 and S9 forming a sub-cluster, and sites S13, S19, and S26 forming the other; whereas sites S3 and S5 constitute a separate cluster. This is also evident for nitrogen-cycling functional genes, where their abundance is influenced by distinct environmental conditions, including water depths (shallower at sites S1 and S9 against deeper at sites S13, S19, and S26) and unique geological features (sites S3 and S5), whereas the vertical distribution of nitrogen-cycling gene abundance generally shows a decreasing trend against sediment depth. Redundancy analysis (RDA) exploring the correlation between the 11 environmental parameters and microbial communities revealed that the NO2--N, C/N ratio, and TN significantly affect microbial community composition (p < 0.05). This study assesses the survival strategies of microorganisms within deep-sea surface sediments and their role in the marine nitrogen cycle.

Diving into the Depths: Uncovering Microplastics in Norwegian Coastal Sediment Cores.

High concentrations of microplastics (MPs) have been documented in the deep-sea surface sediments of the Arctic Ocean. However, studies investigating their high-resolution vertical distribution in sediments from the European waters to the Arctic remain limited. This study examines MPs in five sediment cores from the Norwegian Coastal Current (NCC), encompassing the water-sediment interface and sediment layers up to 19 cm depth. Advanced analytical methods for MP identification down to 11 μm in size were combined with radiometric dating and lithology observations. MPs were present across all sediment cores, including layers predating the introduction of plastics, with concentrations exhibiting significant variation (54-12,491 MP kg-1). The smallest size class (11 μm) predominated in most sediment layers (34-100%). A total of 18 different polymer types were identified across all sediment layers, with polymer diversity and depth correlations varying widely between stations. Our findings suggest that differences in seafloor topography and the impact of anthropogenic activities (e.g., fishing) lead to varying environmental conditions at the sampling sites, influencing the vertical distribution of MPs. This challenges the reliability of using environmental parameters to predict MP accumulation zones and questions the use of MPs in sediment cores as indicators of the Anthropocene.

Fractal modeling for geochemical data of deep-sea surface sediments: A case study from Zhongsha Island, Southern China Sea

This study applied principal component analysis (PCA), concentration-area (C-A) and spectrum-area (S-A) fractal models to identify geochemical element combination anomalies related to heavy metals from the data for 43 geochemical elements in surface sediments of the Zhongsha Islands. The relationships between these 43 elements were first examined by applying correlation and cluster analysis to the surface sediment sample dataset. The multifractal spectral functions of the 43 elements were then calculated and all elements were classified using the curve shape of the spectral function. The results of classification were consistent with that of cluster analysis, thereby verifying the reliability of fractal analysis of the study area. PCA was then used to identify element combination anomalies and to assess high-value areas of element contents, and the S-A model was used to distinguish between the anomaly and background signal. The results of this multiple-analysis approach show that the element combination anomaly is mainly located in the deep-sea plain area, with a few elevated values in the Zhongsha South Basin. This study showed that quantitative evaluation of anomalies of multi-element associations can effectively delineate a target area and that anomalies of element associations extracted by the S-A fractal method can provide a more accurate outline areas containing high contents of combined elements. This study can act as a theoretical reference for the environmental assessment of the Zhongsha sea area.

Vertical heterogeneity of hydrocarbon-degrading bacteria in a core sediment sample from the Central Indian Ridge

Hydrocarbons are ubiquitous in marine environments and might fuel hydrocarbon-metabolizing microbes in the ocean. Numerous studies have documented microbial hydrocarbon degradation in water columns and deep-sea surface sediment. However, the degradation potential and biogeochemical cycling of hydrocarbons in subsurface sediments remain largely unknown. In this study, we used two different hydrocarbons, n-hexadecane (HEX) and methylcyclohexane (MCH), to investigate the distribution and diversity of hydrocarbon-consuming bacteria in a core sediment sample from the Central Indian Ridge (CIR), which is adjacent to mid-ridge hydrothermal vents in the Indian Ocean. We observed different vertical profiles of HEX- and MCH-degrading bacteria in the core sediments. Specifically, HEX-degrading bacteria were universally distributed, while MCH-degrading bacteria were found only in the intermediate layers of the core sediments. Changing factors including dissolved oxygen might affect the natural distribution of different hydrocarbon consumers. We found that a novel species of the genus C1-B045 might play a pivotal role in metabolizing MCH in the CIR deep biosphere. Through amino acid identity comparison with published sequences, we determined that C1-B045 harbors two novel classes of cyclohexanone monooxygenases involved in MCH metabolism. This study sheds light on the structure and function of hydrocarbon-consuming microbes in deep biospheres.

Latitudinal changes in elemental composition of smectite in deep sea sediments and its implication for microbial activity along the transect of equatorial Pacific Ocean

In order to determine the sediment provenance and potential iron (Fe) source in abyssal environment, deep sea surface sediments from a transect of the equatorial Pacific Ocean (0–10°N along ~131°W) were investigated for clay mineral assemblages, the elemental composition of smectite, and biogeochemical characteristics, including total organic carbon (TOC), total nitrogen (TN), and adenosine triphosphate (ATP), all of which are closely related to the specific sediment source and cellular process. Not only the relative composition of clay minerals but also two types of smectite (Fe-rich and Al-rich) were detected along the latitudinal transect. The composition of smectite collected close to the equator (0–6°N) was more Fe-rich compared to that of smectite collected at 7–10°N, which was Al-rich. These two distinct compositional groups indicate the existence of at least two sources of smectite at the study sites: (1) Fe-rich smectite supplied from South America and (2) Al-rich smectite derived from Asia and North America. These results suggest that the elemental composition of smectite can be used alongside other conventional proxies to differentiate the provenances of abyssal sediments in the central Pacific Ocean based on the southernmost latitude with Asian and North American sources (7°N) as the present-day mean Intertropical Convergence Zone (ITCZ) position. Moreover, an increase in the Fe content of smectite (N0: 22.1 wt%, N6: 19.3 wt%, and N10: 16.5 wt%) is positively correlated with the latitudinal distribution of ATP concentrations in surface sediments. Therefore, Fe-rich smectite may be important as a Fe source associated with microbial activity in deep sea environments with potential consequences for microbe–mineral interactions.

Distribution pattern and influencing factors for the microplastics in continental shelf, slope, and deep-sea surface sediments from the South China Sea

Marine microplastic pollution has become a major global concern in recent years and the fate of microplastics in the ocean is a hot issue of research. We investigated microplastic pollution in surface sediments in the northern South China Sea to explore its distribution characteristics and influencing factors across the continental shelf, continental slope, and deep-sea environments. It was found that the microplastic abundance of surface sediments was 130.56 ± 40.48 items/kg. The average abundance of microplastics in all three topographic areas gradually decreased with increasing distance offshore. However, the differences in microplastic diversity indices between the three areas were not significant and were higher than those in other seas of the world, indicating that the waters of the northern South China Sea are rich in microplastics from complex sources, with more pollution input channels. In the continental shelf, fibrous and low density microplastics accounted for the largest amount, with a low degree of microplastic aging, and were mostly transported by suspended-load. These microplastics were mainly influenced by human activities. In the deep sea, microplastics with higher density were the most abundant and the number of fibrous microplastics was fewer, while the average size was larger, mainly influenced by the bottom currents. These microplastics underwent long-term bedload transport. In the continental slope, the main factors affecting the distribution of microplastics were more complex. In addition to pollution by human activities, the slope also receives microplastic materials carried by bottom currents; therefore, the composition of microplastics in the slope combines those characteristics of microplastics in both the continental shelf and deep-sea areas. The findings of this study indicate that the South China Sea is affected by complex pollution sources under the dual effects of human activities and natural conditions; in particular, the pollution situation in the deep-sea area needs extensive attention.

Ecological Distribution and Diversity of Key Functional Genes for Denitrification in Surface Sediments of the Northern South China Sea: Implications for Potential N2O Emissions

Denitrification is an important pathway for nitrogen sink and N2O emissions, but little is known about the ecological distribution of key functional genes of denitrification and their potential N2O emissions in marine sediments. In this study, we analyzed the abundance, ecological distribution, and diversity of key functional genes (nir and nosZ) for denitrification in the northern South China Sea (SCS) surface sediments. Our results showed that the gene abundances varied from 105 to 108 and from 106 to 107 copies·g-1 for the nirS and nirK, respectively. The nosZ II/nosZ I gene abundance ratios were 1.28–9.88 in shallow-sea and deep-sea sediments, suggesting that the nosZ II gene should play a dominant role in N2O reduction in the northern SCS sediments. Moreover, the significantly higher abundance ratios of nir/nosZ in deep-sea surface sediments implied that there might be stronger N2O emissions potential in deep-sea sediments than in shallow-sea sediments. The ecological distribution profiles of the nirS, nosZ I, and nosZ II gene communities varied with water depth, and denitrification genes in shallow-sea and deep-sea sediments differed in their sensitivity to environmental factors. Water temperature was the major factor affecting both the abundance and the community distribution of the nirS gene in deep-sea sediments. Nitrate was the major factor shaping the community of nosZ I and nosZ II genes in shallow-sea sediments. Our study provides a pattern of ecological distribution and diversity for the nir and nosZ genes and emphasizes the role of these key functional genes in potential N2O emissions of the northern SCS surface sediments.

Classification of a Complexly Mixed Magnetic Mineral Assemblage in Pacific Ocean Surface Sediment by Electron Microscopy and Supervised Magnetic Unmixing

Unambiguous magnetic mineral identification in sediments is a prerequisite for reconstructing paleomagnetic and paleoenvironmental information from environmental magnetic parameters. We studied a deep-sea surface sediment sample from the Clarion Fracture Zone region, central Pacific Ocean, by combining magnetic measurements and scanning and transmission electron microscopic analyses. Eight titanomagnetite and magnetite particle types are recognized based on comprehensive documentation of crystal morphology, size, spatial arrangements, and compositions, which are indicative of their corresponding origins. Type-1 particles are detrital titanomagnetites with micron- and submicron sizes and irregular and angular shapes. Type-2 and -3 particles are well-defined octahedral titanomagnetites with submicron and nanometer sizes, respectively, which are likely related to local hydrothermal and volcanic activity. Type-4 particles are nanometer-sized titanomagnetites hosted within silicates, while type-5 particles are typical dendrite-like titanomagnetites that likely resulted from exsolution within host silicates. Type-6 particles are single domain magnetite magnetofossils related to local magnetotactic bacterial activity. Type-7 particles are superparamagnetic magnetite aggregates, while Type-8 particles are defect-rich single crystals composed of many small regions. Electron microscopy and supervised magnetic unmixing reveal that type-1 to -5 titanomagnetite and magnetite particles are the dominant magnetic minerals. In contrast, the magnetic contribution of magnetite magnetofossils appears to be small. Our work demonstrates that incorporating electron microscopic data removes much of the ambiguity associated with magnetic mineralogical interpretations in traditional rock magnetic measurements.

Spatial patterns and co-occurrence networks of microbial communities related to environmental heterogeneity in deep-sea surface sediments around Yap Trench, Western Pacific Ocean

Microbial communities are a large component of abyssal and hadal benthic environments, especially in deep-sea areas like Yap Trench, they provide a continuous source of nutrients and energy in their unique ecosystems. However, due to sampling difficulties, these microbial communities are relatively understudied. In the summer of 2017, sediment samples were collected from 21 stations around Yap Trench in the Western Pacific Ocean (mostly in the West Caroline Basin), at depths ranging from 3156 to 7837 m. Sediment samples from deep water depths and shallow water depths differed in organic matter content, median grain size, silt-clay content, and biodiversity. The structure of the microbial communities in the surface sediments had distinct relationships with environmental factors and their co-occurrence networks exhibited a clear spatial pattern. In addition, for both prokaryotes or eukaryotes, a combination of variables including silt-clay content, organic matter content, median grain size, and depth had the greatest impact on community structure. It was notable that fungi played important roles in the co-occurrence networks of deep water depth sediment samples while bacteria dominated those of shallow water depth samples. The differences in structure and ecological niches in the different networks were due to differences in sediment texture and organic matter content. Since clay had a positive effect on the diversity of bacteria, it had an indirect positive effect on fungi, leading to differences in biodiversity among different groups. More organic matter meant more nutrients were available for the growth and reproduction of microbes, which led to fewer niche overlaps. This study conducted an extensive and systematic sequencing survey of surface sediments around Yap Trench in the Western Pacific Ocean, providing insight into microbial responses to environmental heterogeneity in deep-sea benthic ecosystems.

Diversity and metabolism of Woeseiales bacteria, global members of marine sediment communities

Surveys of 16S rRNA gene sequences derived from marine sediments have indicated that a widely distributed group of Gammaproteobacteria, named “JTB255-Marine Benthic Group” (now the candidate order Woeseiales), accounts for 1–22% of the retrieved sequences. Despite their ubiquity in seafloor communities, little is known about their distribution and specific ecological niches in the deep sea, which constitutes the largest biome globally. Here, we characterized the phylogeny, environmental distribution patterns, abundance, and metabolic potential of Woeseiales bacteria with a focus on representatives from the deep sea. From a phylogenetic analysis of publicly available 16S rRNA gene sequences (≥1400 bp, n = 994), we identified lineages of Woeseiales with greater prevalence in the deep sea than in coastal environments, a pattern corroborated by the distribution of 16S oligotypes recovered from 28 globally distributed sediment samples. Cell counts revealed that Woeseiales bacteria accounted for 5 ± 2% of all microbial cells in deep-sea surface sediments at 23 globally distributed sites. Comparative analyses of a genome, metagenome bins, and single-cell genomes suggested that members of the corresponding clades are likely to grow on proteinaceous matter, potentially derived from detrital cell membranes, cell walls, and other organic remnants in marine sediments.

Bacterial diversity in deep-sea sediments under influence of asphalt seep at the São Paulo Plateau.

Here we investigated the diversity of bacterial communities from deep-sea surface sediments under influence of asphalt seeps at the Sao Paulo Plateau using next-generation sequencing method. Sampling was performed at North São Paulo Plateau using the human occupied vehicle Shinkai 6500 and her support vessel Yokosuka. The microbial diversity was studied at two surficial sediment layers (0-1 and 1-4cm) of five samples collected in cores in water depths ranging from 2456 to 2728m. Bacterial communities were studied through sequencing of 16S rRNA gene on the Ion Torrent platform and clustered in operational taxonomic units. We observed high diversity of bacterial sediment communities as previously described by other studies. When we considered community composition, the most abundant classes were Alphaproteobacteria (27.7%), Acidimicrobiia (20%), Gammaproteobacteria (11.3%) and Deltaproteobacteria (6.6%). Most abundant OTUs at family level were from two uncultured bacteria from Actinomarinales (5.95%) and Kiloniellaceae (3.17%). The unexpected high abundance of Alphaproteobacteria and Acidimicrobiia in our deep-sea microbial communities may be related to the presence of asphalt seep at North São Paulo Plateau, since these bacterial classes contain bacteria that possess the capability of metabolizing hydrocarbon compounds.

Dependence of bacterial magnetosome morphology on chemical conditions in deep-sea sediments

Magnetotactic bacteria (MTB) play an important role in biogeochemical cycles of iron and remanent magnetization acquisition of sediments. It is generally considered that magnetite-producing MTB prefer chemical conditions in the oxic-anoxic transition zone (OATZ). We studied the distribution of fossil MTB magnetite (magnetofossils) and microbes phylogenetically related to MTB within deep-sea surface sediments across the OATZ. Transmission electron microscope (TEM) observations and rock-magnetic proxies show that magnetofossils commonly occur both within the OATZ and above it, even at the top of surface oxidized layers, and that the proportion of magnetofossils with a teardrop morphology increases within the OATZ. Consistent results were obtained from the pyrosequencing of 16S rRNA gene fragments. Operational taxonomic units (OTUs) related to Nitrospirae and OP3 MTB, which produce teardrop-shape magnetosomes, were detected only within the OATZ, whereas OTUs related to alphaproteobacterial MTB, which produce equant or elongated magnetite particles, were distributed above the OATZ. These results suggest that magnetofossil morphology can be used to detect past OATZs, and that some MTB lineages can occur ubiquitously in marine sediments rather than being limited within the OATZ. Our results imply that the timing of remanent magnetization acquisition may depend on the inhabiting MTB lineages.

Unexpectedly high diversity of anammox bacteria detected in deep-sea surface sediments of the South China Sea.

Candidatus Scalindua is an exclusive genus of anammox bacteria known to exhibit low diversity found in deep-sea ecosystems. In this study, the community composition of anammox bacteria in surface sediments of the South China Sea was analyzed using high-throughput sequencing techniques. Results indicated that the dominant operational taxonomic units were related to three different genera of anammox bacteria, identified as Ca. Scalindua (87.29%), Ca. Brocadia (10.27%) and Ca. Kuenenia (2.44%), in order of decreasing abundance. Quantitative PCR analysis of anammox-specific 16S rRNA and hzsB genes confirmed that the abundance of anammox bacteria in deep-sea surface sediments ranged from 4.34 × 105 to 3.91 × 107 and 1.62 × 105 to 1.63 × 108 copies per gram, respectively. The ACE, Chao1 and Shannon estimators for anammox bacteria were significantly higher than those reported in previous studies. Pearson correlation and redundancy analyses indicated that depth and temperature were the key factors affecting the distribution, abundance and diversity of anammox bacteria in deep-sea sediments. We herein report the wide distribution of Ca. Kuenenia and Ca. Brocadia in deep-sea sediments and provide comprehensive information on the distribution and ecological significance of anammox bacteria in deep-sea environments.

Hydrocarbon degradation and response of seafloor sediment bacterial community in the northern Gulf of Mexico to light Louisiana sweet crude oil.

The Deepwater Horizon (DWH) blowout resulted in the deposition to the seafloor of up to 4.9% of 200 million gallons of oil released into the Gulf of Mexico. The petroleum hydrocarbon concentrations near the wellhead were high immediately after the spill, but returned to background levels a few years after the spill. Microbial communities in the seafloor are thought to be responsible for the degradation of hydrocarbons, however, our knowledge is primarily based upon gene diversity surveys and hydrocarbon concentration in field sediment samples. Here, we investigated the oil degradation potential and changes in bacterial community by amending seafloor sediment collected near the DWH site with crude oil and both oil and Corexit dispersant. Polycyclic aromatic hydrocarbons were rapidly degraded during the first 30 days of incubation, while alkanes were degraded more slowly. With the degradation of hydrocarbons, the relative abundances of Colwelliaceae, Alteromonadaceae, Methylococales, Alcanivorax, Bacteriovorax, and Phaeobacter increased remarkably. However, the abundances of oil-degrading bacteria changed with oil chemistry. Colwelliaceae decreased with increasing oil degradation, whereas Alcanivorax and Methylococcales increased considerably. We assembled seven genomes from the metagenome, including ones belonging to Colwellia, Alteromonadaceae, Rhodobacteraceae, the newly reported genus Woeseia, and candidate phylum NC10, all of which possess a repertoire of genes for hydrocarbon degradation. Moreover, genes related to hydrocarbon degradation were highly enriched in the oiled treatment, suggesting that the hydrocarbons were biodegraded, and that the indigenous microflora have a remarkable potential for the natural attenuation of spilled oil in the deep-sea surface sediment.

In-situ measurements of rare earth elements in deep sea sediments using nuclear methods

The prospecting activities for finding new rare earth elements (REE) sources have increased greatly in recent years. One of the main discoveries was announced in 2011 by Japanese researchers who found large quantities of REE on the ocean seafloor at the sea depths greater than 4,000 m. The classic approach to investigate REE in deep sea sediments is to obtain sediment samples by drilling that is followed by laborious laboratory analysis. This is very expensive, time consuming and not appropriate for exploring vast areas. In order to efficiently explore the ocean floor for REE deposits, the further development of affordable sensors is needed. Here, we propose two nuclear techniques for exploring REE in surface deep sea sediments: i) Passive measurement of lutetium-176 radioactivity, appropriate if long-term in-situ measurements are possible, and ii) The use of the neutron sensor attached to a remotely operated vehicle for rapid in-situ measurement of gadolinium by thermal neutron-capture. Since concentrations of lutetium and gadolinium show strong linear correlation to the total REE concentrations in deep sea sediments, it is possible to deduce the total REE content by measuring Lu or Gd concentrations only.

Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria.

The deep ocean floor covers more than 60% of the Earth’s surface, and hosts diverse bacterial communities with important functions in carbon and nutrient cycles. The identification of key bacterial members remains a challenge and their patterns of distribution in seafloor sediment yet remain poorly described. Previous studies were either regionally restricted or included few deep-sea sediments, and did not specifically test biogeographic patterns across the vast oligotrophic bathyal and abyssal seafloor. Here we define the composition of this deep seafloor microbiome by describing those bacterial operational taxonomic units (OTU) that are specifically associated with deep-sea surface sediments at water depths ranging from 1000–5300 m. We show that the microbiome of the surface seafloor is distinct from the subsurface seafloor. The cosmopolitan bacterial OTU were affiliated with the clades JTB255 (class Gammaproteobacteria, order Xanthomonadales) and OM1 (Actinobacteria, order Acidimicrobiales), comprising 21% and 7% of their respective clades, and about 1% of all sequences in the study. Overall, few sequence-abundant bacterial types were globally dispersed and displayed positive range-abundance relationships. Most bacterial populations were rare and exhibited a high degree of endemism, explaining the substantial differences in community composition observed over large spatial scales. Despite the relative physicochemical uniformity of deep-sea sediments, we identified indicators of productivity regimes, especially sediment organic matter content, as factors significantly associated with changes in bacterial community structure across the globe.

The detection of magnetotactic bacteria in deep sea sediments from the east Pacific Manganese Nodule Province

Magnetotactic bacteria (MTB) are distributed ubiquitously in sediments from coastal environments to the deep sea. The Pacific Manganese Nodule Province contains numerous polymetallic nodules mainly composed of manganese, iron, cobalt, copper and nickel. In the present study we used Illumina MiSeq sequencing technology to assess the communities of putative MTB in deep sea surface sediments at nine stations in the east Pacific Manganese Nodule Province. A total of 402 sequence reads from MTB were classified into six operational taxonomic units (OTUs). Among these, OTU113 and OTU759 were affiliated with the genus Magnetospira, OTU2224 and OTU2794 were affiliated with the genus Magnetococcus and Magnetovibrio, respectively, OTU3017 had no known genus affiliation, and OTU2556 was most similar to Candidatus Magnetananas. Interestingly, OTU759 was widely distributed, occurring at all study sites. Magnetism measurements revealed that all sediments were dominated by low coercivity, non-interacting single domain magnetic minerals. Transmission electron microscopy confirmed that the magnetic minerals were magnetosomes. Our data suggest that diverse putative MTB are widely distributed in deep sea surface sediments from the east Pacific Manganese Nodule Province.

N-Alkane distribution and carbon stable isotope composition in leaf waxes of C3 and C4 plants from Angola

Palaeoenvironmental assessment of past C3 and C4 vegetation distributions relies on end member data from plant analyses. In southwestern Africa, end member data of the carbon number distribution of n-alkanes from leaf waxes and their carbon isotopic composition were available for the rainforest and the savannah. To complement this, we analysed the n-alkane parameters of 41 C3 plants and 11 C4 plants from the transition region, i.e., the wood- and shrubland of Angola. The combined results for the rainforest, the wood- and shrubland and the savannah show an increase in the average chain length (ACL) of C3 and C4 plants and an increasingly enriched carbon stable isotope composition for the C3 plants from the equator towards southern Africa. The enlarged database was applied to the data of a north–south transect of deep-sea surface sediments already used in a previous study, which resulted in the proxies showing a good reflection of the vegetation on the adjacent southwest African continent in terms of %C4 plant cover. Applying end member values for ACL and δ13C obtained from the enlarged database by two different averaging methods (arithmetic average and median) to the n-alkane data from the sediment transect yielded similar vegetation reconstructions. In addition, a correlation between ACL and growth height of the plants is discussed, indicating that the ACL may be useful as a tree abundance parameter. Thus, the enlarged end member database strengthens the n-alkane parameters as tools for palaeoenvironmental studies.

Global dispersion and local diversification of the methane seep microbiome

Methane seeps are widespread seafloor ecosystems shaped by the emission of gas from seabed reservoirs. The microorganisms inhabiting methane seeps transform the chemical energy in methane to products that sustain rich benthic communities around the gas leaks. Despite the biogeochemical relevance of microbial methane removal at seeps, the global diversity and dispersion of seep microbiota remain unknown. Here we determined the microbial diversity and community structure of 23 globally distributed methane seeps and compared these to the microbial communities of 54 other seafloor ecosystems, including sulfate-methane transition zones, hydrothermal vents, coastal sediments, and deep-sea surface and subsurface sediments. We found that methane seep communities show moderate levels of microbial richness compared with other seafloor ecosystems and harbor distinct bacterial and archaeal taxa with cosmopolitan distribution and key biogeochemical functions. The high relative sequence abundance of ANME (anaerobic methanotrophic archaea), as well as aerobic Methylococcales, sulfate-reducing Desulfobacterales, and sulfide-oxidizing Thiotrichales, matches the most favorable microbial metabolisms at methane seeps in terms of substrate supply and distinguishes the seep microbiome from other seafloor microbiomes. The key functional taxa varied in relative sequence abundance between different seeps due to the environmental factors, sediment depth and seafloor temperature. The degree of endemism of the methane seep microbiome suggests a high local diversification in these heterogeneous but long-lived ecosystems. Our results indicate that the seep microbiome is structured according to metacommunity processes and that few cosmopolitan microbial taxa mediate the bulk of methane oxidation, with global relevance to methane emission in the ocean.

Examining the diversity of microbes in a deep-sea coral community impacted by the Deepwater Horizon oil spill

Deep-sea surface sediments and flocculent material (floc) associated with corals containing oil originating from the Deepwater Horizon (DWH) oil spill were examined to determine the diversity of microbes and the presence of functional genes involved in oil degradation. For all samples, 16S rRNA clone libraries were constructed to obtain full-length sequences and Illumina amplicon sequencing was used to further probe the diversity of the microbial community. The 16S rRNA gene data obtained by Illumina amplicon sequencing revealed Proteobacteria (55–64%) as the dominant bacteria in both sediment and floc samples. The floc samples were comprised of mostly aerobic or facultative aerobic phylotypes including Rhizobiales, Rhodobacterales, Sphingomonadales, Rickettsiales, Alteromonadales, Pseudomonadales, whereas mixtures of the aforementioned aerobic species and anaerobic phylotypes such as Desulfobacterales, Desulfuromonadales and Desulfarculales were present in the sediment samples. Genera affiliated with oil-degrading bacteria were identified in both sediment and floc samples. To evaluate the potential of the microbial community to degrade oil, clone libraries were constructed for the alkB gene (one of the structural genes of alkane hydroxylase involved in the aerobic degradation of n-alkanes of chain length >C5–C16) and the alkylsuccinate synthase/benzylsuccinate synthases (assA/bssA) gene (involved in the anaerobic degradation of n-alkanes [via assA] and polycyclic aromatic hydrocarbons [PAHs; via bssA]). The alkB gene was present in all samples with the majority of sequences clustering to members of the Proteobacteria closely aligned to environmental sequences from hydrocarbon seep environments. The assA/bssA genes were only detected in sediment samples and were closely affiliated with δ-Proteobacteria previously detected in oil-contaminated sediments and oil-enrichment cultures. These data provide insight into the differences between environments impacted by the DWH oil spill and highlight the functional diversity of oil-degrading microbes associated with a deep-sea coral community.