Non-seep Site Research Articles

Phylogenetic diversity of functional genes in deep-sea cold seeps: a novel perspective on metagenomics

BackgroundLeakages of cold, methane-rich fluids from subsurface reservoirs to the sea floor are termed cold seeps. Recent exploration of the deep sea has shed new light on the microbial communities in cold seeps. However, conventional metagenomic methods largely rely on reference databases and neglect the phylogeny of functional genes.ResultsIn this study, we developed the REMIRGE program to retrieve the full-length functional genes from shotgun metagenomic reads and fully explored the phylogenetic diversity in cold seep sediments. The abundance and diversity of functional genes involved in the methane, sulfur, and nitrogen cycles differed in the non-seep site and five cold seep sites. In one Haima cold seep site, the divergence of functional groups was observed at the centimeter scale of sediment depths, with the surface layer potentially acting as a reservoir of microbial species and functions. Additionally, positive correlations were found between specific gene sequence clusters of relevant genes, indicating coupling occurred within specific functional groups.ConclusionREMIRGE revealed divergent phylogenetic diversity of functional groups and functional pathway preferences in a deep-sea cold seep at finer scales, which could not be detected by conventional methods. Our work highlights that phylogenetic information is conducive to more comprehensive functional profiles, and REMIRGE has the potential to uncover more new insights from shotgun metagenomic data.8PNdJCR5n5eFCnFqsf6X4UVideo

Variations and gradients between methane seep and off-seep microbial communities in a submarine canyon system in the Northeast Pacific.

Methane seeps are highly abundant marine habitats that contribute sources of chemosynthetic primary production to marine ecosystems. Seeps also factor into the global budget of methane, a potent greenhouse gas. Because of these factors, methane seeps influence not only local ocean ecology, but also biogeochemical cycles on a greater scale. Methane seeps host specialized microbial communities that vary significantly based on geography, seep gross morphology, biogeochemistry, and a diversity of other ecological factors including cross-domain species interactions. In this study, we collected sediment cores from six seep and non-seep locations from Grays and Quinault Canyons (46-47°N) off Washington State, USA, as well as one non-seep site off the coast of Oregon, USA (45°N) to quantify the scale of seep influence on biodiversity within marine habitats. These samples were profiled using 16S rRNA gene sequencing. Predicted gene functions were generated using the program PICRUSt2, and the community composition and predicted functions were compared among samples. The microbial communities at seeps varied by seep morphology and habitat, whereas the microbial communities at non-seep sites varied by water depth. Microbial community composition and predicted gene function clearly transitioned from on-seep to off-seep in samples collected from transects moving away from seeps, with a clear ecotone and high diversity where methane-fueled habitats transition into the non-seep deep sea. Our work demonstrates the microbial and metabolic sphere of influence that extends outwards from methane seep habitats.

Methane seeps as refugia during ash falls in the Late Cretaceous Western Interior Seaway of North America

Abstract Methane seeps host rich biotic communities, forming patchy yet highly productive ecosystems across the global ocean. Persistent hydrocarbon emissions fuel chemosynthetic food webs at seeps. Methane seeps were abundant in the Western Interior Seaway of North America during the Late Cretaceous. This area also experienced intermittent ash falls, which negatively impacted the marine fauna. We propose that methane seeps acted as refugia during these environmental perturbations. We report a laterally continuous bentonite within the upper Campanian Baculites compressus Zone of the Pierre Shale in southwestern South Dakota (USA) that fortuitously cuts across a methane seep deposit. We compare the macroinvertebrate record below and above the bentonite at seep and non-seep sites. Our results reveal that the paleocommunity (measured by abundance and diversity) was largely unaffected by the ash fall at the seep site, whereas it was significantly altered at the non-seep site. Thus, methane seeps in the Western Interior Seaway may have provided refuges or served as oases in the aftermath of severe environmental perturbations.

Palaeoecological analysis of a methane seep deposit from the Upper Cretaceous (Maastrichtian) of the U.S. Western Interior

Methane seeps were a common feature in the Late Cretaceous Western Interior Seaway of the United States. We document the occurrence of methane seep deposits in the Pierre Shale on the Cedar Creek Anticline in east-central Montana for the first time. The seep deposits occur in the lowermost part of the Baculites baculus Zone (the Endocostea typica Zone), corresponding to the lowermost Maastrichtian. They are therefore the youngest seeps yet described from the Western Interior Seaway. We conducted a detailed faunal analysis of a single seep deposit, together with geochemical investigation of both seep carbonates and molluscan shell material to determine palaeoenvironmental conditions. Oxygen isotope analysis of well-preserved molluscan shell material reveals water temperatures of between 19 and 27°C, while depleted carbon isotope values of seep carbonates are indicative of the anaerobic oxidation of methane. The morphology of the seep deposit suggests a strong advective flux of methane to the sediment–water interface. Comparison to a nearby contemporaneous non-seep site reveals that similar groups of organisms occur in both settings, albeit with varying relative abundances – the seep is numerically dominated by the lucinid bivalve Nymphalucina occidentalis. Substrate appears to be the major control on the diversity and palaeoecological composition of both seep and non-seep sites.

Faunal and stable isotopic analyses of benthic foraminifera from the Southeast Seep on Kimki Ridge offshore southern California, USA

We investigated the benthic foraminiferal faunal and stable carbon and oxygen isotopic composition of a 15-cm push core (NA075-092b) obtained on a Telepresence-Enabled cruise to the Southeast Seep on Kimki Ridge offshore southern California. The seep core was taken at a depth of 973 m in the vicinity of a Beggiatoa bacterial mat and vesicomyid clams (Calyptogena) and compared to previously published data of living assemblages from ~ 714 m, four reference cores obtained at ~ 1030 m, and another one at 739 m. All of the reference sites are also from the Inner Continental Borderland but with no evidence of methane seepage.No endemic species were found at the seep site and most of the taxa recovered there have been reported previously from other seep or low oxygen environments. Q- and R-mode cluster analyses clearly illustrated differences in the faunal assemblages of the seep and non-seep sites. The living assemblage at Southeast Seep was characterized by abundant Takayanagia delicata, Cassidulina translucens, and Spiroplectammina biformis, whereas the non-seep San Pedro Basin reference assemblage was comprised primarily of Chilostomella oolina and Globobulimina pacifica. Density and species richness were lower at the seep site compared to the non-seep site, reflecting the harsher living conditions there. The dead assemblage at the seep site was dominated by Gyroidina turgida compared to Cassidulina translucens at the ~ 1030 m non-seep site and Cassidulina translucens, Pseudoparrella pacifica, and Takayanagia delicata at the 739 m non-seep site. Density was three times lower at Southeast Seep than at the non-seep sites of comparable water depth but species richness was ~ 30% higher. Stable carbon isotopic values were considerably depleted in the seep samples compared to the non-seep samples, with a progression from lightest to heaviest average δ13C values evident at the seep site reflecting microhabitat preference and vital effect: the deep infaunal species of Globobulimina, the shallow infaunal species Uvigerina peregrina, the epifaunal species Cibicidoides wuellerstorfi, and the shallow infaunal but aragonite-shelled species Hoeglundina elegans. The δ13C values downcore among each benthic species indicates ongoing fluid seepage through at least the last 3800 cal yr B.P. at Southeast Seep. Besides the continual local seepage, evidence from δ13C values of planktic foraminifera in the seep core suggest two pulses of methane (at 3000 and 3700 cal yr B.P.) were released that were large enough to influence much of the water column. Paired benthic and planktic foraminiferal stable oxygen isotope records provide evidence that there were no paleoenvironmental changes such as increased bottom-water temperature or changes in oxygen isotopic composition of bottom and pore waters during this 3800-year record to induce the methane releases. Instead, Southeast Seep appears to be the result of local faulting providing pathways for fluid to flow to the seafloor at a fault stepover or transpressional bend in the regional strike-slip system.

Benthic nematode biodiversity of the Abzu, Tiamat and Michael Ivanov mud volcanoes located along the SWIM fracture zone (Gulf of Cadiz)

Studies that focus on meiofaunal assemblages of deep-sea mud volcanoes show an unpredictable abundance and diversity in a clear response to the different environmental conditions of the seeped sediment. The mud volcanoes Abzu, Tiamat and M. Ivanov (ATI), are located along the SWIM1 fracture zone, in front of the accretionary wedge of the Gulf of Cadiz (AWGC). The geological setting and the fluid geochemical characteristics of the ATI mud volcanoes are different from those located within the AWGC. The main aim of this study is to describe and compare the spatial and vertical distributions of the meiofauna and nematode assemblages from the ATI mud volcanoes, the Porto mud volcano located in the AWGC, and a non-seep site (Site 2) as reference. The pore-water on the uppermost sediment layers has compositions close to the near-bottom seawater. The meiofauna abundances were generally lower and the vertical distribution of the assemblages showed a typical pattern, gradually decreasing towards depth. The lack of spatial patterns of the standing stocks contrasts with the spatial variability of diversity and biomass, related to the differences in the nematode assemblages that are distinct between ATI, Site 2 and the Porto mud volcano. The ATI and Site 2 assemblages are similar to deep-sea non-seep habitats, and are clearly coupled with the environmental conditions of the bottom seawater. No evidence of seep conditions favouring the development of specialised fauna were found. The lower diversity and the presence of higher dominance species could be driven by distinct seepage conditions of the Porto mud volcano.

Novel use of burrow casting as a research tool in deep-sea ecology

Although the deep sea is the largest ecosystem on Earth, its infaunal ecology remains poorly understood because of the logistical challenges. Here we report the morphology of relatively large burrows obtained by in situ burrow casting at a hydrocarbon-seep site and a non-seep site at water depths of 1173 and 1455 m, respectively. Deep and complex burrows are abundant at both sites, indicating that the burrows introduce oxygen-rich sea water into the deep reducing substrate, thereby influencing benthic metabolism and nutrient fluxes, and providing an oxic microhabitat for small organisms. Burrow castings reveal that the solemyid bivalve Acharax johnsoni mines sulphide from the sediment, as documented for related shallow-water species. To our knowledge, this is the first study to examine in situ burrow morphology in the deep sea by means of burrow casting, providing detailed information on burrow structure which will aid the interpretation of seabed processes in the deep sea.

Chemosynthetic trophic support for the benthic community at an intertidal cold seep site at Mocha Island off central Chile

We analyzed C and N stable isotope ratios of benthic fauna and their potential food sources at an intertidal methane seep site and a control site without emanation at Mocha Island (central Chile). The objective was to trace the origin of the main food sources used by the local heterotrophic fauna, based on the hypothesis that chemosynthetic production could be partially fueling the local food web at the seep site. Food sources sampled at both sites included macroalgae, particulate organic matter and bacteria-like filaments found growing over the red algae Gelidium lingulatum within the areas of active methane release. At the control site, located 11 km away from the gas emanation, fauna exhibited moderate δ 13C values ranging from −16.2‰ (in a nereid polychaete) to −14.8‰ (in a cirolanid isopod), which were consistent with those of the potential photosynthetic food sources sampled at this site (−20.2 to −16.5‰). δ 13C values of the photosynthetic food sources at the seep site similarly ranged between −25.4 and −17.9‰. However, a portion of the animals at this site were consistently more 13C-depleted, with δ 13C values close to that of the seeping methane (−43.8‰) and the bacteria-like filaments (−39.2 ± 2.5‰) also collected at this site. Specific examples were the Marphysa sp. polychaetes (δ 13C = −44.7 ± 0.6‰), the Schistomeringos sp. dorvilleid polychaetes (δ 13C = −42.9‰), and the tanaid crustacean Zeuxo marmoratus (δ 13C = −37.3 ± 0.2‰). The significantly higher δ 13C values of the herbivorous gastropod Tegula atra at the seep site (−29.3 ± 3.1‰) than at the control site (−12.6 ± 0.3‰) also indicated differences among sites of the preferred carbon sources of this species. Mixing model estimates indicate that at the seep site bacteria-like filaments could be contributing up to ∼60% of the assimilated diet of selected invertebrates. Furthermore, several indicators of trophic structure, based in isotopic niche metrics, indicate a considerably higher variety of basal resources used at the seep site and a consequent enhanced trophic diversity, compared with the non-seep site. The isotopic data gathered at the seep site clearly and unequivocally reflects the ingestion of a 13C-depleted primary food source, which could be the bacteria-like filaments observed at this site.

Lipid geochemistry of methane-seep-related Black Sea carbonates

Carbonates recovered from anoxic waters between 235 and 1555 m depth in the northwestern Black Sea were analyzed for lipid biomarkers and stable carbon isotopic compositions. In addition, a methane-seep-related microbial mat and a sample of surface sediment recovered from a non-seep site were studied for comparison. High concentrations of strongly 13C-depleted lipids attributed to bacteria and archaea mediating the anaerobic oxidation of methane (AOM) were found in all samples except for the sediment. Differences of the dominant AOM-performing communities between the carbonates indicated by specific lipid patterns appear to be caused by the respective biogeochemical settings. High proportions of ANME-2 consortia are found at sites of assumingly high partial pressures of methane while ANME-1 associations dominate at locations of moderate methane supply. In the sedimentary concretion, a complex mixture of biomarkers for terrestrial and planktonic organisms was found. Different molecular structures along with strong variations in the stable carbon isotopic compositions (δ13C=−20.2‰ to −94.3‰) allow for an estimation of the proportions of tetraether-bound biphytanes derived from planktonic Crenarchaeota and methanotrophic Euryarchaeota. Our data imply that the shape of AOM-derived carbonate precipitates in Black Sea environments is crucially influenced by the respective methane supply. Active AOM-driven chimney-like bioherms, similar to those previously observed on the Ukrainian shelf, might also develop in the deep euxinic zone at 1555 m water depths.

The occurrence of NADPH-ferrihemoprotein reductase in Corbula caribea, from a natural oil seep at La Brea, Trinidad

Corbula caribea is the most common non-polychaete macrofaunal organism identified at a large natural oil seep at La Brea in south Trinidad. It is hypothesized that these animals may possess (NADPH-ferrihemoprotein reductase) a component of the Mixed Function Oxygenase system (MFO), which may allow them to ameliorate the potentially deleterious effects resulting from exposure to the high levels of petroleum hydrocarbons within this environment. This study was designed to determine whether organisms from the seep site showed greater enzyme activity when compared to organisms from a non-seep reference site. NADPH-ferrihemoprotein reductase activity was determined by incubating 10 μm cryostat sections with nitro-blue tetrazolium. The reaction product was determined by visual assessment and quantified by measuring the relative mean stain intensity. The intense staining, indicative of enzyme activity was evident in the digestive epithelia of seep animals. Observations indicated that organisms from the seep showed more intense staining, indicating greater enzyme activity, when compared to animals from a non-seep reference site. The relative stain intensity of NADPH-ferrihemoprotein reductase determined for organisms from the seep was 61.30. This was significantly higher than the stain intensity determined for organisms from the non-seep reference site (7.11). This supported visual assessments, which suggested that the seep organisms showed higher enzyme activity than organisms from the non-seep site. The results suggest that NADPH-ferrihemoprotein reductase may be present in Corbula caribea from the seep site and not in those from the non-seep site. It is possible that this enzyme may contribute to these animals ability to tolerate chronic exposure to petroleum hydrocarbons and offer then a selective advantage for survival the seep environment.