Subsurface Sediments Research Articles

Reconstruction of the late Holocene climate variability from the summer monsoon dominated Bhagirathi valley, western Himalaya

• High resolution proxy data traced late Holocene climate events for western Himalaya. • Sites have traced dry (4.2 ka; Little Ice Age) phases and moist Medieval warm period . • Dry (weak summer monsoon) phases correspond well with decreased solar irradiance. • Traced dry events are more prominent in drier alpine site than moist temperate site. • LIA phase recorded asynchronous response time in Alpine and Temperate pollen data. This study presents a centennial to decadal scale late Holocene climate scenario from the Indian summer monsoon (ISM) dominated region of western Himalaya. The subsurface sediments analyzed for palynology, carbon isotope (δ 13 C org ) and magnetic susceptibility (χlf) were collected from the temperate and alpine meadows, respectively receiving high (low) and relatively low (high) amount of ISM (winter) precipitation. We could identify the dry and moist phases linked to respective weakening and strengthening of ISM. High frequency of steppe pollen ( Ephedra , Amaranthaceae, Asteraceae, Brassicaceae) between 4.4 and 3.8 ka represented a dry phase, coeval to 4.2 ka global dry event. Subsequent low δ 13 C values and high pollen frequency of moist vegetation (Geraniaceae, Cyperaceae, Apiaceae, Ranunculaceae and pteridophytes) till ca. 0.9 ka suggested moist phase but with an intermittent dry episode ca. 2.9–2.5 ka, allowing rise of steppe taxa. Climate ameliorated ca. 1.8 ka and moist conditions further enhanced between 1.5 and 0.9 ka, corresponding to Medieval Warm Period. Sharp increase in δ 13 C org values and steppe vegetation ca. 0.8 ka attributed to dryness that intensified between 0.6 and 0.2 ka and coincide with Little Ice Age (LIA) anomaly. The recorded dry (weak ISM) phases showed correspondence with the low solar irradiance and supported the teleconnection with north Atlantic circulations. Palynological data from both the valleys complement each other throughout late Holocene time. However, the valleys showed temporal inconsistency in their aridity peaks during LIA phase. This indicates response variability of the two physiographically different sites to summer and winter monsoon systems.

Seasonal variability in environmental parameters influence bacterial communities in mangrove sediments along an estuarine gradient

Mangrove ecosystems are repositories of divergent microbial communities which respond differently to environmental characteristics. Hence, it is important to understand the community structure with respect to pertinent controlling environmental factors. Seasonal down-core variations in bacterial communities were investigated at 3 mangrove sites at upstream, mid-stream and mouth region along the economically-important Mandovi estuary, west coast of India. Genomic DNA extracted from 45 sediment samples were analyzed by 454 pyrosequencing. A total of 15008 operational taxonomic units (OTUs) were assigned to 54 phyla and 127 classes re-affirming mangroves to be biodiversity hotspots. Members of class Alphaproteobacteria constituted up to 35% of the tag sequences and showed marked seasonal variability at all locations (Kruskal-Wallis test, p < 0.05). Occurrence of other abundant phyla like Bacteroidetes, Firmicutes, Actinobacteria, Chloroflexi and Acidobacteria at the study sites indicated their participation in biogeochemical cycling. Seasonal fluctuations in the environmental variables influenced the bacterial communities. Statistical analysis revealed that during the monsoon, bacterial communities proximal to the mouth region were largely influenced by pore water NH4+ concentrations due to its accumulation in the sub-surface sediments. At the upstream site, elevated organic carbon and NO2− content during the post-monsoon caused variations in the bacterial community.

Biogeochemistry of three different shallow gas systems in continental shelf sediments of the South-Eastern Baltic Sea (Gulf of Gdańsk): Carbon cycling, origin of methane and microbial community composition

The objective of the study was to describe the biogeochemistry of three different shallow gas systems, with particular emphasis on the content of carbon forms, origin of gas and microbial community composition of sediments. Surface sediments (1–1.2 m) in the areas above geophysically different shallow gas structures located in south-eastern Baltic Sea (Gulf of Gdańsk) were investigated: MET1-MP – an active deepwater pockmark with gas seepage and upward infiltration of freshwater, MET2 – shallow gas regular accumulation with lower availability of sulphates and high input of terrestrial organic matter, and MET3 – shallow gas elongated sub-bottom furrow with sulphate presence in the whole sediment profile. For comparison purposes, a reference site (ZGG) without any gas structures in sediments was included in the study. At each station, the following parameters were examined: CH4, CORG and CINORG in sediments; DIC, DOC, H2S, SO42−, NH4+, Cl− in pore and near-bottom waters; stable isotopes in DIC (δ13C-DIC), in gases (δ13C-CH4, δ13C-CO2, δ2H-CH4), and microbial communities in sediments (16S rRNA). In addition, general physico-chemical conditions in bottom waters (dO2, T, S, pH and Eh) as well as molecular composition of gas emitted from MET1-MP pockmark were determined. In order to be able to better compare the geological background of these shallow gas systems, the sediments were investigated by non-invasive acoustic methods: multi-beam echosounder and sub-bottom profiler. Moreover, relative AOM rates were estimated. The first system (MET1-MP) was characterised by a dramatic decrease in the availability of sulphate down the sediment, acetoclastic methanogenesis taking place in surface sediments, the AOM limited to a very thin topmost sediment layer, average stable isotope values of δ13C-CH4 = −58.9‰, δ2H-CH4 = −310‰, δ13C-CO2 = −6.9‰, carbonate precipitation and both methanogenic as well as methanotrophic Archaea present in the whole sediment profile without clear zonation. In the shallow gas regular accumulation, in a close proximity to the coast (MET2), methane was virtually trapped in subsurface sediment layers, even despite not-high sulphate concentrations resulting from lower salinity (~7.5 PSU). In that area, the bacterial community was, unlike typical marine sediments, dominated by Firmicutes, and average stable isotope values were: δ13C-CH4 = −67.0‰, δ2H-CH4 = −243‰, δ13C-CO2 = −7.9‰. The third shallow gas system (MET3) was characterised by most efficient AOM, mostly due to sulphate presence in a relatively thick sediment layer, even several dozen cm below the SMT. The average stable isotope ratios for gases were as follows: δ13C-CH4 = −75.8‰, δ2H-CH4 = −241‰ and δ13C-CO2 = −11.9‰. Despite high concentrations of methane, the methanogenic Archaea were virtually absent in the sediment profile, while the methanotrophic ones showed clear zonation, with ANME-2a-2b present in shallower sediments and ANME-1 in deeper layers. From the environmental point of view, active pockmark shallow-gas systems can be considered as the least efficient in preventing methane from migration to surface sediment layers and the water column, especially when freshwater infiltration occurs, which additionally dilutes the pool of sulphates available for AOM. In our study, the MET1-MP active pockmark was the most “leaky” in terms of methane release to the water column. In contrast, the shallow gas systems being under influence of additional sources of oxidants (in our case – MET2; influence of riverine discharge introducing Fe(III), together with high concentrations of oxygen in bottom waters) or having sulphate present in a relatively thick sediment layer (e.g. due to sulphide reoxidation below the SMT; in our case – the MET3 system) can be considered efficient in stopping methane within sediments, by its almost complete oxidation before reaching the water column.

Induced-seismicity geomechanics for controlled CO2 storage in the North Sea (IGCCS)

The aim of the current study, IGCCS (2017–2020), is to evaluate the feasibility of micro-seismic (MS) monitoring of CO2 injection into representative storage candidates in the North Sea, based on broad and quantitative characterization of relevant subsurface behavior with respect to geology, geomechanics and seismicity. For this purpose, we first group potential CO2 storage sites in the North Sea into three different depths. Then, advanced triaxial rock mechanical tests are performed together with acoustic emission (AE) acquisition under representative loading for CO2 storage sites in the North Sea and for formations of each depth group, covering shale, mudstone and sandstone cores. Our work focuses particularly on quantifying the effects of injected fluid type and temperature on mechanical behavior and associated MS response of subsurface sediments. The experiment results show that each depth group may behave differently in responses to CO2 injection. Particularly, the occurrence of detectable MS events is expected to increase with depth, as the combined effects of rock stiffness and temperature contrast between the host rock and injected CO2 are increasing. In addition, lithology plays an important role in terms of the MS response, i.e. high AE event rate is observed in sandstones, while aseismicity in shale and mudstone. The test results are then scaled up and applied to advanced coupled flow-geomechanics simulations and a synthetic field-scale MS data study to understand micro-seismicity at fracture, reservoir and regional scales. The numerical simulation of scCO2 injection scenario shows quite different stress-strain changes compared to brine injection, resulting mainly from the thermally-induced behavior. Furthermore, the numerical simulation study via so-called Cohesion Zone Modeling (CZM) approach shows strong potential to improve our understanding of the multiphase-flow-driven fracture propagation. Our synthetic MS data study, focused on slow-earthquake scenario, also suggests that sensors with high sensitivity at low frequency might be necessary for better signal detection and characterization during CO2 injection. This manuscript covers the main findings and insights obtained during the whole study of IGCCS, and refers to relevant publications for more details.

Mussels and Local Conditions Interact to Influence Microbial Communities in Mussel Beds.

Microbiomes are increasingly recognized as widespread regulators of function from individual organism to ecosystem scales. However, the manner in which animals influence the structure and function of environmental microbiomes has received considerably less attention. Using a comparative field study, we investigated the relationship between freshwater mussel microbiomes and environmental microbiomes. We used two focal species of unionid mussels, Amblema plicata and Actinonaias ligamentina, with distinct behavioral and physiological characteristics. Mussel microbiomes, those of the shell and biodeposits, were less diverse than both surface and subsurface sediment microbiomes. Mussel abundance was a significant predictor of sediment microbial community composition, but mussel species richness was not. Our data suggest that local habitat conditions which change dynamically along streams, such as discharge, water turnover, and canopy cover, work in tandem to influence environmental microbial community assemblages at discreet rather than landscape scales. Further, mussel burrowing activity and mussel shells may provide habitat for microbial communities critical to nutrient cycling in these systems.

First description of archaeal communities in carbonate-rich seafloor and subseafloor sediments from the Southwestern Atlantic slope

Deep-sea sediments comprise one of the largest habitats on Earth. The archaeal groups contribute to a large fraction of the deep-sea benthic biomass, playing a key role in biogeochemical cycles. However, their diversity in deep-sea benthic ecosystems remains poorly understood, mostly because only recently novel taxa have been proposed, thus remodeling the phylogenetic tree. Despite the dificulty in obtaining cultivated representatives, the metabolic capabilities of archaea have lately been described through metagenomic data, indicating that archaeal taxa are highly versatile. Here, we aimed to reveal the diversity of archaeal communities in surface (0 to 15 cm depth) and subsurface (200 cm depth) sediments from a carbonate-rich region in the Southwestern Atlantic upper slope. We performed 16S rRNA gene sequencing, and found that the archaeal composition in surface sediments was mainly dominated by ammonia-oxidizing archaea within Nitrososphaeria class. The distribution of Nitrososphaeria ASVs (amplicon sequence variants) indicates the presence of several species or ecotypes. Contrastingly, the subsurface sediment was dominated by uncultivated anaerobic and poorly known archaea, including representatives of all supergroups (Asgard, TACK, DPANN and Euryarchaeota). These archaea have been described as having potentially diverse metabolic capabilities, including autotrophic and heterotrophic pathways, such as acetogenesis, methylotrophy, and degradation of labile and recalcitrant organic compounds. This indicates an important role in the remineralization of organic matter in the SW (Southwest) Atlantic slope. They are likely enriched due to the transport and mixing of sediments by the IWBC (Intermediate Western Boundary Current) along the continental slope. However, further studies are needed to reveal the geochemical and oceanographic drivers of the archaeal distribution. This study provides the first description of the archaeal communities in carbonate-rich sediments in the SW Atlantic slope, and adds new biodiversity insights to this geological feature, which is considered a vulnerable marine ecosystem, thus helping for future conservation strategies.

Temporal monitoring of contamination in three sandy beaches from the 2019 oil spill near Cabo de Santo Agostinho, Northeastern Brazil

In 2019, a massive oil spill impacted coastal ecosystems in eleven Brazilian states; these ecosystems were diverse with regard to their different geological settings (sandy beaches, rocky coasts, estuaries, tidal flats, mangroves, and reef systems) being impacted. Here, we present a temporal analysis on the occurrence of remaining contaminants on three beaches (Paiva, Itapuama, and Enseada) of the Cabo de Santo Agostinho City, Pernambuco State. The approach focuses on the systematic mapping of residues, collection of sediment samples, photographic documentation, and qualitative microscopic analysis. Grain size, calcium carbonate, and total organic matter content analyses provided a faciological and energetic characterization of the environment. The objective was to verify the relationship between the remaining contaminants and the geological setting. The results showed intense weathering of the remaining oil residues due to the high energy environment. We found tar balls reworked by seasonal erosion on the three beaches and no tar residues in shallow subsurface sediments. A large quantity of tar residues remains on rock surfaces in Itapuama Beach, which bears the higher permanence of contamination because it is less affected by weathering and beach erosion. This investigation allowed for an impact assessment of the geological-morphological characteristics of the beaches.

Ostatni epizod vistuliańskiego chłodu: cechy diagnostyczne w obszarach ekstraglacjalnych

The general trend of paleogeographic events is dependent on global climate changes. In the analysis of short geological periods, a large role should be assigned to local conditions, understood both in the regional sense and, above all, at the microscale, i.e. the specificity of sites with different morphological location and lithological properties of the substratum, generating a strictly local course of morphogenetic processes reflected in geological records. In this context, a large role should be assigned to the smallest marks of disturbances. Interpretation difficulties that researchers of the Younger Dryas often encounter result from the small thickness of the sub-surface sediment and its weathering changes. The article shows how a detailed analysis of data from the abiotic sphere can be used to reconstruct the conditions prevailing in short geological periods. The area of study is situated in central Poland in an extraglacial zone of the last Quaternary ice sheet that during the Vistulian remained under periglacial conditions (Fig. 1). Among the diagnostic properties are: sedimentological palaeohydrological marks, traces of permafrost re-aggradation, oversnow deposits, aeolian specificity and random events. Changes in the hydrological regimes in rivers are reflected in changes in the sedimentary record showing effective floods (Fig. 2) and together with raising of groundwater table registered in biogenic baśni point two distinct phases of humidity. Traces of permafrost re-aggradation are scarce and found only in particular localities (e.g., under peatlands), but the environmental context of involutions reported from study sites allow us to conclude a return of frozen substratum (Figs 2, 4). The smallscale fissure and fault network in the deposits of the youngest unit of dry periglacial valleys dated to the Younger Dryas were linked to deposition on patches of frozen snow that lasted for several summers and, afterwards, a collapse of he deposit due to melting (Fig. 5). This process did not require the presence of permafrost. In the aeolian environment, the cool conditions of the Younger Dryas resulted locally in the deposition of thin sand covers (Figs 6, 8), which, in favourable topographic conditions, could even form initial dune ramparts (Fig. 7). In the Younger Dryas environment, morphogenetic processes may have been activated by a random event not necessarily associated with global climatic change. One potential example is traces of wildfires registered in a depositional sequence of the Żabieniec site.

Mineralogy of Alluvial Soils Developed in Narmada River Basin in West Coast of Gujarat

Clay minerals have played a significant role for the plant nutrient management for crop production. Soils of recent and old alluvial plains deposited by Narmada river in Jhagadia block were investigated for their mineralogical makeup. The soils on recent alluvial plains (P1) (Fluventic Haplustepts) are very deep, moderately well drained, very dark grayish brown to very dark brown, silt loam to silt clay loam on level to nearly level slope with clay loam surface and slight erosion. The soils of old alluvial plain (P2) (Vertic Haplustepts) are similar to recent alluvial plain with clayey texture and moderate erosion. The pedons were sampled at one km (recent alluvial plain) and at two km (old alluvial plain) distance from Narmada river stream. The soils of recent alluvial plain are slightly alkaline (pH 7.5-8.5), slightly calcareous (<5% CaCO3) with moderate cation exchange capacity (CEC) and high in base saturation (>90%). The soils of old alluvial plain have high CEC and CaCO3 in sub-surface horizons. This paper presents a detailed study on clay minerals in surface and sub-surface sediments deposited by the Narmada river drainage basin. Clay content was ranged from 30-50% in recent alluvia and 50-60% in old alluvia. The soils of recent alluvia were high in silt fraction (40-47%) which plays an active role in potassium nutrition. The smectite content was significantly higher (weighted mean 64.9%) in old alluvial plain compared with recent plain (weighted mean 37.8%). A reverse pattern of mica distribution was observed in clay fraction of both the plains. The distribution of quartz and K/Na feldspars showed similar trends in sand fraction but wide variability was observed in the case of hydralsite, kenyaite, and boehmite content with depth. The mineralogical study indicated that the clay mineral assemblage of both sites varied in smectites and mica, which imparts heterogeneity to soil properties.

Stage‐Wise Stochastic Deep Learning Inversion Framework for Subsurface Sedimentary Structure Identification

AbstractThe stochastic models and deep‐learning models are the two most commonly used methods for subsurface sedimentary structures identification. The results from the stochastic models typically involve uncertainty due to their nature. For the deep‐learning models, sufficient structure samples are necessary for training, but they are practically difficult to obtain. This study develops an inversion framework to combine the strength of these two models to overcome the limitations. The stochastic model is first adopted to generate the structure samples required by the deep‐learning models by integrating available observations. Then the trained deep‐learning model is utilized to reduce the uncertainty of the structures generated by the stochastic models. This integrated framework can successfully estimate the structures using available observations. Importantly, no additional structure training samples are required in the identification process. To summarize, the combination of the stochastic and the deep‐learning models shows great advantages in identifying subsurface sedimentary structures.

Effects of spatial variations in rock fragments related to tillage on hydrological processes and sediment transport

Cultivation activities play an important role in shaping the spatial distribution of rock fragments in hilly agricultural landscapes. The spatial variation in rock fragment contents (SVRFC) can exert strong effects on the spatial heterogeneity of soil properties with great implications for hydrological fluxes and soil erosion. However, previous research always assumed that rock fragments were homogenously distributed, but little has been known concerning the SVRFC over the hillslope and its influence on hydrological and erosional processes. In this study, simulated rock fragment contents (RFCs) in soil layers at the upper (0.6 kg kg−1) and lower slope positions (0, 0.2, 0.4 and 0.6 kg kg−1) were established in combination with artificial rainfall experiments, to investigate the influence of RFC difference between the upper and lower slope positions on hydrological and erosional processes. Results show that the decreasing RFC difference reduced the yield of surface flow (5–100%), but increased yields of subsurface flow (58–792%) and deep percolation (19–130%). Additionally, the decreasing RFC difference reduced the runoff velocity of surface flow and surface erosion rate, but aggravated subsurface erosion. Especially under the 0 kg kg−1 RFC difference, the intense soil loss occurred at the subsurface which may be due to the highly developed preferential flow. With increasing rainfall intensity, great increments in yields of subsurface flow, deep percolation and subsurface sediments were found under the small RFC difference which had small increments in yields of surface flow and surface sediments. These results suggest that the changing SVRFC related to tillage erosion can exert strong influence on behaviors of hydrological and erosional processes. Our study provides a better understanding of the interaction between agricultural cultivation and soil–water loss in hilly agricultural landscapes.

Sediment characterization in deltas using electrical resistivity tomography: The Ebro delta case

Surface electrical resistivity tomography is a non-invasive and highly competitive technique that can be used to effectively characterize subsurface sediments for different purposes: geological, geotechnical, hydrogeological or subsidence problems. However, due to the strong effect of salinity on resistivity, sediments characterization in deltas (coastal areas) becomes a challenge. In this work, the results of combining extensive surface electrical resistivity tomography measurements and limited borehole logging and geological information in the Ebro delta plain is presented. The methodology used has been critical to reduce uncertainties in the interpretation of the ERT models, allowing to characterize the sedimentary architecture of the Holocene deposits in the Ebro delta plain up to about 60 m depth. The obtained geoelectrical models have been used for the construction of the Ebro delta 3D geological model prior to the delta plain subsidence assessment. Results also highlight the feasibility and capability of the electrical resistivity tomography technique to sediments characterization in extreme environments such as coastal areas and deltas. Additionally, the water quality distribution across the delta plain is also inferred.

Triple oxygen isotope systematics of diagenetic recrystallization of diatom opal-A to opal-CT to microquartz in deep sea sediments

The oxygen-18 isotopic composition (δ18O) of silica preserved in oceanic sediments is an important archive of Earth’s temperature and/or seawater δ18O from the Archean to present. Recent advances in high-precision measurements of both δ18O and δ17O values have been used to provide additional constraints on what the oxygen isotopic composition of chert reflects about past conditions. Here, we examine the effects on the triple oxygen isotopic composition of chert that occurs during transformation and recrystallization of biogenic opal-A to opal-CT to microquartz in deep sea sediments. We studied late Miocene to present samples from the Sea of Japan at ODP Site 795 and measured biogenic diatom opal-A, opal-CT, microquartz chert, and ‘altered’ opal-A samples—previously measured for δ18O values only—for both δ18O and δ17O values. We find that δ18O decreases and Δ′17O increases (where Δ′17O = δ17O – 0.528 × δ18O) with depth, coincident with the conversions from diatom opal-A to opal-CT to microquartz. Silica samples deviate from the trend expected for triple oxygen isotopic equilibrium with modern seawater. To explain these data, we developed a model that shows that local temperature gradients and pore fluid δ18O profiles in combination lower the measured opal-CT and microquartz δ18O values and raise the Δ′17O values relative to the initial opal-A, but deviate from triple oxygen isotopic equilibrium with seawater. We find that a steeper local temperature gradient and a larger influence of hydrothermal alteration of basalt at the base of the sediment column (which lowers pore fluid δ18O values) in the past explain both the measured δ18O and Δ′17O values of the opal-CT and microquartz.These data and our modeling show that the transformation of opal-A to microquartz in marine sediments at elevated temperatures and in the presence of lowered pore water δ18O values leads to an array that falls below the theoretical triple oxygen isotope line of equilibrium for SiO2 with modern seawater. Further, our model indicates that opal-CT and microquartz do form in triple oxygen isotopic equilibrium with pore fluids that are offset in their triple oxygen isotopic composition compared to seawater due to fluid-rock alteration of igneous rocks at the base of the sediment column. The diagenetic processes taking place in the Japan Sea do not explain a large portion of the existing Archean to present triple oxygen isotope chert data, which likely require either changes in the oxygen isotopic composition of the source water (i.e., ocean water) and/or alteration by meteoric fluids. Further, our data demonstrate that the triple oxygen isotopic composition of preserved chert need not represent surface conditions, but instead may reflect processes that occur in subsurface sediments at elevated temperatures and with modified pore fluid oxygen isotopic compositions.

Nitrogen distribution and forms in sediment cores of Daya Bay, China

Sediment was the hotspot of microbial nitrogen sink, affecting the biogeochemical cycle of nitrogen in aquatic ecosystems. However, the distribution and forms of nitrogen in coastal bay subsurface sediments are poorly understood, limiting our knowledge about nitrogen distribution characteristics in subsurface sediments and the implications for nitrogen sinks. Here, the spatial distribution of different forms of nitrogen was examined in the sediment cores of Daya Bay (DYB). The results showed that exchangeable nitrogen (Nex) with an average concentration of 13.14 ± 5.99 mg kg−1, mainly consisted of NO3− and NH4+, occupied only 1.88 ± 0.97% in the total nitrogen (Ntot) in the sediment cores. As the dominant nitrogen form, organic nitrogen (Norg) accounted for 50.52-94.29% in Ntot and displayed a similar decreasing trend with Ntot in sediment cores. No evident change was discovered in the vertical content of fixed ammonia (Nfix) in sediment cores, and the mean concentration of Nfix in the four sediment cores was 97.14 ± 29.08 mg kg−1. These results suggested that Nfix and Norg were the stable recalcitrant nitrogen stocks in the sediment cores, and the labile nitrogen input from anthropogenic activities was transformed by microbial processes, thus reducing the nitrogen pollution efficiently in DYB.

Characterization of bacterial and archaeal community structure in deep subsurface sediments in the Shenhu area, northern South China Sea

Gas hydrate-bearing sediments provide an extreme and unique habitat for bacteria and archaea, but the relationship between the microbial community and gas hydrate formation is poorly known. In the Shenhu area of the northern South China Sea, it was inferred that the gas source is mixed biogenic-thermogenic, and contradictions exist between relatively low total organic carbon content and high saturation of gas hydrates. The synthesized geophysical and geological evidence showed that deep thermogenic fluid could migrate upward through migrating pathways. In this study, samples were collected from Shenhu area from 224 to 271 mbsf (meters below the seafloor), which covered gas hydrate-bearing sediments (GHBS), free gas-bearing sediments (FGBS), and non-gas hydrate-bearing sediments (NGHBS), and 16S rRNA gene sequencing was used to characterize bacterial and archaeal community structure. The results revealed significant differences of microbial community structure among the three sediment types as indicated by alpha (richness and diversity indices) and beta (Bray-Curtis-based non-metric multidimensional scaling) diversity analyses as well as community composition analyses. In bacterial community, abundant genera included Pseudomonas, Halomonas, Alcanivorax, Thiobacillus, Marinobacter, Rhodococcus, and Dietzia, some of which were identified as putative hydrocarbon degraders. Most abundant archaeal genera were potential methanogenic archaea, and the dominant genera between GHBS and FGBS differed. Multiple types of methanogenesis were noted, and the hydrogenotrophic type was inferred to be predominant. Deviations of temperature of methanogens from the geothermal gradient of the study area again suggested the migration of organic matters. Based on the characterization of bacterial and archaeal community structure in the deep subsurface sediments, we proposed a geological model for the gas hydrate formation and accumulation of the gas hydrate reservoir, emphasizing the possibility of microbially-mediated secondary microbial gas formation from deep thermogenic fluid. This study characterized bacterial and archaeal community structure in deep subsurface sediments, which can provide insight into the potential roles of bacteria and archaea including hydrocarbon degradation and methanogenesis in gas hydrate formation and help reevaluate the contribution of deep thermogenic fluid to gas hydrate formation in the Shenhu area of the northern continental slope of the South China Sea.

Complete Genome Sequence of a Novel Dyadobacter sp. Strain, NIV53, Isolated from 2-Meter Deep Subsurface Sediment.

ABSTRACTHere, we provide the complete genome sequence of the subsurface bacterial isolate Dyadobacter sp. strain NIV53, a candidate species from the Spirosomaceae family. The isolate contained one 7,587,604-bp chromosome, with a GC content of 40.4%, and one plasmid, pNIV1, with a size of 12,453 bp.

Porosity mapping of shallow subsurface sediments: a case study in Mahanadi basin, eastern margin of India

Petrophysical properties are the least explored parameters in the Mahanadi basin in the eastern Indian margin. We have used 2D seismic reflection data along a profile AC with available well logs of the Expedition-01 of the Indian National Gas Hydrates Program (NGHP) for the evaluation of lateral variation of porosity – a petrophysical property. The seismic line passes through the Sites NGHP-01-19B in the AB section, and NGHP-01-09A in the BC section. The porosity is estimated using two different approaches based on acoustic impedance (AI) transformation and direct seismic inversion. The AI transformation approach fails to decipher consistent porosity distributions whereas the direct seismic inversion approach provides satisfactory results along seismic line AC (AB and BC) in the Mahanadi Offshore region. The AI transformed porosity section illustrates erroneous porosity values within the target zone, irrespective of a strong coefficient of determination ( R 2 ) of 0.82 and 0.85 between AI and porosity at sites NGHP-01-19B and NGHP-01-9A, respectively. The accuracy of the porosity results obtained from the direct inversion approach depends on the best linear regression fit established between acoustic and porosity reflectivity-based models with a coefficient of determination as 0.91 at Site NGHP-01-19B and 0.94 at Site NGHP-01-9A. The porosity distributions are also corroborated with the density-porosity log values, and it is observed that porosity from direct seismic inversion is consistent with the porosity log information at respective sites. The porosity results at the two sites signify the overall good performance of the direct seismic inversion method and also indicate that the probability of free-gas occurrences in shallow sediments is higher compared to that of gas-hydrates.

Coastal Sediment Nutrient Enrichment Alters Seagrass Blue Carbon Sink Capacity.

The seagrass ecosystem is among the most efficient natural carbon sinks that can contribute to climate change mitigation. However, little is known about the effects of coastal nutrient enrichment caused by anthropogenic activities and/or climate change on the capacity of the seagrass blue carbon sink. Our experimental manipulations of sediment nutrient enrichment shifted the blue carbon sink capabilities of seagrass meadows. Sediment nutrient enrichment significantly increased the nutrient content of seagrass litter, stimulating the decomposition of rhizome + root litter by ∼10% while retarding the decomposition of leaf litter by ∼5%. Sediment N + P enrichment increased seagrass growth and litter production, while enrichment of N or P alone did not. Organic carbon (Corg) stocks in the surface sediments (0-5 cm) were 34% higher than those in the control with N + P enrichment due to high litter production and the low decomposition rate of nutrient-enriched leaf litter. However, Corg stocks in the subsurface sediments (5-20 cm) did not increase with sediment nutrient enrichment, which is likely due to accelerated decomposition of rhizome + root litter. Our findings suggest that nutrient loading in coastal sediments alters the blue carbon sink and storage capacities in seagrass meadows by changing the rates of carbon sequestration and decomposition.

Redefining the Subsurface Biosphere: Characterization of Fungi Isolated From Energy-Limited Marine Deep Subsurface Sediment.

The characterization of metabolically active fungal isolates within the deep marine subsurface will alter current ecosystem models and living biomass estimates that are limited to bacterial and archaeal populations. Although marine fungi have been studied for over fifty years, a detailed description of fungal populations within the deep subsurface is lacking. Fungi possess metabolic pathways capable of utilizing previously considered non-bioavailable energy reserves. Therefore, metabolically active fungi would occupy a unique niche within subsurface ecosystems, with the potential to provide an organic carbon source for heterotrophic prokaryotic populations from the transformation of non-bioavailable energy into substrates, as well as from the fungal necromass itself. These organic carbon sources are not currently being considered in subsurface energy budgets. Sediments from South Pacific Gyre subsurface, one of the most energy-limited environments on Earth, were collected during the Integrated Ocean Drilling Program Expedition 329. Anoxic and oxic sediment slurry enrichments using fresh sediment were used to isolate multiple fungal strains in media types that varied in organic carbon substrates and concentration. Metabolically active and dormant fungal populations were also determined from nucleic acids extracted from in situ cryopreserved South Pacific Gyre sediments. For further characterization of physical growth parameters, two isolates were chosen based on their representation of the whole South Pacific Gyre fungal community. Results from this study show that fungi have adapted to be metabolically active and key community members in South Pacific Gyre sediments and potentially within global biogeochemical cycles.

Potential Activities and Long Lifetimes of Organic Carbon-Degrading Extracellular Enzymes in Deep Subsurface Sediments of the Baltic Sea.

Heterotrophic microorganisms in marine sediments produce extracellular enzymes to hydrolyze organic macromolecules, so their products can be transported inside the cell and used for energy and growth. Therefore, extracellular enzymes may mediate the fate of organic carbon in sediments. The Baltic Sea Basin is a primarily depositional environment with high potential for organic matter preservation. The potential activities of multiple organic carbon-degrading enzymes were measured in samples obtained by the International Ocean Discovery Program Expedition 347 from the Little Belt Strait, Denmark, core M0059C. Potential maximum hydrolysis rates (Vmax) were measured at depths down to 77.9mbsf for the following enzymes: alkaline phosphatase, β-d-xylosidase, β-d-cellobiohydrolase, N-acetyl-β-d-glucosaminidase, β-glucosidase, α-glucosidase, leucyl aminopeptidase, arginyl aminopeptidase, prolyl aminopeptidase, gingipain, and clostripain. Extracellular peptidase activities were detectable at depths shallower than 54.95mbsf, and alkaline phosphatase activity was detectable throughout the core, albeit against a relatively high activity in autoclaved sediments. β-glucosidase activities were detected above 30mbsf; however, activities of other glycosyl hydrolases (β-xylosidase, β-cellobiohydrolase, N-acetyl-β-glucosaminidase, and α-glucosidase) were generally indistinguishable from zero at all depths. These extracellular enzymes appear to be extremely stable: Among all enzymes, a median of 51.3% of enzyme activity was retained after autoclaving for an hour. We show that enzyme turnover times scale with the inverse of community metabolic rates, such that enzyme lifetimes in subsurface sediments, in which metabolic rates are very slow, are likely to be extraordinarily long. A back-of-the-envelope calculation suggests enzyme lifetimes are, at minimum, on the order of 230days, and may be substantially longer. These results lend empirical support to the hypothesis that a population of subsurface microbes persist by using extracellular enzymes to slowly metabolize old, highly degraded organic carbon.