Subsurface Sediments Research Articles

Spatial and Temporal Variation in Deep-Sea Meiofauna at the LTER Observatory HAUSGARTEN in the Fram Strait (Arctic Ocean)

Time-series studies at the LTER (Long-Term Ecological Research) observatory HAUSGARTEN have yielded the world’s longest time-series on deep-sea meiofauna and thus provide a decent basis to investigate the variability in deep-sea meiobenthic communities at different spatial and temporal scales. The main objective of the present study was to investigate whether the sediment-dwelling meiofauna (size range: 32–1000 µm) is controlled by small-scale local environmental conditions, rather than large-scale differences between water depths. Univariate and multivariate statistical analyses, including distance-based linear models (DistLM) and redundancy analysis (dbRDA), revealed that due to their small size, meiofauna tend to mainly respond to micro-scale (centimeter) variations in environmental conditions in surface and subsurface sediment layers. Inter-annual temporal patterns among metazoan meiofauna at higher taxon levels revealed only a weak effect of time, and merely on the rare meiofauna taxa (<2% of the total meiofauna community) at HAUSGARTEN.

Beneath the surface: Application of transparent super absorbent polymer substrates to track faunal activity within the sediment layer

Abstract Tracking the movement of organisms is a fundamental goal of many ecological studies. Several techniques exist in the study of terrestrial and aquatic fauna; however, to date, the ability to monitor aquatic fauna within the sediment layer efficiently and in multiple dimensions is lacking. Given the importance of subsurface sediments in supporting ecosystem functioning, this inability to observe organism behaviour represents a fundamental gap in our knowledge and limits our capability to holistically characterise the response of freshwater systems to stressors. Here we present an experimental study that employs novel transparent super absorbent polymer substrates (c. 8–12 mm in diameter) in combination with computer vision technology, which enables, for the first time, real‐time observation and tracking of organisms within the sediment layer under lotic flow conditions. Use of these substrates allowed the successful extraction of organism trajectories, which enabled the velocity and body orientation of a freshwater amphipod (Gammarus fossarum) in the sediment layer to be calculated in response to a number of vertical hydrological exchange treatments (upwelling, downwelling, and no vertical exchange). Results indicate that under vertical hydrological exchange, a higher proportion of fast velocities (both horizontal and vertical) were recorded for G. fossarum in the sediment layer compared to no vertical exchange (control) conditions. This increase was most marked for upwelling flow exchange. We also observed a change in the body orientation of individuals in the sediment layer from a vertical alignment under no vertical exchange to a more horizontal one under downwelling and more notably upwelling flow exchange. This shift in body position was exacerbated under stronger vertical exchange rates. We identified that following the flow transition of downwelling to upwelling conditions, there was an immediate shift (0–2 min) in both the orientation angle and activity level of individuals. This increased rate of activity was maintained for the individuals' velocity but not for their changing orientation angle. These trends were not apparent within the flow transition of no vertical exchange to downwelling flow. Our new methodological approach enables vital insights into the behaviour of organisms within the sediment layer. Use of super absorbent polymer substrates allows real‐time multi‐directional tracking of multiple organisms in parallel. We believe the method represents an innovative tool that can be employed to tackle a wide range of ecological questions and thereby improve our mechanistic understanding of ecological responses to biotic and abiotic processes/stressors.

Macrofaunal control of microbial community structure in continental margin sediments

Through a process called "bioturbation," burrowing macrofauna have altered the seafloor habitat and modified global carbon cycling since the Cambrian. However, the impact of macrofauna on the community structure of microorganisms is poorly understood. Here, we show that microbial communities across bioturbated, but geochemically and sedimentologically divergent, continental margin sites are highly similar but differ clearly from those in nonbioturbated surface and underlying subsurface sediments. Solid- and solute-phase geochemical analyses combined with modeled bioturbation activities reveal that dissolved O2 introduction by burrow ventilation is the major driver of archaeal community structure. By contrast, solid-phase reworking, which regulates the distribution of fresh, algal organic matter, is the main control of bacterial community structure. In nonbioturbated surface sediments and in subsurface sediments, bacterial and archaeal communities are more divergent between locations and appear mainly driven by site-specific differences in organic carbon sources.

A geophysical, geochemical and microbiological study of a newly discovered pockmark with active gas seepage and submarine groundwater discharge (MET1-BH, central Gulf of Gdańsk, southern Baltic Sea)

High-resolution bathymetric data were collected with a multi-beam echosounder in the southern part of the Baltic Sea (region MET1, Gulf of Gdańsk) revealing the presence of a 10 m deep and 50 m in diameter pockmark (MET1-BH) on the sea bottom (78.7 m). To date, no such structures have been observed to reach this size in the Baltic Sea. The salinity of the near-bottom water in the pockmark was about 2 PSU (about 31.22 mmol/l Cl−), which clearly indicated the presence of a submarine groundwater discharge (SGD). Water column, sediments and the seabed structure were investigated in the MET1-BH area using various hydroacoustic devices: multi-beam and splitbeam echosounders and a sub-bottom profiler. Geochemical analyses of sediment pore waters (CH4, Cl−, Br−, F−, SO42−, Ca2+, Mg2+, K+, Na+, ∑H2S, dP, dSi, NH4+, DIC, DOC) and microbiological analysis of sediments (16S rRNA) were performed. The content of CH4 and CO2 in the outflowing gas and its origin (δ13C-CH4 and δ2D-CH4) were determined. Hydroacoustic data showed that gas was emitted intensively from the inside of the structure. The height and intensity of the gas flares varied depending on the hydrostatic pressure. The gas contained 76.1% of CH4, 17.6% of CO2 and 0.39% of He. Methane source was microbial. Geophysical investigation revealed the presence of dislocations in sub-surface sediment layers in the MET1 region, which could have created a passage for groundwater and gas. Geochemical analyses pointed to intensive processes of organic matter decomposition in this area, active methanogenesis in the surface sediment layer, lack of the sulphate-methane transition, and freshwater seepage at a depth of ~88 m (bottom of the pockmark), probably from Upper Cretaceous deposits. The Prokaryota composition, atypical for marine surface sediments, resulted from the combination of freshwater and high organic matter content, and reflected active in situ methanogensis.

Diverse Thaumarchaeota Dominate Subsurface Ammonia-oxidizing Communities in Semi-arid Floodplains in the Western United States.

Subsurface microbial communities mediate biogeochemical transformations that drive both local and ecosystem-level cycling of essential elements, including nitrogen. However, their study has been largely limited to the deep ocean, terrestrial mines, caves, and topsoils (<30cm). Here, we present regional insights into the microbial ecology of aerobic ammonia oxidation within the terrestrial subsurface of five semi-arid riparian sites spanning a 900-km N-S transect. We sampled sediments, profiled communities to depths of ≤ 10m, and compared them to reveal trends regionally within and surrounding the Upper Colorado River Basin (CRB). The diversity and abundance of ammonia-oxidizing microbial communities were evaluated in the context of subsurface geochemistry by applying a combination of amoA (encoding ammonia monooxygenase subunit A) gene sequencing, quantitative PCR, and geochemical techniques. Analysis of 898 amoA sequences from ammonia-oxidizing archaea (AOA) and bacteria (AOB) revealed extensive ecosystem-scale diversity, including archaeal amoA sequences from four of the five major AOA lineages currently found worldwide as well as distinct AOA ecotypes associated with naturally reduced zones (NRZs) and hydrogeochemical zones (unsaturated, capillary fringe, and saturated). Overall, AOA outnumber AOB by 2- to 5000-fold over this regional scale, suggesting that AOA may play a prominent biogeochemical role in nitrification within terrestrial subsurface sediments.

Microcosm based analysis of arsenic release potential of Bacillus sp. strain IIIJ3-1 under varying redox conditions.

The role of indigenous bacteria in mobilization of sediment bound arsenic (As) into groundwater is investigated using subsurface sediment from Brahmaputra River Basin (BRB) and the Bacillus sp. strain IIIJ3-1, an indigenous species to BRB. Anaerobic sediment microcosms with varying organic carbon sources and terminal electron acceptors (TEAs) are used to illustrate the role of the test bacterium in As mobilization. The aquifer sediment shows an asymmetric distribution of As and Fe in its different phases. Among the TEAs added, NO3 amendment promotes higher cell growth, oxalic acid production and maximum release of sediment bound As. X-ray diffraction analysis further suggests that weathering of As bearing secondary minerals through bacterial action enhances As bioavailability, followed by dissimilatory reduction and thus promotes its mobilization into aqueous phase. Co-release pattern of other elements from the sediment indicates that release of As is decoupled from that of Fe. This study confirms that microbe-mediated mineral weathering followed by respiratory reduction of As facilitates mobilization of sediment hosted As into aqueous phase, and provides a better insight into the catabolic ability of groundwater bacteria in mobilization of sediment hosted As in BRB region.

Trace metal variability controlled by hydrodynamic processes in a polluted inner shelf environment (Besòs prodelta, NW Mediterranean)

Trace metal pollution of coastal sediment is monitored in many countries to control its evolution and the effectiveness of preventive and corrective measures. However, temporal variability of trace metal pollution is not always due to changes in pollution management, as natural processes can induce a significant variability in the trace metal content of sediment and particulate matter, especially in strongly polluted coastal areas. To study this variability, time series of trace metals in particulate matter and bottom sediments were recorded along with hydrographic and hydrodynamic parameters in the most highly polluted zone of the Besòs River prodelta. Two benthic tripods equipped with current meters, turbidimeters and sediment traps were deployed at 20 and 30 m water depth from late-September to mid-June and sediment cores were taken four times at each site during the deployment period. Trace metal content in the trapped particulate matter and the surface sediment increased during storm events, which can resuspend and erode several cm of subsurface sediments with higher pollution levels from earlier industrial times. After the storms, significant accumulation of less polluted sediment began, and near-bottom currents redistributed it, decreasing trace metal contents in surface sediments and trapped particulate matter. Therefore, energy conditions previous to monitoring sampling must be considered in order to evaluate the evolution of trace metals in inner shelf polluted sediments.

Hitchcock’s Leptodactyli, Penetrative Tracks, and Dinosaur Footprint Diversity

ABSTRACT Starting with his first report on fossil footprints from the Connecticut Valley over 180 years ago, Edward Hitchcock described what he interpreted as a burgeoning ancient fauna founded on ever-increasing nominal track diversity. For three decades, Hitchcock made countless contributions to ichnology, but his inference of thin-toed animals (Leptodactyli) from thin-toed tracks is flawed by modern criteria. Leptodactylous tracks are now recognized as variants made by thick-toed feet penetrating into soft, collapsing substrates. Herein, we take a closer look at the creation of such penetrative tracks using computer simulations of particle flow. Classic specimens are used to demonstrate how different modes of surface presentation make penetrative tracks challenging to recognize and interpret. Evaluation of 266 specimens from 43 leptodactylous ichnotaxa reveals that ∼90% are penetrative. We propose that a reliance on a single formation mechanism confounded Hitchcock’s ability to reliably recognize different trackmakers. This is not an old problem applicable only to fossils collected long ago; domination of a transmission-based model continues to bias the field today. Most texts and many publications either omit collapsed penetrative tracks or fail to recognize them as a significant source of variation. Without proper regard for subsurface toe movement and sediment flow, inferences of foot shape from track shape can, as for Hitchcock, be led far astray. The misidentification and misunderstanding of penetrative tracks impact our conception of the diversity of life in the Early Jurassic, as well as in other ichnofaunas worldwide.

Microbially mediated iron redox cycling of subsurface sediments from Hanford Site, Washington State, USA

Abstract: Iron-bearing clay minerals are predominant in soils and sediments, and they undergo oxidation-reduction cycles as a result of natural processes such as wetting/drying cycles and plant root respiration. However, the kinetics and mechanisms of multiple redox cycles of iron in clay-rich sediments and consequences of such cycling on sediment properties are poorly understood. The objective of this study was to understand how multiple redox cycles of Fe in clay-rich sediment affect the rate and extent of Fe bioreduction and the physicochemical properties of the sediment. A natural sediment sample containing Fe-bearing montmorillonite from Hanford, Washington, USA was size-fractionated [2.0 to 0.5 μm (Hanford-C) and 0.5 to 0.02 μm (Hanford-F)] and redox-cycled for four times. Bioreduction was achieved utilizing Geobacter sulfurreducens and re-oxidization was performed with sparged air. Time-course change of total Fe (II) was monitored to measure the rate and extent of Fe (III) bioreduction. Redox-cycled sediments were characterized to determine the physicochemical changes. Both the initial rate and extent of bioreduction fluctuated across the four redox cycles, but they ultimately decreased from 5.3 μmol g−1 h−1 and 22.9% to nearly zero by the fourth cycle. These fluctuation patterns were likely due to a combined effect of reductive dissolution of small/poorly crystalline clay particles (by 3–5%) and clay mineral structural changes, as evidenced by redox induced changes of aqueous chemistry, surface area, cation exchange capacity, mineralogy, and Mossbauer parameters. Once these small/poorly crystalline clay particles were dissolved, structural Fe in residual larger and more crystalline clay particles was largely reversible across additional redox cycles, as revealed by Mossbauer spectroscopy through the first three cycles.

Can we elevate the subsiding coastal plain of the Netherlands with controlled sedimentation?

Abstract. Half the surface area of the coastal plain of the Netherlands has been subsiding below mean sea-level as a result of peatland drainage. At present, the low elevation is sustained, because sedimentation necessary to aggrade the coastal plain back to natural elevations is hampered by engineering structures. Alternatively, controlled sedimentation is a discussed method to elevate the coastal plain. This can either be achieved by allowing water courses to deliver sediments to designated areas, or by anthropogenic deposition. Here, we assess the possibilities of this strategy by determining whether natural systems or anthropogenic deposition are sufficient to elevate the surface to mean high water (MHW), taking into account IPCC projected minimum and maximum forecasted sea-level rise (RCP2.6 and RCP8.5), and predicted future subsidence. We use the 3D geological subsurface model GeoTOP to quantify sediments; i.e. clay and sand that were naturally delivered to the coastal plain by series of tidal inlets and the Rhine river system. Furthermore, we quantify the amount of anthropogenic deposition, and analyze documented supplies. Finally, we discuss the implications of controlled sedimentation in designated areas by providing examples of past embankment breaches. We quantify that 16.98 km3 of sediments are required to elevate the surface to MHW, and between 22.41 and 29.29 km3 at the end of the 21st century. We estimate that 45.30 km3 of sediments were delivered by the tidal systems during 3000 years (52 % sand), 20.18 km3 by the Rhine river system during 8000 years (29 % sand), and 3.59 km3 of anthropogenic deposition. We conclude that the coastal plain of the Netherlands cannot be elevated to more safe levels with controlled sedimentation. Exceptions are areas proximal to tidal systems with high sediment yields. Anthropogenic deposition, combining natural sedimentation with supplied sediments, or allowing peat growth in inundated areas could be viable alternatives as well as.

Spatio-temporal shifts in community structure and activity of nirS-type denitrifiers in the sediment cores of Pearl River Estuary.

Denitrification, an important process in microbial mediated nitrogen cycle, plays important roles in nitrogen loss in estuarine sediments. However, the function of denitrifiers in the estuarine subsurface sediments remained poorly understood. In this study, we analyzed the potential activity, abundance and community structure of nirS-type denitrifiers using 15N-labeled incubation quantitative-PCR and high throughput sequencing techniques in sediment cores from Pearl River Estuary (PRE). Results showed that subsurface sediments had nearly same level denitrification potential activity compare to surface sediments, although the abundance of nirS gene decreased sharply from surface to bottom in sediment cores. Meanwhile, nirS gene abundance exhibit significant temporal variations, which is consistent with denitrification potential activity. Moreover, the community structure and diversity of nirS-type denitrifiers in sediment cores exhibited remarkable temporal shift pattern. For spatial variation, no significant difference was observed of denitrifiers community structure in each sediment core from the surface to the subsurface, while there were significant different diversity characteristic among different cores. Redundancy analysis (RDA) showed that multiple environmental factors including salinity, pH, oxidation-reduction potential, nutrient content and organic substances synergistically shaped the diversity and distribution of nirS-type denitrifers in PRE sediments. Our results showed that nirS-type denitrifers played important roles in the nitrogen removal in subsurface sediments of PRE.

Metagenomic views of microbial dynamics influenced by hydrocarbon seepage in sediments of the\xa0Gulf of Mexico

Microbial cells in the seabed are thought to persist by slow population turnover rates and extremely low energy requirements. External stimulations such as seafloor hydrocarbon seeps have been demonstrated to significantly boost microbial growth; however, the microbial community response has not been fully understood. Here we report a comparative metagenomic study of microbial response to natural hydrocarbon seeps in the Gulf of Mexico. Subsurface sediments (10–15 cm below seafloor) were collected from five natural seep sites and two reference sites. The resulting metagenome sequencing datasets were analyzed with both gene-based and genome-based approaches. 16S rRNA gene-based analyses suggest that the seep samples are distinct from the references by both 16S rRNA fractional content and phylogeny, with the former dominated by ANME-1 archaea (~50% of total) and Desulfobacterales, and the latter dominated by the Deltaproteobacteria, Planctomycetes, and Chloroflexi phyla. Sulfate-reducing bacteria (SRB) are present in both types of samples, with higher relative abundances in seep samples than the references. Genes for nitrogen fixation were predominantly found in the seep sites, whereas the reference sites showed a dominant signal for anaerobic ammonium oxidation (anammox). We recovered 49 metagenome-assembled genomes and assessed the microbial functional potentials in both types of samples. By this genome-based analysis, the seep samples were dominated by ANME-1 archaea and SRB, with the capacity for methane oxidation coupled to sulfate reduction, which is consistent with the 16S rRNA-gene based characterization. Although ANME-1 archaea and SRB are present in low relative abundances, genome bins from the reference sites are dominated by uncultured members of NC10 and anammox Scalindua, suggesting a prevalence of nitrogen transformations for energy in non-seep pelagic sediments. This study suggests that hydrocarbon seeps can greatly change the microbial community structure by stimulating nitrogen fixation, inherently shifting the nitrogen metabolism compared to those of the reference sediments.

Communicating Simulation Outputs of Mesoscale Coastal Evolution to Specialist and Non-Specialist Audiences

Coastal geomorphologists and engineers worldwide are increasingly facing the non-trivial challenge of visualising and communicating mesoscale modelling assumptions, uncertainties and outcomes to both coastal specialists and decision-makers. Visualisation of simulation outcomes is a non-trivial problem because the more abstract scientific visualisation techniques favoured by specialists for data exploration and hypothesis-testing are not always as successful at engaging decision-makers and planners. In this paper, we show how the risk of simulation model outcomes becoming disconnected from more realistic visualisations of model outcomes can be minimised by using the Coastal Modelling Environment (CoastalME). CoastalME is a modelling framework for coastal mesoscale morphological modelling that can achieve close linkages between the scientific model abstractions, in the form of lines, areas and volumes, and the 3D representation of topographic and bathymetric surfaces and shallow sub-surface sediment composition. We propose and illustrate through the study case of Happisburgh (eastern England, UK), a transparent methodology to merge the required variety of data types and formats into a 3D-thickness model that is used to initialise a simulation. We conclude by highlighting some of the barriers to the adoption of the methodology proposed.

Microbial Community Structures in Terrestrial Subsurface Sediments from the Southern Kanto Plain, Japan

Microbial community structure reflects the surrounding natural environment and changes to that environment. Although the subsurface at 5–100 m depth is important for human activities and there are potential risks of environmental pollution in this region, there have been only a few reports of subsurface microbial community structures in terrestrial areas. We investigated the diversity and community compositions of Bacteria and Archaea in boring cores collected from various depths at three different sites in the southern Kanto Plain, Japan. The results of 16S rRNA gene amplicon sequencing using MiSeq showed that the microbial community composition varied with the geological unit. Proteobacteria (Alphaproteobacteria and Gammaproteobacteria) were dominant members within sediments accumulated during the Pleistocene in the Musashino Upland. In contrast, Acidobacteria and Chloroflexi characteristically appeared in the Holocene layers of the Arakawa Lowland. These data suggest that the subsurface microbial composition is controlled by the geological features of the sediments.

Enhanced Extraction of AFFF-Associated PFASs from Source Zone Soils.

Poly- and perfluoroalkyl substances (PFASs) derived from aqueous film-forming foam (AFFF) are increasingly recognized as groundwater contaminants, though the composition and distribution of AFFF-derived PFASs associated with soils and subsurface sediments remain largely unknown. This is particularly true for zwitterionic and cationic PFASs, which may be incompletely extracted from subsurface solids by analytical methods developed for anionic PFASs. Therefore, a method involving sequential basic and acidic methanol extractions was developed and evaluated for recovery of anionic, cationic, and zwitterionic PFASs from field-collected, AFFF-impacted soils. The method was validated by spike-recovery experiments with equilibrated soil-water-AFFF and analytical standards. To determine the relative importance of PFASs lacking commercially available analytical standards, their concentrations were estimated by a novel semiquantitation approach. Total PFAS concentrations determined by semiquantitation were compared with concentrations determined by the total oxidizable precursor assay. Finally, the described method was applied to two soil cores from former fire-training areas in which cations and zwitterions were found to contribute up to 97% of the total PFAS mass. This result demonstrates the need for extraction and analysis methods, such as the ones presented here, that are capable of quantifying cationic and zwitterionic PFASs in AFFF-impacted source zone soils.

Cenomanian/Turonian oceanic anoxic event 2 in October oil field, central Gulf of Suez, Egypt

Gulf of Suez is one of the world most prolific Cretaceous and Miocene oil provinces in Egypt. In this basin the Late Cenomanian/Early Turonian organic rich limestone and shale sediments are referred to oceanic anoxic event 2 (OAE2). Two oil-cored wells (GS 197-2 and OCT-A8) have encountered the Late Cenomanian/Early Turonian Abu Qada Formation in October Field, central part of Gulf of Suez. The aim of this work is to pick the global Cenomanian/Turonian anoxic boundary in the subsurface sediments within the Gulf of Suez basin. Consequently, the core samples of the studied wells have been investigated in order to recognize the lithofacies, biostratigraphy, geochemistry and isotope content of upper Raha, Abu Qada and lower Wata formations. The microfacies association of anoxic middle to outer shelf marine were recognized. In addition, remarkable turnover and significant change in biostratigraphy and ichnological diversity and abundance were confirmed the abrupt change in oxidation and nutrition the Cenomanian-Turonian boundary. The recorded positive δ13C excursion (1.8‰) matched with maximum TOC value encountered to mark OAE2 as well as source rock maturity and potentiality of Abu Qada Formation. The neighboring exposed section of Abu Qada Formation in Gabal Nezzazat show similar isotopic and biostratigraphic characteristics that recorded in the studied wells. This work define the Cenomanian-Turonian OAE2 as material based chronostratigraphic surface boundary in Nezzazat Group from surface to subsurface integrated data to improve sequence stratigraphic interpretation of the heterogeneous Upper Cretaceous shallow marine reservoirs in Gulf of Suez.

Evidence of recurrent wildfire from the Permian coal deposits of India: Petrographic, scanning electron microscopic and palynological analyses of fossil charcoal

In India hitherto fossil charcoal has been reported from Kashmir, Damodar Basin, and Mahanadi Basin. This work documents recurrent Cisuralian wildfire based on the occurrence of fossil charcoal from India. The authors used petrographical, palynological and SEM studies to analyze the anatomy of charred wood fragments and temperature of their formation. The fossil charcoal has been retrieved from the Cisuralian coal bearing subsurface sediments of Lower Barakar Formation (Artinskian) from Auranga Coalfield of Damodar Basin. Evidences of recurrent wildfire have been observed by the occurrence of charcoal at four levels of clastic sediments in Borehole 2N. The charcoal was subjected to petrographical, palynological and SEM studies to understand the burning temperature, fuel source and plant anatomy respectively. Petrographic studies indicate high frequency of semifusinite vis-à-vis fusinite having reflectance values ranging from 2.87% to 4.1%. The majority of the fusinite reflectance values fall in the range of 2.9%–3.5% indicating the temperature of formation of these charcoals to be at approximately 500°C. High temperature is also indicated by homogenization of cell walls under SEM. They also reveal fungal infestation and degradation in all charcoal samples. Moderate to high degree of preservation of charcoal indicates lesser transportation/post-depositional degradation suggesting a hypo-autochthonous nature. The botanical affinity of recovered spores and pollen suggest that the hinterland was dominated by gymnosperms and sub-dominated by filicopsids, sphenopsids, and lycopsids which contributed to the fuel source.

Recycling and metabolic flexibility dictate life in the lower oceanic crust.

The lithified lower oceanic crust is one of Earth's last biological frontiers as it is difficult to access. It is challenging for microbiota that live in marine subsurface sediments or igneous basement to obtain sufficient carbon resources and energy to support growth1-3 or to meet basal power requirements4 during periods of resource scarcity. Here we show how limited and unpredictable sources of carbon and energy dictate survival strategies used by low-biomass microbial communities that live 10-750m below the seafloor at Atlantis Bank, Indian Ocean, where Earth's lower crust is exposed at the seafloor. Assays of enzyme activities, lipid biomarkers, marker genes and microscopy indicate heterogeneously distributed and viable biomass with ultralow cell densities (fewer than 2,000 cells per cm3). Expression of genes involved in unexpected heterotrophic processes includes those with a role inthe degradation of polyaromatic hydrocarbons, use of polyhydroxyalkanoates as carbon-storage molecules and recycling of amino acids to produce compounds that can participate in redox reactions and energy production. Our study provides insights into how microorganisms in the plutonic crust are able to survive within fractures or porous substrates by coupling sources of energy to organic and inorganic carbon resources that are probably delivered through the circulation of subseafloor fluids or seawater.

Biosurfactant Production in Sub-Oxic Conditions Detected in Hydrocarbon-Degrading Isolates from Marine and Estuarine Sediments.

Hydrocarbon bioremediation in anoxic sediment layers is still challenging not only because it involves metabolic pathways with lower energy yields but also because the production of biosurfactants that contribute to the dispersion of the pollutant is limited by oxygen availability. This work aims at screening populations of culturable hydrocarbonoclastic and biosurfactant (BSF) producing bacteria from deep sub-seafloor sediments (mud volcanos from Gulf of Cadiz) and estuarine sub-surface sediments (Ria de Aveiro) for strains with potential to operate in sub-oxic conditions. Isolates were retrieved from anaerobic selective cultures in which crude oil was provided as sole carbon source and different supplements were provided as electron acceptors. Twelve representative isolates were obtained from selective cultures with deep-sea and estuary sediments, six from each. These were identified by sequencing of 16S rRNA gene fragments belonging to Pseudomonas, Bacillus, Ochrobactrum, Brevundimonas, Psychrobacter, Staphylococcus, Marinobacter and Curtobacterium genera. BSF production by the isolates was tested by atomized oil assay, surface tension measurement and determination of the emulsification index. All isolates were able to produce BSFs under aerobic and anaerobic conditions, except for isolate DS27 which only produced BSF under aerobic conditions. These isolates presented potential to be applied in bioremediation or microbial enhanced oil recovery strategies under conditions of oxygen limitation. For the first time, members of Ochrobactrum, Brevundimonas, Psychrobacter, Staphylococcus, Marinobacter and Curtobacterium genera are described as anaerobic producers of BSFs.

The shuttling effects and associated mechanisms of different types of iron oxide nanoparticles for Cu(II) reduction by Geobacter sulfurreducens

Iron oxide nanoparticles (IONPs), commonly occurring in soils, aquifers and subsurface sediments, may serve as important electron shuttles for the biotransformation of coexisting toxic metals. Here, we explored the impact of different IONPs (low-crystallinity goethite and ferrihydrite, high-crystallinity magnetite and hematite) on the reduction of Cu(II) by Geobacter sulfurreducens and the associated electron shuttle mechanisms. All four IONPs tested can function as electron shuttles to enhance long distance electron transfer from bacteria to Cu(II). Upon IONPs addition, the rate of Cu(II) reduction increased from 14.9 to 65.0–83.8 % in solution after 7 days of incubation. Formation of both Cu(I) and Cu(0) on the iron oxide nanoparticles was revealed by the X-ray absorption near-edge spectroscopy. The IONPs can be utilized as conduits by bacteria to directly transfer electrons and they can also reversibly accept and donate electrons as batteries through a charging-discharging cycle to transfer electron. The latter mechanism (geo-battery) played an important role in all four types of IONPs while the former one (geo-conductor) can only be found in the magnetite and hematite treatments due to the higher crystallinity. Our results shed new light on the biogeochemically mediated electron flux in microbe-IONPs-metal networks under anaerobic iron-reduction conditions.