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1.  Linking Geology and Microbiology: Inactive Pockmarks Affect Sediment Microbial Community Structure 
PLoS ONE  2014;9(1):e85990.
Pockmarks are geological features that are found on the bottom of lakes and oceans all over the globe. Some are active, seeping oil or methane, while others are inactive. Active pockmarks are well studied since they harbor specialized microbial communities that proliferate on the seeping compounds. Such communities are not found in inactive pockmarks. Interestingly, inactive pockmarks are known to have different macrofaunal communities compared to the surrounding sediments. It is undetermined what the microbial composition of inactive pockmarks is and if it shows a similar pattern as the macrofauna. The Norwegian Oslofjord contains many inactive pockmarks and they are well suited to study the influence of these geological features on the microbial community in the sediment. Here we present a detailed analysis of the microbial communities found in three inactive pockmarks and two control samples at two core depth intervals. The communities were analyzed using high-throughput amplicon sequencing of the 16S rRNA V3 region. Microbial communities of surface pockmark sediments were indistinguishable from communities found in the surrounding seabed. In contrast, pockmark communities at 40 cm sediment depth had a significantly different community structure from normal sediments at the same depth. Statistical analysis of chemical variables indicated significant differences in the concentrations of total carbon and non-particulate organic carbon between 40 cm pockmarks and reference sample sediments. We discuss these results in comparison with the taxonomic classification of the OTUs identified in our samples. Our results indicate that microbial communities at the sediment surface are affected by the water column, while the deeper (40 cm) sediment communities are affected by local conditions within the sediment.
doi:10.1371/journal.pone.0085990
PMCID: PMC3901666  PMID: 24475066
2.  Fine-Scale Community Structure Analysis of ANME in Nyegga Sediments with High and Low Methane Flux 
To obtain knowledge on how regional variations in methane seepage rates influence the stratification, abundance, and diversity of anaerobic methanotrophs (ANME), we analyzed the vertical microbial stratification in a gravity core from a methane micro-seeping area at Nyegga by using 454-pyrosequencing of 16S rRNA gene tagged amplicons and quantitative PCR. These data were compared with previously obtained data from the more active G11 pockmark, characterized by higher methane flux. A down core stratification and high relative abundance of ANME were observed in both cores, with transition from an ANME-2a/b dominated community in low-sulfide and low methane horizons to ANME-1 dominance in horizons near the sulfate-methane transition zone. The stratification was over a wider spatial region and at greater depth in the core with lower methane flux, and the total 16S rRNA copy numbers were two orders of magnitude lower than in the sediments at G11 pockmark. A fine-scale view into the ANME communities at each location was achieved through operational taxonomical units (OTU) clustering of ANME-affiliated sequences. The majority of ANME-1 sequences from both sampling sites clustered within one OTU, while ANME-2a/b sequences were represented in unique OTUs. We suggest that free-living ANME-1 is the most abundant taxon in Nyegga cold seeps, and also the main consumer of methane. The observation of specific ANME-2a/b OTUs at each location could reflect that organisms within this clade are adapted to different geochemical settings, perhaps due to differences in methane affinity. Given that the ANME-2a/b population could be sustained in less active seepage areas, this subgroup could be potential seed populations in newly developed methane-enriched environments.
doi:10.3389/fmicb.2012.00216
PMCID: PMC3375579  PMID: 22715336
ANME; pyrosequencing; AOM; community structure; Nyegga; cold seep; stratification
3.  Activity and Diversity of Methanotrophic Bacteria at Methane Seeps in Eastern Lake Constance Sediments ▿  
The activity and community structure of aerobic methanotrophic communities were investigated at methane seeps (pockmarks) in the littoral and profundal zones of an oligotrophic freshwater lake (Lake Constance, Germany). Measurements of potential methane oxidation rates showed that sediments inside littoral pockmarks are hot spots of methane oxidation. Potential methane oxidation rates at littoral pockmark sites exceeded the rates of the surrounding sediment by 2 orders of magnitude. Terminal restriction fragment length polymorphism (T-RFLP) analysis of the pmoA gene revealed major differences in the methanotrophic community composition between littoral pockmarks and the surrounding sediments. Clone library analysis confirmed that one distinct Methylobacter-related group dominates the community at littoral pockmarks. In profundal sediments, the differences between pockmarks and surrounding sediments were found to be less pronounced.
doi:10.1128/AEM.02776-10
PMCID: PMC3126381  PMID: 21335392
4.  Novel Alkane Hydroxylase Gene (alkB) Diversity in Sediments Associated with Hydrocarbon Seeps in the Timor Sea, Australia▿  
Applied and Environmental Microbiology  2009;75(23):7391-7398.
Hydrocarbon seeps provide inputs of petroleum hydrocarbons to widespread areas of the Timor Sea. Alkanes constitute the largest proportion of chemical components found in crude oils, and therefore genes involved in the biodegradation of these compounds may act as bioindicators for this ecosystem's response to seepage. To assess alkane biodegradation potential, the diversity and distribution of alkane hydroxylase (alkB) genes in sediments of the Timor Sea were studied. Deduced AlkB protein sequences derived from clone libraries identified sequences only distantly related to previously identified AlkB sequences, suggesting that the Timor Sea maybe a rich reservoir for novel alkane hydroxylase enzymes. Most sequences clustered with AlkB sequences previously identified from marine Gammaproteobacteria though protein sequence identities averaged only 73% (with a range of 60% to 94% sequence identities). AlkB sequence diversity was lower in deep water (>400 m) samples off the continental slope than in shallow water (<100 m) samples on the continental shelf but not significantly different in response to levels of alkanes. Real-time PCR assays targeting Timor Sea alkB genes were designed and used to quantify alkB gene targets. No correlation was found between gene copy numbers and levels of hydrocarbons measured in sediments using sensitive gas chromatography-mass spectrometry techniques, probably due to the very low levels of hydrocarbons found in most sediment samples. Interestingly, however, copy numbers of alkB genes increased substantially in sediments exposed directly to active seepage even though only low or undetectable concentrations of hydrocarbons were measured in these sediments in complementary geochemical analyses due to efficient biodegradation.
doi:10.1128/AEM.01370-09
PMCID: PMC2786413  PMID: 19820158
5.  A metagenomic study of methanotrophic microorganisms in Coal Oil Point seep sediments 
BMC Microbiology  2011;11:221.
Background
Methane oxidizing prokaryotes in marine sediments are believed to function as a methane filter reducing the oceanic contribution to the global methane emission. In the anoxic parts of the sediments, oxidation of methane is accomplished by anaerobic methanotrophic archaea (ANME) living in syntrophy with sulphate reducing bacteria. This anaerobic oxidation of methane is assumed to be a coupling of reversed methanogenesis and dissimilatory sulphate reduction. Where oxygen is available aerobic methanotrophs take part in methane oxidation. In this study, we used metagenomics to characterize the taxonomic and metabolic potential for methane oxidation at the Tonya seep in the Coal Oil Point area, California. Two metagenomes from different sediment depth horizons (0-4 cm and 10-15 cm below sea floor) were sequenced by 454 technology. The metagenomes were analysed to characterize the distribution of aerobic and anaerobic methanotrophic taxa at the two sediment depths. To gain insight into the metabolic potential the metagenomes were searched for marker genes associated with methane oxidation.
Results
Blast searches followed by taxonomic binning in MEGAN revealed aerobic methanotrophs of the genus Methylococcus to be overrepresented in the 0-4 cm metagenome compared to the 10-15 cm metagenome. In the 10-15 cm metagenome, ANME of the ANME-1 clade, were identified as the most abundant methanotrophic taxon with 8.6% of the reads. Searches for particulate methane monooxygenase (pmoA) and methyl-coenzyme M reductase (mcrA), marker genes for aerobic and anaerobic oxidation of methane respectively, identified pmoA in the 0-4 cm metagenome as Methylococcaceae related. The mcrA reads from the 10-15 cm horizon were all classified as originating from the ANME-1 clade.
Conclusions
Most of the taxa detected were present in both metagenomes and differences in community structure and corresponding metabolic potential between the two samples were mainly due to abundance differences.
The results suggests that the Tonya Seep sediment is a robust methane filter, where taxa presently dominating this process could be replaced by less abundant methanotrophic taxa in case of changed environmental conditions.
doi:10.1186/1471-2180-11-221
PMCID: PMC3197505  PMID: 21970369
6.  Bacterial Communities in Polluted Seabed Sediments: A Molecular Biology Assay in Leghorn Harbor 
The Scientific World Journal  2013;2013:165706.
Seabed sediments of commercial ports are often characterized by high pollution levels. Differences in number and distribution of bacteria in such areas can be related to distribution of pollutants in the port and to sediment conditions. In this study, the bacterial communities of five sites from Leghorn Harbor seabed were characterized, and the main bacterial groups were identified. T-RFLP was used for all samples; two 16S rRNA libraries and in silico digestion of clones were used to identify fingerprint profiles. Library data, phylogenetic analysis, and T-RFLP coupled with in silico digestion of the obtained sequences evidenced the dominance of Proteobacteria and the high percentage of Bacteroidetes in all sites. The approach highlighted similar bacterial communities between samples coming from the five sites, suggesting a modest differentiation among bacterial communities of different harbor seabed sediments and hence the capacity of bacterial communities to adapt to different levels and types of pollution.
doi:10.1155/2013/165706
PMCID: PMC3817660  PMID: 24227997
7.  Metagenomic analysis and metabolite profiling of deep–sea sediments from the Gulf of Mexico following the Deepwater Horizon oil spill 
Marine subsurface environments such as deep-sea sediments, house abundant and diverse microbial communities that are believed to influence large-scale geochemical processes. These processes include the biotransformation and mineralization of numerous petroleum constituents. Thus, microbial communities in the Gulf of Mexico are thought to be responsible for the intrinsic bioremediation of crude oil released by the Deepwater Horizon (DWH) oil spill. While hydrocarbon contamination is known to enrich for aerobic, oil-degrading bacteria in deep-seawater habitats, relatively little is known about the response of communities in deep-sea sediments, where low oxygen levels may hinder such a response. Here, we examined the hypothesis that increased hydrocarbon exposure results in an altered sediment microbial community structure that reflects the prospects for oil biodegradation under the prevailing conditions. We explore this hypothesis using metagenomic analysis and metabolite profiling of deep-sea sediment samples following the DWH oil spill. The presence of aerobic microbial communities and associated functional genes was consistent among all samples, whereas, a greater number of Deltaproteobacteria and anaerobic functional genes were found in sediments closest to the DWH blowout site. Metabolite profiling also revealed a greater number of putative metabolites in sediments surrounding the blowout zone relative to a background site located 127 km away. The mass spectral analysis of the putative metabolites revealed that alkylsuccinates remained below detection levels, but a homologous series of benzylsuccinates (with carbon chain lengths from 5 to 10) could be detected. Our findings suggest that increased exposure to hydrocarbons enriches for Deltaproteobacteria, which are known to be capable of anaerobic hydrocarbon metabolism. We also provide evidence for an active microbial community metabolizing aromatic hydrocarbons in deep-sea sediments of the Gulf of Mexico.
doi:10.3389/fmicb.2013.00050
PMCID: PMC3598227  PMID: 23508965
Deepwater Horizon; metagenomics; metabolomics; oil-degradation
8.  Metabolic stratification driven by surface and subsurface interactions in a terrestrial mud volcano 
The ISME Journal  2012;6(12):2280-2290.
Terrestrial mud volcanism represents the prominent surface geological feature, where fluids and hydrocarbons are discharged along deeply rooted structures in tectonically active regimes. Terrestrial mud volcanoes (MVs) directly emit the major gas phase, methane, into the atmosphere, making them important sources of greenhouse gases over geological time. Quantification of methane emission would require detailed insights into the capacity and efficiency of microbial metabolisms either consuming or producing methane in the subsurface, and establishment of the linkage between these methane-related metabolisms and other microbial or abiotic processes. Here we conducted geochemical, microbiological and genetic analyses of sediments, gases, and pore and surface fluids to characterize fluid processes, community assemblages, functions and activities in a methane-emitting MV of southwestern Taiwan. Multiple lines of evidence suggest that aerobic/anaerobic methane oxidation, sulfate reduction and methanogenesis are active and compartmentalized into discrete, stratified niches, resembling those in marine settings. Surface evaporation and oxidation of sulfide minerals are required to account for the enhanced levels of sulfate that fuels subsurface sulfate reduction and anaerobic methanotrophy. Methane flux generated by in situ methanogenesis appears to alter the isotopic compositions and abundances of thermogenic methane migrating from deep sources, and to exceed the capacity of microbial consumption. This metabolic stratification is sustained by chemical disequilibria induced by the mixing between upward, anoxic, methane-rich fluids and downward, oxic, sulfate-rich fluids.
doi:10.1038/ismej.2012.61
PMCID: PMC3504961  PMID: 22739492
metabolic stratification; terrestrial mud volcano; sulfate-to-methane transition zone; methanogenesis; 16S rRNA gene clone library; metagenome
9.  Metagenomics of the subsurface Brazos-Trinity Basin (IODP site 1320): comparison with other sediment and pyrosequenced metagenomes 
The ISME journal  2011;5(6):1038-1047.
The Brazos-Trinity Basin on the slope of the Gulf of Mexico passive margin was drilled during Integrated Ocean Drilling Progam Expedition 308. The buried anaerobic sediments of this basin are largely organic-poor and have few microbial inhabitants compared with the organic-rich sediments with high cell counts from the Peru Margin that were drilled during Ocean Drilling Program Leg 201. Nucleic acids were extracted from Brazos-Trinity Basin sediments and were subjected to whole-genome amplification and pyrosequencing. A comparison of the Brazos-Trinity Basin metagenome, consisting of 105 Mbp, and the existing Peru Margin metagenome revealed trends linking gene content, phylogenetic content, geological location and geochemical regime. The major microbial groups (Proteobacteria, Firmicutes, Euryarchaeota and Chloroflexi) occur consistently throughout all samples, yet their shifting abundances allow for discrimination between samples. The cluster of orthologous groups category abundances for some classes of genes are correlated with geochemical factors, such as the level of ammonia. Here we describe the sediment metagenome from the oligotrophic Brazos-Trinity Basin (Site 1320) and show similarities and differences with the dataset from the Pacific Peru Margin (Site 1229) and other pyrosequenced datasets. The microbial community found at Integrated Ocean Drilling Program Site 1320 likely represents the subsurface microbial inhabitants of turbiditic slopes that lack substantial upwelling.
doi:10.1038/ismej.2010.199
PMCID: PMC3131849  PMID: 21209666
comparative metagenomics; pyrosequencing; subseafloor; microbial ecology
10.  Comparative Composition, Diversity and Trophic Ecology of Sediment Macrofauna at Vents, Seeps and Organic Falls 
PLoS ONE  2012;7(4):e33515.
Sediments associated with hydrothermal venting, methane seepage and large organic falls such as whale, wood and plant detritus create deep-sea networks of soft-sediment habitats fueled, at least in part, by the oxidation of reduced chemicals. Biological studies at deep-sea vents, seeps and organic falls have looked at macrofaunal taxa, but there has yet to be a systematic comparison of the community-level attributes of sediment macrobenthos in various reducing ecosystems. Here we review key similarities and differences in the sediment-dwelling assemblages of each system with the goals of (1) generating a predictive framework for the exploration and study of newly identified reducing habitats, and (2) identifying taxa and communities that overlap across ecosystems. We show that deep-sea seep, vent and organic-fall sediments are highly heterogeneous. They sustain different geochemical and microbial processes that are reflected in a complex mosaic of habitats inhabited by a mixture of specialist (heterotrophic and symbiont-associated) and background fauna. Community-level comparisons reveal that vent, seep and organic-fall macrofauna are very distinct in terms of composition at the family level, although they share many dominant taxa among these highly sulphidic habitats. Stress gradients are good predictors of macrofaunal diversity at some sites, but habitat heterogeneity and facilitation often modify community structure. The biogeochemical differences across ecosystems and within habitats result in wide differences in organic utilization (i.e., food sources) and in the prevalence of chemosynthesis-derived nutrition. In the Pacific, vents, seeps and organic-falls exhibit distinct macrofaunal assemblages at broad-scales contributing to ß diversity. This has important implications for the conservation of reducing ecosystems, which face growing threats from human activities.
doi:10.1371/journal.pone.0033515
PMCID: PMC3319539  PMID: 22496753
11.  Resource quality affects carbon cycling in deep-sea sediments 
The ISME Journal  2012;6(9):1740-1748.
Deep-sea sediments cover ∼70% of Earth's surface and represent the largest interface between the biological and geological cycles of carbon. Diatoms and zooplankton faecal pellets naturally transport organic material from the upper ocean down to the deep seabed, but how these qualitatively different substrates affect the fate of carbon in this permanently cold environment remains unknown. We added equal quantities of 13C-labelled diatoms and faecal pellets to a cold water (−0.7 °C) sediment community retrieved from 1080 m in the Faroe-Shetland Channel, Northeast Atlantic, and quantified carbon mineralization and uptake by the resident bacteria and macrofauna over a 6-day period. High-quality, diatom-derived carbon was mineralized >300% faster than that from low-quality faecal pellets, demonstrating that qualitative differences in organic matter drive major changes in the residence time of carbon at the deep seabed. Benthic bacteria dominated biological carbon processing in our experiments, yet showed no evidence of resource quality-limited growth; they displayed lower growth efficiencies when respiring diatoms. These effects were consistent in contrasting months. We contend that respiration and growth in the resident sediment microbial communities were substrate and temperature limited, respectively. Our study has important implications for how future changes in the biochemical makeup of exported organic matter will affect the balance between mineralization and sequestration of organic carbon in the largest ecosystem on Earth.
doi:10.1038/ismej.2012.14
PMCID: PMC3498925  PMID: 22378534
bacterial growth efficiency; biogeochemistry; carbon mineralization; deep sea; resource quality; stable isotope
12.  A Comparison of Supervised Classification Methods for the Prediction of Substrate Type Using Multibeam Acoustic and Legacy Grain-Size Data 
PLoS ONE  2014;9(4):e93950.
Detailed seabed substrate maps are increasingly in demand for effective planning and management of marine ecosystems and resources. It has become common to use remotely sensed multibeam echosounder data in the form of bathymetry and acoustic backscatter in conjunction with ground-truth sampling data to inform the mapping of seabed substrates. Whilst, until recently, such data sets have typically been classified by expert interpretation, it is now obvious that more objective, faster and repeatable methods of seabed classification are required. This study compares the performances of a range of supervised classification techniques for predicting substrate type from multibeam echosounder data. The study area is located in the North Sea, off the north-east coast of England. A total of 258 ground-truth samples were classified into four substrate classes. Multibeam bathymetry and backscatter data, and a range of secondary features derived from these datasets were used in this study. Six supervised classification techniques were tested: Classification Trees, Support Vector Machines, k-Nearest Neighbour, Neural Networks, Random Forest and Naive Bayes. Each classifier was trained multiple times using different input features, including i) the two primary features of bathymetry and backscatter, ii) a subset of the features chosen by a feature selection process and iii) all of the input features. The predictive performances of the models were validated using a separate test set of ground-truth samples. The statistical significance of model performances relative to a simple baseline model (Nearest Neighbour predictions on bathymetry and backscatter) were tested to assess the benefits of using more sophisticated approaches. The best performing models were tree based methods and Naive Bayes which achieved accuracies of around 0.8 and kappa coefficients of up to 0.5 on the test set. The models that used all input features didn't generally perform well, highlighting the need for some means of feature selection.
doi:10.1371/journal.pone.0093950
PMCID: PMC3974812  PMID: 24699553
13.  Metagenomics of Hydrocarbon Resource Environments Indicates Aerobic Taxa and Genes to be Unexpectedly Common 
Environmental Science & Technology  2013;47(18):10708-10717.
Oil in subsurface reservoirs is biodegraded by resident microbial communities. Water-mediated, anaerobic conversion of hydrocarbons to methane and CO2, catalyzed by syntrophic bacteria and methanogenic archaea, is thought to be one of the dominant processes. We compared 160 microbial community compositions in ten hydrocarbon resource environments (HREs) and sequenced twelve metagenomes to characterize their metabolic potential. Although anaerobic communities were common, cores from oil sands and coal beds had unexpectedly high proportions of aerobic hydrocarbon-degrading bacteria. Likewise, most metagenomes had high proportions of genes for enzymes involved in aerobic hydrocarbon metabolism. Hence, although HREs may have been strictly anaerobic and typically methanogenic for much of their history, this may not hold today for coal beds and for the Alberta oil sands, one of the largest remaining oil reservoirs in the world. This finding may influence strategies to recover energy or chemicals from these HREs by in situ microbial processes.
doi:10.1021/es4020184
PMCID: PMC3864245  PMID: 23889694
14.  Biomarkers in Natural Fish Populations Indicate Adverse Biological Effects of Offshore Oil Production 
PLoS ONE  2011;6(5):e19735.
Background
Despite the growing awareness of the necessity of a sustainable development, the global economy continues to depend largely on the consumption of non-renewable energy resources. One such energy resource is fossil oil extracted from the seabed at offshore oil platforms. This type of oil production causes continuous environmental pollution from drilling waste, discharge of large amounts of produced water, and accidental spills.
Methods and principal findings
Samples from natural populations of haddock (Melanogrammus aeglefinus) and Atlantic cod (Gadus morhua) in two North Sea areas with extensive oil production were investigated. Exposure to and uptake of polycyclic aromatic hydrocarbons (PAHs) were demonstrated, and biomarker analyses revealed adverse biological effects, including induction of biotransformation enzymes, oxidative stress, altered fatty acid composition, and genotoxicity. Genotoxicity was reflected by a hepatic DNA adduct pattern typical for exposure to a mixture of PAHs. Control material was collected from a North Sea area without oil production and from remote Icelandic waters. The difference between the two control areas indicates significant background pollution in the North Sea.
Conclusion
It is most remarkable to obtain biomarker responses in natural fish populations in the open sea that are similar to the biomarker responses in fish from highly polluted areas close to a point source. Risk assessment of various threats to the marine fish populations in the North Sea, such as overfishing, global warming, and eutrophication, should also take into account the ecologically relevant impact of offshore oil production.
doi:10.1371/journal.pone.0019735
PMCID: PMC3100293  PMID: 21625421
15.  Metabolically active microbial communities in marine sediment under high-CO2 and low-pH extremes 
The ISME Journal  2012;7(3):555-567.
Sediment-hosting hydrothermal systems in the Okinawa Trough maintain a large amount of liquid, supercritical and hydrate phases of CO2 in the seabed. The emission of CO2 may critically impact the geochemical, geophysical and ecological characteristics of the deep-sea sedimentary environment. So far it remains unclear whether microbial communities that have been detected in such high-CO2 and low-pH habitats are metabolically active, and if so, what the biogeochemical and ecological consequences for the environment are. In this study, RNA-based molecular approaches and radioactive tracer-based respiration rate assays were combined to study the density, diversity and metabolic activity of microbial communities in CO2-seep sediment at the Yonaguni Knoll IV hydrothermal field of the southern Okinawa Trough. In general, the number of microbes decreased sharply with increasing sediment depth and CO2 concentration. Phylogenetic analyses of community structure using reverse-transcribed 16S ribosomal RNA showed that the active microbial community became less diverse with increasing sediment depth and CO2 concentration, indicating that microbial activity and community structure are sensitive to CO2 venting. Analyses of RNA-based pyrosequences and catalyzed reporter deposition-fluorescence in situ hybridization data revealed that members of the SEEP-SRB2 group within the Deltaproteobacteria and anaerobic methanotrophic archaea (ANME-2a and -2c) were confined to the top seafloor, and active archaea were not detected in deeper sediments (13–30 cm in depth) characterized by high CO2. Measurement of the potential sulfate reduction rate at pH conditions of 3–9 with and without methane in the headspace indicated that acidophilic sulfate reduction possibly occurs in the presence of methane, even at very low pH of 3. These results suggest that some members of the anaerobic methanotrophs and sulfate reducers can adapt to the CO2-seep sedimentary environment; however, CO2 and pH in the deep-sea sediment were found to severely impact the activity and structure of the microbial community.
doi:10.1038/ismej.2012.124
PMCID: PMC3578575  PMID: 23096400
CO2 seep; low pH; anaerobic oxidation of methane; acidophilic sulfate reduction
16.  Recovery of Benthic Megafauna from Anthropogenic Disturbance at a Hydrocarbon Drilling Well (380 m Depth in the Norwegian Sea) 
PLoS ONE  2012;7(10):e44114.
Recovery from disturbance in deep water is poorly understood, but as anthropogenic impacts increase in deeper water it is important to quantify the process. Exploratory hydrocarbon drilling causes physical disturbance, smothering the seabed near the well. Video transects obtained by remotely operated vehicles were used to assess the change in invertebrate megafaunal density and diversity caused by drilling a well at 380 m depth in the Norwegian Sea in 2006. Transects were carried out one day before drilling commenced and 27 days, 76 days, and three years later. A background survey, further from the well, was also carried out in 2009. Porifera (45% of observations) and Cnidaria (40%) dominated the megafauna. Porifera accounted for 94% of hard-substratum organisms and cnidarians (Pennatulacea) dominated on the soft sediment (78%). Twenty seven and 76 days after drilling commenced, drill cuttings were visible, extending over 100 m from the well. In this area there were low invertebrate megafaunal densities (0.08 and 0.10 individuals m−2) in comparison to pre-drill conditions (0.21 individuals m−2). Three years later the visible extent of the cuttings had reduced, reaching 60 m from the well. Within this area the megafaunal density (0.05 individuals m−2) was lower than pre-drill and reference transects (0.23 individuals m−2). There was a significant increase in total megafaunal invertebrate densities with both distance from drilling and time since drilling although no significant interaction. Beyond the visible disturbance there were similar megafaunal densities (0.14 individuals m−2) to pre-drilling and background surveys. Species richness, Shannon-Weiner diversity and multivariate techniques showed similar patterns to density. At this site the effects of exploratory drilling on megafaunal invertebrate density and diversity seem confined to the extent of the visible cuttings pile. However, elevated Barium concentration and reduced sediment grain size suggest persistence of disturbance for three years, with unclear consequences for other components of the benthic fauna.
doi:10.1371/journal.pone.0044114
PMCID: PMC3466215  PMID: 23056177
17.  Modelling potential impacts of bottom trawl fisheries on soft sediment biogeochemistry in the North Sea† 
Bottom trawling causes physical disturbance to sediments particularly in shelf areas. The disturbance due to trawling is most significant in deeper areas with softer sediments where levels of natural disturbance due to wave and tidal action are low. In heavily fished areas, trawls may impact the same area of seabed more than four times per year. A single pass of a beam trawl, the heaviest gear routinely used in shelf sea fisheries, can kill 5–65% of the resident fauna and mix the top few cm of sediment. We expect that sediment community function, carbon mineralisation and biogeochemical fluxes will be strongly affected by trawling activity because the physical effects of trawling are equivalent to those of an extreme bioturbator, and yet, unlike bioturbating macrofauna, trawling does not directly contribute to community metabolism. We used an existing box-model of a generalised soft sediment system to examine the effects of trawling disturbance on carbon mineralisation and chemical concentrations. We contrasted the effects of a natural scenario, where bioturbation is a function of macrobenthos biomass, with an anthropogenic impact scenario where physical disturbance results from trawling rather than the action of bioturbating macrofauna. Simulation results suggest that the effects of low levels of trawling disturbance will be similar to those of natural bioturbators but that high levels of trawling disturbance prevent the modelled system from reaching equilibrium due to large carbon fluxes between oxic and anoxic carbon compartments. The presence of macrobenthos in the natural disturbance scenario allowed sediment chemical storage and fluxes to reach equilibrium. This is because the macrobenthos are important carbon consumers in the system whose presence reduces the magnitude of available carbon fluxes. In soft sediment systems, where the level physical disturbance due to waves and tides is low, model results suggest that intensive trawling disturbance could cause large fluctuations in benthic chemical fluxes and storage.
doi:10.1186/1467-4866-2-112
PMCID: PMC1475597  PMID: 16759420
18.  Characterization of Microbial Population Shifts during Sample Storage 
The objective of this study was to determine shifts in the microbial community structure and potential function based on standard Integrated Ocean Drilling Program (IODP) storage procedures for sediment cores. Standard long-term storage protocols maintain sediment temperature at 4°C for mineralogy, geochemical, and/or geotechnical analysis whereas standard microbiological sampling immediately preserves sediments at −80°C. Storage at 4°C does not take into account populations may remain active over geologic time scales at temperatures similar to storage conditions. Identification of active populations within the stored core would suggest geochemical and geophysical conditions within the core change over time. To test this potential, the metabolically active fraction of the total microbial community was characterized from IODP Expedition 325 Great Barrier Reef sediment cores prior to and following a 3-month storage period. Total RNA was extracted from complementary 2, 20, and 40 m below sea floor sediment samples, reverse transcribed to complementary DNA and then sequenced using 454 FLX sequencing technology, yielding over 14,800 sequences from the six samples. Interestingly, 97.3% of the sequences detected were associated with lineages that changed in detection frequency during the storage period including key biogeochemically relevant lineages associated with nitrogen, iron, and sulfur cycling. These lineages have the potential to permanently alter the physical and chemical characteristics of the sediment promoting misleading conclusions about the in situ biogeochemical environment. In addition, the detection of new lineages after storage increases the potential for a wider range of viable lineages within the subsurface that may be underestimated during standard community characterizations.
doi:10.3389/fmicb.2012.00049
PMCID: PMC3281211  PMID: 22363327
sediment microbial ecology; pyrosequencing; geobiology; sediment core storage
19.  New Hydrocarbon Degradation Pathways in the Microbial Metagenome from Brazilian Petroleum Reservoirs 
PLoS ONE  2014;9(2):e90087.
Current knowledge of the microbial diversity and metabolic pathways involved in hydrocarbon degradation in petroleum reservoirs is still limited, mostly due to the difficulty in recovering the complex community from such an extreme environment. Metagenomics is a valuable tool to investigate the genetic and functional diversity of previously uncultured microorganisms in natural environments. Using a function-driven metagenomic approach, we investigated the metabolic abilities of microbial communities in oil reservoirs. Here, we describe novel functional metabolic pathways involved in the biodegradation of aromatic compounds in a metagenomic library obtained from an oil reservoir. Although many of the deduced proteins shared homology with known enzymes of different well-described aerobic and anaerobic catabolic pathways, the metagenomic fragments did not contain the complete clusters known to be involved in hydrocarbon degradation. Instead, the metagenomic fragments comprised genes belonging to different pathways, showing novel gene arrangements. These results reinforce the potential of the metagenomic approach for the identification and elucidation of new genes and pathways in poorly studied environments and contribute to a broader perspective on the hydrocarbon degradation processes in petroleum reservoirs.
doi:10.1371/journal.pone.0090087
PMCID: PMC3935994  PMID: 24587220
20.  The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs 
The ISME Journal  2012;6(12):2257-2268.
Microorganisms mediate geochemical processes in deep-sea hydrothermal vent plumes, which are a conduit for transfer of elements and energy from the subsurface to the oceans. Despite this important microbial influence on marine geochemistry, the ecology and activity of microbial communities in hydrothermal plumes is largely unexplored. Here, we use a coordinated metagenomic and metatranscriptomic approach to compare microbial communities in Guaymas Basin hydrothermal plumes to background waters above the plume and in the adjacent Carmen Basin. Despite marked increases in plume total RNA concentrations (3–4 times) and microbially mediated manganese oxidation rates (15–125 times), plume and background metatranscriptomes were dominated by the same groups of methanotrophs and chemolithoautotrophs. Abundant community members of Guaymas Basin seafloor environments (hydrothermal sediments and chimneys) were not prevalent in the plume metatranscriptome. De novo metagenomic assembly was used to reconstruct genomes of abundant populations, including Marine Group I archaea, Methylococcaceae, SAR324 Deltaproteobacteria and SUP05 Gammaproteobacteria. Mapping transcripts to these genomes revealed abundant expression of genes involved in the chemolithotrophic oxidation of ammonia (amo), methane (pmo) and sulfur (sox). Whereas amo and pmo gene transcripts were abundant in both plume and background, transcripts of sox genes for sulfur oxidation from SUP05 groups displayed a 10–20-fold increase in plumes. We conclude that the biogeochemistry of Guaymas Basin hydrothermal plumes is mediated by microorganisms that are derived from seawater rather than from seafloor hydrothermal environments such as chimneys or sediments, and that hydrothermal inputs serve as important electron donors for primary production in the deep Gulf of California.
doi:10.1038/ismej.2012.63
PMCID: PMC3504965  PMID: 22695860
metagenomics; metatranscriptomics; deep sea; vents; plume; hydrothermal
21.  Comparative metagenomics of bathypelagic plankton and bottom sediment from the Sea of Marmara 
The ISME journal  2010;5(2):285-304.
To extend comparative metagenomic analyses of the deep-sea, we produced metagenomic data by direct 454 pyrosequencing from bathypelagic plankton (1000 m depth) and bottom sediment of the Sea of Marmara, the gateway between the Eastern Mediterranean and the Black Seas. Data from small subunit ribosomal RNA (SSU rRNA) gene libraries and direct pyrosequencing of the same samples indicated that Gamma- and Alpha-proteobacteria, followed by Bacteroidetes, dominated the bacterial fraction in Marmara deep-sea plankton, whereas Planctomycetes, Delta- and Gamma-proteobacteria were the most abundant groups in high bacterial-diversity sediment. Group I Crenarchaeota/Thaumarchaeota dominated the archaeal plankton fraction, although group II and III Euryarchaeota were also present. Eukaryotes were highly diverse in SSU rRNA gene libraries, with group I (Duboscquellida) and II (Syndiniales) alveolates and Radiozoa dominating plankton, and Opisthokonta and Alveolates, sediment. However, eukaryotic sequences were scarce in pyrosequence data. Archaeal amo genes were abundant in plankton, suggesting that Marmara planktonic Thaumarchaeota are ammonia oxidizers. Genes involved in sulfate reduction, carbon monoxide oxidation, anammox and sulfatases were over-represented in sediment. Genome recruitment analyses showed that Alteromonas macleodii ‘surface ecotype', Pelagibacter ubique and Nitrosopumilus maritimus were highly represented in 1000 m-deep plankton. A comparative analysis of Marmara metagenomes with ALOHA deep-sea and surface plankton, whale carcasses, Peru subsurface sediment and soil metagenomes clustered deep-sea Marmara plankton with deep-ALOHA plankton and whale carcasses, likely because of the suboxic conditions in the deep Marmara water column. The Marmara sediment clustered with the soil metagenome, highlighting the common ecological role of both types of microbial communities in the degradation of organic matter and the completion of biogeochemical cycles.
doi:10.1038/ismej.2010.113
PMCID: PMC3105693  PMID: 20668488
deep-sea; anaerobic respiration; carbon fixation; carbon cycle; sulfate reduction; ammonia oxidation
22.  Novel Cardiolipins from Uncultured Methane-Metabolizing Archaea 
Archaea  2012;2012:832097.
Novel cardiolipins from Archaea were detected by screening the intact polar lipid (IPL) composition of microbial communities associated with methane seepage in deep-sea sediments from the Pakistan margin by high-performance liquid chromatography electrospray ionization mass spectrometry. A series of tentatively identified cardiolipin analogues (dimeric phospholipids or bisphosphatidylglycerol, BPG) represented 0.5% to 5% of total archaeal IPLs. These molecules are similar to the recently described cardiolipin analogues with four phytanyl chains from extreme halophilic archaea. It is worth noting that cardiolipin analogues from the seep archaeal communities are composed of four isoprenoidal chains, which may contain differences in chain length (20 and 25 carbon atoms) and degrees of unsaturation and the presence of a hydroxyl group. Two novel diether lipids, structurally related to the BPGs, are described and interpreted as degradation products of archaeal cardiolipin analogues. Since archaeal communities in seep sediments are dominated by anaerobic methanotrophs, our observations have implications for characterizing structural components of archaeal membranes, in which BPGs are presumed to contribute to modulation of cell permeability properties. Whether BPGs facilitate interspecies interaction in syntrophic methanotrophic consortia remains to be tested.
doi:10.1155/2012/832097
PMCID: PMC3359654  PMID: 22654563
23.  A Spatial-Spectral Approach for Visualization of Vegetation Stress Resulting from Pipeline Leakage 
Sensors (Basel, Switzerland)  2008;8(6):3733-3743.
Hydrocarbon leakage into the environment has large economic and environmental impact. Traditional methods for investigating seepages and their resulting pollution, such as drilling, are destructive, time consuming and expensive. Remote sensing is an efficient tool that offers a non-destructive investigation method. Optical remote sensing has been extensively tested for exploration of onshore hydrocarbon reservoirs and detection of hydrocarbons at the Earth's surface. In this research, we investigate indirect manifestations of pipeline leakage by way of visualizing vegetation anomalies in airborne hyperspectral imagery. Agricultural land-use causes a heterogeneous landcover; variation in red edge position between fields was much larger than infield red edge position variation that could be related to hydrocarbon pollution. A moving and growing kernel procedure was developed to normalzie red edge values relative to values of neighbouring pixels to enhance pollution related anomalies in the image. Comparison of the spatial distribution of anomalies with geochemical data obtained by drilling showed that 8 out of 10 polluted sites were predicted correctly while 2 out of 30 sites that were predicted clean were actually polluted.
doi:10.3390/s8063733
PMCID: PMC3714662
pipeline; hydrocarbon; vegetation stress; hyperspectral; spatial
24.  Spatial Structure and Activity of Sedimentary Microbial Communities Underlying a Beggiatoa spp. Mat in a Gulf of Mexico Hydrocarbon Seep 
PLoS ONE  2010;5(1):e8738.
Background
Subsurface fluids from deep-sea hydrocarbon seeps undergo methane- and sulfur-cycling microbial transformations near the sediment surface. Hydrocarbon seep habitats are naturally patchy, with a mosaic of active seep sediments and non-seep sediments. Microbial community shifts and changing activity patterns on small spatial scales from seep to non-seep sediment remain to be examined in a comprehensive habitat study.
Methodology/Principal Findings
We conducted a transect of biogeochemical measurements and gene expression related to methane- and sulfur-cycling at different sediment depths across a broad Beggiatoa spp. mat at Mississippi Canyon 118 (MC118) in the Gulf of Mexico. High process rates within the mat (∼400 cm and ∼10 cm from the mat's edge) contrasted with sharply diminished activity at ∼50 cm outside the mat, as shown by sulfate and methane concentration profiles, radiotracer rates of sulfate reduction and methane oxidation, and stable carbon isotopes. Likewise, 16S ribosomal rRNA, dsrAB (dissimilatory sulfite reductase) and mcrA (methyl coenzyme M reductase) mRNA transcripts of sulfate-reducing bacteria (Desulfobacteraceae and Desulfobulbaceae) and methane-cycling archaea (ANME-1 and ANME-2) were prevalent at the sediment surface under the mat and at its edge. Outside the mat at the surface, 16S rRNA sequences indicated mostly aerobes commonly found in seawater. The seep-related communities persisted at 12–20 cm depth inside and outside the mat. 16S rRNA transcripts and V6-tags reveal that bacterial and archaeal diversity underneath the mat are similar to each other, in contrast to oxic or microoxic habitats that have higher bacterial diversity.
Conclusions/Significance
The visual patchiness of microbial mats reflects sharp discontinuities in microbial community structure and activity over sub-meter spatial scales; these discontinuities have to be taken into account in geochemical and microbiological inventories of seep environments. In contrast, 12–20 cm deep in the sediments microbial communities performing methane-cycling and sulfate reduction persist at lower metabolic rates regardless of mat cover, and may increase activity rapidly when subsurface flow changes.
doi:10.1371/journal.pone.0008738
PMCID: PMC2806916  PMID: 20090951
25.  Metagenomic Analysis of Viral Communities in (Hado)Pelagic Sediments 
PLoS ONE  2013;8(2):e57271.
In this study, we analyzed viral metagenomes (viromes) in the sedimentary habitats of three geographically and geologically distinct (hado)pelagic environments in the northwest Pacific; the Izu-Ogasawara Trench (water depth = 9,760 m) (OG), the Challenger Deep in the Mariana Trench (10,325 m) (MA), and the forearc basin off the Shimokita Peninsula (1,181 m) (SH). Virus abundance ranged from 106 to 1011 viruses/cm3 of sediments (down to 30 cm below the seafloor [cmbsf]). We recovered viral DNA assemblages (viromes) from the (hado)pelagic sediment samples and obtained a total of 37,458, 39,882, and 70,882 sequence reads by 454 GS FLX Titanium pyrosequencing from the virome libraries of the OG, MA, and SH (hado)pelagic sediments, respectively. Only 24−30% of the sequence reads from each virome library exhibited significant similarities to the sequences deposited in the public nr protein database (E-value <10−3 in BLAST). Among the sequences identified as potential viral genes based on the BLAST search, 95−99% of the sequence reads in each library were related to genes from single-stranded DNA (ssDNA) viral families, including Microviridae, Circoviridae, and Geminiviridae. A relatively high abundance of sequences related to the genetic markers (major capsid protein [VP1] and replication protein [Rep]) of two ssDNA viral groups were also detected in these libraries, thereby revealing a high genotypic diversity of their viruses (833 genotypes for VP1 and 2,551 genotypes for Rep). A majority of the viral genes predicted from each library were classified into three ssDNA viral protein categories: Rep, VP1, and minor capsid protein. The deep-sea sedimentary viromes were distinct from the viromes obtained from the oceanic and fresh waters and marine eukaryotes, and thus, deep-sea sediments harbor novel viromes, including previously unidentified ssDNA viruses.
doi:10.1371/journal.pone.0057271
PMCID: PMC3584133  PMID: 23468952

Results 1-25 (340050)