Microbially-driven methane and sulfur cycling in a Gulf of Mexico methane seep and the White Oak River estuary

Methane is a globally relevant greenhouse gas, but many key questions remain about the microbes that produce it, and the microorganisms responsible for oxidizing it anaerobically to CO2 via sulfate reduction. I used DNA- and RNA-based techniques coupled to geochemistry to study the spatial relationship and functions of microbes at a Gulf of Mexico deep-sea hydrocarbon seep, and methane-cycling archaea in the shallow White Oak River estuary, North Carolina. In particular, I concentrated on ribosomal RNA for the small 16S subunit and messenger RNA encoding Dissimilatory Sulfite Reductase or Methyl Coenzyme M Reductase, which are key enzymes in sulfate reduction or anaerobic methane production/oxidation. First, I examined different nucleic acid extraction techniques and found that avoiding silica column purification procedures appears to be necessary to avoid yield loss in humic acid-rich samples like the White Oak. In the Gulf of Mexico, Mississippi Canyon 118 (MC118), subseafloor hydrocarbon seeps fuel large Beggiatoa spp. mats at the sediment-water interface. In a transect of cores across a Beggiatoa spp. mat, I found that the mat accurately circumscribes near-surface hydrocarbon seepage and surface microbial communities, but deeper in the sediments, seep-related communities appear uncoupled from the immediate presence of either seeping fluids or sulfate as an electron acceptor. In the White Oak River estuary, I found that the organisms thought to mediate the anaerobic oxidation of methane transcribe genes and maintain stable population sizes well into the methane production zone, agreeing with previous indications from the literature that they are also capable of methane production. After making primers specific for the uncultured Miscellaneous Crenarchaeotal Group (MCG), I found that they dominate the archaeal DNA and RNA content of White Oak River estuary sediments, although their RNA content may decrease after sulfate is depleted. Altogether this work has shown that microbial distribution patterns are relevant at deep-sea hydrocarbon seeps, anaerobic methane oxidizing archaea are most likely capable of methane production as well, and that the MCG group may be quite important to biogeochemistry

A pilot investigation of load-carrying on the head and bone mineral density in premenopausal, black African women

Although the influence of weight bearing activity on bone mass has been widely investigated in white women, few studies have been conducted in black, African populations. We investigated bone mineral density (BMD) in black South African women, with and without a history of load-carrying on the head. We also investigated whether load carrying may offer protection against low BMD in users of injectable progestin contraception (IPC). Participants were 32 black, South African women (22.4±3.2 yrs). Load carrying history was determined by questionnaire and interview and participants were grouped as load carriers (LC; n=18) or non load carriers (NLC; n=14). Ten women were using IPC and 6 were load-carriers. Total body (TB), lumbar spine (LS) and total hip (H) BMD were measured by dual energy X-ray absorptiometry. There were no differences in BMD between LC and NLC, and after controlling for age and BMI using two-tailed partial correlations. IPC users had lower BMD at all sites compared to non IPC users (p<0.05) and there were no associations between load carrying and BMD in this group. When IPC users were excluded from analysis, LC had higher LS BMD than NLC (p<0.005). Correlations were found between the weight of load carried and LS BMD (r=0.743, p<0.005), and between years of load carrying and LS and TB BMD (r=0.563, r=0.538 respectively; both p<0.05). Load carrying on the head may offer osteogenic benefits to the spine but these benefits did not appear in women using IPC

Quantitative PCR data from sediment samples from MPSV GREATSHIP MANISHA IODP-347 cruise in the Baltic Sea in 2013 (IODP-347 Microbial Quantification project)

Dataset: qPCRThese data include the quantification of specific microbial taxa within the sediments collected during Integrated Ocean Drilling Program (IODP) Expedition 347: Baltic Sea. DNA was extracted from the interior of frozen whole round cores sampled from Little Belt, Anholt Loch, Landsort Deep, and Bornholm Basin at The University of Tennessee. For a more detailed description of drill sites, access the data set, "IODP-347 drill site locations". Primers specifically targeting the 16S rRNA gene of bacteria, archaea, anaerobic methane oxidizers (ANME-1), and Miscellaneous Crenarchaeota Group (MCG; taxonomically reassigned as the Bathyarchaeota phylum of Archaea) were used to assess abundance of these microbial groups. Abundance data was generated using quantitative-PCR (qPCR) and a non-specific, intercalating DNA stain, SYBR Green. Values were compared against a standard curve to generate copies/uL. These data were collected by Alex Shumaker as part of Dr. Karen Lloyd and Dr. Andrew Steen’s project funded by the National Science Foundation entitled, "Quantifying the contribution of the deep biosphere in the marine sediment carbon cycle using deep-sea sediment cores from the Baltic Sea". For a complete list of measurements, refer to the supplemental document 'Field_names.pdf', and a full dataset description is included in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: http://www.bco-dmo.org/dataset/641358NSF Division of Ocean Sciences (NSF OCE) OCE-143159

Drill site locations from MPSV GREATSHIP MANISHA IODP-347 cruise in the Baltic Sea in 2013 (IODP-347 Microbial Quantification project)

Dataset: IODP-347 drill site locationsIn 2013, Integrated Ocean Drilling Program Expedition 347 sampled six subbasins within the Baltic Sea Basin in an effort to understand the sedimentological record of climate dynamics over the last 140,000 years. These sites, including Bornholm Basin (BSB-7), Lille Belt (BSB-3), and Anholt Loch (BSB-9), were selected because they contain varved, rapidly deposited sediments that represent an archive of paleoclimatological information spanning from the last glacial cycle. This expedition was led by Dr. Bo Barker Jørgensen of Aarhus University and Dr. Thomas Andrén of Södertörn University aboard the vessel MPSV GREATSHIP MANISHA. Data included here are dates sampled, latitude and longitude, and depth of overlying water. For a complete list of measurements, refer to the supplemental document 'Field_names.pdf', and a full dataset description is included in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: http://www.bco-dmo.org/dataset/641342NSF Division of Ocean Sciences (NSF OCE) OCE-143159

The Guaymas Basin hiking guide to hydrothermal mounds, chimneys, and microbial mats : complex seafloor expressions of subsurface hydrothermal circulation

© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 7 (2016): 75, doi:10.3389/fmicb.2016.00075.The hydrothermal mats, mounds, and chimneys of the southern Guaymas Basin are the surface expression of complex subsurface hydrothermal circulation patterns. In this overview, we document the most frequently visited features of this hydrothermal area with photographs, temperature measurements, and selected geochemical data; many of these distinct habitats await characterization of their microbial communities and activities. Microprofiler deployments on microbial mats and hydrothermal sediments show their steep geochemical and thermal gradients at millimeter-scale vertical resolution. Mapping these hydrothermal features and sampling locations within the southern Guaymas Basin suggest linkages to underlying shallow sills and heat flow gradients. Recognizing the inherent spatial limitations of much current Guaymas Basin sampling calls for comprehensive surveys of the wider spreading region.AT acknowledges a W. Reynolds research leave from UNC, Guaymas-relevant support from the Center for Dark Energy Biosphere Investigations (C-DEBI) at the University of Southern Californi

Spatial Structure and Activity of Sedimentary Microbial Communities Underlying a Beggiatoa spp. Mat in a Gulf of Mexico Hydrocarbon Seep

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 eac

Biological methane production and accumulation under sulfate-rich conditions at Cape Lookout Bight, NC

IntroductionAnaerobic oxidation of methane (AOM) is hypothesized to occur through reverse hydrogenotrophic methanogenesis in marine sediments because sulfate reducers pull hydrogen concentrations so low that reverse hydrogenotrophic methanogenesis is exergonic. If true, hydrogenotrophic methanogenesis can theoretically co-occur with sulfate reduction if the organic matter is so labile that fermenters produce more hydrogen than sulfate reducers can consume, causing hydrogen concentrations to rise. Finding accumulation of biologically-produced methane in sulfate-containing organic-rich sediments would therefore support the theory that AOM occurs through reverse hydrogenotrophic methanogenesis since it would signal the absence of net AOM in the presence of sulfate.Methods16S rRNA gene libraries were compared to geochemistry and incubations in high depth-resolution sediment cores collected from organic-rich Cape Lookout Bight, North Carolina.ResultsWe found that methane began to accumulate while sulfate is still abundant (6–8 mM). Methane-cycling archaea ANME-1, Methanosarciniales, and Methanomicrobiales also increased at these depths. Incubations showed that methane production in the upper 16 cm in sulfate-rich sediments was biotic since it could be inhibited by 2-bromoethanosulfonoic acid (BES).DiscussionWe conclude that methanogens mediate biological methane production in these organic-rich sediments at sulfate concentrations that inhibit methanogenesis in sediments with less labile organic matter, and that methane accumulation and growth of methanogens can occur under these conditions as well. Our data supports the theory that H2 concentrations, rather than the co-occurrence of sulfate and methane, control whether methanogenesis or AOM via reverse hydrogenotrophic methanogenesis occurs. We hypothesize that the high amount of labile organic matter at this site prevents AOM, allowing methane accumulation when sulfate is low but still present in mM concentrations

Distinct biogeographic patterns for archaea, bacteria, and fungi along the vegetation gradient at the continental scale in Eastern China

© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in mSystems 2 (2017): e00174-16, doi:10.1128/mSystems.00174-16.The natural forest ecosystem in Eastern China, from tropical forest to boreal forest, has declined due to cropland development during the last 300 years, yet little is known about the historical biogeographic patterns and driving processes for the major domains of microorganisms along this continental-scale natural vegetation gradient. We predicted the biogeographic patterns of soil archaeal, bacterial, and fungal communities across 110 natural forest sites along a transect across four vegetation zones in Eastern China. The distance decay relationships demonstrated the distinct biogeographic patterns of archaeal, bacterial, and fungal communities. While historical processes mainly influenced bacterial community variations, spatially autocorrelated environmental variables mainly influenced the fungal community. Archaea did not display a distance decay pattern along the vegetation gradient. Bacterial community diversity and structure were correlated with the ratio of acid oxalate-soluble Fe to free Fe oxides (Feo/Fed ratio). Fungal community diversity and structure were influenced by dissolved organic carbon (DOC) and free aluminum (Ald), respectively. The role of these environmental variables was confirmed by the correlations between dominant operational taxonomic units (OTUs) and edaphic variables. However, most of the dominant OTUs were not correlated with the major driving variables for the entire communities. These results demonstrate that soil archaea, bacteria, and fungi have different biogeographic patterns and driving processes along this continental-scale natural vegetation gradient, implying different community assembly mechanisms and ecological functions for archaea, bacteria, and fungi in soil ecosystems.This research was financially supported by the National Natural Science Foundation of China (grant number 41520104001), the 111 Project, and the Fundamental Research Funds for the Central Universities