Similar Microbial Communities Found on Two Distant Seafloor Basalts.

The oceanic crust forms two thirds of the Earth's surface and hosts a large phylogenetic and functional diversity of microorganisms. While advances have been made in the sedimentary realm, our understanding of the igneous rock portion as a microbial habitat has remained limited. We present the first comparative metagenomic microbial community analysis from ocean floor basalt environments at the Lō'ihi Seamount, Hawai'i, and the East Pacific Rise (EPR; 9°N). Phylogenetic analysis indicates the presence of a total of 43 bacterial and archaeal mono-phyletic groups, dominated by Alpha- and Gammaproteobacteria, as well as Thaumarchaeota. Functional gene analysis suggests that these Thaumarchaeota play an important role in ammonium oxidation on seafloor basalts. In addition to ammonium oxidation, the seafloor basalt habitat reveals a wide spectrum of other metabolic potentials, including CO2 fixation, denitrification, dissimilatory sulfate reduction, and sulfur oxidation. Basalt communities from Lō'ihi and the EPR show considerable metabolic and phylogenetic overlap down to the genus level despite geographic distance and slightly different seafloor basalt mineralogy

The Deep Subsurface Biosphere in Igneous Ocean Crust: Frontier Habitats for Microbiological Exploration

We discuss ridge flank environments in the ocean crust as habitats for subseafloor microbial life. Oceanic ridge flanks, areas far from the magmatic and tectonic influence of seafloor spreading, comprise one of the largest and least explored microbial habitats on the planet. We describe the nature of selected ridge flank crustal environments, and present a framework for delineating a continuum of conditions and processes that are likely to be important for defining subseafloor microbial "provinces." The basis for this framework is three governing conditions that help to determine the nature of subseafloor biomes: crustal age, extent of fluid flow, and thermal state. We present a brief overview of subseafloor conditions, within the context of these three characteristics, for five field sites where microbial studies have been done, are underway, or have been proposed. Technical challenges remain and likely will limit progress in studies of microbial ridge flank ecosystems, which is why it is vital to select and design future studies so as to leverage as much general understanding as possible from work focused at a small number of sites. A characterization framework such that as presented in this paper, perhaps including alternative or additional physical or chemical characteristics, is essential for achieving the greatest benefit from multidisciplinary microbial investigations of oceanic ridge flanks

Quantifying microbial utilization of petroleum hydrocarbons in salt-marsh sediments using the ^(13)C content of bacterial rRNA

Natural remediation of oil spills is catalyzed by complex microbial consortia. Here we take a whole-community approach to investigate bacterial incorporation of petroleum hydrocarbons from a simulated oil spill. We utilized the natural difference in carbon-isotopic abundance between a salt marsh ecosystem supported by the ^(13)C-enriched C4 grass, Spartina alterniflora, and the ^(13)C-depleted composition of petroleum to monitor changes in the ^(13)C content of biomass. Magnetic-bead capture methods for the selective recovery of bacterial RNA were used to monitor the ^(13)C content of bacterial biomass during a two-week experiment. The data show that by the end of the experiment, up to 26% of bacterial biomass derived from consumption of the freshly-spilled oil. The results contrast with the inertness of a nearby relict spill, which occurred in 1969 in West Falmouth, MA. Sequences of 16S rRNA genes from our experimental samples also were consistent with previous reports suggesting the importance of {gamma}- and {delta}-Proteobacteria and Firmicutes in the remineralization of hydrocarbons. The magnetic-bead capture approach makes it possible to quantify uptake of petroleum hydrocarbons by microbes in-situ. Although employed here at the Domain level, RNA-capture procedures can be highly specific. The same strategy could be used with genus-level specificity, something which is not currently possible using the ^(13)C content of biomarker lipids

Integrated Fe- and S-isotope study of seafloor hydrothermal vents at East Pacific Rise 9–10°N

Author Posting. © Elsevier B.V., 2008. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Chemical Geology 252 (2008): 214-227, doi:10.1016/j.chemgeo.2008.03.009.In this study, we report on coupled Fe- and S-isotope systematics of hydrothermal fluids and sulfide deposits from the East Pacific Rise at 9-10°N to better constrain processes affecting Fe- isotope fractionation in hydrothermal environments. We aim to address three fundamental questions: (1) is there significant Fe isotope fractionation during sulfide precipitation? (2) Is there significant variability of Fe-isotope composition of the hydrothermal fluids reflecting sulfide precipitation in subsurface environments? (3) Are there any systematics between Fe- and S- isotopes in sulfide minerals? The results show that chalcopyrite, precipitating in the interior wall of a hydrothermal chimney displays a limited range of δ56Fe values and δ34S values, between –0.11 to –0.33‰ and 2.2 to 2.6‰ respectively. The δ56Fe values are, on average, slightly higher by 0.14‰ relative to coeval vent fluid composition while δ34S values suggest significant S-isotope fractionation (-0.6±0.2‰) during chalcopyrite precipitation. In contrast, systematically lower δ56Fe and δ34S values relative to hydrothermal fluids, by up to 0.91‰ and 2.0‰ respectively, are observed in pyrite and marcasite precipitating in the interior of active chimneys. These results suggest isotope disequilibrium in both Fe- and S-isotopes due to S-isotopic exchange between hydrothermal H2S and seawater SO42- followed by rapid formation of pyrite from FeS precursors, thus preserving the effects of a strong kinetic Fe-isotope fractionation during FeS precipitation. In contrast, δ56Fe and δ34S values of pyrite from inactive massive sulfides, which show evidence of extensive late-stage reworking, are essentially similar to the hydrothermal fluids. Multiple stages of remineralization of ancient chimney deposits at the seafloor appear to produce minimal Fe-isotope fractionation. Similar affects are indicated during subsurface sulfide precipitation as demonstrated by the lack of systematic differences between δ56Fe values in both high-temperature, Fe-rich black smokers and lower temperature, Fe-depleted vents.Support for W. Bach and K. Edwards was provided by NSF grant OCE-0241791 and support for O. Rouxel was provided by funding from the WHOI Deep Ocean Exploration Institute and NSF grant OCE-0622982 and OCE-0647948

Characterization of Attachment and Growth of Thiobacillus denitrificans on Pyrite Surfaces

Anaerobic growth and attachment of the autotrophic denitrifying bacterium Thiobacillus denitrificans on pyrite surfaces were studied. Polished pyrite slabs were exposed to T. denitrificans for 1 to 9 weeks. The reacted pyrite surfaces were imaged with scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM). Cells were observed as isolated attached cells, cells in division and cells forming microcolonies embedded in organic films. Bacteria began to colonize pyrite surfaces after 1 week, forming microcolonies after 3 weeks. The rate of colonization of the pyrite surface was around 35 cells mm−2 h−1 for the 3-week period. After 9 weeks, larger areas of the pyrite surface were covered by organic films. Bacterial enumeration on the pyrite surface and in solution showed that most of the cells were not attached to the mineral surface. Nevertheless, both attached and free-living bacteria probably contributed to pyrite-driven denitrification. The results may be applied to the natural environment to better understand pyrite-driven denitrification in aquifers and to improve the long-term performance of bioremediation processes using pyrite

Time-series analysis of two hydrothermal plumes at 9°50′N East Pacific Rise reveals distinct, heterogeneous bacterial populations

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in Geobiology 10 (2012): 178-192, doi:10.1111/j.1472-4669.2011.00315.xWe deployed sediment traps adjacent to two active hydrothermal vents at 9°50’N on the East Pacific Rise (EPR) to assess variability in bacterial community structure associated with plume particles on the time scale of weeks to months, to determine if an endemic population of plume microbes exists, and to establish ecological relationships between bacterial populations and vent chemistry. Automated rRNA intergenic spacer analysis (ARISA) indicated there are separate communities at the two different vents and temporal community variations between each vent. Correlation analysis between chemistry and microbiology indicated that shifts in the coarse particulate (>1 mm) Fe/(Fe+Mn+Al), Cu, V, Ca, Al, 232Th, and Ti as well as fine-grained particulate (<1 mm) Fe/(Fe+Mn+Al), Fe, Ca and Co are reflected in shifts in microbial populations. 16S rRNA clone libraries from each trap at three time points revealed a high percentage of Epsilonproteobacteria clones and hyperthermophilic Aquificae. There is a shift towards the end of the experiment to more Gammaproteobacteria and Alphaproteobacteria, many of whom likely participate in Fe and S cycling. The particle attached plume environment is genetically distinct from the surrounding seawater. While work to date in hydrothermal environments has focused on determining the microbial communities on hydrothermal chimneys and the basaltic lavas that form the surrounding seafloor, little comparable data exists on the plume environment that physically and chemically connects them. By employing sediment traps for a time series approach to sampling, we show that bacterial community composition on plume particles changes on time scales much shorter than previously known.This work was supported by the NSF Marine Geology and Geophysics program, the Science and Technology program, and the Gordon and Betty Moore Foundation

Not All Play Equipment Is Created Equal: Associations Between Equipment at Home and Children’s Physical Activity

Background: Play equipment at home could be targeted in interventions to increase children’s physical activity (PA), but evidence is mixed, potentially because current methods do not reflect children’s lived experience. This study investigated associations between combinations of equipment and PA. Methods: Data were from the Mothers and their Children’s Health study and the Australian Longitudinal Study on Women’s Health. Mothers (n = 2409) indicated the types of fixed active (eg, trampolines), portable active (eg, bicycles), and electronic (eg, computers) equipment at home, and the number of days children (n = 4092, aged 5–12 y, 51% boys) met PA guidelines. Latent class analysis was used to identify combinations of equipment, and linear regressions were used to investigate associations with PA. Results: Compared with children with high active (fixed and portable) and medium electronic equipment, children with portable active and medium (B = −0.53; 95% confidence interval, −0.72 to −0.34) or high (B = −0.58; 95% confidence interval, −0.83 to −0.33) electronic equipment met the guidelines on fewer days. Children with similar active equipment (but more electronic equipment) met the PA guidelines on fewer days (mean difference = −0.51, SE = 0.14, P = .002). Conclusion: Having the right combination of play equipment at home may be important for children’s PA

Prospects for the Study of Evolution in the Deep Biosphere

Since the days of Darwin, scientists have used the framework of the theory of evolution to explore the interconnectedness of life on Earth and adaptation of organisms to the ever-changing environment. The advent of molecular biology has advanced and accelerated the study of evolution by allowing direct examination of the genetic material that ultimately determines the phenotypes upon which selection acts. The study of evolution has been furthered through examination of microbial evolution, with large population numbers, short generation times, and easily extractable DNA. Such work has spawned the study of microbial biogeography, with the realization that concepts developed in population genetics may be applicable to microbial genomes (Martiny et al., 2006; Manhes and Velicer, 2011). Microbial biogeography and adaptation has been examined in many different environments. Here we argue that the deep biosphere is a unique environment for the study of evolution and list specific factors that can be considered and where the studies may be performed. This publication is the result of the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) theme team on Evolution (www.darkenergybiosphere.org)

Evidence for microbial mediation of subseafloor nitrogen redox processes at Loihi Seamount, Hawaii

© The Author(s), 2016. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Geochimica et Cosmochimica Acta 198 (2017): 131-150, doi:10.1016/j.gca.2016.10.029.The role of nitrogen cycling in submarine hydrothermal systems is far less studied than that of other biologically reactive elements such as sulfur and iron. In order to address this knowledge gap, we investigated nitrogen redox processes at Loihi Seamount, Hawaii, using a combination of biogeochemical and isotopic measurements, bioenergetic calculations and analysis of the prokaryotic community composition in venting fluids sampled during four cruises in 2006, 2008, 2009 and 2013. Concentrations of NH4+ were positively correlated to dissolved Si and negatively correlated to NO3-+NO2-, while NO2- was not correlated to NO3-+NO2-, dissolved Si or NH4+. This is indicative of hydrothermal input of NH4+ and biological mediation influencing NO2- concentrations. The stable isotope ratios of NO3- (d15N and d18O) was elevated with respect to background seawater, with d18O values exhibiting larger changes than corresponding d15N values, reflecting the occurrence of both production and reduction of NO3- by an active microbial community. d15N-NH4+ values ranged from 0‰ to +16.7‰, suggesting fractionation during consumption and potentially N-fixation as well. Bioenergetic calculations reveal that several catabolic strategies involving the reduction of NO3- and NO2- coupled to sulfide and iron oxidation could provide energy to microbes in Loihi fluids, while 16S rRNA gene sequencing of Archaea and Bacteria in the fluids reveals groups known to participate in denitrification and N-fixation. Taken together, our data support the hypothesis that microbes are mediating N-based redox processes in venting hydrothermal fluids at Loihi Seamount.This work was supported by the NSF Microbial Observatories program (MCB 0653265), the Gordon and Betty Moore Foundation (GBMF1609), NSF-OCE 0648287, the Center for Dark Energy Biosphere Investigations (C-DEBI) and the NASA Astrobiology Institute — Life Underground (NAI-LU). Sequence data was generated as part of the Alfred P. Sloan Foundation's ICoMM field project and the W. M. Keck Foundation