Kirkpatrick John B.

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Kirkpatrick
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John B.
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  • Article
    Bacterial diversity and community composition from seasurface to subseafloor
    (Nature Publishing Group, 2015-10-02) Walsh, Emily A. ; Kirkpatrick, John B. ; Rutherford, Scott D. ; Smith, David C. ; Sogin, Mitchell L. ; D'Hondt, Steven
    We investigated compositional relationships between bacterial communities in the water column and those in deep-sea sediment at three environmentally distinct Pacific sites (two in the Equatorial Pacific and one in the North Pacific Gyre). Through pyrosequencing of the v4–v6 hypervariable regions of the 16S ribosomal RNA gene, we characterized 450 104 pyrotags representing 29 814 operational taxonomic units (OTUs, 97% similarity). Hierarchical clustering and non-metric multidimensional scaling partition the samples into four broad groups, regardless of geographic location: a photic-zone community, a subphotic community, a shallow sedimentary community and a subseafloor sedimentary community (greater than or equal to1.5 meters below seafloor). Abundance-weighted community compositions of water-column samples exhibit a similar trend with depth at all sites, with successive epipelagic, mesopelagic, bathypelagic and abyssopelagic communities. Taxonomic richness is generally highest in the water-column O2 minimum zone and lowest in the subseafloor sediment. OTUs represented by abundant tags in the subseafloor sediment are often present but represented by few tags in the water column, and represented by moderately abundant tags in the shallow sediment. In contrast, OTUs represented by abundant tags in the water are generally absent from the subseafloor sediment. These results are consistent with (i) dispersal of marine sedimentary bacteria via the ocean, and (ii) selection of the subseafloor sedimentary community from within the community present in shallow sediment.
  • Article
    Microbial activity in the marine deep biosphere : progress and prospects
    (Frontiers Media, 2013-07-11) Orcutt, Beth N. ; LaRowe, Douglas E. ; Biddle, Jennifer F. ; Colwell, Frederick S. ; Glazer, Brian T. ; Kiel Reese, Brandi ; Kirkpatrick, John B. ; Lapham, Laura L. ; Mills, Heath J. ; Sylvan, Jason B. ; Wankel, Scott D. ; Wheat, C. Geoffrey
    The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists—all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these “extreme” environments survive (or even thrive). Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) “theme team” on microbial activity (www.darkenergybiosphere.org).
  • Article
    Relationship of bacterial richness to organic degradation rate and sediment age in subseafloor sediment
    (American Society for Microbiology, 2016-06-10) Walsh, Emily A. ; Kirkpatrick, John B. ; Pockalny, Robert ; Sauvage, Justine ; Spivack, Arthur J. ; Murray, Richard W. ; Sogin, Mitchell L. ; D'Hondt, Steven
    Subseafloor sediment hosts a large, taxonomically rich and metabolically diverse microbial ecosystem. However, the factors that control microbial diversity in subseafloor sediment have rarely been explored. Here we show that bacterial richness varies with organic degradation rate and sediment age. At three open-ocean sites (in the Bering Sea and equatorial Pacific) and one continental margin site (Indian Ocean), richness decreases exponentially with increasing sediment depth. The rate of decrease in richness with depth varies from site to site. The vertical succession of predominant terminal electron acceptors correlates to abundance-weighted community composition, but does not drive the vertical decrease in richness. Vertical patterns of richness at the open-ocean sites closely match organic degradation rates; both properties are highest near the seafloor and decline together as sediment depth increases. This relationship suggests that (i) total catabolic activity and/or electron donor diversity exerts a primary influence on bacterial richness in marine sediment, and (ii) many bacterial taxa that are poorly adapted for subseafloor sedimentary conditions are degraded in the geologically young sediment where respiration rates are high. Richness consistently takes a few hundred thousand years to decline from near-seafloor values to much lower values in deep anoxic subseafloor sediment, regardless of sedimentation rate, predominant terminal electron acceptor, or oceanographic context.
  • Article
    Net community production and gross primary production rates in the western equatorial Pacific
    (American Geophysical Union, 2010-10-12) Stanley, Rachel H. R. ; Kirkpatrick, John B. ; Cassar, Nicolas ; Barnett, Bruce A. ; Bender, Michael L.
    Net community production (NCP) and gross primary production (GPP) are two key metrics for quantifying the biological carbon cycle. In this study, we present a detailed characterization of NCP and GPP in the western equatorial Pacific during August and September 2006. We use continuous measurements of dissolved gases (O2 and Ar) in the surface water in order to quantify NCP at subkilometer scale resolution. We constrain GPP in discrete samples using the triple isotopic composition of O2. We find the average NCP in the western equatorial Pacific is 5.9 ± 0.9 mmol O2 m−2 d−1 (equivalent to 1.5 ± 0.2 mol C m−2 yr−1 with error estimates reflecting 1σ confidence levels) and the average GPP is 121 ± 34 mmol O2 m−2 d−1 (equivalent to 32 ± 9 mol C m−2 yr−1). The measurements reveal significant spatial variability on length scales as small as 50 km. The NCP/GPP ratio is 5.7% ± 1.8%. We also present results for NCP and GPP in the coastal area off Papua New Guinea and for GPP in the central Pacific along the equator.