C-DEBI Newsletter – February 1, 2016

Publications

Frontiers in Microbiology
Structural Iron (II) of Basaltic Glass as an Energy Source for Zetaproteobacteria in an Abyssal Plain Environment, Off the Mid Atlantic Ridge
Pauline A. Henri, Céline Rommevaux-Jestin, Françoise Lesongeur, Adam Mumford, David Emerson*, Anne Godfroy and Bénédicte Ménez
*C-DEBI Contribution 290

To explore the capability of basaltic glass to support the growth of chemosynthetic microorganisms, complementary in situ and in vitro colonization experiments were performed. Microbial colonizers containing synthetic tholeitic basaltic glasses, either enriched in reduced or oxidized iron, were deployed off-axis from the Mid Atlantic Ridge on surface sediments of the abyssal plain (35°N; 29°W). In situ microbial colonization was assessed by sequencing of the 16S rRNA gene and basaltic glass alteration was characterized using Scanning Electron Microscopy, micro-X-ray Absorption Near Edge Structure at the Fe-K-edge and Raman microspectroscopy. The colonized surface of the reduced basaltic glass was covered by a rind of alteration made of iron-oxides trapped in a palagonite-like structure with thicknesses up to 150 μm. The relative abundance of the associated microbial community was dominated (39% of all reads) by a single operational taxonomic unit (OTU) that shared 92% identity with the iron-oxidizer Mariprofundus ferrooxydans PV-1. Conversely, the oxidized basaltic glass showed the absence of iron-oxides enriched surface deposits and correspondingly there was a lack of known iron-oxidizing bacteria in the inventoried diversity. In vitro, a similar reduced basaltic glass was incubated in artificial seawater with a pure culture of the iron-oxidizing M. ferrooxydans DIS-1 for 2 weeks, without any additional nutrients or minerals. Confocal Laser Scanning Microscopy revealed that the glass surface was covered by twisted stalks characteristic of this iron-oxidizing Zetaproteobacteria. This result supported findings of the in situ experiments indicating that the Fe(II) present in the basalt was the energy source for the growth of representatives of Zetaproteobacteria in both the abyssal plain and the in vitro experiment. In accordance, the surface alteration rind observed on the reduced basaltic glass incubated in situ could at least partly result from their activity.

Biogeosciences
Nitrogen cycling in the deep sedimentary biosphere: nitrate isotopes in porewaters underlying the oligotrophic North Atlantic
S.D. Wankel*, C. Buchwald, W. Ziebis*, C.B. Wenk, and M.F. Lehmann
*C-DEBI Contribution 295

Nitrogen (N) is a key component of fundamental biomolecules. Hence, its cycling and availability are central factors governing the extent of ecosystems across the Earth. In the organic-lean sediment porewaters underlying the oligotrophic ocean, where low levels of microbial activity persist despite limited organic matter delivery from overlying water, the extent and modes of nitrogen transformations have not been widely investigated. Here we use the N and oxygen (O) isotopic composition of porewater nitrate (NO₃⁻) from a site in the oligotrophic North Atlantic (Integrated Ocean Drilling Program – IODP) to determine the extent and magnitude of microbial nitrate production (via nitrification) and consumption (via denitrification). We find that NO₃^– accumulates far above bottom seawater concentrations (~ 21 μM) throughout the sediment column (up to ~ 50 μM) down to the oceanic basement as deep as 90 m b.s.f. (below sea floor), reflecting the predominance of aerobic nitrification/remineralization within the deep marine sediments. Large changes in the δ¹⁵N and δ¹⁸O of nitrate, however, reveal variable influence of nitrate respiration across the three sites. We use an inverse porewater diffusion–reaction model, constrained by the N and O isotope systematics of nitrification and denitrification and the porewater NO₃⁻ isotopic composition, to estimate rates of nitrification and denitrification throughout the sediment column. Results indicate variability of reaction rates across and within the three boreholes that are generally consistent with the differential distribution of dissolved oxygen at this site, though not necessarily with the canonical view of how redox thresholds separate nitrate regeneration from dissimilative consumption spatially. That is, we provide stable isotopic evidence for expanded zones of co-occurring nitrification and denitrification. The isotope biogeochemical modeling also yielded estimates for the δ¹⁵N and δ¹⁸O of newly produced nitrate (δ¹⁵N_NTR (NTR, referring to nitrification) and δ¹⁸O_NTR), as well as the isotope effect for denitrification (¹⁵ϵ_DNF) (DNF, referring to denitrification), parameters with high relevance to global ocean models of N cycling. Estimated values of δ¹⁵N_NTR were generally lower than previously reported δ¹⁵N values for sinking particulate organic nitrogen in this region. We suggest that these values may be, in part, related to sedimentary N2 fixation and remineralization of the newly fixed organic N. Values of δ¹⁸O_NTR generally ranged between −2.8 and 0.0 ‰, consistent with recent estimates based on lab cultures of nitrifying bacteria. Notably, some δ¹⁸O_NTR values were elevated, suggesting incorporation of ¹⁸O-enriched dissolved oxygen during nitrification, and possibly indicating a tight coupling of NH₄⁺ and NO₂⁻ oxidation in this metabolically sluggish environment. Our findings indicate that the production of organic matter by in situ autotrophy (e.g., nitrification, nitrogen fixation) supplies a large fraction of the biomass and organic substrate for heterotrophy in these sediments, supplementing the small organic-matter pool derived from the overlying euphotic zone. This work sheds new light on an active nitrogen cycle operating, despite exceedingly low carbon inputs, in the deep sedimentary biosphere.

Frontiers in Microbiology
Similar Microbial Communities Found on Two Distant Seafloor Basalts
Esther Singer*, Lauren S. Chong, John F. Heidelberg* and Katrina J. Edwards*
*C-DEBI Contribution 296

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.

Frontiers in Microbiology
The Irony of Iron – Biogenic Iron Oxides as an Iron Source to the Ocean
David Emerson*
*C-DEBI Contribution 297

Primary productivity in at least a third of the sunlit open ocean is thought to be iron-limited. Primary sources of dissolved iron (dFe) to the ocean are hydrothermal venting, flux from the sediments along continental margins, and airborne dust. This article provides a general review of sources of hydrothermal and sedimentary iron to the ocean, and speculates upon the role that iron-cycling microbes play in controlling iron dynamics from these sources. Special attention is paid to iron-oxidizing bacteria (FeOB) that live by oxidizing iron and producing biogenic iron oxides as waste products. The presence and ubiquity of FeOB both at hydrothermal systems and in sediments is only beginning to be appreciated. The biogenic oxides they produce have unique properties that could contribute significantly to the dynamics of dFe in the ocean. Changes in the physical and chemical characteristics of the ocean due to climate change and ocean acidification will undoubtedly impact the microbial iron cycle. A better understanding of the contemporary role of microbes in the iron cycle will help in predicting how these changes could ultimately influence marine primary productivity.

Frontiers in Microbiology
Hydrogen Utilization Potential in Subsurface Sediments
Rishi R. Adhikari, Clemens Glombitza, Julia C. Nickel, Chloe H. Anderson, Ann G. Dunlea, Arthur J. Spivack, Richard W. Murray, Steven D’Hondt* and Jens Kallmeyer
*C-DEBI Contribution 317

Subsurface microbial communities undertake many terminal electron-accepting processes, often simultaneously. Using a tritium-based assay, we measured the potential hydrogen oxidation catalyzed by hydrogenase enzymes in several subsurface sedimentary environments (Lake Van, Barents Sea, Equatorial Pacific, and Gulf of Mexico) with different predominant electron-acceptors. Hydrogenases constitute a diverse family of enzymes expressed by microorganisms that utilize molecular hydrogen as a metabolic substrate, product, or intermediate. The assay reveals the potential for utilizing molecular hydrogen and allows qualitative detection of microbial activity irrespective of the predominant electron-accepting process. Because the method only requires samples frozen immediately after recovery, the assay can be used for identifying microbial activity in subsurface ecosystems without the need to preserve live material. We measured potential hydrogen oxidation rates in all samples from multiple depths at several sites that collectively span a wide range of environmental conditions and biogeochemical zones. Potential activity normalized to total cell abundance ranges over five orders of magnitude and varies, dependent upon the predominant terminal electron acceptor. Lowest per-cell potential rates characterize the zone of nitrate reduction and highest per-cell potential rates occur in the methanogenic zone. Possible reasons for this relationship to predominant electron acceptor include (i) increasing importance of fermentation in successively deeper biogeochemical zones and (ii) adaptation of H₂ases to successively higher concentrations of H₂ in successively deeper zones.

Frontiers in Microbiology
The Guaymas Basin hiking guide to hydrothermal mounds, chimneys and microbial mats: complex seafloor expressions of subsurface hydrothermal circulation
Andreas Teske*,  Dirk De Beer,  Luke McKay*,  Margaret K. Tivey,  Jennifer F. Biddle*, Daniel Hoer, Karen G. Lloyd*,  Mark A. Lever, Hans Røy, Daniel B. Albert, Howard P. Mendlovitz and Barbara J. MacGregor*
*C-DEBI Contribution 319

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 heatflow gradients. Recognizing the inherent spatial limitations of much current Guaymas Basin sampling calls for a wider survey of the entire spreading region.

Proposal Calls

IODP: Call for Scientific Drilling Proposals
The International Ocean Discovery Program (IODP) explores Earth’s climate history, structure, dynamics, and deep biosphere as described at www.iodp.org/Science-Plan-for-2013-2023. IODP provides opportunities for international and interdisciplinary research on transformative and societally relevant topics using the ocean drilling, coring, and downhole measurement facilities D/V JOIDES Resolution (JR), D/V Chikyu and Mission-Specific Platforms (MSP). The JR is planned to operate 10 months per year in 2018 and 2019 under a long-term, global circumnavigation track based on proposal pressure. Future JR expeditions are projected to follow a path from the southwestern Pacific Ocean, through the Southern Ocean, and into the Atlantic Ocean for opportunities starting there in 2019. The JR is then expected to operate in the Atlantic, Mediterranean, Caribbean, and Gulf of Mexico starting in 2020. Although JR proposals for any region are welcomed, pre- and full proposals for these future operational areas are strongly encouraged. MSP expeditions are planned to operate once per year on average, and proposals for any ocean are welcomed. Chikyu operations will be project-based, and new proposals to use Chikyu in riser mode must be Complementary Project Proposals (with cost-sharing). IODP aims to foster joint projects with the International Continental Drilling Program (ICDP). We therefore also invite proposals that coordinate drilling on land and at sea. Next proposal submission deadline: April 01, 2016.

NAS: Gulf Research Program Exploratory Grants
Letter of Intent due February 17, 2016. 

National Academies: Research Associateships for Graduate, Postdoctoral and Senior Researchers
There are four annual review cycles and the next closes February 01, 2016.

National Academies of Science: Gulf Research Program Early-Career Research Fellowships
Application deadline: February 17, 2016.

Shell: Ocean Discovery XPRIZE
Regular registration deadline: June 30, 2016.

NSF: Geobiology and Low-Temperature Geochemistry Program Solicitation
Proposals accepted anytime.

Employment

University of Hawaii at Manoa: Post Doctoral and Graduate Student Research
Positions
The Rappé laboratory at the University of Hawaii at Manoa’s Hawaii Institute of Marine Biology is seeking a postdoctoral researcher and one to two graduate students (M.S. or Ph.D.) to join a project investigating the population genomics of planktonic marine bacteria. The selected individuals will apply recent advances in DNA sequencing technology, bioinformatics, and a high throughput extinction culturing approach in order to investigate the evolutionary characteristics of genomes from populations of globally important marine bacterial lineages. The extramural research grants supporting these positions require the selected individuals to spend one to three months performing research in the field per year. Applicants should have in interest in microbial diversity, speciation, and/or the population genetics of marine microorganisms. Postdoctoral researchers should hold a Ph.D. in microbiology, marine science, oceanography, or computer sicence/bioinformatics. Graduate student applicants should hold a B.S. or M.S. in a relevant field (see above), and must meet all of the requirements for acceptance into the Department of Oceanography, Department of Microbiology, or Marine Biology graduate programs at the University of Hawaii at Manoa. All appointments are initially for one year, renewable for up to three years based on performance. Review of applications will begin immediately; to ensure full consideration, apply by February 25, 2016.

LMU Munich: Postdoctoral Research Fellowship Program
The Orsi lab at the University of Munich is inviting interested graduate students and postdocs to apply for the LMU Postdoctoral Research Fellowship Program, to study the activity, biochemistry, and genomics of bacteria in subseafloor sediment. Informal inquiries should be sent to Bill Orsi (william.orsi@gmail.com). The deadline for applications is February 29, 2016.

IFREMER: Life at the extremes: microbial EcoGenomics of deep-sea extremophiles: Postdoctoral position (starting immediately) 
The Lab for Microbiology of Extreme environments in Brest (France) has an 18-month postdoctoral position available to carry out research in the ecology of bacterial and archaeal communities in deep-sea brine lakes and hydrothermal vent systems. The appointment should start no later than April 1 2016. Please send inquiries and application to Loïs Maignien (lois.maignien@univ-brest.fr) and A.M. Eren (meren@mbl.edu).