C-DEBI Newsletter – February 1, 2016 This newsletter is also accessible via our website.
Atlantis Massif Expedition Update
Expedition to the Atlantis Massif Recovers Mantle Rocks with Signs of Life An international team of scientists – recently returned from a 47-day research expedition to the middle of the Atlantic Ocean – have collected an unprecedented sequence of rock samples from the shallow mantle of the ocean crust that bear signs of life, unique carbon cycling, and ocean crust movement. Led by Co-Chief Scientists Gretchen Früh-Green (ETH Zurich, Switzerland) and Beth Orcutt (Bigelow Laboratory for Ocean Sciences, USA, and C-DEBI Phase II Senior Scientist) the team collected these unique rock samples using seabed rock drills from Germany and the UK – the first time in the history of the decades-long scientific ocean drilling program that such technology has been utilized.
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.
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 (δ15NNTR (NTR, referring to nitrification) and δ18ONTR), as well as the isotope effect for denitrification (15ϵDNF) (DNF, referring to denitrification), parameters with high relevance to global ocean models of N cycling. Estimated values of δ15NNTR 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 δ18ONTR generally ranged between −2.8 and 0.0 ‰, consistent with recent estimates based on lab cultures of nitrifying bacteria. Notably, some δ18ONTR 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.
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.
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.
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.
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.
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.
C-DEBI: Applications Now Open for the 2016 Summer Undergraduate GEM Course The GEM Course is an all-expenses paid, four-week intensive introductory course in Global Environmental Microbiology (GEM) geared for early career undergraduates from 2 and 4 year institutions. The course focuses on microbes found in aquatic environments investigated through authentic research experiences (students collect, process & interpret data). This residential course includes lectures, labs and fieldwork at USC, the Eastern Sierra Mountains, and on Santa Catalina Island. The application deadline is February 02, 2016.
C-DEBI NSF REU: Community College Cultivation Cohort (C4) C-DEBI’s NSF REU, C4, is a 9-week research internship targeting community college students nationwide. Students will spend their summer doing cutting edge research as they help grow, isolate, and describe previously unknown microorganisms. C4 students will work in teams in laboratories at USC, learning state-of-the-art techniques ranging from DNA sequencing to microscopy and sterile techniques to analytical chemistry. Applications due February 15, 2016.
C-DEBI: The Community College Research Internship for Scientific Engagement, June 13 – August 5, 2016 CC-RISE is an eight-week, paid, summer research internship program for community college students run by the Center for Dark Energy Biosphere Investigations. Students will gain firsthand exposure to the scientific process by working in a faculty-led research lab at the University of California Santa Cruz or at the Marine Biological Laboratory in Woods Hole, MA. In addition to research, students will participate in activities focusing on how to transition from a two-year college to a university and information on graduate school. At the end of the program, students will present their results to an audience of peers and mentors. Applications due March 18, 2016.
USC: Wrigley Institute International GeoBiology Course The International GeoBiology Course is an intense, multidisciplinary summer course exploring the coevolution of the Earth and it’s biosphere, with an emphasis on how microbial processes affect the environment and leave imprints on the rock record. Participants get hands-on experience in cutting-edge geobiological techniques including molecular biology, bioinformatics, geochemistry, petrology and sedimentology, and work in research groups to solve relevant questions. GeoBiology 2016 is open to students and researchers at any level, although we give preference to graduate students in their early to mid years of study. Applications are due February 12, 2016.
UNOLS: STEMSEAS Program The STEM workforce is crucial to the U.S. health and economy, yet retention rates in STEM fields are poor and the Geoscience community in particular is faced with a looming workforce shortage. The Geoscience community continues to lack the diversity of the population at large. The STEMSEAS project is an NSF-funded initiative aimed at addressing these issues. STEMSEAS takes advantage of unused berthing capacity available during transits between expeditions on the federally funded research vessel network, the University National Oceanographic Laboratory System (UNOLS). These short (~5-12 day) transits offer a mobile classroom setting where undergraduate non-STEM, undecided-STEM, and geoscience majors can be exposed to geoscience professional practice and career exploration. During Spring and Summer 2016, undergraduates will sail on one of three different transits aboard state-of-the art research vessels. Students over the age of 18 who are enrolled in 2- or 4-year institutions who are interested in STEM fields but are unsure of their exact direction are encouraged to apply. Students from traditionally under-represented communities in STEM are also strongly encouraged to apply, as are those pursuing degrees in art, journalism, film studies, English and pre-law. If accepted, all expenses are paid by the program. Deadline to apply is February 19, 2016
Session 14g: Deep Biosphere: Biogeochemical Elemental Cycles, Serpentinization and Evolution of Life in the Earth’s Interior Conveners: Fumio Inagaki (JAMSTEC), Shuhai Ono (MIT), Yohey Suzuki (Univ. Tokyo), Li-Hung Lin (National Taiwan Univ.), Mitch Sogin (MBL), Fengping Wang (Shanghai Jiaotong Univ.) Keynote speaker: Kai-Uwe Hinrichs (Univ. Bremen)
Summary: Multiple lines of evidence for the presence and activity in the deep biosphere have transformed our view of Earth’s ecosystems and biogeochemical elemental cycles. Over the past decade, extensive research opportunities of the marine and terrestrial deep biosphere demonstrated the occurrence of aerobic and anaerobic subsurface microbial habitats, whereas environmental factors that limit population, diversity, and activity of deep life remain largely unknown. While the occurrence of heterotrophic microbial ecosystems has been documented up to a few km-deep subseafloor sediments, water-rock reactions (e.g., serpentinization, water radiolysis, fault activity) can also fuel deep subsurface biospheres in terrestrial and marine settings. Genomic information of subsurface microbial communities has drastically increased at single-cell to community levels on regional to global scales. However, some key issues remain largely elusive: e.g., genetic and metabolic functions, eco-physiology and community networks, strategies for long-term survival on geological time scales, and origins and evolution of deep life and the biosphere. In this session, we would like to create a forum for recent exciting results in the deep-biosphere geomicrobiology and biogeochemistry. We welcome papers studying Archaea, Bacteria, Eukarya, and viruses in both crustal and sedimentary subsurface environments, biogeochemical processes of serpentinization (e.g., origins of methane and hydrogen, local and global flux) and its microbial habitat, ecosystem consequence to tectonic activities, genetic and functional characteristics and evolution, energetic and other constraints that may define biotic-abiotic transition zones, and topics relevant to new cultivation and analytical techniques that will enhance exploration of deep-biosphere frontiers.
Societé Francaise de Minéralogie: Serpentine Days The next edition of Serpentine Days will be held in Sète (France) – September 25-29, 2016. The Serpentine Days is an international workshop supported by the Societé Francaise de Minéralogie (French mineralogical society); it aims primarily at favoring multidisciplinary research on serpentines and serpentinization. The workshop will bring together scientists with an interest in the geological, physical and (bio-)chemical processes of serpentinization and the life it sustains as well as scientists working on its impact for the development of mineral resources and new energy sources and the environmental and societal impact of their exploration and exploitation. If you are interested in participating in this workshop, please fill the pre-registration form. Participation will be limited to 120 international attendees. For the organizing committee: Marguerite Godard (Géosciences Montpellier), Bénedicte Ménez (IPGP), José-Alberto Padron-Navarta (Géosciences Montpellier), Bruno Reynard (LST Lyon). Contact : firstname.lastname@example.org. Deadline for pre-registration: March 01, 2016.
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 (email@example.com). The deadline for applications is February 29, 2016.