C-DEBI Newsletter – May 2, 2016

Publications

Frontiers in Microbiology
Deep subsurface life from North Pond: enrichment, isolation, characterization and genomes of heterotrophic bacteria
Joseph A. Russell*, Rosa León-Zayas*, Kelly Wrighton and Jennifer F. Biddle*
*C-DEBI Contribution 325

Studies of subsurface microorganisms have yielded few environmentally relevant isolates for laboratory studies. In order to address this lack of cultivated microorganisms, we initiated several enrichments on sediment and underlying basalt samples from North Pond, a sediment basin ringed by basalt outcrops underlying an oligotrophic water-column west of the Mid-Atlantic Ridge at 22°N. In contrast to anoxic enrichments, growth was observed in aerobic, heterotrophic enrichments from sediment of IODP site U1382B at 4 and 68 meters below seafloor (mbsf). These sediment depths, respectively, correspond to the fringes of oxygen penetration from overlying seawater in the top of the sediment column and upward migration of oxygen from oxic seawater from the basalt aquifer below the sediment. Here we report the enrichment, isolation, and initial characterizations of three isolated aerobic heterotrophs from North Pond sediments; an Arthrobacter species from 4 mbsf, and Paracoccus and Pseudomonas species from 68 mbsf. These cultivated bacteria are represented in the amplicon 16S rRNA gene libraries created from whole sediments, albeit at low (up to 2%) relative abundance. We provide genomic evidence from our isolates demonstrating that the Arthrobacter and Pseudomonas isolates have the potential to respire nitrate and oxygen, though dissimilatory nitrate reduction could not be confirmed in laboratory cultures. The cultures from this study represent members of environmentally significant phyla, and allow for further studies into geochemical factors impacting life in the deep subsurface.

Frontiers in Microbiology
Nanocalorimetric Characterization of Microbial Activity in Deep Subsurface Oceanic Crustal Fluids
Alberto Robador*, Douglas E. LaRowe*, Sean P. Jungbluth*, Huei-Ting Lin*, Michael S. Rappé*, Kenneth H. Nealson and Jan P. Amend*
*C-DEBI Contribution 327

Although fluids within the upper oceanic basaltic crust harbor a substantial fraction of the total prokaryotic cells on Earth, the energy needs of this microbial population are unknown. In this study, a nanocalorimeter (sensitivity down to 1.2 nW ml^-1) was used to measure the enthalpy of microbially catalyzed reactions as a function of temperature in samples from two distinct crustal fluid aquifers. Microorganisms in unamended, warm (63°C) and geochemically altered anoxic fluids taken from 292 meters sub-basement (msb) near the Juan de Fuca Ridge produced 267.3 mJ of heat over the course of 97 h during a step-wise isothermal scan from 35.5 to 85.0°C. Most of this heat signal likely stems from the germination of thermophilic endospores (6.66 × 104 cells ml^-1_FLUID) and their subsequent metabolic activity at temperatures greater than 50°C. The average cellular energy consumption (5.68 pW cell^-1) reveals the high metabolic potential of a dormant community transported by fluids circulating through the ocean crust. By contrast, samples taken from 293 msb from cooler (3.8°C), relatively unaltered oxic fluids, produced 12.8 mJ of heat over the course of 14 h as temperature ramped from 34.8 to 43.0°C. Corresponding cell-specific energy turnover rates (0.18 pW cell^-1) were converted to oxygen uptake rates of 24.5 nmol O2 ml^-1_FLUID d^-1, validating previous model predictions of microbial activity in this environment. Given that the investigated fluids are characteristic of expansive areas of the upper oceanic crust, the measured metabolic heat rates can be used to constrain boundaries of habitability and microbial activity in the oceanic crust.

International Ocean Discovery Program Expedition 366 Scientific Prospectus
Mariana serpentinite mud volcanism: geochemical, tectonic, and biological processes
Patricia Fryer, C. Geoffrey Wheat, Trevor Williams

International Ocean Discovery Program (IODP) Expedition 366 has two primary science objectives. The first objective is devoted to coring a series of sites at the summit and flanks of three large (up to 50 km diameter and 2 km high) serpentinite mud volcanoes in the Mariana forearc (within 100 km west of the Mariana Trench). This objective addresses the broad scientific aim of examining processes of mass transport within the subduction zone of a nonaccretionary convergent margin. In detail, the plan is to recover mudflow materials to (1) examine processes of mass transport and geochemical cycling within the forearc of a nonaccretionary convergent margin; (2) ascertain the spatial variability of slab-related fluids within the forearc environment as a means of tracing dehydration, decarbonation, and water-rock reactions in subduction and suprasubduction zone environments; (3) study the metamorphic and tectonic history of this nonaccretionary forearc region; (4) investigate the physical properties of the subduction zone in relation to dehydration reactions and seismicity; (5) document microbial activity associated with subduction zone material from great depth; and (6) explore linkages among these subduction-related processes, including seismicity, while placing the effects of these processes within a historical context. The second objective establishes long-term seafloor observatory sites by emplacing cased boreholes at summit (conduit) holes in three mud volcanoes (at Expedition 366 proposed Sites MAF-11A, MAF-9B, and MAF-15A) and removing the circulation obviation retrofit kit (CORK) body from Ocean Drilling Program Hole 1200C. These activities set the foundation for future deployments of sensors and samplers with the possibility of deploying a CORK-Lite structure within the boreholes. CORK-Lites provide a framework for conducting temporal observations that will allow one to “take the pulse of subduction” in an active nonaccretionary convergent plate margin and establish a platform for in situ experimentation.

Meetings & Activities

C-DEBI 2015-2016 Networked Speaker Series: Thursday, May 26, 2016, 12:30pm PT online!

Stephanie Carr, Bigelow Laboratory for Ocean Sciences
Methanosaeta, are you my methanogen?
Add to:  iCal  •  gCal  •  Outlook  •  Outlook Online  •  Yahoo!

The Adélie Basin, located ~100km off shore of Antarctica’s Wilkes Land Margin, is an anoxic, eutrophic sedimentary environment. During IODP Expedition 318, a 103 m sediment core was collected for microbiological and geochemical studies. Stable carbon isotope analysis of dissolved CO₂ indicates an enrichment of δ¹³C values with depth. This enrichment is indicative of the autotrophic selection of dissolved ¹²CO₂ over ¹³CO₂ , which corresponds to increasing methane concentrations suggesting methanogenesis (a maximum of 12.8 mM at 18 meters below sea floor). Surprisingly, previous pyrosequencing of SSU rRNA gene amplicons identified relatively low amounts of known archaea (<7%) and very few sequences from known methanogens (<0.2%). An additional PCR screen for the gene mcrA also failed to recognize the presence of potential methanogens. This unsatisfying dearth of genomic evidence for methanogens precludes a deeper understanding of CH₄ cycling in this environment. To better identify the missing methanogenic community of this basin, an integrated approach of metagenomics, single cell genomics, and stable carbon isotope analysis of intact polar lipid techniques was applied to these sediments. Lipid analyses identified isotopically light hydroxyarchaeol and glycerol dialkyl glycerol tetraether (GDGT) phospholipids, both suspected to be of methanogenic origin. Metagenomic analyses identified coding regions for both acetoclastic and autotrophic methanogenesis pathways. The majority of these coding regions were classified to the genus Methanosaeta, a well-known acetoclastic methanogen. This presentation takes a thorough look at the genus Methanosaeta, especially their methanogenic potential and their role in these and other marine subsurface environments.

Goldschmidt/DCO/Jamstec: IODP “T-Limit” Project Workshop – Expedition 370: T-Limit of the Deep Biosphere off Muroto
One of the key scientific objectives in studies of deep life and carbon is to understand environmental factors that constrain population, activity, diversity and ecological function of microbial communities, and the extent of habitable zones in the Earth’s interior. To better constrain the temperature limit of life in the deep biosphere, the International Ocean Discovery Program (IODP) is preparing one of two expeditions with the Japanese drilling vessel Chikyu to revisit Ocean Drilling Program (ODP) Site 1174 in the Nankai Trough subduction zone off Cape Muroto, Japan (water depth: 4731 m), which was drilled by ODP Legs 190/196 15 years ago. Anomalously high heat flow results in temperatures of ~100ºC at the décollement (870 to 900 m below seafloor [mbsf]) and of ~130ºC at the sediment-basement interface (1,210 mbsf). After drilling, multiple-temperature sensors will be installed into the borehole, allowing ~1 year monitoring of formation temperature in situ. In this workshop, we will discuss how to achieve some important scientific objectives regarding the limits of the deep biosphere during the upcoming IODP Expedition 370. Contributions related to microbiology and biogeochemistry of the deep biosphere, as well as thermodynamics, fluid flow regimes, and subduction geology would be very welcome, as we aim to maximize the scientific return of this challenging IODP T-Limit project through multidisciplinary research coordination. Please register online by June 21, 2016. Registration may close sooner if the maximum number of participants have registered. Participation is limited to 50 scientists (including guests, operators, etc.).

DCO Symposium in Yokohama: Deep Life, Deep Energy, Reservoirs and Flues, and Extreme Physics and Chemistry, June 26, 2016
Register by June 21, 2016.

IODP-USSP: Host An Ocean Discovery Lecture
Are you interested in having an Ocean Discovery Lecturer like C-DEBI researchers Andy Fisher and Jason Sylvan speak at your institution? We accept applications from any U.S. college, university, or nonprofit organization, and the application period is open until May 20, 2016.

Proposal Calls

IODP: Apply to Sail: Expedition 370, T-Limit of the Deep Biosphere off Muroto
The International Ocean Discovery Program (IODP) is now accepting applications for Expedition 370 T-Limit of the Deep Biosphere off Moroto. Using the drilling vessel Chikyu, Expedition 370 will explore the limits of subseafloor life and the biosphere in the protothrust zone of the Nankai accretionary prism off Cape Muroto, Japan. Expedition 370 aims to: (1) study the factors that control biomass, activity and diversity of microbial communities in a subseafloor environment where temperatures increase from ~30°C to ~130°C and which thus likely encompasses the biotic-abiotic transition zone, and (2) determine geochemical, geophysical and hydrogeological characteristics in sediments and the underlying basaltic basement and elucidate if the supply of fluids containing thermogenic and/or geogenic nutrient and energy substrates may support subseafloor microbial communities in the Nankai accretionary complex. To achieve these scientific objectives, the expedition will retrieve sediment and basalt core samples from a site near ODP Site 1174 (Leg 190 in 2000), located in the landward protothrust zone of the Nankai Trough accretionary prism down to ~1.2 km below seafloor (water depth: 4730 m). After coring operations, a string of multiple temperature sensor-loggers will be installed into the borehole down to the basement to monitor the temperature profile for 1-2 years. Opportunities exist for researchers (and graduate students) in the following specialties: microbiology, organic and inorganic geochemistry/biogeochemistry, physical properties, sedimentology, structural geology, paleontology, paleomagnetism, petrology, and hydrogeology. Additional information about this expedition can be found here and in the summary prospectus on the Expedition 370 webpage. U.S.-affiliated scientists interested in participating in this expedition should apply to sail through the U.S. Science Support Program, by visiting http://usoceandiscovery.org/expeditions. The deadline to apply is June 10, 2016.

IODP: Special Call for Applications for Expeditions 367 & 368
The International Ocean Discovery Program (IODP) is seeking scientists with expertise in sedimentology, petrology, organic geochemistry, and nannofossil, foraminifer, and diatom micropaleontology to sail on Expeditions 367/368 South China Sea Rifted Margin aboard the JOIDES Resolution. These two expeditions aim to understand the mechanisms of lithospheric breakup at a non-volcanic rifted margin. The deadline to apply for this special call is Today, May 02, 2016.

DCO/AGI: Diversity Engagement Grants
Please submit all materials by Today, May 02, 2016. 

IODP: Call for Sample Requests, Expedition 365
As part of contingency operations made possible by the completion of primary objectives ahead of schedule, IODP Expedition 365 (NanTroSEIZE Shallow Megasplay Long-Term Borehole Monitoring System, LTBMS) will drill and collect core at IODP Site C0010 from ~300-600 meters below seafloor. A description of Site C0010 is available at: http://publications.iodp.org/proceedings/319/104/104_.htm. The core will be analyzed and described at a post-expedition sampling party in summer 2016 at the Kochi Core Center. This is an open call for sample and data requests for the Expedition 365 core. Details for requesting samples/data can be found at: https://www.iodp.org/access-data-and-samples. The deadline for requests is May 20, 2016.

IODP-USSSP: Proposals for Pre-Drilling Activities and Workshops
The U.S. Science Support Program (USSSP) accepts proposals on a rolling basis for pre-drilling activities and semi-annually for workshops (next call due June 01, 2016), related to the International Ocean Discovery Program (IODP).

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

Rutgers University Deep Sea Microbiology Lab: Bioinformatics Postdoctoral Position
The postdoc will participate in a project to investigate the evolution of early and acquired metabolism in T. ammonificans, a thermophilic, chemolithoautotrophic bacterium that we isolated in my laboratory from a deep-sea hydrothermal vent. In this project we are leveraging different types of culture approaches (including batch and continuous culture techniques) with comparative genomic and proteomic analyses of T. ammonificans and related organisms. Experience with bioinformatics (and some microbiology background) is an essential requirement, as this project entails the analyses large sequence data. More info about the lab at: http://marine.rutgers.edu/deep-seamicrobiology/. The position is available immediately and potential candidates should contact group leader Constantino Vetriani directly at vetriani@marine.rutgers.edu.

Montana State University, Thermal Biology Institute: Two Postdoctoral Scholar Positions Open
Applications will be reviewed starting March 21, 2016 and will continue until positions are filled.

IODP at Texas A&M: Assistant Research Scientist
We will begin reviewing applications on May 16, 2016, but will continue to accept applications until candidates are selected for interviews.

Station Biologique de Roscoff (SBR) 2 PhD positions available