C-DEBI Newsletter – April 1, 2016

Publications

Frontiers in Microbiology
Temperature and Redox Effect on Mineral Colonization in Juan de Fuca Ridge Flank Subsurface Crustal Fluids
Jean-Paul M. Baquiran, Gustavo A. Ramírez, Amanda G. Haddad, Brandy M. Toner, Samuel Hulme, Charles G. Wheat*, Katrina J. Edwards* and Beth N. Orcutt*
*C-DEBI Contribution 285

To examine microbe-mineral interactions in subsurface oceanic crust, we evaluated microbial colonization on crustal minerals that were incubated in borehole fluids for 1 year at the seafloor wellhead of a crustal borehole observatory (IODP Hole U1301A, Juan de Fuca Ridge flank) as compared to an experiment that was not exposed to subsurface crustal fluids (at nearby IODP Hole U1301B). In comparison to previous studies at these same sites, this approach allowed assessment of the effects of temperature, fluid chemistry, and/or mineralogy on colonization patterns of different mineral substrates, and an opportunity to verify the approach of deploying colonization experiments at an observatory wellhead at the seafloor instead of within the borehole. The Hole U1301B deployment did not have biofilm growth, based on microscopy and DNA extraction, thereby confirming the integrity of the colonization design against bottom seawater intrusion. In contrast, the Hole U1301A deployment supported biofilms dominated by Epsilonproteobacteria (43.5% of 370 16S rRNA gene clone sequences) and Gammaproteobacteria (29.3%). Sequence analysis revealed overlap in microbial communities between different minerals incubated at the Hole U1301A wellhead, indicating that mineralogy did not separate biofilm structure within the 1-year colonization experiment. Differences in the Hole U1301A wellhead biofilm community composition relative to previous studies from within the borehole using similar mineral substrates suggest that temperature and the diffusion of dissolved oxygen through plastic components influenced the mineral colonization experiments positioned at the wellhead. This highlights the capacity of low abundance crustal fluid taxa to rapidly establish communities on diverse mineral substrates under changing environmental conditions such as from temperature and oxygen.

Environmental Microbiology Reports
Transcriptional analysis of sulfate reducing and chemolithoautotrophic sulfur oxidizing bacteria in the deep subseafloor
William D. Orsi*, Bo Barker Jørgensen, Jennifer F. Biddle*
*C-DEBI Contribution 318

Sulfate reducing bacteria (SRB) oxidize a significant proportion of subseafloor organic carbon, but their metabolic activities and subsistence mechanisms are poorly understood. Here, we report in depth phylogenetic and metabolic analyses of SRB transcripts in the Peru Margin subseafloor and interpret these results in the context of sulfate reduction activity in the sediment. Relative abundance of overall SRB gene transcripts declines strongly whereas relative abundance of ribosomal protein transcripts from sulfate reducing δ-proteobacteria peak at 90 meters below seafloor (mbsf) within a deep sulfate methane transition zone (SMT). This coincides with isotopically heavy δ³⁴S values of pore water sulfate (70‰), indicating active subseafloor microbial sulfate reduction. Within the shallow sulfate reduction zone (0-5 mbsf), a transcript encoding the beta subunit of dissimilatory sulfite reductase (dsrB) was related to Desulfitobacterium dehalogenans and environmental sequences from Aarhus Bay (Denmark). At 159 mbsf we discovered a transcript encoding the reversely operating dissimilatory sulfite reductase α-subunit (rdsrA), with basal phylogenetic relation to the chemolithoautotrophic SUP05 Group II clade. A diversity of SRB transcripts involved in cellular maintenance point toward potential subsistence mechanisms under low-energy over long time periods, and provide a detailed new picture of SRB activities underlying sulfur cycling in the deep subseafloor.

Applied and Environmental Microbiology
Comparative Single-Cell Genomics of Chloroflexi from the Okinawa Trough Deep Subsurface Biosphere
Heather Fullerton and Craig L. Moyer*
*C-DEBI Contribution 322

Chloroflexi SSU rRNA gene sequences are frequently recovered from subseafloor environments, but the metabolic potential of this phylum is poorly understood. The phylum Chloroflexi is represented by isolates with diverse metabolic strategies including, anoxic phototrophy, fermentation and reductive dehalogenation; therefore, function cannot be attributed to these organisms based solely on phylogeny. Single cell genomics can provide metabolic insights into uncultured organisms, like the deep-subsurface Chloroflexi. Nine SSU rRNA gene sequences were identified from single-cell sorts of whole-round core material collected as part of IODP Expedition 331 (Deep Hot Biosphere) from the Okinawa Trough at Iheya North hydrothermal field. Previous studies of subsurface Chloroflexi single amplified genomes (SAGs) suggest heterotrophic or lithotrophic metabolisms and provide no evidence for growth by reductive dehalogenation. Our nine Chloroflexi SAGs (of which seven are Anaerolineales) indicate that in addition to encoding genes for the Wood-Ljungdahl pathway, exogenous carbon sources can be actively transported into the cells. At least one subunit for the pyruvate ferredoxin oxidoreductase was found in four of the Chloroflexi SAGs. This protein can provide a link between the Wood-Ljungdahl pathway and other carbon anabolic pathways. Finally, one of the seven Anaerolineales SAGs contains a distinct reductive dehalogenase homologous (rdhA) gene; suggesting reductive dehalogenation is not limited to the Dehalococcoidia class of Chloroflexi.

Frontiers in Microbiology
Diversity and Metabolic Potentials of Subsurface Crustal Microorganisms from the Western Flank of the Mid-Atlantic Ridge
Xinxu Zhang, Xiaoyuan Feng and Fengping Wang

Deep-sea oceanic crust constitutes the largest region of the earth’s surface. Accumulating evidence suggests that unique microbial communities are supported by iron cycling processes, particularly in the young (4 cells cm^-3 of basaltic rock, with higher cell densities occurring between 115 and 145 m below seafloor. Similar bacterial community structures, which are dominated by Gammaproteobacterial and Sphingobacterial species closely related to iron oxidizers, were detected regardless of variations in sampling depth. The metabolic potentials of the crust microbiota were assayed by metagenomic analysis of two basalt enrichments which showed similar bacterial structure with the original sample. Genes coding for energy metabolism involved in hydrocarbon degradation, dissimilatory nitrate reduction to ammonium, denitrification and hydrogen oxidation were identified. Compared with other marine environments, the metagenomes from the basalt-hosted environments were enriched in pathways for Fe³⁺ uptake, siderophore synthesis and uptake, and Fe transport, suggesting that iron metabolism is an important energy production and conservation mechanism in this system. Overall, we provide evidence that the North Pond crustal biosphere is dominated by unique bacterial groups with the potential for iron-related biogeochemical cycles.

Education & Outreach

C-DEBI: K-16 Educator Small Grants
The K-16 Educator Small program supports K-16 teachers who have attended a C-DEBI educator training program and have incorporated C-DEBI content into their classrooms. These awards up to $2500 support items including but not limited to the following: funds for student field trips, classroom supplies, travel for presenting C-DEBI curriculum at educator meetings, or additional professional development directly related to C-DEBI research. Proposals for funding should indicate how C-DEBI research content is being translated into the classroom and how the proposed activities connect to that content. Applications due May 01, 2016.

IODP-USSSP: ECORD Summer School 2016: Petrophysics
To apply for U.S. travel support, visit the USSSP webpage and scroll down to “Participation” to submit an online application. The deadline to apply for travel support and for the course is April 01, 2016.

The Data Incubator: Data Science Fellowship
Regular deadline: April, 04 2016.

MBL: Strategies and Techniques for Analyzing Microbial Population Structures (STAMPS), August 3 – August 13, 2016
Application deadline: April 08, 2016.

MARUM: ECORD Summer School 2016: Submarine Geohazards – Mapping, Monitoring, and Modelling
The application deadline is May 05, 2016.

Summer Institutes on Undergraduate STEM Education
The Summer Institutes model the scientific teaching principles they teach. We invite college and university faculty, instructional staff, and future faculty to develop teaching skills at multi-day workshops to transform the undergraduate classroom. They draw on the expertise of participants and presenters. Current research, active learning, assessment, and inclusive teaching are woven into the program, creating a forum to share ideas and develop innovative instructional materials to be implemented upon returning home.

Proposal Calls

DCO: Census of Deep Life Sequencing Opportunities – Call for Proposals
Since 2011, the Deep Carbon Observatory’s Deep Life Community has sponsored the Census of Deep Life (CoDL) that has supported surveys of the diversity of microbes present in several deep continental and subseafloor environments. The first surveys (2011-2012) were conducted using 454 pyrosequencing and subsequently (2013) Illumina sequencing strategies were adopted. Through this initiative, the Deep Life Community has allowed the characterization of diversity of subsurface microbial communities at numerous sites worldwide including the subseafloor and deep continental locations from a range of geologic settings (e.g., large igneous provinces, subglacial lakes, methane hydrate-rich sediments, cratons). The Illumina platform provides increased numbers of reads for more samples at reduced cost. For DNA samples submitted to the CoDL for sequencing, proponents have the option of obtaining 400-450 nt bacterial sequences that span the V4V5 region of Bacterial and Archaeal rRNA coding regions or a greater number of reads for V6 regions that through complete overlap of forward and reverse reads allows detection of lower abundance taxa with reduced stochastic error rates. Shotgun metagenomic DNA sequencing for key samples can also be performed. Deadline April 30, 2016.

IODP: Call for Scientific Drilling Proposals
Next proposal submission deadline: April 01, 2016.

DCO/AGI: Diversity Engagement Grants
AGI (American Geosciences Institute) has received funding from the Alfred P. Sloan Foundation to bolster participation of traditionally underrepresented geoscientists within the Deep Carbon Observatory (DCO) community. Please submit all materials by May 02, 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.

DCO: Deep Life Cultivation Internship Program
The DLC will support early-carrier researchers to visit some key laboratories (Inagaki – Kochi, Japan, Bartlett – La Jolla, USA, and others) to learn and practice newly developed cultivation and cultivation-dependent molecular/biogeochemical techniques using samples from the DLC’s field missions. Financial support includes $5,400 per person for travel and lodging costs and host lab research supply reimbursement.

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

Montana State University, Thermal Biology Institute: Two Postdoctoral Scholar Positions Open
Two recently funded Postdoctoral Scholar positions are available immediately in the Thermal Biology Institute (TBI) (www.TBI.montana.edu) at Montana State University (MSU).  One position will focus on metagenomics and microbial ecology, and a closely aligned position to focus on proteomics and metabolomics of these same systems. TBI conducts research on the biology and interrelated physical and chemical processes of geothermal environments in the Greater Yellowstone Ecosystem, and was established in 1999 and has a successful history of high quality, interdisciplinary biological research in geothermal environments. For one position, applications are particularly welcome from candidates who have additional experience on the physiology and ecology of thermophilic bacteria and archaea, expertise using molecular methods and bioinformatics to assess phylogenetic and/or functional diversity of biota in natural systems, annotation of microbial genomes and/or metagenomes of environmental samples. For the second position, expertise in liquid chromatography-mass spectrometry (LC-MS/MS), gas chromatography mass spectrometry (GC-MS), metabolite profiling by NMR, standard proteomics and/or metabolomics work flows, biological statistics, and/or microbial metabolism is highly desired. Research objectives will focus on the characterization and isolation of novel hyperthermophilic archaea found in geothermal alkaline springs of Yellowstone National Park. Applications will be reviewed starting March 21, 2016 and will continue until positions are filled.

Station Biologique de Roscoff (SBR) 2 PhD positions available
Over the last 7 years, the EPEP team @SBR, France, has been coordinating global oceans sampling and analyses of marine planktonic protists in the Tara-Oceans/OCEANOMICS expeditions and project. For the first time in ecology, a small but highly interdisciplinary consortium has assembled a holistic, standardized eco-morpho-genetic dataset across a planetary biome, comprising >30,000 biological samples and associated contextual data from 220 sites, 3 depths, and 11 organismal size-fractions from viruses to small animals (Karsenti et al. 2011, Bork et al. 2015). We have then generated the largest meta-omics dataset available to date (>40 Terabases!), including >1,000 viral, prokaryotic, and eukaryotic-enriched metagenomes and metatranscriptomes, as well >4 billion eukaryotic and prokaryotic metabarcodes from >3,000 size-fractionated, worldwide plankton communities. This dataset covering global geographic and taxonomic scales represents today a unique opportunity to explore the boundaries of a planetary ecosystem at the crossroad between biodiversity, ecology, and evolution. The 2 PhD projects proposed here aims at further exploring the symbiotic/mixotrophic structure of protistan diversity across Life’s kingdoms and global oceans biogeography and hydrography, as well as understanding the acclimation and adaptation patterns of the key protist players in these ecosystems which cover 71% of our planet and generate half its oxygen. Both students will apply innovative protocols combining eco-bioinformatics, single-cell-omics, and advanced imaging. They will integrate the Tara Oceans/Oceanomics international consortium (http://oceans.taraexpeditions.org/en/, http://www.oceanomics.eu/), and benefit from the great and long-standing pluridisciplinary expertise developed over the last 7 years in the collaborative network.

Bigelow: Research Technician
Review of applicants will begin on April 11, 2016.

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.