C-DEBI Newsletter – July 1, 2013
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Dear C-DEBI,
As part of our "deep" appreciation of the challenges that accompany microbiological investigations and the study of biogeochemical processes in the subseafloor biosphere, we invite proposals for biomolecular projects in a special call due July 31 (see below for more information).  We are also pleased to announce that we will be funding 13 proposals from this spring's small grants and fellowships calls (3 grad student fellowships, 3 postdoctoral fellowships, 5 small research grants and 2 education and outreach grants) out of over 50 submissions.  The competition has grown due to your great interest in C-DEBI; look for details on who has been funded on our website over the next couple months as these awards become official. Much thanks goes out to the Theme Team Leaders who develop the calls and the review panels (chairs and reviewers) who continue to make these calls a success.
Call for Proposals

C-DEBI invites proposals for one-year biomolecular projects that will significantly advance understanding in one or more of the central research themes of C-DEBI. C-DEBI intends to fund 2-3 proposals in response to this call, at levels of $100,000-$150,000. Successful proposals will support one or more state-of-the-art biomolecular approaches, be innovative, and aim to answer one or more fundamental research questions and/or contribute to the development of new hypotheses and goals for future studies. Relevant molecular approaches include, but are not limited to: metagenomics, single cell genomics, tag pyrosequencing, functional gene surveys, transcriptomics, proteomics and metabolomics. Proposed research can address the deep biosphere from one or more perspectives, e.g., molecular interrogation of subseafloor samples, analysis of lab‐based experiments with deep biosphere organisms, or study of organisms grown under deep subsurface conditions. Please see the website or PDF for more details. Submissions are due 7/31/13.
Scientific Activities and Programs

Thinking about attending this fall's AGU meeting? Submit your abstracts to session B020: Deep biosphere research: presence, diversity and activity of microbes (conveners M. Lever, J. Biddle, J. Fang and M. Rappe), which will encapsulate all aspects of deep biosphere research, from microbiological characterizations to hydrogeological and geochemical controls on microbial communities, the diversity and structure of resident communities, the evolutionary characteristics of individuals or populations, activity measurements, manipulation experiments, data syntheses and comparisons, and technological advances. Other subsurface-elated sessions to consider include B073: Windows Into to the Deep Subsurface Biosphere: Coupled Geochemical and Biological Investigations of Terrestrial Hot Spring Ecosystems (conveners E. Boyd and E. Shock), B028: Geobiological Perspectives on the Energetic Limits of Life (conveners J. Marlow and S. McGlynn), and B015: Carbon Transformations in Hydrothermal Systems (conveners F. Klein, E. Reeves, F. Schubotz, W. Orsi). Abstracts are due August 6, 2013 and please let us know if there are any other sessions you'd like to advertise to the C-DEBI community!
Join the International Society for Subsurface Microbiology for it's Ninth International Symposium on Subsurface Microbiology (ISSM 2014), a week-long conference that will explore the link between microbiology, the subsurface environment, and microbial ecosystems. The conference will be held October 5-10, 2014, at Asilomar State Beach and Conference Grounds in Pacific Grove, California, U.S.A. ISSM is held every 3 years to exchange ideas, advance the science and will showcase the latest developments and breakthroughs in the rapidly expanding field of subsurface microbiology. The program includes four plenary sessions and 10 topic sessions divided into dual tracks. Additionally, two networking receptions will highlight poster presentations. Early registration opens in August, and more information is available at
New C-DEBI Contributed Publications

The biogeochemical processes that occur in marine sediments on continental margins are complex; however, from one perspective they can be considered with respect to three geochemical zones based on the presence and form of methane: sulfate–methane transition (SMTZ), gas hydrate stability zone (GHSZ), and free gas zone (FGZ). These geochemical zones may harbor distinct microbial communities that are important in biogeochemical carbon cycles. The objective of this study by C-DEBI Postdoctoral Fellow Briggs, et al. was to describe the microbial communities in sediments from the SMTZ, GHSZ, and FGZ using molecular ecology methods (i.e. PhyloChip microarray analysis and terminal restriction fragment length polymorphism (T-RFLP)) and examining the results in the context of non-biological parameters in the sediments. Non-metric multidimensional scaling and multi-response permutation procedures were used to determine whether microbial community compositions were significantly different in the three geochemical zones and to correlate samples with abiotic characteristics of the sediments. This analysis indicated that microbial communities from all three zones were distinct from one another and that variables such as sulfate concentration, hydrate saturation of the nearest gas hydrate layer, and depth (or unmeasured variables associated with depth e.g. temperature, pressure) were correlated to differences between the three zones. The archaeal anaerobic methanotrophs typically attributed to performing anaerobic oxidation of methane were not detected in the SMTZ; however, the marine benthic group-B, which is often found in SMTZ, was detected. Within the GHSZ, samples that were typically closer to layers that contained higher hydrate saturation had indicator sequences related to Vibrio-type taxa. These results suggest that the biogeographic patterns of microbial communities in marine sediments are distinct based on geochemical zones defined by methane.
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, C-DEBI Activity Theme Team Leader Orcutt, et al. 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.
C-DEBI Co-Investigator Wheat, et al. describe systematic differences in sediment thermal and pore water chemical profiles from Integrated Ocean Drilling Program Site U1363 document mixing and reaction within the basaltic crust adjacent to Grizzly Bare outcrop, a site of hydrothermal recharge into 3.6 My-old basaltic crust. A transect of seven holes was drilled ~50 m to ~750 m away from the base of the outcrop. Temperatures at the sediment-basement interface increase from ~6°C to >30°C with increasing distance from the outcrop, and heat flow is suppressed within several hundred meters from the outcrop. Calculated fluid compositions at the sediment-basement interface are generally explained by mixing between bottom seawater and altered crustal basement fluids, with a composition similar but not identical to fluids from seeps at Baby Bare outcrop, located ~45 km to the northeast. Reactions within upper basement and overlying sediment affect a variety of ions (Mn, Fe, Mo, Si, PO43-, V, and U) and δ13DIC, indicating a diagenetic influence and diffusive exchange with overlying sediment pore waters. The apparent 14C age of basal pore fluids is much older than bottom seawater. Collectively, these results are consistent with seawater recharge at Grizzly Bare outcrop; however, there are strong gradients in fluid composition within 50 m of the outcrop, providing evidence for complex flow paths and vigorous mixing of young, recently recharged seawater with much older, more reacted basement fluid. The proximity of these altered fluids to the edge of the outcrop raises the possibility for fluid seepage from the outcrop in addition to seawater recharge.
Microbial processes within the subseafloor can be examined during the ephemeral and uncommonly observed phenomena known as snowblower venting. Snowblowers are characterized by the large quantity of white floc that is expelled from the seafloor following mid-ocean ridge eruptions. During these eruptions, rapidly cooling lava entrains seawater and hydrothermal fluids enriched in geochemical reactants, creating a natural bioreactor that supports a subseafloor microbial “bloom.” Previous studies hypothesized that the eruption-associated floc was made by sulfide-oxidizing bacteria; however, the microbes involved were never identified. Here C-DEBI Postdoctoral Fellow Meyer, et al. present the first molecular analysis combined with microscopy of microbial communities in snowblower vents from samples collected shortly after the 2011 eruption at Axial Seamount, an active volcano on the Juan de Fuca Ridge. They obtained fluid samples and white flocculent material from active snowblower vents as well as orange flocculent material found on top of newly formed lava flows. Both flocculent types revealed diverse cell types and particulates when examined by phase contrast and scanning electron microscopy (SEM). Distinct archaeal and bacterial communities were detected in each sample type through Illumina tag sequencing of 16S rRNA genes and through sequencing of the sulfide oxidation gene, soxB. In fluids and white floc, the dominant bacteria were sulfur-oxidizing Epsilonproteobacteria and the dominant archaea were thermophilic Methanococcales. In contrast, the dominant organisms in the orange floc were Gammaproteobacteria and Thaumarchaeota Marine Group I. In all samples, bacteria greatly outnumbered archaea. The presence of anaerobic methanogens and microaerobic Epsilonproteobacteria in snowblower communities provides evidence that these blooms are seeded by subseafloor microbes, rather than from microbes in bottom seawater. These eruptive events thus provide a unique opportunity to observe subseafloor microbial communities.
The formation and maintenance of deep-sea ferromanganese/polymetallic nodules still remains a mystery 140 years after their discovery. The wealth of rare metals concentrated in these nodules has spurred global interest in exploring the mining potential of these resources. The prevailing theory of abiotic formation has been called into question and the role of microbial metabolisms in nodule development is now an area of active research. To understand the community structure of microbes associated with nodules and their surrounding sediment, C-DEBI Graduate Fellow Tully and Heidelberg performed targeted sequencing of the V4 hypervariable region of the 16S rRNA gene from three nodules collected from the central South Pacific. Results have shown that the microbial communities of the nodules are significantly distinct from the communities in the surrounding sediments, and that the interiors of the nodules harbor communities different from the exterior. This suggests not only differences in potential metabolisms between the nodule and sediment communities, but also differences in the dominant metabolisms of interior and exterior communities. They identified several operational taxonomic units (OTUs) unique to both the nodule and sediment environments. The identified OTUs were assigned putative taxonomic identifications, including two OTUs only found associated with the nodules, which were assigned to the α-Proteobacteria. Finally, they explored the diversity of the most assigned taxonomic group, the Thaumarchaea MG-1, which revealed novel OTUs compared to previous research from the region and suggests a potential role as a source of fixed carbon for ammonia oxidizing archaea in the environment.
Few studies have directly measured sulfate reduction at hydrothermal vents, and relatively little is known about how environmental or ecological factors influence rates of sulfate reduction in vent environments. A better understanding of microbially mediated sulfate reduction in hydrothermal vent ecosystems may be achieved by integrating ecological and geochemical data with metabolic rate measurements. Here C-DEBI Graduate Fellow Frank, et al. present rates of microbially mediated sulfate reduction from three distinct hydrothermal vents in the Middle Valley vent field along the Juan de Fuca Ridge, as well as assessments of bacterial and archaeal diversity, estimates of total biomass and the abundance of functional genes related to sulfate reduction, and in situ geochemistry. Maximum rates of sulfate reduction occurred at 90 °C in all three deposits. Pyrosequencing and functional gene abundance data revealed differences in both biomass and community composition among sites, including differences in the abundance of known sulfate-reducing bacteria. The abundance of sequences for Thermodesulfovibro-like organisms and higher sulfate reduction rates at elevated temperatures suggests that Thermodesulfovibro-like organisms may have a role in sulfate reduction in warmer environments. The rates of sulfate reduction presented here suggest that—within anaerobic niches of hydrothermal deposits—heterotrophic sulfate reduction may be quite common and might contribute substantially to secondary productivity, underscoring the potential role of this process in both sulfur and carbon cycling at vents.
C-DEBI Limits to Life Theme Team Leader McCollom and Seewald explain that the process of serpentinization creates strongly reducing conditions and produces fluids that are highly enriched in molecular hydrogen and methane. Some microorganisms are able to exploit these compounds to gain metabolic energy and to generate biomass, leading to the development of biological communities based on chemical energy rather than photosynthesis. The abundance of chemical energy and favorable conditions for organic synthesis make serpentinites a strong candidate for the site of the origin of life on Earth, as well as a prime target in the search for life elsewhere in our Solar System.
High-temperature water–rock reactions produce large quantities of hydrogen, which must be transported to cooler settings to sustain life. Based on the recent Mayhew, et al. paper in Nature Geoscience (see below) C-DEBI Co-Investigator D'Hondt considers that lower-temperature hydrogen generation could potentially support life in situ and free subsurface microbes from photosynthetic constraints.

Share your C-DEBI-supported publications with the community and request a contribution number! Contact Matt Janicak ( for details.

Other New Publications

Hydrogen is commonly produced during the high-temperature hydration of mafic and ultramafic rocks, owing to the oxidation of reduced iron present in the minerals. Hydrothermal hydrogen is known to sustain microbial communities in submarine vent and terrestrial hot-spring systems. However, the rates and mechanisms of hydrogen generation below temperatures of 150 °C are poorly constrained. As such, the existence and extent of hydrogen-fuelled ecosystems in subsurface terrestrial and oceanic aquifers has remained uncertain. Here, Mayhew, et al. report results from laboratory experiments in which they reacted ground ultramafic and mafic rocks and minerals—specifically peridotite, pyroxene, olivine and magnetite—with anoxic fluids at 55 and 100 °C, and monitored hydrogen gas production. They used synchrotron-based micro-X-ray fluorescence and X-ray absorption near-edge structure spectroscopy to identify changes in the speciation of iron in the materials. They report a strong correlation between molecular hydrogen generation and the presence of spinel phases—oxide minerals with the general formula [M2+M23+]O4 and a cubic crystal structure—in the reactants. They also identify Fe(III)-(hydr)oxide reaction products localized on the surface of the spinel phases, indicative of iron oxidation. They propose that the transfer of electrons between Fe(II) and water adsorbed to the spinel surfaces promotes molecular hydrogen generation at low temperatures. They suggest that these localized sites of hydrogen generation in ultramafic aquifers in the oceanic and terrestrial crust could support hydrogen-based microbial life.
Planktonic bacteria dominate surface ocean biomass and influence global biogeochemical processes, but remain poorly characterized owing to difficulties in cultivation. Using large-scale single cell genomics, Swan, et al. obtained insight into the genome content and biogeography of many bacterial lineages inhabiting the surface ocean. They found that, compared with existing cultures, natural bacterioplankton have smaller genomes, fewer gene duplications, and are depleted in guanine and cytosine, noncoding nucleotides, and genes encoding transcription, signal transduction, and noncytoplasmic proteins. These findings provide strong evidence that genome streamlining and oligotrophy are prevalent features among diverse, free-living bacterioplankton, whereas existing laboratory cultures consist primarily of copiotrophs. The apparent ubiquity of metabolic specialization and mixotrophy, as predicted from single cell genomes, also may contribute to the difficulty in bacterioplankton cultivation. Using metagenome fragment recruitment against single cell genomes, they show that the global distribution of surface ocean bacterioplankton correlates with temperature and latitude and is not limited by dispersal at the time scales required for nucleotide substitution to exceed the current operational definition of bacterial species. Single cell genomes with highly similar small subunit rRNA gene sequences exhibited significant genomic and biogeographic variability, highlighting challenges in the interpretation of individual gene surveys and metagenome assemblies in environmental microbiology. Their study demonstrates the utility of single cell genomics for gaining an improved understanding of the composition and dynamics of natural microbial assemblages.
October 2013 brings a new scientific ocean drilling program to the community, one founded on the principle that excellent scientific outcomes, combined with practical planning and efficient operations, will provide outstanding opportunities for future generations of researchers and educators. Despite an identical acronym to its predecessor (the Integrated Ocean Drilling Program), this new program, called the International Ocean Discovery Program (IODP), constitutes a forward looking and societally relevant roadmap for scientific ocean drilling. This opinion article is written by Susan Humphris (the new chair of the new JOIDES Resolution Facility Board) and Anthony Koppers (the outgoing chair of the US Advisory Committee to IODP) and is relevant to cruise planning for IODP.

Don’t forget to email me with any items you'd like to share in future newsletters! You are what makes our deep biosphere community!
Matthew Janicak
Administrative Assistant
Center for Dark Energy Biosphere Investigations (C-DEBI)
University of Southern California
3616 Trousdale Pkwy, AHF 209, Los Angeles, CA 90089-0371
Phone: 708-691-9563, Fax: 213-740-2437

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