C-DEBI Newsletter – April 1, 2015

Hot Off the Press: Bacillus rigiliprofundi sp. nov., an endospore forming, Mn-oxidizing, moderately halophilic bacterium isolated from deep subseafloor basaltic crust (C-DEBI Contribution 257) in the International Journal of Systematic and Evolutionary Microbiology
Authors: C-DEBI researcher Sylvan et al. A facultatively anaerobic bacterium, designated strain 1MBB1T, was isolated from basaltic breccia collected from 341 meters below seafloor by seafloor drilling of Rigil Guyot during Integrated Ocean Drilling Program Expedition 330. The cells were straight rods 0.5 μm wide and 1-3 μm long that occurred singly and in chains. Strain 1MBB1T stained Gram-positive. Catalase and oxidase were produced. The isolate grew optimally at 30˚C and pH 7.5, and could grow with up to 12% (w/v) NaCl. The DNA G+C base composition was 40.5 mol%. The major cellular fatty acids were C16:1ω11c (26.5%), anteiso-C15:0 (19.5%), C16:0 (18.7%) and iso-C15:0 (10.4%), and the cell wall diamino acid was meso¬-diaminopimelic acid. Endospores of strain 1MBB1T oxidized Mn(II) to Mn(IV), and siderophore production by vegetative cells was positive. Phylogenetic analysis of the 16S rRNA gene indicated that strain 1MBB1T was a member of the family Bacillaceae, with Bacillus foraminis CV53T and Bacillus novalis LMG21837T being the closest phylogenetic neighbors (96.5 and 96.2% similarity, respectively). This is the first new species described from deep subseafloor basaltic crust. On the basis of polyphasic analysis, we conclude that strain 1MBB1T is a novel species of the genus Bacillus, for which we propose the name Bacillus rigiliprofundi sp. nov. The type strain is 1MBB1T (=NCMA B78T =LMG 28275T).

Hot Off the Press: Chapter 7: Current perspectives on microbial strategies for survival under extreme nutrient starvation: evolution and ecophysiology (C-DEBI Contribution 243) in Life in Extreme Environments 2: Microbial Evolution under Extreme Conditions, ed. Bakermans, De Gruyter
Authors: C-DEBI researchers Glass, Batmalle Kretz et al. [From the book description:] Today’s microorganisms represent the vast majority of biodiversity on Earth and have survived nearly 4 billion years of evolutionary change. However, we still know little about the processes of evolution as applied to microorganisms and microbial populations. Microbial evolution occurred and continues to take place in a vast variety of environmental conditions that range from anoxic to oxic, from hot to cold, from free-living to symbiotic, etc. Some of these physicochemical conditions are considered “extreme”, particularly when inhabitants are limited to microorganisms. It is easy to imagine that microbial life in extreme environments is somehow more constrained and perhaps subjected to different evolutionary pressures. But what do we actually know about microbial evolution under extreme conditions and how can we apply that knowledge to other conditions? Appealingly, extreme environments with their relatively limited numbers of inhabitants can serve as good model systems for the study of evolutionary processes.

Global dispersion and local diversification of the methane seep microbiome, in PNAS
Co-authors include C-DEBI researcher Biddle and Extent Theme Team Leader Teske. Methane seeps are widespread seafloor ecosystems shaped by the emission of gas from seabed reservoirs. The microorganisms inhabiting methane seeps transform the chemical energy in methane to products that sustain rich benthic communities around the gas leaks. Despite the biogeochemical relevance of microbial methane removal at seeps, the global diversity and dispersion of seep microbiota remain unknown. Here we determined the microbial diversity and community structure of 23 globally distributed methane seeps and compared these to the microbial communities of 54 other seafloor ecosystems, including sulfate–methane transition zones, hydrothermal vents, coastal sediments, and deep-sea surface and subsurface sediments. We found that methane seep communities show moderate levels of microbial richness compared with other seafloor ecosystems and harbor distinct bacterial and archaeal taxa with cosmopolitan distribution and key biogeochemical functions. The high relative sequence abundance of ANME (anaerobic methanotrophic archaea), as well as aerobic Methylococcales, sulfate-reducing Desulfobacterales, and sulfide-oxidizing Thiotrichales, matches the most favorable microbial metabolisms at methane seeps in terms of substrate supply and distinguishes the seep microbiome from other seafloor microbiomes. The key functional taxa varied in relative sequence abundance between different seeps due to the environmental factors, sediment depth and seafloor temperature. The degree of endemism of the methane seep microbiome suggests a high local diversification in these heterogeneous but long-lived ecosystems. Our results indicate that the seep microbiome is structured according to metacommunity processes and that few cosmopolitan microbial taxa mediate the bulk of methane oxidation, with global relevance to methane emission in the ocean.

Biological oceanography: Life in the deepest depths, in Nature Geoscience: News and Views
Author: C-DEBI Activity Theme Team Lead Orcutt; companion piece to C-DEBI Contribution 254 (C-DEBI Co-I D’Hondt et al.). Deep abyssal clay sediments in organic-poor regions of the ocean present challenging conditions for life. Techniques for identifying cells at extremely low concentrations demonstrate that aerobic microbes are found throughout these deep clays in as much of 37% of the global ocean. 

Frontiers in Microbiology: Seeking Contributions for Special Topic on Ocean Crust Geomicrobiology
A special issue of Frontiers in Microbiology journal on the topic of “Recent Advances in Geomicrobiology of the Ocean Crust” is seeking contributions from the C-DEBI community. Articles in the research topic are in tribute to the late Katrina J. Edwards, who was a pioneer in diverse aspects of exploring life in oceanic crust. For more information, contact topic editors Beth Orcutt, Cara Santelli, or Jason Sylvan, or visit the journal webpage.

Simons Foundation, Howard Hughes Medical Institute and Bill & Melinda Gates Foundation: 2016 Faculty Scholars Competition
Three of the nation’s largest philanthropies, the Howard Hughes Medical Institute (HHMI), the Bill & Melinda Gates Foundation, and the Simons Foundation are announcing a new partnership to provide much needed research support to outstanding early-career scientists in the United States. Through the new Faculty Scholars Program, the philanthropies will invest a total of $148 million in research support over the program’s first five years. They will award up to 70 grants every 2.5 years to promising scientists who have great potential to make unique contributions to their field. This is the first collaboration between HHMI, the Bill & Melinda Gates Foundation, and the Simons Foundation. Awardees will receive a five-year, non-renewable grant whose size will be based on several factors, including the amount of external funding the scientist has at the time of the grant. The grants will range from $100,000 to $400,000 per year for direct costs. The awardee’s institution will be given an additional 20 percent of the yearly grant for indirect (or administrative) costs. Faculty Scholars are required to devote at least 50 percent of their total effort to the direct conduct of research. The competition is open to basic researchers and physician scientists at more than 220 eligible U.S. institutions. Applicants must be using molecular, genetic, computational or theoretical approaches to address fundamental biological or biomedical problems. Applicants must have more than four but fewer than 10 years of post-training professional experience. Application deadline: July 28, 2015.

DCO: Deep Life Community Call for Proposals 
The Deep Life Community (DLC) of the Deep Carbon Observatory invites proposals for short-term funding of exploratory projects and/or activities aimed at addressing the DLC’s decadal goals and/or strengthening the international DLC community and its abilities to generate funding for new and ongoing initiatives. The DLC, which explores the evolutionary and functional diversity of Earth’s deep biosphere and its interactions with the carbon cycle, embraces three primary Decadal Goals: 1) Determine the processes that define the diversity and distribution of deep life as it relates to the carbon cycle; 2) Determine the environmental limits of deep life; and 3) Determine the interactions between deep life and carbon cycling. The DLC has identified a number of key tasks of direct relevance to our ability to reach our decadal goals. For example, we must improve life detection capabilities, develop new tracer approaches to track the flow of carbon into biomolecules and cells, and advance our ability to measure the interrelationship between composition of carbonaceous materials and deep life. The DLC Steering Committee encourages submission of ideas for modest short-term support that will address these and other relevant or meritorious efforts with high potential to attract new funding. Examples of supported activities include: 1) Laboratory research; 2) Travel to field sites to collect samples of key importance; 3) Support of working groups and workshops to synthesize data for publication of Deep Life research, and/or to develop interdisciplinary collaborations; 4) Travel to work with collaborators on the preparation of new proposals; or 5) Other activities that would advance Deep Life Science. A successful proposal will meet the following criteria: 1) Requests for support must address unresolved questions related to deep life and its decadal goals; 2) Requests must identify the potential for attracting additional funding resources and the description must outline a plan for seeking new research support; 3) the amount of requested support can range from $1000 to $25,000; and 4) The supported project/activity must conclude within six-months of receiving the award. Application deadline: May 01, 2015.

DCO: Call for Proposals Census of Deep Life Sequencing Opportunities
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 or Bacterial and Archaeal sequences of very high quality that span V6 regions. The V6 analyses allow accurate sequence determinations and provide rich datasets in terms of numbers of reads per sample. These data can be compared at the taxonomic level when targeting different hypervariable regions but cluster/diversity analyses will be restricted to comparisons of samples for which there are data available from the very same hypervariable region. Shotgun metagenomic DNA sequencing for key samples can also be performed. Application deadline: June 01, 2015.

IODP: Apply to sail on Expedition 364 Chicxulub Impact Crater
Expedition 364 will address several questions related to large impact crater formation on Earth and other planets and the effects of large impacts on the Earth’s environment and ecology. The expedition target is the unique Chicxulub impact crater, Mexico, which is the only known terrestrial impact structure that has been directly linked to a mass extinction event (the K-Pg mass extinction). This expedition aims to drill and core into the Chicxulub impact structure to recover cores from, and above, the peak ring. The expedition objectives are to understand what rocks comprise a topographic peak ring and how peak rings formed, how rocks are weakened during large impacts to allow them to collapse and form relatively wide, flat craters, what caused the environmental changes that led to a mass extinction and what insights arise from biologic recovery in the Paleogene, and gain insight into what effect a large impact has on the deep subsurface biosphere and if impacts generate habitats for chemosynthetic life. Opportunities exist for researchers, including graduate students, in the following fields: paleontology, sedimentology, microbiology, organic geochemistry, inorganic geochemistry, structural geology, impact petrology, metamorphic petrology, paleomagnetics, physical properties, geophysics and petrophysics/downhole logging. Other areas of expertise may be considered. Additional information on this expedition can be found here: http://www.eso.ecord.org/expeditions/364/364.php. The deadline to apply is May 08, 2015.

NSF: Geobiology and Low-Temperature Geochemistry Program Solicitation
The Geobiology and Low-Temperature Geochemistry Program focuses on geochemical processes in terrestrial Earth’s surface environmental systems, as well as the interaction of geochemical and biological processes. The program supports field, laboratory, theoretical, and modeling studies of these processes and related mechanisms at all spatial and temporal scales. Studies may address: 1) inorganic and/or organic geochemical processes occurring at or near the Earth’s surface now and in the past, and across the broad spectrum of interfaces ranging in scale from planetary and regional to mineral-surface and supramolecular; 2) the role of life in the transformation and evolution of Earth’s geochemical cycles; 3) surficial chemical and biogeochemical systems and cycles, including their modification through environmental change and human activities; 4) low-temperature aqueous geochemical processes; 5) mineralogy and chemistry of earth materials; 6) geomicrobiology and biomineralization processes; and 7) medical mineralogy and geochemistry. The Program encourages research that focuses on geochemical processes as they are coupled with physical and biological processes in the critical zone. The Program also supports work on the development of tools, methods, and models for the advancement of low-temperature geochemistry and geobiology. Proposals accepted anytime.

NSF: Dimensions of Biodiversity Program Solicitation
Full proposal deadline: April 09, 2015.

Meetings, Workshops and Activities

• Submit an abstract but do not make payment
• Complete the form
• Give details of a referee
• Ensure your referee replies to our email