C-DEBI Newsletter – September 3, 2019

Publications & Press

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Frontiers in Microbiology
Ecology of Subseafloor Crustal Biofilms – NEW!
Gustavo A. Ramírez*, Arkadiy I. Garber, Aurélien Lecoeuvre, Timothy D’Angelo, Charles Geoffrey Wheat*, Beth N. Orcutt*
*C-DEBI Contribution 455

The crustal subseafloor is the least explored and largest biome on Earth. Interrogating crustal life is difficult due to habitat inaccessibility, low-biomass and contamination challenges. Subseafloor observatories have facilitated the study of planktonic life in crustal aquifers, however, studies of life in crust-attached biofilms are rare. Here, we investigate biofilms grown on various minerals at different temperatures over 1–6 years at subseafloor observatories in the Eastern Pacific. To mitigate potential sequence contamination, we developed a new bioinformatics tool – TaxonSluice. We explore ecological factors driving community structure and potential function of biofilms by comparing our sequence data to previous amplicon and metagenomic surveys of this habitat. We reveal that biofilm community structure is driven by temperature rather than minerology, and that rare planktonic lineages colonize the crustal biofilms. Based on 16S rRNA gene overlap, we partition metagenome assembled genomes into planktonic and biofilm fractions and suggest that there are functional differences between these community types, emphasizing the need to separately examine each to accurately describe subseafloor microbe-rock-fluid processes. Lastly, we report that some rare lineages present in our warm and anoxic study site are also found in cold and oxic crustal fluids in the Mid-Atlantic Ridge, suggesting global crustal biogeography patterns.

Geochimica et Cosmochimica Acta
Carbon cycling in low temperature hydrothermal systems: The Dorado Outcrop – NEW!
James McManus*, Charles Geoffrey Wheat*, Wolfgang Bach
*C-DEBI Contribution 486

We sampled low temperature (<15 °C) hydrothermal fluids that discharge from the Dorado Outcrop on the eastern flank of the Cocos Ridge. Our sampling techniques included discrete sample collection using DSV Alvin and autonomous time-series samplers deployed using RSV Jason II. The sampled fluids are enriched in dissolved inorganic carbon (DIC) by ∼0.10 mM and have a δ¹³C_DICthat is on average between 0.2 and 0.5‰ lower than the surrounding bottom seawater. Assuming that the measured DIC enrichment is representative of low temperature hydrothermal systems, the magnitude of the DIC source to the ocean would be 1 × 10¹² mol C/y, which is roughly the same magnitude as the high temperature hydrothermal source, but is more than a factor of three smaller than the estimated rate of carbon removal via carbonate precipitation within the ocean crust. Based on an isotope balance of the discharging fluids, which considers added sources of both basalt-derived inorganic and marine-derived organic carbon, the net DIC carbon isotope signature of vent fluids is most consistent with a primary carbon source from seawater (95.9%), plus a component from the weathering of basalt (3.4%) with a δ¹³C value of −6‰, and a component from organic matter degradation (0.7%), with a δ¹³C value of −22‰. This particular balance places the upper limit of organic carbon respiration at ∼0.3 × 10¹² mol C/y; however, if our DIC input estimate is too high, then the isotope balance requires a larger organic carbon component, which is not consistent with the dissolved oxygen and nitrate data. Although low temperature hydrothermal systems are often thought to be important locations for carbonate precipitation, there is little evidence for current carbonate precipitation at Dorado Outcrop. Similar trends in DIC are observed at North Pond, another low temperature (<15 °C) ridge flank hydrothermal system. These data suggest that much of the current ridge flank discharge is a source of DIC to the ocean.

mSphere
Quantitatively Partitioning Microbial Genomic Traits among Taxonomic Ranks across the Microbial Tree of Life – NEW!
Taylor Royalty*, Andrew D. Steen
*C-DEBI Contribution 487

Widely used microbial taxonomies, such as the NCBI taxonomy, are based on a combination of sequence homology among conserved genes and historically accepted taxonomies, which were developed based on observable traits such as morphology and physiology. A recently proposed alternative taxonomy database, the Genome Taxonomy Database (GTDB), incorporates only sequence homology of conserved genes and attempts to partition taxonomic ranks such that each rank implies the same amount of evolutionary distance, regardless of its position on the phylogenetic tree. This provides the first opportunity to completely separate taxonomy from traits and therefore to quantify how taxonomic rank corresponds to traits across the microbial tree of life. We quantified the relative abundances of clusters of orthologous group functional categories (COG-FCs) as a proxy for traits within the lineages of 13,735 cultured and uncultured microbial lineages from a custom-curated genome database. On average, 41.4% of the variation in COG-FC relative abundance is explained by taxonomic rank, with domain, phylum, class, order, family, and genus explaining, on average, 3.2%, 14.6%, 4.1%, 9.2%, 4.8%, and 5.5% of the variance, respectively (P < 0.001 for all). To our knowledge, this is the first work to quantify the variance in metabolic potential contributed by individual taxonomic ranks. A qualitative comparison between the COG-FC relative abundances and genus-level phylogenies, generated from published concatenated protein sequence alignments, further supports the idea that metabolic potential is taxonomically coherent at higher taxonomic ranks. The quantitative analyses presented here characterize the integral relationship between diversification of microbial lineages and the metabolisms which they host.

Environmental Microbiology
Minireview: demystifying microbial reaction energetics – NEW!
Jan P. Amend*, Douglas E. LaRowe*
*C-DEBI Contribution 489

The biology literature is rife with misleading information on how to quantify catabolic reaction energetics. The principal misconception is that the sign and value of the standard Gibbs energy (ΔG_r⁰) define the direction and energy yield of a reaction; they do not. ΔG_r⁰ is one part of the actual Gibbs energy of a reaction (ΔG_r), with a second part accounting for deviations from the standard composition. It is also frequently assumed that ΔG_r⁰ applies only to 25 °C and 1 bar; it does not. ΔG_r⁰ is a function of temperature and pressure. Here, we review how to determine ΔG_r as a function of temperature, pressure and chemical composition for microbial catabolic reactions, including a discussion of the effects of ionic strength on ΔG_r and highlighting the large effects when multi‐valent ions are part of the reaction. We also calculate ΔG_r for five example catabolisms at specific environmental conditions: aerobic respiration of glucose in freshwater, anaerobic respiration of acetate in marine sediment, hydrogenotrophic methanogenesis in a laboratory batch reactor, anaerobic ammonia oxidation in a wastewater reactor and aerobic pyrite oxidation in acid mine drainage. These examples serve as templates to determine the energy yields of other catabolic reactions at environmentally relevant conditions.

Frontiers in Microbiology
Differences in Applied Redox Potential on Cathodes Enrich for Diverse Electrochemically Active Microbial Isolates From a Marine Sediment – NEW!
Bonita R. Lam, Casey R. Barr, Annette R. Rowe*, Kenneth H. Nealson
*C-DEBI Contribution 490

The diversity of microbially mediated redox processes that occur in marine sediments is likely underestimated, especially with respect to the metabolisms that involve solid substrate electron donors or acceptors. Though electrochemical studies that utilize poised potential electrodes as a surrogate for solid substrate or mineral interactions have shed some much needed light on these areas, these studies have traditionally been limited to one redox potential or metabolic condition. This work seeks to uncover the diversity of microbes capable of accepting cathodic electrons from a marine sediment utilizing a range of redox potentials, by coupling electrochemical enrichment approaches to microbial cultivation and isolation techniques. Five lab-scale three-electrode electrochemical systems were constructed, using electrodes that were initially incubated in marine sediment at cathodic or electron-donating voltages (five redox potentials between −400 and −750 mV versus Ag/AgCl) as energy sources for enrichment. Electron uptake was monitored in the laboratory bioreactors and linked to the reduction of supplied terminal electron acceptors (nitrate or sulfate). Enriched communities exhibited differences in community structure dependent on poised redox potential and terminal electron acceptor used. Further cultivation of microbes was conducted using media with reduced iron (Fe⁰, FeCl₂) and sulfur (S⁰) compounds as electron donors, resulting in the isolation of six electrochemically active strains. The isolates belong to the genera Vallitalea of the Clostridia, Arcobacter of the Epsilonproteobacteria, Desulfovibrio of the Deltaproteobacteria, and Vibrio and Marinobacter of the Gammaproteobacteria. Electrochemical characterization of the isolates with cyclic voltammetry yielded a wide range of midpoint potentials (99.20 to −389.1 mV versus Ag/AgCl), indicating diverse metabolic pathways likely support the observed electron uptake. Our work demonstrates culturing under various electrochemical and geochemical regimes allows for enhanced cultivation of diverse cathode-oxidizing microbes from one environmental system. Understanding the mechanisms of solid substrate oxidation from environmental microbes will further elucidation of the ecological relevance of these electron transfer interactions with implications for microbe-electrode technologies.
 

Meetings & Activities

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C-DEBI: Networked Speaker Series Seminar, THIS THURSDAY, September 5, 2019, 12:30pm PDT – NEW!
Join us online for our latest Networked Speaker Series Seminar with Taylor Royalty (University of Tennessee) on "Quantitatively partitioning microbial genomic traits among taxonomic ranks: implications for subsurface microbial communities."

UNOLS: Deep Submergence Science Committee (DeSSC) Call for Nominations
Applications due September 13, 2019.

ISSM: Submit your abstracts to the 11th ISSM conference, June 14-19, 2020, Utrecht, The Netherlands
Abstracts due in September 2019.

UCSD: Guaymas Science Symposium, September 16, 2019, Scripps Forum

Ongoing Activities:

• C-DEBI: Rolling call for Community Workshop support
• C-DEBI: Protocols.io Group Page
• C-DEBI: Subseafloor Cultures Database
• C-DEBI: Join us on LinkedIn

 

Best, 

 

Matt

 

— 

Matthew Janicak

Data Manager

Center for Dark Energy Biosphere Investigations (C-DEBI)

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