C-DEBI Newsletter – February 18, 2020

Publications & Press

mSystems
Validating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of Zetaproteobacteria Iron Mats at Marine Hydrothermal Vents – NEW!
Sean M. McAllister, Shawn W. Polson, David A. Butterfield, Brian T. Glazer, Jason B. Sylvan*, Clara S. Chan
*C-DEBI Contribution 501

Zetaproteobacteria create extensive iron (Fe) oxide mats at marine hydrothermal vents, making them an ideal model for microbial Fe oxidation at circumneutral pH. Comparison of neutrophilic Fe oxidizer isolate genomes has revealed a hypothetical Fe oxidation pathway, featuring a homolog of the Fe oxidase Cyc2 from Acidithiobacillus ferrooxidans. However, Cyc2 function is not well verified in neutrophilic Fe oxidizers, particularly in Fe-oxidizing environments. Toward this, we analyzed genomes and metatranscriptomes of Zetaproteobacteria, using 53 new high-quality metagenome-assembled genomes reconstructed from Fe mats at Mid-Atlantic Ridge, Mariana Backarc, and Loihi Seamount (Hawaii) hydrothermal vents. Phylogenetic analysis demonstrated conservation of Cyc2 sequences among most neutrophilic Fe oxidizers, suggesting a common function. We confirmed the widespread distribution of cyc2 and other model Fe oxidation pathway genes across all represented Zetaproteobacteria lineages. High expression of these genes was observed in diverse Zetaproteobacteria under multiple environmental conditions and in incubations. The putative Fe oxidase gene cyc2 was highly expressed in situ, often as the top expressed gene. The cyc2 gene showed increased expression in Fe(II)-amended incubations, with corresponding increases in carbon fixation and central metabolism gene expression. These results substantiate the Cyc2-based Fe oxidation pathway in neutrophiles and demonstrate its significance in marine Fe-mineralizing environments.

Frontiers in Environmental Science
Using Cathodic Poised Potential Experiments to Investigate Extracellular Electron Transport in the Crustal Deep Biosphere of North Pond, Mid-Atlantic Ridge – NEW!
Rose M. Jones, Timothy D’Angelo, Beth N. Orcutt*
*C-DEBI Contribution 503

The crustal sub-seafloor covers a large portion of the Earth’s surface but is poorly understood as a habitat for life. It is unclear what metabolisms support the microscopic cells that have been observed, and how they survive under resource limitation. As the deep crustal subsurface represents a significant portion of the Earth’s surface, microbially mediated reactions may therefore be significant contributors to biogeochemical cycling. In the present study, we used electrochemical techniques to investigate the possibility that crustal subsurface microbial groups can use the solid rock matrix (basalts, etc.) as a source of electrons for redox reactions via extracellular electron transfer (EET). Subsurface crustal fluids and mineral colonization experiments from the cool and oxic basaltic crustal subsurface at the North Pond site on the western flank of the Mid-Atlantic Ridge were used as inocula in cathodic poised potential experiments. Electrodes in oxic microbial fuel cells (MFCs) were poised at −200 mV versus a standard hydrogen electrode to mimic the delivery of electrons in an energy range equivalent to iron oxidation. In this way, microbes that use reduced iron in solid minerals for energy were selected for from the general community onto the electrode surface for interrogation of EET activity, and potential identification by scanning electron microscopy (SEM) and DNA sequencing. The results document that there are cathodic EET-capable microbial groups in the low biomass crustal subsurface at this site. The patterns of current generation in the experiments indicate that these microbial groups are active but likely not growing under the low-resource condition of the experiments, consistent with other studies of activity versus growth in the deep biosphere. Lack of growth stymied attempts to determine the phylogeny of EET-capable microbial groups from this habitat, but the results indicate that these microbial groups are a small part of the overall crustal deep biosphere community. This first demonstration of using electromicrobiology techniques to investigate microbial metabolic potential in the crustal deep biosphere reveals the challenges and opportunities for studying EET in the crustal deep biosphere.

The ISME Journal
Metabolic potentials of archaeal lineages resolved from metagenomes of deep Costa Rica sediments – NEW!
Ibrahim F. Farag, Jennifer F. Biddle*, Rui Zhao, Amanda J. Martino*, Christopher H. House*, Rosa León-Zayas
*C-DEBI Contribution 517

Numerous archaeal lineages are known to inhabit marine subsurface sediments, although their distributions, metabolic capacities, and interspecies interactions are still not well understood. Abundant and diverse archaea were recently reported in Costa Rica (CR) margin subseafloor sediments recovered during IODP Expedition 334. Here, we recover metagenome-assembled genomes (MAGs) of archaea from the CR margin and compare them to their relatives from shallower settings. We describe 31 MAGs of six different archaeal lineages (Lokiarchaeota, Thorarchaeota, Heimdallarchaeota, Bathyarcheota, Thermoplasmatales, and Hadesarchaea) and thoroughly analyze representative MAGs from the phyla Lokiarchaeota and Bathyarchaeota. Our analysis suggests the potential capability of Lokiarchaeota members to anaerobically degrade aliphatic and aromatic hydrocarbons. We show it is genetically possible and energetically feasible for Lokiarchaeota to degrade benzoate if they associate with organisms using nitrate, nitrite, and sulfite as electron acceptors, which suggests a possibility of syntrophic relationships between Lokiarchaeota and nitrite and sulfite reducing bacteria. The novel Bathyarchaeota lineage possesses an incomplete methanogenesis pathway lacking the methyl coenzyme M reductase complex and encodes a noncanonical acetogenic pathway potentially coupling methylotrophy to acetogenesis via the methyl branch of Wood–Ljungdahl pathway. These metabolic characteristics suggest the potential of this Bathyarchaeota lineage to be a transition between methanogenic and acetogenic Bathyarchaeota lineages. This work expands our knowledge about the metabolic functional repertoire of marine benthic archaea.