Oceanic Crustal Fluid Single Cell Genomics Complements Metagenomic and Metatranscriptomic Surveys With Orders of Magnitude Less Sample Volume

Abstract

Fluids circulating through oceanic crust play important roles in global biogeochemical cycling mediated by their microbial inhabitants, but studying these sites is challenged by sampling logistics and low biomass. Borehole observatories installed at the North Pond study site on the western flank of the Mid-Atlantic Ridge have enabled investigation of the microbial biosphere in cold, oxygenated basaltic oceanic crust. Here we test a methodology that applies redox-sensitive fluorescent molecules for flow cytometric sorting of cells for single cell genomic sequencing from small volumes of low biomass (approximately 103 cells ml–1) crustal fluid. We compare the resulting genomic data to a recently published paired metagenomic and metatranscriptomic analysis from the same site. Even with low coverage genome sequencing, sorting cells from less than one milliliter of crustal fluid results in similar interpretation of dominant taxa and functional profiles as compared to ‘omics analysis that typically filter orders of magnitude more fluid volume. The diverse community dominated by Gammaproteobacteria, Bacteroidetes, Desulfobacterota, Alphaproteobacteria, and Zetaproteobacteria, had evidence of autotrophy and heterotrophy, a variety of nitrogen and sulfur cycling metabolisms, and motility. Together, results indicate fluorescence activated cell sorting methodology is a powerful addition to the toolbox for the study of low biomass systems or at sites where only small sample volumes are available for analysis.

Comparative proteomics of a versatile, marine, iron‐oxidizing chemolithoautotroph

“…Some genera implicated in microbially influenced corrosion (MIC) (e.g., Desulfobulbus and Desulfovibrio ) and/or characterized by Fe‐reduction function (e.g., Geobacter ) also contain homologs of GrcJ. Metagenome‐assembled‐genomes and single‐cell amplified genomes associated with uncultivated Nitrospirae , Betaproteobacteria , and Zetaproteobacteria from terrestrial groundwater, marine subsurface, and marine hydrothermal environments also expand the diversity of grcJ (Anantharaman et al, 2016; D'Angelo et al, 2022; McAllister et al, 2020; Probst et al, 2017; Tian et al, 2020; Tully et al, 2018). Other notable chemolithoautotrophic microorganisms that contain homologs of grcJ include the recently described Mn‐oxidizing “ Candidatus Manganitrophus noduliformans” and Ramlibacter lithotrophicus (Yu & Leadbetter, 2020).…”

Transformation of low‐molecular‐weight organic acids by microbial endoliths in subsurface mafic and ultramafic igneous rock

“…Nevertheless, continued efforts based on recently published techniques [e.g. using FACS to concentrate biomass prior to molecular characterization (Goordial et al ., 2021; D'Angelo et al ., 2022)] could be employed to overcome such limitations in the future.…”