ENVIRONMENTAL GENOMICS REVEALS ABUNDANT AUTOTROPHIC AND SULFATE-REDUCING NITROSPIROTA BACTERIA INHABITING DEEP SUBSEAFLOOR CRUSTAL FLUIDS FROM THE JUAN DE FUCA RIDGE FLANK
ENVIRONMENTAL GENOMICS REVEALS ABUNDANT AUTOTROPHIC AND SULFATE-REDUCING NITROSPIROTA BACTERIA INHABITING DEEP SUBSEAFLOOR CRUSTAL FLUIDS FROM THE JUAN DE FUCA RIDGE FLANK
Date
2021
Authors
Sullivan, Clarisse Eleanor Santos
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Rappé, Michael S.
Department
Oceanography
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Abstract
Along the eastern flank of the Juan de Fuca Ridge (JdFR), boreholes drilled through sediment and into the oceanic crust access deep subseafloor fluids that support a unique microbiome. One group of bacteria that has been previously detected in high relative abundance in gene- and genome-based surveys of JdFR crustal fluids belong to the phylum Nitrospirota. In this study, metagenomes from crustal fluids collected from boreholes along the JdFR were used to recover Nitrospirota metagenome-assembled genomes (MAGs), which were subsequently interrogated by phylogenomics, metabolic reconstruction, and for population genetic characteristics. Nine Nitrospirota MAGs ranging in size from 0.60 mega base pairs (Mbp) to 2.34 Mbp were recovered, including five high quality genomes that were at least 95% complete. Genome phylogenies based on concatenated alignments of single-copy core genes placed the JdFR Nitrospirota into three distinct lineages within the Class Thermodesulfovibrionia, and revealed that the JdFR Nitrospirota are closely related to Nitrospirota MAGs previously recovered from sulfide deposits and solid substrates incubated within a JdFR borehole. Competitive recruitment of metagenome sequence reads revealed a single lineage dominated the Nitrospirota fraction of the crustal fluid microbiome. Metabolic reconstructions indicated the shared presence of genes involved in dissimilatory sulfate reduction, carbon fixation, and gluconeogenesis. Fine-scale genetic heterogeneity was investigated within two highly similar (>99% average nucleotide identity) Nitrospirota genomes recovered from separate boreholes along the JdFR flank. Read recruitment and whole genome comparisons revealed little intrapopulation variation, but subtle genetic discontinuity in the subsurface environment in JdFR.
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Biological oceanography,
Crustal fluids,
Dissimilatory sulfate reduction,
Juan de Fuca Ridge,
Nitrospirota,
Subsurface,
Wood-Ljungdahl pathway
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65 pages
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