Geochemical and Metagenomic Characterization of Jinata Onsen, a Proterozoic-Analog Hot Spring, Reveals Novel Microbial Diversity including Iron-Tolerant Phototrophs and Thermophilic Lithotrophs

Abstract

Hydrothermal systems, including terrestrial hot springs, contain diverse geochemical conditions that vary over short spatial scales due to progressive interactions between reducing hydrothermal fluids, the oxygenated atmosphere, and, in some cases, seawater. At Jinata Onsen on Shikinejima Island, Japan, an intertidal, anoxic, iron-rich hot spring mixes with the oxygenated atmosphere and seawater over short spatial scales, creating diverse chemical potentials and redox pairs over a distance of ~10 m. We characterized geochemical conditions along the outflow of Jinata Onsen as well as the microbial communities present in biofilms, mats, and mineral crusts along its traverse using 16S rRNA gene amplicon and genome-resolved shotgun metagenomic sequencing. Microbial communities significantly changed downstream as temperatures and dissolved iron concentrations decreased and dissolved oxygen increased. Biomass was more limited near the spring source than downstream, and primary productivity appeared to be fueled by the oxidation of ferrous iron and molecular hydrogen by members of Zetaproteobacteria and Aquificae. The microbial community downstream was dominated by oxygenic Cyanobacteria. Cyanobacteria are abundant and active even at ferrous iron concentrations of ~150 μM, which challenges the idea that iron toxicity limited cyanobacterial expansion in Precambrian oceans. Several novel lineages of Bacteria are also present at Jinata Onsen, including previously uncharacterized members of the phyla Chloroflexi and Calditrichaeota, positioning Jinata Onsen as a valuable site for the future characterization of these clades.

Genomic Insights of “Candidatus Nitrosocaldaceae” Based on Nine New Metagenome-Assembled Genomes, Including “Candidatus Nitrosothermus” Gen Nov. and Two New Species of “Candidatus Nitrosocaldus”

“…N. cavascurensis SCU2” ( Abby et al, 2018 ) and “ Ca. N. islandicus” ( Daebeler et al, 2018 ), a MAG (Thaumarchaeota archaeon J079) obtained from a Japanese hot spring ( Ward et al, 2019 ) was also assigned to this family based on phylogenetic analysis. In phylogenetic trees based on alignments of 122 archaeal marker genes ( Figure 1A ), a monophyletic group containing the two cultivated members of “ Ca .…”

“…Nitrosothermus” ( Supplementary Table S4 ). These two enzymes could potentially provide ammonia under aerobic conditions ( Abdelal et al, 1982 ), which could be valuable given the low concentration of ammonia in these springs ( Hedlund et al, 2012 ; Hou et al, 2013 ; Ward et al, 2019 ) and many other alkaline geothermal springs ( Holloway et al, 2011 ). However, the potential function of these genes in ammonia production in “ Ca.…”

Genomic sequence analysis of Dissulfurirhabdus thermomarina SH388 and proposed reassignment to Dissulfurirhabdaceae fam. nov.

“…Phylogenetic analyses followed methods described previously [16, 17], and summarized here. Additional Desulfobulbales genomes were downloaded from the National Center for Biotechnology Information (NCBI) GenBank and WGS databases.…”

Taxonomic Novelty and Distinctive Genomic Features of Hot Spring Cyanobacteria

“…Several strategies have been used to recover partial genomes of hot spring cyanobacteria from metagenomes, including mapping contigs against reference genomes (Bhaya et al, 2007) and the use of binning tools (Thiel et al, 2017;Alcorta et al, 2018;Ward et al, 2019). Metagenomes from the binning-based studies were reanalyzed here, allowing for better genome recovery in terms of contig numbers and completeness.…”