Genomic evidence for distinct carbon substrate preferences and ecological niches of Bathyarchaeota in estuarine sediments

Abstract

Investigations of the biogeochemical roles of benthic Archaea in marine sediments are hampered by the scarcity of cultured representatives. In order to determine their metabolic capacity, we reconstructed the genomic content of four widespread uncultured benthic Archaea recovered from estuary sediments at 48% to 95% completeness. Four genomic bins were found to belong to different subgroups of the former Miscellaneous Crenarcheota Group (MCG) now called Bathyarchaeota: MCG-6, MCG-1, MCG-7/17 and MCG-15. Metabolic predictions based on gene content of the different genome bins indicate that subgroup 6 has the ability to hydrolyse extracellular plant-derived carbohydrates, and that all four subgroups can degrade detrital proteins. Genes encoding enzymes involved in acetate production as well as in the reductive acetyl-CoA pathway were detected in all four genomes inferring that these Archaea are organo-heterotrophic and autotrophic acetogens. Genes involved in nitrite reduction were detected in all Bathyarchaeota subgroups and indicate a potential for dissimilatory nitrite reduction to ammonium. Comparing the genome content of the different Bathyarchaeota subgroups indicated preferences for distinct types of carbohydrate substrates and implicitly, for different niches within the sedimentary environment.

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

“…They are more complete than those typically derived using single-cell genomics 4 and are of similar quality to those reported in other studies considering MAGs 10,11,44 . We have focused on these genomes, which represent only ~12% of the 64,295 recovered bins, as they are of sufficient quality to inform analyses such as resolving phylogenetic relationships 4,30 and comparing inter-and intralineage genomic features [45][46][47] . Importantly, these results demonstrate that a large amount of microbial diversity remains to be genomically described across the tree of life, even within existing metagenomic samples, and that this diversity is readily recovered using current tools and methodologies.…”

Carbon isotopes of dissolved inorganic carbon reflect utilization of different carbon sources by microbial communities in two limestone aquifer assemblages

“…Chemolithoautotrophic microorganisms, i.e., microbes that metabolize CO 2 instead of organic carbon, have been shown to be key players and important primary producers in groundwater microbial communities (Alfreider et al, 2012;Hutchins et al, 2016;Kellermann et al, 2012). A high potential for microbial CO 2 fixation has already been demonstrated in our studied aquifers by molecular analyses (Herrmann et al, 2015;Lazar et al, 2016a;Schwab et al, 2017b). We hypothesized that turnover of OM derived from chemoautotrophic microorganisms should be reflected in DIC isotopes, since OM derived from CO 2 fixation should be isotopically distinct from other sources like surface-derived OM or sedimentary organic matter.…”

Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota

“…The 16S rRNA genes identified in V1-V5 and Bathyarchaeota genomes 12,27 were aligned with full-length 16S rRNA sequences in the GreenGenes database 43 classified as Crenarchaeota, Bathyarchaeota (former Miscellaneous Crenarchaeota Group), Terrestrial Hot Spring Crenarchaeota Group (THSCG) and Aigarchaeota. The multiple sequence alignment from SSU-ALIGN (ref.…”

“…3b). The presence of multiple genes encoding peptide and amino-acid transporters suggests that the Verstraetearchaeota are capable of importing these compounds, which can then be degraded to keto-acids by various endopeptidases (PepB, PepD, PepP and PepT), glutamate dehydrogenase (Gdh) and aminotransferases (AspB, ArgD, GabT, IlvE, GlmS and HisC) 26,27 . The ketoacids could be converted to acetyl-CoA by 2-oxoacid: ferredoxin oxidoreductases (Kor, Ior, Por and Vor) and aldehydeferredoxin oxidoreductases (Aor) 12,26 (Fig.…”