Metagenomic investigation of the geologically unique Hellenic Volcanic Arc reveals a distinctive ecosystem with unexpected physiology

Abstract

SummaryHydrothermal vents represent a deep, hot, aphotic biosphere where chemosynthetic primary producers, fuelled by chemicals from Earth's subsurface, form the basis of life. In this study, we examined microbial mats from two distinct volcanic sites within the Hellenic Volcanic Arc (HVA). The HVA is geologically and ecologically unique, with reported emissions of CO2-saturated fluids at temperatures up to 220°C and a notable absence of macrofauna. Metagenomic data reveals highly complex prokaryotic communities composed of chemolithoautotrophs, some methanotrophs, and to our surprise, heterotrophs capable of anaerobic degradation of aromatic hydrocarbons. Our data suggest that aromatic hydrocarbons may indeed be a significant source of carbon in these sites, and instigate additional research into the nature and origin of these compounds in the HVA. Novel physiology was assigned to several uncultured prokaryotic lineages; most notably, a SAR406 representative is attributed with a role in anaerobic hydrocarbon degradation. This dataset, the largest to date from submarine volcanic ecosystems, constitutes a significant resource of novel genes and pathways with potential biotechnological applications.

Coupled Carbon, Sulfur, and Nitrogen Cycles Mediated by Microorganisms in the Water Column of a Shallow-Water Hydrothermal Ecosystem

“…The rTCA cycle is universal in hydrothermal vent environments; it is performed by chemoautotrophic Epsilonbacteraeota ( Hügler et al, 2005 ), and is the most economical pathway of carbon fixation in bacteria ( Mangiapia and Scott, 2016 ). This pathway is particularly advantageous in an energy-limited environment ( Oulas et al, 2016 ). The CBB cycle was the first carbon fixation pathway to be discovered about 60 years ago ( Wilson and Calvin, 1955 ), and autotrophic Gammaproteobacteria mainly perform carbon fixation through this pathway ( Hügler and Sievert, 2011 ).…”

Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes

“…Tara Ocean metagenomes were downloaded from the European Nucleotide Archive using accession numbers provided in [32] and [21]. Read data used from Vik et al [33], Hollibaugh et al [34], Thrash et al [35], and Oulas et al [36] were downloaded from iVirus, the National Center for Biotechnology Information (NCBI) Short Read Archive (SRA), or the Joint Genome Institute's (JGI) Integrated Microbial Genomes & Microbiomes (IMG/M) website using accessions or file names provided in those studies. amoC reads were assigned as cellular or viral by "placement" of reads on the reference amoC tree (Fig.…”

Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data

“…• We binned six metagenomic samples with the highest number of candidate viral sequences (not satisfying the high-confidence threshold of the number of hits to protein models) using emergent self-organizing maps by Ultsch, as described previously 44,45 . • We manually checked the contig sets outside the bins corresponding to cellular organisms and identified 66 long putative novel metagenomic viral contigs from diverse habitat types (freshwater, wastewater, thermal vents, and marine), which were added to the training set.…”