Single-Cell Genomics of Novel Actinobacteria With the Wood-Ljungdahl Pathway Discovered in a Serpentinizing System.

Nancy Merino,Shawn E. McGlynn,Kenneth H. Nealson,Eric S. Boyd,Daniel R. Colman,Yuichi Hongoh,Ken Kurokawa,Mikihiko Kawai

doi:10.3389/fmicb.2020.01031

Abstract

Serpentinite-hosted systems represent modern-day analogs of early Earth environments. In these systems, water-rock interactions generate highly alkaline and reducing fluids that can contain hydrogen, methane, and low-molecular-weight hydrocarbons-potent reductants capable of fueling microbial metabolism. In this study, we investigated the microbiota of Hakuba Happo hot springs (∼50°C; pH∼10.5–11), located in Nagano (Japan), which are impacted by the serpentinization process. Analysis of the 16S rRNA gene amplicon sequences revealed that the bacterial community comprises Nitrospirae (47%), “Parcubacteria” (19%), Deinococcus-Thermus (16%), and Actinobacteria (9%), among others. Notably, only 57 amplicon sequence variants (ASV) were detected, and fifteen of these accounted for 90% of the amplicons. Among the abundant ASVs, an early-branching, uncultivated actinobacterial clade identified as RBG-16-55-12 in the SILVA database was detected. Ten single-cell genomes (average pairwise nucleotide identity: 0.98–1.00; estimated completeness: 33–93%; estimated genome size: ∼2.3 Mb) that affiliated with this clade were obtained. Taxonomic classification using single copy genes indicates that the genomes belong to the actinobacterial class-level clade UBA1414 in the Genome Taxonomy Database. Based on metabolic pathway predictions, these actinobacteria are anaerobes, capable of glycolysis, dissimilatory nitrate reduction and CO2 fixation via the Wood–Ljungdahl (WL) pathway. Several other genomes within UBA1414 and two related class-level clades also encode the WL pathway, which has not yet been reported for the Actinobacteria phylum. For the Hakuba actinobacterium, the energy metabolism related to the WL pathway is likely supported by a combination of the Rnf complex, group 3b and 3d [NiFe]-hydrogenases, [FeFe]-hydrogenases, and V-type (H+/Na+ pump) ATPase. The genomes also harbor a form IV ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) complex, also known as a RubisCO-like protein, and contain signatures of interactions with viruses, including clustered regularly interspaced short palindromic repeat (CRISPR) regions and several phage integrases. This is the first report and detailed genome analysis of a bacterium within the Actinobacteria phylum capable of utilizing the WL pathway. The Hakuba actinobacterium is a member of the clade UBA1414/RBG-16-55-12, formerly within the group “OPB41.” We propose to name this bacterium ‘Candidatus Hakubanella thermoalkaliphilus.’

Highlights

The serpentinization reaction is fundamental to one of the leading hypotheses regarding the emergence of life on Earth, known as the submarine alkaline hydrothermal vent model (Russell et al, 2010; Branscomb and Russell, 2018)
The dominant bacterial phyla were Nitrospirae (47%), “Parcubacteria” (19%), Deinococcus-Thermus (16%), and Actinobacteria (9%), followed by Firmicutes (5%), Bacteroidetes (2%), among others (
We present a genomic characterization of a dominant member in the Hakuba Happo hot spring ecosystem that belongs to the early-branching actinobacterial clade UBA1414

Summary

Introduction

The serpentinization reaction is fundamental to one of the leading hypotheses regarding the emergence of life on Earth, known as the submarine alkaline hydrothermal vent model (Russell et al, 2010; Branscomb and Russell, 2018) It follows that contemporary serpentinite-hosted systems might provide a window into early life. Several studies have examined the microbial communities present in serpentinite-influenced environments, including in the Samail ophiolite (Rempfert et al, 2017; Fones et al, 2019), the Cedars (Suzuki et al, 2013), the Cabeço de Vide Aquifer (Tiago and Veríssimo, 2013), the Coast Range Ophiolite Microbial Observatory (Crespo-Medina et al, 2014; Twing et al, 2017), the Voltri Massif (Quéméneur et al, 2015; Brazelton et al, 2017), and the Zambales ophiolite (Meyer-Dombard et al, 2018) These can be distant locations from each other, Meyer-Dombard et al (2018) identified a ‘principal community’ amongst serpentinizing environments, consisting of key members in the phyla Firmicutes (e.g., Dethiobacter sp.) and Proteobacteria (e.g., Serpentinomonas sp.)

Methods

Results

Conclusion