Respiratory Pathways Reconstructed by Multi-Omics Analysis in Melioribacter roseus, Residing in a Deep Thermal Aquifer of the West-Siberian Megabasin

Abstract

Melioribacter roseus, a representative of recently proposed Ignavibacteriae phylum, is a metabolically versatile thermophilic bacterium, inhabiting subsurface biosphere of the West-Siberian megabasin and capable of growing on various substrates and electron acceptors. Genomic analysis followed by inhibitor studies and membrane potential measurements of aerobically grown M. roseus cells revealed the activity of aerobic respiratory electron transfer chain comprised of respiratory complexes I and IV, and an alternative complex III. Phylogeny reconstruction revealed that oxygen reductases belonged to atypical cc(o/b)o3-type and canonical cbb3–type cytochrome oxidases. Also, two molybdoenzymes of M. roseus were affiliated either with Ttr or Psr/Phs clades, but not with typical respiratory arsenate reductases of the Arr clade. Expression profiling, both at transcripts and protein level, allowed us to assign the role of the terminal respiratory oxidase under atmospheric oxygen concentration for the cc(o/b)o3 cytochrome oxidase, previously proposed to serve for oxygen detoxification only. Transcriptomic analysis revealed the involvement of both molybdoenzymes of M. roseus in As(V) respiration, yet differences in the genomic context of their gene clusters allow to hypothesize about their distinct roles in arsenate metabolism with the ‘Psr/Phs’-type molybdoenzyme being the most probable candidate respiratory arsenate reductase. Basing on multi-omics data, the pathways for aerobic and arsenate respiration were proposed. Our results start to bridge the vigorously increasing gap between homology-based predictions and experimentally verified metabolic processes, what is especially important for understudied microorganisms of novel lineages from deep subsurface environments of Eurasia, which remained separated from the rest of the biosphere for several geological periods.

Microbial Communities of Polymetallic Deposits’ Acidic Ecosystems of Continental Climatic Zone With High Temperature Contrasts

“…The two known cultured ignavibacteria are facultatively anaerobic organotrophs that use various carbon sources. One of them, Melioribacter roseus , possesses а high hydrolytic potential along with capabilities of arsenate, nitrite and Fe(III) reduction (Podosokorskaya et al, 2013; Gavrilov et al, 2017), suggesting a possible involvement of Ignavibacteriae -related organisms in iron, nitrogen and mixed valence elements cycling in Sherlovaya Gora lake. Clones belonging to the class and phylum of the same name, Elusimicrobia , have been previously detected in various environments with high organic matter content, as well as in the groundwater of a deep subsurface gold mine (Magnabosco et al, 2016).…”

Expression of Genes and Proteins Involved in Arsenic Respiration and Resistance in Dissimilatory Arsenate-Reducing Geobacter sp. Strain OR-1

“…Although it was genetically characterized in S. enterica as a protein essential for anaerobic tetrathionate (S 4 O 6 2Ϫ ) respiration (35,36), TtrA-like proteins may also be involved in dissimilatory As(V) reduction in archaea such as Pyrobaculum aerophilum and Pyrobaculum calidifontis (37). In addition, TtrA is one of candidates for respiratory As(V) reductase in dissimilatory As(V)-reducing bacteria, such as Melioribacter roseus (38) and Citrobacter sp. strain TSA-1 (39), both of which lack homologs of arrA in their genomes.…”

Novel Extracellular Electron Transfer Channels in a Gram-Positive Thermophilic Bacterium

“…Such a metabolic strategy could represent a widespread response of microorganisms to sharp changes in the availability of electron acceptors. In particular, constitutive expression has been reported for different terminal oxidoreductases of a thermophilic iron-reducer Melioribacter roseus from a deep subsurface aquifer ( Gavrilov et al, 2017 ), as well as for several multihemes involved in electron transfer to different electron acceptors in a mesophilic iron-reducing soil bacterium Geobacter soli ( Cai et al, 2018 ). A modular principle of the respiratory system organization, which implies differential activity of various multihemes, has been previously proposed for S. oneidensis ( Coursolle and Gralnick, 2010 ) and Geobacter species ( Butler et al, 2010 ; Aklujkar et al, 2013 ; Cai et al, 2018 ).…”