Detection of anaerobic carbon monoxide-oxidizing thermophiles in hydrothermal environments

Using custom-built primers and nanopore sequencing to evaluate CO-utilizer bacterial and archaeal populations linked to bioH2 production

The microbial community composition of five distinct thermophilic hot springs was effectively described in this work, using broad-coverage nanopore sequencing (ONT MinION sequencer). By examining environmental samples from the same source, but from locations with different temperatures, bioinformatic analysis revealed dramatic changes in microbial diversity and archaeal abundance. More specifically, no archaeal presence was reported with universal bacterial primers, whereas a significant archaea presence and also a wider variety of bacterial species were reported. These results revealed the significance of primer preference for microbiomes in extreme environments. Bioinformatic analysis was performed by aligning the reads to 16S microbial databases for identification using three different alignment methods, Epi2Me (Fastq 16S workflow), Kraken, and an in-house BLAST tool, including comparison at the genus and species levels. As a result, this approach to data analysis had a significant impact on the genera identified, and thus, it is recommended that use of multiple analysis tools to support findings on taxonomic identification using the 16S region until more precise bioinformatics tools become available. This study presents the first compilation of the ONT-based inventory of the hydrogen producers in the designated hot springs in Türkiye.

Construction of multiple metagenome assembled genomes containing carbon monoxide dehydrogenases from anaerobic carbon monoxide enrichment cultures

Despite its toxicity to many organisms, including most prokaryotes, carbon monoxide (CO) is utilized by some aerobic and anaerobic prokaryotes. Hydrogenogenic CO utilizers employ carbon monoxide dehydrogenase (CODH) and energy-converting hydrogenase (ECH) to oxidize CO and reduce protons to produce H2. Those prokaryotes constitute a rare biosphere and are difficult to detect even with PCR amplification and with metagenomic analyses. In this study, anaerobic CO-enrichment cultures followed by construction of metagenome assembled genomes (MAGs) detected high-quality MAGs from potential hydrogenogenic CO utilizers. Of 32 MAGs constructed, 5 were potential CO utilizer harboring CODH genes. Of the five MAGs, two were classified into the genus Thermolithobacter on the basis of 16S rRNA sequence identity, related to Carboxydocella tharmautotrophica 41, with an average nucleotide identity (ANI) of approximately 72%. Additionally, two were related to Geoglobus acetivorans with ANI values ranging from 75 to 77% to G. acetivorans SBH6, and one MAG was identified as Desulfotomaculum kuznetsovii with an ANI > 96% to D. kuznetsovii DSM 6115. The two Thermolithobacter MAGs identified in this study contained CODH-ECH gene clusters, and were therefore identified as potential hydrogenogenic CO utilizers. However, these MAGs harbored three CODH gene clusters that showed distinct physiological functions in addition to CODH-ECH gene clusters. In total, the five potential CO utilizer MAGs contained sixteen CODH genes. Among those CODHs, four sets did not cluster with any known CODH protein sequences (with an identity of > 90%), and the CODH database was expanded.

Distribution and diversity of anaerobic thermophiles and putative anaerobic nickel-dependent carbon monoxide-oxidizing thermophiles in mesothermal soils and sediments

Even though thermophiles are best known from geothermal and other heated systems, numerous studies have demonstrated that they occur ubiquitously in mesothermal and permanently cold soils and sediments. Cultivation based studies of the latter have revealed that the thermophiles within them are mostly spore-forming members of the Firmicutes. Since the geographic distribution of spores is presumably unconstrained by transport through the atmosphere, similar communities (composition and diversity) of thermophiles might be expected to emerge in mesothermal habitats after they are heated. Alternatively, thermophiles might experience environmental selection before or after heating leading to divergent communities. After demonstrating the ubiquity of anaerobic thermophiles and CO uptake in a variety of mesothermal habitats and two hot springs, we used high throughput sequencing of 16S rRNA genes to assess the composition and diversity of populations that emerged after incubation at 60°C with or without headspace CO concentrations of 25%. Anaerobic Firmicutes dominated relative abundances at most sites but anaerobic thermophilic members of the Acidobacteria and Proteobacteria were also common. Nonetheless, compositions at the amplicon sequence variant (ASV) level varied among the sites with no convergence resulting from heating or CO addition as indicated by beta diversity analyses. The distinctions among thermophilic communities paralleled patterns observed for unheated "time zero" mesothermal soils and sediments. Occupancy analyses showed that the number of ASVs occupying each of n sites decreased unimodally with increasing n; no ASV occupied all 14 sites and only one each occupied 11 and 12 sites, while 69.3% of 1873 ASVs occupied just one site. Nonetheless, considerations of distances among the sites occupied by individual ASVs along with details of their distributions indicated that taxa were not dispersal limited but rather were constrained by environmental selection. This conclusion was supported by βMNTD and βNTI analyses, which showed dispersal limitation was only a minor contributor to taxon distributions.

Putative Nickel-Dependent Anaerobic Carbon Monoxide Uptake Occurs Commonly in Soils and Sediments at Ambient Temperature and Might Contribute to Atmospheric and Sub-Atmospheric Carbon Monoxide Uptake During Anoxic Conditions

Carbon monoxide (CO) occurs naturally in the atmosphere where it plays a critical role in tropospheric chemistry. Atmospheric CO uptake by soils has been well documented as an important CO sink and has been attributed to a group of aerobic bacteria that possess a molybdenum-dependent CO dehydrogenase (Mo-CODH). CO can also be oxidized by obligate Ni-dependent anaerobes (Ni-COX) that possess nickel-dependent CODHs (Ni-CODH) but relatively little is known about their ecology or their potential to contribute to CO dynamics within soils and sediments or to soil-atmosphere CO exchanges. Results from a series of assays undertaken with diverse soils and sediments and CO concentrations of 10 ppm and 25% with incubation temperatures of 10, 25, and 60°C revealed anaerobic uptake rates with 10 ppm CO that were comparable to those measured under oxic conditions; further, anaerobic CO uptake occurred without a lag and at atmospheric and sub-atmospheric CO concentrations. Assays with 25% CO revealed previously undocumented activity at 10°C and showed extensive activity at 25°C. Results from prior studies with isolates and soils suggest that anaerobic uptake at both 10 ppm and 25% CO concentrations might be attributed to Ni-COX. Collectively the results considerably expand the ecological range for Ni-COX and indicate that they could play previously unsuspected roles in soil CO dynamics.

Functional genome-centric view of the CO-driven anaerobic microbiome

CO is a promising substrate for producing biochemicals and biofuels through mixed microbial cultures, where carboxydotrophs play a crucial role. The previous investigations of mixed microbial cultures focused primarily on overall community structures, but under-characterized taxa and intricate microbial interactions have not yet been precisely explicated. Here, we undertook DNA-SIP based metagenomics to profile the anaerobic CO-driven microbiomes under 95 and 35% CO atmospheres. The time-series analysis of the isotope-labeled amplicon sequencing revealed the essential roles of Firmicutes and Proteobacteria under high and low CO pressure, respectively, and Methanobacterium was the predominant archaeal genus. The functional enrichment analysis based on the isotope-labeled metagenomes suggested that the microbial cultures under high CO pressure had greater potential in expressing carboxylate metabolism and citrate cycle pathway. The genome-centric metagenomics reconstructed 24 discovered and 24 under-characterized metagenome-assembled genomes (MAGs), covering more than 94% of the metagenomic reads. The metabolic reconstruction of the MAGs described their potential functions in the CO-driven microbiomes. Some under-characterized taxa might be versatile in multiple processes; for example, under-characterized Rhodoplanes sp. and Desulfitobacterium_A sp. could encode the complete enzymes in CO oxidation and carboxylate production, improving functional redundancy. Finally, we proposed the putative microbial interactions in the conversion of CO to carboxylates and methane.

Diversity analysis of thermophilic hydrogenogenic carboxydotrophs by carbon monoxide dehydrogenase amplicon sequencing using new primers

The microbial H₂-producing (hydrogenogenic) carbon monoxide (CO)-oxidizing activity by the membrane-associated CO dehydrogenase (CODH)/energy-converting hydrogenase (ECH) complex is an important metabolic process in the microbial community. However, the studies on hydrogenogenic carboxydotrophs had to rely on inherently cultivation and isolation methods due to their rare abundance, which was a bottleneck in ecological study. Here, we provided gene-targeted sequencing method for the diversity estimation of thermophilic hydrogenogenic carboxydotrophs. We designed six new degenerate primer pairs which effectively amplified the coding regions of CODH genes forming gene clusters with ECH genes (CODHech genes) in Firmicutes which includes major thermophilic hydrogenogenic carboxydotrophs in terrestrial thermal habitats. Amplicon sequencing by these primers using DNAs from terrestrial hydrothermal sediments and CO-gas-incubated samples specifically detected multiple CODH genes which were identical or phylogenetically related to the CODHech genes in Firmictes. Furthermore, we found that phylogenetically distinct CODHech genes were enriched in CO-gas-incubated samples, suggesting that our primers detected uncultured hydrogenogenic carboxydotrophs as well. The new CODH-targeted primers provided us with a fine-grained (~ 97.9% in nucleotide sequence identity) diversity analysis of thermophilic hydrogenogenic carboxydotrophs by amplicon sequencing and will bolster the ecological study of these microorganisms.

Anaerobic Carbon Monoxide Uptake by Microbial Communities in Volcanic Deposits at Different Stages of Successional Development on O-yama Volcano, Miyake-jima, Japan

Research on Kilauea and O-yama Volcanoes has shown that microbial communities and their activities undergo major shifts in response to plant colonization and that molybdenum-dependent CO oxidizers (Mo-COX) and their activities vary with vegetation and deposit age. Results reported here reveal that anaerobic CO oxidation attributed to nickel-dependent CO oxidizers (Ni-COX) also occurs in volcanic deposits that encompass different developmental stages. Ni-COX at three distinct sites responded rapidly to anoxia and oxidized CO from initial concentrations of about 10 ppm to sub-atmospheric levels. CO was also actively consumed at initial 25% concentrations and 25 °C, and during incubations at 60 °C; however, uptake under the latter conditions was largely confined to an 800-year-old forested site. Analyses of microbial communities based on 16S rRNA gene sequences in treatments with and without 25% CO incubated at 25 °C or 60 °C revealed distinct responses to temperature and CO among the sites and evidence for enrichment of known and potentially novel Ni-COX. The results collectively show that CO uptake by volcanic deposits occurs under a wide range of conditions; that CO oxidizers in volcanic deposits may be more diverse than previously imagined; and that Ni-dependent CO oxidizers might play previously unsuspected roles in microbial succession.

Hydrogen and Carbon Monoxide-Utilizing Kyrpidia spormannii Species From Pantelleria Island, Italy

Volcanic and geothermal areas are hot and often acidic environments that emit geothermal gasses, including H₂, CO and CO₂. Geothermal gasses mix with air, creating conditions where thermoacidophilic aerobic H₂- and CO-oxidizing microorganisms could thrive. Here, we describe the isolation of two Kyrpidia spormannii strains, which can grow autotrophically by oxidizing H₂ and CO with oxygen. These strains, FAVT5 and COOX1, were isolated from the geothermal soils of the Favara Grande on Pantelleria Island, Italy. Extended physiology studies were performed with K. spormannii FAVT5, and showed that this strain grows optimally at 55°C and pH 5.0. The highest growth rate is obtained using H₂ as energy source (μ_max 0.19 ± 0.02 h^–1, doubling time 3.6 h). K. spormannii FAVT5 can additionally grow on a variety of organic substrates, including some alcohols, volatile fatty acids and amino acids. The genome of each strain encodes for two O₂-tolerant hydrogenases belonging to [NiFe] group 2a hydrogenases and transcriptome studies using K. spormannii FAVT5 showed that both hydrogenases are expressed under H₂ limiting conditions. So far no Firmicutes except K. spormannii FAVT5 have been reported to exhibit a high affinity for H₂, with a K_s of 327 ± 24 nM. The genomes of each strain encode for one putative CO dehydrogenase, belonging to Form II aerobic CO dehydrogenases. The genomic potential and physiological properties of these Kyrpidia strains seem to be quite well adapted to thrive in the harsh environmental volcanic conditions.

Anaerobic and hydrogenogenic carbon monoxide-oxidizing prokaryotes: Versatile microbial conversion of a toxic gas into an available energy

Carbon monoxide (CO) is a gas that is toxic to various organisms including humans and even microbes; however, it has low redox potential, which can fuel certain microbes, namely, CO oxidizers. Hydrogenogenic CO oxidizers utilize an energy conservation system via a CO dehydrogenase/energy-converting hydrogenase complex to produce hydrogen gas, a zero emission fuel, by CO oxidation coupled with proton reduction. Biochemical and molecular biological studies using a few model organisms have revealed their enzymatic reactions and transcriptional response mechanisms using CO. Biotechnological studies for CO-dependent hydrogen production have also been carried out with these model organisms. In this chapter, we review recent advances in the studies of these microbes, which reveal their unique and versatile metabolic profiles and provides future perspectives on ecological roles and biotechnological applications. Over the past decade, the number of isolates has doubled (37 isolates in 5 phyla, 20 genera, and 32 species). Some of the recently isolated ones show broad specificity to electron acceptors. Moreover, accumulating genomic information predicts their unique physiologies and reveals their phylogenomic relationships with novel potential hydrogenogenic CO oxidizers. Combined with genomic database surveys, a molecular ecological study has unveiled the wide distribution and low abundance of these microbes. Finally, recent biotechnological applications of hydrogenogenic CO oxidizers have been achieved via diverse approaches (e.g., metabolic engineering and co-cultivation), and the identification of thermophilic facultative anaerobic CO oxidizers will promote industrial applications as oxygen-tolerant biocatalysts for efficient hydrogen production by genomic engineering.

Transcriptome analysis of a thermophilic and hydrogenogenic carboxydotroph Carboxydothermus pertinax

A thermophilic and hydrogenogenic carboxydotroph, Carboxydothermus pertinax, performs hydrogenogenic CO metabolism in which CODH-II couples with distally encoded ECH. To enhance our knowledge of its hydrogenogenic CO metabolism, we performed whole transcriptome analysis of C. pertinax grown under 100% CO or 100% N2 using RNA sequencing. Of the 2577 genes, 36 and 64 genes were differentially expressed genes (DEGs) with false discovery rate adjusted P value < 0.05 when grown under 100% CO or 100% N2, respectively. Most of the DEGs were components of 23 gene clusters, suggesting switch between metabolisms via intensive expression changes in a relatively low number of gene clusters. Of the 9 significantly expressed gene clusters under 100% CO, CODH-II and ECH gene clusters were found. Only the ECH gene cluster was regulated by the CO-responsive transcriptional factor CooA, suggesting that others were separately regulated in the same transcriptional cascade as the ECH gene cluster. Of the 14 significantly expressed gene clusters under 100% N2, ferrous iron transport gene cluster involved in anaerobic respiration and prophage region were found. Considering that the expression of the temperate phage was strictly repressed under 100% CO, hydrogenogenic CO metabolism might be stable for C. pertinax.

Diversity and distribution of thermophilic hydrogenogenic carboxydotrophs revealed by microbial community analysis in sediments from multiple hydrothermal environments in Japan

In hydrothermal environments, carbon monoxide (CO) utilisation by thermophilic hydrogenogenic carboxydotrophs may play an important role in microbial ecology by reducing toxic levels of CO and providing H₂ for fuelling microbial communities. We evaluated thermophilic hydrogenogenic carboxydotrophs by microbial community analysis. First, we analysed the correlation between carbon monoxide dehydrogenase (CODH)–energy-converting hydrogenase (ECH) gene cluster and taxonomic affiliation by surveying an increasing genomic database. We identified 71 genome-encoded CODH–ECH gene clusters, including 46 whose owners were not reported as hydrogenogenic carboxydotrophs. We identified 13 phylotypes showing > 98.7% identity with these taxa as potential hydrogenogenic carboxydotrophs in hot springs. Of these, Firmicutes phylotypes such as Parageobacillus, Carboxydocella, Caldanaerobacter, and Carboxydothermus were found in different environmental conditions and distinct microbial communities. The relative abundance of the potential thermophilic hydrogenogenic carboxydotrophs was low. Most of them did not show any symbiotic networks with other microbes, implying that their metabolic activities might be low.

Life on the fringe: microbial adaptation to growth on carbon monoxide

Microbial adaptation to extreme conditions takes many forms, including specialized metabolism which may be crucial to survival in adverse conditions. Here, we analyze the diversity and environmental importance of systems allowing microbial carbon monoxide (CO) metabolism. CO is a toxic gas that can poison most organisms because of its tight binding to metalloproteins. Microbial CO uptake was first noted by Kluyver and Schnellen in 1947, and since then many microbes using CO via oxidation have emerged. Many strains use molecular oxygen as the electron acceptor for aerobic oxidation of CO using Mo-containing CO oxidoreductase enzymes named CO dehydrogenase. Anaerobic carboxydotrophs oxidize CO using CooS enzymes that contain Ni/Fe catalytic centers and are unrelated to CO dehydrogenase. Though rare on Earth in free form, CO is an important intermediate compound in anaerobic carbon cycling, as it can be coupled to acetogenesis, methanogenesis, hydrogenogenesis, and metal reduction. Many microbial species—both bacteria and archaea—have been shown to use CO to conserve energy or fix cell carbon or both. Microbial CO formation is also very common. Carboxydotrophs thus glean energy and fix carbon from a “metabolic leftover” that is not consumed by, and is toxic to, most microorganisms. Surprisingly, many species are able to thrive under culture headspaces sometimes exceeding 1 atmosphere of CO. It appears that carboxydotrophs are adapted to provide a metabolic “currency exchange” system in microbial communities in which CO arising either abiotically or biogenically is converted to CO ₂ and H ₂ that feed major metabolic pathways for energy conservation or carbon fixation. Solventogenic CO metabolism has been exploited to construct very large gas fermentation plants converting CO-rich industrial flue emissions into biofuels and chemical feedstocks, creating renewable energy while mitigating global warming. The use of thermostable CO dehydrogenase enzymes to construct sensitive CO gas sensors is also in progress.

Genomic Insights Into Energy Metabolism of Carboxydocella thermautotrophica Coupling Hydrogenogenic CO Oxidation With the Reduction of Fe(III) Minerals

The genus Carboxydocella forms a deeply branching family in the class Clostridia and is currently represented by three physiologically diverse species of thermophilic prokaryotes. The type strain of the type species, Carboxydocella thermautotrophica 41T, is an obligate chemolithoautotroph growing exclusively by hydrogenogenic CO oxidation. Another strain, isolated from a hot spring at Uzon caldera, Kamchatka in the course of this work, is capable of coupling carboxydotrophy and dissimilatory reduction of Fe(III) from oxic and phyllosilicate minerals. The processes of carboxydotrophy and Fe(III) reduction appeared to be interdependent in this strain. The genomes of both isolates were sequenced, assembled into single chromosome sequences (for strain 41T a plasmid sequence was also assembled) and analyzed. Genome analysis revealed that each of the two strains possessed six genes encoding diverse Ni,Fe-containing CO dehydrogenases (maximum reported in complete prokaryotic genomes), indicating crucial role of carbon monoxide in C. thermautotrophica metabolism. Both strains possessed a set of 30 multiheme c-type cytochromes, but only the newly isolated Fe-reducing strain 019 had one extra gene of a 17-heme cytochrome, which is proposed to represent a novel determinant of dissimilatory iron reduction in prokaryotes. Mössbauer studies revealed that strain 019 induced reductive transformation of the abundant ferric/ferrous-mica mineral glauconite to siderite during carboxydotrophic growth. Reconstruction of the C. thermautotrophica strains energy metabolism is the first comprehensive genome analysis of a representative of the deep phylogenetic branch Clostridia Incertae Sedis, family V. Our data provide insights into energy metabolism of C. thermautotrophica with an emphasis on its ecological implications.

Comparative Analysis of Carbon Monoxide Tolerance among Thermoanaerobacter Species

An anaerobic thermophilic strain (strain PCO) was isolated from a syngas-converting enrichment culture. Syngas components cannot be used by strain PCO, but the new strain is very tolerant to carbon monoxide (pCO = 1.7 × 10(5) Pa, 100% CO). 16S rRNA gene analysis and DNA-DNA hybridization revealed that strain PCO is a strain of Thermoanaerobacter thermohydrosulfuricus. The physiology of strain PCO and other Thermoanaerobacter species was compared, focusing on their tolerance to carbon monoxide. T. thermohydrosulfuricus, T. brockii subsp. finnii, T. pseudethanolicus, and T. wiegelii were exposed to increased CO concentrations in the headspace, while growth, glucose consumption and product formation were monitored. Remarkably, glucose conversion rates by Thermoanaerobacter species were not affected by CO. All the tested strains fermented glucose to mainly lactate, ethanol, acetate, and hydrogen, but final product concentrations differed. In the presence of CO, ethanol production was generally less affected, but H2 production decreased with increasing CO partial pressure. This study highlights the CO resistance of Thermoanaerobacter species.