Methane oxidation activity and diversity of aerobic methanotrophs in pH-neutral and semi-neutral thermal springs of the Kunashir Island, Russian Far East

Methylococcus mesophilus sp. nov., the first non-thermotolerant methanotroph of the genus Methylococcus, from a rice field

Strain 16-5T, a mesophilic methanotroph of the genus Methylococcus, was isolated from rice field soil sampled in Chungcheong Province, Republic of Korea. Strain 16-5T had both particulate and soluble methane monooxygenases and could only grow on methane and methanol as electron donors. Strain 16-5 T cells are Gram-negative, white to light tan in color, non-motile, non-flagellated, diplococcoid to cocci, and have the typical type I intracytoplasmic membrane system. Strain 16-5T grew at 18-38 °C (optimum, 27 °C) and at pH 5.0-8.0 (optimum, pH 6.5-7.0). C16 : 1 ω7c (38.8%), C16 : 1  ω5c (18.8%), C16 : 1  ω6c (16.8%) and C16 : 0 (16.9%) were the major fatty acids, and phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unidentified phospholipid were the major polar lipids. The main respiratory quinone was methylene-ubiquinone-8. Strain 16-5T displayed the highest 16S rRNA gene sequence similarities to other taxonomically recognized members of the genus Methylococcus, i.e. Methylococcus capsulatus TexasT (98.62%) and Methylococcus geothermalis IM1T (98.49 %), which were its closest relatives. It did, however, differ from all other taxonomically described Methylococcus species due to some phenotypic differences, most notably its inability to grow at temperatures above 38 °C, where other Methylococcus species thrive. Its 4.34 Mbp-sized genome has a DNA G+C content of 62.47 mol%, and multiple genome-based properties such as average nucleotide identity and digital DNA-DNA hybridization value distanced it from its closest relatives. Based on the data presented above, this strain represents the first non-thermotolerant species of the genus Methylococcus. The name Methylococcus mesophilus sp. nov. is proposed, and 16-5T (=JCM 35359T=KCTC 82050T) is the type strain.

Thermophilic methane oxidation is widespread in Aotearoa-New Zealand geothermal fields

Geothermal areas represent substantial point sources for greenhouse gas emissions such as methane. While it is known that methanotrophic microorganisms act as a biofilter, decreasing the efflux of methane in most soils to the atmosphere, the diversity and the extent to which methane is consumed by thermophilic microorganisms in geothermal ecosystems has not been widely explored. To determine the extent of biologically mediated methane oxidation at elevated temperatures, we set up 57 microcosms using soils from 14 Aotearoa-New Zealand geothermal fields and show that moderately thermophilic (>40°C) and thermophilic (>60°C) methane oxidation is common across the region. Methane oxidation was detected in 54% (n = 31) of the geothermal soil microcosms tested at temperatures up to 75°C (pH 1.5-8.1), with oxidation rates ranging from 0.5 to 17.4 μmol g-1 d-1 wet weight. The abundance of known aerobic methanotrophs (up to 60.7% Methylacidiphilum and 11.2% Methylothermus) and putative anaerobic methanotrophs (up to 76.7% Bathyarchaeota) provides some explanation for the rapid rates of methane oxidation observed in microcosms. However, not all methane oxidation was attributable to known taxa; in some methane-consuming microcosms we detected methanotroph taxa in conditions outside of their known temperature range for growth, and in other examples, we observed methane oxidation in the absence of known methanotrophs through 16S rRNA gene sequencing. Both of these observations suggest unidentified methane oxidizing microorganisms or undescribed methanotrophic syntrophic associations may also be present. Subsequent enrichment cultures from microcosms yielded communities not predicted by the original diversity studies and showed rates inconsistent with microcosms (≤24.5 μmol d-1), highlighting difficulties in culturing representative thermophilic methanotrophs. Finally, to determine the active methane oxidation processes, we attempted to elucidate metabolic pathways from two enrichment cultures actively oxidizing methane using metatranscriptomics. The most highly expressed genes in both enrichments (methane monooxygenases, methanol dehydrogenases and PqqA precursor peptides) were related to methanotrophs from Methylococcaceae, Methylocystaceae and Methylothermaceae. This is the first example of using metatranscriptomics to investigate methanotrophs from geothermal environments and gives insight into the metabolic pathways involved in thermophilic methanotrophy.

Taxonomic Diversity of the Microbial Biofilms Collected along the Thermal Streams on Kunashir Island

Hot springs are known as highly adverse extreme environments where thermophilic and hyperthermophilic microorganisms can survive. We describe taxonomic diversity of several microbial biofilms collected along water temperature gradient in hot streams in the aquatic system of the Stolbovskie hot springs on Kunashir Island, Kurils, Russia. The taxonomic composition of the studied microbial communities was assessed by the 16S rRNA gene metabarcoding for bacteria and archaea, and by the 18S rRNA gene metabarcoding for protists. Richness and diversity of bacteria in the geothermal microbial communities decreased with the increase of temperature, while for archaea, the tendency was the opposite. Ciliophora was the most represented taxon of protists. The biofilms of various kinds that we found in a very local area of the geothermal system were different from each other by taxonomic composition, and the level of their taxonomic diversity was significantly influenced by water temperature.

Expanding Characterized Diversity and the Pool of Complete Genome Sequences of Methylococcus Species, the Bacteria of High Environmental and Biotechnological Relevance

The bacterial genus Methylococcus, which comprises aerobic thermotolerant methanotrophic cocci, was described half-a-century ago. Over the years, a member of this genus, Methylococcus capsulatus Bath, has become a major model organism to study genomic and metabolic basis of obligate methanotrophy. High biotechnological potential of fast-growing Methylococcus species, mainly as a promising source of feed protein, has also been recognized. Despite this big research attention, the currently cultured Methylococcus diversity is represented by members of the two species, M. capsulatus and M. geothermalis, while finished genome sequences are available only for two strains of these methanotrophs. This study extends the pool of phenotypically characterized Methylococcus strains with good-quality genome sequences by contributing four novel isolates of these bacteria from activated sludge, landfill cover soil, and freshwater sediments. The determined genome sizes of novel isolates varied between 3.2 and 4.0Mb. As revealed by the phylogenomic analysis, strains IO1, BH, and KN2 affiliate with M. capsulatus, while strain Mc7 may potentially represent a novel species. Highest temperature optima (45-50°C) and highest growth rates in bioreactor cultures (up to 0.3h-1) were recorded for strains obtained from activated sludge. The comparative analysis of all complete genomes of Methylococcus species revealed 4,485 gene clusters. Of these, pan-genome core comprised 2,331 genes (on average 51.9% of each genome), with the accessory genome containing 846 and 1,308 genes in the shell and the cloud, respectively. Independently of the isolation source, all strains of M. capsulatus displayed surprisingly high genome synteny and a striking similarity in gene content. Strain Mc7 from a landfill cover soil differed from other isolates by the high content of mobile genetic elements in the genome and a number of genome-encoded features missing in M. capsulatus, such as sucrose biosynthesis and the ability to scavenge phosphorus and sulfur from the environment.

A Novel Moderately Thermophilic Type Ib Methanotroph Isolated from an Alkaline Thermal Spring in the Ethiopian Rift Valley

Aerobic moderately thermophilic and thermophilic methane-oxidizing bacteria make a substantial contribution in the control of global warming through biological reduction of methane emissions and have a unique capability of utilizing methane as their sole carbon and energy source. Here, we report a novel moderately thermophilic Methylococcus-like Type Ib methanotroph recovered from an alkaline thermal spring (55.4 °C and pH 8.82) in the Ethiopian Rift Valley. The isolate, designated LS7-MC, most probably represents a novel species of a new genus in the family Methylococcaceae of the class Gammaproteobacteria. The 16S rRNA gene phylogeny indicated that strain LS7-MC is distantly related to the closest described relative, Methylococcus capsulatus (92.7% sequence identity). Growth was observed at temperatures of 30–60 °C (optimal, 51–55 °C), and the cells possessed Type I intracellular membrane (ICM). The comparison of the pmoA gene sequences showed that the strain was most closely related to M.capsulatus (87.8%). Soluble methane monooxygenase (sMMO) was not detected, signifying the biological oxidation process from methane to methanol by the particulate methane monooxygenase (pMMO). The other functional genes mxaF, cbbL and nifH were detected by PCR. To our knowledge, the new strain is the first isolated moderately thermophilic methanotroph from an alkaline thermal spring of the family Methylococcaceae. Furthermore, LS7-MC represents a previously unrecognized biological methane sink in thermal habitats, expanding our knowledge of its ecological role in methane cycling and aerobic methanotrophy.

Thermophilic methanotrophs: in hot pursuit

Methane is a potent greenhouse gas responsible for 20–30% of global climate change effects. The global methane budget is ∼500–600 Tg y−1, with the majority of methane produced via microbial processes, including anthropogenic-mediated sources such as ruminant animals, rice fields, sewage treatment facilities and landfills. It is estimated that microbially mediated methane oxidation (methanotrophy) consumes >50% of global methane flux each year. Methanotrophy research has primarily focused on mesophilic methanotrophic representatives and cooler environments such as freshwater, wetlands or marine habitats from which they are sourced. Nevertheless, geothermal emissions of geological methane, produced from magma and lithosphere degassing micro-seepages, mud volcanoes and other geological sources, contribute an estimated 33–75 Tg y−1 to the global methane budget. The aim of this review is to summarise current literature pertaining to the activity of thermophilic and thermotolerant methanotrophs, both proteobacterial (Methylocaldum, Methylococcus, Methylothermus) and verrucomicrobial (Methylacidiphilum). We assert, on the basis of recently reported molecular and geochemical data, that geothermal ecosystems host hitherto unidentified species capable of methane oxidation at higher temperatures.

Microbial Ecology on Solar Panels in Berkeley, CA, United States

Solar panels can be found practically all over the world and represent a standard surface that can be colonized by microbial communities that are resistant to harsh environmental conditions, including high irradiation, temperature fluctuations and desiccation. These properties make them not only ideal sources of stress-resistant bacteria, but also standard devices to study the microbial communities and their colonization process from different areas of Earth. We report here a comprehensive description of the microbial communities associated with solar panels in Berkeley, CA, United States. Cultivable bacteria were isolated to characterize their adhesive capabilities, and UV- and desiccation-resistance properties. Furthermore, a parallel culture-independent metagenomic and metabolomic approach has allowed us to gain insight on the taxonomic and functional nature of these communities. Metagenomic analysis was performed using the Illumina HiSeq2500 sequencing platform, revealing that the bacterial population of the Berkeley solar panels is composed mainly of Actinobacteria, Bacteroidetes and Proteobacteria, as well as lower amounts of Deinococcus-Thermus and Firmicutes. Furthermore, a clear predominance of Hymenobacter sp. was also observed. A functional analysis revealed that pathways involved in the persistence of microbes on solar panels (i.e., stress response, capsule development, and metabolite repair) and genes assigned to carotenoid biosynthesis were common to all metagenomes. On the other hand, genes involved in photosynthetic pathways and general autotrophic subsystems were rare, suggesting that these pathways are not critical for persistence on solar panels. Metabolomics was performed using a liquid chromatography tandem mass spectrometry (LC-MS/MS) approach. When comparing the metabolome of the solar panels from Berkeley and from Valencia (Spain), a very similar composition in polar metabolites could be observed, although some metabolites appeared to be differentially represented (for example, trigonelline, pantolactone and 5-valerolactone were more abundant in the samples from Valencia than in the ones from Berkeley). Furthermore, triglyceride metabolites were highly abundant in all the solar panel samples, and both locations displayed similar profiles. The comparison of the taxonomic profile of the Californian solar panels with those previously described in Spain revealed striking similarities, highlighting the central role of both selective pressures and the ubiquity of microbial populations in the colonization and establishment of microbial communities.

Methane Oxidation and Molecular Characterization of Methanotrophs from a Former Mercury Mine Impoundment

The Herman Pit, once a mercury mine, is an impoundment located in an active geothermal area. Its acidic waters are permeated by hundreds of gas seeps. One seep was sampled and found to be composed of mostly CO₂ with some CH₄ present. The δ¹³CH₄ value suggested a complex origin for the methane: i.e., a thermogenic component plus a biological methanogenic portion. The relatively ¹²C-enriched CO₂ suggested a reworking of the ebullitive methane by methanotrophic bacteria. Therefore, we tested bottom sediments for their ability to consume methane by conducting aerobic incubations of slurried materials. Methane was removed from the headspace of live slurries, and subsequent additions of methane resulted in faster removal rates. This activity could be transferred to an artificial, acidic medium, indicating the presence of acidophilic or acid-tolerant methanotrophs, the latter reinforced by the observation of maximum activity at pH = 4.5 with incubated slurries. A successful extraction of sterol and hopanoid lipids characteristic of methanotrophs was achieved, and their abundances greatly increased with increased sediment methane consumption. DNA extracted from methane-oxidizing enrichment cultures was amplified and sequenced for pmoA genes that aligned with methanotrophic members of the Gammaproteobacteria. An enrichment culture was established that grew in an acidic (pH 4.5) medium via methane oxidation.