Methylocystis bryophila sp. nov., a facultatively methanotrophic bacterium from acidic Sphagnum peat, and emended description of the genus Methylocystis (ex Whittenbury et al. 1970) Bowman et al. 1993

Isolation of a facultative methanotroph Methylocystis iwaonis SD4 from rice rhizosphere and establishment of rapid genetic tools for it

Methanotrophs of the genus Methylocystis are frequently found in rice paddies. Although more than ten facultative methanotrophs have been reported since 2005, none of these strains was isolated from paddy soil. Here, a facultative methane-oxidizing bacterium, Methylocystis iwaonis SD4, was isolated and characterized from rhizosphere samples of rice plants in Nanjing, China. This strain grew well on methane or methanol but was able to grow slowly using acetate or ethanol. Moreover, strain SD4 showed sustained growth at low concentrations of methane (100 and 500 ppmv). M. iwaonis SD4 could utilize diverse nitrogen sources, including nitrate, urea, ammonium as well as dinitrogen. Strain SD4 possessed genes encoding both the particulate methane monooxygenase and the soluble methane monooxygenase. Simple and rapid genetic manipulation methods were established for this strain, enabling vector transformation and unmarked genetic manipulation. Fast growth rate and efficient genetic tools make M. iwaonis SD4 an ideal model to study facultative methanotrophs, and the ability to grow on low concentration of methane implies its potential in methane removal.

Targeting methanotrophs and isolation of a novel psychrophilic Methylobacter species from a terrestrial Arctic alkaline methane seep in Lagoon Pingo, Central Spitsbergen (78° N)

The microbial diversity associated with terrestrial groundwater seepage through permafrost soils is tightly coupled to the geochemistry of these fluids. Terrestrial alkaline methane seeps from Lagoon Pingo, Central Spitsbergen (78°N) in Norway, with methane-saturated and oxygen-limited groundwater discharge providing a potential habitat for methanotrophy. Here, we report on the microbial community's comparative analyses and distribution patterns at two sites close to Lagoon Pingo's methane emission source. To target methane-oxidizing bacteria from this system, we analysed the microbial community pattern of replicate samples from two sections near the main methane seepage source. DNA extraction, metabarcoding and subsequent sequencing of 16S rRNA genes revealed microbial communities where the major prokaryotic phyla were Pseudomonadota (42-47%), Gemmatimonadota (4-14%) and Actinobacteriota (7-11%). Among the Pseudomonadota, members of the genus Methylobacter were present at relative abundances between 1.6 and 4.7%. Enrichment targeting the methane oxidising bacteria was set up using methane seep sediments as inoculum and methane as the sole carbon and energy source, and this resulted in the isolation of a novel psychrophilic methane oxidizer, LS7-T4AT. The optimum growth temperature for the isolate was 13 °C and the pH optimum was 8.0. The morphology of cells was short rods, and TEM analysis revealed intracytoplasmic membranes arranged in stacks, a distinctive feature for Type I methanotrophs in the family Methylomonadaceae of the class Gammaproteobacteria. The strain belongs to the genus Methylobacter based on high 16S rRNA gene similarity to the psychrophilic species of Methylobacter psychrophilus Z-0021T (98.95%), the psychrophilic strain Methylobacter sp. strain S3L5C (99.00%), and the Arctic mesophilic species of Methylobacter tundripaludum SV96T (99.06%). The genome size of LS7-T4AT was 4,338,157 bp with a G + C content of 47.93%. The average nucleotide identities (ANIb) of strain LS7-T4AT to 10 isolated strains of genus Methylobacter were between 75.54 and 85.51%, lower than the species threshold of 95%. The strain LS7-T4AT represents a novel Arctic species, distinct from other members of the genus Methylobacter, for which the name Methylobacter svalbardensis sp. nov. is proposed. The type of strain is LS7-T4AT (DSMZ:114308, JCM:39463).

Methylocystis suflitae sp. nov., a novel type II methanotrophic bacterium isolated from landfill cover soil

A bacterial strain, designated NLS-7T, was isolated through enrichment of landfill cover soil in methane-oxidizing conditions. Strain NLS-7T is a Gram-stain negative, non-motile rod, approximately 0.8 µm wide by 1.3 µm long. Phylogenetic analysis based on 16S rRNA gene sequencing places it within the genus Methylocystis, with its closest relatives being M. hirsuta, M. silviterrae and M. rosea, with 99.9, 99.7 and 99.6 % sequence similarity respectively. However, average nucleotide identity and average amino acid identity values below the 95 % threshold compared to all the close relatives and digital DNA-DNA hybridization values between 20.9 and 54.1 % demonstrate that strain NLS-7T represents a novel species. Genome sequencing generated 4.31 million reads and genome assembly resulted in the generation of 244 contigs with a total assembly length of 3 820 957 bp (N50, 37 735 bp; L50, 34). Genome completeness is 99.5 % with 3.98 % contamination. It is capable of growth on methane and methanol. It grows optimally at 30 °C between pH 6.5 and 7.0. Strain NLS-7T is capable of atmospheric dinitrogen fixation and can use ammonium (as NH4Cl), l-aspartate, l-arginine, yeast extract, nitrate, l-leucine, l-proline, l-methionine, l-lysine and l-alanine as nitrogen sources. The major fatty acids are C18:1 ω8c and C18:1 ω7c. Based upon this polyphasic taxonomic study, strain NLS-7T represents a novel species of the genus Methylocystis, for which the name Methylocystis suflitae sp. nov. is proposed. The type strain is NLS-7T (=ATCC TSD-256T=DSM 112294T). The 16S rRNA gene and genome sequences of strain NLS-7T have been deposited in GenBank under accession numbers ON715489 and GCA_024448135.1, respectively.

Ferrihydrite-mediated methanotrophic nitrogen fixation in paddy soil under hypoxia

Biological nitrogen fixation (BNF) by methanotrophic bacteria has been shown to play an important role in maintaining fertility. However, this process is still limited to aerobic methane oxidation with sufficient oxygen. It has remained unknown whether and how methanotrophic BNF proceeds in hypoxic environments. Herein, we incubated paddy soils with a ferrihydrite-containing mineral salt medium to enrich methanotrophic bacteria in the presence of methane (20%, v/v) under oxygen constraints (0.27%, v/v). The resulting microcosms showed that ferrihydrite-dependent aerobic methane oxidation significantly contributed (81%) to total BNF, increasing the 15N fixation rate by 13-fold from 0.02 to 0.28 μmol 15N2 (g dry weight soil) -1 d-1. BNF was reduced by 97% when ferrihydrite was omitted, demonstrating the involvement of ferrihydrite in methanotrophic BNF. DNA stable-isotope probing indicated that Methylocystis, Methylophilaceae, and Methylomicrobium were the dominant methanotrophs/methylotrophs that assimilated labeled isotopes (13C or 15N) into biomass. Metagenomic binning combined with electrochemical analysis suggested that Methylocystis and Methylophilaceae had the potential to perform methane-induced BNF and likely utilized riboflavin and c-type cytochromes as electron carriers for ferrihydrite reduction. It was concluded that ferrihydrite mediated methanotrophic BNF by methanotrophs/methylotrophs solely or in conjunction with iron-reducing bacteria. Overall, this study revealed a previously overlooked yet pronounced coupling of iron-dependent aerobic methane oxidation to BNF and improves our understanding of methanotrophic BNF in hypoxic zones.

One Step Closer to Enigmatic USCα Methanotrophs: Isolation of a Methylocapsa-like Bacterium from a Subarctic Soil

The scavenging of atmospheric trace gases has been recognized as one of the lifestyle-defining capabilities of microorganisms in terrestrial polar ecosystems. Several metagenome-assembled genomes of as-yet-uncultivated methanotrophic bacteria, which consume atmospheric CH4 in these ecosystems, have been retrieved in cultivation-independent studies. In this study, we isolated and characterized a representative of these methanotrophs, strain D3K7, from a subarctic soil of northern Russia. Strain D3K7 grows on methane and methanol in a wide range of temperatures, between 5 and 30 °C. Weak growth was also observed on acetate. The presence of acetate in the culture medium stimulated growth at low CH4 concentrations (~100 p.p.m.v.). The finished genome sequence of strain D3K7 is 4.15 Mb in size and contains about 3700 protein-encoding genes. According to the result of phylogenomic analysis, this bacterium forms a common clade with metagenome-assembled genomes obtained from the active layer of a permafrost thaw gradient in Stordalen Mire, Abisco, Sweden, and the mineral cryosol at Axel Heiberg Island in the Canadian High Arctic. This clade occupies a phylogenetic position in between characterized Methylocapsa methanotrophs and representatives of the as-yet-uncultivated upland soil cluster alpha (USCα). As shown by the global distribution analysis, D3K7-like methanotrophs are not restricted to polar habitats but inhabit peatlands and soils of various climatic zones.

Type-specific quantification of particulate methane monooxygenase gene of methane-oxidizing bacteria at the oxic-anoxic interface of a surface paddy soil by digital PCR

Aerobic methane-oxidizing bacteria (MOB) play an important role in mitigating methane emissions from paddy fields. In this study, we developed a differential quantification method for the copy number of pmoA genes of type Ia, Ib, and IIa MOB in paddy field soil using chip-based digital PCR. Three probes specific to the pmoA of type Ia, Ib, and IIa MOB worked well in digital PCR quantification when genomic DNA of MOB isolates and PCR-amplified DNA fragments of pmoA were examined as templates. When pmoA genes in the surface soil layer of a flooded paddy were quantified by digital PCR, the copy numbers of type Ia, Ib, and IIa MOB were 105 -106 , 105 -106 , and 107 copies g-1 dry soil, respectively, with the highest values in the top 0-2-mm soil layer. Especially, the copy numbers of type Ia and Ib MOB increased by 240% and 380% at the top layer after soil flooding, suggesting that the soil circumstances at the oxic-anoxic interfaces were more preferential for growth of type I MOB than type II MOB. Thus, type I MOB likely play an important role in the methane consumption at the surface paddy soil.

Methylocystis iwaonis sp. nov., a type II methane-oxidizing bacterium from surface soil of a rice paddy field in Japan, and emended description of the genus Methylocystis (ex Whittenbury et al. 1970) Bowman et al. 1993

A novel methane-oxidizing bacterial strain SS37A-ReT was isolated from surface soil of a rice paddy field in Japan. Cells were Gram-stain-negative, motile rods with single polar flagellum and type II intracytoplasmic membrane arrangement. The strain grew on methane or methanol as the sole carbon and energy source. It grew at 15–37 °C (optimum 25–30 °C), pH 6.0–9.0 (optimum 7.0–8.0) and with 0–0.1 % (w/w) NaCl (no growth at 0.5 % or above). Cells formed cysts, but not exospores. The results of sequence analysis of the 16S rRNA gene indicated that SS37A-ReT represented a member of the family Methylocystaceae , with the highest similarity (98.9 %) to Methylocystis parva corrig. OBBPT. Phylogenetic analysis of pmoA and mxaF genes and core genes in the genome indicated that the strain was closely related to the members of the genus Methylocystis , while the analysis of the mmoX gene indicated the close relationships with the genus Methylosinus . The values of genome relatedness between SS37A-ReT and species of the genera Methylocystis and Methylosinus were 78.6–82.5% and 21.7–24.9 % estimated by the average nucleotide identity and digital DNA–DNA hybridisation, respectively, showing the highest values with Methylocystis echinoides LMG 27198T. The DNA G+C content was 63.2 mol% (genome). The major quinone and fatty acids were Q-8 and, C18 : 1 (C18 : 1ω8t and C18 : 1ω8c) and C18 : 2, respectively. On the basis of the phenotypic and phylogenetic features, the strain represents a novel species of the genus Methylocystis , for which the name Methylocystis iwaonis sp. nov. is proposed. The type strain is SS37A-ReT (=JCM 34278T =NBRC 114996T=KCTC 82710T).

Activity and abundance of methanotrophic bacteria in a northern mountainous gradient of wetlands

Methane uptake and diversity of methanotrophic bacteria was investigated across six hydrologically connected wetlands in a mountainous forest landscape upstream of lake Langtjern, southern Norway. From floodplain through shrubs, forest and sedges to a Sphagnum covered site, growing season CH4 production was insufficiently consumed to balance release into the atmosphere. Emission increased by soil moisture ranging 0.6-6.8 mg CH4 m-2  h-1 . Top soils of all sites consumed CH4 including at the lowest 78 ppmv CH4 supplied, thus potentially oxidizing 17-51 nmol CH4 g-1 dw h-1 , with highest Vmax 440 nmol g-1 dw h-1 under Sphagnum and lowest Km 559 nM under hummocked Carex. Nine genera and several less understood type I and type II methanotrophs were detected by the key functional gene pmoA involved in methane oxidation. Microarray signal intensities from all sites revealed Methylococcus, the affiliated Lake Washington cluster, Methylocaldum, a Japanese rice cluster, Methylosinus, Methylocystis and the affiliated Peat264 cluster. Notably enriched by site was a floodplain Methylomonas and a Methylocapsa-affiliated watershed cluster in the Sphagnum site. The climate sensitive water table was shown to be a strong controlling factor highlighting its link with the CH4 cycle in elevated wetlands.

Distinct responses of soil methanotrophy in hummocks and hollows to simulated glacier meltwater and temperature rise in Tibetan glacier foreland

Glacier foreland soils are known to be essential methane (CH₄) consumers. However, global warming and increased glacier meltwater have turned some foreland meadows into swamp meadows. The potential impact of this change on the function of foreland soils in methane consumption remains unclear. Therefore, we collected Tibetan glacier foreland soils in the non-melting season from typical microtopography in swamp meadows (hummock and hollow). Three soil moisture conditions (moist, saturated, and submerged) were set by adding glacier runoff water. Soil samples were then incubated in the laboratory for two weeks at 10 °C and 20 °C. About 5 % of ¹³CH₄/¹²CH₄ was added to the incubation bottles, and daily methane concentrations were measured. DNA stable isotope probing (DNA-SIP) and high-throughput sequencing were combined to target the active methanotroph populations. The results showed that type Ia methanotrophs, including Crenothrix, Methylobacter, and an unclassified Methylomonadaceae cluster, actively oxidized methane at 10 °C and 20 °C. There were distinct responses of methanotrophs to soil moisture rises in hummock and hollow soils, resulting in different methane oxidation potentials. In both hummock and hollow soils, the methane oxidation potential was positively correlated with temperature. Furthermore, saturated hummock soils exhibited the highest methane oxidation potential and methanotroph populations, while submerged hollow soils had the lowest. This suggests that the in-situ hummock soils, generally saturated with water, are more essential than in-situ hollows, typically submerged in water, for alleviating the global warming potential of swamp meadows in the Tibetan glacier foreland during the growing season.

Attenuation of Methane Oxidation by Nitrogen Availability in Arctic Tundra Soils

CH₄ emission in the Arctic has large uncertainty due to the lack of mechanistic understanding of the processes. CH₄ oxidation in Arctic soil plays a critical role in the process, whereby removal of up to 90% of CH₄ produced in soils by methanotrophs can occur before it reaches the atmosphere. Previous studies have reported on the importance of rising temperatures in CH₄ oxidation, but because the Arctic is typically an N-limited system, fewer studies on the effects of inorganic nitrogen (N) have been reported. However, climate change and an increase of available N caused by anthropogenic activities have recently been reported, which may cause a drastic change in CH₄ oxidation in Arctic soils. In this study, we demonstrate that excessive levels of available N in soil cause an increase in net CH₄ emissions via the reduction of CH₄ oxidation in surface soil in the Arctic tundra. In vitro experiments suggested that N in the form of NO₃^- is responsible for the decrease in CH₄ oxidation via influencing soil bacterial and methanotrophic communities. The findings of our meta-analysis suggest that CH₄ oxidation in the boreal biome is more susceptible to the addition of N than in other biomes. We provide evidence that CH₄ emissions in Arctic tundra can be enhanced by an increase of available N, with profound implications for modeling CH₄ dynamics in Arctic regions.

Comparative genomic analysis of Methylocystis sp. MJC1 as a platform strain for polyhydroxybutyrate biosynthesis

Biodegradable polyhydroxybutyrate (PHB) can be produced from methane by some type II methanotroph such as the genus Methylocystis. This study presents the comparative genomic analysis of a newly isolated methanotroph, Methylocystis sp. MJC1 as a biodegradable PHB-producing platform strain. Methylocystis sp. MJC1 accumulates up to 44.5% of PHB based on dry cell weight under nitrogen-limiting conditions. To facilitate its development as a PHB-producing platform strain, the complete genome sequence of Methylocystis sp. MJC1 was assembled, functionally annotated, and compared with genomes of other Methylocystis species. Phylogenetic analysis has shown that Methylocystis parvus to be the closest species to Methylocystis sp. MJC1. Genome functional annotation revealed that Methylocystis sp. MJC1 contains all major type II methanotroph biochemical pathways such as the serine cycle, EMC pathway, and Krebs cycle. Interestingly, Methylocystis sp. MJC1 has both particulate and soluble methane monooxygenases, which are not commonly found among Methylocystis species. In addition, this species also possesses most of the RuMP pathway reactions, a characteristic of type I methanotrophs, and all PHB biosynthetic genes. These comparative analysis would open the possibility of future practical applications such as the development of organism-specific genome-scale models and application of metabolic engineering strategies to Methylocystis sp. MJC1.

Higher pH is associated with enhanced co-occurrence network complexity, stability and nutrient cycling functions in the rice rhizosphere microbiome

The rice rhizosphere microbiota is crucial for crop yields and nutrient use efficiency. However, little is known about how co-occurrence patterns, keystone taxa and functional gene assemblages relate to soil pH in the rice rhizosphere soils. Using shotgun metagenome analysis, the rice rhizosphere microbiome was investigated across 28 rice fields in east-central China. At higher pH sites, the taxonomic co-occurrence network of rhizosphere soils was more complex and compact, as defined by higher average degree, graph density and complexity. Network stability was greatest at medium pH (6.5 < pH < 7.5), followed by high pH (7.5 < pH). Keystone taxa were more abundant at higher pH and correlated significantly with key ecosystem functions. Overall functional genes involved in C, N, P and S cycling were at a higher relative abundance in higher pH rhizosphere soils, excepting C degradation genes (e.g. key genes involved in starch, cellulose, chitin and lignin degradation). Our results suggest that the rice rhizosphere soil microbial network is more complex and stable at higher pH, possibly indicating increased efficiency of nutrient cycling. These observations may indicate routes towards more efficient soil management and understanding of the potential effects of soil acidification on the rice rhizosphere system.

Effects of municipal wastewater effluents on the digestive gland microbiome of wild freshwater mussels (Lasmigona costata)

Gut microbial communities are vital for maintaining host health, and are sensitive to diet, environment, and chemical exposures. Wastewater treatment plants (WWTPs) release effluents containing antimicrobials, pharmaceuticals, and other contaminants that may negatively affect the gut microbiome of downstream organisms. This study investigated changes in the diversity and composition of the digestive gland microbiome of flutedshell mussels (Lasmigona costata) from upstream and downstream of two large (service >100,000) WWTPs. Mussel digestive gland microbiome was analyzed following the extraction, PCR amplification, and sequencing of bacterial DNA using the V3-V4 hypervariable regions of the 16 S rRNA gene. Bacterial alpha diversity decreased at sites downstream of the second WWTP and these sites were dissimilar in beta diversity from sites upstream and downstream of the first upstream WWTP. The microbiomes of mussels collected downstream of the first WWTP had increased relative abundances of Actinobacteria, Bacteroidetes, and Firmicutes, with a decrease in Cyanobacteria, compared to upstream mussels. Meanwhile, those collected downstream of the second WWTP increased in Proteobacteria and decreased in Actinobacteria, Bacteroidetes, and Tenericutes. Increased Proteobacteria has been linked to adverse effects in mammals, but their functions in mussels is currently unknown. Finally, effluent-derived bacteria were found in the microbiome of mussels downstream of both WWTPs but not in those from upstream. Overall, results show that the digestive gland microbiome of mussels collected upstream and downstream of WWTPs differed, which has implications for altered host health and the transport of WWTP-derived bacteria through aquatic ecosystems.

Methylocystis silviterrae sp.nov., a high-affinity methanotrophic bacterium isolated from the boreal forest soil

A novel species is proposed for a high-affinity methanotrophic representative of the genus Methylocystis. Strain FS^T was isolated from a weakly acidic (pH 5.3) mixed forest soil of the southern Moscow area. Cells of FS^T are aerobic, Gram-negative, non-motile, curved coccoids or short rods that contain an intracytoplasmic membrane system typical of type-II methanotrophs. Only methane and methanol are used as carbon sources. FS^T grew at a temperature range of 4-37 °C (optimum 25-30 °C) and a pH range of 4.5 to 7.5 (optimum pH 6.0-6.5). The major fatty acids were C_{18  :  1}ω8c, C_{18  :  1}ω7c and C_{18  :  0}; the major quinone as Q-8. FS^T displays 16S rRNA gene sequences similarity to other taxonomically recognized members of the genus Methylocystis, with Methylocystis hirsuta CSC1^T (99.6 % similarity) and Methylocystis rosea SV97^T (99.3 % similarity) as its closest relatives. The genome comprises 3.85 Mbp and has a DNA G+C content of 62.6 mol%. Genomic analyses and DNA-DNA relatedness with genome-sequenced members of the genus Methylocystis demonstrated that FS^T could be separated from its closest relatives. FS^T possesses two particulate methane monooxygenases (pMMO): low-affinity pMMO1 and high-affinity pMMO2. In laboratory experiments, it was demonstrated that FS^T might oxidize methane at atmospheric concentration. The genome contained various genes for nitrogen fixation, polyhydroxybutyrate synthesis, antibiotic resistance and detoxification of arsenic, cyanide and mercury. On the basis of genotypic, phenotypic and chemotaxonomic characteristics, it is proposed that the isolate represents a novel species, Methylocystis silviterrae sp. nov. The type strain is FS^T (=KCTC 82935^T=VKM B-3535^T).

Selection of methanotrophic platform for methanol production using methane and biogas

To develop biotechnological process for methane to methanol conversion, selection of a suitable methanotrophic platform is an important aspect. Systematic approach based on literature and public databases was developed to select representative methanotrophs Methylotuvimicrobium alcaliphilum, Methylomonas methanica, Methylosinus trichosporium and Methylocella silvestris. Selected methanotrophs were further investigated for methanol tolerance and methanol production on pure methane as well as biogas along with key enzyme activities involved in methane utilization. Among selected methanotrophs M. alcaliphilum showed maximum methanol tolerance of 6% v/v along with maximum methanol production of 307.90 mg/L and 247.37 mg/L on pure methane and biogas respectively. Activity of methane monooxygenase and formate dehydrogenase enzymes in M.alcaliphilum was significantly higher up to 98.40 nmol/min/mg cells and 0.87 U/mg protein, respectively. Biotransformation trials in 14 L fermentor resulted in increased methanol production up to 418 and 331.20 mg/L, with yield coefficient 0.83 and 0.71 mg methanol/mg of pure methane and biogas respectively. The systematic selection resulted in haloalkaliphilic strain M. alcaliphilum as one of the potential methanotroph for bio-methanol production.

Unexpected metabolic versatility among type II methanotrophs in the Alphaproteobacteria

Aerobic methane-oxidizing bacteria, or methanotrophs, play a crucial role in the global methane cycle. Their methane oxidation activity in various environmental settings has a great mitigation effect on global climate change. Alphaproteobacterial methanotrophs were among the first to be taxonomically characterized, nowadays unified in the Methylocystaceae and Beijerinckiaceae families. Originally thought to have an obligate growth requirement for methane and related one-carbon compounds as a source of carbon and energy, it was later shown that various alphaproteobacterial methanotrophs are facultative, able to grow on multi-carbon compounds such as acetate. Most recently, we expanded our knowledge of the metabolic versatility of alphaproteobacterial methanotrophs. We showed that Methylocystis sp. strain SC2 has the capacity for mixotrophic growth on H2 and CH4. This mini-review will summarize the change in perception from the long-held paradigm of obligate methanotrophy to today's recognition of alphaproteobacterial methanotrophs as having both facultative and mixotrophic capabilities.

Verrucomicrobial methanotrophs grow on diverse C3 compounds and use a homolog of particulate methane monooxygenase to oxidize acetone

Short-chain alkanes (SCA; C2-C4) emitted from geological sources contribute to photochemical pollution and ozone production in the atmosphere. Microorganisms that oxidize SCA and thereby mitigate their release from geothermal environments have rarely been studied. In this study, propane-oxidizing cultures could not be grown from acidic geothermal samples by enrichment on propane alone, but instead required methane addition, indicating that propane was co-oxidized by methanotrophs. “Methylacidiphilum” isolates from these enrichments did not grow on propane as a sole energy source but unexpectedly did grow on C3 compounds such as 2-propanol, acetone, and acetol. A gene cluster encoding the pathway of 2-propanol oxidation to pyruvate via acetol was upregulated during growth on 2-propanol. Surprisingly, this cluster included one of three genomic operons (pmoCAB3) encoding particulate methane monooxygenase (PMO), and several physiological tests indicated that the encoded PMO3 enzyme mediates the oxidation of acetone to acetol. Acetone-grown resting cells oxidized acetone and butanone but not methane or propane, implicating a strict substrate specificity of PMO3 to ketones instead of alkanes. Another PMO-encoding operon, pmoCAB2, was induced only in methane-grown cells, and the encoded PMO2 could be responsible for co-metabolic oxidation of propane to 2-propanol. In nature, propane probably serves primarily as a supplemental growth substrate for these bacteria when growing on methane.

A Novel Laboratory-Scale Mesocosm Setup to Study Methane Emission Mitigation by Sphagnum Mosses and Associated Methanotrophs

Degraded peatlands are often rewetted to prevent oxidation of the peat, which reduces CO₂ emission. However, the created anoxic conditions will boost methane (CH₄) production and thus emission. Here, we show that submerged Sphagnum peat mosses in rewetted-submerged peatlands can reduce CH₄ emission from peatlands with 93%. We were able to mimic the field situation in the laboratory by using a novel mesocosm set-up. By combining these with 16S rRNA gene amplicon sequencing and qPCR analysis of the pmoA and mmoX genes, we showed that submerged Sphagnum mosses act as a niche for CH₄ oxidizing bacteria. The tight association between Sphagnum peat mosses and methane oxidizing bacteria (MOB) significantly reduces CH₄ emissions by peatlands and can be studied in more detail in the mesocosm setup developed in this study.

Genomic and Physiological Properties of a Facultative Methane-Oxidizing Bacterial Strain of Methylocystis sp. from a Wetland

Methane-oxidizing bacteria are crucial players in controlling methane emissions. This study aimed to isolate and characterize a novel wetland methanotroph to reveal its role in the wetland environment based on genomic information. Based on phylogenomic analysis, the isolated strain, designated as B8, is a novel species in the genus Methylocystis. Strain B8 grew in a temperature range of 15 °C to 37 °C (optimum 30–35 °C) and a pH range of 6.5 to 10 (optimum 8.5–9). Methane, methanol, and acetate were used as carbon sources. Hydrogen was produced under oxygen-limited conditions. The assembled genome comprised of 3.39 Mbp and 59.9 mol% G + C content. The genome contained two types of particulate methane monooxygenases (pMMO) for low-affinity methane oxidation (pMMO1) and high-affinity methane oxidation (pMMO2). It was revealed that strain B8 might survive atmospheric methane concentration. Furthermore, the genome had various genes for hydrogenase, nitrogen fixation, polyhydroxybutyrate synthesis, and heavy metal resistance. This metabolic versatility of strain B8 might enable its survival in wetland environments.

Facultative methanotrophs - diversity, genetics, molecular ecology and biotechnological potential: a mini-review

Methane-oxidizing bacteria (methanotrophs) play a vital role in reducing atmospheric methane emissions, and hence mitigating their potent global warming effects. A significant proportion of the methane released is thermogenic natural gas, containing associated short-chain alkanes as well as methane. It was one hundred years following the description of methanotrophs that facultative strains were discovered and validly described. These can use some multi-carbon compounds in addition to methane, often small organic acids, such as acetate, or ethanol, although Methylocella strains can also use short-chain alkanes, presumably deriving a competitive advantage from this metabolic versatility. Here, we review the diversity and molecular ecology of facultative methanotrophs. We discuss the genetic potential of the known strains and outline the consequent benefits they may obtain. Finally, we review the biotechnological promise of these fascinating microbes.

Methanobactin from methanotrophs: genetics, structure, function and potential applications

Aerobic methane-oxidizing bacteria of the Alphaproteobacteria have been found to express a novel ribosomally synthesized post-translationally modified polypeptide (RiPP) termed methanobactin (MB). The primary function of MB in these microbes appears to be for copper uptake, but MB has been shown to have multiple capabilities, including oxidase, superoxide dismutase and hydrogen peroxide reductase activities, the ability to detoxify mercury species, as well as acting as an antimicrobial agent. Herein, we describe the diversity of known MBs as well as the genetics underlying MB biosynthesis. We further propose based on bioinformatics analyses that some methanotrophs may produce novel forms of MB that have yet to be characterized. We also discuss recent findings documenting that MBs play an important role in controlling copper availability to the broader microbial community, and as a result can strongly affect the activity of microbes that require copper for important enzymatic transformations, e.g. conversion of nitrous oxide to dinitrogen. Finally, we describe procedures for the detection/purification of MB, as well as potential medical and industrial applications of this intriguing RiPP.

Pan-Genome-Based Analysis as a Framework for Demarcating Two Closely Related Methanotroph Genera Methylocystis and Methylosinus

The Methylocystis and Methylosinus are two of the five genera that were included in the first taxonomic framework of methanotrophic bacteria created half a century ago. Members of both genera are widely distributed in various environments and play a key role in reducing methane fluxes from soils and wetlands. The original separation of these methanotrophs in two distinct genera was based mainly on their differences in cell morphology. Further comparative studies that explored various single-gene-based phylogenies suggested the monophyletic nature of each of these genera. Current availability of genome sequences from members of the Methylocystis/Methylosinus clade opens the possibility for in-depth comparison of the genomic potentials of these methanotrophs. Here, we report the finished genome sequence of Methylocystis heyeri H2^T and compare it to 23 currently available genomes of Methylocystis and Methylosinus species. The phylogenomic analysis confirmed that members of these genera form two separate clades. The Methylocystis/Methylosinus pan-genome core comprised 1173 genes, with the accessory genome containing 4941 and 11,192 genes in the shell and the cloud, respectively. Major differences between the genome-encoded environmental traits of these methanotrophs include a variety of enzymes for methane oxidation and dinitrogen fixation as well as genomic determinants for cell motility and photosynthesis.

The effect of methane and odd-chain fatty acids on 3-hydroxybutyrate (3HB) and 3-hydroxyvalerate (3HV) synthesis by a Methylosinus-dominated mixed culture

A methanotrophic community was enriched in a semi-continuous reactor under non-aseptic conditions with methane and ammonia as carbon and nitrogen source. After a year of operation, Methylosinus sp., accounted for 80% relative abundance of the total sequences identified from potential polyhydroxyalkanoates (PHAs) producers, dominated the methane-fed enrichment. Prior to induction of PHA accumulation, cells harvested from the parent reactor contained low level of PHA at 4.0 ± 0.3 wt%. The cells were later incubated in the absence of ammonia with various combinations of methane, propionic acid, and valeric acid to induce biosynthesis of poly(3-hydroxybutyrate) (PHB) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV). Previous studies reported that methanotrophic utilization of odd-chain fatty acids for the production of PHAs requires reducing power from methane oxidation. However, our findings demonstrated that the PHB-containing methanotrophic enrichment does not require methane availability to generate 3-hydroxybutyrate (3HB) and 3-hydroxyvalerate (3HV)—when odd-chain fatty acids are presented. The enrichment yielded up to 14 wt% PHA with various mole fractions of 3HV monomer depending on the availability of methane and odd-fatty acids. Overall, the addition of valeric acid resulted in a higher PHA content and a higher 3HV fraction. The highest 3HV fraction (up to 65 mol%) was obtained from the methane–valeric acid experiment, which is higher than those previously reported for PHA-producing methanotrophic mixed microbial cultures.

The gut microbiome of freshwater Unionidae mussels is determined by host species and is selectively retained from filtered seston

Freshwater mussels are a species-rich group of aquatic invertebrates that are among the most endangered groups of fauna worldwide. As filter-feeders that are constantly exposed to new microbial inoculants, mussels represent an ideal system to investigate the effects of species or the environment on gut microbiome composition. In this study, we examined if host species or site exerts a greater influence on microbiome composition. Individuals of four co-occurring freshwater mussel species, Cyclonaias asperata, Fusconaia cerina, Lampsilis ornata, and Obovaria unicolor were collected from six sites along a 50 km stretch of the Sipsey River in Alabama, USA. High throughput 16S rRNA gene sequencing revealed that mussel gut bacterial microbiota were distinct from bacteria on seston suspended in the water column, and that the composition of the gut microbiota was influenced by both host species and site. Despite species and environmental variation, the most frequently detected sequences within the mussel microbiota were identified as members of the Clostridiales. Sequences identified as the nitrogen-fixing taxon Methylocystis sp. were also abundant in all mussel species, and sequences of both bacterial taxa were more abundant in mussels than in water. Site physicochemical conditions explained almost 45% of variation in seston bacterial communities but less than 8% of variation in the mussel bacterial microbiome. Together, these findings suggest selective retention of bacterial taxa by the freshwater mussel host, and that both species and the environment are important in determining mussel gut microbiome composition.

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.

Activity and Identification of Methanotrophic Bacteria in Arable and No-Tillage Soils from Lublin Region (Poland)

Methanotrophic bacteria are able to use methane (CH₄) as a sole carbon and energy source. Photochemical oxidation of methane takes place in the stratosphere, whereas in the troposphere, this process is carried out by methanotrophic bacteria. On the one hand, it is known that the efficiency of biological CH₄ oxidation is dependent on the mode of land use but, on the other hand, the knowledge of this impact on methanotrophic activity (MTA) is still limited. Thus, the aim of the study was to determine the CH₄ oxidation ability of methanotrophic bacteria inhabiting selected arable and no-tillage soils from the Lublin region (Albic Luvisol, Brunic Arenosol, Haplic Chernozem, Calcaric Cambisol) and to identify bacteria involved in this process. MTA was determined based on incubation of soils in air with addition of methane at the concentrations of 0.002, 0.5, 1, 5, and 10%. The experiment was conducted in a temperature range of 10-30 °C. Methanotrophs in soils were identified by next-generation sequencing (NGS). MTA was confirmed in all investigated soils (in the entire range of the tested methane concentrations and temperatures, except for the arable Albic Luvisol). Importantly, the MTA values in the no-tillage soil were nearly two-fold higher than in the cultivated soils. Statistical analysis indicated a significant influence of land use, type of soil, temperature, and especially methane concentration (p < 0.05) on MTA. Metagenomic analysis confirmed the presence of methanotrophs from the genus Methylocystis (Alphaproteobacteria) in the studied soils (except for the arable Albic Luvisol). Our results also proved the ability of methanotrophic bacteria to oxidize methane although they constituted only up to 0.1% of the total bacterial community.

Electron donor-driven bacterial and archaeal community patterns along forest ring edges in Ontario, Canada

Forest rings are 50-1600 m diameter circular structures found in boreal forests around the globe. They are believed to be chemically reducing chimney features, having an accumulation of reduced species in the middle of the ring and oxidation processes occurring at the ring's edges. It has been suggested that microorganisms could be responsible for charge transfer from the inside to the outside of the ring. To explore this, we focused on the changes in bacterial and archaeal communities in the ring edges of two forest rings, the 'Bean' and the 'Thorn North' ring, in proximity to each other in Ontario, Canada. The drier samples from the methane-sourced Bean ring were characterized by the abundance of bacteria from the classes Deltaproteobacteria and Gemmatimonadetes. Geobacter spp. and methanotrophs, such as Candidatus Methylomirabilis and Methylobacter, were highly abundant in these samples. The Thorn North ring, centred on an H₂ S accumulation in groundwater, had wetter samples and its communities were dominated by the classes Alphaproteobacteria and Anaerolineae. This ring's microbial communities showed an overall higher microbial diversity supported by higher available free energy. For both rings, the species diversity was highest near the borders of the 20-30 m broad ring edges.

Unusual Genomic Traits Suggest Methylocystis bryophila S285 to Be Well Adapted for Life in Peatlands

The genus Methylocystis belongs to the class Alphaproteobacteria, the family Methylocystaceae, and encompasses aerobic methanotrophic bacteria with the serine pathway of carbon assimilation. All Methylocystis species are able to fix dinitrogen and several members of this genus are also capable of using acetate or ethanol in the absence of methane, which explains their wide distribution in various habitats. One additional trait that enables their survival in the environment is possession of two methane-oxidizing isozymes, the conventional particulate methane monooxygenase (pMMO) with low-affinity to substrate (pMMO1) and the high-affinity enzyme (pMMO2). Here, we report the finished genome sequence of Methylocystis bryophila S285, a pMMO2-possessing methanotroph from a Sphagnum-dominated wetland, and compare it to the genome of Methylocystis sp. strain SC2, which is the first methanotroph with confirmed high-affinity methane oxidation potential. The complete genome of Methylocystis bryophila S285 consists of a 4.53 Mb chromosome and one plasmid, 175 kb in size. The genome encodes two types of particulate MMO (pMMO1 and pMMO2), soluble MMO and, in addition, contains a pxmABC-like gene cluster similar to that present in some gammaproteobacterial methanotrophs. The full set of genes related to the serine pathway, the tricarboxylic acid cycle as well as the ethylmalonyl-CoA pathway is present. In contrast to most described methanotrophs including Methylocystis sp. strain SC2, two different types of nitrogenases, that is, molybdenum–iron and vanadium–iron types, are encoded in the genome of strain S285. This unique combination of genome-based traits makes Methylocystis bryophila well adapted to the fluctuation of carbon and nitrogen sources in wetlands.

Genomic Insights Into the Acid Adaptation of Novel Methanotrophs Enriched From Acidic Forest Soils

Soil acidification is accelerated by anthropogenic and agricultural activities, which could significantly affect global methane cycles. However, detailed knowledge of the genomic properties of methanotrophs adapted to acidic soils remains scarce. Using metagenomic approaches, we analyzed methane-utilizing communities enriched from acidic forest soils with pH 3 and 4, and recovered near-complete genomes of proteobacterial methanotrophs. Novel methanotroph genomes designated KS32 and KS41, belonging to two representative clades of methanotrophs (Methylocystis of Alphaproteobacteria and Methylobacter of Gammaproteobacteria), were dominant. Comparative genomic analysis revealed diverse systems of membrane transporters for ensuring pH homeostasis and defense against toxic chemicals. Various potassium transporter systems, sodium/proton antiporters, and two copies of proton-translocating F1F0-type ATP synthase genes were identified, which might participate in the key pH homeostasis mechanisms in KS32. In addition, the V-type ATP synthase and urea assimilation genes might be used for pH homeostasis in KS41. Genes involved in the modification of membranes by incorporation of cyclopropane fatty acids and hopanoid lipids might be used for reducing proton influx into cells. The two methanotroph genomes possess genes for elaborate heavy metal efflux pumping systems, possibly owing to increased heavy metal toxicity in acidic conditions. Phylogenies of key genes involved in acid adaptation, methane oxidation, and antiviral defense in KS41 were incongruent with that of 16S rRNA. Thus, the detailed analysis of the genome sequences provides new insights into the ecology of methanotrophs responding to soil acidification.

Improved methane removal in exhaust gas from biogas upgrading process using immobilized methane-oxidizing bacteria

Methane in exhaust gas from biogas upgrading process, which is a greenhouse gas, could cause global warming. The biofilter with immobilized methane-oxidizing bacteria (MOB) is a promising approach for methane removal, and the selections of inoculated MOB culture and support material are vital for the biofilter. In this work, five MOB consortia were enriched at different methane concentrations. The MOB-20 consortium enriched at the methane concentration of 20.0% (v/v) was then immobilized on sponge and two particle sizes of volcanic rock in biofilters to remove methane in exhaust gas from biogas upgrading process. Results showed that the immobilized MOB performed more admirable methane removal capacity than suspended cells. The immobilized MOB on sponge reached the highest methane removal efficiency (RE) of 35%. The rough surface, preferable hydroscopicity, appropriate pore size and particle size of support material might favor the MOB immobilization and accordingly methane removal.

Drinking water microbiome assembly induced by water stagnation

What happens to tap water when you are away from home? Day-to-day water stagnation in building plumbing can potentially result in water quality deterioration (e.g., lead release or pathogen proliferation), which is a major public health concern. However, little is known about the microbial ecosystem processes in plumbing systems, hindering the development of biological monitoring strategies. Here, we track tap water microbiome assembly in situ, showing that bacterial community composition changes rapidly from the city supply following ~6-day stagnation, along with an increase in cell count from 10³ cells/mL to upwards of 7.8 × 10⁵ cells/mL. Remarkably, bacterial community assembly was highly reproducible in this built environment system (median Spearman correlation between temporal replicates = 0.78). Using an island biogeography model, we show that neutral processes arising from the microbial communities in the city water supply (i.e., migration and demographic stochasticity) explained the island community composition in proximal pipes (Goodness-of-fit = 0.48), yet declined as water approached the faucet (Goodness-of-fit = 0.21). We developed a size-effect model to simulate this process, which indicated that pipe diameter drove these changes by mediating the kinetics of hypochlorite decay and cell detachment, affecting selection, migration, and demographic stochasticity. Our study challenges current water quality monitoring practice worldwide which ignore biological growth in plumbing, and suggests the island biogeography model as a useful framework to evaluate building water system quality.

Positive diversity-functioning relationships in model communities of methanotrophic bacteria

Biodiversity enhances ecosystem functions such as biomass production and nutrient cycling. Although the majority of the terrestrial biodiversity is hidden in soils, very little is known about the importance of the diversity of microbial communities for soil functioning. Here, we tested effects of biodiversity on the functioning of methanotrophs, a specialized group of soil bacteria that plays a key role in mediating greenhouse gas emissions from soils. Using pure strains of methanotrophic bacteria, we assembled artificial communities of different diversity levels, with which we inoculated sterile soil microcosms. To assess the functioning of these communities, we measured methane oxidation by gas chromatography throughout the experiment and determined changes in community composition and community size at several time points by quantitative PCR and sequencing. We demonstrate that microbial diversity had a positive overyielding effect on methane oxidation, in particular at the beginning of the experiment. This higher assimilation of CH₄ at high diversity translated into increased growth and significantly larger communities towards the end of the study. The overyielding of mixtures with respect to CH₄ consumption and community size were positively correlated. The temporal CH₄ consumption profiles of strain monocultures differed, raising the possibility that temporal complementarity of component strains drove the observed community-level strain richness effects; however, the community niche metric we derived from the temporal activity profiles did not explain the observed strain richness effect. The strain richness effect also was unrelated to both the phylogenetic and functional trait diversity of mixed communities. Overall, our results suggest that positive biodiversity-ecosystem-function relationships show similar patterns across different scales and may be widespread in nature. Additionally, biodiversity is probably also important in natural methanotrophic communities for the ecosystem function methane oxidation. Therefore, maintaining soil conditions that support a high diversity of methanotrophs may help to reduce the emission of the greenhouse gas methane.

Diversity and Habitat Preferences of Cultivated and Uncultivated Aerobic Methanotrophic Bacteria Evaluated Based on pmoA as Molecular Marker

Methane-oxidizing bacteria are characterized by their capability to grow on methane as sole source of carbon and energy. Cultivation-dependent and -independent methods have revealed that this functional guild of bacteria comprises a substantial diversity of organisms. In particular the use of cultivation-independent methods targeting a subunit of the particulate methane monooxygenase (pmoA) as functional marker for the detection of aerobic methanotrophs has resulted in thousands of sequences representing "unknown methanotrophic bacteria." This limits data interpretation due to restricted information about these uncultured methanotrophs. A few groups of uncultivated methanotrophs are assumed to play important roles in methane oxidation in specific habitats, while the biology behind other sequence clusters remains still largely unknown. The discovery of evolutionary related monooxygenases in non-methanotrophic bacteria and of pmoA paralogs in methanotrophs requires that sequence clusters of uncultivated organisms have to be interpreted with care. This review article describes the present diversity of cultivated and uncultivated aerobic methanotrophic bacteria based on pmoA gene sequence diversity. It summarizes current knowledge about cultivated and major clusters of uncultivated methanotrophic bacteria and evaluates habitat specificity of these bacteria at different levels of taxonomic resolution. Habitat specificity exists for diverse lineages and at different taxonomic levels. Methanotrophic genera such as Methylocystis and Methylocaldum are identified as generalists, but they harbor habitat specific methanotrophs at species level. This finding implies that future studies should consider these diverging preferences at different taxonomic levels when analyzing methanotrophic communities.

Core-satellite populations and seasonality of water meter biofilms in a metropolitan drinking water distribution system

Drinking water distribution systems (DWDSs) harbor the microorganisms in biofilms and suspended communities, yet the diversity and spatiotemporal distribution have been studied mainly in the suspended communities. This study examined the diversity of biofilms in an urban DWDS, its relationship with suspended communities and its dynamics. The studied DWDS in Urbana, Illinois received conventionally treated and disinfected water sourced from the groundwater. Over a 2-year span, biomass were sampled from household water meters (n=213) and tap water (n=20) to represent biofilm and suspended communities, respectively. A positive correlation between operational taxonomic unit (OTU) abundance and occupancy was observed. Examined under a 'core-satellite' model, the biofilm community comprised 31 core populations that encompassed 76.7% of total 16 S rRNA gene pyrosequences. The biofilm communities shared with the suspended community highly abundant and prevalent OTUs, which related to methano-/methylotrophs (i.e., Methylophilaceae and Methylococcaceae) and aerobic heterotrophs (Sphingomonadaceae and Comamonadaceae), yet differed by specific core populations and lower diversity and evenness. Multivariate tests indicated seasonality as the main contributor to community structure variation. This pattern was resilient to annual change and correlated to the cyclic fluctuations of core populations. The findings of a distinctive biofilm community assemblage and methano-/methyltrophic primary production provide critical insights for developing more targeted water quality monitoring programs and treatment strategies for groundwater-sourced drinking water systems.

Uncultivated Methylocystis Species in Paddy Soil Include Facultative Methanotrophs that Utilize Acetate

Methanotrophs are crucial in regulating methane emission from rice field systems. Type II methanotrophs in particular are often observed in high abundance in paddy soil. Some cultivated species of Methylocystis are able to grow on acetate in the absence of methane. We hypothesize that the dominant type II methanotrophs in paddy soil might facultatively utilize acetate for growth, which we evaluate in the present study. The measurement of methane oxidation rates showed that the methanotrophic activity in paddy soil was inhibited by the addition of acetate compared to the continuous supplementation of methane, but the paddy soil maintained the methane oxidation capacity and recovered following methane supplementation. Terminal restriction fragment length polymorphism analysis (T-RFLP) combined with cloning and sequencing of pmoA genes showed that Methylocystis was enriched after incubation with added acetate, while the type I methanotrophs Methylocaldum/Methylococcus and Methylobacter were enriched by methane supplementation. A comparison of pmoA sequences obtained in this study with those in the public database indicated that they were globally widespread in paddy soils or in associated with rice roots. Furthermore, we performed stable isotope probing (SIP) of pmoA messenger RNA (mRNA) to investigate the assimilation of (13)C-acetate by paddy soil methanotrophs. RNA-SIP revealed that Methylocystis-related methanotrophs which shared the same genotype of the above enriched species were significantly labelled. It indicates that these methanotrophs actively assimilated the labelled acetate in paddy soil. Altogether, these results suggested that uncultivated Methylocystis species are facultative methanotrophs utilizing acetate as a secondary carbon source in paddy soil.

Bioenergetic evolution in proteobacteria and mitochondria

Mitochondria are the energy-producing organelles of our cells and derive from bacterial ancestors that became endosymbionts of microorganisms from a different lineage, together with which they formed eukaryotic cells. For a long time it has remained unclear from which bacteria mitochondria actually evolved, even if these organisms in all likelihood originated from the α lineage of proteobacteria. A recent article (Degli Esposti M, et al. 2014. Evolution of mitochondria reconstructed from the energy metabolism of living bacteria. PLoS One 9:e96566) has presented novel evidence indicating that methylotrophic bacteria could be among the closest living relatives of mitochondrial ancestors. Methylotrophs are ubiquitous bacteria that live on single carbon sources such as methanol and methane; in the latter case they are called methanotrophs. In this review, I examine their possible ancestry to mitochondria within a survey of the common features that can be found in the central and terminal bioenergetic systems of proteobacteria and mitochondria. I also discuss previously overlooked information on methanotrophic bacteria, in particular their intracytoplasmic membranes resembling mitochondrial cristae and their capacity of establishing endosymbiotic relationships with invertebrate animals and archaic plants. This information appears to sustain the new idea that mitochondrial ancestors could be related to extant methanotrophic proteobacteria, a possibility that the genomes of methanotrophic endosymbionts will hopefully clarify.

Remarkable recovery and colonization behaviour of methane oxidizing bacteria in soil after disturbance is controlled by methane source only

Little is understood about the relationship between microbial assemblage history, the composition and function of specific functional guilds and the ecosystem functions they provide. To learn more about this relationship we used methane oxidizing bacteria (MOB) as model organisms and performed soil microcosm experiments comprised of identical soil substrates, hosting distinct overall microbial diversities(i.e., full, reduced and zero total microbial and MOB diversities). After inoculation with undisturbed soil, the recovery of MOB activity, MOB diversity and total bacterial diversity were followed over 3 months by methane oxidation potential measurements and analyses targeting pmoA and 16S rRNA genes. Measurement of methane oxidation potential demonstrated different recovery rates across the different treatments. Despite different starting microbial diversities, the recovery and succession of the MOB communities followed a similar pattern across the different treatment microcosms. In this study we found that edaphic parameters were the dominant factor shaping microbial communities over time and that the starting microbial community played only a minor role in shaping MOB microbial community.

Gammaproteobacterial methanotrophs dominate cold methane seeps in floodplains of West Siberian rivers

A complex system of muddy fluid-discharging and methane (CH4)-releasing seeps was discovered in a valley of the river Mukhrinskaya, one of the small rivers of the Irtysh Basin, West Siberia. CH4 flux from most (90%) of these gas ebullition sites did not exceed 1.45 g CH4 h(-1), while some seeps emitted up to 5.54 g CH4 h(-1). The δ(13)C value of methane released from these seeps varied between -71.1 and -71.3‰, suggesting its biogenic origin. Although the seeps were characterized by low in situ temperatures (3.5 to 5°C), relatively high rates of methane oxidation (15.5 to 15.9 nmol CH4 ml(-1) day(-1)) were measured in mud samples. Fluorescence in situ hybridization detected 10(7) methanotrophic bacteria (MB) per g of mud (dry weight), which accounted for up to 20.5% of total bacterial cell counts. Most (95.8 to 99.3%) methanotroph cells were type I (gammaproteobacterial) MB. The diversity of methanotrophs in this habitat was further assessed by pyrosequencing of pmoA genes, encoding particulate methane monooxygenase. A total of 53,828 pmoA gene sequences of seep-inhabiting methanotrophs were retrieved and analyzed. Nearly all of these sequences affiliated with type I MB, including the Methylobacter-Methylovulum-Methylosoma group, lake cluster 2, and several as-yet-uncharacterized methanotroph clades. Apparently, microbial communities attenuating methane fluxes from these local but strong CH4 sources in floodplains of high-latitude rivers have a large proportion of potentially novel, psychrotolerant methanotrophs, thereby providing a challenge for future isolation studies.

Descriptions of Roseiarcus fermentans gen. nov., sp. nov., a bacteriochlorophyll a-containing fermentative bacterium related phylogenetically to alphaproteobacterial methanotrophs, and of the family Roseiarcaceae fam. nov

A light-pink-pigmented, microaerophilic bacterium was obtained from a methanotrophic consortium enriched from acidic Sphagnum peat and designated strain Pf56(T). Cells of this bacterium were Gram-negative, non-motile, thick curved rods that contained a vesicular intracytoplasmic membrane system characteristic of some purple non-sulfur alphaproteobacteria. The absorption spectrum of acetone/methanol extracts of cells grown in the light showed maxima at 363, 475, 505, 601 and 770 nm; the peaks at 363 and 770 nm are characteristic of bacteriochlorophyll a. However, in contrast to purple non-sulfur bacteria, strain Pf56(T) was unable to grow phototrophically under anoxic conditions in the light. Best growth occurred on some sugars and organic acids under micro-oxic conditions by means of fermentation. The fermentation products were propionate, acetate and hydrogen. Slow chemo-organotrophic growth was also observed under fully oxic conditions. Light stimulated growth. C1 substrates were not utilized. Strain Pf56(T) grew at pH 4.0-7.0 (optimum pH 5.5-6.5) and at 15-30 °C (optimum 22-28 °C). The major cellular fatty acids were 19 : 0 cyclo ω8c and 18 : 1ω7c; quinones were represented by ubiquinone Q-10. The G+C content of the DNA was 70.0 mol%. Strain Pf56 displays 93.6-94.7 and 92.7-93.7% 16S rRNA gene sequence similarity to members of the families Methylocystaceae and Beijerinckiaceae, respectively, and belongs to a large cluster of environmental sequences retrieved from various wetlands and forest soils in cultivation-independent studies. Phenotypic, genotypic and chemotaxonomic characteristics of strain Pf56(T) suggest that it represents a novel genus and species of bacteriochlorophyll a-containing fermentative bacteria, for which the name Roseiarcus fermentans gen. nov., sp. nov. is proposed. Strain Pf56(T) ( = DSM 24875(T) = VKM B-2876(T)) is the type strain of Roseiarcus fermentans, and is also the first characterized member of a novel family within the class Alphaproteobacteria, Roseiarcaceae fam. nov.

Alsobacter metallidurans gen. nov., sp. nov., a thallium-tolerant soil bacterium in the order Rhizobiales

A thallium-tolerant, aerobic bacterium, designated strain SK200a-9(T), isolated from a garden soil sample was characterized using a polyphasic approach. Comparative analysis of 16S rRNA gene sequences revealed that strain SK200a-9(T) was affiliated with an uncultivated lineage within the Alphaproteobacteria and the nearest cultivated neighbours were bacteria in genera in the family Methylocystaceae (93.3-94.4% 16S rRNA gene sequence similarity) and the family Beijerinckiaceae (92.3-93.1%) in the order Rhizobiales. Cells of strain SK200a-9(T) were Gram-stain-negative, non-motile, non-spore-forming, poly-β-hydroxybutyrate-accumulating rods. The strain was a chemo-organotrophic bacterium, which was incapable of growth on C1 substrates. Catalase and oxidase were positive. Atmospheric nitrogen fixation and nitrate reduction were negative. The strain contained ubiquinone Q-10 and cellular fatty acids C18 : 1ω7c, C18 : 0, C16 : 1ω7c and C16 : 0 as predominant components. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content was 64.8 mol%. On the basis of the information described above, strain SK200a-9(T) is considered to represent a novel species of a new genus in the order Rhizobiales, for which the name Alsobacter metallidurans gen. nov., sp. nov. is proposed. The type strain of Alsobacter metallidurans is SK200a-9(T) ( = NBRC 107718(T) = CGMCC 1.12214(T)).