Methylomarinovum tepidoasis sp. nov., a moderately thermophilic methanotroph of the family Methylothermaceae isolated from a deep-sea hydrothermal field

A novel aerobic methanotrophic bacterium, designated as strain IN45T, was isolated from in situ colonisation systems deployed at the Iheya North deep-sea hydrothermal field in the mid-Okinawa Trough. IN45T was a moderately thermophilic obligate methanotroph that grew only on methane or methanol at temperatures between 25 and 56 °C (optimum 45-50 °C). It was an oval-shaped, Gram-reaction-negative, motile bacterium with a single polar flagellum and an intracytoplasmic membrane system. It required 1.5-4.0 % (w/v) NaCl (optimum 2-3 %) for growth. The major phospholipid fatty acids were C16 : 1ω7c, C16 : 0 and C18 : 1ω7c. The major isoprenoid quinone was Q-8. The 16S rRNA gene sequence comparison revealed 99.1 % sequence identity with Methylomarinovum caldicuralii IT-9T, the only species of the genus Methylomarinovum with a validly published name within the family Methylothermaceae. The complete genome sequence of IN45T consisted of a 2.42-Mbp chromosome (DNA G+C content, 64.1 mol%) and a 20.5-kbp plasmid. The genome encodes genes for particulate methane monooxygenase and two types of methanol dehydrogenase (mxaFI and xoxF). Genes involved in the ribulose monophosphate pathway for carbon assimilation are encoded, but the transaldolase gene was not found. The genome indicated that IN45T performs partial denitrification of nitrate to N2O, and its occurrence was indirectly confirmed by N2O production in cultures grown with nitrate. Genomic relatedness indices between the complete genome sequences of IN45T and M. caldicuralii IT-9T, such as digital DNA-DNA hybridisation (51.2 %), average nucleotide identity (92.94 %) and average amino acid identity (93.21 %), indicated that these two methanotrophs should be separated at the species level. On the basis of these results, strain IN45T represents a novel species, for which we propose the name Methylomarinovum tepidoasis sp. nov. with IN45T (=JCM 35101T =DSM 113422T) as the type strain.

Effects of Aeriscardovia aeriphila on growth performance, antioxidant functions, immune responses, and gut microbiota in broiler chickens

Aeriscardovia aeriphila, also known as Bifidobacterium aerophilum, was first isolated from the caecal contents of pigs and the faeces of cotton-top tamarin. Bifidobacterium species play important roles in preventing intestinal infections, decreasing cholesterol levels, and stimulating the immune system. In this study, we isolated a strain of bacteria from the duodenal contents of broiler chickens, which was identified as A. aeriphila, and then evaluated the effects of A. aeriphila on growth performance, antioxidant functions, immune functions, and gut microbiota in commercial broiler chickens. Chickens were orally gavaged with A. aeriphila (1×109 CFU/mL) for 21 d. The results showed that A. aeriphila treatment significantly increased the average daily gain and reduced the feed conversion ratio (P<0.001). The levels of serum growth hormone (GH) and insulin-like growth factor 1 (IGF-1) were significantly increased following A. aeriphila treatment (P<0.05). Blood urea nitrogen and aspartate aminotransferase levels were decreased, whereas glucose and creatinine levels increased as a result of A. aeriphila treatment. Furthermore, the levels of serum antioxidant enzymes, including catalase (P<0.01), superoxide dismutase (P<0.001), and glutathione peroxidase (P<0.05), and total antioxidant capacity (P<0.05) were enhanced following A. aeriphila treatment. A. aeriphila treatment significantly increased the levels of serum immunoglobulin A (IgA) (P<0.05), IgG (P<0.01), IgM (P<0.05), interleukin-1 (IL-1) (P<0.05), IL-4 (P<0.05), and IL-10 (P<0.05). The broiler chickens in the A. aeriphila group had higher secretory IgA (SIgA) levels in the duodenum (P<0.01), jejunum (P<0.001), and cecum (P<0.001) than those in the control group. The messenger RNA (mRNA) relative expression levels of IL-10 (P<0.05) and IL-4 (P<0.001) in the intestinal mucosa of chickens were increased, while nuclear factor-‍κB (NF‍-‍κB) (P<0.001) expression was decreased in the A. aeriphila group compared to the control group. Phylum-level analysis revealed Firmicutes as the main phylum, followed by Bacteroidetes, in both groups. The data also found that Phascolarctobacterium and Barnesiella were increased in A. aeriphila-treated group. In conclusion, oral administration of A. aeriphila could improve the growth performance, serum antioxidant capacity, immune modulation, and gut health of broilers. Our findings may provide important information for the application of A. aeriphila in poultry production.

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.

Judicial Opinions 112–122

Opinion 112 denies the request to place Seliberia Aristovskaya and Parinkina 1963 (Approved Lists 1980) on the list of rejected names because the information provided is insufficient. For the same reason, Opinion 113 denies the request to reject Shewanella irciniae Lee et al. 2006 and Opinion 114 denies the request to reject the name Enterobacter siamensis Khunthongpan et al. 2014. Opinion 115 rejects the epithet of Moorella thermoautotrophica (Wiegel et al. 1981) Collins et al. 1994, which is regarded as a nomen confusum. To assess the consequences of Rule 8, Opinion 116 revisits names of taxa above the rank of genus which should comprise the stem of the name of a nomenclatural type and a category-specific ending but fail to do so. Such names should be orthographically corrected if the sole error is the inadvertent usage of an incorrect stem or be regarded as illegitimate if otherwise. The necessary corrections are made for a number of names. In Opinion 117, the request to designate Methylothermus subterraneus Hirayama et al. 2011 as the type species of the genus Methylothermus is denied because an equivalent action compatible with the Code was already conducted. In Opinion 118, the possible orthographical correction of the name Flaviaesturariibacter is treated, as are the analogous cases of Fredinandcohnia and Hydrogeniiclostidium . The genus names are corrected to Flaviaestuariibacter, Ferdinandcohnia and Hydrogeniiclostridium , respectively. Opinion 119 concludes that assigning Actinomycetales Buchanan 1917 (Approved Lists 1980) as nomenclatural type of the class Actinobacteria Stackebrandt et al. 1997 would not render that name legitimate if Rule 8 remained retroactive. The request is granted but Actinomycetales is also assigned as type of Actinomycetes Krassilnikov 1949 (Approved Lists 1980). In Opinion 120, the possible orthographical correction of the name Amycolatopsis albidoflavus is treated. It is grammatically corrected to Amycolatopsis albidoflava. Six names which could according to Rule 61 be grammatically corrected by anyone are also corrected. Opinion 121 denies the request to revise Opinion 69 and notes that Opinion 69 does not have the undesirable consequences emphasized in the request. In Opinion 122, the request to reject various taxon names of Mollicutes proposed in 2018 is denied because it is based on misinterpretations of the Code, which are clarified. Alternative ways to solve the perceived problems are outlined. These Opinions were ratified by the voting members of the International Committee on Systematics of Prokaryotes.

Cultivation of Important Methanotrophs From Indian Rice Fields

Methanotrophs are aerobic to micro-aerophilic bacteria, which oxidize and utilize methane, the second most important greenhouse gas. The community structure of the methanotrophs in rice fields worldwide has been studied mainly using culture-independent methods. Very few studies have focused on culturing methanotrophs from rice fields. We developed a unique method for the cultivation of methanotrophs from rice field samples. Here, we used a modified dilute nitrate mineral salts (dNMS) medium, with two cycles of dilution till extinction series cultivation with prolonged incubation time, and used agarose in the solid medium. The cultivation approach resulted in the isolation of methanotrophs from seven genera from the three major groups: Type Ia (Methylomonas, Methylomicrobium, and Methylocucumis), Type Ib (Methylocaldum and Methylomagnum), and Type II (Methylocystis and Methylosinus). Growth was obtained till 10^–6–10^–8 dilutions in the first dilution series, indicating the culturing of dominant methanotrophs. Our study was supported by 16S rRNA gene-based next-generation sequencing (NGS) of three of the rice samples. Our analyses and comparison with the global scenario suggested that the cultured members represented the major detected taxa. Strain RS1, representing a putative novel species of Methylomicrobium, was cultured; and the draft genome sequence was obtained. Genome analysis indicated that RS1 represented a new putative Methylomicrobium species. Methylomicrobium has been detected globally in rice fields as a dominant genus, although no Methylomicrobium strains have been isolated from rice fields worldwide. Ours is one of the first extensive studies on cultured methanotrophs from Indian rice fields focusing on the tropical region, and a unique method was developed. A total of 29 strains were obtained, which could be used as models for studying methane mitigation from rice fields and for environmental and biotechnological applications.

Verrucomicrobial methanotrophs: ecophysiology of metabolically versatile acidophiles

Methanotrophs are an important group of microorganisms that counteract methane emissions to the atmosphere. Methane-oxidising bacteria of the Alpha- and Gammaproteobacteria have been studied for over a century, while methanotrophs of the phylum Verrucomicrobia are a more recent discovery. Verrucomicrobial methanotrophs are extremophiles that live in very acidic geothermal ecosystems. Currently, more than a dozen strains have been isolated, belonging to the genera Methylacidiphilum and Methylacidimicrobium. Initially, these methanotrophs were thought to be metabolically confined. However, genomic analyses and physiological and biochemical experiments over the past years revealed that verrucomicrobial methanotrophs, as well as proteobacterial methanotrophs, are much more metabolically versatile than previously assumed. Several inorganic gases and other molecules present in acidic geothermal ecosystems can be utilised, such as methane, hydrogen gas, carbon dioxide, ammonium, nitrogen gas and perhaps also hydrogen sulfide. Verrucomicrobial methanotrophs could therefore represent key players in multiple volcanic nutrient cycles and in the mitigation of greenhouse gas emissions from geothermal ecosystems. Here, we summarise the current knowledge on verrucomicrobial methanotrophs with respect to their metabolic versatility and discuss the factors that determine their diversity in their natural environment. In addition, key metabolic, morphological and ecological characteristics of verrucomicrobial and proteobacterial methanotrophs are reviewed.

Methylococcus geothermalis sp. nov., a methanotroph isolated from a geothermal field in the Republic of Korea

A Gram-stain-negative, aerobic, non-motile and coccoid methanotroph, strain IM1^T, was isolated from hot spring soil. Cells of strain IM1^T were catalase-negative, oxidase-positive and displayed a characteristic intracytoplasmic membrane arrangement of type I methanotrophs. The strain possessed genes encoding both membrane-bound and soluble methane monooxygenases and grew only on methane or methanol. The strain was capable of growth at temperatures between 15 and 48 °C (optimum, 30-45 °C) and pH values between pH 4.8 and 8.2 (optimum, pH 6.2-7.0). Based on phylogenetic analysis of 16S rRNA gene and PmoA sequences, strain IM1^T was demonstrated to be affiliated to the genus Methylococcus. The 16S rRNA gene sequence of this strain was most closely related to the sequences of an uncultured bacterium clone FD09 (100 %) and a partially described cultured Methylococcus sp. GDS2.4 (99.78 %). The most closely related taxonomically described strains were Methylococcus capsulatus Texas^T (97.92 %), Methylococcus capsulatus Bath (97.86 %) and Methyloterricola oryzae 73a^T (94.21 %). Strain IM1^T shared average nucleotide identity values of 85.93 and 85.62 % with Methylococcus capsulatus strains Texas^T and Bath, respectively. The digital DNA-DNA hybridization value with the closest type strain was 29.90 %. The DNA G+C content of strain IM1^T was 63.3 mol% and the major cellular fatty acids were C_16 : 0 (39.0 %), C_16 : 1  ω7c (24.0 %), C_16 : 1  ω6c (13.6 %) and C_16 : 1  ω5c (12.0 %). The major ubiquinone was methylene-ubiquinone-8. On the basis of phenotypic, genetic and phylogenetic data, strain IM1^T represents a novel species of the genus Methylococcus for which the name Methylococcus geothermalis sp. nov. is proposed, with strain IM1^T (=JCM 33941^T=KCTC 72677^T) as the type strain.

Methane Elimination Using Biofiltration Packed With Fly Ash Ceramsite as Support Material

Methane is a greenhouse gas and significantly contributes to global warming. Methane biofiltration with immobilized methane-oxidizing bacteria (MOB) is an efficient and eco-friendly approach for methane elimination. To achieve high methane elimination capacity (EC), it is necessary to use an exceptional support material to immobilize MOB. The MOB consortium was inoculated in biofilters to continuusly eliminate 1% (v/v) of methane. Results showed that the immobilized MOB cells outperformed than the suspended MOB cells. The biofilter packed with fly ash ceramsite (FAC) held the highest average methane EC of 4.628 g h^–1 m^–3, which was 33.4% higher than that of the biofilter with the suspended MOB cells. The qPCR revealed that FAC surface presented the highest pmoA gene abundance, which inferred that FAC surface immobilized the most MOB biomass. The XPS and contact angle measurement indicated that the desirable surface elemental composition and stronger surface hydrophilicity of FAC might favor MOB immobilization and accordingly improve methane elimination.

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.

Novel approaches and reasons to isolate methanotrophic bacteria with biotechnological potentials: recent achievements and perspectives

The recent drop in the price of natural gas has rekindled the interests in methanotrophs, the organisms capable of utilizing methane as the sole electron donor and carbon source, as biocatalysts for various industrial applications. As heterologous expression of the methane monooxygenases in more amenable hosts has been proven to be nearly impossible, future success in methanotroph biotechnology largely depends on securing phylogenetically and phenotypically diverse methanotrophs with relatively high growth rates. For long, isolation of methanotrophs have relied on repeated single colony picking after initial batch enrichment with methane, which is a very rigorous and time-consuming process. In this review, three unconventional isolation methods devised for facilitation of the isolation process, diversification of targeted methanotrophs, and/or screening of rapid growers are summarized. The soil substrate membrane method allowed for isolation of previously elusive methanotrophs and application of high-throughput extinction plating technique facilitated the isolation procedure. Use of a chemostat with gradually increased dilution rates proved effective in screening for the fastest-growing methanotrophs from environmental samples. Development of new isolation technologies incorporating microfluidics and single-cell techniques may lead to discovery of previously unculturable methanotrophs with unexpected metabolic potentials and thus, certainly warrant future investigation.

Comparative Analysis of Microbial Communities in Iron-Dominated Flocculent Mats in Deep-Sea Hydrothermal Environments

It has been suggested that iron is one of the most important energy sources for photosynthesis-independent microbial ecosystems in the ocean crust. Iron-metabolizing chemolithoautotrophs play a key role as primary producers, but little is known about their distribution and diversity and their ecological role as submarine iron-metabolizing chemolithotrophs, particularly the iron oxidizers. In this study, we investigated the microbial communities in several iron-dominated flocculent mats found in deep-sea hydrothermal fields in the Mariana Volcanic Arc and Trough and the Okinawa Trough by culture-independent molecular techniques and X-ray mineralogical analyses. The abundance and composition of the 16S rRNA gene phylotypes demonstrated the ubiquity of zetaproteobacterial phylotypes in iron-dominated mat communities affected by hydrothermal fluid input. Electron microscopy with energy-dispersive X-ray microanalysis and X-ray absorption fine structure (XAFS) analysis revealed the chemical and mineralogical signatures of biogenic Fe-(oxy)hydroxide species and the potential contribution of Zetaproteobacteria to the in situ generation. These results suggest that putative iron-oxidizing chemolithoautotrophs play a significant ecological role in producing iron-dominated flocculent mats and that they are important for iron and carbon cycles in deep-sea low-temperature hydrothermal environments.

IMPORTANCE

We report novel aspects of microbiology from iron-dominated flocculent mats in various deep-sea environments. In this study, we examined the relationship between Zetaproteobacteria and iron oxides across several hydrothermally influenced sites in the deep sea. We analyzed iron-dominated mats using culture-independent molecular techniques and X-ray mineralogical analyses. The scanning electron microscopy-energy-dispersive X-ray spectroscopy SEM-EDS analysis and X-ray absorption fine structure (XAFS) analysis revealed chemical and mineralogical signatures of biogenic Fe-(oxy)hydroxide species as well as the potential contribution of the zetaproteobacterial population to the in situ production. These key findings provide important information for understanding the mechanisms of both geomicrobiological iron cycling and the formation of iron-dominated mats in deep-sea hydrothermal fields.

Acid-Tolerant Moderately Thermophilic Methanotrophs of the Class Gammaproteobacteria Isolated From Tropical Topsoil with Methane Seeps

Terrestrial tropical methane seep habitats are important ecosystems in the methane cycle. Methane oxidizing bacteria play a key role in these ecosystems as they reduce methane emissions to the atmosphere. Here, we describe the isolation and initial characterization of two novel moderately thermophilic and acid-tolerant obligate methanotrophs, assigned BFH1 and BFH2 recovered from a tropical methane seep topsoil habitat. The new isolates were strictly aerobic, non-motile, coccus-shaped and utilized methane and methanol as sole carbon and energy source. Isolates grew at pH range 4.2–7.5 (optimal 5.5–6.0) and at a temperature range of 30–60°C (optimal 51–55°C). 16S rRNA gene phylogeny placed them in a well-separated branch forming a cluster together with the genus Methylocaldum as the closest relatives (93.1–94.1% sequence similarity). The genes pmoA, mxaF, and cbbL were detected, but mmoX was absent. Strains BFH1 and BFH2 are, to our knowledge, the first isolated acid-tolerant moderately thermophilic methane oxidizers of the class Gammaproteobacteria. Each strain probably denotes a novel species and they most likely represent a novel genus within the family Methylococcaceae of type I methanotrophs. Furthermore, the isolates increase our knowledge of acid-tolerant aerobic methanotrophs and signify a previously unrecognized biological methane sink in tropical ecosystems.

Methylomagnum ishizawai gen. nov., sp. nov., a mesophilic type I methanotroph isolated from rice rhizosphere

An aerobic, methane-oxidizing bacterium (strain RS11D-PrT) was isolated from rice rhizosphere. Cells of strain RS11D-PrT were Gram-stain-negative, motile rods with a single polar flagellum and contained an intracytoplasmic membrane system typical of type I methanotrophs. The strain utilized methane and methanol as sole carbon and energy sources. It could grow at 20–37 °C (optimum 31–33 °C), at pH 6.8–7.4 (range 5.5–9.0) and with 0–0.2 % (w/v) NaCl (there was no growth at above 0.5 % NaCl). pmoA and mmoX genes were present. The ribulose monophosphate and/or ribulose bisphosphate pathways were used for carbon assimilation. Results of sequence analysis of 16S rRNA genes showed that strain RS11D-PrT is related closely to the genera Methylococcus, Methylocaldum, Methyloparacoccus and Methylogaea in the family Methylococcaceae. The similarity was low (94.6 %) between strain RS11D-PrT and the most closely related type strain (Methyloparacoccus murrellii R-49797T). The DNA G+C content was 64.1 mol%. Results of phylogenetic analysis of the pmoA gene and chemotaxonomic data regarding the major cellular fatty acids (C16 : 1ω7c, C16 : 0 and C14 : 0) and the major respiratory quinone (MQ-8) also indicated the affiliation of strain RS11D-PrT to the Methylococcus–Methylocaldum–Methyloparacoccus–Methylogaea clade. On the basis of phenotypic, genotypic and phylogenetic characteristics, strain RS11D-PrT is considered to represent a novel genus and species within the family Methylococcaceae, for which the name Methylomagnum ishizawai gen. nov., sp. nov. is proposed. The type strain is RS11D-PrT ( = JCM 18894T = NBRC 109438T = DSM 29768T = KCTC 4681T).

Influence of nutrients on oxidation of low level methane by mixed methanotrophic consortia

Low-level methane emissions from coal mine ventilation air (CMV-CH4; i.e., 1 % CH4) can significantly contribute to global climate change, and therefore, treatment is important to reduce impacts. To investigate CMV-CH4 abatement potential, five different mixed methanotrohic consortia (MMCs) were established from soil/sediment sources, i.e., landfill top cover soil, bio-solid compost, vegetated humus soil, estuarine and marine sediments. Enrichment conditions for MMCs were as follows: nitrate mineral salt (NMS) medium, pH ~ 6.8; 25 °C; 20-25 % CH4; agitation 200 rpm; and culture period 20 days, in mini-bench-top bioreactors. The enriched cultures were supplemented with extra carbon (methanol 0.5-1.5 %, formate 5-15 mM, and acetate 5-15 mM), nitrogen (nitrate 0.5-1.5 g L(-1), ammonium 0.1-0.5 g L(-1), or urea: 0.1-0.5 g L(-1)), and trace elements (copper 1-5 μM, iron 1-5 μM, and zinc 1-5 μM) in different batch experiments to improve low-level CH4 abatement. Average CH4 oxidation capacities (MOCs) of MMCs varied between 1.712 ± 0.032 and 1.963 ± 0.057 mg g(-1)DWbiomass h(-1). Addition of formate improved the MOCs of MMCs, but the dose-response varied for different MMCs. Acetate, nitrate and copper had no significant effect on MOCs, while addition of methanol, ammonium, urea, iron and zinc impacted negatively. Overall, MMCs enriched from marine sediments and landfill top cover soil showed high MOCs which were largely resilient to nutrient supplementation, suggesting a strong potential for biofilter development for industrial low-level CH4 abatement, such as those present in CMV.

Microbiology and potential applications of aerobic methane oxidation coupled to denitrification (AME-D) process: A review

Aerobic methane oxidation coupled to denitrification (AME-D) is an important link between the global methane and nitrogen cycles. This mini-review updates discoveries regarding aerobic methanotrophs and denitrifiers, as a prelude to spotlight the microbial mechanism and the potential applications of AME-D. Until recently, AME-D was thought to be accomplished by a microbial consortium where denitrifying bacteria utilize carbon intermediates, which are excreted by aerobic methanotrophs, as energy and carbon sources. Potential carbon intermediates include methanol, citrate and acetate. This mini-review presents microbial thermodynamic estimations and postulates that methanol is the ideal electron donor for denitrification, and may serve as a trophic link between methanotrophic bacteria and denitrifiers. More excitingly, new discoveries have revealed that AME-D is not only confined to the conventional synergism between methanotrophic bacteria and denitrifiers. Specifically, an obligate aerobic methanotrophic bacterium, Methylomonas denitrificans FJG1, has been demonstrated to couple partial denitrification with methane oxidation, under hypoxia conditions, releasing nitrous oxide as a terminal product. This finding not only substantially advances the understanding of AME-D mechanism, but also implies an important but unknown role of aerobic methanotrophs in global climate change through their influence on both the methane and nitrogen cycles in ecosystems. Hence, further investigation on AME-D microbiology and mechanism is essential to better understand global climate issues and to develop niche biotechnological solutions. This mini-review also presents traditional microbial techniques, such as pure cultivation and stable isotope probing, and powerful microbial techniques, such as (meta-) genomics and (meta-) transcriptomics, for deciphering linked methane oxidation and denitrification. Although AME-D has immense potential for nitrogen removal from wastewater, drinking water and groundwater, bottlenecks and potential issues are also discussed.

Genomic Reconstruction of an Uncultured Hydrothermal Vent Gammaproteobacterial Methanotroph (Family Methylothermaceae) Indicates Multiple Adaptations to Oxygen Limitation

Hydrothermal vents are an important contributor to marine biogeochemistry, producing large volumes of reduced fluids, gasses, and metals and housing unique, productive microbial and animal communities fueled by chemosynthesis. Methane is a common constituent of hydrothermal vent fluid and is frequently consumed at vent sites by methanotrophic bacteria that serve to control escape of this greenhouse gas into the atmosphere. Despite their ecological and geochemical importance, little is known about the ecophysiology of uncultured hydrothermal vent-associated methanotrophic bacteria. Using metagenomic binning techniques, we recovered and analyzed a near-complete genome from a novel gammaproteobacterial methanotroph (B42) associated with a white smoker chimney in the Southern Lau basin. B42 was the dominant methanotroph in the community, at ∼80x coverage, with only four others detected in the metagenome, all on low coverage contigs (7x–12x). Phylogenetic placement of B42 showed it is a member of the Methylothermaceae, a family currently represented by only one sequenced genome. Metabolic inferences based on the presence of known pathways in the genome showed that B42 possesses a branched respiratory chain with A- and B-family heme copper oxidases, cytochrome bd oxidase and a partial denitrification pathway. These genes could allow B42 to respire over a wide range of oxygen concentrations within the highly dynamic vent environment. Phylogenies of the denitrification genes revealed they are the result of separate horizontal gene transfer from other Proteobacteria and suggest that denitrification is a selective advantage in conditions where extremely low oxygen concentrations require all oxygen to be used for methane activation.

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.

Inmirania thermothiophila gen. nov., sp. nov., a thermophilic, facultatively autotrophic, sulfur-oxidizing gammaproteobacterium isolated from a shallow-sea hydrothermal vent

A novel thermophilic, facultatively autotrophic bacterium, strain S2479T, was isolated from a thermal spring located in a tidal zone of a geothermally heated beach (Kuril Islands, Russia). Cells of strain S2479T were rod-shaped and motile with a Gram-negative cell-wall type. The temperature range for growth was 35-68 °C (optimum 65 °C), and the pH range for growth was pH 5.5-8.8 (optimum pH 6.5). Growth of strain S2479T was observed in the presence of NaCl concentrations ranging from 0.5 to 3.5 % (w/v) (optimum 1.5-2.0 %). The strain oxidized sulfur and thiosulfate as sole energy sources for autotrophic growth under anaerobic conditions with nitrate as electron acceptor. Strain S2479T was also capable of heterotrophic growth by reduction of nitrate with oxidation of low-chain fatty acids and a limited number of other carboxylic acids or with complex proteinaceous compounds. Nitrate was reduced to N2. Sulfur compounds were oxidized to sulfate. Strain S2479T did not grow aerobically during incubation at atmospheric concentration of oxygen but was able to grow microaerobically (1 % of oxygen in gas phase). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain was a member of the family Ectothiorhodospiraceae, order Chromatiales, class Gammaproteobacteria. On the basis of phylogenetic and phenotypic properties, strain S2479T represents a novel species of a new genus, for which the name Inmirania thermothiophila gen. nov., sp. nov. is proposed. The type strain of the type species is S2479T ( = DSM 100275T = VKM B-2962T).

Geomicrobiology of sublacustrine thermal vents in Yellowstone Lake: geochemical controls on microbial community structure and function

Yellowstone Lake (Yellowstone National Park, WY, USA) is a large high-altitude (2200 m), fresh-water lake, which straddles an extensive caldera and is the center of significant geothermal activity. The primary goal of this interdisciplinary study was to evaluate the microbial populations inhabiting thermal vent communities in Yellowstone Lake using 16S rRNA gene and random metagenome sequencing, and to determine how geochemical attributes of vent waters influence the distribution of specific microorganisms and their metabolic potential. Thermal vent waters and associated microbial biomass were sampled during two field seasons (2007–2008) using a remotely operated vehicle (ROV). Sublacustrine thermal vent waters (circa 50–90°C) contained elevated concentrations of numerous constituents associated with geothermal activity including dissolved hydrogen, sulfide, methane and carbon dioxide. Microorganisms associated with sulfur-rich filamentous “streamer” communities of Inflated Plain and West Thumb (pH range 5–6) were dominated by bacteria from the Aquificales, but also contained thermophilic archaea from the Crenarchaeota and Euryarchaeota. Novel groups of methanogens and members of the Korarchaeota were observed in vents from West Thumb and Elliot's Crater (pH 5–6). Conversely, metagenome sequence from Mary Bay vent sediments did not yield large assemblies, and contained diverse thermophilic and nonthermophilic bacterial relatives. Analysis of functional genes associated with the major vent populations indicated a direct linkage to high concentrations of carbon dioxide, reduced sulfur (sulfide and/or elemental S), hydrogen and methane in the deep thermal ecosystems. Our observations show that sublacustrine thermal vents in Yellowstone Lake support novel thermophilic communities, which contain microorganisms with functional attributes not found to date in terrestrial geothermal systems of YNP.

Novel Methanotrophs of the Family Methylococcaceae from Different Geographical Regions and Habitats

Terrestrial methane seeps and rice paddy fields are important ecosystems in the methane cycle. Methanotrophic bacteria in these ecosystems play a key role in reducing methane emission into the atmosphere. Here, we describe three novel methanotrophs, designated BRS-K6, GFS-K6 and AK-K6, which were recovered from three different habitats in contrasting geographic regions and ecosystems: waterlogged rice-field soil and methane seep pond sediments from Bangladesh; and warm spring sediments from Armenia. All isolates had a temperature range for growth of 8–35 °C (optimal 25–28 °C) and a pH range of 5.0–7.5 (optimal 6.4–7.0). 16S rRNA gene sequences showed that they were new gammaproteobacterial methanotrophs, which form a separate clade in the family Methylococcaceae. They fell into a cluster with thermotolerant and mesophilic growth tendency, comprising the genera Methylocaldum-Methylococcus-Methyloparacoccus-Methylogaea. So far, growth below 15 °C of methanotrophs from this cluster has not been reported. The strains possessed type I intracytoplasmic membranes. The genes pmoA, mxaF, cbbL, nifH were detected, but no mmoX gene was found. Each strain probably represents a novel species either belonging to the same novel genus or each may even represent separate genera. These isolates extend our knowledge of methanotrophic Gammaproteobacteria and their physiology and adaptation to different ecosystems.

The origin, source, and cycling of methane in deep crystalline rock biosphere

The emerging interest in using stable bedrock formations for industrial purposes, e.g., nuclear waste disposal, has increased the need for understanding microbiological and geochemical processes in deep crystalline rock environments, including the carbon cycle. Considering the origin and evolution of life on Earth, these environments may also serve as windows to the past. Various geological, chemical, and biological processes can influence the deep carbon cycle. Conditions of CH4 formation, available substrates and time scales can be drastically different from surface environments. This paper reviews the origin, source, and cycling of methane in deep terrestrial crystalline bedrock with an emphasis on microbiology. In addition to potential formation pathways of CH4, microbial consumption of CH4 is also discussed. Recent studies on the origin of CH4 in continental bedrock environments have shown that the traditional separation of biotic and abiotic CH4 by the isotopic composition can be misleading in substrate-limited environments, such as the deep crystalline bedrock. Despite of similarities between Precambrian continental sites in Fennoscandia, South Africa and North America, where deep methane cycling has been studied, common physicochemical properties which could explain the variation in the amount of CH4 and presence or absence of CH4 cycling microbes were not found. However, based on their preferred carbon metabolism, methanogenic microbes appeared to have similar spatial distribution among the different sites.

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

Aerobic methane oxidation has been mostly studied in environments with moderate to low temperatures. However, the process also occurs in terrestrial thermal springs, where little research on the subject has been done to date. The potential activity of methane oxidation and diversity of aerobic methanotrophic bacteria were studied in sediments of thermal springs with various chemical and physical properties, sampled across the Kunashir Island, the Kuriles archipelago. Activity was measured by means of the radioisotope tracer technique utilizing (14)C-labeled methane. Biodiversity assessments were based on the particulate methane monooxygenase (pmoA) gene, which is found in all known thermophilic and thermotolerant methanotrophs. We demonstrated the possibility of methane oxidation in springs with temperature exceeding 74 °C, and the most intensive methane uptake was shown in springs with temperatures about 46 °C. PmoA was detected in 19 out of 30 springs investigated and the number of pmoA gene copies varied between 10(4) and 10(6) copies per ml of sediment. Phylogenetic analysis of PmoA sequences revealed the presence of methanotrophs from both the Alpha- and Gammaproteobacteria. Our results suggest that methanotrophs inhabiting thermal springs with temperature exceeding 50 °C may represent novel thermophilic and thermotolerant species of the genera Methylocystis and Methylothermus, as well as previously undescribed Gammaproteobacteria.

Methylomarinovum caldicuralii gen. nov., sp. nov., a moderately thermophilic methanotroph isolated from a shallow submarine hydrothermal system, and proposal of the family Methylothermaceae fam. nov

A novel methane-oxidizing bacterium, strain IT-9(T), was isolated from a shallow submarine hydrothermal system occurring in a coral reef in Japan. Strain IT-9(T) was a Gram-negative, aerobic, motile, coccoid or oval-shaped bacterium with the distinctive intracytoplasmic membrane arrangement of a type I methanotroph. Strain IT-9(T) was a moderately thermophilic, obligate methanotroph that grew on methane and methanol at 30-55 °C (optimum 45-50 °C). The strain possessed the particulate methane monooxygenase (pMMO). The ribulose monophosphate pathway was operative for carbon assimilation. NaCl was required for growth within a concentration range of 1-5 % (optimum 3 %). The hao gene encoding hydroxylamine oxidoreductase (HAO) involved in nitrification was detected by a PCR experiment. The major phospholipid fatty acids were C16 : 0 and C18 : 1ω7c. The major isoprenoid quinone was Q-8. The DNA G+C content was 66.0 mol%. The 16S rRNA gene sequence of strain IT-9(T) was only moderately related to the sequences of members of the closest genera Methylohalobius (94.1 % similarity) and Methylothermus (91.7-91.9 % similarity); however, those sequences formed a deeply branching monophyletic group within the order Methylococcales. Phylogenies based on 16S rRNA gene sequences, deduced partial PmoA sequences and deduced partial Hao sequences and physiological and chemotaxonomic characteristics revealed that strain IT-9(T) represents a novel species of a new genus, for which the name Methylomarinovum caldicuralii gen. nov., sp. nov. is proposed. The type strain of Methylomarinovum caldicuralii is IT-9(T) ( = JCM 13666(T) = DSM 19749(T)). In addition, we propose a new family, Methylothermaceae fam. nov., in the order Methylococcales, to accommodate the genera Methylothermus, Methylohalobius and Methylomarinovum. The genera Methylothermus and Methylohalobius have been recognized as being distinct from other genera in the methane-oxidizing order Methylococcales in the class Gammaproteobacteria. These genera form a distinctive monophyletic lineage within the order on the basis of 16S rRNA gene sequence phylogeny. This seems consistent with their distinctive physiological traits; the genus Methylothermus includes the most thermophilic species, and the genus Methylohalobius includes the most halophilic species, within the order. Although these two genera include only three species at the time of writing, similar sequences of 16S rRNA genes and pmoA genes encoding pMMO have been detected in a geothermal area or deep-sea hydrothermal vent fields by studies using culture-independent techniques. This suggests that unknown methanotrophs of this lineage inhabit various extreme environments.

Prerequisites for amplicon pyrosequencing of microbial methanol utilizers in the environment

The commercial availability of next generation sequencing (NGS) technologies facilitated the assessment of functional groups of microorganisms in the environment with high coverage, resolution, and reproducibility. Soil methylotrophs were among the first microorganisms in the environment that were assessed with molecular tools, and nowadays, as well with NGS technologies. Studies in the past years re-attracted notice to the pivotal role of methylotrophs in global conversions of methanol, which mainly originates from plants, and is involved in oxidative reactions and ozone formation in the atmosphere. Aerobic methanol utilizers belong to Bacteria, yeasts, Ascomycota, and molds. Numerous bacterial methylotrophs are facultatively aerobic, and also contribute to anaerobic methanol oxidation in the environment, whereas strict anaerobic methanol utilizers belong to methanogens and acetogens. The diversity of enzymes catalyzing the initial oxidation of methanol is considerable, and comprises at least five different enzyme types in aerobes, and one in strict anaerobes. Only the gene of the large subunit of pyrroloquinoline quinone (PQQ)-dependent methanol dehydrogenase (MDH; mxaF) has been analyzed by environmental pyrosequencing. To enable a comprehensive assessment of methanol utilizers in the environment, new primers targeting genes of the PQQ MDH in Methylibium (mdh2), of the nicotinamide adenine dinucleotide-dependent MDH (mdh), of the methanol oxidoreductase of Actinobacteria (mdo), of the fungal flavin adenine nucleotide-dependent alcohol oxidase (mod1, mod2, and homologs), and of the gene of the large subunit of the methanol:corrinoid methyltransferases (mtaC) in methanogens and acetogens need to be developed. Combined stable isotope probing of nucleic acids or proteins with amplicon-based NGS are straightforward approaches to reveal insights into functions of certain methylotrophic taxa in the global methanol cycle.

Unique substrate specificity of a thermostable glycosyl hydrolase from an uncultured Anaerolinea, derived from bacterial mat on a subsurface geothermal water stream

To investigate novel extremozymes encoded by sequenced metagenes from a microbial community in an extreme environment, we have characterized a recombinant glycosyl hydrolase (rGH) from an uncultured bacterium within the order Chloroflexi. rGH formed insoluble bodies in an Escherichia coli protein expression system. The protein was partially dissolved by a surfactant and was enzymatically characterized. The MW of the monomeric peptide was ~62 kDa, and it formed a homodimers in buffer. It was optimally active at 65 °C and from pH 4 to 8. rGH showed hydrolytic activity for α-1,1, α-1,2 and α-1,6 linkages, including isomaltose, but not α-1,4 and β-linkages.

Methylomarinum vadi gen. nov., sp. nov., a methanotroph isolated from two distinct marine environments

Two aerobic methane-oxidizing bacterial strains were isolated from distinct marine environments in Japan. Strains IT-4(T) and T2-1 were Gram-stain-negative, aerobic, motile, plump short rods or oval-shaped bacteria with a single polar flagellum and type I intracytoplasmic membranes. They were obligate methanotrophs that grew only on methane or methanol. Each strain possessed the particulate methane monooxygenase (pMMO). The ribulose monophosphate pathway was operative for carbon assimilation. The strains grew best at 37 °C, and did not grow at 45 °C. NaCl was required for growth within a concentration range of 1-8 % (w/v). The major phospholipid fatty acids were C16 : 0, C16 : 1ω7c, and C16 : 1ω5t. The major isoprenoid quinone was MQ-8. The DNA G+C content was 50.9-51.7 mol%. The 16S rRNA gene sequences of the strains showed 99.4 % similarity to each other, and DNA-DNA hybridization analysis indicated that the strains were representatives of the same species. The 16S rRNA gene sequences were highly similar to some marine environmental sequences (94.0-97.7 % similarity), but did not show similarities more than 94 % with sequences of members of other related genera, such as Methylomicrobium, Methylobacter, Methylomonas and Methylosarcina. Phylogenies based on 16S rRNA gene sequences and deduced partial PmoA sequences, and the physiological and chemotaxonomic characteristics revealed that strains IT-4(T) and T2-1 represent a novel species of a new genus in the family Methylococcaceae, for which the name Methylomarinum vadi gen. nov., sp. nov. is proposed. The type strain is IT-4(T) ( = JCM 13665(T) = DSM 18976(T)).

Domain-level identification and quantification of relative prokaryotic cell abundance in microbial communities by Micro-FTIR spectroscopy

Domain-level identification of microbial cells or cell-like structures is crucial for investigating natural microbial communities and their ecological significance. By using micro-Fourier transform infrared (micro-FTIR) spectroscopy, we established a technical basis for the domain-level diagnosis and quantification of prokaryotic cell abundance in natural microbial communities. Various prokaryotic cultures (12 species of bacteria and 10 of archaea) were examined using micro-FTIR spectroscopic analysis. The aliphatic CH3 /CH2 absorbance ratios (R3/2 ) showed domain-specific signatures, possibly reflecting distinctive cellular lipid compositions. The signatures were preserved even after chemical cell fixation (formaldehyde) and nucleic acid staining (DAPI) processes - techniques that are essential in studying microbial ecology. The micro-FTIR technique was successfully applied for quantification of the bacteria/archaea abundance ratio in an active microbial mat community in a subsurface hot aquifer stream. We conclude that the micro-FTIR R3/2 measurement is both fast and effective for domain-level diagnosis and quantification of first-order prokaryotic community structures.