Over 200 years ago Alexander von Humboldt (1808) observed that plant and animal diversity peaks at tropical latitudes and decreases toward the poles, a trend he attributed to more favorable ...temperatures in the tropics. Studies to date suggest that this temperature-diversity gradient is weak or nonexistent for Bacteria and Archaea. To test the impacts of temperature as well as pH on bacterial and archaeal diversity, we performed pyrotag sequencing of 16S rRNA genes retrieved from 165 soil, sediment and biomat samples of 36 geothermal areas in Canada and New Zealand, covering a temperature range of 7.5-99 °C and a pH range of 1.8-9.0. This represents the widest ranges of temperature and pH yet examined in a single microbial diversity study. Species richness and diversity indices were strongly correlated to temperature, with R(2) values up to 0.62 for neutral-alkaline springs. The distributions were unimodal, with peak diversity at 24 °C and decreasing diversity at higher and lower temperature extremes. There was also a significant pH effect on diversity; however, in contrast to previous studies of soil microbial diversity, pH explained less of the variability (13-20%) than temperature in the geothermal samples. No correlation was observed between diversity values and latitude from the equator, and we therefore infer a direct temperature effect in our data set. These results demonstrate that temperature exerts a strong control on microbial diversity when considered over most of the temperature range within which life is possible.
The alphaproteobacterial family Beijerinckiaceae contains generalists that grow on a wide range of substrates, and specialists that grow only on methane and methanol. We investigated the evolution of ...this family by comparing the genomes of the generalist organotroph Beijerinckia indica, the facultative methanotroph Methylocella silvestris and the obligate methanotroph Methylocapsa acidiphila. Highly resolved phylogenetic construction based on universally conserved genes demonstrated that the Beijerinckiaceae forms a monophyletic cluster with the Methylocystaceae, the only other family of alphaproteobacterial methanotrophs. Phylogenetic analyses also demonstrated a vertical inheritance pattern of methanotrophy and methylotrophy genes within these families. Conversely, many lateral gene transfer (LGT) events were detected for genes encoding carbohydrate transport and metabolism, energy production and conversion, and transcriptional regulation in the genome of B. indica, suggesting that it has recently acquired these genes. A key difference between the generalist B. indica and its specialist methanotrophic relatives was an abundance of transporter elements, particularly periplasmic-binding proteins and major facilitator transporters. The most parsimonious scenario for the evolution of methanotrophy in the Alphaproteobacteria is that it occurred only once, when a methylotroph acquired methane monooxygenases (MMOs) via LGT. This was supported by a compositional analysis suggesting that all MMOs in Alphaproteobacteria methanotrophs are foreign in origin. Some members of the Beijerinckiaceae subsequently lost methanotrophic functions and regained the ability to grow on multicarbon energy substrates. We conclude that B. indica is a recidivist multitroph, the only known example of a bacterium having completely abandoned an evolved lifestyle of specialized methanotrophy.
Aerobic methanotrophic bacteria are considered strict aerobes but are often highly abundant in hypoxic and even anoxic environments. Despite possessing denitrification genes, it remains to be ...verified whether denitrification contributes to their growth. Here, we show that acidophilic methanotrophs can respire nitrous oxide (N
O) and grow anaerobically on diverse non-methane substrates, including methanol, C-C substrates, and hydrogen. We study two strains that possess N
O reductase genes: Methylocella tundrae T4 and Methylacidiphilum caldifontis IT6. We show that N
O respiration supports growth of Methylacidiphilum caldifontis at an extremely acidic pH of 2.0, exceeding the known physiological pH limits for microbial N
O consumption. Methylocella tundrae simultaneously consumes N
O and CH
in suboxic conditions, indicating robustness of its N
O reductase activity in the presence of O
. Furthermore, in O
-limiting conditions, the amount of CH
oxidized per O
reduced increases when N
O is added, indicating that Methylocella tundrae can direct more O
towards methane monooxygenase. Thus, our results demonstrate that some methanotrophs can respire N
O independently or simultaneously with O
, which may facilitate their growth and survival in dynamic environments. Such metabolic capability enables these bacteria to simultaneously reduce the release of the key greenhouse gases CO
, CH
and N
O.
Summary
Described genera of methanotrophic bacteria are present in most upland soils, but it is not known whether these are sufficiently oligotrophic to oxidize methane at its trace atmospheric ...mixing ratio of 1.75 ppmv. Members of the genera Methylocystis, Methylosinus, Methylocaldum and Methylobacter were isolated from different upland soils and compared with type strains for growth and activity under low methane mixing ratios. The specific affinity (a0s) varied by about one order of magnitude among different methanotrophs. It was highest in some Methylocystis spp., suggesting that these were the most oligotrophic. In direct tests, the threshold mixing ratio of methane required by most methanotrophs for growth ranged from 100 to greater than 1000 ppmv. However, two Methylocystis strains grew at only 10–100 ppmv of methane and one oxidized atmospheric methane for > 3 months with little or no decline in the absolute rate. The results show that some cultivated methanotrophic bacteria are much more oligotrophic than others, and may contribute to atmospheric methane oxidation in soils. However, it is likely that these need additional energy sources for long‐term survival, and that uncultivated groups of methanotrophic bacteria are primarily responsible for the process in soils possessing high methane oxidation rates.
Copper membrane monooxygenases (CuMMOs) oxidize ammonia, methane and some short-chain alkanes and alkenes. They are encoded by three genes, usually in an operon of
. We aligned
operons from 66 ...microbial genomes, including members of the
-,
-, and
and the candidate phylum NC10. Phylogenetic and compositional analyses were used to reconstruct the evolutionary history of the enzyme and detect potential lateral gene transfer (LGT) events. The phylogenetic analyses showed at least 10 clusters corresponding to a combination of substrate specificity and bacterial taxonomy, but with no overriding structure based on either function or taxonomy alone. Adaptation of the enzyme to preferentially oxidize either ammonia or methane has occurred more than once. Individual phylogenies of all three genes,
and
, closely matched, indicating that this operon evolved or was consistently transferred as a unit, with the possible exception of the methane monooxygenase operons in
, where the
gene has a distinct phylogeny from
and
. Compositional analyses indicated that some clusters of
operons (for example, the
in gammaproteobacterial methanotrophs and the
in betaproteobacterial nitrifiers) were compositionally very different from their genomes, possibly indicating recent lateral transfer of these operons. The combined phylogenetic and compositional analyses support the hypothesis that an ancestor of the nitrifying bacterium
was the donor of methane monooxygenase (pMMO) to both the alphaproteobacterial and gammaproteobacterial methanotrophs, but that before this event the gammaproteobacterial methanotrophs originally possessed another CuMMO (Pxm), which has since been lost in many species.
Summary
Recently, methanotrophic members of the phylum Verrucomicrobia have been described, but little is known about their distribution in nature. We surveyed methanotrophic bacteria in geothermal ...springs and acidic wetlands via pyrosequencing of 16S rRNA gene amplicons. Putative methanotrophic Verrucomicrobia were found in samples covering a broad temperature range (22.5–81.6°C), but only in acidic conditions (pH 1.8–5.0) and only in geothermal environments, not in acidic bogs or fens. Phylogenetically, three 16S rRNA gene sequence clusters of putative methanotrophic Verrucomicrobia were observed. Those detected in high‐temperature geothermal samples (44.1–81.6°C) grouped with known thermoacidiphilic ‘Methylacidiphilum’ isolates. A second group dominated in moderate‐temperature geothermal samples (22.5–40.1°C) and a representative mesophilic methanotroph from this group was isolated (strain LP2A). Genome sequencing verified that strain LP2A possessed particulate methane monooxygenase, but its 16S rRNA gene sequence identity to ‘Methylacidiphilum infernorum’ strain V4 was only 90.6%. A third group clustered distantly with known methanotrophic Verrucomicrobia. Using pmoA‐gene targeted quantitative polymerase chain reaction, two geothermal soil profiles showed a dominance of LP2A‐like pmoA sequences in the cooler surface layers and ‘Methylacidiphilum'‐like pmoA sequences in deeper, hotter layers. Based on these results, there appears to be a thermophilic group and a mesophilic group of methanotrophic Verrucomicrobia. However, both were detected only in acidic geothermal environments.
Analysis of the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data ...collected globally to discover a novel bacterial phylum ('Candidatus Kryptonia') found exclusively in high-temperature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic 'blind spot' because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestyle with conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery.
Biofiltration of methane La, Helen; Hettiaratchi, J. Patrick A.; Achari, Gopal ...
Bioresource technology,
11/2018, Letnik:
268
Journal Article
Recenzirano
Display omitted
•Critical review of methane biofiltration studies performed to date.•Long-term performance monitoring should consider methanotroph community dynamics.•Nitrogen metabolism influences ...methanotroph community and system performance.•Methane biofiltration requires low energy input and inexpensive packing medium.•Opportunity to displace fossil fuels by harvesting biomass for biocarbon.
The on-going annual increase in global methane (CH4) emissions can be largely attributed to anthropogenic activities. However, as more than half of these emissions are diffuse and possess a concentration less than 3% (v/v), physical-chemical treatments are inefficient as an abatement technology. In this regard, biotechnologies, such as biofiltration using methane-oxidizing bacteria, or methanotrophs, are a cost-effective and efficient means of combating diffuse CH4 emissions. In this review, a number of abiotic factors including temperature, pH, water content, packing material, empty-bed residence time, inlet gas flow rate, CH4 concentration, as well biotic factors, such as biomass development, are reviewed based on empirical findings on CH4 biofiltration studies that have been performed in the last decades.
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