The (d)evolution of methanotrophy in the Beijerinckiaceae--a comparative genomics analysis

Nematodes alter the taxonomic and functional profiles of benthic bacterial communities: A metatranscriptomic approach

Marine sediments cover 70% of the Earth's surface, and harbour diverse bacterial communities critical for marine biogeochemical processes, which affect climate change, biodiversity and ecosystem functioning. Nematodes, the most abundant and species-rich metazoan organisms in marine sediments, in turn, affect benthic bacterial communities and bacterial-mediated ecological processes, but the underlying mechanisms by which they affect biogeochemical cycles remain poorly understood. Here, we demonstrate using a metatranscriptomic approach that nematodes alter the taxonomic and functional profiles of benthic bacterial communities. We found particularly strong stimulation of nitrogen-fixing and methane-oxidizing bacteria in the presence of nematodes, as well as increased functional activity associated with methane metabolism and degradation of various carbon compounds. This study provides empirical evidence that the presence of nematodes results in taxonomic and functional shifts in active bacterial communities, indicating that nematodes may play an important role in benthic ecosystem processes.

Acetylene Tunes Microbial Growth During Aerobic Cometabolism of Trichloroethene

Microbial aerobic cometabolism is a possible treatment approach for large, dilute trichloroethene (TCE) plumes at groundwater contaminated sites. Rapid microbial growth and bioclogging pose a persistent problem in bioremediation schemes. Bioclogging reduces soil porosity and permeability, which negatively affects substrate distribution and contaminant treatment efficacy while also increasing the operation and maintenance costs of bioremediation. In this study, we evaluated the ability of acetylene, an oxygenase enzyme-specific inhibitor, to decrease biomass production while maintaining aerobic TCE cometabolism capacity upon removal of acetylene. We first exposed propane-metabolizing cultures (pure and mixed) to 5% acetylene (v v-1) for 1, 2, 4, and 8 d and we then verified TCE aerobic cometabolic activity. Exposure to acetylene overall decreased biomass production and TCE degradation rates while retaining the TCE degradation capacity. In the mixed culture, exposure to acetylene for 1-8 d showed minimal effects on the composition and relative abundance of TCE cometabolizing bacterial taxa. TCE aerobic cometabolism and incubation conditions exerted more notable effects on microbial ecology than did acetylene. Acetylene appears to be a viable approach to control biomass production that may lessen the likelihood of bioclogging during TCE cometabolism. The findings from this study may lead to advancements in aerobic cometabolism remediation technologies for dilute plumes.

Forest top canopy bacterial communities are influenced by elevation and host tree traits

BACKGROUND

The phyllosphere microbiome is crucial for plant health and ecosystem functioning. While host species play a determining role in shaping the phyllosphere microbiome, host trees of the same species that are subjected to different environmental conditions can still exhibit large degrees of variation in their microbiome diversity and composition. Whether these intra-specific variations in phyllosphere microbiome diversity and composition can be observed over the broader expanse of forest landscapes remains unclear. In this study, we aim to assess the variation in the top canopy phyllosphere bacterial communities between and within host tree species in the temperate European forests, focusing on Fagus sylvatica (European beech) and Picea abies (Norway spruce).

RESULTS

We profiled the bacterial diversity, composition, driving factors, and discriminant taxa in the top canopy phyllosphere of 211 trees in two temperate forests, Veluwe National Parks, the Netherlands and Bavarian Forest National Park, Germany. We found the bacterial communities were primarily shaped by host species, and large variation existed within beech and spruce. While we showed that there was a core microbiome in all tree species examined, community composition varied with elevation, tree diameter at breast height, and leaf-specific traits (e.g., chlorophyll and P content). These driving factors of bacterial community composition also correlated with the relative abundance of specific bacterial families.

CONCLUSIONS

While our results underscored the importance of host species, we demonstrated a substantial range of variation in phyllosphere bacterial diversity and composition within a host species. Drivers of these variations have implications at both the individual host tree level, where the bacterial communities differed based on tree traits, and at the broader forest landscape level, where drivers like certain highly plastic leaf traits can potentially link forest canopy bacterial community variations to forest ecosystem processes. We eventually showed close associations between forest canopy phyllosphere bacterial communities and host trees exist, and the consistent patterns emerging from these associations are critical for host plant functioning.

Exploring ecological effects of arsenic and cadmium combined exposure on cropland soil: from multilevel organisms to soil functioning by multi-omics coupled with high-throughput quantitative PCR

Arsenic (As) and cadmium (Cd) pose potential ecological threats to cropland soils; however, few studies have investigated their combined effects on multilevel organisms and soil functioning. Here, we used collembolans and soil microbiota as test organisms to examine their responses to soil As and Cd co-contamination at the gene, individual, and community levels, respectively, and further uncovered ecological relationships between pollutants, multilevel organisms, and soil functioning. At the gene level, collembolan transcriptome revealed that elevated As concentrations stimulated As-detoxifying genes AS3MT and GST, whereas the concurrent Cd restrained GST gene expression. At the individual level, collembolan reproduction was sensitive to pollutants while collembolan survival wasn't. At the community level, significant but inconsistent correlations were observed between the biodiversity of different soil keystone microbial clusters and soil As levels. Moreover, soil functioning related to nutrient (e.g., carbon, nitrogen, phosphorus, and sulfur) cycles was inhibited under As and Cd co-exposure only through the mediation of plant pathogens. Overall, these findings suggested multilevel bioindicators (i.e., AS3MT gene expression in collembolans, collembolan reproduction, and biodiversity of soil keystone microbial clusters) in cropland soils co-contaminated with As and Cd, thus improving the understanding of the ecotoxicological impact of heavy metal co-contamination on soil ecosystems.

Microbial Ecosystems in Movile Cave: An Environment of Extreme Life

Movile Cave, situated in Romania close to the Black Sea, constitutes a distinct and challenging environment for life. Its partially submerged ecosystem depends on chemolithotrophic processes for its energetics, which are fed by a continuous hypogenic inflow of mesothermal waters rich in reduced chemicals such as hydrogen sulfide and methane. We sampled a variety of cave sublocations over the course of three years. Furthermore, in a microcosm experiment, minerals were incubated in the cave waters for one year. Both endemic cave samples and extracts from the minerals were subjected to 16S rRNA amplicon sequencing. The sequence data show specific community profiles in the different subenvironments, indicating that specialized prokaryotic communities inhabit the different zones in the cave. Already after one year, the different incubated minerals had been colonized by specific microbial communities, indicating that microbes in Movile Cave can adapt in a relatively short timescale to environmental opportunities in terms of energy and nutrients. Life can thrive, diversify and adapt in remote and isolated subterranean environments such as Movile Cave.

Methanotrophs: Metabolic versatility from utilization of methane to multi-carbon sources and perspectives on current and future applications

The development of biorefineries for a sustainable bioeconomy has been driven by the concept of utilizing environmentally friendly and cost-effective renewable energy sources. Methanotrophic bacteria with a unique capacity to utilize methane as a carbon and energy source can serve as outstanding biocatalysts to develop C1 bioconversion technology. By establishing the utilization of diverse multi-carbon sources, integrated biorefinery platforms can be created for the concept of the circular bioeconomy. An understanding of physiology and metabolism could help to overcome challenges for biomanufacturing. This review summaries fundamental gaps for methane oxidation and the capability to utilize multi-carbon sources in methanotrophic bacteria. Subsequently, breakthroughs and challenges in harnessing methanotrophs as robust microbial chassis for industrial biotechnology were compiled and overviewed. Finally, capabilities to exploit the inherent advantages of methanotrophs to synthesize various target products in higher titers are proposed.

Acidophilic methanotrophs: Occurrence, diversity, and possible bioremediation applications

Methanotrophs have been identified and isolated from acidic environments such as wetlands, acidic soils, peat bogs, and groundwater aquifers. Due to their methane (CH₄ ) utilization as a carbon and energy source, acidophilic methanotrophs are important in controlling the release of atmospheric CH₄ , an important greenhouse gas, from acidic wetlands and other environments. Methanotrophs have also played an important role in the biodegradation and bioremediation of a variety of pollutants including chlorinated volatile organic compounds (CVOCs) using CH₄ monooxygenases via a process known as cometabolism. Under neutral pH conditions, anaerobic bioremediation via carbon source addition is a commonly used and highly effective approach to treat CVOCs in groundwater. However, complete dechlorination of CVOCs is typically inhibited at low pH. Acidophilic methanotrophs have recently been observed to degrade a range of CVOCs at pH < 5.5, suggesting that cometabolic treatment may be an option for CVOCs and other contaminants in acidic aquifers. This paper provides an overview of the occurrence, diversity, and physiological activities of methanotrophs in acidic environments and highlights the potential application of these organisms for enhancing contaminant biodegradation and bioremediation.

Elucidating performance failure in the use of an Anaerobic-Oxic-Anoxic (AOA) plug-flow system for biological nutrient removal

The Anaerobic-oxic-anoxic (AOA) process is a carbon-saving and high-efficiency way to treat municipal wastewater and gets more attention. Recent reports suggest that in the AOA process, well-performed endogenous denitrification (ED), conducted by glycogen accumulating organisms (GAOs), is crucial to advanced nutrient removal. However, the consensuses about starting up and optimizing AOA, and in-situ enriching GAOs, are still lacking. Hence, this study tried to verify whether AOA could be established in an ongoing anaerobic-oxic (AO) system. For this aim, a lab-scale plug-flow reactor (working volume of 40 L) previously operated under AO mode for 150 days, during that 97.87 % of ammonium was oxidized to nitrate and 44.4 % of orthophosphate was absorbed. Contrary to expectations, under AOA mode, little nitrate reduction (only 6.3 mg/L within 5.33 h) indicated the failure of ED. According to high-throughput sequencing analysis, GAOs (Candidatus_Competibacter and Defluviicoccus) were enriched within the AO period (14.27 % and 3 %) and then still dominated during the AOA period (13.9 % and 10.07 %) but contributed little to ED. Although apparent alternate orthophosphate variations existed in this reactor, no typical phosphorus accumulating organisms were abundant (< 2 %). More than that, within the long-term AOA operation (109 days), the nitrification weakened (merely 40.11 % of ammonium been oxidized) since the dual effects of low dissolved oxygen and long unaerated duration. This work reveals the necessity of developing practical strategies for starting and optimizing AOA, and then three aspects in future studying are pointed out.

Maintaining grass coverage increases methane uptake in Amazonian pastures, with a reduction of methanogenic archaea in the rhizosphere

Cattle ranching is the largest driver of deforestation in the Brazilian Amazon. The rainforest-to-pasture conversion affects the methane cycle in upland soils, changing it from sink to source of atmospheric methane. However, it remains unknown if management practices could reduce the impact of land-use on methane cycling. In this work, we evaluated how pasture management can regulate the soil methane cycle either by maintaining continuous grass coverage on pasture soils, or by liming the soil to amend acidity. Methane fluxes from forest and pasture soils were evaluated in moisture-controlled greenhouse experiments with and without grass cover (Urochloa brizantha cv. Marandu) or liming. We also assessed changes in the soil microbial community structure of both bare (bulk) and rhizospheric pasture soils through high throughput sequencing of the 16S rRNA gene, and quantified the methane cycling microbiota by their respective marker genes related to methane generation (mcrA) or oxidation (pmoA). The experiments used soils from eastern and western Amazonia, and concurrent field studies allowed us to confirm greenhouse data. The presence of a grass cover not only increased methane uptake by up to 35% in pasture soils, but also reduced the abundance of the methane-producing community. In the grass rhizosphere this reduction was up to 10-fold. Methane-producing archaea belonged to the genera Methanosarcina sp., Methanocella sp., Methanobacterium sp., and Rice Cluster I. Further, we showed that soil liming to increasing pH compromised the capacity of forest and pasture soils to be a sink for methane, and instead converted formerly methane-consuming forest soils to become methane sources in only 40-80 days. Liming reduced the relative abundance of Beijerinckiacea family in forest soils, which account for many known methanotrophs. Our results demonstrate that pasture management that maintains grass coverage can mitigate soil methane emissions, compared to bare (bulk) pasture soil.

Sulfur and methane oxidation by a single microorganism

Wetlands are the major natural source of methane, an important greenhouse gas. The sulfur and methane cycles in wetlands are linked—e.g., a strong sulfur cycle can inhibit methanogenesis. Although there has historically been a clear distinction drawn between methane and sulfur oxidizers, here, we isolated a methanotroph that also performed respiratory oxidization of sulfur compounds. We experimentally demonstrated that thiotrophy and methanotrophy are metabolically compatible, and both metabolisms could be expressed simultaneously in a single microorganism. These findings suggest that mixotrophic methane/sulfur-oxidizing bacteria are a previously overlooked component of environmental methane and sulfur cycles. This creates a framework for a better understanding of these redox cycles in natural and engineered wetlands.

Natural and anthropogenic wetlands are major sources of the atmospheric greenhouse gas methane. Methane emissions from wetlands are mitigated by methanotrophic bacteria at the oxic–anoxic interface, a zone of intense redox cycling of carbon, sulfur, and nitrogen compounds. Here, we report on the isolation of an aerobic methanotrophic bacterium, ‘Methylovirgula thiovorans' strain HY1, which possesses metabolic capabilities never before found in any methanotroph. Most notably, strain HY1 is the first bacterium shown to aerobically oxidize both methane and reduced sulfur compounds for growth. Genomic and proteomic analyses showed that soluble methane monooxygenase and XoxF-type alcohol dehydrogenases are responsible for methane and methanol oxidation, respectively. Various pathways for respiratory sulfur oxidation were present, including the Sox–rDsr pathway and the S₄I system. Strain HY1 employed the Calvin–Benson–Bassham cycle for CO₂ fixation during chemolithoautotrophic growth on reduced sulfur compounds. Proteomic and microrespirometry analyses showed that the metabolic pathways for methane and thiosulfate oxidation were induced in the presence of the respective substrates. Methane and thiosulfate could therefore be independently or simultaneously oxidized. The discovery of this versatile bacterium demonstrates that methanotrophy and thiotrophy are compatible in a single microorganism and underpins the intimate interactions of methane and sulfur cycles in oxic–anoxic interface environments.

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.

Bacterial communities associated with wood rot fungi that use distinct decomposition mechanisms

Wood decomposer fungi are grouped by how they extract sugars from lignocellulose. Brown rot fungi selectively degrade cellulose and hemicellulose, leaving lignin intact, and white rot fungi degrade all components. Many trees are susceptible to both rot types, giving carbon in Earth's woody biomass, specifically lignin, a flexible fate that is affected not only by the fungal decomposition mechanism but also the associated microbial community. However, little is understood about how rot type may influence the microbial community in decaying wood. In this study, we quantified bacterial communities associated with Fomes fomentarius (white rot) and Fomitopsis betulina (brown rot) found on a shared tree host species, birch (Betula papyrifera). We collected 25 wood samples beneath sporocarps  of F. fomentarius (n = 13) and F. betulina (n = 12) on standing dead trees, and coupled microbial DNA sequencing with chemical signatures of rot type (pH and lignin removal). We found that bacterial communities for both fungi were dominated by Proteobacteria, a commonly reported association. However, rot type exerted significant influence on less abundant taxa in ways that align logically with fungal traits. Amplicon sequence variants (ASVs) were enriched in Firmicutes in white-rotted wood, and were enriched in Alphaproteobacteria, Actinobacteria and Acidobacteria in lower pH brown rot. Our results suggest that wood decomposer strategies may exert significant selection effects on bacteria, or vice versa, among less-abundant taxa that have been overlooked when using abundance as the only measure of influence.

Gaseous isopropanol removal in a microbial fuel cell with deoxidizing anode: Performance, anode characteristics and microbial community

A deoxidizing packing material (DPM) with an encapsulated deoxidizing agent (DA) was developed to construct the packed anodes of a trickle-bed microbial fuel cell (TB-MFC) for treating waste gas. The encapsulated DA can consume O₂ in waste gas and increase the voltage output and power density (PD) of the constructed TB-MFC. The DPM effectively enables the circulating water in TB-MFC for maintaining a low level of dissolved oxygen for 80 h. The results revealed that when the concentration of isopropanol (IPA) in waste gas was 0.74 g/m³, the TB-MFC (DPM with DA) exhibited an IPA removal efficiency (RE) of up to 99.7%. When DPM with DA was used as the packing material of the TB-MFC (486.6 mW/m³), the PD was 2.54 times that obtained when using coke as the packing material (191.6 mW/m³). The next-generation sequencing results demonstrated that because the oxygen content of the MFC anode chamber decreased over time in the TB-MFC, the richness of anaerobic electrogens (Pseudoxanthomonas, Flavobacterium, and Ferruginibacter) in the packing materials was increased. These electrogens mainly attached to the DPM, and IPA-degraders appeared in the circulating water of the TB-MFC. This enabled the TB-MFC to simultaneously achieve a high voltage output and IPA RE.

Functional trait relationships demonstrate life strategies in terrestrial prokaryotes

Functional, physiological traits are the underlying drivers of niche differentiation. A common framework related to niches occupied by terrestrial prokaryotes is based on copiotrophy or oligotrophy, where resource investment is primarily in either rapid growth or stress tolerance, respectively. A quantitative trait-based approach sought relationships between taxa, traits and niche in terrestrial prokaryotes. With 175 taxa from 11 Phyla and 35 Families (n = 5 per Family), traits were considered as discrete counts of shared genome-encoded proteins. Trait composition strongly supported non-random functional distributions as preferential clustering of related taxa via unweighted pair-group method with arithmetic mean. Trait similarity between taxa increased as taxonomic rank decreased. A suite of Random Forest models identified traits significantly enriched or depleted in taxonomic groups. These traits conveyed functions related to rapid growth, nutrient acquisition and stress tolerance consistent with their presence in copiotroph-oligotroph niches. Hierarchical clustering of traits identified a clade of competitive, copiotrophic Families resilient to oxidative stress versus glycosyltransferase-enriched oligotrophic Families resistant to antimicrobials and environmental stress. However, the formation of five clades suggested a more nuanced view to describe niche differentiation in terrestrial systems is necessary. We suggest considering traits involved in both resource investment and acquisition when predicting niche.

Linking prokaryotic community composition to carbon biogeochemical cycling across a tropical peat dome in Sarawak, Malaysia

Tropical peat swamp forest is a global store of carbon in a water-saturated, anoxic and acidic environment. This ecosystem holds diverse prokaryotic communities that play a major role in nutrient cycling. A study was conducted in which a total of 24 peat soil samples were collected in three forest types in a tropical peat dome in Sarawak, Malaysia namely, Mixed Peat Swamp (MPS), Alan Batu (ABt), and Alan Bunga (ABg) forests to profile the soil prokaryotic communities through meta 16S amplicon analysis using Illumina Miseq. Results showed these ecosystems were dominated by anaerobes and fermenters such as Acidobacteria, Proteobacteria, Actinobacteria and Firmicutes that cover 80-90% of the total prokaryotic abundance. Overall, the microbial community composition was different amongst forest types and depths. Additionally, this study highlighted the prokaryotic communities' composition in MPS was driven by higher humification level and lower pH whereas in ABt and ABg, the less acidic condition and higher organic matter content were the main factors. It was also observed that prokaryotic diversity and abundance were higher in the more oligotrophic ABt and ABg forest despite the constantly waterlogged condition. In MPS, the methanotroph Methylovirgula ligni was found to be the major species in this forest type that utilize methane (CH4), which could potentially be the contributing factor to the low CH4 gas emissions. Aquitalea magnusonii and Paraburkholderia oxyphila, which can degrade aromatic compounds, were the major species in ABt and ABg forests respectively. This information can be advantageous for future study in understanding the underlying mechanisms of environmental-driven alterations in soil microbial communities and its potential implications on biogeochemical processes in relation to peatland management.

Comparative study of the hemolymph microbiome between live and recently dead American lobsters Homarus americanus

Lobsters and other crustaceans do not have sterile hemolymph. Despite this, little is known about the microbiome in the hemolymph of the lobster Homarus americanus. The purpose of this study was to characterize the hemolymph microbiome in lobsters. The lobsters were part of a larger study on the effect of temperature on epizootic shell disease, and several died during the course of the study, providing an opportunity to examine differences in the microbiomes between live and recently dead (1-24 h) animals. The hemolymph microbiomes of live lobsters was different from those in dead animals and both were different from the tank microbiome in which the animals had been held. The microbiomes of live lobsters were more diverse and had a different suite of bacteria than those from dead animals. The dominant taxa in live lobsters belonged to Flavobacteriaceae and Rhodobacteraceae, whereas Vibrionaceae and Enterobacteriaceae were predominant in the dead lobsters. Although aquarium microbiomes overlapped with the hemolymph microbiomes, there was less overlap and lower abundance of taxa in comparison with hemolymph from live lobsters. Previous studies reporting bacteria in the digestive tract of lobsters suggested that Vibrionaceae and Enterobacteriaceae had invaded the hemolymph via the gut. Our study suggests that hemolymph bacteria abundant in live lobsters do not originate from the tank milieu and comprise a rich, natural, or native background of bacterial constituents.

Soil Bacterial Diversity Is Positively Correlated with Decomposition Rates during Early Phases of Maize Litter Decomposition

This study aimed to investigate the effects of different levels of soil- and plant-associated bacterial diversity on the rates of litter decomposition, and bacterial community dynamics during its early phases. We performed an incubation experiment where soil bacterial diversity (but not abundance) was manipulated by autoclaving and reinoculation. Natural or autoclaved maize leaves were applied to the soils and incubated for 6 weeks. Bacterial diversity was assessed before and during litter decomposition using 16S rRNA gene metabarcoding. We found a positive correlation between litter decomposition rates and soil bacterial diversity. The soil with the highest bacterial diversity was dominated by oligotrophic bacteria including Acidobacteria, Nitrospiraceae, and Gaiellaceae, and its community composition did not change during the incubation. In the less diverse soils, those taxa were absent but were replaced by copiotrophic bacteria, such as Caulobacteraceae and Beijerinckiaceae, until the end of the incubation period. SourceTracker analysis revealed that litter-associated bacteria, such as Beijerinckiaceae, only became part of the bacterial communities in the less diverse soils. This suggests a pivotal role of oligotrophic bacteria during the early phases of litter decomposition and the predominance of copiotrophic bacteria at low diversity.

Meta-analysis cum machine learning approaches address the structure and biogeochemical potential of marine copepod associated bacteriobiomes

Copepods are the dominant members of the zooplankton community and the most abundant form of life. It is imperative to obtain insights into the copepod-associated bacteriobiomes (CAB) in order to identify specific bacterial taxa associated within a copepod, and to understand how they vary between different copepods. Analysing the potential genes within the CAB may reveal their intrinsic role in biogeochemical cycles. For this, machine-learning models and PICRUSt2 analysis were deployed to analyse 16S rDNA gene sequences (approximately 16 million reads) of CAB belonging to five different copepod genera viz., Acartia spp., Calanus spp., Centropages sp., Pleuromamma spp., and Temora spp.. Overall, we predict 50 sub-OTUs (s-OTUs) (gradient boosting classifiers) to be important in five copepod genera. Among these, 15 s-OTUs were predicted to be important in Calanus spp. and 20 s-OTUs as important in Pleuromamma spp.. Four bacterial s-OTUs Acinetobacter johnsonii, Phaeobacter, Vibrio shilonii and Piscirickettsiaceae were identified as important s-OTUs in Calanus spp., and the s-OTUs Marinobacter, Alteromonas, Desulfovibrio, Limnobacter, Sphingomonas, Methyloversatilis, Enhydrobacter and Coriobacteriaceae were predicted as important s-OTUs in Pleuromamma spp., for the first time. Our meta-analysis revealed that the CAB of Pleuromamma spp. had a high proportion of potential genes responsible for methanogenesis and nitrogen fixation, whereas the CAB of Temora spp. had a high proportion of potential genes involved in assimilatory sulphate reduction, and cyanocobalamin synthesis. The CAB of Pleuromamma spp. and Temora spp. have potential genes accountable for iron transport.

Isolation and characterisation of Methylocystis spp. for poly-3-hydroxybutyrate production using waste methane feedstocks

Waste plastic and methane emissions are two anthropogenic by-products exacerbating environmental pollution. Methane-oxidizing bacteria (methanotrophs) hold the key to solving these problems simultaneously by utilising otherwise wasted methane gas as carbon source and accumulating the carbon as poly-3-hydroxybutyrate, a biodegradable plastic polymer. Here we present the isolation and characterisation of two novel Methylocystis strains with the ability to produce up to 55.7 ± 1.9% poly-3-hydroxybutyrate of cell dry weight when grown on methane from different waste sources such as landfill and anaerobic digester gas. Methylocystis rosea BRCS1 isolated from a recreational lake and Methylocystis parvus BRCS2 isolated from a bog were whole genome sequenced using PacBio and Illumina genome sequencing technologies. In addition to potassium nitrate, these strains were also shown to grow on ammonium chloride, glutamine and ornithine as nitrogen source. Growth of Methylocystis parvus BRCS2 on Nitrate Mineral Salt (NMS) media with 0.1% methanol vapor as carbon source was demonstrated. The genetic tractability by conjugation was also determined with conjugation efficiencies up to 2.8 × 10^–2 and 1.8 × 10^–2 for Methylocystis rosea BRCS1 and Methylocystis parvus BRCS2 respectively using a plasmid with ColE1 origin of replication. Finally, we show that Methylocystis species can produce considerable amounts of poly-3-hydroxybutyrate on waste methane sources without impaired growth, a proof of concept which opens doors to their use in integrated bio-facilities like landfills and anaerobic digesters.

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.

Anaerobic oxidation of methane and associated microbiome in anoxic water of Northwestern Siberian lakes

Arctic lakes emit methane (CH₄) to the atmosphere. The magnitude of this flux could increase with permafrost thaw but might also be mitigated by microbial CH₄ oxidation. Methane oxidation in oxic water has been extensively studied, while the contribution of anaerobic oxidation of methane (AOM) to CH₄ mitigation is not fully understood. We have investigated four Northern Siberian stratified lakes in an area of discontinuous permafrost nearby Igarka, Russia. Analyses of CH₄ concentrations in the water column demonstrated that 60 to 100% of upward diffusing CH₄ was oxidized in the anoxic layers of the four lakes. A combination of pmoA and mcrA gene qPCR and 16S rRNA gene metabarcoding showed that the same taxa, all within Methylomonadaceae and including the predominant genus Methylobacter as well as Crenothrix, could be the major methane-oxidizing bacteria (MOB) in the anoxic water of the four lakes. Correlation between Methylomonadaceae and OTUs within Methylotenera, Geothrix and Geobacter genera indicated that AOM might occur in an interaction between MOB, denitrifiers and iron-cycling partners. We conclude that MOB within Methylomonadaceae could have a crucial impact on CH₄ cycling in these Siberian Arctic lakes by mitigating the majority of produced CH₄ before it leaves the anoxic zone. This finding emphasizes the importance of AOM by Methylomonadaceae and extends our knowledge about CH₄ cycle in lakes, a crucial component of the global CH₄ cycle.

The origin of aerobic methanotrophy within the Proteobacteria

Aerobic methanotrophs play critical roles in the global carbon cycle, but despite their environmental ubiquity, they are phylogenetically restricted. Via bioinformatic analyses, it is shown that methanotrophy likely arose from methylotrophy from the lateral gene transfer of either of the two known forms of methane monooxygenase (particulate and soluble methane monooxygenases). Moreover, it appears that both known forms of pyrroloquinoline quinone-dependent methanol dehydrogenase (MeDH) found in methanotrophs-the calcium-containing Mxa-MeDH and the rare earth element-containing Xox-MeDH-were likely encoded in the genomes before the acquisition of the methane monooxygenases (MMOs), but that some methanotrophs subsequently received an additional copy of Xox-MeDH-encoding genes via lateral gene transfer. Further, data are presented that indicate the evolution of methanotrophy from methylotrophy not only required lateral transfer of genes encoding for methane monooxygenases, but also likely the pre-existence of a means of collecting copper. Given the emerging interest in valorizing methane via biological platforms, it is recommended that future strategies for heterologous expression of methane monooxygenase for conversion of methane to methanol also include cloning of genes encoding mechanism(s) of copper uptake, especially for expression of particulate methane monooxygenase.

Biotic and Environmental Drivers of Plant Microbiomes Across a Permafrost Thaw Gradient

Plant-associated microbiomes are structured by environmental conditions and plant associates, both of which are being altered by climate change. The future structure of plant microbiomes will depend on the, largely unknown, relative importance of each. This uncertainty is particularly relevant for arctic peatlands, which are undergoing large shifts in plant communities and soil microbiomes as permafrost thaws, and are potentially appreciable sources of climate change feedbacks due to their soil carbon (C) storage. We characterized phyllosphere and rhizosphere microbiomes of six plant species, and bulk peat, across a permafrost thaw progression (from intact permafrost, to partially- and fully-thawed stages) via 16S rRNA gene amplicon sequencing. We tested the hypothesis that the relative influence of biotic versus environmental filtering (the role of plant species versus thaw-defined habitat) in structuring microbial communities would differ among phyllosphere, rhizosphere, and bulk peat. Using both abundance- and phylogenetic-based approaches, we found that phyllosphere microbial composition was more strongly explained by plant associate, with little influence of habitat, whereas in the rhizosphere, plant and habitat had similar influence. Network-based community analyses showed that keystone taxa exhibited similar patterns with stronger responses to drivers. However, plant associates appeared to have a larger influence on organisms belonging to families associated with methane-cycling than the bulk community. Putative methanogens were more strongly influenced by plant than habitat in the rhizosphere, and in the phyllosphere putative methanotrophs were more strongly influenced by plant than was the community at large. We conclude that biotic effects can be stronger than environmental filtering, but their relative importance varies among microbial groups. For most microbes in this system, biotic filtering was stronger aboveground than belowground. However, for putative methane-cyclers, plant associations have a stronger influence on community composition than environment despite major hydrological changes with thaw. This suggests that plant successional dynamics may be as important as hydrological changes in determining microbial relevance to C-cycling climate feedbacks. By partitioning the degree that plant versus environmental filtering drives microbiome composition and function we can improve our ability to predict the consequences of warming for C-cycling in other arctic areas undergoing similar permafrost thaw transitions.

Bioremediation of Unconventional Oil Contaminated Ecosystems under Natural and Assisted Conditions: A Review

It is a general understanding that unconventional oil is petroleum-extracted and processed into petroleum products using unconventional means. The recent growth in the United States shale oil production and the lack of refineries in Canada built for heavy crude processes have resulted in a significant increase in U.S imports of unconventional oil since 2018. This has increased the risk of incidents and catastrophic emergencies during the transportation of unconventional oils using transmission pipelines and train rails. A great deal of effort has been made to address the remediation of contaminated soil/sediment following the traditional oil spills. However, spill response and cleanup techniques (e.g., oil recuperation, soil-sediment-water treatments) showed slow and inefficient performance when it came to unconventional oil, bringing larger associated environmental impacts in need of investigation. To the best of our knowledge, there is no coherent review available on the biodegradability of unconventional oil, including Dilbit and Bakken oil. Hence, in view of the insufficient information and contrasting results obtained on the remediation of petroleum, this review is an attempt to fill the gap by presenting the collective understanding and critical analysis of the literature on bioremediation of products from the oil sand and shale (e.g., Dilbit and Bakken oil). This can help evaluate the different aspects of hydrocarbon biodegradation and identify the knowledge gaps in the literature.

Lanthanide-Dependent Methylotrophs of the Family Beijerinckiaceae: Physiological and Genomic Insights

Methylotrophic bacteria use methanol and related C₁ compounds as carbon and energy sources. Methanol dehydrogenases are essential for methanol oxidation, while lanthanides are important cofactors of many pyrroloquinoline quinone-dependent methanol dehydrogenases and related alcohol dehydrogenases. We describe here the physiological and genomic characterization of newly isolated Beijerinckiaceae bacteria that rely on lanthanides for methanol oxidation. A broad physiological diversity was indicated by the ability to metabolize a wide range of multicarbon substrates, including various sugars, and organic acids, as well as diverse C₁ substrates such as methylated amines and methylated sulfur compounds. Methanol oxidation was possible only in the presence of low-mass lanthanides (La, Ce, and Nd) at submicromolar concentrations (>100 nM). In a comparison with other Beijerinckiaceae, genomic and transcriptomic analyses revealed the usage of a glutathione- and tetrahydrofolate-dependent pathway for formaldehyde oxidation and channeling methyl groups into the serine cycle for carbon assimilation. Besides a single xoxF gene, we identified two additional genes for lanthanide-dependent alcohol dehydrogenases, including one coding for an ExaF-type alcohol dehydrogenase, which was so far not known in Beijerinckiaceae Homologs for most of the gene products of the recently postulated gene cluster linked to lanthanide utilization and transport could be detected, but for now it remains unanswered how lanthanides are sensed and taken up by our strains. Studying physiological responses to lanthanides under nonmethylotrophic conditions in these isolates as well as other organisms is necessary to gain a more complete understanding of lanthanide-dependent metabolism as a whole.IMPORTANCE We supplemented knowledge of the broad metabolic diversity of the Beijerinckiaceae by characterizing new members of this family that rely on lanthanides for methanol oxidation and that possess additional lanthanide-dependent enzymes. Considering that lanthanides are critical resources for many modern applications and that recovering them is expensive and puts a heavy burden on the environment, lanthanide-dependent metabolism in microorganisms is an exploding field of research. Further research into how isolated Beijerinckiaceae and other microbes utilize lanthanides is needed to increase our understanding of lanthanide-dependent metabolism. The diversity and widespread occurrence of lanthanide-dependent enzymes make it likely that lanthanide utilization varies in different taxonomic groups and is dependent on the habitat of the microbes.

Molecular Analyses of the Distribution and Function of Diazotrophic Rhizobia and Methanotrophs in the Tissues and Rhizosphere of Non-Leguminous Plants

Biological nitrogen fixation (BNF) by plants and its bacterial associations represent an important natural system for capturing atmospheric dinitrogen (N₂) and processing it into a reactive form of nitrogen through enzymatic reduction. The study of BNF in non-leguminous plants has been difficult compared to nodule-localized BNF in leguminous plants because of the diverse sites of N₂ fixation in non-leguminous plants. Identification of the involved N₂-fixing bacteria has also been difficult because the major nitrogen fixers were often lost during isolation attempts. The past 20 years of molecular analyses has led to the identification of N₂ fixation sites and active nitrogen fixers in tissues and the rhizosphere of non-leguminous plants. Here, we examined BNF hotspots in six reported non-leguminous plants. Novel rhizobia and methanotrophs were found to be abundantly present in the free-living state at sites where carbon and energy sources were predominantly available. In the carbon-rich apoplasts of plant tissues, rhizobia such as Bradyrhizobium spp. microaerobically fix N₂. In paddy rice fields, methane molecules generated under anoxia are oxidized by xylem aerenchyma-transported oxygen with the simultaneous fixation of N₂ by methane-oxidizing methanotrophs. We discuss the effective functions of the rhizobia and methanotrophs in non-legumes for the acquisition of fixed nitrogen in addition to research perspectives.

Novel facultative Methylocella strains are active methane consumers at terrestrial natural gas seeps

BACKGROUND

Natural gas seeps contribute to global climate change by releasing substantial amounts of the potent greenhouse gas methane and other climate-active gases including ethane and propane to the atmosphere. However, methanotrophs, bacteria capable of utilising methane as the sole source of carbon and energy, play a significant role in reducing the emissions of methane from many environments. Methylocella-like facultative methanotrophs are a unique group of bacteria that grow on other components of natural gas (i.e. ethane and propane) in addition to methane but a little is known about the distribution and activity of Methylocella in the environment. The purposes of this study were to identify bacteria involved in cycling methane emitted from natural gas seeps and, most importantly, to investigate if Methylocella-like facultative methanotrophs were active utilisers of natural gas at seep sites.

RESULTS

The community structure of active methane-consuming bacteria in samples from natural gas seeps from Andreiasu Everlasting Fire (Romania) and Pipe Creek (NY, USA) was investigated by DNA stable isotope probing (DNA-SIP) using ¹³C-labelled methane. The 16S rRNA gene sequences retrieved from DNA-SIP experiments revealed that of various active methanotrophs, Methylocella was the only active methanotrophic genus common to both natural gas seep environments. We also isolated novel facultative methanotrophs, Methylocella sp. PC1 and PC4 from Pipe Creek, able to utilise methane, ethane, propane and various non-gaseous multicarbon compounds. Functional and comparative genomics of these new isolates revealed genomic and physiological divergence from already known methanotrophs, in particular, the absence of mxa genes encoding calcium-containing methanol dehydrogenase. Methylocella sp. PC1 and PC4 had only the soluble methane monooxygenase (sMMO) and lanthanide-dependent methanol dehydrogenase (XoxF). These are the first Alphaproteobacteria methanotrophs discovered with this reduced functional redundancy for C-1 metabolism (i.e. sMMO only and XoxF only).

CONCLUSIONS

Here, we provide evidence, using culture-dependent and culture-independent methods, that Methylocella are abundant and active at terrestrial natural gas seeps, suggesting that they play a significant role in the biogeochemical cycling of these gaseous alkanes. This might also be significant for the design of biotechnological strategies for controlling natural gas emissions, which are increasing globally due to unconventional exploitation of oil and gas.

Genomic Evidence for Simultaneous Optimization of Transcription and Translation through Codon Variants in the pmoCAB Operon of Type Ia Methanotrophs

Microbial methane oxidation plays a fundamental role in the biogeochemical cycle of Earth’s system. Recent reports have provided evidence for the acquisition of methane monooxygenases by horizontal gene transfer in methane-oxidizing bacteria from different environments, but how evolution has shaped the coding sequences to execute methanotrophy efficiently remains unexplored. In this work, we provide genomic evidence that among the different types of methanotrophs, type Ia methanotrophs possess a unique coding sequence of the pmoCAB operon that is under positive selection for optimal resource allocation and efficient synthesis of transcripts and proteins. This adaptive trait possibly enables type Ia methanotrophs to respond robustly to fluctuating methane availability and explains their global prevalence.

Understanding the interplay between genotype and phenotype is a fundamental goal of functional genomics. Methane oxidation is a microbial phenotype with global-scale significance as part of the carbon biogeochemical cycle and a sink for greenhouse gas. Microorganisms that oxidize methane (methanotrophs) are taxonomically diverse and widespread around the globe. In methanotrophic bacteria, enzymes in the methane oxidation metabolic module (KEGG module M00174, conversion of methane to formaldehyde) are encoded in four operons (pmoCAB, mmoXYZBCD, mxaFI, and xoxF). Recent reports have suggested that methanotrophs in Proteobacteria acquired methane monooxygenases through horizontal gene transfer. Here, we used a genomic meta-analysis to infer the transcriptional and translational advantages of coding sequences from the methane oxidation metabolic modules of different types of methanotrophs. By analyzing isolate and metagenome-assembled genomes from phylogenetically and geographically diverse sources, we detected an anomalous nucleotide composition bias in the coding sequences of particulate methane monooxygenase genes (pmoCAB) from type Ia methanotrophs. We found that this nucleotide bias increases the level of codon bias by decreasing the GC content in the third base of codons, a strategy that contrasts with that of other coding sequences in the module. Further codon usage analyses uncovered that codon variants of the type Ia pmoCAB coding sequences deviate from the genomic signature to match ribosomal protein-coding sequences. Subsequently, computation of transcription and translation metrics revealed that the pmoCAB coding sequences of type Ia methanotrophs optimize the usage of codon variants to maximize translation efficiency and accuracy, while minimizing the synthesis cost of transcripts and proteins.

IMPORTANCE Microbial methane oxidation plays a fundamental role in the biogeochemical cycle of Earth’s system. Recent reports have provided evidence for the acquisition of methane monooxygenases by horizontal gene transfer in methane-oxidizing bacteria from different environments, but how evolution has shaped the coding sequences to execute methanotrophy efficiently remains unexplored. In this work, we provide genomic evidence that among the different types of methanotrophs, type Ia methanotrophs possess a unique coding sequence of the pmoCAB operon that is under positive selection for optimal resource allocation and efficient synthesis of transcripts and proteins. This adaptive trait possibly enables type Ia methanotrophs to respond robustly to fluctuating methane availability and explains their global prevalence.

Widespread soil bacterium that oxidizes atmospheric methane

The global atmospheric level of methane (CH₄), the second most important greenhouse gas, is currently increasing by ∼10 million tons per year. Microbial oxidation in unsaturated soils is the only known biological process that removes CH₄ from the atmosphere, but so far, bacteria that can grow on atmospheric CH₄ have eluded all cultivation efforts. In this study, we have isolated a pure culture of a bacterium, strain MG08 that grows on air at atmospheric concentrations of CH₄ [1.86 parts per million volume (p.p.m.v.)]. This organism, named Methylocapsa gorgona, is globally distributed in soils and closely related to uncultured members of the upland soil cluster α. CH₄ oxidation experiments and ¹³C-single cell isotope analyses demonstrated that it oxidizes atmospheric CH₄ aerobically and assimilates carbon from both CH₄ and CO₂ Its estimated specific affinity for CH₄ (a⁰ _s) is the highest for any cultivated methanotroph. However, growth on ambient air was also confirmed for Methylocapsa acidiphila and Methylocapsa aurea, close relatives with a lower specific affinity for CH₄, suggesting that the ability to utilize atmospheric CH₄ for growth is more widespread than previously believed. The closed genome of M. gorgona MG08 encodes a single particulate methane monooxygenase, the serine cycle for assimilation of carbon from CH₄ and CO₂, and CO₂ fixation via the recently postulated reductive glycine pathway. It also fixes dinitrogen and expresses the genes for a high-affinity hydrogenase and carbon monoxide dehydrogenase, suggesting that atmospheric CH₄ oxidizers harvest additional energy from oxidation of the atmospheric trace gases carbon monoxide (0.2 p.p.m.v.) and hydrogen (0.5 p.p.m.v.).

A review on the advanced leachate treatment technologies and their performance comparison: an opportunity to keep the environment safe

Landfill application is the most common approach for biowaste treatment via leachate treatment system. When municipal solid waste deposited in the landfills, microbial decomposition breaks down the wastes generating the end products, such as carbon dioxide, methane, volatile organic compounds, and liquid leachate. However, due to the landfill age, the fluctuation in the characteristics of landfill leachate is foreseen in the leachate treatment plant. The focuses of the researchers are keeping leachate from contaminating groundwater besides keeping potent methane emissions from reaching the atmosphere. To address the above issues, scientists are required to adopt green biological methods to keep the environment safe. This review focuses on the assorting of research papers on organic content and nitrogen removal from the leachate via recent effective biological technologies instead of conventional nitrification and denitrification process. The published researches on the characteristics of various Malaysian landfill sites were also discussed. The understanding of the mechanism behind the nitrification and denitrification process will help to select an optimized and effective biological treatment option in treating the leachate waste. Recently, widely studied technologies for the biological treatment process are aerobic methane oxidation coupled to denitrification (AME-D) and partial nitritation-anammox (PN/A) process, and both were discussed in this review article. This paper gives the idea of the modification of the conventional treatment technologies, such as combining the present processes to make the treatment process more effective. With the integration of biological process in the leachate treatment, the effluent discharge could be treated in shortcut and novel pathways, and it can lead to achieving "3Rs" of reduce, reuse, and recycle approach.

Seasonal and ecohydrological regulation of active microbial populations involved in DOC, CO2, and CH4 fluxes in temperate rainforest soil

The Pacific coastal temperate rainforest (PCTR) is a global hot-spot for carbon cycling and export. Yet the influence of microorganisms on carbon cycling processes in PCTR soil is poorly characterized. We developed and tested a conceptual model of seasonal microbial carbon cycling in PCTR soil through integration of geochemistry, micro-meteorology, and eukaryotic and prokaryotic ribosomal amplicon (rRNA) sequencing from 216 soil DNA and RNA libraries. Soil moisture and pH increased during the wet season, with significant correlation to net CO₂ flux in peat bog and net CH₄ flux in bog forest soil. Fungal succession in these sites was characterized by the apparent turnover of Archaeorhizomycetes phylotypes accounting for 41% of ITS libraries. Anaerobic prokaryotes, including Syntrophobacteraceae and Methanomicrobia increased in rRNA libraries during the wet season. Putatively active populations of these phylotypes and their biogeochemical marker genes for sulfate and CH₄ cycling, respectively, were positively correlated following rRNA and metatranscriptomic network analysis. The latter phylotype was positively correlated to CH₄ fluxes (r = 0.46, p < 0.0001). Phylotype functional assignments were supported by metatranscriptomic analysis. We propose that active microbial populations respond primarily to changes in hydrology, pH, and nutrient availability. The increased microbial carbon export observed over winter may have ramifications for climate-soil feedbacks in the PCTR.

Evolutionary History of Copper Membrane Monooxygenases

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 xmoCAB. We aligned xmo operons from 66 microbial genomes, including members of the Alpha-, Beta-, and Gamma-proteobacteria, Verrucomicrobia, Actinobacteria, Thaumarchaeota 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, xmoA, xmoB and xmoC, closely matched, indicating that this operon evolved or was consistently transferred as a unit, with the possible exception of the methane monooxygenase operons in Verrucomicrobia, where the pmoB gene has a distinct phylogeny from pmoA and pmoC. Compositional analyses indicated that some clusters of xmoCAB operons (for example, the pmoCAB in gammaproteobacterial methanotrophs and the amoCAB 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 Nitrosococcus 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.

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.

Horizontal gene transfer of three co-inherited methane monooxygenase systems gave rise to methanotrophy in the Proteobacteria

The critical role that bacterial methanotrophs have in regulating the environmental concentrations of the potent greenhouse gas, methane, under aerobic conditions is dependent on monooxygenase enzymes which oxidise the substrate as both a carbon and energy source. Despite the importance of these organisms, the evolutionary origins of aerobic methane oxidation capability and its relationship to proteobacterial evolution is not well understood. Here we investigated the phylogenetic relationship of proteobacterial methanotrophs with related, non-methanotrophic bacteria using 16S rRNA and the evolution of two forms of methane monooxygenase: membrane bound (pMMO and pXMO) and cytoplasmic (sMMO). Through analysis we have concluded that extant proteobacterial methanotrophs evolved from up to five ancestral species, and that all three methane monooxygenase systems, pMMO, pXMO and sMMO, were likely present in the ancestral species (although pXMO and sMMO are not present in most of the present day methanotrophs). Here we propose that the three monooxygenase systems entered the ancestral species by horizontal gene transfer, with these likely to have pre-existing physiological and metabolic attributes that supported conversion to methanotrophy. Further, we suggest that prior to these enzyme systems developing methane oxidation capabilities, the membrane-bound and cytoplasmic monooxygenases were already both functionally and phylogenetically associated. These results not only suggest that sMMO and pXMO have a far greater role in methanotrophic evolution than previously understood but also implies that the co-inheritance of membrane bound and cytoplasmic monooxygenases have roles additional to that of supporting methanotrophy.

Methanotrophy across a natural permafrost thaw environment

The fate of carbon sequestered in permafrost is a key concern for future global warming as this large carbon stock is rapidly becoming a net methane source due to widespread thaw. Methane release from permafrost is moderated by methanotrophs, which oxidise 20-60% of this methane before emission to the atmosphere. Despite the importance of methanotrophs to carbon cycling, these microorganisms are under-characterised and have not been studied across a natural permafrost thaw gradient. Here, we examine methanotroph communities from the active layer of a permafrost thaw gradient in Stordalen Mire (Abisko, Sweden) spanning three years, analysing 188 metagenomes and 24 metatranscriptomes paired with in situ biogeochemical data. Methanotroph community composition and activity varied significantly as thaw progressed from intact permafrost palsa, to partially thawed bog and fully thawed fen. Thirteen methanotroph population genomes were recovered, including two novel genomes belonging to the uncultivated upland soil cluster alpha (USCα) group and a novel potentially methanotrophic Hyphomicrobiaceae. Combined analysis of porewater δ¹³C-CH₄ isotopes and methanotroph abundances showed methane oxidation was greatest below the oxic-anoxic interface in the bog. These results detail the direct effect of thaw on autochthonous methanotroph communities, and their consequent changes in population structure, activity and methane moderation potential.

Facultative methanotrophs are abundant at terrestrial natural gas seeps

BACKGROUND

Natural gas contains methane and the gaseous alkanes ethane, propane and butane, which collectively influence atmospheric chemistry and cause global warming. Methane-oxidising bacteria, methanotrophs, are crucial in mitigating emissions of methane as they oxidise most of the methane produced in soils and the subsurface before it reaches the atmosphere. Methanotrophs are usually obligate, i.e. grow only on methane and not on longer chain alkanes. Bacteria that grow on the other gaseous alkanes in natural gas such as propane have also been characterised, but they do not grow on methane. Recently, it was shown that the facultative methanotroph Methylocella silvestris grew on ethane and propane, other components of natural gas, in addition to methane. Therefore, we hypothesised that Methylocella may be prevalent at natural gas seeps and might play a major role in consuming all components of this potent greenhouse gas mixture before it is released to the atmosphere.

RESULTS

Environments known to be exposed to biogenic methane emissions or thermogenic natural gas seeps were surveyed for methanotrophs. 16S rRNA gene amplicon sequencing revealed that Methylocella were the most abundant methanotrophs in natural gas seep environments. New Methylocella-specific molecular tools targeting mmoX (encoding the soluble methane monooxygenase) by PCR and Illumina amplicon sequencing were designed and used to investigate various sites. Functional gene-based assays confirmed that Methylocella were present in all of the natural gas seep sites tested here. This might be due to its ability to use methane and other short chain alkane components of natural gas. We also observed the abundance of Methylocella in other environments exposed to biogenic methane, suggesting that Methylocella has been overlooked in the past as previous ecological studies of methanotrophs often used pmoA (encoding the alpha subunit of particulate methane monooxygenase) as a marker gene.

CONCLUSION

New biomolecular tools designed in this study have expanded our ability to detect, and our knowledge of the environmental distribution of Methylocella, a unique facultative methanotroph. This study has revealed that Methylocella are particularly abundant at natural gas seeps and may play a significant role in biogeochemical cycling of gaseous hydrocarbons.

Impacts of Glutaraldehyde on Microbial Community Structure and Degradation Potential in Streams Impacted by Hydraulic Fracturing

The environmental impacts of hydraulic fracturing, particularly those of surface spills in aquatic ecosystems, are not fully understood. The goals of this study were to (1) understand the effect of previous exposure to hydraulic fracturing fluids on aquatic microbial community structure and (2) examine the impacts exposure has on biodegradation potential of the biocide glutaraldehyde. Microcosms were constructed from hydraulic fracturing-impacted and nonhydraulic fracturing-impacted streamwater within the Marcellus shale region in Pennsylvania. Microcosms were amended with glutaraldehyde and incubated aerobically for 56 days. Microbial community adaptation to glutaraldehyde was monitored using 16S rRNA gene amplicon sequencing and quantification by qPCR. Abiotic and biotic glutaraldehyde degradation was measured using ultra-performance liquid chromatography--high resolution mass spectrometry and total organic carbon. It was found that nonhydraulic fracturing-impacted microcosms biodegraded glutaraldehyde faster than the hydraulic fracturing-impacted microcosms, showing a decrease in degradation potential after exposure to hydraulic fracturing activity. Hydraulic fracturing-impacted microcosms showed higher richness after glutaraldehyde exposure compared to unimpacted streams, indicating an increased tolerance to glutaraldehyde in hydraulic fracturing impacted streams. Beta diversity and differential abundance analysis of sequence count data showed different bacterial enrichment for hydraulic fracturing-impacted and nonhydraulic fracturing-impacted microcosms after glutaraldehyde addition. These findings demonstrated a lasting effect on microbial community structure and glutaraldehyde degradation potential in streams impacted by hydraulic fracturing operations.

Response of Aquatic Bacterial Communities to Hydraulic Fracturing in Northwestern Pennsylvania: A Five-Year Study

Horizontal drilling and hydraulic fracturing extraction procedures have become increasingly present in Pennsylvania where the Marcellus Shale play is largely located. The potential for long-term environmental impacts to nearby headwater stream ecosystems and aquatic bacterial assemblages is still incompletely understood. Here, we perform high-throughput sequencing of the 16 S rRNA gene to characterize the bacterial community structure of water, sediment, and other environmental samples (n = 189) from 31 headwater stream sites exhibiting different histories of fracking activity in northwestern Pennsylvania over five years (2012-2016). Stream pH was identified as a main driver of bacterial changes within the streams and fracking activity acted as an environmental selector for certain members at lower taxonomic levels within stream sediment. Methanotrophic and methanogenic bacteria (i.e. Methylocystaceae, Beijerinckiaceae, and Methanobacterium) were significantly enriched in sites exhibiting Marcellus shale activity (MSA+) compared to MSA- streams. This study highlighted potential sentinel taxa associated with nascent Marcellus shale activity and some of these taxa remained as stable biomarkers across this five-year study. Identifying the presence and functionality of specific microbial consortia within fracking-impacted streams will provide a clearer understanding of the natural microbial community's response to fracking and inform in situ remediation strategies.

Chloromethane Degradation in Soils: A Combined Microbial and Two-Dimensional Stable Isotope Approach

Chloromethane (CHCl, methyl chloride) is the most abundant volatile halocarbon in the atmosphere and involved in stratospheric ozone depletion. The global CHCl budget, and especially the CHCl sink from microbial degradation in soil, still involves large uncertainties. These may potentially be resolved by a combination of stable isotope analysis and bacterial diversity studies. We determined the stable isotope fractionation of CHCl hydrogen and carbon and investigated bacterial diversity during CHCl degradation in three soils with different properties (forest, grassland, and agricultural soils) and at different temperatures and headspace mixing ratios of CHCl. The extent of chloromethane degradation decreased in the order forest > grassland > agricultural soil. Rates ranged from 0.7 to 2.5 μg g dry wt. d for forest soil, from 0.1 to 0.9 μg g dry wt. d for grassland soil, and from 0.1 to 0.4 μg g dry wt. d for agricultural soil and increased with increasing temperature and CHCl supplementation. The measured mean stable hydrogen enrichment factor of CHCl of -50 ± 13‰ was unaffected by temperature, mixing ratio, or soil type. In contrast, the stable carbon enrichment factor depended on CHCl degradation rates and ranged from -38 to -11‰. Bacterial community composition correlated with soil properties was independent from CHCl degradation or isotope enrichment. Nevertheless, increased abundance after CHCl incubation was observed in 21 bacterial operational taxonomical units (OTUs at the 97% 16S RNA sequence identity level). This suggests that some of these bacterial taxa, although not previously associated with CHCl degradation, may play a role in the microbial CHCl sink in soil.

Current Trends in Methylotrophy

Methylotrophy is a field of study dealing with microorganisms capable of utilization of compounds devoid of carbon-carbon bonds (C1 compounds). In this review, we highlight several emerging trends in methylotrophy. First, we discuss the significance of the recent discovery of lanthanide-dependent alcohol dehydrogenases for understanding both the occurrence and the distribution of methylotrophy functions among bacteria, and then we discuss the newly appreciated role of lanthanides in biology. Next, we describe the detection of other methylotrophy pathways across novel bacterial taxa and insights into the evolution of methylotrophy. Further, data are presented on the occurrence and activity of aerobic methylotrophs in hypoxic and anoxic environments, questioning the prior assumptions on niche separation of aerobic and anaerobic methylotrophy. The concept of communal function in aerobic methane oxidation is also briefly discussed. Finally, we review recent research in engineering methylotrophs for biotechnological applications as well as recent progress in engineering synthetic methylotrophy.

Unravelling the Identity, Metabolic Potential and Global Biogeography of the Atmospheric Methane-Oxidizing Upland Soil Cluster α

Understanding of global methane sources and sinks is a prerequisite for the design of strategies to counteract global warming. Microbial methane oxidation in soils represents the largest biological sink for atmospheric methane. However, still very little is known about the identity, metabolic properties and distribution of the microbial group proposed to be responsible for most of this uptake, the uncultivated upland soil cluster α (USCα). Here, we reconstructed a draft genome of USCα from a combination of targeted cell sorting and metagenomes from forest soil, providing the first insights into its metabolic potential and environmental adaptation strategies. The 16S rRNA gene sequence recovered was distinctive and suggests this crucial group as a new genus within the Beijerinckiaceae, close to Methylocapsa. Application of a fluorescently labelled suicide substrate for the particulate methane monooxygenase enzyme (pMMO) coupled to 16S rRNA fluorescence in situ hybridisation (FISH) allowed for the first time a direct link of the high‐affinity activity of methane oxidation to USCα cells in situ. Analysis of the global biogeography of this group further revealed its presence in previously unrecognized habitats, such as subterranean and volcanic biofilm environments, indicating a potential role of these environments in the biological sink for atmospheric methane.

Acidotolerant Bacteria and Fungi as a Sink of Methanol-Derived Carbon in a Deciduous Forest Soil

Methanol is an abundant atmospheric volatile organic compound that is released from both living and decaying plant material. In forest and other aerated soils, methanol can be consumed by methanol-utilizing microorganisms that constitute a known terrestrial sink. However, the environmental factors that drive the biodiversity of such methanol-utilizers have been hardly resolved. Soil-derived isolates of methanol-utilizers can also often assimilate multicarbon compounds as alternative substrates. Here, we conducted a comparative DNA stable isotope probing experiment under methylotrophic (only [¹³C₁]-methanol was supplemented) and combined substrate conditions ([¹²C₁]-methanol and alternative multi-carbon [¹³C_u]-substrates were simultaneously supplemented) to (i) identify methanol-utilizing microorganisms of a deciduous forest soil (European beech dominated temperate forest in Germany), (ii) assess their substrate range in the soil environment, and (iii) evaluate their trophic links to other soil microorganisms. The applied multi-carbon substrates represented typical intermediates of organic matter degradation, such as acetate, plant-derived sugars (xylose and glucose), and a lignin-derived aromatic compound (vanillic acid). An experimentally induced pH shift was associated with substantial changes of the diversity of active methanol-utilizers suggesting that soil pH was a niche-defining factor of these microorganisms. The main bacterial methanol-utilizers were members of the Beijerinckiaceae (Bacteria) that played a central role in a detected methanol-based food web. A clear preference for methanol or multi-carbon substrates as carbon source of different Beijerinckiaceae-affiliated phylotypes was observed suggesting a restricted substrate range of the methylotrophic representatives. Apart from Bacteria, we also identified the yeasts Cryptococcus and Trichosporon as methanol-derived carbon-utilizing fungi suggesting that further research is needed to exclude or prove methylotrophy of these fungi.

Draft Genome Sequence of Methylocapsa palsarum NE2T, an Obligate Methanotroph from Subarctic Soil

Methylocapsa palsarum NE2^T is an aerobic, mildly acidophilic, obligate methanotroph. Similar to other Methylocapsa species, it possesses only a particulate methane monooxygenase and is capable of atmospheric nitrogen fixation. The genome sequence of this typical inhabitant of subarctic wetlands and soils also contains genes indicative of aerobic anoxygenic photosynthesis.