Microbial megacities fueled by methane oxidation in a mineral spring cave

Resilience of aerobic methanotrophs in soils; spotlight on the methane sink under agriculture

Aerobic methanotrophs are a specialized microbial group, catalyzing the oxidation of methane. Disturbance-induced loss of methanotroph diversity/abundance, thus results in the loss of this biological methane sink. Here, we synthesized and conceptualized the resilience of the methanotrophs to sporadic, recurring, and compounded disturbances in soils. The methanotrophs showed remarkable resilience to sporadic disturbances, recovering in activity and population size. However, activity was severely compromised when disturbance persisted or reoccurred at increasing frequency, and was significantly impaired following change in land use. Next, we consolidated the impact of agricultural practices after land conversion on the soil methane sink. The effects of key interventions (tillage, organic matter input, and cover cropping) where much knowledge has been gathered were considered. Pairwise comparisons of these interventions to nontreated agricultural soils indicate that the agriculture-induced impact on the methane sink depends on the cropping system, which can be associated to the physiology of the methanotrophs. The impact of agriculture is more evident in upland soils, where the methanotrophs play a more prominent role than the methanogens in modulating overall methane flux. Although resilient to sporadic disturbances, the methanotrophs are vulnerable to compounded disturbances induced by anthropogenic activities, significantly affecting the methane sink function.

Unique architecture of microbial snottites from a methane driven biofilm revealed by confocal microscopy

Microbial biofilms occur in many shapes and different dimensions. In natural and semi-artificial caves they are forming pendulous structures of 10 cm and more. In this study a methane driven microbial community of a former medicinal spring was investigated. The habitat was completely covered by massive biofilms and snottites with a wobbly, gelatinous appearance. By using fluorescence techniques in combination with confocal laser scanning microscopy the architecture of these so far unknown snottites was examined. The imaging approaches applied comprised reflection of geogenic and cellular origin, possible autofluorescence, nucleic acid staining for bacterial cells, protein staining for bacteria and extracellular fine structures, calcofluor white for β 1 → 3, β 1 → 4 polysaccharide staining for possible fungi as well as lectin staining for the extracellular biofilm matrix glycoconjugates. The results showed a highly complex, intricate structure with voluminous, globular, and tube-like glycoconjugates of different dimensions and densities. In addition, filamentous bacteria seem to provide additional strength to the snottites. After screening with all commercially available lectins, by means of fluorescence lectin barcoding and subsequent fluorescence lectin binding analysis, the AAL, PNA, LEA, and Ban lectins identified α-Fuc, β-Gal, β-GlcNAc, and α-Man with α-Fuc as a major component. Examination of the outer boundary with fluorescent beads revealed a potential outer layer which could not be stained by any of the fluorescent probes applied. Finally, suggestions are made to further elucidate the characteristics of these unusual microbial biofilms in form of snottites. RESEARCH HIGHLIGHTS: The gelatinous snottites revealed at the microscale a highly complex structure not seen before. The extracellular matrix of the snottite biofilm was identified as clusters of different shape and density. The matrix of snottites was examined by taking advantage of 78 fluorescently-labeled lectins. The extracellular matrix glycoconjugates of snottites identified comprised: α-Fuc, β-Gal, β-GlcNAc, and α-Man. Probing the snottite outer surface indicated an additional unknown stratum.

Shifts in functional traits and interactions patterns of soil methane-cycling communities following forest-to-pasture conversion in the Amazon Basin

Deforestation threatens the integrity of the Amazon biome and the ecosystem services it provides, including greenhouse gas mitigation. Forest-to-pasture conversion has been shown to alter the flux of methane gas (CH₄ ) in Amazonian soils, driving a switch from acting as a sink to a source of atmospheric CH₄ . This study aimed to better understand this phenomenon by investigating soil microbial metagenomes, focusing on the taxonomic and functional structure of methane-cycling communities. Metagenomic data from forest and pasture soils were combined with measurements of in situ CH₄ fluxes and soil edaphic factors and analysed using multivariate statistical approaches. We found a significantly higher abundance and diversity of methanogens in pasture soils. As inferred by co-occurrence networks, these microorganisms seem to be less interconnected within the soil microbiota in pasture soils. Metabolic traits were also different between land uses, with increased hydrogenotrophic and methylotrophic pathways of methanogenesis in pasture soils. Land-use change also induced shifts in taxonomic and functional traits of methanotrophs, with bacteria harbouring genes encoding the soluble form of methane monooxygenase enzyme (sMMO) depleted in pasture soils. Redundancy analysis and multimodel inference revealed that the shift in methane-cycling communities was associated with high pH, organic matter, soil porosity and micronutrients in pasture soils. These results comprehensively characterize the effect of forest-to-pasture conversion on the microbial communities driving the methane-cycling microorganisms in the Amazon rainforest, which will contribute to the efforts to preserve this important biome.

The biofilm matrix: multitasking in a shared space

The biofilm matrix can be considered to be a shared space for the encased microbial cells, comprising a wide variety of extracellular polymeric substances (EPS), such as polysaccharides, proteins, amyloids, lipids and extracellular DNA (eDNA), as well as membrane vesicles and humic-like microbially derived refractory substances. EPS are dynamic in space and time and their components interact in complex ways, fulfilling various functions: to stabilize the matrix, acquire nutrients, retain and protect eDNA or exoenzymes, or offer sorption sites for ions and hydrophobic substances. The retention of exoenzymes effectively renders the biofilm matrix an external digestion system influencing the global turnover of biopolymers, considering the ubiquitous relevance of biofilms. Physico-chemical and biological interactions and environmental conditions enable biofilm systems to morph into films, microcolonies and macrocolonies, films, ridges, ripples, columns, pellicles, bubbles, mushrooms and suspended aggregates - in response to the very diverse conditions confronting a particular biofilm community. Assembly and dynamics of the matrix are mostly coordinated by secondary messengers, signalling molecules or small RNAs, in both medically relevant and environmental biofilms. Fully deciphering how bacteria provide structure to the matrix, and thus facilitate and benefit from extracellular reactions, remains the challenge for future biofilm research.

A novel Methylomirabilota methanotroph potentially couples methane oxidation to iodate reduction

Methane oxidizing microbes play a key role in reducing the emission of this potent greenhouse gas to the atmosphere. The known versatility of the recently discovered anaerobic Methylomirabilota methanotrophs is limited. Here, we report a novel uncultured Methylomirabilis species, Candidatus Methylomirabilis iodofontis, with the genetic potential of iodate respiration from biofilm in iodine-rich cavern spring water. Star-like cells resembling Methylomirabilis oxyfera were directly observed from the biofilm and a high-quality metagenome-assembled genome (MAG) of Ca. M. iodofontis was assembled. In addition to oxygenic denitrification and aerobic methane oxidation pathways, the M. iodofontis MAG also indicated its iodate-reducing potential, a capability that would enable the bacterium to use iodate other than nitrite as an electron acceptor, a hitherto unrecognized metabolic potential of Methylomirabilota methanotrophs. The results advance the current understanding of the ecophysiology of anaerobic Methylomirabilota methanotrophs and may suggest an additional methane sink, especially in iodate-rich ecosystems.

Occurrence of methane-oxidizing bacteria and methanogenic archaea in earth’s cave systems—A metagenomic analysis

Karst ecosystems represent up to 25% of the land surface and recent studies highlight their potential role as a sink for atmospheric methane. Despite this, there is limited knowledge of the diversity and distribution of methane-oxidizing bacteria (MOB) or methanogens in karst caves and the sub-surface environment in general. Here, we performed a survey of 14 shotgun metagenomes from cave ecosystems covering a broad set of environmental conditions, to compare the relative abundance and phylogenetic diversity of MOB and methanogens, targeting biomarker genes for methane monooxygenase (pmoA and mmoX) and methyl-coenzyme M reductase (mcrA). Taxonomic analysis of metagenomes showed 0.02–1.28% of classified reads were related to known MOB, of which Gammaproteobacterial MOB were the most abundant making up on average 70% of the surveyed caves’ MOB community. Potential for biogenic methane production in caves was also observed, with 0.008–0.39% of reads classified to methanogens and was dominated by sequences related to Methanosarcina. We have also generated a cave ecosystems protein database (CEPD) based on protein level assembly of cave metagenomes that can be used to profile genes of interest.

Matrix glycoconjugate characterization in multispecies biofilms and bioaggregates from the environment by means of fluorescently-labeled lectins

Environmental biofilms represent a complex mixture of different microorganisms. Their identity is usually analyzed by means of nucleic acid-based techniques. However, these biofilms are also composed of a highly complex extracellular matrix produced by the microbes within a particular biofilm system. The biochemical identity of this extracellular matrix remains in many cases an intractable part of biofilms and bioaggregates. Consequently, there is a need for an approach that will give access to the fully hydrated structure of the extracellular matrix or at least a major part of it. A crucial compound of the matrix identified as carbohydrate-based polymers represents major structural and functional constituents. These glycoconjugates can be characterized by using fluorescently-labeled lectins in combination with confocal laser scanning microscopy. The lectin approach is defined previously, as fluorescence lectin barcoding (FLBC) and fluorescence lectin-binding analysis (FLBA), where FLBC is equal to the screening of a particular sample with all the commercially available lectins and FLBA is the actual analysis of the matrix throughout an experiment with a selected panel of lectins. As the application of immune-based techniques in environmental biofilm systems is impossible, the lectin approach is currently the only option for probing lectin-specific glycoconjugates in complex biofilms and bioaggregates. From all the commercially available lectins tested, the lectins such as AAL, HAA, WGA, ConA, IAA, HPA, and LEA showed the highest binding efficiency. Furthermore, 20 of the overall lectins tested showed an intermediate signal intensity, nevertheless very useful for the assessment of matrix glycoconjugates. With the data compiled, we shall virtually shed more light on the dark matter of the extracellular matrix and their 3-dimensional distribution in environmental biofilm systems. The results will be helpful in future studies with a focus on the extracellular matrix glycoconjugates present in environmental microbial communities.

Metagenome-Assembled Genomes from Monte Cristo Cave (Diamantina, Brazil) Reveal Prokaryotic Lineages As Functional Models for Life on Mars

Microbial communities have been explored in various terrestrial subsurface ecosystems, showing metabolic potentials that could generate noteworthy morphological and molecular biosignatures. Recent advancements in bioinformatic tools have allowed for descriptions of novel and yet-to-be cultivated microbial lineages in different ecosystems due to the genome reconstruction approach from metagenomic data. Using shotgun metagenomic data, we obtained metagenome-assembled genomes related to cultivated and yet-to-be cultivated prokaryotic lineages from a silica and iron-rich cave (Monte Cristo) in Minas Gerais State, Brazil. The Monte Cristo Cave has been shown to possess a high diversity of genes involved with different biogeochemical cycles, including reductive and oxidative pathways related to carbon, sulfur, nitrogen, and iron. Three genomes were selected for pangenomic analysis, assigned as Truepera sp., Ca. Methylomirabilis sp., and Ca. Koribacter sp. based on their lifestyles (radiation resistance, anaerobic methane oxidation, and potential iron oxidation). These bacteria exhibit genes involved with multiple DNA repair strategies, starvation, and stress response. Because these groups have few reference genomes deposited in databases, our study adds important genomic information about these lineages. The combination of techniques applied in this study allowed us to unveil the potential relationships between microbial genomes and their ecological processes with the cave mineralogy and highlight the lineages involved with anaerobic methane oxidation, iron oxidation, and radiation resistance as functional models for the search for extant life-forms outside our planet in silica- and iron-rich environments and potentially on Mars.

Bacteriome composition analysis of selected mineral water occurrences in Serbia

Bacterial metabarcoding analysis by 16S rDNA of five occurrences of mineral waters in Serbia (Torda, Slankamen Banja, Lomnicki Kiseljak, Velika Vrbnica and Obrenovacka Banja) indicated the presence of a high percentage of the Proteobacteria phylum, followed by the Bacteroidetes phylum. The families Rhodobacteraceae, Burkholderiaceae, Pseudomonadaceae, Methylophilaceae and Moraxellaceae were the most dominant in the bacterial flora of the selected occurrences, whereas the most represented genera were Acinetobacter, Pseudorhodobacter, Pseudomonas, Limnohabitans, Massilia, Limnobacter and Methylotenera. The presence of coliform bacteria was not detected. Alpha diversity analysis revealed that Slankamen Banja and Lomnicki Kiseljak were the richest of the selected occurrences, while the mineral waters of Torda, Velika Vrbnica and Obrenovacka Banja were characterized by similar diversity of bacterial communities determined by beta diversity analysis. Physical-chemical analysis revealed the value of total dissolved solids above 1 g/L, as well as elevated concentrations of some metals and non-metals. The research concluded that specific bacteria contribute to the development of biocorrosion and biofouling processes of water intake facilities. In addition, some of these bacteria might be potential indicators of the organic sources of pollution and/or biotechnological natural remediators in the treatment of contaminated waters.

Methane-dependent selenate reduction by a bacterial consortium

Methanotrophic microorganisms play a critical role in controlling the flux of methane from natural sediments into the atmosphere. Methanotrophs have been shown to couple the oxidation of methane to the reduction of diverse electron acceptors (e.g., oxygen, sulfate, nitrate, and metal oxides), either independently or in consortia with other microbial partners. Although several studies have reported the phenomenon of methane oxidation linked to selenate reduction, neither the microorganisms involved nor the underlying trophic interaction has been clearly identified. Here, we provide the first detailed evidence for interspecies electron transfer between bacterial populations in a bioreactor community where the reduction of selenate is linked to methane oxidation. Metagenomic and metaproteomic analyses of the community revealed a novel species of Methylocystis as the most abundant methanotroph, which actively expressed proteins for oxygen-dependent methane oxidation and fermentation pathways, but lacked the genetic potential for selenate reduction. Pseudoxanthomonas, Piscinibacter, and Rhodocyclaceae populations appeared to be responsible for the observed selenate reduction using proteins initially annotated as periplasmic nitrate reductases, with fermentation by-products released by the methanotrophs as electron donors. The ability for the annotated nitrate reductases to reduce selenate was confirmed by gene knockout studies in an isolate of Pseudoxanthomonas. Overall, this study provides novel insights into the metabolic flexibility of the aerobic methanotrophs that likely allows them to thrive across natural oxygen gradients, and highlights the potential role for similar microbial consortia in linking methane and other biogeochemical cycles in environments where oxygen is limited.

Syntrophic co-culture of a methanotroph and heterotroph for the efficient conversion of methane to mevalonate

As the bioconversion of methane becomes increasingly important for bio-industrial and environmental applications, methanotrophs have received much attention for their ability to convert methane under ambient conditions. This includes the extensive reporting of methanotroph engineering for the conversion of methane to biochemicals. To further increase methane usability, we demonstrated a highly flexible and efficient modular approach based on a synthetic consortium of methanotrophs and heterotrophs mimicking the natural methane ecosystem to produce mevalonate (MVA) from methane. In the methane-conversion module, we used Methylococcus capsulatus Bath as a highly efficient methane biocatalyst and optimized the culture conditions for the production of high amounts of organic acids. In the MVA-synthesis module, we used Escherichia coli SBA01, an evolved strain with high organic acid tolerance and utilization ability, to convert organic acids to MVA. Using recombinant E. coli SBA01 possessing genes for the MVA pathway, 61 mg/L (0.4 mM) of MVA was successfully produced in 48 h without any addition of nutrients except methane. Our platform exhibited high stability and reproducibility with regard to cell growth and MVA production. We believe that this versatile system can be easily extended to many other value-added processes and has a variety of potential applications.

Response of a methane-driven interaction network to stressor intensification

Microorganisms may reciprocally select for specific interacting partners, forming a network with interdependent relationships. The methanotrophic interaction network, comprising methanotrophs and non-methanotrophs, is thought to modulate methane oxidation and give rise to emergent properties beneficial for the methanotrophs. Therefore, microbial interaction may become relevant for community functioning under stress. However, empirical validation of the role and stressor-induced response of the interaction network remains scarce. Here, we determined the response of a complex methane-driven interaction network to a stepwise increase in NH4Cl-induced stress (0.5-4.75 g L-1, in 0.25-0.5 g L-1 increments) using enrichment of a naturally occurring complex community derived from a paddy soil in laboratory-scale incubations. Although ammonium and intermediates of ammonium oxidation are known to inhibit methane oxidation, methanotrophic activity was unexpectedly detected even in incubations with high ammonium levels, albeit rates were significantly reduced. Sequencing analysis of the 16S rRNA and pmoA genes consistently revealed divergent communities in the reference and stressed incubations. The 16S rRNA-based co-occurrence network analysis revealed that NH4Cl-induced stress intensification resulted in a less complex and modular network, likely driven by less stable interaction. Interestingly, the non-methanotrophs formed the key nodes, and appear to be relevant members of the community. Overall, stressor intensification unravels the interaction network, with adverse consequences for community functioning.

Cultivation of methanotrophic bacteria in a novel bubble-free membrane bioreactor for microbial protein production

Microbial protein is proposed as an alternative protein source with low environmental impact. Methane oxidizing bacteria are already produced at commercial scale from natural gas. However, their productivity is limited because of the creation of explosive atmospheres in the fermenters during production. This work demonstrates the applicability of bioreactors with a membrane-based gas supply via diffusion. Methanotrophic bacteria were successfully cultivated, with growth yields from 0.26 to 0.43 g-VSS g-CH₄^-1, slightly below those observed in analogous fermenters relying on bubbling. However, ammonia yields ranged from 5.2 to 6.9 g-VSS g-NH₃^-1, indicating higher nitrogen assimilation than in conventional fermenters. Indeed, protein content increased during the operational period reaching up to 51% of dry weight. The amino acid profile included the majority of the essential amino acids, demonstrating suitability as feed ingredient. Never during the operational period was an explosive atmosphere established in the reactor. Thus, bubble-free membrane bioreactors are a promising technology for microbial protein production relying on explosive gas mixtures.

Microbial Ecology of Methanotrophy in Streams Along a Gradient of CH4 Availability

Despite the recognition of streams and rivers as sources of methane (CH₄) to the atmosphere, the role of CH₄ oxidation (MOX) in these ecosystems remains poorly understood to date. Here, we measured the kinetics of MOX in stream sediments of 14 sites to resolve the ecophysiology of CH₄ oxidizing bacteria (MOB) communities. The streams cover a gradient of land cover and associated physicochemical parameter and differed in stream- and porewater CH₄ concentrations. Michealis–Menten kinetic parameter of MOX, maximum reaction velocity (V_max), and CH₄ concentration at half V_max (K_S) increased with CH₄ supply. K_S values in the micromolar range matched the CH₄ concentrations measured in shallow stream sediments and indicate that MOX is mostly driven by low-affinity MOB. 16S rRNA gene sequencing identified MOB classified as Methylococcaceae and particularly Crenothrix. Their relative abundance correlated with pmoA gene counts and MOX rates, underscoring their pivotal role as CH₄ oxidizers in stream sediments. Building on the concept of enterotypes, we identify two distinct groups of co-occurring MOB. While there was no taxonomic difference among the members of each cluster, one cluster contained abundant and common MOB, whereas the other cluster contained rare operational taxonomic units (OTUs) specific to a subset of streams. These integrated analyses of changes in MOB community structure, gene abundance, and the corresponding ecosystem process contribute to a better understanding of the distal controls on MOX in streams.

Methanol-linked synergy between aerobic methanotrophs and denitrifiers enhanced nitrate removal efficiency in a membrane biofilm reactor under a low O2:CH4 ratio

Nitrate removal efficiency of aerobic methane oxidation coupled with denitrification (AME-D) process was elevated by enhancing the methanol-linked synergy in a membrane biofilm reactor (MBfR) under a low O₂:CH₄ ratio. After 140 days' enrichment, the nitrate removal rate increased significantly from 3 to 4 mg-N L^-1 d^-1 to 22.09 ± 1.21 mg-N L^-1 d^-1 and the indicator, mol CH₄ consumed/mol reduced NO₃^--N (C/N ratio), decreased to 1.79 which was very close to the theoretical minimum value (1.27-1.39). The increased nitrate removal efficiency was largely related to the enhanced relationship between aerobic methanotrophs and methanol-utilizing denitrifiers. Type I methanotrophs and some denitrifiers, especially those potential methanol-utilizing denitrifiers from Methylobacillus, Methylotenera, Methylophilus and Methyloversatilis, were abundant in the MBfR sludge. Aerobic methanotrophs and potential methanol-utilizing denitrifiers were closely associated in many globular aggregates (5-10 μm diameter) in the MBfR sludge, which may have promoted the denitrifiers to capture methanol released by methanotrophs efficiently. If we assume methanol is the only cross-feeding intermediate in the MBfR, about 38-60% of the CH₄ supplied would be converted to methanol and secreted rather than continuing to be oxidized. At least 63% of this secreted methanol should be utilized for denitrification instead of being oxidized by oxygen in the MBfR. These findings suggest that the nitrate removal efficiency of the AME-D process could be significantly improved.

Chlorine Isotope Fractionation of the Major Chloromethane Degradation Processes in the Environment

Chloromethane (CH₃Cl) is an important source of chlorine in the stratosphere, but detailed knowledge of the magnitude of its sources and sinks is missing. Here, we measured the stable chlorine isotope fractionation (ε_Cl) associated with the major abiotic and biotic CH₃Cl sinks in the environment, namely, CH₃Cl degradation by hydroxyl (^·OH) and chlorine (^·Cl) radicals in the troposphere and by reference bacteria Methylorubrum extorquens CM4 and Leisingera methylohalidivorans MB2 from terrestrial and marine environments, respectively. No chlorine isotope fractionation was detected for reaction of CH₃Cl with ^·OH and ^·Cl radicals, whereas a large chlorine isotope fractionation (ε_Cl) of -10.9 ± 0.7‰ (n = 3) and -9.4 ± 0.9 (n = 3) was found for CH₃Cl degradation by M. extorquens CM4 and L. methylohalidivorans MB2, respectively. The large difference in chlorine isotope fractionation observed between tropospheric and bacterial degradation of CH₃Cl provides an effective isotopic tool to characterize and distinguish between major abiotic and biotic processes contributing to the CH₃Cl sink in the environment. Our findings demonstrate the potential of emerging triple-element isotopic approaches including chlorine to carbon and hydrogen analysis for the assessment of global cycling of organochlorines.

Methane oxidising bacteria to upcycle effluent streams from anaerobic digestion of municipal biowaste

Conventional microbial protein production relies on the usage of pure chemicals and gases. Natural gas, which is a fossil resource, is the common input gas for bacterial protein production. Alternative sources for gas feedstock and nutrients can sufficiently decrease the operational cost and environmental impact of microbial protein production processes. In the present study, the effluents streams of municipal biowaste anaerobic digestion, were used to grow methane oxidising bacteria which can be used as protein source. Results demonstrated that a 40:60 CH₄:O₂ (v/v) gas feeding resulted in microbial biomass production of 0.95 g-DM/L by a Methylophilus dominated community. When raw biogas was used as input for methane corresponding to the same initial methane partial pressure as before, instead of pure methane, the growth was partially hindered (0.61 g-DM/L) due to the presence of H₂S (IC₅₀: 1376 ppm). Hence, desulfurization is suggested before using biogas for microbial protein production. At semi-continuous mode, results showed that the produced biomass had relatively high protein content (>40% of dry weight) and the essential amino acids lysine, valine, leucine and histidine were detected at high levels.

Upland soil cluster γ dominates the methanotroph communities in the karst Heshang Cave

Microorganisms are thought to play a critical role in methane (CH4) consumption in karst caves and yet the presence and diversity of methane-oxidizing bacteria (MOB) remain a mystery. In Heshang Cave, CH4 concentration decreases from 1.9 ppm at the entrance to 0.65 ppm inside the cave. To explore the presence and diversity of MOB in this cave, weathered rocks and sediment samples were collected from the cave and subjected to molecular analysis. The abundances of MOB were 107-108 copies g-1 dry sample via quantification of the pmoA gene, which are comparable to or even higher than those reported in other terrestrial environments, and account for up to 20% of the total microbial communities. Phylogenetically, MOB communities were dominated by the 'high-affinity' upland soil cluster γ (USCγ), although the predominance of Type Ia MOB was also detected in the permanently waterlogged stream sediment. The estimated CH4 oxidation potential varied dramatically among samples in the range of 0.6-80 CH4 m-3 d-1. Collectively, this study provides compelling evidence that the high-affinity MOB capable of oxidizing CH4 at the atmospheric level are present in Heshang Cave, which may play an important role in the CH4 consumption, and supports karst caves as important atmospheric CH4 sinks.

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.

The plethora of membrane respiratory chains in the phyla of life

The diversity of microbial cells is reflected in differences in cell size and shape, motility, mechanisms of cell division, pathogenicity or adaptation to different environmental niches. All these variations are achieved by the distinct metabolic strategies adopted by the organisms. The respiratory chains are integral parts of those strategies especially because they perform the most or, at least, most efficient energy conservation in the cell. Respiratory chains are composed of several membrane proteins, which perform a stepwise oxidation of metabolites toward the reduction of terminal electron acceptors. Many of these membrane proteins use the energy released from the oxidoreduction reaction they catalyze to translocate charges across the membrane and thus contribute to the establishment of the membrane potential, i.e. they conserve energy. In this work we illustrate and discuss the composition of the respiratory chains of different taxonomic clades, based on bioinformatic analyses and on biochemical data available in the literature. We explore the diversity of the respiratory chains of Animals, Plants, Fungi and Protists kingdoms as well as of Prokaryotes, including Bacteria and Archaea. The prokaryotic phyla studied in this work are Gammaproteobacteria, Betaproteobacteria, Epsilonproteobacteria, Deltaproteobacteria, Alphaproteobacteria, Firmicutes, Actinobacteria, Chlamydiae, Verrucomicrobia, Acidobacteria, Planctomycetes, Cyanobacteria, Bacteroidetes, Chloroflexi, Deinococcus-Thermus, Aquificae, Thermotogae, Deferribacteres, Nitrospirae, Euryarchaeota, Crenarchaeota and Thaumarchaeota.

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.

Natural Selection in Synthetic Communities Highlights the Roles of Methylococcaceae and Methylophilaceae and Suggests Differential Roles for Alternative Methanol Dehydrogenases in Methane Consumption

We describe experiments that follow species dynamics and gene expression patterns in synthetic bacterial communities including species that compete for the single carbon substrate supplied, methane, and species unable to consume methane, which could only succeed through cooperative interactions. We demonstrate that these communities mostly select for two functional guilds, methanotrophs of the family Methylococcaceae and non-methanotrophic methylotrophs of the family Methylophilaceae, these taxonomic guilds outcompeting all other species included in the synthetic mix. The metatranscriptomics analysis uncovered that in both Methylococcaceae and Methylophilaceae, some of the most highly transcribed genes were the ones encoding methanol dehydrogenases (MDH). Remarkably, expression of alternative MDH genes (mxaFI versus xoxF), previously shown to be subjects to the rare Earth element switch, was found to depend on environmental conditions such as nitrogen source and methane and O₂ partial pressures, and also to be species-specific. Along with the xoxF genes, genes encoding divergent cytochromes were highly expressed in both Methylophilaceae and Methylococcaceae, suggesting their function in methanol metabolism, likely encoding proteins serving as electron acceptors from XoxF enzymes. The research presented tested a synthetic community model that is much simplified compared to natural communities consuming methane, but more complex than the previously utilized two-species model. The performance of this model identifies prominent species for future synthetic ecology experiments and highlights both advantages of this approach and the challenges that it presents.