FEMS Microbiology Ecology (original) (raw)
Aerobic methanotrophs are frequently detected in oxygen-limited, stratified coastal environments. Known adaptations, including high-affinity terminal oxidases and oxygen-binding bacteriohemerythrins, help explain methane oxidation at extremely low oxygen concentrations, yet their activity and ecological role under fully anoxic conditions remain uncertain. Here, we show that an anoxic, poised-anode bioelectrochemical system inoculated with a methane-oxidizing sediment enrichment produced methane-dependent current, with rapid current loss upon methane removal and recovery after re-addition. Metagenomic analysis revealed the selective enrichment of a Methylobacter population encoding a porin-cytochrome complex and numerous multiheme _c_-type cytochromes, suggesting extracellular electron transfer potential. A complementary phylogenomic survey across Methylococcales identified homologs of this gene cluster in multiple lineages, but with a scattered phylogenetic distribution indicative of modular acquisition. Comparative synteny further revealed conserved gene order across genomes, supporting horizontal transfer of the locus as a functional unit. Together, these results demonstrate that aerobic methanotrophs may employ extracellular electron transfer strategies to dissipate methane-derived electrons when oxygen-dependent respiration is constrained.
The rapid emergence and global dissemination of antimicrobial resistance pose a serious threat to public health, environmental sustainability, and economic development. Central to this crisis is the resistome, defined as the collection of all antimicrobial resistance genes (ARGs) present in pathogenic and non-pathogenic micro-organisms across clinical, agricultural, and natural ecosystems. The environmental resistome plays a crucial role in the evolution and transmission of resistance, serving as both a reservoir and a conduit for ARG exchange through horizontal gene transfer. This review provides a comprehensive overview of the structure, diversity, and dynamics of the resistome, with emphasis on the interconnected water–soil–air continuum. Key mechanisms driving resistome dissemination, including mobile genetic elements such as plasmids, integrons, transposons, and bacteriophages, are discussed alongside the major routes of gene transfer, conjugation, transformation, and transduction. The review highlights anthropogenic drivers that intensify resistome expansion, including antibiotic misuse, wastewater discharge, agricultural runoff, and exposure to heavy metals, pesticides, and disinfectants, which promote co-selection. Advances in resistome profiling approaches, such as quantitative PCR, metagenomics, long-read sequencing, and functional metagenomics, are critically evaluated for their capacity to resolve ARG diversity, mobility, and host associations.
The macronutrients in our diets including non-starch polysaccharides such as β-mannans, found in plant cell walls, can impact on human gut health. There is however a paucity of data regarding the ability of gut bacteria, in particular those belonging to the Bacillota (previously Firmicutes) phylum, to depolymerise and ferment β-mannans. In this study, we tested a total of 12 strains, including nine Bacillota, for their ability to metabolise and cross-feed on β-mannans. Three of the six butyrate-producing Bacillota strains, namely Roseburia intestinalis L1-82, Roseburia faecis M72/1, and Coprococcus eutactus ART55/1, were able to metabolise carob galactomannan, konjac glucomannan, and softwood spruce acetylated galactoglucomannan, which corresponded with their carbohydrate active enzyme profiles, whilst Faecalibacterium prausnitzii S3L/3 only grew well on β-mannan endo-mannanase digests. To investigate competition and microbial cross-feeding on β-mannans, growth assays were conducted with co-cultures of up to six strains belonging to both the Bacillota phylum and a Bacteroidetes β-mannan utilising strain, Bacteroides ovatus V975. All strains in the mixes were able to co-exist, including the non-mannan degrading butyrate producers, with butyrate being formed as one of the major fermentation products. These studies suggest that β-mannans may offer a notable prebiotic approach to promoting butyrate-producing bacteria and gut health.
Volcanic soils provide a unique environment for studying microbial colonization and succession due to their extreme conditions and distinct geochemical profiles. This study focused on carbon monoxide (CO)-oxidizing microbial communities in volcanic soils at Piton De La Fournaise, Réunion Island. Soil samples from three sites (corresponding to eruptions in 1401, 1559, and 2007) were analysed to assess microbial community structure using 16S rRNA gene sequencing and metagenomic analysis to identify functional genes involved in CO oxidation. Phylum-level analysis showed higher relative abundance of Acidobacteriota and Chloroflexota, lower abundances of Actinomycetota and Bacteroidota, and relatively stable levels of Pseudomonadota, while class-level patterns included rising Alphaproteobacteria and Acidobacteriia, with Ktenobacteria emerging in the 1401 site. CO dehydrogenase-related genes were found in 17 metagenome-assembled genomes across all sites. The CO consumption rate by microbes in soils was measured. CO-oxidizing microbes were present across soil ages, with detectable activity in the 2007 site and greatest activity in the 1401 site, suggesting that these microbes actively use CO as an energy source even in soils with primary vegetation, contrary to general understanding. The findings suggest intricate dynamics of microbial succession in volcanic soils and may challenge conventional expectations about community complexity over time.
The poles represent Earth’s most climate-sensitive biomes, where microbial communities and viruses drive fundamental ecological processes. Within these extreme environments, giant viruses of the phylum Nucleocytoviricota have emerged as key regulators of microbial mortality and biogeochemical cycling. This review synthesizes current knowledge on polar giant viruses, emphasizing their diversity, endemism, genomic adaptations, and ecological roles across polar habitats. Polar systems harbour highly structured, habitat-specific viral assemblages characterized by significant endemism and sharp ecological boundaries, shaped by strong environmental filtering, host biogeography, virus–virus interactions and spatial isolation. Genomic analyses show that these viruses possess unique adaptations to persistent cold, including proteomic shifts consistent with psychrophily and the enrichment of auxiliary metabolic genes. Interactions with giant virus parasites (virophages) further contribute to the complexity of polar giant virus ecology. However, rapid warming and the loss of perennial ice threaten to destabilize these ancient refugia and their giant virus populations. Changes in temperature, hydrological connectivity and ecosystem structure may alter virus–host dynamics and weaken the strong viral endemism. These environmental shifts risk the extinction of unique lineages and the disruption of the critical biogeochemical roles they perform, highlighting the urgent need to understand viral dynamics in rapidly changing polar and cryospheric ecosystems.
FEMS Microbiology Ecology. June 23, 2026: 102(7)
Aerobic methanotrophs are frequently detected in oxygen-limited, stratified coastal environments. Known adaptations, including high-affinity terminal oxidases and oxygen-binding bacteriohemerythrins, help explain methane oxidation at extremely low oxygen concentrations, yet their activity and ecological role under fully anoxic conditions remain uncertain. Here, we show that an anoxic, poised-anode bioelectrochemical system inoculated with a methane-oxidizing sediment enrichment produced methane-dependent current, with rapid current loss upon methane removal and recovery after re-addition. Metagenomic analysis revealed the selective enrichment of a Methylobacter population encoding a porin-cytochrome complex and numerous multiheme _c_-type cytochromes, suggesting extracellular electron transfer potential. A complementary phylogenomic survey across Methylococcales identified homologs of this gene cluster in multiple lineages, but with a scattered phylogenetic distribution indicative of modular acquisition. Comparative synteny further revealed conserved gene order across genomes, supporting horizontal transfer of the locus as a functional unit. Together, these results demonstrate that aerobic methanotrophs may employ extracellular electron transfer strategies to dissipate methane-derived electrons when oxygen-dependent respiration is constrained.
FEMS Microbiology Ecology. June 22, 2026: 102(7)
Plastic has introduced a novel and persistent substrate into natural ecosystems, rapidly colonized by microbial biofilms collectively termed the plastisphere. Since its introduction, the concept has catalyzed interdisciplinary research and shaped scientific and public discourse on plastic pollution. Yet, a central question remains unresolved: Do plastisphere communities represent a fundamentally distinct ecological entity, or are they conventional biofilms forming on an unconventional material? Here, we synthesize current evidence across marine and terrestrial systems to argue that plastisphere communities are not consistently taxonomically or functionally unique. Instead, they largely reflect established biofilm assembly processes governed by environmental conditions, source communities, and successional dynamics. Claims of plastic biodegradation, pathogen enrichment, or antimicrobial resistance hotspots remain context-dependent and often lack robust comparative frameworks. We propose that the ecological significance of the plastisphere lies not in microbial novelty, but in the properties of the substrate itself. Plastics are uniquely persistent and, in many environments, highly mobile, enabling microbial communities to disperse across ecosystems and extend residence times beyond those of natural particles. By reframing the plastisphere as a condition of microbial life on durable, mobile substrates, we retain its conceptual value while aligning it with ecological theory and advancing a more precise research agenda.
FEMS Microbiology Ecology. June 22, 2026: 102(7)
Research on the respiratory microbiome has moved beyond the sterile-lung paradigm, but disease-associated microbial patterns are still often described as static signatures. In this mini-review, we synthesize current evidence within a dynamic state-transition framework in which respiratory microbial communities are shaped by microbial immigration, elimination, local growth conditions, and host inflammatory tone. This framework traces the respiratory microbiome from early-life assembly and homeostatic maintenance to perturbation, recovery, or persistence in alternative ecological states. We discuss how barrier integrity, mucociliary clearance, mucus and nutrient landscapes, inflammatory feedback, microbial metabolites, and the gut–lung axis regulate microbial stability and disease susceptibility. Across asthma, chronic obstructive pulmonary disease, cystic fibrosis, bronchiectasis, and respiratory infection, dysbiosis is interpreted not as a set of disease-specific taxa, but as a context-dependent outcome of shared ecological mechanisms. We also highlight methodological and translational priorities, including contamination control in low-biomass samples, longitudinal sampling, multi-omics integration, spatial host profiling, and cautious interpretation of association versus causality. Viewing the respiratory microbiome as an ecological system in motion may better connect microbial dynamics with disease heterogeneity, risk stratification, and future microbiome-directed interventions.