Microbial community dynamics are central to the functioning of freshwater ecosystems, yet short-term surveys fail to capture long-term ecological trajectories. Here, we present a five-year monthly time series of microbial communities and environmental variables in Lake Soyang, a model oligotrophic freshwater ecosystem in South Korea. We identified six distinct clusters of seasonally recurring microbes that drive a predictable annual microbial cycle, which operates alongside episodic populations that transiently occupy ephemeral niches. Crucially, the genome-streamlined acI and acIVclades of Actinomycetota exhibited extensive spatiotemporal niche differentiation, with recurring lineages partitioning into previously undescribed low-oxygen- and winter-associated subgroups, while specific members emerged as episodic bloomers, thereby expanding our understanding of their ecological versatility. Network analysis further revealed dense interconnectivity among diverse populations, indicative of finely coordinated, time-dependent succession. By linking short-term fluctuations to multiyear trends, this study highlights the value of long-term monitoring and offers a baseline for incorporating microbial indicators into freshwater management and conservation.
Antimicrobial resistance (AMR) in wildlife is a One Health concern, yet research has largely focused on anthropogenic contexts and animal species in close contact with humans. How AMR carriage affects wildlife hosts themselves remains poorly understood. The class 1 integron is a clinically important, anthropogenically associated genetic element that captures and disseminates antibiotic resistance genes primarily among Gram-negative bacteria. As the gut microbiome is a key reservoir for antibiotic resistance genes, the relationship between antibiotic resistance carriage and microbiome composition is an important dimension for understanding the integration, persistence, and evolution of antibiotic resistance in bacteria. This study investigated whether carriage of class 1 integrons was associated with gut microbiome composition in wild koalas. Koala faecal samples (n = 62) from Belair National Park, South Australia, categorised by presence and absence of class 1 integrons (intI1 gene), underwent 16S rRNA gene amplicon sequencing. Findings revealed no significant differences in alpha or beta diversity between integron-positive and integron-negative groups. Non-metric multidimensional scaling indicated no association between community composition and integron carriage. Differential abundance analysis revealed no significantly different taxa between groups. These results indicate that class 1 integron presence alone is not related to significant gut microbiome changes in this antibiotic-naïve koala population. These findings contribute to understanding how antibiotic resistance carriage relates to gut microbiome composition in wildlife not exposed to antibiotic selection pressure.
Soil acidity and nutrient deficiencies limit sustainable sugarcane production in KwaZulu-Natal (KZN), South Africa, where small-scale growers (SSGs) often lack access to lime and fertilizers, leading to progressive soil degradation. This study assessed the potential of Vigna unguiculata L. Walp., a versatile African legume, to support restoration of soil health during fallow periods in acidic, nutrient-poor sugarcane soils. A pot experiment was conducted using soils from four sugarcane sites characterized by low pH and nitrogen (N) and phosphorus (P) deficiencies. Vigna unguiculata cultivation was associated with increased soil pH, reduced exchangeable acidity, and improved N and P availability at several sites. Elevated acid phosphatase and nitrate reductase activities indicated enhanced nutrient cycling. 16 S rRNA sequencing revealed diverse symbiotic bacteria (Bacillus, Lysinibacillus, Paenibacillus, Pseudomonas) and post-cultivation enrichment of free-living N fixers (Burkholderia, Herbaspirillum), N-cyclers (Novosphingobium, Paenibacillus), and P-solubilizers (Agrobacterium, Bacillus, Sphingomonas), taxa previously associated with supporting soil fertility functions. Vigna unguiculata demonstrated high N use efficiency and strong reliance on symbiotically fixed N (35–61
Early-life wheezing in children has been associated with microbial alterations along the gut-airway axis, yet studies simultaneously investigating bacterial communities in both compartments remain scarce. The aim of this cross-sectional exploratory pilot study (n = 25) was to characterize and compare nasal and stool bacterial communities in preschool children aged 1–4 years with recurrent wheezing and healthy controls using 16S rRNA gene metabarcoding. Across participants, nasal and stool bacteriomes were highly individualized and taxonomically diverse. Overall richness, evenness, and community composition did not differ significantly between healthy children and wheezers in either compartment. However, wheezers displayed markedly higher within-group variability, particularly in nasal communities. Stratification based on microbiome similarity to healthy samples revealed increased Moraxella and reduced commensal genera including Prevotella spp. and Veillonella, along with lower richness and evenness (all p < 0.001) in nasal samples with divergent bacterial communities. Stool alterations were more subtle but included trends toward reduced Bacteroides, Faecalibacterium, and Alistipes in wheezers more divergent from healthy controls. Community assembly in both compartments was largely governed by stochastic processes but accompanied by less complex and more fragmented bacterial interaction networks in wheezing children. Cross-compartment correlations were also altered, most prominently involving stool Lactococcus showing stronger and more numerous correlations with nasal taxa in wheezers than in healthy controls. Divergent wheezers exhibited distinct modular network structure and cross-compartment profiles, consistent with a differentiated microbial organization. Together, these findings suggest compartment-specific differences in microbial interaction patterns across the gut–airway axis in early-life wheezing, despite limited differences in overall community diversity.
The rhizosphere microbiome is associated with plant health and may contribute to interactions between rice and the rice blast pathogen, Magnaporthe oryzae. In this greenhouse study, 16 S rDNA amplicon sequencing was used to compare rhizobacterial communities associated with blast-resistant and blast-susceptible rice cultivars before and after pathogen infection. Significant differences in rhizobacterial diversity and community composition were observed between resistant and susceptible cultivars, with distinct community shifts following pathogen challenge. Differential microbial enrichment patterns were detected across cultivars and disease conditions. Notably, Bacillus spp. were consistently enriched in healthy plants of resistant cultivars and in infected plants of susceptible cultivars, indicating their association with disease status and potential ecological roles in the rice rhizosphere. Network analysis further showed that cultivar resistance was associated with differences in rhizosphere microbial community structure. Additionally, a bacterial strain, Bacillus velezensis H2, was isolated from the same rhizosphere of healthy rice plants and characterized using morphological, biochemical, and genomic analyses, including 16 S rRNA sequencing and SNP profiling. Whole-genome analysis using antiSMASH identified multiple biosynthetic gene clusters involved in secondary metabolite production, including nonribosomal peptide synthetases. In addition, B. velezensis H2 exhibited strong in vitro antifungal activity against M. oryzae, supporting its potential as a biocontrol candidate. Overall, this study describes rhizosphere bacterial community shifts associated with rice blast resistance and identifies B. velezensis H2 as a promising antagonistic bacterium for the sustainable management of rice blast disease.
Microplastics (MPs) can influence soil microbial communities, this may further affect the transformation of soil organic carbon (SOC) in saline-alkali soils. However, the combined effects of MPs and varying salinity on this process remain unclear. We combined incubation experiments with metagenomic sequencing to investigate the impacts of polyethylene (PE) and biodegradable polylactic acid (PLA) MPs on SOC dynamics and microbial metabolic functions. The study was conducted across a salinity gradient (EC: 4.75, 20, and 40 mS/cm) with varying MPs addition (0
Studying the microbiota of closely related species can provide important insights into the essential roles of symbiotic microbes in the physiology of organisms. We have studied the bacterial microbiota of four polistine species (Vespidae: Polistinae), from India, using 16S rRNA amplicon sequencing on the Oxford Nanopore platform. Many polistine species have been studied from behavioural, genetic, physiological and ecological perspectives. However, few of them were used for studying their microbiota. A recent study on the microbiota of Polistes wattii revealed that its microbiota is similar to Vespa (Vespidae: Vespinae). However, the microbiota of a single species from a single geographic location did not provide a holistic assessment of the genus’s microbiota. Therefore, here we studied and compared the microbial community of four polistine species. We used P. wattii and P. indicus from northern India and P. wattii, P. olivaceous, and Ropalidia spatulata from eastern India to compare the microbiota of different polistine species. We show that the microbiota of P. wattii from different geographic locations were more similar to each other than the other three species. Contrary to our expectation, sympatric species showed more distinct bacterial community profiles while P. wattii samples from two different locations were more similar to each other. We further conducted a multivariate analysis to assess the gut microbiota of different hymenopteran species. We show that the gut microbial communities of polistine wasps are more similar to those of Asian Vespine wasps (both carnivorous) than to those of omnivorous ants and herbivorous bees, indicating that diet is an important determinant of their bacterial microbiota.
Far-red light-utilizing cyanobacteria (FRLCyano) extend oxygenic photosynthesis beyond the visible spectrum, yet their detection in natural environments remains challenging. Traditional pigment-based and culture-dependent methods are time-consuming and limited by factors such as inducible phenotypes, often underestimating FRLCyano abundance and distribution. Here, we applied the Far-Red Cyanobacteria Identification (FRCI), a customized 16S rRNA gene database and classification framework, to investigate FRLCyano communities in hot spring ecosystems. Using a comprehensive dataset from Taiwanese hot springs, we further validated this 16S-based approach against two functional lines of evidence: consistency with the FRL-specific marker gene apcE2, which introduces a validation marker not included in the initial FRCI framework, and a significant positive correlation with chlorophyll f concentrations. The FRCI approach identified 11 distinct FRLCyano amplicon sequence variants, primarily affiliated with Leptolyngbya and Calothrix, and revealed that their relative abundance is driven by higher pH and lower temperatures. Extending this framework to global hot spring datasets revealed distinct biogeographical signatures, notably the rarity of Fischerella in Taiwan compared to other regions. Furthermore, the isolation of a novel FRL strain, Chroococcidiopsis sp. GD1, highlights the essential, complementary role of cultivation in comprehensive surveys. This study provides a robust, multi-method validated framework for assessing the distribution and ecological correlates of FRLCyano.
Biting midges are important medical and veterinary vector insects that can transmit a range of zoonotic viruses. The Beijing-Tianjin-Hebei (BTH) region, as the core area in northern China, is rich in tourism resources, but the characteristics of the virome of biting midges in this region remain unclear. A total of 12,152 biting midges individuals were collected, and 7 species of Culicoides were identified. Culicoides punctatus (67.02
As seagrasses decline, parasites continue to threaten remaining populations. Upon observing galls in Hawaiian seagrasses, efforts were undertaken to identify their cause, resulting in the first identification of infections by the seagrass parasite Marinomyxa halophilae in Halophila hawaiiana and in Hawaiian populations of H. decipiens. In both hosts, M. halophilae could be found year-round and was relatively common. Samples were taken from three sites per host, and sequencing of the ribosomal 18S gene revealed two strains, each specific to the host species. New gall morphology was identified for Marinomyxa infections in Halophila, namely, infections of H. decipiens with reduced internodes and infections of H. hawaiiana extending beyond petioles into fruits, representing a potential threat to seed-based restoration efforts.
Aquirufa is a widespread and diverse bacterial genus inhabiting freshwater ecosystems. Analyses of genomes from cultured strains and metagenome-assembled genomes (MAGs) of the genus revealed four phylogenetically distinct branches that differed markedly in the proportions of cultured strains and MAGs they contained. In total, 56 species or species-like taxa were identified, including eight novel species described here. Proteorhodopsin genes were detected in many of the genomes and were found across a wide range of habitat types, but their prevalence differed considerably among the four phylogenetic branches. Detailed analyses of two branches with markedly different proteorhodopsin gene frequencies suggested differences in the occurrence, size, structure, and pangenomes of their populations. Comparative whole-genome analyses showed that proteorhodopsin genes in Aquirufa consistently co-occurred with two key genes involved in retinal chromophore biosynthesis. These three genes exhibited distinct evolutionary patterns, most likely reflecting differences in recombination and co-evolution. Phylogenetic analyses placed the Aquirufa proteorhodopsins within the proteorhodopsin-xanthorhodopsin clade, specifically in a lineage comprising proteorhodopsins from species of the phylum Bacteroidota. Extending the analyses to related proteorhodopsins revealed additional patterns. Thirteen distinct gene arrangement types and all three common spectral-tuning residues were identified, with variation occurring not only among genera but occasionally even among species within the same genus. Overall, our findings indicated that the evolution, acquisition, horizontal transfer, and recombination of proteorhodopsin genes and associated genes have proceeded differently across taxonomic groups.
Estuaries are dynamic ecosystems influenced by fluctuating environmental conditions and sediment-associated contamination, which may affect host-associated microbiomes. This study investigated the gut microbiome of the bivalve Cerastoderma edule across three estuarine sites differing in anthropogenic pressure. Bacterial 16S rRNA and fungal ITS metabarcoding data were integrated with sediment physicochemical parameters to assess spatial and seasonal variation in gut microbial diversity and composition. Bacterial communities showed clear differences among sites and seasons, with stronger variation in areas characterized by higher organic matter and trace metal concentrations. Fungal communities also varied among samples, although their interpretation was limited by the high proportion of unassigned ITS taxa. Multivariate analyses indicated associations between gut microbial composition and sediment parameters, including organic matter, salinity, and trace metals such as mercury (Hg), zinc (Zn), and lead (Pb). Putative bacterial functional profiles were inferred from taxonomic data using FAPROTAX, suggesting potential involvement in nitrogen, sulfur, and carbon cycling, as well as organic compound degradation. Nevertheless, it is important to note that these functional predictions should be interpreted as indicators of potential metabolic capacity rather than direct evidence of activity. Ultimately, these findings demonstrate that the C. edule gut microbiome has strong potential as a complementary tool for the assessment of estuarine environmental conditions and host–environment interactions.
Bats harbour diverse genera containing zoonotic species, yet whether colonisation by these genera reflects stable host–microbe associations or transient environmental exposure remains unresolved. We propose that bat bacterial communities are shaped by three axes of variation: body site defines the microbial niche, host species imposes ecological and phylogenetic constraints, and seasonal life-history transitions alter exposure regimes. We tested four predictions: (1) each body site would (2) host species would show different bacterial profiles associated with differences in roosting ecology, colony density, and foraging behavior; (3) active and hibernation periods would differ in community structure and predicted metabolic function; and (4) zoonotic genera would show predominantly transient detection across years within individuals. Using 16 S rRNA gene amplicon sequencing of 2,747 oral, skin, and gut (stool) samples from eight insectivorous bat species across four seasons (2021–2024) in South Korea, all four predictions were supported. Body site was the strongest determinant of community structure: mean zoonotic genus relative abundance was 10-fold higher in gut (6.91
Understanding the core microbiome has potential applications on biomonitoring and conservation. We explore whether closely related xerophytes from the Mammillaria haageana species complex (MHSC), a recently diverged group (ca. 2 mya) that occupy geographically distant and contrasting environments, share a bacterial core microbiome (BCM) that could help them to thrive through an aridity gradient. We sampled the rhizosheath and the surrounding bulk soil, performed 16S rRNA (v3-v4 region) metabarcoding, and analyzed soil properties, bacterial diversity and functional predictions, to compare between soil compartments and describe the BCM associated to the MHSC rhizosheath. We observed that bacterial communities differed among bulk soils but MHSC species display a trend to select for the same bacteria. Despite environmental differences, we found that all four species shared a BCM composed of 17 bacterial taxa, assigned to genera Dactylosporangium, Microvirga, and Rubrobacter; as well as 14 predicted functional processes. This BCM could enhance rhizosheath nutrient acquisition and stress responses, thus helping the plant-bacteria holobiont to thrive in arid environments and help us understand the rapid evolution and diversification of the MHSC across an aridity gradient
Plant microbiomes are shaped by hierarchical ecological filters in which compartmentalization through the progressive selection of microbial communities along the soil-root-leaf continuum, emerges as the strongest structuring force. Despite the agronomic importance of oil palm (Elaeis guineensis Jacq.) as an important oil crop, compartment-resolved characterizations of its microbiome remain scarce, and the microbiome of the interspecific hybrid OxG (E. oleifera × E. guineensis), widely planted in Latin America to sustain production in disease-affected areas, had not been previously described. Here, we used 16S rRNA (V3-V4) and ITS (ITS2) metabarcoding to survey bacterial, archaeal, and fungal communities across bulk soil, rhizosphere, roots, and leaves of productive plots of E. guineensis and OxG hybrid palms under two soil consociations in Colombia. Sequencing produced 10,298,116 raw reads, of which 79.83
Studies on microbiomes are essential for understanding the various roles microbes play in the health of bees, yet many wild bees including cleptoparasitic species and their microbiomes continue to be underexplored. To alleviate this gap, we analyzed bacterial and fungal microbiomes of cleptoparasitic species with 16 S rRNA and ITS1 metabarcoding and compared results to the microbiomes of their hosts and other wild bees across families and functional traits. We found that a parasitic lifestyle was associated with a significantly more diverse bacterial microbiome compared to other social or dietary traits, and that ground-nesting bees have a richer bacterial microbiome than stem-nesting bees. Fungal diversity was only found to be greater in solitary bees compared to eusocial species. Hosts and cleptoparasites had broadly similar bacterial and fungal microbiomes, with a few exceptions. N. articulata had a significantly more diverse bacterial microbiome compared to its hosts Agapostemon virescens and A. sericeus, and H. calliopsidis boasted greater bacterial diversity compared to its host Calliopsis andreniformis. Fungal communities were also different for N. illinoensis – Andrena crataegi and for N. articulata – A. virescens, whereas several host-cleptoparasite pairs harboured distinct bacterial communities. Individual cleptoparasites were also uniquely associated with several understudied bacterial microbes. Our study is the first to assess the microbiomes of six cleptoparasitic species and reveals important insight into the unique and shared microbes in wild bees and host-cleptoparasite pairs.
The complex relationship between insects and their gut microbiota has become a central theme in host–microbe ecology, revealing profound effects on host fitness and interactions. Yet, how gut microbial communities—and their primary determinant, diet—vary across space and time in natural insect populations remains largely unexplored. Understanding these dynamics is essential for linking microbial variation with host biology. We investigated bacterial gut microbiota and dietary patterns in two odonate species, Sympetrum vulgatum and Lestes sponsa, across their flight season and three locations in southern Finland. Using faecal DNA metabarcoding of the cytochrome c oxidase subunit I (COI) gene for diet and 16 S rRNA gene for gut microbiota, we examined spatiotemporal changes and their associations. Season, location, and host species affected both dietary and bacterial diversity. The observed parallel responses of dietary composition and microbial communities highlight that the same ecological factors shaping insect feeding behaviour also influence their associated microbiota, illustrating the dynamic and context-dependent nature of insect–microbe interactions in the wild and emphasizing the need for broader ecological perspectives in microbiome research.
Fusarium species are major contributors to Fusarium head blight (FHB) and mycotoxin contamination in cereal production. To characterize microbial co-occurrence associated with toxin accumulation in oats, the Fusarium, fungal, and bacterial communities of 51 Finnish oat grain samples were analyzed using a multi-marker metabarcoding approach targeting Fusarium translation elongation factor 1‑alpha (EF1α), fungal ITS2, and bacterial 16 S regions. Microbial profiles were compared between grains with high and low deoxynivalenol (DON) concentrations. High‑DON samples were dominated by F. graminearum, whereas F. langsethiae prevailed in low‑DON grains. Bacterial diversity was higher in high‑DON samples, while fungal diversity remained similar across groups. Several bacterial genera, including Pseudomonas, Paenibacillus, Massilia, and Curtobacterium, exhibited negative correlations with Fusarium species, indicating competition in the same niche, whereas Duganella and Xylophilus showed positive association with Fusarium abundance. Microdochium consistently co-occurred with Fusarium. Results show differences in microbial communities associated with mycotoxin levels and Fusarium community composition, identifying taxa that may influence FHB or indicate mycotoxin risk.
Biological nitrogen fixation (BNF) by diazotrophs contributes to increasing nitrogen (N) availability in nutrient-poor deadwood during the decomposition process. However, chronically elevated atmospheric N deposition may increase N availability, thereby reshaping diazotrophic community and suppressing BNF. We simulated high N deposition by repeatedly applying ammonium-nitrate solution to deadwood of 13 tree species over 9 years (N addition) and compared diazotrophic community composition and BNF rates with untreated controls. Deadwood N concentrations increased over time in both control and N addition, with N addition resulting in higher N concentrations at the final sampling, although significant treatment effects were detected only in Tilia and Pinus. Chronic high-N addition was associated with reduced BNF activity, with significant suppression primarily observed in coniferous deadwood, while responses among broadleaved species were weak, variable, or absent. The N addition altered diazotroph richness and community composition by increasing the abundance of Bradyrhizobium and by reducing Methylocapsa across all tree species. Under N addition, BNF correlated positively with nifH gene copy numbers in broadleaved deadwood but negatively in coniferous deadwood. Co-occurrence networks were more interconnected and modular under N addition, with diazotrophs (e.g., Azospirillum) central in broadleaved deadwood and fungi (e.g., Meliniomyces, Athelia) central in coniferous deadwood. Tree clade (coniferous vs. broadleaved) strongly shaped richness and community response, with broadleaved and coniferous species showing distinct patterns.Overall, the largely robust diversity and community composition of diazotrophs and BNF activity under high N addition suggest that moderately increasing N deposition has little influence on fungal deadwood decomposition and the function of deadwood as a carbon pool in forest ecosystems.
Protozoa are major bacterial predators in aquatic, soil and host-associated environments. During feeding, bacteria are internalised into food vacuoles, which normally mature into digestive vacuoles containing the molecular machinery required for bacterial digestion. However, several bacterial species can resist this process and are instead expelled from protozoa packaged within these vacuoles now commonly referred to as expelled food vacuoles (EFVs), and previously described as “expelled vesicles”, “faecal pellets” or “multilamellar bodies”. Rather than being viewed simply as waste products of protozoan digestion, EFVs should be considered as biologically generated reservoirs that package, protect and transmit viable pathogenic bacteria. In this review, we synthesise evidence from studies in Vibrio cholerae, Salmonella enterica, Legionella pneumophila, Campylobacter jejuni, Listeria monocytogenes, Escherichia coli, Burkholderia cenocepacia and Mycobacterium smegmatis indicating that EFV-associated bacteria display increased resistance to acid, starvation, antibiotics, biocides, oxidative stress and desiccation, together with enhanced infectivity and horizontal gene transfer. Based on this research, we propose that EFVs create a distinct environmental transmission state in which bacteria that survive protozoan digestion are packaged into protective vesicles and exit the predator already primed for persistence, dissemination and host colonisation. This process connects environmental persistence with infection biology and suggests that EFV-associated pathogens could serve as useful targets for water surveillance and outbreak prediction.
