The nutritional strategy of phago-mixotrophy among pigmented eukaryotes has been widely recognized and characterized across various taxonomic lineages. While their ecological role as bacterivores in different aquatic environments is acknowledged, establishing a clear connection between phago-mixotrophic activities and taxonomy within natural communities remains challenging. In this study, we utilized a combination of microscopy and fluorescence-activated single-cell sorting techniques to investigate the diversity and temporal variations of bacteria-feeding mixotrophs in a freshwater habitat. We identified four groups of mixotrophs using both methods: Pedinellales (Dictyochophyceae), Cryptomonas (Cryptophyceae), Dinobryon (Chrysophyceae) and a single-chloroplast bearing group within Chlorophyta. Together, these groups accounted for 58%-96% and 54%-95% of total mixotrophs detected by microscopy and cell sorting, respectively. Samples collected in different seasons demonstrated that Pedinellales and Chlorophyta were more abundant in spring and summer/autumn, while Dinobryon was only present in winter when temperatures were lowest and light intensity was moderate. Our findings, with 6 classes and 12 genera identified as bacterivorous mixotrophs, highlight the promising potential of single-cell techniques in aquatic microbiology. This approach reveals the taxonomic identity and feeding activities of phago-mixotrophs in situ, thereby enhancing our understanding of their functional ecological roles within microbial food webs.
ABSTRACT Understanding how multiple biotic stressors shape host‐associated bacteriomes is essential for predicting ecological outcomes. This study examined interactions among the cattle tick Rhipicephalus microplus , the pathogen Anaplasma marginale and the entomopathogenic fungus Metarhizium anisopliae . Across treatments involving fungal exposure alone or combined with A. marginale , the gut bacteriome comprised 698 ASVs, of which 28.2% formed a stable core dominated by Bacteroidota and Bacillota. Fungal‐associated stress drove functional shifts, including enrichment of SCFA‐producing taxa such as Akkermansia muciniphila and Lachnospiraceae , indicating reorganization preceding major taxonomic changes. Co‐occurrence networks were restructured under fungal and combined pressures, showing high connectivity, predominance of negative correlations and antagonistic interactions driven by keystone taxa like Prevotella . The combined‐stressor network showed greater robustness, cohesion and communication efficiency than single‐stressor conditions. Functional predictions revealed conserved metabolic profiles, yet co‐exposure increased functional diversity and gene abundance, with A. marginale exerting dominant influence. In silico removal of A. marginale from the co‐exposure condition indicated a persistent ecological imprint, preventing reversion to the basal fungal‐only configuration and retaining structural traces of prior colonization. Overall, simultaneous pathogen–fungus pressures reorganize microbial networks, tightening interactions and enhancing stability, underscoring the dual role of M. anisopliae as a biocontrol agent and potential modulator of bacteriome resilience.
ABSTRACT Alpine meadows (AM) and desert steppes (DS) are major grassland types in northern Qiangtang that support ecosystem functioning, livestock production and pastoral livelihoods. However, how Tibetan sheep coordinate dietary, microbial and metabolic responses across these contrasting forage environments remains unclear. We used vegetation surveys, organic matter intake (OMI) estimation, faecal DNA metabarcoding, 16S rRNA gene sequencing and untargeted metabolomics to compare female Tibetan sheep grazing AM or DS. The DS had lower forage biomass and concentrations of several nutrients, whereas DS sheep had higher OMI, lower dietary plant diversity and greater representation of Rosaceae ( p < 0.05). Faecal bacterial communities differed between groups. Plant‐family composition, rather than dietary alpha diversity, was associated with bacterial variation; Rosaceae and Tamaricaceae showed the strongest associations ( r 2 = 0.929 and 0.836, respectively; p = 0.001). Selected bacterial genera were associated with Rosaceae (Mantel R = 0.59, p = 0.001). Among 3819 detected metabolites, 1177 differed between groups and were mainly enriched in flavonoid‐ and phenylpropanoid‐related pathways (adjusted p < 0.05). These findings reveal coordinated associations among diet, faecal microbiota and metabolites and identify plant‐family composition as a key correlate of habitat‐related microbial and metabolic variation.
ABSTRACT This study describes the isolation and characterization of two biofilm‐forming bacterial strains, Pseudomonas aeruginosa MD3 and Bacillus toyonensis LD07, capable of degrading chlorpyrifos. These isolates demonstrated remarkable phenotypic plasticity, maintaining biofilm formation across varying pH, temperature and salinity levels. To maximize microbial stability and metabolic efficiency, sugarcane bagasse was utilized as a support matrix. Analytical characterization (EDX, BET and XRD) confirmed that the bagasse possesses a highly porous architecture, serving as a protective scaffold and an auxiliary carbon source for synergistic co‐metabolism. A bio‐product formulated via solid‐state fermentation on this matrix exhibited exceptional bioremediation efficacy, eliminating 99% of chlorpyrifos at an extreme concentration of 4500 ppm within 35 days. Furthermore, 16S rRNA gene amplicon sequencing of coffee‐growing soils across different treatments (natural control, pesticide‐stressed and 10% bio‐product amended) with accession numbers PRJNA1529359 revealed distinct shifts in microbial community dynamics. While the taxonomic landscape was broadly dominated by Bacillota, Pseudomonadota and Actinomycetota, the bio‐product amendment caused P. aeruginosa and B. toyonensis to become the dominant taxa. Ultimately, these insights underscore the viability of cost‐effective agricultural by‐products for cell immobilization and highlight metagenomics as a powerful predictive framework for monitoring the remediation of anthropogenically stressed ecosystems.
ABSTRACT Anoxygenic phototrophs are metabolically flexible bacteria. However, it is unclear how Fe(II) oxidation is affected by the simultaneous availability of organic or inorganic substrates. We therefore cultivated six green‐ and purple non‐sulfur photoferrotrophs from freshwater and marine environments with 2 mM Fe(II), amended with 0.6 mM organic co‐substrate or H 2 . We found that photoferrotrophs generally utilized organics and Fe(II) simultaneously, and that two marine strains preferred Fe(II) over H 2 . For some photoferrotrophs, Fe(II) oxidation rates were significantly enhanced by acetate, lactate, and glucose, whereas H 2 typically slowed Fe(II) oxidation. All phototrophic Fe(II)‐oxidizers oxidized 80%–100% of the Fe(II) by the end of the experiment except for R. robiginosum , where Fe(II) oxidation reached only 52%–73%. We further observed for the first time that R. palustris TIE‐1 can grow with butyrate and glucose and that R. iodosum can utilize glucose. Comparison of genomic predictions with experimentally observed substrate consumption revealed discrepancies in four strains. Overall, our results demonstrate that Fe(II) remains an important electron donor despite the availability of alternative substrates, suggesting that maintaining photoferrotrophy is a common trait of photoferrotrophs and likely contributes to iron cycling in natural environments.
