Environmental Microbiology Reports最新文献

Chronic non-point nitrogen (N) and phosphorus (P) loads reshape sediment microbial biogeochemical cycling in headwater systems, altering ecosystem function. This study integrates DNA and RNA amplicon sequencing with metatranscriptomics to examine microbial taxonomic and functional responses to nutrient inputs in lower Great Lakes watersheds, focusing on N, P, and sulphur (S) metabolism. RNA-based taxa showed a stronger correlation with metabolic functions than DNA-based taxa, highlighting RNA-based approaches as valuable tools for assessing active microbial responses to nutrients. Site-specific analyses revealed distinct microbial metabolic profiles linked to watershed fertiliser sources and seasonal variation. Inorganic fertiliser inputs were associated with tightly coupled N reduction and sulphur oxidation, driven by differential expression of dissimilatory nitrate reduction to ammonia (DNRA) and sox genes. In contrast, a manure-amended site exhibited elevated nitrosative stress and sulphur assimilation pathways, consistent with detection of ammonia-oxidising genera. The low-impact reference site demonstrated intermediate functional turnover, enhanced nitrogen fixation, and the highest microbial diversity, suggesting greater ecosystem resilience. Seasonally, functional turnover increased in fall, with fewer shared core taxa across sites compared to summer. These findings highlight the impact of chronic nutrient enrichment on site-specific microbial adaptations and underscore the importance of temporal dynamics in assessing freshwater sediment microbial communities.

Chronic non-point nitrogen (N) and phosphorus (P) loads reshape sediment microbial biogeochemical cycling in headwater systems, altering ecosystem function. This study integrates DNA and RNA amplicon sequencing with metatranscriptomics to examine microbial taxonomic and functional responses to nutrient inputs in lower Great Lakes watersheds, focusing on N, P, and sulphur (S) metabolism. RNA-based taxa showed a stronger correlation with metabolic functions than DNA-based taxa, highlighting RNA-based approaches as valuable tools for assessing active microbial responses to nutrients. Site-specific analyses revealed distinct microbial metabolic profiles linked to watershed fertiliser sources and seasonal variation. Inorganic fertiliser inputs were associated with tightly coupled N reduction and sulphur oxidation, driven by differential expression of dissimilatory nitrate reduction to ammonia (DNRA) and sox genes. In contrast, a manure-amended site exhibited elevated nitrosative stress and sulphur assimilation pathways, consistent with detection of ammonia-oxidising genera. The low-impact reference site demonstrated intermediate functional turnover, enhanced nitrogen fixation, and the highest microbial diversity, suggesting greater ecosystem resilience. Seasonally, functional turnover increased in fall, with fewer shared core taxa across sites compared to summer. These findings highlight the impact of chronic nutrient enrichment on site-specific microbial adaptations and underscore the importance of temporal dynamics in assessing freshwater sediment microbial communities.

Mondia whitei (Hook.f.) Skeels is an essential medicinal plant in African societies. However, little is known about the plant's metabolome and its microbiota. Here, we examine the root endosphere and rhizosphere from five locations in Uganda using high-throughput amplicon sequencing, qPCR and multifactorial modelling. Root metabolite profiles obtained with GC/LC–MS were comprehensively catalogued through a deep literature survey using 516 sources. Plant roots were inhabited by microbiota ranging between 50 and 500 ASVs, also with an average microbial abundance of 10¹¹ gene (16SrRNA or ITS) copies per gram. The microbiota was dominated by Gammaproteobacteria, Alphaproteobacteria and Actinobacteria, as well as Sordariomycetes, Dothideomycota, Eurotiomycetes and Agaricomycetes. We identified that a major portion of the microbiome (i.e., 45%–70%) was potentially transferred from the rhizosphere into the roots. Therefore, the root microbiota showed a strong location-specific microbial and metabolite fingerprint. Fraxin, 4-methoxy-benzaldehyde, monobutyl phthalate, 2-hydroxy-4-methoxybenzaldehyde, and scopoletin were among the 86 compounds found in plant roots that were strongly correlated with the root microbiota. Moreover, the identified plant compounds have been shown to mediate microbe, plant, and animal interactions. Our research advances the research frontiers of endangered African herbal plants, through providing insights into the microbiome and potential compounds of M. whitei, a medicinal plant used in sub-Saharan Africa.

Mondia whitei (Hook.f.) Skeels is an essential medicinal plant in African societies. However, little is known about the plant's metabolome and its microbiota. Here, we examine the root endosphere and rhizosphere from five locations in Uganda using high-throughput amplicon sequencing, qPCR and multifactorial modelling. Root metabolite profiles obtained with GC/LC–MS were comprehensively catalogued through a deep literature survey using 516 sources. Plant roots were inhabited by microbiota ranging between 50 and 500 ASVs, also with an average microbial abundance of 10¹¹ gene (16SrRNA or ITS) copies per gram. The microbiota was dominated by Gammaproteobacteria, Alphaproteobacteria and Actinobacteria, as well as Sordariomycetes, Dothideomycota, Eurotiomycetes and Agaricomycetes. We identified that a major portion of the microbiome (i.e., 45%–70%) was potentially transferred from the rhizosphere into the roots. Therefore, the root microbiota showed a strong location-specific microbial and metabolite fingerprint. Fraxin, 4-methoxy-benzaldehyde, monobutyl phthalate, 2-hydroxy-4-methoxybenzaldehyde, and scopoletin were among the 86 compounds found in plant roots that were strongly correlated with the root microbiota. Moreover, the identified plant compounds have been shown to mediate microbe, plant, and animal interactions. Our research advances the research frontiers of endangered African herbal plants, through providing insights into the microbiome and potential compounds of M. whitei, a medicinal plant used in sub-Saharan Africa.

Vibrio cholerae is a globally distributed, free-living bacterium in aquatic ecosystems. While non-O1/non-O139 serogroups typically do not produce cholera toxin, they have the potential to cause diarrhoea. These strains may act as reservoirs of antibiotic resistance in rivers, lakes and oceans. Understanding their genetic resistance and virulence can shed light on their role in spreading antimicrobial resistance and their pathogenicity. In this study, we characterised 60 V. cholerae non-O1/non-O139 strains from 16 freshwater bodies located throughout the Province of Córdoba, Argentina. We found none of the strains carried cholera toxin and identified ampicillin resistance as the most prevalent phenotype. Whole genome sequencing revealed that all ampicillin-resistant strains (n = 10) carried CARB β-lactamases, leading to the identification of new CARB variants (CARB-59 to CARB-62) likely associated with the V. cholerae superintegron. Two strains were notably related and exhibited enhanced virulence due to an unusual genetic arrangement of the VPI-1 pathogenicity island, encoding both the toxin co-regulated pilus and a type VI secretion system cluster subclass i5, commonly found in non-cholera Vibrio species. These findings provide significant insights into the genetic diversity and virulent potential of ampicillin-resistant environmental V. cholerae non-O1/non-O139 and enhance our understanding of the evolution of CARB β-lactamases within the species.

Vibrio cholerae is a globally distributed, free-living bacterium in aquatic ecosystems. While non-O1/non-O139 serogroups typically do not produce cholera toxin, they have the potential to cause diarrhoea. These strains may act as reservoirs of antibiotic resistance in rivers, lakes and oceans. Understanding their genetic resistance and virulence can shed light on their role in spreading antimicrobial resistance and their pathogenicity. In this study, we characterised 60 V. cholerae non-O1/non-O139 strains from 16 freshwater bodies located throughout the Province of Córdoba, Argentina. We found none of the strains carried cholera toxin and identified ampicillin resistance as the most prevalent phenotype. Whole genome sequencing revealed that all ampicillin-resistant strains (n = 10) carried CARB β-lactamases, leading to the identification of new CARB variants (CARB-59 to CARB-62) likely associated with the V. cholerae superintegron. Two strains were notably related and exhibited enhanced virulence due to an unusual genetic arrangement of the VPI-1 pathogenicity island, encoding both the toxin co-regulated pilus and a type VI secretion system cluster subclass i5, commonly found in non-cholera Vibrio species. These findings provide significant insights into the genetic diversity and virulent potential of ampicillin-resistant environmental V. cholerae non-O1/non-O139 and enhance our understanding of the evolution of CARB β-lactamases within the species.

The use of beneficial soil fungi or their natural products offers a more sustainable alternative to synthetic fungicides for pathogen management in crops. Volatile organic compounds (VOCs) produced by such fungi act as semiochemicals that inhibit pathogens, with VOC production influenced by physical interactions between competing fungi. This study explores the interaction between the beneficial soil fungus Trichoderma hamatum GD12 strain (GD12), previously shown to antagonise crop pathogens such as Sclerotinia sclerotiorum, to test the hypothesis that its antagonistic effect is mediated by volatile chemical signalling. In dual-culture confrontation assays, co-inoculation of GD12 and S. sclerotiorum led to fungistatic interactions after 7 days. VOCs collected from individual and co-cultures were analysed by gas chromatography–flame ionisation detector (GC-FID) analysis and coupled GC-mass spectrometry (GC–MS), revealing significant differences in VOC production between treatments, with VOC production notably upregulated in the GD12 + S. sclerotiorum co-culture. Peak VOC production occurred 17 days post-inoculation. Synthetic VOC assays revealed several compounds inhibitory to S. sclerotiorum, including 1-octen-3-one, which also arrested the growth of other fungal crop pathogens (Botrytis cinerea, Pyrenopeziza brassicae, and Gaeumannomyces tritici). Structural insights into 1-octen-3-one's antifungal activity against S. sclerotiorum are also presented. These findings support the hypothesis that the antagonistic properties of T. hamatum GD12 against crop fungal pathogens can, in part, be attributed to VOC production. Further research is needed to assess the potential of these semiochemicals as tools for pathogen management in agriculture.

Free-living amoebae are phagotrophic protists that prey on bacteria. However, under certain conditions, some bacteria can resist phagocytosis and become pathogenic. Environmental parameters altered by climate change may impact amoebae and bacterial diversity, as well as their pathogenicity. In our study, we monitored amoebae and bacterial abundance both temporally, over 1 year, and spatially, along a river estuary, while also recording key environmental parameters. Naegleria was the most represented amoebae genus, present year-round from the river to the estuary. Similarly, Vibrio was the most dominant bacterial genus. Salinity, and to a lesser extent dissolved oxygen, influenced amoebae and bacterial abundance. In particular, the genera Naegleria, Paramoeba, Pseudomonas and Legionella were the most affected. In conclusion, this study highlights the impact of salinity on amoebae diversity, suggesting that this parameter, as a key factor in coastal environments, will impact both amoebae and the associated bacterial communities.

Free-living amoebae are phagotrophic protists that prey on bacteria. However, under certain conditions, some bacteria can resist phagocytosis and become pathogenic. Environmental parameters altered by climate change may impact amoebae and bacterial diversity, as well as their pathogenicity. In our study, we monitored amoebae and bacterial abundance both temporally, over 1 year, and spatially, along a river estuary, while also recording key environmental parameters. Naegleria was the most represented amoebae genus, present year-round from the river to the estuary. Similarly, Vibrio was the most dominant bacterial genus. Salinity, and to a lesser extent dissolved oxygen, influenced amoebae and bacterial abundance. In particular, the genera Naegleria, Paramoeba, Pseudomonas and Legionella were the most affected. In conclusion, this study highlights the impact of salinity on amoebae diversity, suggesting that this parameter, as a key factor in coastal environments, will impact both amoebae and the associated bacterial communities.

Biological soil crusts (biocrusts) are associations of microorganisms coexisting in the top millimetres of soil, which are found predominantly in arid biomes. Recently, a new type of biocrust, termed grit crust, of the coastal range of the Atacama Desert was discovered. Here, we explore the culturable microbiome of the grit crust based on an integrative isolation approach combining morphological and phylogenetic analyses, focusing on cyanobacteria, green algae and the often overlooked non-lichenised fungi with climate records and soil data. The 122 generated isolates from four contrasting locations were distributed over three organismic groups: cyanobacteria (38), green algae (26) and non-lichenised fungi (58). The distribution of the organisms among the four locations followed a water availability gradient as shown by relative air humidity data, resulting in communities shaping the biochemistry of the substrate in terms of texture, carbon and nitrogen contents. Novel species, genera and the functional roles of the different organisms within the biocrust environment are discussed. The high abundance of endemic and presumably new species, including five potentially new genera within the cyanobacterial order of the Chroococcidiopsidales—not found in other deserts—underpins the uniqueness and further distinguishes the grit crust from other biocrusts in extreme environments.