Environmental Microbiology Reports最新文献_第4页

Stable Bacterial Cores and Patchy Eukaryotic Communities Shape the Summer Microbiomes of Patagonian Fjord Ecosystems Across Spatial, Functional and Temporal Gradients 稳定的细菌核心和斑块状的真核生物群落塑造了巴塔哥尼亚峡湾生态系统夏季微生物群的空间、功能和时间梯度。

IF 3.1 4区生物学

Environmental Microbiology Reports Pub Date : 2026-09-08 DOI: 10.1111/1758-2229.70412

Nicole Trefault, Susana Rodríguez-Marconi, María Fernanda Manrique-de-la-Cuba, Patricio Flores-Herrera, Clara Natalia Rodríguez-Flórez, Bernd Krock

{"title":"Stable Bacterial Cores and Patchy Eukaryotic Communities Shape the Summer Microbiomes of Patagonian Fjord Ecosystems Across Spatial, Functional and Temporal Gradients","authors":"Nicole Trefault, Susana Rodríguez-Marconi, María Fernanda Manrique-de-la-Cuba, Patricio Flores-Herrera, Clara Natalia Rodríguez-Flórez, Bernd Krock","doi":"10.1111/1758-2229.70412","DOIUrl":"10.1111/1758-2229.70412","url":null,"abstract":"Patagonian fjord ecosystems are shaped by a combination of glacial, oceanographic and climatic factors that generate physical and chemical gradients. In these environments, microbial communities play essential roles in ecosystem functioning, with temporal and depth-related compositional shifts often linked to glacial meltwater input. In this study, we characterised microbial communities from southern Patagonia and the Drake Passage using high-throughput sequencing of the 16S and 18S rRNA genes across seven study areas. We found that bacterial and eukaryotic communities differed across the sampling areas, with salinity showing the strongest association with community composition in both microbial domains. Bacterial core communities, defined here using a combined occupancy–abundance approach, were widespread throughout fjords and channels, whereas eukaryotic core communities were spatially restricted. Network analyses revealed contrasting modes of community organisation across these fjord systems, with land-terminating glaciers displaying more hub microorganisms (highly connected bacteria and microbial eukaryotes) than water-terminating glaciers. Short-term analyses identified microbial taxa that varied significantly in abundance over a 10-day period and were present in inter-domain co-occurrence networks. Together, these results identify a small set of abundant and well-connected microorganisms that structure summer microbiomes in Patagonian fjords and may link glacial runoff regimes into distinct modes of community interactions.","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 5","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1758-2229.70412","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148910148","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Seasonal Baseline Evaluation of Physicochemical Parameters and Culturable Bacterial Characteristics in Northwestern Himalayan Ramsar Sites 喜马拉雅拉姆萨尔湿地西北部理化参数和可培养细菌特征的季节性基线评价

IF 3.1 4区生物学

Environmental Microbiology Reports Pub Date : 2026-09-01 DOI: 10.1111/1758-2229.70409

Shagufta Butt, Chandresh Kumari, Rakesh Kumar Shukla, Sunil Puri, Sadanand Pandey, Adane Woldemedhin Kalsido

{"title":"Seasonal Baseline Evaluation of Physicochemical Parameters and Culturable Bacterial Characteristics in Northwestern Himalayan Ramsar Sites","authors":"Shagufta Butt, Chandresh Kumari, Rakesh Kumar Shukla, Sunil Puri, Sadanand Pandey, Adane Woldemedhin Kalsido","doi":"10.1111/1758-2229.70409","DOIUrl":"10.1111/1758-2229.70409","url":null,"abstract":"Freshwater wetlands in the Himalayan region are ecologically sensitive and microbiologically diverse ecosystems, yet their seasonal dynamics remain insufficiently characterised. This study investigated seasonal variations in physicochemical properties and bacterial diversity of two Ramsar wetlands in northwestern India, Renuka Ji Lake and Asan Conservation Reserve. Water samples were collected during pre-monsoon (June), monsoon (August) and post-monsoon (November) seasons. Physicochemical parameters were analysed using standardised IS:3025, APHA 24th Edition and SLS/SOP protocols. Bacterial isolation was performed by serial dilution–pour plating on nutrient agar, followed by Gram staining, biochemical characterisation and 16S rRNA gene sequencing. Both wetlands exhibited pronounced seasonal fluctuations in water chemistry. At both sites, dissolved oxygen (Renuka Ji), turbidity and dissolved oxygen (Asan Conservation Reserve) exceeded CPCB permissible limits during specific seasons. Eleven bacterial isolates were identified, predominantly representing freshwater associated genera. Agrobacterium cavarae was comparatively uncommon in freshwater environments. No bacterial colonies were recovered from Renuka Ji Lake during post-monsoon sampling within the tested dilution range (101–104). Overall, culturable bacterial communities showed seasonal variation and were dominated by a limited number of genera. These findings highlight the ecological sensitivity of Himalayan Ramsar wetlands and emphasise the need for continuous physicochemical and microbiological monitoring for effective conservation and sustainable management.","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 5","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13533594/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148872359","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genomic Characterization of Aeromonas dhakensis Isolated From a Fatal Dolphin Case 从致命性海豚病例分离的达肯气单胞菌的基因组特征。

IF 3.1 4区生物学

Environmental Microbiology Reports Pub Date : 2026-08-31 DOI: 10.1111/1758-2229.70410

Kohei Yamazaki, Yu Takahashi, Yuki Yoneda, Takashige Kashimoto, Tsutomu Kakuda

{"title":"Genomic Characterization of Aeromonas dhakensis Isolated From a Fatal Dolphin Case","authors":"Kohei Yamazaki, Yu Takahashi, Yuki Yoneda, Takashige Kashimoto, Tsutomu Kakuda","doi":"10.1111/1758-2229.70410","DOIUrl":"10.1111/1758-2229.70410","url":null,"abstract":"Aeromonas dhakensis has emerged as a significant pathogen affecting both aquatic animals and humans; however, genomic data for isolates from marine mammals remain scarce. In this study, we characterised the genome of A. dhakensis strain KDL-001, isolated from a fatal dolphin case, using whole-genome sequencing and comparative genomics. Taxonomic analyses, including MLST and average nucleotide identity (ANI), confirmed the isolate as A. dhakensis. Core-genome phylogeny further revealed that KDL-001 is closely related to strains derived from fish and aquatic environments. Notably, in silico screening of virulence-associated genes showed that the virulence-associated gene profile of the dolphin isolate was broadly comparable to those of other A. dhakensis strains, with no isolate-specific virulence-associated genes being identified within the limits of this analysis. These findings demonstrate that the dolphin-derived isolate is genomically comparable to previously described A. dhakensis strains and possesses conserved virulence-associated genes commonly found within the species.","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 5","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13529358/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148862962","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Biofilm Source Shapes the Tolerance to Short-Term Ciprofloxacin Exposure 生物膜源形成对短期环丙沙星暴露的耐受性。

IF 3.1 4区生物学

Environmental Microbiology Reports Pub Date : 2026-08-30 DOI: 10.1111/1758-2229.70408

Clara Benavent-Celma, Sophie Oster, Sebastian Pietz, Sabine Filker, Mirco Bundschuh, Timo Mühlhaus, Alexander Feckler

{"title":"Biofilm Source Shapes the Tolerance to Short-Term Ciprofloxacin Exposure","authors":"Clara Benavent-Celma, Sophie Oster, Sebastian Pietz, Sabine Filker, Mirco Bundschuh, Timo Mühlhaus, Alexander Feckler","doi":"10.1111/1758-2229.70408","DOIUrl":"10.1111/1758-2229.70408","url":null,"abstract":"Periphytic biofilms are key mediators of freshwater ecosystem processes but are increasingly exposed to anthropogenic stressors. We compared biofilms sampled upstream and downstream of a wastewater treatment plant (WWTP) effluent, two source communities presumed to differ in prior exposure to wastewater-associated press disturbance, to examine differences in tolerance to ciprofloxacin (CIP) exposure. We assessed biomass, photosynthetic pigments and fatty acid (FA) profiles as well as microbial community structure using qPCR and metabarcoding. Downstream-sourced biofilms exhibited higher biomass stability, reduced pigment and FA losses and fewer bacterial and eukaryotic community shifts under CIP exposure than upstream-sourced biofilms. Upstream-sourced communities, despite higher baseline pigment and FA contents, showed pronounced sensitivity to CIP, including biomass declines and reduced prokaryotic diversity. Taxon-specific responses revealed stress-tolerant Chlorophyceae, cyanobacteria and heterotrophic taxa, which may have contributed to higher functional stability under the tested conditions. Our findings show that biofilm responses to CIP varied with source site and community composition. While not a direct test of environmental filtering, the observed patterns are consistent with its predictions. The results further suggest that legacy effects and spatial heterogeneity may influence biofilm vulnerability to antibiotic exposure, although this requires validation across multiple WWTP-impacted and reference sites.","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 5","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13526528/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148860449","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Correction to ‘Geographic Variability of Fish Carcass–Associated Microbial Communities’ 修正“鱼类尸体相关微生物群落的地理变异”

IF 3.1 4区生物学

Environmental Microbiology Reports Pub Date : 2026-08-26 DOI: 10.1111/1758-2229.70407

引用次数: 0

Correction to ‘Geographic Variability of Fish Carcass–Associated Microbial Communities’ 修正“鱼类尸体相关微生物群落的地理变异”

IF 3.1 4区生物学

Environmental Microbiology Reports Pub Date : 2026-08-26 DOI: 10.1111/1758-2229.70407

引用次数: 0

Plant Defence Metabolite Detoxification by a Pathogenic Fungus Opens Necrotic Tissue to Diverse Bacteria in Arabidopsis thaliana 植物防御代谢物解毒的病原真菌打开坏死组织对多种细菌在拟南芥

IF 3.1 4区生物学

Environmental Microbiology Reports Pub Date : 2026-08-19 DOI: 10.1111/1758-2229.70401

Shubhangi Sharma, Jingyuan Chen, Matthew Agler

{"title":"Plant Defence Metabolite Detoxification by a Pathogenic Fungus Opens Necrotic Tissue to Diverse Bacteria in Arabidopsis thaliana","authors":"Shubhangi Sharma, Jingyuan Chen, Matthew Agler","doi":"10.1111/1758-2229.70401","DOIUrl":"https://doi.org/10.1111/1758-2229.70401","url":null,"abstract":"Foliar necrotic fungal pathogens pose a constant threat to plant health. Their virulence can be affected by both the host immune system, as well as diverse host-associated bacteria. Generally, how these factors interact is not well studied, but may provide insights toward sustainable plant protection. Sclerotinia sclerotiorum (Ssc) is a devastating, broad host range necrotrophic pathogen with limited control options. Here, we find that necrotic Ssc lesions strongly enrich diverse bacterial taxa. Arabidopsis thaliana, like other Brassica plants including crops, produce and store large amounts of aliphatic glucosinolates (aGLS). Upon Ssc invasion and tissue damage, myrosinase enzymes transform aGLS into toxic metabolites, including aliphatic isothiocyanates (aITCs). Adapted Ssc strains can detoxify aITCs by hydrolyzing them with the enzyme SaxA, which is important for its virulence. Here, we find that this detoxification is critical for bacterial enrichment in necrotic lesions, since a SaxA-deficient strain does not alter the bacteriome. Additionally, our results suggest that both aliphatic and other GLSs likely contribute specific effects to this phenomenon. Thus, we demonstrate a mechanism in which the interaction of host and pathogen factors together shape a pathogen-associated bacteriome, providing directions to better understand interactions of host bacteria with foliar necrotic pathogens.","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 4","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1758-2229.70401","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148783833","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Plant Defence Metabolite Detoxification by a Pathogenic Fungus Opens Necrotic Tissue to Diverse Bacteria in Arabidopsis thaliana 植物防御代谢物解毒的病原真菌打开坏死组织对多种细菌在拟南芥

IF 3.1 4区生物学

Environmental Microbiology Reports Pub Date : 2026-08-19 DOI: 10.1111/1758-2229.70401

Shubhangi Sharma, Jingyuan Chen, Matthew Agler

{"title":"Plant Defence Metabolite Detoxification by a Pathogenic Fungus Opens Necrotic Tissue to Diverse Bacteria in Arabidopsis thaliana","authors":"Shubhangi Sharma, Jingyuan Chen, Matthew Agler","doi":"10.1111/1758-2229.70401","DOIUrl":"https://doi.org/10.1111/1758-2229.70401","url":null,"abstract":"Foliar necrotic fungal pathogens pose a constant threat to plant health. Their virulence can be affected by both the host immune system, as well as diverse host-associated bacteria. Generally, how these factors interact is not well studied, but may provide insights toward sustainable plant protection. Sclerotinia sclerotiorum (Ssc) is a devastating, broad host range necrotrophic pathogen with limited control options. Here, we find that necrotic Ssc lesions strongly enrich diverse bacterial taxa. Arabidopsis thaliana, like other Brassica plants including crops, produce and store large amounts of aliphatic glucosinolates (aGLS). Upon Ssc invasion and tissue damage, myrosinase enzymes transform aGLS into toxic metabolites, including aliphatic isothiocyanates (aITCs). Adapted Ssc strains can detoxify aITCs by hydrolyzing them with the enzyme SaxA, which is important for its virulence. Here, we find that this detoxification is critical for bacterial enrichment in necrotic lesions, since a SaxA-deficient strain does not alter the bacteriome. Additionally, our results suggest that both aliphatic and other GLSs likely contribute specific effects to this phenomenon. Thus, we demonstrate a mechanism in which the interaction of host and pathogen factors together shape a pathogen-associated bacteriome, providing directions to better understand interactions of host bacteria with foliar necrotic pathogens.","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 4","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1758-2229.70401","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148783962","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Using Ongoing Wildlife Surveillance Programs to Monitor Antibiotic Resistant Bacteria in the Environment 利用正在进行的野生动物监测项目来监测环境中的抗生素耐药细菌。

IF 3.1 4区生物学

Environmental Microbiology Reports Pub Date : 2026-08-16 DOI: 10.1111/1758-2229.70404

María Rincón-Gracia, Stefan Börjesson, Robert Söderlund, Hanna Woksepp, Aleksija Neimanis, Henrik Uhlhorn, Thomas Rosendal, David Winlund, Hugo Uddströmer, Josef D. Järhult, Jonas Bonnedahl

{"title":"Using Ongoing Wildlife Surveillance Programs to Monitor Antibiotic Resistant Bacteria in the Environment","authors":"María Rincón-Gracia, Stefan Börjesson, Robert Söderlund, Hanna Woksepp, Aleksija Neimanis, Henrik Uhlhorn, Thomas Rosendal, David Winlund, Hugo Uddströmer, Josef D. Järhult, Jonas Bonnedahl","doi":"10.1111/1758-2229.70404","DOIUrl":"10.1111/1758-2229.70404","url":null,"abstract":"The need to include wildlife in surveillance programs for antibiotic resistance has been previously highlighted. In the present study, we explored the possibility of sampling Swedish wildlife in conjunction with ongoing monitoring programs for wildlife health and disease to evaluate the occurrence of antibiotic resistance. The animals included in the study represented different trophic levels and degrees of interaction with humans, namely bears, eagles, wolves, foxes, otters, and hares. Samples were screened for ESBL-, pAmpC-, and carbapenemase-producing Escherichia coli using selective media, and indicator E. coli was also isolated from each sample. All isolates were tested for antimicrobial susceptibility, and a subset of isolates was genome sequenced. Two samples from foxes were found to carry ESBL- or pAmpC-producing isolates, while no carbapenemase-producing E. coli could be detected. Geographical information on the samples and genetic characterization of the ESBL- and pAmpC-producing isolates suggest that proximity to anthropogenic settings could play a role in the occurrence of antibiotic resistance in wildlife. In addition, the study demonstrated that the use of ongoing wildlife surveillance programs presents a cost-efficient possibility to monitor antibiotic resistance in wild animals. However, future studies and monitoring programs should take careful consideration regarding selection of animal species and distribution.","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 4","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13477815/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148758362","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Soil Microbiomes Across Depth and Ecosystems in Dubai, UAE: Potential Environmental Signatures for Forensic Geolocation 阿联酋迪拜深度和生态系统的土壤微生物组：法医地理定位的潜在环境特征

IF 3.1 4区生物学

Environmental Microbiology Reports Pub Date : 2026-08-14 DOI: 10.1111/1758-2229.70403

Abdulla Albastaki, Mohammed Naji, Mohamed Moussa, Judith Smith

{"title":"Soil Microbiomes Across Depth and Ecosystems in Dubai, UAE: Potential Environmental Signatures for Forensic Geolocation","authors":"Abdulla Albastaki, Mohammed Naji, Mohamed Moussa, Judith Smith","doi":"10.1111/1758-2229.70403","DOIUrl":"https://doi.org/10.1111/1758-2229.70403","url":null,"abstract":"Soil microbial communities exhibit strong sensitivity to environmental gradients, yet their distribution across depth and land-use types in hyper-arid environments remains poorly characterised. Using whole-genome shotgun metagenomics via Oxford Nanopore Technologies long-read sequencing, we profiled soil microbial communities across six contrasting land-use sites in Dubai, UAE: urban, industrial (two locations), marine, desert and agricultural, where each sampled at three depth intervals (0–25 cm, 25–50 cm and 50–100 cm). Marine soils exhibited extreme salinity (EC 23.7–30.7 dS m−1) and the highest organic matter content (1.19%–1.76%), while desert soils were nutrient-poor with minimal salinity. Actinomycetota and Pseudomonadota co-dominated across all sites, collectively accounting for 77%–96% of classified sequences. Actinomycetota prevailed in undisturbed desert horizons (up to 53.4%), while Pseudomonadota dominated nutrient-enriched environments, reaching 69.4% at industrial sites. A notable compositional reversal was observed in the desert deep horizon (50–100 cm), where Pseudomonadota increased to 56.8%, departing from the expected oligotrophic depth gradient. PERMANOVA confirmed land use as the primary driver of community composition (p = 0.001), with depth exerting a secondary but significant effect (p ≤ 0.01). NMDS ordination revealed strong site-specific clustering, with each environment harbouring a distinctive microbial fingerprint with promising forensic geolocation potential.","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 4","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1758-2229.70403","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148753816","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0