Environmental Microbiology Reports最新文献

{"title":"The Indoor Microbiome: Sampling, Analysis and Emerging Trends","authors":"Iva Šunić,&nbsp;Jelena Šarac,&nbsp;Dubravka Havaš Auguštin,&nbsp;Sofya Pozdniakova,&nbsp;Robert M. W. Ferguson,&nbsp;Matijana Jergović,&nbsp;David Visentin,&nbsp;Sílvia Borràs,&nbsp;Elizabeth Archer,&nbsp;Drew K. Henderson,&nbsp;Sandra Vitko,&nbsp;Adna Ašić,&nbsp;Anja Bošnjaković,&nbsp;Željka Maglica,&nbsp;Carla Viegas,&nbsp;Natalija Novokmet,&nbsp;Nina Karlović,&nbsp;Damir Marjanović,&nbsp;Adam Muszyński,&nbsp;Yuxi Liu,&nbsp;Piia Karisola,&nbsp;Harri Alenius,&nbsp;Lukasz Krych,&nbsp;Mario Lovrić","doi":"10.1111/1758-2229.70272","DOIUrl":"10.1111/1758-2229.70272","url":null,"abstract":"<p>Indoor spaces contain diverse microbial communities that shape human health. These microorganisms are particularly relevant to respiratory diseases, including asthma and allergies. Despite growing recognition of the importance of indoor microbial exposures, research in this field is slowed by differences in methods. These inconsistencies make it difficult to compare results and draw conclusions. This systematic review analyses 106 studies published between 2000 and 2025 that investigated indoor microbiomes in dust, air, and other matrices across homes, schools, and other built environments. We assessed sampling strategies, DNA extraction protocols, sequencing technologies, and bioinformatic pipelines, identifying trends, inconsistencies, and areas requiring harmonisation. Passive sampling, particularly dust collection, was the most common approach, while Illumina-based 16S rRNA and ITS amplicon sequencing dominated molecular analyses. However, variations in targeted gene regions, extraction kits, and analytical tools limited cross-study comparability. Ecological findings revealed consistent detection of bacterial taxa such as <i>Staphylococcus</i>, <i>Streptococcus</i>, and <i>Corynebacterium</i>, and fungal taxa including <i>Cladosporium</i>, <i>Aspergillus</i>, and <i>Penicillium</i>, with diversity shaped by building characteristics, ventilation, humidity, occupancy, and presence of pets. This review highlights the need for standardised protocols in indoor microbiome research to facilitate reproducibility, enable meta-analyses, and inform health-related guidelines for indoor environments.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 2","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13054241/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147626681","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}

{"title":"Analysis of Bacterial Wilt Management Strategies From the Dynamic Perspective of Environmental Adaptation Approaches of Ralstonia solanacearum.","authors":"Mingzhao Han, Xin Liu, Guixiang Li, Peng Li","doi":"10.1111/1758-2229.70335","DOIUrl":"10.1111/1758-2229.70335","url":null,"abstract":"<p><p>The Ralstonia solanacearum species complex (RSSC) ranks among the most destructive plant pathogens worldwide, due to its broad host range, extensive geographic distribution and remarkable environmental adaptability. Its persistence in soil and colonization of plant vascular tissues severely limits the effectiveness of conventional chemical control, posing significant challenges for disease management. This review highlights recent advances in understanding the environmental adaptation mechanisms of RSSC. Key topics include the dynamic evolution of pathogenicity, niche-specific survival strategies and virulence regulation mediated by quorum sensing, and complex interactions with surrounding microbial communities that shape its behaviour and fitness. We further provide a comprehensive assessment of current control strategies from an ecological perspective, encompassing physical, chemical, genetic, agronomic and microbial approaches, with critical evaluation of their mechanisms, potential and limitations. Meanwhile, we discuss the major challenges in bacterial wilt management and outline future directions, with an emphasis on multi-omics-informed precision breeding, microbiome engineering and intelligent integrated disease management (IDM). These emerging strategies hold promise for the sustainable and effective long-term control of bacterial wilt disease caused by RSSC.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 2","pages":"e70335"},"PeriodicalIF":2.7,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13052101/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147615465","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}

{"title":"Soil Microbiome of Tropical Seasonal and Permanent Small Wetlands.","authors":"Karen Luko-Sulato, Everton Tiago Sulato, Jorge R Osman, Pedro Nolasco-Jiménez, Daniela Morales, Graziela Silva Rezende, Cassy Anne Rodrigues, Sandra Imaculada Maintinguer, Anderson Ferreira da Cunha, Vania Rosolen","doi":"10.1111/1758-2229.70306","DOIUrl":"10.1111/1758-2229.70306","url":null,"abstract":"<p><p>Characterisation of the microbial communities of two small tropical wetlands under two distinct hydrological regimes (permanent and seasonal), across a rainy and dry season was performed by 16S rRNA amplicon sequencing. We identified 48 bacterial phyla across the two wetland types, seasons and depths and 83% of the bacterial sequences consistently corresponded to six phyla: Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Proteobacteria and Verrucomicrobia. The seasonal wetland presented a predominance of Chloroflexi, Nitrospirae, Actinobacteria and Acidobacteria, whereas the permanent wetland showed higher relative abundances of Planctomycetes, Bacteroidetes, Proteobacteria and Firmicutes. Archaeal communities also differed, with Crenarchaeota predominating in the seasonal and Euryarchaeota in the permanent wetland. Microbial communities showed pronounced compositional shifts across wetland type, season and depth, while maintaining stable alpha diversity, with depth was the dominant driver. Functional inference suggested that aerobic ammonia oxidation, nitrate reduction and sulphur compound respiration were the predominant putative metabolic pathways in the seasonal wetland and methanogenesis, fermentation, dark hydrogen oxidation, nitrogen fixation, photoautotrophy, ureolysis and hydrocarbon degradation in the permanent wetland. The permanent wetland exhibited sparse correlation with environmental drivers, consistent with long-term saturation and chronic nutrient limitation, while the seasonal wetland presented influence of pH, nutrients and SOC on microbial community structure.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 2","pages":"e70306"},"PeriodicalIF":2.7,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13053137/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147579998","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}

{"title":"Examining Short Temporal Changes in Intertidal Macroalgal Microbiomes at 'Ewa Beach, O'Ahu, Hawai'i: Some Hosts Varied While Others Remained Stable.","authors":"Evan S Dunn, Heather L Spalding, Kristina M Hill-Spanik, Heather Fullerton","doi":"10.1111/1758-2229.70333","DOIUrl":"10.1111/1758-2229.70333","url":null,"abstract":"<p><p>Understanding the temporal variability of microbiomes is crucial for predicting dynamics within macroalgal communities under future climate change scenarios, rising temperatures, and increased marine heatwave events. Short-term variation has been observed in human- and coral-associated microbes, but these dynamics are less understood in macroalgae. Intertidal macroalgal communities are ideal systems for investigating microbiome temporal variation due to their exposure to daily fluctuations in abiotic conditions. We characterised and examined the variability in the microbiota of seven macroalgal species, with representatives from three different phyla, across five sequential low tides in May 2021 at a single intertidal bench at 'Ewa Beach, O'ahu, Hawai'i, USA. Bacterial community compositions found in two red algae, Acanthophora spicifera and Laurencia dendroidea, and one brown alga, Dictyota sandvicensis, had variable abundances of several amplicon sequence variants contributing to significant dissimilarity through time. Two green macroalgae (Avrainvillea lacerata and Halimeda discoidea) were stable over time. Temporal stability of the macroalgal microbiotas, therefore, was variable amongst macroalgal species, but may be dependent on its horizontal or vertical positioning within the intertidal zone, which can vary the level of environmental stress (e.g., temperature, light, desiccation). Additional work exploring the drivers of the temporal variability observed herein is needed.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 2","pages":"e70333"},"PeriodicalIF":2.7,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13052502/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147626670","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}

{"title":"Correction to 'Enhancing Biodiversity-Function Relationships in Field Retting: Towards Key Microbial Indicators for Retting Control'.","authors":"","doi":"10.1111/1758-2229.70334","DOIUrl":"10.1111/1758-2229.70334","url":null,"abstract":"","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 2","pages":"e70334"},"PeriodicalIF":2.7,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13052130/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147621187","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}

{"title":"Viral Diversity of Coastal Restinga Soils From Southern Brazil.","authors":"Janaína Paula Back, Vinícius Klain, Val Oliveira Pintro, Fernanda Cortez Lopes, Ana Luiza Marques, Jair Kray, Walter Orlando Beys-da-Silva, Lucélia Santi, Augusto Schrank, Fabiana Quoos Mayer, Marilene Henning Vainstein","doi":"10.1111/1758-2229.70343","DOIUrl":"10.1111/1758-2229.70343","url":null,"abstract":"<p><p>Coastal ecotones are highly dynamic environments for viral studies due to their extreme abiotic conditions, transitional nature between marine and terrestrial domains and high biodiversity. In Brazil, the Restinga is a coastal ecotone along the shoreline, characterized by nutrient-poor sandy soils, high salinity, strong winds and intense solar radiation, hosting poorly explored microbial communities essential for ecological balance. This exploratory study provides a preliminary characterization of viral diversity across three Restinga localities in southern Brazil (Imbé, Cidreira and Mostardas) using metagenomics. We identified 261 viral families, 2023 genera and 6064 species, with 'Unknown' representing 44%-46% of families and ~9% of genera. Among known taxa, Mimiviridae was most frequent (15%-16%), followed by Phycodnaviridae (9%), Peduoviridae (5%) and Kyanoviridae (4%-5%). Genera such as Tupanvirus and Fadolivirus were abundant (~5%), with Fadolivirus algeromassiliense and Donellivirus gee among the most frequent species. Although alpha diversity and composition did not differ significantly among sites, landscape features influenced viral communities. Viral richness and abundance increased with urban land cover and isolation but decreased with Restinga cover and patch fragmentation.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 2","pages":"e70343"},"PeriodicalIF":2.7,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13078860/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147687307","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}

{"title":"Phage Cocktail Designed for Wastewater Bioremediation Has Limited Effect on Crustacean Filtrator Microbiome Diversity and Health.","authors":"Marta Grabska, Adrian Gorecki, Hannah V Pye, Evelien M Adriaenssens, Malgorzata Grzesiuk","doi":"10.1111/1758-2229.70329","DOIUrl":"10.1111/1758-2229.70329","url":null,"abstract":"<p><p>In this study we investigated the impact of a phage cocktail on Daphnia magna microbiome and the life-history parameters. A mixture of four phages able to infect strains of Klebsiella pneumoniae, Enterobacter sp. and Pseudomonas aeruginosa was tested on three D. magna clones. The host-associated microbiome composition in both the examined variants and the control was analysed using 16S rRNA amplicon sequencing. Additionally, the survival, growth rate, age, size at the first reproduction, and neonate per female were assessed. The analysis revealed minor shifts in microbial composition following phage exposure. Nevertheless, results showed that the phage cocktail increased microbiome diversity. None of the life-history parameters studied were affected by the presence of the phage cocktail, and no adverse effects were observed. The results indicated that under laboratory conditions the phage cocktail is safe for D. magna and its microbiome.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 2","pages":"e70329"},"PeriodicalIF":2.7,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13058927/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147631980","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}

{"title":"Aquatic Bacterial Community Responses to Aquatic Contaminants Revealed by 16S rRNA Metabarcoding in Field-Based Microcosms.","authors":"A S Flynn, A M Osborn, V Pettigrove, J Shimeta, S M Long","doi":"10.1111/1758-2229.70328","DOIUrl":"10.1111/1758-2229.70328","url":null,"abstract":"<p><p>In this study we used environmental DNA metabarcoding and field-based microcosms to assess three classes of aquatic contaminants (metals (copper), pesticides (diuron), and pharmaceuticals (venlafaxine)) and their impact on the structure of freshwater wetland sedimentary bacterial communities. Our results showed that copper had the most influence on bacterial community structure, followed by venlafaxine, then diuron. We also saw that the addition of copper facilitated the release of other sediment-bound metals (barium, zinc, and vanadium), also having significant impacts on community structure. The bacterial communities were mostly dominated by Proteobacteria, Cyanobacteria, Bacteroidota, and Verrucomicrobiota, which were key drivers of variation among treatments, along with Actinobacteriota. Our findings indicate that the ideal taxonomic level for the assessment and identification of bacterial bioindicators is family, with constraints at lower taxonomic levels. We identified five phyla, 13 families, and three species which show strong potential to be either diagnostic bioindicators of one or more of the chemicals assessed or broad bioindicators of common urban contaminants, eight of which are novel bioindicators. Our study highlights the effectiveness of eDNA metabarcoding to efficiently characterise sedimentary bacterial community assemblages and emphasises its value in aquatic ecosystem assessments, particularly for the prediction of contaminants driving ecosystem change.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 2","pages":"e70328"},"PeriodicalIF":2.7,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13140830/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147525145","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}

{"title":"Bacterial Resilience and Vulnerability to Neonicotinoid Seed Treatments in Soil: Short-Term Community Responses.","authors":"Sharmin Akter, Julia Jasonsmith, Nilantha R Hulugalle, Craig L Strong","doi":"10.1111/1758-2229.70339","DOIUrl":"10.1111/1758-2229.70339","url":null,"abstract":"<p><p>We explored the short-term impacts of three neonicotinoids (imidacloprid, thiamethoxam, and clothianidin) on soil bacterial community composition and diversity in wheat-planted microcosms. Neonicotinoids were applied as seed treatments, and soil samples were collected over 10 days. Overall alpha diversity metrics showed no significant treatment- or time-dependent shifts; however, post hoc analyses revealed transient, treatment-specific responses at individual sampling time points. Thiamethoxam and clothianidin significantly increased diversity and evenness at early time points, while imidacloprid reduced diversity by Day 10. Clothianidin was also associated with a short-term increase in estimated species richness. Actinobacteriota and Proteobacteria dominated across treatments, with Firmicutes increasing and Bacteroidota declining with time. The minor phylum Methylomirabilota exhibited a significant treatment effect. Sampling day and day-treatment interaction significantly influenced community structure. Mesorhizobium enriched under all neonicotinoids. Imidacloprid enhanced Massilia and suppressed Solirubrobacterales and Chloroflexia. Thiamethoxam enriched Gaiella, Solirubrobacter, and Massilia but suppressed Nitrospira. Clothianidin enriched Solirubrobacter and Lysobacter but suppressed Methyloceanibacter and Nitrospira. Haliangiaceae were positively correlated with sampling days, while Flavobacteriaceae and Microscillaceae were negatively correlated. Yersiniaceae and Solirubrobacteraceae were negatively correlated with imidacloprid and Mycobacteriaceae with thiamethoxam. These findings highlight the need for longer-term and functional investigations into neonicotinoid impacts on soil microbial communities and ecosystem health.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 2","pages":"e70339"},"PeriodicalIF":2.7,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13056401/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147631985","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}

{"title":"Diversity and Dispersal of Fungi Along a Subtropical Land-to-Sea Continuum.","authors":"M Meyneng, L Tedersoo, G Burgaud, V Mikryukov, F Carriconde, H Lemonnier, R Siano","doi":"10.1111/1758-2229.70297","DOIUrl":"10.1111/1758-2229.70297","url":null,"abstract":"<p><p>This study examines the fungal and fungal-like stramenopile communities along the land-to-sea continuum to explore microbial connectivity across terrestrial and marine ecosystems. In addition to providing new ecological knowledge on coastal communities, the objectives were to assess the presence of terrestrial fungi and evaluate their potential as bioindicators of riverine influence on marine environments. Conducted in New Caledonia (southwest Pacific), the research involved 113 marine samples (water and sediment) and 148 additional soil samples from tropical/subtropical Pacific regions. Sampling spanned spatial and temporal gradients, including dry periods and a post-cyclone runoff event. We used high-throughput long-read amplicon sequencing of the full-length ITS rRNA gene, complemented by inference of fungal ecological traits from genus-level annotations. In total, 1653 fungal OTUs were identified in marine samples, with distinct communities in sediment and water. Terrestrial fungal taxa were also detected in marine environments, with 306 genera exhibiting varying occurrence across sample types and periods. The cyclone runoff temporarily increased the richness of terrestrial fungal taxa by up to threefold, underscoring the impact of extreme events on marine coastal assemblages. Overall, this work provides the first study of fungal communities along New Caledonia's coastlines, highlighting fungal dispersal as a key component of land-to-sea connectivity.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 2","pages":"e70297"},"PeriodicalIF":2.7,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13052330/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147615523","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}