{"title":"Genomic Survey of Carbon Monoxide Dehydrogenases Reveals Their Widespread Distribution in Marine Habitats.","authors":"Nipa Chongdar, Anand Goyal, Samir R Damare","doi":"10.1111/1758-2229.70375","DOIUrl":"10.1111/1758-2229.70375","url":null,"abstract":"<p><p>Most carbon monoxide (CO) produced in the ocean is consumed by microorganisms encoding carbon monoxide dehydrogenases (CODHs), thereby significantly reducing the flux of CO from the ocean to the atmosphere. CODHs are of two types based on the metal content of their active sites: the oxygen-sensitive, nickel-containing Ni-CODH and the oxygen-tolerant, molybdenum-copper-containing Mo-CODH. Although CODHs have been reported from specific marine environments, their combined distribution across ocean ecosystems remains unclear. Here, we analyzed the NCBI non-redundant protein database and identified 1969 Ni-CODH and 864 Mo-CODH genes from marine prokaryotes spanning diverse oceanic ecosystems. Using metagenomic analyses across three marine biomes, we showed that oxygen availability selectively constrains Ni-CODH gene abundance, but not Mo-CODHs. Thus, Ni-CODHs are restricted to oxygen-limited niches, while Mo-CODHs occur across both oxygenated and oxygen-limited marine environments. Phylogenetic analyses indicated that all previously described CODH clades are represented in the marine ecosphere, highlighting their evolutionary diversity. Genome context analyses suggest that approximately 50% of the marine Ni-CODH potentially participate in carbon fixation via the Wood-Ljungdahl pathway, whereas most marine Mo-CODH likely contribute to the supplementary energy conservation. Together, these results provide an integrated view of CODH distribution and potential function in marine ecosystems.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 3","pages":"e70375"},"PeriodicalIF":3.1,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13240472/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148154662","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 Diversity and Functional Dynamics in the Soybean (Glycine max L.) Rhizosphere Under Different Organic Fertilisation.","authors":"Ijeoma Emelda Osuji, Akinlolu Olalekan Akanmu, Olubukola Oluranti Babalola","doi":"10.1111/1758-2229.70370","DOIUrl":"10.1111/1758-2229.70370","url":null,"abstract":"<p><p>Soybean (Glycine max L.) is a globally important legume for oil and protein production, yet its responses to specific organic fertilisation practices remain insufficiently understood. Organic amendments such as cattle dung and poultry manure are sustainable alternatives to inorganic fertilisers, but their effects on the soybean rhizosphere microbiome remain poorly characterised. This study investigated microbial community structure and functional diversity under poultry manure and cattle dung treatments. Rhizospheric soils were collected from treated plots, untreated controls and bulk soil and then subjected to physicochemical analysis. DNA extracted from samples was analysed using 16S rRNA gene sequencing on the Illumina NovaSeq 6000 platform, with data processed in QIIME 2 (v2019.1). Poultry manure increased available phosphorus (28%) and calcium (19%), while cattle dung enhanced potassium (22%) and magnesium (17%). Microbial community composition shifted significantly, with poultry manure promoting copiotrophic taxa such as Burkholderia and Cupriavidus and cattle dung enriching decomposers including Paenibacillus and Treponema. Alpha diversity was highest in poultry manure (Shannon index 6.2) and bulk soil (6.0) and lowest in cattle dung (5.1). Functional predictions indicated retention of core metabolic pathways, suggesting functional redundancy. Overall, organic fertilisation reshapes microbial communities while maintaining essential functions, supporting sustainable soybean cultivation.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 3","pages":"e70370"},"PeriodicalIF":3.1,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13239308/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148136263","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}
Amanda Simão Dias, Sílvia Dias de Oliveira, Renata Medina-Silva
{"title":"High Resistance and Biofilm Tolerance to Antimicrobials of Marine Bacteria From Brazilian Deep-Sea Sediment.","authors":"Amanda Simão Dias, Sílvia Dias de Oliveira, Renata Medina-Silva","doi":"10.1111/1758-2229.70364","DOIUrl":"10.1111/1758-2229.70364","url":null,"abstract":"<p><p>Antimicrobial resistance studies have focused on clinical bacteria, neglecting the role of resistant isolates in natural environments. However, oceans are daily contaminated with high loads of antimicrobials and resistant bacteria from agro-industrial and urban activities. Deep-sea sediment is a challenging environment that may select microbial strains with resistance to chemicals and ability to form biofilms, becoming a potential reservoir of resistance genes. We evaluated the susceptibility to antimicrobials of six Pseudomonas sp., five Bacillus sp., two Brevibacillus sp. and two Paenibacillus sp. from deep-sea sediments of the Pelotas Basin (Brazil) by the disk diffusion and microdilution tests. Pseudomonas and Bacillales were tested against 11 and 7 antimicrobials, respectively. Biofilms of susceptible isolates were exposed to antimicrobials to determine the minimum biofilm inhibitory concentration (MBIC) and the minimum biofilm eradication concentration (MBEC). All Pseudomonas were resistant to aztreonam at very high concentrations (up to 2048 μg/mL). MBIC values were significantly higher than respective MICs, and only one third of biofilms were eradicated. These results underscore the importance of the study, as one of the first reporting antimicrobial tolerance of biofilms of cultivable bacteria from deep-sea sediments, contributing to the knowledge of bacterial resistance in these environments, concerning One Health issues.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 3","pages":"e70364"},"PeriodicalIF":3.1,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13580871/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147968989","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}
Elham Lashani, Hamid Moghimi, Raymond J Turner, Mohammad Ali Amoozegar
{"title":"Effect of Metal Cations on Selenite Bioreduction by a Consortium of Halophilic/Halotolerant Bacteria and/or Yeast.","authors":"Elham Lashani, Hamid Moghimi, Raymond J Turner, Mohammad Ali Amoozegar","doi":"10.1111/1758-2229.70320","DOIUrl":"10.1111/1758-2229.70320","url":null,"abstract":"<p><p>Selenium oxyanion pollution in the environment, often originating from anthropogenic industrial activities, causes significant risks to human health and the ecosystem. The selenite bioreduction to the less toxic form of selenium, Se (0), by microbial species and consortia offers a promising approach for bioremediation of polluted environments. This study explores the effects of potentially toxic co-contaminating metal cations, including cadmium (Cd), lead (Pb), and zinc (Zn), on the bioreduction of selenite by a consortium of halotolerant and halophilic bacteria and yeast. The effectiveness of the consortium in reducing selenite was investigated in conditions that mimic multi-metal pollution found in the real world, with varying levels of the different metals. The results showed that Pb and Cd had negative effects on the mixed consortium efficacy, while Zn showed an augmenting effect on the bacterial consortia. Also, molybdate significantly reduced selenite removal in all consortia. Kinetic analyses using the Michaelis-Menten model were applied for evaluating the rate of selenite reduction. Also, selenium biosorption and dispersion in microbial cells were studied using electron microscopy and EDS analysis. The findings provide insights into the use of microbial consortia in contaminated environments and highlight the potential for bioremediation strategies that can cope with multiple pollutants.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 3","pages":"e70320"},"PeriodicalIF":3.1,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13580820/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147968921","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}
Rosalina Stancheva, Cecilio Valadez-Cano, Benoit Van Aken, Gordon M Selckmann, Janice Lawrence, A Bruce Cahoon
{"title":"Limnofasciculus delicatus (Coleofasciculaceae, Coleofasciculales), a Novel Mat-Forming Cyanobacterium From Shenandoah River, Virginia, USA.","authors":"Rosalina Stancheva, Cecilio Valadez-Cano, Benoit Van Aken, Gordon M Selckmann, Janice Lawrence, A Bruce Cahoon","doi":"10.1111/1758-2229.70377","DOIUrl":"10.1111/1758-2229.70377","url":null,"abstract":"<p><p>Benthic cyanobacterial mats in flowing waters are complex communities typically composed of taxa from the orders Coleofasciculales and Oscillatoriales, many of which have unresolved taxonomic positions and poorly characterized toxic potential. We collected field mats of a benthic non-heterocytous filamentous cyanobacterium from the North and South Forks of the Shenandoah River in Northern Virginia (USA) that were dominated by a novel morphotype. Whole-genome and 16S rRNA gene phylogenetic analyses placed this cyanobacterium within the recently described genus Limnofasciculus (Coleofasciculaceae). Genome-based species delimitation metrics fell below accepted thresholds for bacterial species delineation relative to Limnofasciculus baicalensis, the only formally described species in the genus to date, supporting recognition of the cyanobacterium from Shenandoah River as a distinct species. Furthermore, the two Limnofasciculus species exhibited marked structural differences in the Box B helix of the 16S-23S ITS region. Comparative genomic analyses revealed a genome size similar to L. baicalensis and a conserved core gene repertoire alongside substantial divergence in biosynthetic gene cluster composition. Neither species contains biosynthetic gene clusters associated with the production of known cyanotoxins. Based on morphological, phylogenetic and genomic evidence, we describe Limnofasciculus delicatus sp. nov., supported by light microscopy and whole-genome characterization.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 3","pages":"e70377"},"PeriodicalIF":3.1,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13283753/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148292776","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, Composition and Resilience of the Root Microbiome of Tomato Plants in a Hydroponic Rockwool System.","authors":"Phil Thomas, Brian Sindel, Gal Winter","doi":"10.1111/1758-2229.70380","DOIUrl":"10.1111/1758-2229.70380","url":null,"abstract":"<p><p>In hydroponic horticulture, where soil is replaced by a sterile artificial substrate, attention to microorganisms is primarily focused on the suppression of plant pathogens and the application of potentially beneficial organisms. This study examined the ecology of the root microbiome of tomato plants which were grown to maturity in a hydroponic rockwool system and then treated with a Trichoderma-based biocontrol product. The bacterial community was species-rich but was dominated by a small number of Alphaproteobacteria, Gammaproteobacteria and Bacteroidia species. The fungal community was less diverse and consisted almost exclusively of Ascomycota and Rozellomycota species. Biocontrol treatment did not have a significant effect on bacterial diversity, but the microbiome composition changed distinctly over the period of sampling in both treated and untreated plants. These results support the view that mineral substrates in a hydroponic system can support a complex and resilient root microbiome. Understanding the microorganisms that thrive in this unique environment may help identify effective biological treatments, and enable the development of rockwool-specific practices for monitoring, protecting and promoting plant health.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 3","pages":"e70380"},"PeriodicalIF":3.1,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13283755/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148292793","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 'On the Difficulty to Detect Carbapenem Resistance in the Environment: Characterisation of Escherichia coli With Reduced Carbapenem Susceptibility Isolated in a French River'.","authors":"","doi":"10.1111/1758-2229.70378","DOIUrl":"10.1111/1758-2229.70378","url":null,"abstract":"","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 3","pages":"e70378"},"PeriodicalIF":3.1,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13250460/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148209379","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}
Mansoureh Esfandiyari Doolaby, Mohammad Javad Mehdipour Moghaddam, Akbar Norastehnia
{"title":"Modulation of Quorum Sensing and Virulence Gene Expression in Escherichia coli by Extracts of Physalis alkekengi.","authors":"Mansoureh Esfandiyari Doolaby, Mohammad Javad Mehdipour Moghaddam, Akbar Norastehnia","doi":"10.1111/1758-2229.70371","DOIUrl":"10.1111/1758-2229.70371","url":null,"abstract":"<p><p>The rise of multidrug-resistant (MDR) bacteria underscores the need for new antimicrobials. In uropathogenic Escherichia coli, quorum sensing and adhesion play central roles in pathogenicity; therefore, luxS and fimH were selected as virulence targets. This study examined the antibacterial, antibiofilm and gene-modulating effects of ethanolic and aqueous root extracts of Physalis alkekengi L. against three E. coli isolates (EC1, EC2, EC3). Phytochemical analysis confirmed the presence of phenolics, flavonoids, flavonols and anthocyanins, along with measurable antioxidant capacity. Antimicrobial activity was assessed using agar well diffusion, disk diffusion and broth microdilution on the MDR isolate EC2. Biofilm inhibition was quantified using a microtiter plate, and changes in luxS and fimH expression were evaluated by real-time PCR. The ethanolic extract contained higher flavonoid and flavonol levels, whereas the aqueous extract was richer in phenolics. Anthocyanins and DPPH activity were undetectable in both extracts. The ethanolic extract completely inhibited EC3 at 10 mg/mL, although no MBC was observed for EC1, EC2 or any isolate exposed to the aqueous extract. In EC2, the ethanolic extract produced larger but variable inhibition zones, reduced biofilm by approximately 63% and significantly downregulated luxS and fimH (p < 0.05), supporting the potential of P. alkekengi as a natural antivirulence agent.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 3","pages":"e70371"},"PeriodicalIF":3.1,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13239241/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148141995","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}
Zbigniew Bełkot, Mateusz G Adamski, Zuzanna J Strzałkowska, Ewa D Domańska, Daria Kłosińska, Grzegorz Kunstman, Dawid Skoczek, Joanna Pławińska-Czarnak
{"title":"Full-Length 16S and 18S rRNA Long-Read Sequencing Reveals Gut Microbiome Diversity in the European Brown Hare (Lepus europaeus).","authors":"Zbigniew Bełkot, Mateusz G Adamski, Zuzanna J Strzałkowska, Ewa D Domańska, Daria Kłosińska, Grzegorz Kunstman, Dawid Skoczek, Joanna Pławińska-Czarnak","doi":"10.1111/1758-2229.70358","DOIUrl":"10.1111/1758-2229.70358","url":null,"abstract":"<p><p>The European brown hare (Lepus europaeus) is a declining wildlife species of ecological and epidemiological importance, yet its intestinal microbiome remains poorly characterized. Here, Oxford Nanopore long-read sequencing was used to analyse full-length 16S and 18S rRNA genes from pooled large-intestine contents of 30 healthy hares divided into three groups. Comparative taxonomic assignment at 95% and 80% sequence identity thresholds revealed striking differences in diversity estimates, with the lower threshold uncovering up to ten-fold more taxa. Across all samples, 40 phyla, 360 families, 1027 genera, and 3373 species were identified, including 30 taxa not previously reported in lagomorphs. These included Monoglobus pectinilyticus, Ruminococcus champanellensis, Odoribacter splanchnicus, Butyricimonas virosa, and Akkermansia muciniphila, associated with pectin degradation, cellulose hydrolysis, butyrate production, mucin degradation, bile acid transformation, and nitrogen recycling. Several taxa relevant to both animal and human health were also detected, supporting hares as sentinels of environmental microbiota within a One Health framework. These findings show that analytical parameter selection strongly shapes microbiome interpretation and provide the most comprehensive gut microbiome profile of the European brown hare to date. The study expands lagomorph microbial ecology and highlights long-read sequencing as a valuable tool for wildlife microbiome surveillance in undercharacterized host species globally.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 3","pages":"e70358"},"PeriodicalIF":3.1,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13239162/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148012727","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}
Ludmila López Arias, Juan José Herrera, Daiana Betsabé Monzón Bechara Roucos, Nadia Stefania Alvarez, Melisa Leone
{"title":"Detection of Potentially Toxic Elements and Tolerant Native Fungi Presence in an Urban Stream in Argentina.","authors":"Ludmila López Arias, Juan José Herrera, Daiana Betsabé Monzón Bechara Roucos, Nadia Stefania Alvarez, Melisa Leone","doi":"10.1111/1758-2229.70350","DOIUrl":"10.1111/1758-2229.70350","url":null,"abstract":"<p><p>Potentially toxic elements (PTEs) represent a critical threat to aquatic and terrestrial ecosystems and human health. This study assessed the presence of PTEs and the tolerance capacity of native filamentous fungi inhabiting contaminated freshwater-associated soils. Soil and water samples were collected from four sites along the urban stream (Buenos Aires, Argentina), and PTEs concentrations were quantified. Thirteen fungal isolates were obtained from contaminated soils and characterised using phenotypic traits, while molecular identification was achieved for a subset of isolates through analyses of the internal transcribed spacer (ITS) region and the translation elongation factor 1-alpha (TEF1-α) gene. Probable tolerance to manganese (Mn), zinc (Zn), copper (Cu), lead (Pb), chromium (Cr) and cadmium (Cd) was evaluated on solid media using a tolerance index (TI). All isolates exhibited tolerance to at least one of the tested PTEs. Notably, three Fusarium strains showed tolerance to Pb, with Fusarium equiseti-like IR2.1 and Purpureocillium lavendulum-like MR2.8 exhibiting high tolerance across multiple PTEs. The detection of multi-PTEs tolerance in P. lavendulum-like isolates expand previous evidence largely limited to Cd and underscores the adaptive capacity of native fungal communities in contaminated urban freshwater systems, supporting their future, more detailed evaluation for potential bioremediation applications.</p>","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 3","pages":"e70350"},"PeriodicalIF":3.1,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13240332/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147985994","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}