Environmental Microbiome最新文献

{"title":"The composition and function succession of lignocellulose-degrading microbial consortia drives in situ decomposition of rice straw in paddy fields.","authors":"Binhan Zhao, Wenjun Dong, Yang Yu, Xin Zhao, Zhanjun Cai, Haoyue Zhang, Shaojie Li, Xianyun Sun","doi":"10.1186/s40793-026-00888-6","DOIUrl":"10.1186/s40793-026-00888-6","url":null,"abstract":"<p><strong>Background: </strong>Straw incorporation into soil can increase soil organic matter content and improve soil structure. However, the in situ decomposition mechanisms of straw in field remain unclear.</p><p><strong>Results: </strong>The decomposition mechanisms of straw in paddy fields within the black soil region of Northeast China were investigated by analyzing the composition and functional succession of lignocellulose-degrading microbial consortia (LDMC). Straw decomposition predominantly occurred from May to September, coinciding with warmer temperatures. The alternating paddy-upland field patterns and temperature fluctuations significantly influenced soil microbial community diversity and function, thereby impacting straw decomposition. Through literature analysis, microbial isolation, and enzymatic activity assays, LDMC comprising 18 bacterial genera and 41 fungal genera were proposed. A comprehensive analysis of the dynamics of straw decomposition rates, microbial composition succession, enzymatic profiles, and the abundance of corresponding enzyme genes in soil revealed unique functional succession patterns of LDMC. During the paddy field phase (May-August), Pseudarthrobacter, Bacillus, Nocardioides, Tausonia, Mortierella, Pseudeurotium, etc. were the dominant microbial taxa driving straw decomposition. Tausonia, Mortierella and Pseudeurotium primarily contributed to cellulose degradation, while Bacillus and Nocardioides were involved in the breakdown of both cellulose and hemicellulose. In contrast, Pseudarthrobacter played a major role in lignin degradation. This phase was characterized by a high abundance of cellulase and hemicellulase genes, indicating that decomposition primarily targets these components. During the upland field phase in September, Bacillus, Bradyrhizobium, Mortierella, Mrakia, Pseudeurotium, etc. were the predominant decomposers. Mortierella and Mrakia contributed to the degradation of straw lignocellulose, while Bacillus and Pseudeurotium played a key role in the degradation of cellulose and hemicellulose. In contrast, Bradyrhizobium was predominantly involved in lignin degradation. This phase exhibited a higher abundance of ligninase genes, suggesting a shift towards lignin degradation as the dominant process.</p><p><strong>Conclusions: </strong>These findings provide novel insights into the ecological succession and functional roles of LDMC in rice straw decomposition. They offer a theoretical basis for identifying key lignocellulose-degrading microorganisms active at different phases, thereby laying a foundation for improving the efficiency of rice straw return to fields.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13188402/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147634760","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unraveling plasmid contributions to phosphorus acquisition in soil microbiomes.","authors":"Pablo Bruna, Patricio Javier Barra, Matías García, Ivan Liachko, María de la Luz Mora, Bas E Dutilh, Michel Abanto","doi":"10.1186/s40793-026-00887-7","DOIUrl":"10.1186/s40793-026-00887-7","url":null,"abstract":"<p><strong>Background: </strong>Phosphorus (P) is a fundamental macronutrient for plant and microbial growth, but its availability in soils is often constrained by strong interactions with minerals and organic matter. While the role of bacteriophages in P cycling has gained attention, plasmids remain comparatively underexplored despite their central role in horizontal gene transfer. This study aimed to investigate the occurrence, diversity, and ecological relevance of plasmid-borne genes involved in P acquisition across soils with contrasting P availability.</p><p><strong>Results: </strong>Using curated plasmid databases and soil metagenomes from diverse biomes, we identified a broad repertoire of plasmid-encoded P-acquisition genes. These genes encompassed regulatory pathways, transport systems, organic P mineralization, and inorganic P solubilization. Regulatory and transporter genes were the most abundant categories, with phoB, phoP, and ugpC among the most frequently detected. When additional analyses were performed using habitat-specific P classifications and continuous P gradients, these associations appeared weak and were not significant after multiple-testing correction. These results suggest that plasmid-encoded P-acquisition genes are broadly distributed across environments rather than tightly constrained by measured soil P levels, while taxonomic assignment revealed that Pseudomonadota were the predominant plasmid hosts, followed by Bacillota and Actinobacteriota, suggesting broad host diversity.</p><p><strong>Conclusions: </strong>This study provides a genomic overview of plasmid-borne genes associated with P acquisition in soils. Our results show that these genes are widespread across plasmids from diverse environments and host taxa, suggesting that the soil mobilome may represent an important reservoir of functions related to microbial P metabolism. While the presence and relative abundance of these genes indicate their potential ecological relevance, functional expression and ecological impact remain to be experimentally validated. These findings expand current knowledge of plasmid contributions to nutrient cycling and highlight the mobilome as a potential target for future studies aiming to better understand microbial strategies for P acquisition in soil ecosystems.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13188316/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147628797","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial functional traits in the hyperaccumulating Noccaea praecox rhizobiome are metal-dependent and host-driven.","authors":"Valentina Bočaj, Paula Pongrac, Matevž Likar","doi":"10.1186/s40793-026-00890-y","DOIUrl":"10.1186/s40793-026-00890-y","url":null,"abstract":"<p><strong>Background: </strong>Noccaea praecox is a zinc (Zn), cadmium (Cd), and lead (Pb) hyperaccumulating plant native to the Italian peninsula and Western Balkans, where it occurs naturally in both metalliferous and non-metalliferous soils. In the present study, we investigated the effects of soil metal concentrations and the plant host on microbial functional traits, specifically the resistome (i.e., microbial functions associated with metal tolerance and resistance) in two soil compartments: the roots and rhizosphere of N. praecox. For this, we collected four plants from each metalliferous and non-metalliferous site and used a metagenomic sequencing approach to characterise microbial functions from paired root and rhizosphere samples, with three root samples per site obtained due to limited biomass, and four rhizosphere samples.</p><p><strong>Results: </strong>The compartment was the primary driver of the general microbial functional structure. By contrast, the soil metal concentrations and root compartment significantly shaped the microbial resistome. Functions associated with the cobalt-zinc-cadmium efflux system and copper-transporting P-type ATPase V were significantly enriched at the metalliferous compared to the non-metalliferous site, with log₂ fold change being 2.62 and 1.72, respectively. Transporters associated with manganese/iron and cobalt/nickel were shaped by the host, regardless of soil metal levels, consistent with host-mediated filtering of microbial functions. Notably, several Zn transporter-related microbial functions associated with the ZIP family were more abundant in the rhizosphere, potentially supporting the plant's high Zn demand.</p><p><strong>Conclusion: </strong>Overall, our results demonstrate that both environmental conditions and plant host play interactive roles in shaping the microbial functional potential, with the host sometimes exerting a stronger influence than soil metal content. The enrichment of Zn transporters (Zrt-/Irt-like proteins) in the rhizosphere of the Zn-hyperaccumulating N. praecox suggests a specific microbial adaptation that may facilitate Zn uptake. These findings provide new insight into the functional dynamics of plant-microbe interactions that support the N. praecox lifestyle.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13188454/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147624512","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prosystemin-derived signals: bridging leaf microbiome dynamics and defense activation.","authors":"Valeria Castaldi, Wisnu Adi Wicaksono, Martina Chiara Criscuolo, Liberata Gualtieri, Emma Langella, Ilaria Di Lelio, Simona Maria Monti, Francesca De Filippis, Gabriele Berg, Rosa Rao","doi":"10.1186/s40793-026-00885-9","DOIUrl":"10.1186/s40793-026-00885-9","url":null,"abstract":"<p><strong>Background: </strong>Plant-derived peptides can act as resistance inducers and represent promising tools for sustainable crop protection. Despite growing interest and application, their broader effects on plant-associated microbiomes remain insufficiently characterized. Here, we investigated the impact of an immunomodulatory peptide derived from the tomato defense protein Prosystemin on the tomato phyllosphere microbiome and leaf volatilome.</p><p><strong>Results: </strong>The peptide was applied as a foliar spray at biweekly intervals from planting to two months post-germination to approximate common agricultural practices. Shotgun metagenomic sequencing combined with qPCR revealed abundant bacterial communities (up to 4.6 log₁₀ bacterial 16S rRNA gene copies) dominated by Actino-, Alphaproteo- and Gammaproteobacteria across all samples. Peptide treatment was associated with a significant shift in community structure, characterized by reduced alpha diversity and increased microbial associations. Several genera, including Acinetobacter, Sphingobium, Sphingomonas, Brevundimonas, and Massilia, increased in relative abundance following treatment. Functional profiling indicated rearrangements in gene categories related to stress response and metabolic adaptation. Notably, volatilome analysis further revealed elevated monoterpene emissions in peptide treated plants, consistent with activation of defense-associated metabolism. Members of the Sphingomonadaceae family, particularly Sphingobium yanoikuyae, appear well suited to persist under peptide-associated conditions and may therefore contribute to the observed community restructuring, although causal mechanisms remain to be tested.</p><p><strong>Conclusion: </strong>Beyond its established role in protecting tomato against pests and necrotrophic fungi, the Prosystemin-derived peptide provides an opportunity to investigate peptide-triggered plant responses and their interactions with the plant microbiota.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13188736/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147619178","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of heat-assisted sample desiccation on microbiome surveys.","authors":"Claire E Mullin, Stilianos Louca","doi":"10.1186/s40793-026-00889-5","DOIUrl":"10.1186/s40793-026-00889-5","url":null,"abstract":"<p><p>Sample preservation remains a challenge in microbiome surveys, particularly in remote areas. Drying samples eliminates the need for cold chains and preservatives, but sophisticated desiccation tools such as lyophilization are impractical in the field. Further, the effects of sample drying on modern analyses, such as gene-centric metagenomics and metagenome-assembled genome (MAG) recovery, remain poorly understood. Here we explore heat-assisted sample desiccation followed by storage at room temperature as a cost-effective and practical solution in the field. We assess its effects relative to freezing on typical metagenomic and 16 S rRNA amplicon sequence analyses of bacterial and archaeal communities, using 60 samples from 6 different source materials (soils from 3 locations, feces from 3 animals). We consider multiple metrics related to the success of DNA extraction, sequencing, contig assembly, OTU clustering, gene annotation and MAG recovery, as well as impacts on inferred microbial community composition. We find that, while desiccation had a significant negative impact on multiple metrics related to DNA extraction success, its impacts on downstream metrics such as OTU richness, Shannon diversity, gene annotation and MAG recovery were more nuanced and often insignificant. Further, while the preservation method had a significant influence on the inferred microbial community composition, samples from different source materials (e.g., soils from different locations, or feces from different individuals) remained clearly distinguishable. We conclude that heat-assisted desiccation can be a viable sample preservation method for microbiome studies, when a high consistency with frozen samples is not a requirement.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13188285/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147624483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phytoplankton community dynamics and their role in naphthenic acid transformation within a constructed wetland system treating oil sands process-affected water.","authors":"Dilini M Atugala, Lisa M Gieg","doi":"10.1186/s40793-026-00876-w","DOIUrl":"10.1186/s40793-026-00876-w","url":null,"abstract":"<p><p>Bitumen extraction from oil sands surface mining in northern Alberta generates vast amounts of oil sands process-affected water (OSPW) containing naphthenic acid fraction compounds (NAFCs) that require treatment due to their persistence and toxicity. The use of constructed wetland treatment systems (CWTS) is a promising strategy for reducing NAFC concentrations in OSPW. Photosynthetic microalgae and cyanobacteria are present in CWTS, yet their contributions to this ecosystem and NAFC degradation remain understudied. We investigated the temporal dynamics of phytoplankton communities within a pilot CWTS treating OSPW to characterize these organisms and their potential contributions to NAFC transformation. Phytoplankton taxa identified were comparable to those found in natural boreal lakes, including Chlorophyta, Cryptophyta, and photosynthetic Stramenopiles/marine algae (e.g., Chrysophyceae, Xanthophyceae, and Eustigmatophyceae) and Cyanobacteria. Water chemistry, particularly pH, calcium, magnesium, sodium, temperature, electrical conductivity, and NAFC concentrations, played a key role in shaping phytoplankton communities. While magnesium and calcium supported long-term algal growth and resilience, NAFC concentrations strongly influenced early-stage community composition. As NAFC concentrations declined over time, their direct impact lessened, highlighting phytoplankton adaptability to shifting environmental conditions. Over the operational season, NAFC concentrations in the CWTS decreased by approximately 35%, accompanied by a shift in NAFC class distribution. The toxic O2 class declined, while higher-oxygenated, less toxic classes (O3, O4, O5, O6) increased, suggesting microbial and algal-mediated transformation. Several algal genera exhibited significant correlations with heteroatom composition at different time points, with Ankistrodesmus, Scotinosphaera, and Chloroidium significantly associated with NAFC biodegradation products at the end of the CWTS operating season. These findings suggest that phytoplankton may contribute to NAFC transformation, supporting their contribution to degradation of OSPW components in constructed wetlands.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13181954/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147619273","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Generalist phyllosphere taxa dominate microbial communities on macrophytes across a natural salinity gradient.","authors":"Daniel P R Herlemann, David J Riedinger, Victor Fenández-Juárez, Luis F Delgado, Anders F Andersson, Christian Pansch, Lasse Riemann, Mia M Bengtsson, Greta Gyraite, Thorsten B H Reusch, Marija Katarzyte, Sandra Kube, Georg Martin, Marcin Rakowski, Matthias Labrenz","doi":"10.1186/s40793-026-00881-z","DOIUrl":"10.1186/s40793-026-00881-z","url":null,"abstract":"<p><strong>Background: </strong>Shallow coastal habitats are characterized by diverse macrophytes and often feature steep abiotic gradients, including salinity variations, which can shape the leaf- surface epi-microbiome (phyllosphere). To elucidate the effect of salinity and host identity on the phyllosphere of aquatic macrophytes in shallow water, we sampled the leaf surface microbiota across a salinity range of 6-15. Samples included the eelgrass Zostera marina, as well as the Eurasian water milfoil (Myriophyllum spicatum), muskgrass (Chara spp.), and sago pondweed (Stuckenia pectinata) in the brackish Baltic Sea during the summer of 2022. Microbial communities were characterized using 16S and 18S rRNA gene amplicon sequencing.</p><p><strong>Result: </strong>As hypothesized, the phyllosphere bacterial and protist community composition was distinct from the surrounding seawater microbiome. Typically associated taxa included the genera Loktanella, Pseudorhodobacter, the methylotrophic genus Methylotenera, unclassified Synechococcales, and Rhodobacteriaceae. Protist genera such as Picochlorum were consistently detected across all macrophyte hosts, while Cocconeis, Cyclotella, Mondous and unclassified Bacillariophyceae were present in all phyllospheres except Chara spp. Both, salinity and host species significantly influenced the composition and prevalence of the microbiota, primarily through shifts in the abundance of typical phyllosphere taxa. However, only 4-11% of phyllosphere taxa were uniquely associated with a specific salinity or macrophyte host.</p><p><strong>Conclusions: </strong>Our results demonstrate that aquatic macrophytes harbor a distinct and characteristic phyllosphere microbiome. The low proportion of host- or salinity specific taxa suggests that the most abundant members of this community are generalists, broadly adapted to the phyllosphere niche rather than being narrowly specialized. This implies that the presence of the macrophyte itself, providing a stable, nutrient-rich surface, exerts a stronger deterministic influence on the microbial community than the host identity or salinity fluctuations. Consequently, the phyllosphere appears relatively resilient to environmental variability, particularly salinity fluctuations. This highlights the robust nature of host-microbiome interactions and their importance for conservation of aquatic macrophyte ecosystems.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13067490/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147619238","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Associations between phloem microbiota and metabolomes in three North American ash species (Fraxinus spp.) susceptible to emerald ash borer (Agrilus planipennis).","authors":"Judith Mogouong Tambue, Claire Yager, Kathryn E Bushley","doi":"10.1186/s40793-026-00884-w","DOIUrl":"10.1186/s40793-026-00884-w","url":null,"abstract":"<p><strong>Background: </strong>Microorganisms play crucial roles in the survival and fitness of their plant and insects hosts, including invasive species. The emerald ash borer (Agrilus planipennis, Fairmaire; EAB) is an invasive insect from Asia. It represents a significant threat to North American forest ecosystems, causing widespread mortality in susceptible native ash (Fraxinus) species. While previous studies have shown differences in specific plant defense metabolites between susceptible North American ash species and their more resistant Asian counterparts, widely targeted metabolite profiles and their interactions with phloem microbiota in response to EAB infestation has thus far received little attention. This study aimed to profile microbial communities associated with ash phloem and EAB larval guts and their relationship to ash phloem metabolites in three native susceptible North American ash species: F. pennsylvanica (green ash), F. nigra (black ash) and F. americana (white ash).</p><p><strong>Results: </strong>Using metabarcoding to characterize the microbial communities associated with the larval gut and host tree phloem and widely targeted metabolomics to establish the first global metabolomic profile of phloem in these ash species, we examined interspecies differences in profiles and associations of ash phloem microbiota and metabolites in relation to EAB infestation. Multivariate analysis revealed that fungal communities were distinct in all ash species, while F. pennsylvanica (green ash) harbored bacterial communities distinct from black ash. Only black ash showed a phloem profile significantly associated with EAB attack symptoms and had the largest number of differentially abundant bacterial taxa. In contrast, larval gut bacterial communities from green ash were distinct from those in other ash species. Green ash displayed a distinct global metabolite profile from the other two species and had the highest number of differentially regulated metabolites, while black ash had the least. Green and white ash shared a strong upregulation of terpenoid compounds, several of which were among compounds significantly associated with microbial communities in green ash phloem or the EAB larval gut.</p><p><strong>Conclusions: </strong>Our results provide the first comparative analysis of phloem-associated microbial communities and metabolomes across three susceptible North American ash species and their response to EAB. We found that microbiota and metabolites in green ash showed a distinct response to EAB infestation from the other ash species and we identified specific metabolites exhibiting significant correlations with microbial communities in ash phloem or the EAB larval gut. These findings contribute novel insights into interspecies variability in host-associated microbial communities and metabolomes and their response to an invasive insect.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13169598/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147595581","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phenotypic resistance profiles and resistome variations between endophytic and epiphytic bacteria in apple fruits.","authors":"Denis Kiplimo, Ana María Sánchez, Dinesh Kumar Ramakrishnan, Wisnu Adi Wicaksono, Romano Mwirichia, Neus Teixidó, Gabriele Berg, Ahmed Abdelfattah","doi":"10.1186/s40793-026-00880-0","DOIUrl":"10.1186/s40793-026-00880-0","url":null,"abstract":"<p><strong>Background: </strong>In recent years, there has been increasing concerns about antibiotic resistance. Although studies have investigated resistance in food-associated bacteria, fresh produce microbes remain underexplored as potential hub of resistance genes capable for horizontal transfer to human via consumption. To this end, we tested the antibiotic resistance profiles of bacterial isolates recovered from Golden Reinders and Mandy apple cultivars. We aimed to investigate the effects of orchard-cultivar combinations and microbial lifestyle on the antibiotic resistance profiles. The apples (Golden Reinders and Mandy) were sampled from four separate orchards (EEL-Lleida, Esterri, Fruits-de-Ponent and Gotarta) in Spain. We used combination of culture-dependent and whole genome sequencing approaches to analyse the antibiotic resistance profiles.</p><p><strong>Results: </strong>A total of 516 bacterial isolates were screened for susceptibility against seven different classes of antibiotics. Results showed that 272 isolates were resistant to at least one antibiotic. From those, 203 were epiphytes and 95 classified as endophytes (isolated from surface-sterilized apple peels), whereas 26 isolates were shared between the groups. The resistance profiles varied across the antibiotics, with over 50% of the isolates exhibiting resistance to tetracycline, quinolones and cephalosporins. In contrast, none of the isolates showed resistance to imipenem. Whole genome sequencing (WGS) was performed on 18 isolates, however, only 10 genomes passed quality-control thresholds and were included in subsequent resistome analyses. We found ARGs encoding resistance to 14 main antibiotic classes, with the majority of the confirmed resistances attributed to multidrug resistance (MDR). Only few target-specific ARGs were annotated, including (Rif)iri (rifampicin), lnu(A) (lincomycin) and FosD (Fosfomycin). Pantoea agglomerans possessed higher number of ARGs, while Staphylococcus arlettae exhibited notable prevalence of plasmid-encoded ARGs.</p><p><strong>Conclusion: </strong>Overall, the study highlights the prevalence of antibiotic resistance in apple microbiomes. The presence of multidrug-resistance (MDR) genes further underscores the persistent threat of 'antibiotic resistance', underlining the necessity for deeper insight into antibiotic resistance within food chain.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13063563/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147595636","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rare taxa enhance microbial network complexity and drive nitrification and denitrification processes in river ecosystems.","authors":"Xiaoliang Jiang, Xiang Xiong, Miaomiao Cai, Gang He, Quanfa Zhang, Wenzhi Liu","doi":"10.1186/s40793-026-00879-7","DOIUrl":"10.1186/s40793-026-00879-7","url":null,"abstract":"<p><strong>Background: </strong>Microbial communities, which drive most ecological processes and functions, contain not only a few highly abundant species but also a large number of rare species. However, little is known about the relative importance of abundant and rare microorganisms to network complexity and biogeochemical cycling, especially at large spatial scales. Here, we investigated nitrifying and denitrifying communities using high-throughput sequencing of archaeal amoA and bacterial amoA, nirK, and nirS genes, and we determined nitrification and denitrification rates in channel sediments, riparian rhizosphere soils, and riparian bulk soils of 30 rivers across China.</p><p><strong>Results: </strong>Rare nitrifiers and denitrifiers exhibited broader environmental thresholds than abundant taxa. Co-occurrence network analysis revealed that all topological features (e.g., node degree and eigenvector centrality) had higher values for rare taxa than for abundant taxa. In addition, major modules (i.e., clusters of closely interconnected microbes) in the network were mainly composed of rare taxa, indicating that rare taxa play a vital role in maintaining the network complexity of nitrifying and denitrifying communities. Random forest analysis showed that nitrification rates were significantly associated only with the β-diversity of rare bacterial nitrifiers. Denitrification rates were largely influenced by the β-diversity of both rare and abundant nirK-type denitrifiers. These results suggested that rare microbial taxa play an important but previously underestimated role in biogeochemical processes.</p><p><strong>Conclusions: </strong>Overall, this study highlights that, compared with abundant taxa, rare taxa contribute more to microbial network complexity and nitrogen cycling processes in river ecosystems at the continental scale.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13151270/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147533550","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}