Environmental Microbiology Reports最新文献_第2页

Shift Towards Syndiniales Prevalence in Protist Communities During a Marine Heatwave. 海洋热浪中原生群落向Syndiniales流行的转变。

IF 3.1 4区生物学

Environmental Microbiology Reports Pub Date : 2026-10-01 DOI: 10.1111/1758-2229.70430

Hanneloor Heynderickx, Ro Allen, Tina C Summerfield, Kim Currie, Linn J Hoffmann

{"title":"Shift Towards Syndiniales Prevalence in Protist Communities During a Marine Heatwave.","authors":"Hanneloor Heynderickx, Ro Allen, Tina C Summerfield, Kim Currie, Linn J Hoffmann","doi":"10.1111/1758-2229.70430","DOIUrl":"10.1111/1758-2229.70430","url":null,"abstract":"Marine heatwaves (MHWs) are becoming more frequent and severe, yet their impact on natural marine protist communities remains poorly understood. Using 18S rRNA gene amplicon sequencing, we examined the effects of the extreme 2017/2018 Austral summer MHW on protist communities in three water masses off the southeast coast of New Zealand. During the MHW, alpha diversity declined significantly in Subtropical Waters (Shannon: 1.78 ± 0.42, p = 0.03) and the Front (Shannon: 3.26 ± 0.19, p = 0.05), driven by reduced evenness in Subtropical Waters (Pielou: 0.36 ± 0.06, p = 0.03) and by both richness and evenness in the Front. Communities also became more homogeneous, with lower dispersion among samples, and the water mass driven structuring of communities seen in non-MHW summers disappeared during the MHW. The taxonomic composition shifted substantially: the parasitic dinoflagellate Syndiniales became the most dominant group in Subtropical Waters and the Southland Front (up 68 and 30 percentage points, respectively), while Dinophyceae decreased by 47% and 20%, respectively. Since host-parasitoid interactions play a significant role in carbon and nutrient cycling, the strong increase in relative abundance of Syndiniales underscores the need to consider biotic interactions, including host-parasitoid relationships, when studying MHW impacts on marine protists.","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 5","pages":"e70430"},"PeriodicalIF":3.1,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13655307/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149164180","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

Neighbour Effects and Dynamics of Plant-Associated Microbiomes in a Strip-Crop System. 带状作物系统中植物相关微生物组的邻域效应和动态。

IF 3.1 4区生物学

Environmental Microbiology Reports Pub Date : 2026-10-01 DOI: 10.1111/1758-2229.70423

Enoch Narh Kudjordjie, Mette Vestergård, Mesfin Tsegaye Gebremikael, Otto Nielsen, Mogens Nicolaisen

{"title":"Neighbour Effects and Dynamics of Plant-Associated Microbiomes in a Strip-Crop System.","authors":"Enoch Narh Kudjordjie, Mette Vestergård, Mesfin Tsegaye Gebremikael, Otto Nielsen, Mogens Nicolaisen","doi":"10.1111/1758-2229.70423","DOIUrl":"https://doi.org/10.1111/1758-2229.70423","url":null,"abstract":"While multi-cropping systems, such as strip-cropping, assemble complex microbial communities that contribute to ecosystem resilience, we have limited understanding of their assembly and functions at field scale. Here, we examined the dynamics and site-specific assembly of soil and phyllosphere microbiomes in a rotational faba bean (Vicia faba) and spring barley (Hordeum vulgare) strip-system during two seasons. Using bacterial 16S and fungal ITS amplicon sequencing, we analysed microbial communities across gradients from the centre towards strip edges. We found that phyllosphere microbiomes are more affected by strip-cropping than soil microbiomes. Neighbouring crops harbour different microbial communities, but with increasing proximity, their phyllosphere microbiomes share more specific microbial taxa. Likewise, we observed gradient-specific microbial distribution, including fungal pathogen taxa. For instance, Puccinia was more abundant in the centre of the spring barley strips and gradually declined towards the edge. Correlation and co-occurrence network analyses revealed distinct microbial interaction patterns across soil and phyllosphere gradients. These networks were more resilient at the edge of the strips compared to central networks of spring barley. Altogether, our findings revealed neighbour-effects modulating host-associated microbiomes across strips that could be harnessed for designing optimal cropping systems, for example, to reduce leaf pathogens.","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 5","pages":"e70423"},"PeriodicalIF":3.1,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13631382/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149101701","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

Metagenomic Characterisation of Antibiotic Resistance in Anaerobic Digesters and Their Implications for Environmental Health 厌氧消化器抗生素耐药性的宏基因组特征及其对环境健康的影响。

IF 3.1 4区生物学

Environmental Microbiology Reports Pub Date : 2026-10-01 DOI: 10.1111/1758-2229.70400

Olasunbo Aina Olasupo, Oluwaseyi Paul Olaniyan, Sunday Babatunde Akinde, Ademola Ayodele Adesoye, Fatimah Adenike Ajadi, Omokaro Obire, Elijah Kolawole Oladipo, Waidi Folorunso Sule, Olamilekan Emmanuel Oyinloye, Adedolapo Aishat Salami, Emmanuel Sunday Fajoyegbe, Adejoke Janet Ajani, Olabisi Ojo

{"title":"Metagenomic Characterisation of Antibiotic Resistance in Anaerobic Digesters and Their Implications for Environmental Health","authors":"Olasunbo Aina Olasupo, Oluwaseyi Paul Olaniyan, Sunday Babatunde Akinde, Ademola Ayodele Adesoye, Fatimah Adenike Ajadi, Omokaro Obire, Elijah Kolawole Oladipo, Waidi Folorunso Sule, Olamilekan Emmanuel Oyinloye, Adedolapo Aishat Salami, Emmanuel Sunday Fajoyegbe, Adejoke Janet Ajani, Olabisi Ojo","doi":"10.1111/1758-2229.70400","DOIUrl":"10.1111/1758-2229.70400","url":null,"abstract":"Antimicrobial resistance (AMR) in environmental systems represents an emerging One Health challenge, with anaerobic digesters potentially serving as reservoirs of resistance-associated genetic features. This study analysed four publicly available anaerobic digester shotgun metagenomic datasets (M2, M3, M12 and M17) retrieved from the NCBI Sequence Read Archive to characterise microbial functions, resistance-associated annotations and antibiotic target loci. The datasets were generated using Illumina HiSeq 2000 sequencing and analysed through quality assessment, assembly, functional annotation and resistome profiling. A total of 1082 resistance-associated annotations were identified, with the highest abundance detected in M2 (348), followed by M12 (276), M17 (259) and M3 (205). Detected annotations were associated with diverse antimicrobial categories, including aminoglycosides, quinolones, beta-lactams, tetracyclines, glycopeptides, macrolides and sulfonamides. Several frequently detected loci, including rpoB, rpoC, gyrA, gyrB, EF-Tu, EF-G, Ddl and KasA, were interpreted as antibiotic target or housekeeping loci rather than confirmed acquired resistance genes. Exploratory co-abundance analysis identified strong associations among functionally linked loci, including rpoB-rpoC and gyrA-gyrB, likely reflecting shared genomic occurrence or functional relationships. These findings highlight the resistome potential of anaerobic digesters while emphasising the need for host-resolved metagenomics, mobile genetic element analysis and mutation-level characterisation to clarify environmental AMR risks.","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 5","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13628450/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149101620","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

Drivers of Soil Community Composition in Apple Orchards: Insights From Environmental Metabarcoding. 苹果园土壤群落组成的驱动因素：来自环境元条形码的见解。

IF 3.1 4区生物学

Environmental Microbiology Reports Pub Date : 2026-10-01 DOI: 10.1111/1758-2229.70422

Ulrike Obertegger, Emanuela Coller, Sara Zanoni, Roberto Zanzotti, Raffaella Morelli, Massimo Pindo, Loris Marchel, Daniele Prodorutti

{"title":"Drivers of Soil Community Composition in Apple Orchards: Insights From Environmental Metabarcoding.","authors":"Ulrike Obertegger, Emanuela Coller, Sara Zanoni, Roberto Zanzotti, Raffaella Morelli, Massimo Pindo, Loris Marchel, Daniele Prodorutti","doi":"10.1111/1758-2229.70422","DOIUrl":"https://doi.org/10.1111/1758-2229.70422","url":null,"abstract":"Soil biodiversity in apple orchards plays a vital role for productivity. We studied the biodiversity of prokaryotes, protists and fungi of 26 apple orchards belonging to the same regional growers' association in Northern-Italy by environmental DNA metabarcoding (16S, 18S, ITS). We assessed alpha- and beta-diversity, distance decay relationships, immigration rates and community assembly processes, variance partitioning between space and environment and putative prokaryotic and fungal functions from the upper 20 cm of soil during summer 2023. Despite uniform management practices, orchards showed a huge variability in alpha diversity, with single orchards having only a small part of total diversity. Protists showed the lowest mean beta-diversity, followed by prokaryotes and fungi. Although immigration rates were low across all organismal groups-reflecting the low number of taxa co-occurring across all orchards-prokaryotes and protists still displayed relatively higher rates than fungi, in support of the size-plasticity hypothesis. Community assembly was governed primarily by stochastic processes, even though deterministic processes were also important. Turnover dominated community composition for all organismal groups. Putative functions of prokaryotes pertained mainly to carbon and nitrogen cycling. Our study provided mechanistic insights into the diversity of soil organisms across different trophic levels found in apple orchards.","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 5","pages":"e70422"},"PeriodicalIF":3.1,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13635805/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149101570","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

What is in the Dust? Species-Level Profiling Reveals Pathogenic and Protective Potential of Microbial Communities in Daycare and Home Environments. 尘埃里有什么？物种水平分析揭示了日托和家庭环境中微生物群落的致病和保护潜力。

IF 3.1 4区生物学

Environmental Microbiology Reports Pub Date : 2026-10-01 DOI: 10.1111/1758-2229.70433

Jill A McKay, Richard Harding-Crooks, Vartul Sangal

{"title":"What is in the Dust? Species-Level Profiling Reveals Pathogenic and Protective Potential of Microbial Communities in Daycare and Home Environments.","authors":"Jill A McKay, Richard Harding-Crooks, Vartul Sangal","doi":"10.1111/1758-2229.70433","DOIUrl":"10.1111/1758-2229.70433","url":null,"abstract":"Indoor environments are rich in microbial diversity, which is influenced by multiple factors, including human activities, occupancy levels and the presence of pets. Environment-associated taxa were found to be prevalent in daycare and human-associated taxa in home environments during the COVID-19 pandemic, a period marked by profoundly altered social mixing and hygiene practices. In this study, we investigated the structure of microbial communities and their ecological profiles in daycare and home dust in the post-COVID-19 era. Microbial communities in household dust remain more heterogeneous, with a higher prevalence of human-associated species, than daycare samples. Full-length 16S rRNA gene sequencing enabled species-level taxonomic resolution, yet approximately 40% of amplicon sequence variants remained unclassified, underscoring the vast, novel microbial diversity within our indoor environments encountered in everyday life. AI-assisted ecological profiling revealed a higher burden of pathogens and opportunistic pathogens in home environments than in daycares. Interestingly, the presence of pets had limited influence on microbial diversity in household dust. Finally, several species with known probiotic properties and immunostimulatory potential were present in both environments, reinforcing the notion that microbial exposure during the critical window of early childhood may confer protection against various non-communicable diseases including asthma, childhood leukaemia and other cancers.","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 5","pages":"e70433"},"PeriodicalIF":3.1,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13668400/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149178294","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

Bacillus tropicus and Bacillus safensis: A Potential Siderophore Producing Rhizospheric Bacteria: Its Characterisation and Optimisation. 热带芽孢杆菌和萨福芽孢杆菌：一种潜在的产铁菌根际细菌：其特性和优化。

IF 3.1 4区生物学

Environmental Microbiology Reports Pub Date : 2026-10-01 DOI: 10.1111/1758-2229.70388

Anita Tilwari, Sanober Kalam

{"title":"Bacillus tropicus and Bacillus safensis: A Potential Siderophore Producing Rhizospheric Bacteria: Its Characterisation and Optimisation.","authors":"Anita Tilwari, Sanober Kalam","doi":"10.1111/1758-2229.70388","DOIUrl":"10.1111/1758-2229.70388","url":null,"abstract":"Siderophore-Producing Rhizobacteria (SPR) have emerged as a viable approach to plant protection and crop health management in agriculture. It brings iron molecules into bacterial cells for use in a variety of metabolic processes, with applications in agriculture, medicine, industry, and the environment. In this study, 22 bacteria were isolated and screened for siderophore production from maize field soil. Seven of the 22 bacterial isolates showed discrete zones of orange colour, indicating siderophore production. However, only two potent siderophore-producing strains, Bacillus safensis (BMS-01) and Bacillus tropicus (BMS-15), were optimised and identified using physiological characteristics and 16S rDNA sequencing. After optimising siderophore production with glucose and sucrose as carbon sources and NaNO3 and (NH4)2NO3 as nitrogen sources, Bacillus safensis (BMS-01) and Bacillus tropicus (BMS-15) were found to have a significant ability to yield siderophore (60%-70% units) under ideal conditions of pH 8, 28°C. The study concludes that the strains Bacillus safensis and Bacillus tropicus show potential for siderophore production, which may warrant further investigation as biocontrol agents and plant growth promoters in future field trials.","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 5","pages":"e70388"},"PeriodicalIF":3.1,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13675655/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149206395","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

Volatile Emissions From Diverse Estuarine Bacteria Share Core Compounds With a Subset of Strain-Specific, Low Abundance Compounds. 来自不同河口细菌的挥发性排放物与一组菌株特异性低丰度化合物共享核心化合物。

IF 3.1 4区生物学

Environmental Microbiology Reports Pub Date : 2026-10-01 DOI: 10.1111/1758-2229.70439

Eve Galen, Kajsa Roslund, Riikka Rinnan, Lasse Riemann

{"title":"Volatile Emissions From Diverse Estuarine Bacteria Share Core Compounds With a Subset of Strain-Specific, Low Abundance Compounds.","authors":"Eve Galen, Kajsa Roslund, Riikka Rinnan, Lasse Riemann","doi":"10.1111/1758-2229.70439","DOIUrl":"10.1111/1758-2229.70439","url":null,"abstract":"Biogenic volatile organic compounds (BVOCs) are gases that influence atmospheric chemistry, nutrient cycling and species interactions, yet the contribution of heterotrophic marine bacteria to marine BVOC emissions remains poorly constrained. In addition, the extent to which the volatilome is linked to bacterial phylogeny is unknown. Here, we characterize the volatilome of 16 heterotrophic bacterial strains isolated from Baltic Sea surface water, spanning Alphaproteobacteria, Gammaproteobacteria, Betaproteobacteria, Bacteroidota and Actinomycetes. Headspace BVOCs were quantified under standardized growth conditions using Proton Transfer Reaction Time-of-Flight Mass Spectrometry (PTR-TOF-MS). A broadly overlapping bacterial volatilome was identified, with compound composition and proportional abundance similar across many strains, irrespective of phylogeny. Namely, most strains shared a set of core compounds with a subset of strain-specific, low abundance compounds. Acetone accounted for more than 50% of the emissions in most volatilomes. The remaining fraction of emissions was primarily comprised of other low-molecular-weight oxygenated compounds. Interestingly, two strains demonstrated strain-specific emission patterns, significantly diverging from the group in their emission rate and compound composition. Together, these findings suggest that marine heterotrophic bacteria may contribute a broadly conserved collection of BVOCs to the ocean-atmosphere interface, highlighting their role as a widespread source of trace gases in marine ecosystems.","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 5","pages":"e70439"},"PeriodicalIF":3.1,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13677163/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149219788","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

Inferring Adaptation at Community Composition Level From the Relationship Between Succession Rate and Global Change Intensity 从演替速率与全球变化强度的关系推断群落组成水平上的适应。

IF 3.1 4区生物学

Environmental Microbiology Reports Pub Date : 2026-09-30 DOI: 10.1111/1758-2229.70426

Tingting Li, Rong Mao, Yang Zhang, Ximei Zhang

{"title":"Inferring Adaptation at Community Composition Level From the Relationship Between Succession Rate and Global Change Intensity","authors":"Tingting Li, Rong Mao, Yang Zhang, Ximei Zhang","doi":"10.1111/1758-2229.70426","DOIUrl":"10.1111/1758-2229.70426","url":null,"abstract":"In response to anthropogenic environmental changes, biological communities often undergo compositional changes, which are traditionally thought to represent adaptation. However, this hypothesis and its mechanism remain surprisingly underexplored. In this study, we conducted a 10-year nitrogen deposition experiment in the Eurasian steppe, manipulating nine intensities under two management strategies (fencing or mowing). As the intensity increased from 0–20 to 50 g N m−2 yr−1, the succession rates of both plant and soil microbial communities first increased but then decreased, implying that high intensities of N deposition exceed the capacity of community adaptation. In addition, both the succession rate of the deterministic component of community compositional variation and the succession rate of soil physicochemical characteristics increased and then decreased with increasing N intensity. They were positively correlated, demonstrating that adaptation is primarily driven by deterministic ecological processes. Meanwhile, mowing promoted the plant community's adaptation, while fencing promoted adaptation of the microbial community, both by restraining stochastic processes. Overall, to enable biological communities to adapt compositionally to environmental changes, we should aim to limit the intensity of changes below certain thresholds, and implement reasonable strategies, whether deterministic (e.g., restoring soil physicochemical conditions) or stochastic (e.g., adding seeds of adaptive species).","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 5","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13626865/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149101642","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

Effects of Antibiotic and Temperature Treatments on Phycosphere Bacterial Communities of Kelp Gametophytes 抗生素和温度处理对海带配子体藻球细菌群落的影响。

IF 3.1 4区生物学

Environmental Microbiology Reports Pub Date : 2026-09-30 DOI: 10.1111/1758-2229.70425

Yuewen Zhang, Shanshan Liang, Huiling Xia, Xiaoyu Zhong, Yi Zheng

{"title":"Effects of Antibiotic and Temperature Treatments on Phycosphere Bacterial Communities of Kelp Gametophytes","authors":"Yuewen Zhang, Shanshan Liang, Huiling Xia, Xiaoyu Zhong, Yi Zheng","doi":"10.1111/1758-2229.70425","DOIUrl":"10.1111/1758-2229.70425","url":null,"abstract":"Microbiome dysbiosis represents a critical bottleneck in sustainable kelp aquaculture, yet the distinct regulatory mechanisms of antibiotics and temperature remain poorly characterized. This study systematically elucidates the divergent effects of penicillin–streptomycin exposure and temperature gradients on Saccharina japonica gametophytes and their epiphytic microbiota. Antibiotic treatment significantly reduced Proteobacteria from 93.02% to 49.70% and increased Bacteroidetes from 6.98% to 49.20%, replacing beneficial Sulfitobacter and Colwellia with opportunistic Kordia and Klebsiella, indicating severe dysbiosis driven by the creation of unoccupied ecological niches. In contrast, temperature variation did not alter dominant phyla: Proteobacteria remained predominant, but Vibrio peaked at 15°C (44.11%) alongside the maximal gametophyte specific growth rate of 5.21% per day, concurrently elevating pathogenic loads of Vibrio and Pseudomonas. These findings reveal that antibiotics disrupt core community architecture, whereas temperature modulates metabolic rates within stable taxonomic frameworks. Consequently, we propose a stratified preservation strategy: short-term seedling cultivation at 15°C requires stringent antimicrobial measures to mitigate disease risk, while lower temperatures are preferable for long-term germplasm storage to minimize contamination potential. This framework provides essential insights for precision microbial management, balancing growth promotion with disease control in kelp aquaculture systems.","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 5","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13625041/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149079060","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

Diagnosing Anaerobic Digesters' Function and Performance: From Meta-Omics to Integrated Meta-Omics Analyses 诊断厌氧消化器的功能和性能：从元组学到综合元组学分析。

IF 3.1 4区生物学

Environmental Microbiology Reports Pub Date : 2026-09-24 DOI: 10.1111/1758-2229.70417

Kevin Iyere Ehiosun, Olivier Chapleur, Laurent Mazéas

{"title":"Diagnosing Anaerobic Digesters' Function and Performance: From Meta-Omics to Integrated Meta-Omics Analyses","authors":"Kevin Iyere Ehiosun, Olivier Chapleur, Laurent Mazéas","doi":"10.1111/1758-2229.70417","DOIUrl":"10.1111/1758-2229.70417","url":null,"abstract":"Anaerobic digestion (AD) of organic wastes by microorganisms into biomethane contributes significantly towards bioenergy generation. However, the bioprocess remains challenging due to its complex microbial ecology, dynamic biochemical pathways and sensitivity to perturbations. Over the past decade, using meta-omics like metataxonomics, metagenomics, metatranscriptomics, metaproteomics and metabolomics to diagnose its functioning has become necessary and common. However, a single meta-omics method can only provide limited biological understanding of the bioprocess. This led to the use of multi-meta-omics analyses in tandem; however, most studies still examine and interpret each meta-omics separately, limiting their ability to uncover functional interactions across molecular levels. Currently, the frontier is integrated meta-omics, where multi-meta-omics and process data are systematically combined into a single and interpretable system to unlock mechanistic understanding, diagnostic and predictive control of AD. This review critically examines specific application of meta-omics in AD, discussing their strengths, limitations and distinct position in integrated meta-omics approach. Importantly, it explores the computational frameworks, methodologies and challenges of integrated meta-omics. Discovering diagnostic biomarkers with high predictive power and transferability across AD systems through cross-omics validation is highlighted. As workflows standardise and technologies mature, integrated meta-omics would significantly contribute to the advancement of AD bioprocess for bioenergy.","PeriodicalId":163,"journal":{"name":"Environmental Microbiology Reports","volume":"18 5","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1758-2229.70417","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149029510","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