Frontiers in Microbiology最新文献

{"title":"Evolution and transmission landscape of the staphylococcal <i>msrA</i> gene mediating resistance to 14-membered macrolides and type B streptogramins.","authors":"Davit Janelidze, Saba Kobakhidze, Tinatin Elbakidze, Mamuka Kotetishvili","doi":"10.3389/fmicb.2026.1815688","DOIUrl":"https://doi.org/10.3389/fmicb.2026.1815688","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Introduction: &lt;/strong&gt;&lt;i&gt;Staphylococcus&lt;/i&gt; species, particularly &lt;i&gt;Staphylococcus aureus&lt;/i&gt;, are leading opportunistic pathogens responsible for a wide range of infections, with antimicrobial resistance-including high rates of macrolide resistance-severely limiting treatment options. The &lt;i&gt;msrA&lt;/i&gt; gene encodes the ABC-F protein MsrA, which mediates inducible resistance to 14-membered macrolides and type B streptogramins. Despite its clinical and epidemiological relevance, the evolutionary forces, selective pressures, and transmission routes shaping &lt;i&gt;msrA&lt;/i&gt; in staphylococci remain insufficiently understood.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods: &lt;/strong&gt;Six hundred and one complete staphylococcal &lt;i&gt;msrA&lt;/i&gt; coding sequences (CDSs) were retrieved from GenBank. Evolutionary analyses of &lt;i&gt;msrA&lt;/i&gt; included nucleotide diversity (&lt;i&gt;π&lt;/i&gt;), selection metrics (&lt;i&gt;d&lt;sub&gt;N&lt;/sub&gt;-d&lt;sub&gt;S&lt;/sub&gt;&lt;/i&gt; , π&lt;sub&gt;a&lt;/sub&gt;/π&lt;sub&gt;s&lt;/sub&gt;, Tajima's D, Fu's Fs, FUBAR, MEME, and aBSREL), and conservation mapping using DnaSP in relation to MsrA functional domains (UniProt P23212). Linkage disequilibrium (LD) was assessed using ZnS, Za, ZZ, and Wall's statistics. Recombination and transmission pathways were inferred using GARD, RDP4-embedded algorithms, SplitsTree network analysis, and the PHI test.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;Forty-one &lt;i&gt;msrA&lt;/i&gt; allelic variants were determined, with five predominant alleles accounting for approximately 90% of CDSs; allele 19 was almost exclusive to &lt;i&gt;S. aureus&lt;/i&gt;. Nucleotide diversity was moderate (&lt;i&gt;π&lt;/i&gt; ≈ 0.039-0.042), and strong purifying selection predominated (π&lt;sub&gt;a&lt;/sub&gt;/π&lt;sub&gt;s&lt;/sub&gt; ≈ 0.169; &lt;i&gt;d&lt;sub&gt;N&lt;/sub&gt;-d&lt;sub&gt;S&lt;/sub&gt;&lt;/i&gt;  = -0.138 ± 0.016; strongly negative Fu's Fs), with only four codons showing evidence of episodic positive selection. Three highly conserved regions were identified, mainly overlapping the inter-domain linker and the second nucleotide-binding domain across MsrA. Moderate-to-high LD with minimal decay indicated the persistence of only a limited number of successful allelic variants. Predominant &lt;i&gt;msrA&lt;/i&gt; alleles were largely plasmid-associated. Recombination analyses revealed frequent interspecies transfer within &lt;i&gt;Staphylococcus&lt;/i&gt;, with &lt;i&gt;S. aureus&lt;/i&gt; acting as a central donor to &lt;i&gt;Staphylococcus chromogenes&lt;/i&gt; and &lt;i&gt;Staphylococcus saprophyticus&lt;/i&gt;, as well as rare intergeneric transfers involving &lt;i&gt;Citrobacter&lt;/i&gt;, &lt;i&gt;Enterococcus&lt;/i&gt;, &lt;i&gt;Corynebacterium&lt;/i&gt;, and &lt;i&gt;Pseudomonas&lt;/i&gt;.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusion: &lt;/strong&gt;These findings support a dual evolutionary strategy for &lt;i&gt;msrA&lt;/i&gt;: strong purifying selection preserves its essential ribosomal-protection function, while plasmid-mediated dissemination promotes the spread of fit alleles. &lt;i&gt;S. aureus&lt;/i&gt; appears to be a key reservoir and vector, facilitating both interspecies and intergeneric transmission. Clinically, this underscores the need for surveillance of plasmid-borne &lt;i&gt;msrA&lt;/i&gt; and targeted control of &lt;i&gt;S. aureus&lt;","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"17 ","pages":"1815688"},"PeriodicalIF":4.0,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13144154/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147835954","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Acute high-intensity exercise alters gut microbiota composition and energy metabolism in different strains of mice.","authors":"Ruolin Gao, Jie Wang, Jiajia Song, Wenlong Zhang, Lei Quan","doi":"10.3389/fmicb.2026.1790697","DOIUrl":"https://doi.org/10.3389/fmicb.2026.1790697","url":null,"abstract":"<p><strong>Introduction: </strong>The gut microbiota is a critical modulator of host energy metabolism and immune regulation. Although exercise modulates microbial composition, the temporal dynamics and strain-specific impact of acute high-intensity exercise remains unclear.</p><p><strong>Methods: </strong>This study investigated dynamic alterations in gut microbiota following acute high-intensity exercise in BALB/c and C57BL/6 mice, focusing on energy and gut health-related genera. Age-matched male mice underwent a 30-min high-intensity treadmill run. To capture temporal dynamics, colonic content samples were collected at 0, 30, and 60 min post-exercise for 16S rRNA gene sequencing.</p><p><strong>Results: </strong>Exercise induced significant remodeling of gut microbiota composition in both strains, with a notable post-exercise elevation in the <i>Bacteroidetes/Firmicutes</i> ratio, particularly in C57BL/6 mice (C57Cr vs. C57T0, <i>p</i> < 0.01; C57Cr vs. C57T60, <i>p</i> < 0.05; BCCr vs. BCT30, <i>p</i> < 0.05). Both alpha and beta diversity metrics revealed significant exercise-induced microbial changes, with C57BL/6 mice showing a more pronounced increase in diversity at 30 and 60 min post-exercise (OTUs and observed species, all <i>p</i> < 0.001) compared to BALB/c mice. Functional analysis revealed strain-specific responses: BALB/c mice exhibited upregulated enzymes involved in energy metabolism but impaired immune regulation, indicating compromised intestinal barrier integrity and delayed energy recovery. In contrast, C57BL/6 mice displayed enhanced anti-inflammatory capacity, accelerated energy recovery through enrichment of energy metabolism-related genera, and maintained gut integrity through the proliferation of beneficial bacteria. The potential important genus <i>Muribaculum</i> identified as a key exercise-responsive taxon across time points, potentially associated with gut motility. The role of <i>Muribaculum</i> warrants further using multi-omics investigation.</p><p><strong>Discussion: </strong>These findings provide a foundation for identifying genetic loci influencing exercise microbiota interactions, thereby providing a theoretical basis for microbiota-based personalized exercise interventions.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"17 ","pages":"1790697"},"PeriodicalIF":4.0,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13148273/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147836055","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rock surfaces as reservoirs for airborne halophilic microorganisms in the Bochnia Salt Mine.","authors":"Magdalena Kowalewicz-Kulbat, Gabriela Arciszewska, Maciej Manecki, Dominika Drzewiecka, Michalina Rachubik, Karolina Stępniak, Luciana Albuquerque, Conceição Egas, Krzysztof Krawczyk, Camille Locht, Aleksandra Puławska","doi":"10.3389/fmicb.2026.1813537","DOIUrl":"https://doi.org/10.3389/fmicb.2026.1813537","url":null,"abstract":"<p><p>Airborne halophilic archaea have recently been detected in subterranean salt mines, yet their origin in such dynamic environments remains unclear. We investigated whether exposed salt rock surfaces may serve as biological reservoirs for airborne halophilic microorganisms. Rock surfaces were sampled at three underground sites in the Bochnia Salt Mine (southern Poland), spanning a gradient of distance from the mine entrance and human influence. Surface swabs were collected from rock salt and salty claystone during summer and winter, representing contrasting warm-humid and cool-dry microclimatic conditions, and analyzed using cultivation-based methods combined with 16S rRNA gene sequencing. Across all sites, seasons, and both rock types considered together, halophilic microorganisms dominated rock-associated communities, occurring at approximately 1.2 × 10³ to 4.3 × 10³ CFU/25 cm². In contrast, non-halophilic microorganisms were present at only about 0.5-1.3 × 10² CFU/25 cm². Mean halophilic abundance was approximately 3.8 × 10³ CFU/25 cm² in summer and 1.4 × 10³ CFU/25 cm² in winter, indicating less than two-fold seasonal variation on rock surfaces. In contrast, airborne communities from the same sites previously showed up to 13-fold summer-winter variation. A total of 11 halophilic archaeal species were identified on rock surfaces, dominated by members of the genus <i>Halococcus</i> (<i>Hcc. salifodinae</i>, <i>Hcc. hamelinensis</i>, <i>Hcc. morrhuae</i> and <i>Hcc. dombrowskii</i>), as well as <i>Natrinema versiforme</i> and <i>Halalkalicoccus paucihalophilus</i>. Most taxa detected on rock surfaces overlapped with those previously identified in the mine air. These results indicate that exposed salty rock surfaces constitute favorable habitats and likely persistent reservoirs for halophilic archaea, whereas the mine atmosphere appears to represent a transient, environmentally filtered compartment that receives only a subset of the rock-associated community.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"17 ","pages":"1813537"},"PeriodicalIF":4.0,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13144014/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147836102","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characteristic rhizosphere metabolites of low-cadmium-accumulating rice drive microbially induced soil cadmium speciation transformation.","authors":"Junyang Zhao, Yuhang Qiu, Xiaowen Feng, Guanchun Qin, Shunpiao Meng, Yongzhi Chen, Liyu Shi, Guoyuan Li, Yongcheng Ma, Bing He, Ronghui Wen","doi":"10.3389/fmicb.2026.1832350","DOIUrl":"https://doi.org/10.3389/fmicb.2026.1832350","url":null,"abstract":"<p><strong>Introduction: </strong>Cadmium (Cd) contamination in paddy soils threatens global rice safety. However, the mechanisms by which interactions between rhizosphere metabolites and microorganisms regulate Cd bioavailability in the rhizosphere microecosystem of low-Cd-accumulating rice (LAR) remain unclear.</p><p><strong>Methods: </strong>To elucidate the mechanisms by which metabolite-microbe interactions in the rhizosphere microenvironment of LAR regulate Cd bioavailability, a microplot experiment was performed to classify fifteen rice cultivars into LAR (<i>n</i> = 4) and high-Cd-accumulating rice (HAR, <i>n</i> = 3) groups.</p><p><strong>Results: </strong>Rhizosphere omics analyses revealed that LAR tends to form a highly specialized metabolite profile and microbial community at the cost of overall diversity, thereby promoting Cd immobilization. Multiomics integrated analysis demonstrated that characteristic LAR metabolites (Compared with HAR, the rhizosphere metabolites significantly enriched in LAR) serve as carbon sources to enrich Cd-immobilizing bacteria (<i>Desulfopila aestuarii</i> and <i>Paludibacter</i> sp.) while inhibiting Cd-mobilizing bacteria (<i>Sulfuriferula</i> sp. AH1, <i>Nocardioides deserti</i>, and <i>Nocardioides glacieisoli</i>) through antimicrobial activity. These interactions establish a microecological mechanism that suppresses Cd mobilization and enhances immobilization. Moreover, LAR metabolites increase the abundance of microbial genes encoding enzymes for sinapic acid and biotin biosynthesis-including caffeoyl-CoA O-methyltransferase (EC: 2.1.1.104) and 6-carboxyhexanoate-CoA ligase (EC: 6.2.1.14)-and promote the enrichment of related functional microorganisms such as Candidatus Sulfobium mesophilum and Deltaproteobacteria bacterium, thereby further regulating Cd speciation. Validation experiments revealed that a consortium of 23 characteristic LAR metabolites (e.g., sinapic acid, biotin, isosteviol, hydroxyisocaproic acid, 2-hydroxyhexanoic acid, lumichrome, and hypoxanthine) reduced exchangeable Cd by 10-21% and increased Fe-Mn oxide-bound Cd by 28-56% in both natural and sterilized soils.</p><p><strong>Conclusion: </strong>These findings reveal that characteristic LAR metabolites directly promote Cd immobilization and drive directional microbial assembly and functional optimization, thereby providing novel insights that can facilitate the establishment of a rhizosphere ecological barrier that can increase resistance to Cd stress in rice.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"17 ","pages":"1832350"},"PeriodicalIF":4.0,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13144023/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147836134","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative analysis of rhizobacterial communities across five medicinal plants in Xinjiang.","authors":"Jing Wu, Ru Bai, Oren Akhberdi, Liping Xu","doi":"10.3389/fmicb.2026.1785383","DOIUrl":"https://doi.org/10.3389/fmicb.2026.1785383","url":null,"abstract":"<p><p>Five medicinal plants with various therapeutic effects in Xinjiang (<i>Helichrysum thianschanicum</i> Regel, <i>Taraxacum kok-saghyz</i> Rodin<i>, Artemisia rupestris</i> L.<i>, Arnebia euchroma</i> Johnst, <i>and Hyssopus officinalis</i> L.) are considered as promising raw materials of pharmaceutical, cosmetic, and fragrance industries. Understanding the characteristics of rhizosphere bacterial communities can be critical in regulating the growth process of these medicinal plants. To clarify the plant-specificity of rhizobacterial assemblages and related driving factors of five medicinal plants, we compared their rhizosphere bacterial communities with those of non-planted soil (CK). Soil physicochemical properties were analyzed, and bacterial communities were characterized using high-throughput sequencing of the 16S rRNA gene V3-V4 region. Results showed that rhizosphere soils of medicinal plants had significantly higher organic matter (OM), total nitrogen (TN), and total phosphorus (TP) than CK, with TP increasing by 2.6-2.9 times. Each medicinal plant rhizosphere harbored a highly specific bacterial community, with unique Amplicon Sequence Variants (ASVs) accounting for 34.04-46.70% of total ASVs, while only 449 core ASVs were shared among all five plants. At the phylum level, <i>Proteobacteria</i>, <i>Bacteroidota</i>, and <i>Acidobacteriota</i> dominated the rhizosphere, in contrast to the dominance of <i>Actinobacteriota</i> in CK. <i>Chitinophagaceae</i>, <i>Sphingomonas</i>, <i>Pseudomonas</i> and <i>RB41</i> were selectively enriched in different plant rhizospheres. Total potassium (TK), TN, and TP were the key edaphic drivers, with TK negatively correlated with bacterial diversity, and TN/TP regulating the distribution of dominant genera. This study demonstrates high plant-specificity of rhizobacterial communities in Xinjiang medicinal plants and the dominant role of soil TK, TN, and TP, providing a scientific basis for the precise cultivation of medicinal plants and the development of specialized microbial agents.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"17 ","pages":"1785383"},"PeriodicalIF":4.0,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13144048/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147836141","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Root-associated bacterial community dynamics and assembly mechanisms in healthy and root rot-infected soybeans.","authors":"Chunjing Yu, Mengdan Wang, Ming Zhao, Song Zhang, Minghui Cao, Zhiting Liu, Jiaping Jiang, Yi Zhang, Yu Pan, Xiaoyu Zhao","doi":"10.3389/fmicb.2026.1789440","DOIUrl":"https://doi.org/10.3389/fmicb.2026.1789440","url":null,"abstract":"<p><strong>Introduction: </strong>Soybean root rot, a devastating soil-borne disease, severely limits global soybean yield and quality. Traditional control measures cause environmental pollution and have regional limitations. Root-associated microbiomes are vital for plant health, but most studies use relative abundance sequencing that distorts actual microbial quantities. This study used absolute quantitative high-throughput sequencing to clarify soil chemical properties and bacterial community assembly in healthy and diseased soybeans, laying a theoretical foundation for microbiome-based root rot management.</p><p><strong>Methods: </strong>Samples were collected from bulk soil, and the endosphere, rhizoplane, rhizosphere of healthy and diseased soybeans in black soil fields of Heilongjiang. Soil chemical properties, including pH, soil organic carbon (SOC), total nitrogen (TN), available nitrogen (AN), available phosphorus (AP), and available potassium (AK), were determined. Absolute quantitative sequencing of bacterial 16S rRNA V4-V5 region was performed, combined with qPCR for absolute abundance calibration. Bioinformatics analyses included α/β diversity, co-occurrence network, community assembly (βNTI & RCbray), random forest and correlation analysis to identify key taxa and their relationships with environmental factors.</p><p><strong>Results: </strong>Root rot significantly reduced rhizosphere SOC (by 29.13%), TN (8.57%), AN (24.18%), AP (18.86%), while increased AK (12.82%) and pH. However, the contents of certain bacterial taxa at the genus levels showed significant differences in both absolute and relative abundances. The bacterial co-occurrence network indicate that the interaction in the healthy soybean (H) group was more complex than that in the diseased soybean (S) group. Specifically, 1 module hub and 21 connectors were identified in the H group, whereas 55 connectors were detected in the S group. Community assembly in both the H and S groups was governed by deterministic processes, with homogeneous selection primarily observed in the S group. Random forest and correlation heatmap analyses revealed ASV115 (<i>Candidatus Koribacter</i>) in H group was positively correlated with SOC, pH and AN; ASV16 (<i>Streptomyces</i>), ASV42 (<i>Agrobacterium</i>) and ASV46 (<i>Mesorhizobium</i>) were keystones in S group.</p><p><strong>Discussion: </strong>Root rot destroyed rhizosphere nutrient balance and reshaped bacterial community structure, reducing network complexity. Absolute quantification effectively compensated for the defects of relative abundance, accurately reflecting community changes. These findings clarify the microecological mechanism of soybean root rot, supporting the development of biocontrol strategies targeting rhizosphere microbiome for sustainable soybean production.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"17 ","pages":"1789440"},"PeriodicalIF":4.0,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13144118/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147836084","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Preceding crops may reduce denitrification potential and enhance ammonium assimilation pathways.","authors":"Juan Li, Ming Liu, Chengwei Yang, Zhiyong Fan, Jiaen Su, Yanxia Hu, Yinju Yang, Junying Li, Yi Pu, Erdeng Ma, Xiaopeng Deng, Junwei Sun","doi":"10.3389/fmicb.2026.1808894","DOIUrl":"https://doi.org/10.3389/fmicb.2026.1808894","url":null,"abstract":"<p><strong>Background: </strong>Soil microorganisms are pivotal to nitrogen (N) cycling in croplands, yet how preceding crops modulate their functional profiles remains unclear.</p><p><strong>Objective: </strong>This field study aimed to quantify the effects of barley (BT) and rapeseed (RT) preceding crops (vs. no preceding crop, CK) on soil microbial functions and N-metabolic pathways in tobacco fields.</p><p><strong>Results: </strong>High-throughput metagenomics revealed that BT and RT significantly increased soil microbial richness (Chao1 index) compared to CK. At the genus level, CK contained 64% and 24% fewer unique taxa than BT and RT, respectively. While the top five KEGG functional pathways (e.g., Metabolic pathways, Biosynthesis of secondary metabolites) were conserved across treatments, their relative abundances differed. Critically, preceding crops reduced soil denitrification rates and increased glutamine dehydrogenase activity. Redundancy analysis confirmed that ammonium-N concentration was the key edaphic factor strongly correlated with microbial community structure and function (<i>P</i> < 0.01).</p><p><strong>Conclusion: </strong>Our findings demonstrate that barley and rapeseed preceding crops enhance microbial richness and activity, thereby inhibiting denitrification and promoting N fixation via altered ammonium-N dynamics.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"17 ","pages":"1808894"},"PeriodicalIF":4.0,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13144092/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147836079","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Alkaline autofermentation of <i>Nostoc muscorum</i> enhances organic acid production and antimicrobial activity against <i>Salmonella enterica</i> and <i>Campylobacter jejuni</i>.","authors":"Mohana Krishnan Neelakrishnan, Brahmaiah Pendyala, Akhil Rautela, Ankit Patras","doi":"10.3389/fmicb.2026.1830932","DOIUrl":"https://doi.org/10.3389/fmicb.2026.1830932","url":null,"abstract":"<p><p>Foodborne pathogens such as <i>Salmonella enterica</i> and <i>Campylobacter jejuni</i> remain leading causes of bacterial gastroenteritis and are frequently associated with poultry production systems. Increasing restrictions on antibiotic use in animal agriculture have intensified the need for sustainable antimicrobial alternatives. Cyanobacteria represent a promising resource for producing antimicrobial metabolites; however, their antimicrobial potential has primarily been explored using solvent extracts derived from fresh biomass. While alkaline autofermentation and organic acid production in cyanobacteria have been previously reported, including in our earlier work, the antimicrobial potential of autofermentation-derived aqueous extracts, which are primarily composed of organic acids, remains largely unexplored. This study establishes, for the first time, a dual-product autofermentation framework in <i>Nostoc muscorum</i> that enhances antimicrobial activity through the generation of organic acid-rich extracts and metabolite-enriched residual biomass. Autofermentation was conducted at pH 8.4 and 10.3, and organic acid production and antimicrobial activity against <i>S. enterica</i> and <i>C. jejuni</i> were evaluated using minimum inhibitory concentration assays. Alkaline autofermentation significantly enhanced metabolite production, yielding 12.31 g L^-1 total organic acids after 24 h at pH 10.3, a 1.6-fold increase compared with pH 8.4. Butyric acid was the dominant fermentation product, reaching 9.11 g L^-1 under alkaline conditions (pH 10.3), and contributed substantially to antimicrobial activity. Organic acid-rich extracts inhibited both pathogens, while methanolic extracts from autofermented biomass exhibited greater potency than fresh biomass extracts. These findings demonstrate that alkaline autofermentation enhances the antimicrobial potential of cyanobacterial biomass and highlight <i>N. muscorum</i> as a promising platform for developing antibiotic-free pathogen control strategies in poultry production systems.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"17 ","pages":"1830932"},"PeriodicalIF":4.0,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13144051/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147836115","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 functional traits: a key driver of soil organic carbon dynamics during reductive soil disinfestation.","authors":"Risheng Xu, Haijiao Liu, Juan Liu, Yafei Chen, Ruiwei Ran, Lina Gao, Weizhen Zhao, Xing Chen, Tengfei Ma","doi":"10.3389/fmicb.2026.1784827","DOIUrl":"https://doi.org/10.3389/fmicb.2026.1784827","url":null,"abstract":"<p><p>Reductive soil disinfestation (RSD) significantly enhanced SOC content. However, its microbial mechanisms mediated through changes in microbial necromass carbon, particularly under different organic amendments, remain poorly understood. Here, we evaluated the effects of RSD combined with two types of organic amendments (wheat <i>vs</i>. soybean straw) on soil chemical properties, SOC fractions, microbial community composition and diversity, 16S rRNA gene operon (<i>rrn</i>) copy number, co-occurrence networks, and functional profiles. The results showed that microbial necromass carbon increased markedly after RSD treatment and accounted for up to 75% of the total SOC. Compared to wheat straw, soybean straw amendment resulted in higher relative abundances of Firmicutes (47.70%), Halobacterota (506.99%), and Euryarchaeota (1671.36%), intensified anaerobic conditions during RSD, improved suppression of aerobic fungi, and preferentially promoted the accumulation of fungal necromass carbon (33.25%). Conversely, the wheat straw treatment induced moderate anaerobic conditions, less pronounced than with soybean straw but stronger than the control, while sustaining higher bacterial abundance and promoting more robust bacterial succession, thereby preferentially leading to accumulation of bacterial necromass carbon (141.74%). These findings underscore the important role of bacteria functional traits in mediating carbon sequestration under anaerobic straw incorporation and provide new insights for optimizing organic amendment strategies in RSD practices to enhance soil carbon sequestration efficiently.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"17 ","pages":"1784827"},"PeriodicalIF":4.0,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13143972/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147836107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Plant microbiome engineering: from inoculation to genome editing.","authors":"Jyoti Yadav, Pushpa Gehlot, Priya Soni, Tripta Jain","doi":"10.3389/fmicb.2026.1781381","DOIUrl":"https://doi.org/10.3389/fmicb.2026.1781381","url":null,"abstract":"<p><p>Plant-associated microbiomes are central to crop productivity, nutrient efficiency, and stress resilience, yet conventional microbiome manipulation strategies, largely based on microbial inoculation and agronomic management, often suffer from inconsistent field performance and limited persistence. Although several recent reviews have discussed CRISPR-mediated plant-microbe engineering and synthetic microbial community (SynCom) design separately, few reviews integrate genome editing, ecological stability of microbiomes, and climate-resilient agricultural applications within a unified conceptual framework. Recent advances in molecular biotechnology are transforming this landscape by enabling precision engineering of plant-microbe interactions at genetic, metabolic, and community levels. In particular, synthetic biology tools including CRISPR/Cas genome editing, RNA interference, and synthetic microbial communities (SynComs), now allow targeted modification of plant traits governing microbial recruitment, microbial pathways underpinning nutrient cycling and stress tolerance, and community-level functional complementarity. This review integrates molecular genetics, microbial ecology, and systems-level microbiome design to frame the plant and its microbiome as an engineerable holobiont. We integrate insights from genome editing in plants and microbes, omics-guided SynCom design, climate-resilience mechanisms, and emerging AI-assisted decision frameworks, including machine learning and ecological modeling approaches used to analyze multi-omics datasets, and predict plant-microbiome interactions across experimental and field-based studies. Importantly, we critically assess limitations related to ecological stability, trait trade-offs, biosafety, and regulatory challenges that constrain large-scale deployment. By bridging genome-enabled microbiome manipulation with ecological design principles, this review proposes an integrative framework for climate-smart microbiome engineering and identifies key research priorities required to transition from empirical inoculation toward predictive, sustainable, and socially responsible agricultural biotechnology.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":"17 ","pages":"1781381"},"PeriodicalIF":4.0,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13144036/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147836133","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}