Sustainable microbiology最新文献

{"title":"Evidence of biological nitrification inhibition in barley to support sustainable nitrogen management.","authors":"Jack Henderson, Xiaoping Fan, Ellen Elizabeth Smith, Marcel Jaspars, Timothy S George, Cécile Gubry-Rangin","doi":"10.1093/sumbio/qvag034","DOIUrl":"10.1093/sumbio/qvag034","url":null,"abstract":"<p><p>Nitrification drives nitrogen loss in agricultural systems, resulting in leached nitrate and increased emissions of the greenhouse gas nitrous oxide, thereby reducing nitrogen use efficiency (NUE). Biological nitrification inhibition (BNI) provides a promising nature-based solution to low-NUE by suppressing nitrifying microorganisms via plant-exuded bioactive metabolites. Although BNI is well documented in several major cereal grasses, evidence of BNI in barley (<i>Hordeum vulgare</i>) is lacking. This study demonstrates barley BNI activity through suppression of rhizosphere ammonia-oxidizer abundance, without a corresponding inhibition of the total prokaryotic community. Several barley lines exhibited strong inhibition of rhizosphere ammonia oxidizers consistent with high-BNI efficiency. The impact of BNI on the rhizosphere microbial community revealed clear differential effects across multiple phylogenetic clades of ammonia oxidizers, revealing that nitrifier clades differ in sensitivity to BNI in the rhizosphere. This led to a decrease in ammonia-oxidizer community richness correlating with BNI activity. The selective inhibition of rhizosphere ammonia oxidizers suggests that further research across diverse soils is needed. This study clearly demonstrates barley BNI activity in soil through suppression of rhizosphere ammonia oxidizers, identifying promising high-BNI lines, and providing a foundation for developing high-BNI barley cultivars to enhance NUE and increase agricultural sustainability.</p>","PeriodicalId":516860,"journal":{"name":"Sustainable microbiology","volume":"3 3","pages":"qvag034"},"PeriodicalIF":0.0,"publicationDate":"2026-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13520126/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148842680","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbiome modulation for sustainable crop production and climate resilience.","authors":"Malek Marian, Ioannis Stringlis, Eleonora Rolli, Christopher James Barnes, Stéphane Compant, Angela Sessitsch","doi":"10.1093/sumbio/qvag032","DOIUrl":"10.1093/sumbio/qvag032","url":null,"abstract":"<p><p>The microbiome is fundamental to plant performance in agroecosystems, influencing primary productivity and climate resilience. Microbiome modulation refers to the targeted manipulation (or steering) and optimization of microbiota features, including taxonomic structure, diversity, composition, assembly dynamics, stability, functional capacity, interactions, and network architecture. Here, we review the current state-of-the-art knowledge and strategies used for microbiome modulation, encompassing biological interventions such as bacteria, fungi, protists, nematodes, and phages, as well metabolites, compounds, and nutrients derived from plants. We further discuss emerging tools and strategies for next-generation microbiome modulation, including function-oriented, multitrophic defined microbial communities assembled based on ecological traits and interactions across multiple trophic levels to enable their establishment and function within the phytobiome; temperate phages; microbiome transplantation and breeding; and functional synbiotics, defined as combinations of beneficial microorganisms and compounds that improve microbiome health and function. In addition, we highlight key knowledge gaps and research priorities for advancing precision microbiome modulation. Addressing current challenges will require integrated frameworks combining experimental validation <i>in planta</i> and reductionist approaches with <i>in silico</i> modeling and multiomics analyses to better predict, design, and sustain beneficial plant-microbiome outcomes. Overall, microbiome modulation represents a paradigm shift in advancing sustainable and climate-resilient agri-food systems.</p>","PeriodicalId":516860,"journal":{"name":"Sustainable microbiology","volume":"3 3","pages":"qvag032"},"PeriodicalIF":0.0,"publicationDate":"2026-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13520125/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148842696","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lignin enrichment selects specialized fungal communities from contrasting soils.","authors":"Vitória Pinheiro Balestrini, Sílvia Belém Gonçalves, Ricardo Henrique Krüger, Betania Ferraz Quirino","doi":"10.1093/sumbio/qvag031","DOIUrl":"10.1093/sumbio/qvag031","url":null,"abstract":"<p><p>Despite growing interest in microbial lignin degradation, the ecological and taxonomic dynamics of fungal communities enriched under ligninolytic conditions remain poorly understood. We hypothesized that sequential enrichment on lignin would select specialized fungal communities, with assembly shaped by inoculum source, temperature, and lignin type. Fungal consortia from backyard compost soil and a commercial substrate were enriched on alkaline-extracted or Kraft lignin as the sole carbon source at 30°C or 37°C through six successive passages. Internal Transcribed Spacer amplicon sequencing assessed fungal diversity, taxonomic composition, and predicted ecological guilds. Richness and diversity progressively declined, indicating strong selective pressure and enrichment of specialized communities. Community composition was primarily influenced by temperature and inoculum source, whereas lignin type had limited and statistically nonsignificant effects at the genus level. Ascomycota dominated all enriched consortia, while several taxa initially detected in the source materials were progressively lost. Functional predictions indicated a predominance of saprotrophic guilds, although most assignments had moderate or low confidence. These findings highlight the importance of temperature and inoculum source in shaping fungal community assembly during lignin enrichment and provide guidance for designing and optimizing ligninolytic consortia for biotechnological applications.</p>","PeriodicalId":516860,"journal":{"name":"Sustainable microbiology","volume":"3 3","pages":"qvag031"},"PeriodicalIF":0.0,"publicationDate":"2026-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13463638/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148727486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Community Dynamics in a Changing World: highlights from the 1st Puerto Rico & Caribbean Microbiome Symposium and vision for a new microbiome hub.","authors":"Filipa Godoy-Vitorino","doi":"10.1093/sumbio/qvag030","DOIUrl":"10.1093/sumbio/qvag030","url":null,"abstract":"<p><p>The Puerto Rico Center for Microbiome Sciences (PR-CMS) seeks to become a leading hub for multiomics research and host-microbiota symbiosis in the Caribbean. As part of this effort, PR-CMS organizes an annual symposium that convenes international leaders, regional experts, and the local scientific community to address key challenges in microbiome science. The 1st Microbiome Symposium of Puerto Rico and the Caribbean, titled \"Community Dynamics in a Changing World,\" took place in San Juan in February 2026. The event brought together more than 200 participants, including researchers, trainees, and stakeholders from clinical, environmental, computational, and translational fields. Topics highlighted the role of microbiomes in human health, disease, biodiversity, and ecosystem resilience, covering host-microbiome interactions, cancer, infectious diseases, diet-immune dynamics, environmental microbiology, and bioinformatics. Through keynote talks, invited presentations, and student research, the symposium emphasized integrating multiomics, data science, and translational approaches. It strengthened collaborative networks locally and globally, positioning PR-CMS as a regional leader in microbiome innovation. This meeting report also emphasizes the vision and mission of the PR-CMS as a new regional and global hub for the study of biodiversity.</p>","PeriodicalId":516860,"journal":{"name":"Sustainable microbiology","volume":"3 3","pages":"qvag030"},"PeriodicalIF":0.0,"publicationDate":"2026-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13463629/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148727542","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hidden pesticidal diversity within the <i>Bacillus cereus</i> group: expanding the concept beyond <i>Bacillus thuringiensis</i>.","authors":"Diego Herman Sauka, Leopoldo Palma","doi":"10.1093/sumbio/qvag029","DOIUrl":"10.1093/sumbio/qvag029","url":null,"abstract":"<p><p>For over a century, <i>Bacillus thuringiensis</i> has been regarded as the primary microbial source of pesticidal proteins used in agriculture and vector control. Its defining phenotype, the production of parasporal crystals composed mainly of Cry and Cyt proteins, has shaped both scientific understanding and regulatory frameworks. However, advances in whole genome sequencing reveal that pesticidal traits are not restricted to a single species but are distributed across members of the <i>Bacillus cereus</i> group. This distribution is largely driven by the mobility of toxin-associated genetic elements across closely related genomic backgrounds. Here, we propose that this observation reflects a broader, dynamic, and largely unexplored functional diversity. Using the emerging case of <i>Bacillus toyonensis</i> biovar Thuringiensis, we argue that the current species centered paradigm may be limiting the discovery of novel pesticidal diversity and propose a shift toward a function centered framework in microbial biocontrol. We suggest that embracing this perspective will not only refine our understanding of microbial evolution but also open new avenues for the development of sustainable, next generation biopesticides. Furthermore, it may facilitate the systematic discovery of previously overlooked pesticidal diversity hidden within historical microbial collections.</p>","PeriodicalId":516860,"journal":{"name":"Sustainable microbiology","volume":"3 3","pages":"qvag029"},"PeriodicalIF":0.0,"publicationDate":"2026-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13439580/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148709220","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial solutions for a changing world.","authors":"Zahra F Islam, Paul Sainsbury, Chris Greening","doi":"10.1093/sumbio/qvag011","DOIUrl":"10.1093/sumbio/qvag011","url":null,"abstract":"<p><p><i>Microbial Solutions for a Changing World</i> was an inaugural international conference hosted at Monash University, Melbourne, and presented by Applied Microbiology International. The meeting brought together researchers from across the Asia-Pacific region to examine how microbiological research informs responses to climate-related challenges across environmental, health, and applied contexts. Recognizing the central role of microorganisms in regulating greenhouse gas fluxes, shaping disease dynamics, and underpinning ecosystem function, it provided a forum for focused exchange at the intersection of microbiology and climate research. The programme was organized around three thematic areas: greenhouse gas cycling and mitigation, health impacts and pathogen control, and environmental impacts and ecosystem restoration. Plenary lectures and contributed presentations addressed microbial processes operating across managed, natural, and extreme environments, alongside discussion of how microbiological insight can inform mitigation, disease management, and restoration strategies under changing environmental conditions. Early-career researchers were placed at the centre of the programme, with structured activities aimed at supporting interaction and collaboration. By convening researchers working across diverse sub-disciplines, the conference highlighted common challenges and opportunities in aligning microbiology with climate response efforts. <i>Microbial Solutions for a Changing World</i> demonstrated the value of dedicated forums for advancing sustainable microbiology within the Asia-Pacific region and beyond.</p>","PeriodicalId":516860,"journal":{"name":"Sustainable microbiology","volume":"3 3","pages":"qvag011"},"PeriodicalIF":0.0,"publicationDate":"2026-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13375366/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148709256","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbiome stewardship: definition and guiding principles for implementation.","authors":"Kieran C O'Doherty, Mikaela Beijbom, Emma Allen-Vercoe, Mallory J Choudoir, Diego S Silva, Carla Bonilla, Justine Debelius, Sarah Elton, Aviâja Lyberth Hauptmann, Andreas Heyland, Nicolae Morar, Derek Skillings, Zhongzhi Sun, Patricia G Wolf, Robert G Beiko, Suzanne Lynn Ishaq","doi":"10.1093/sumbio/qvag028","DOIUrl":"10.1093/sumbio/qvag028","url":null,"abstract":"<p><p>Microbiomes are essential for ecosystem, plant, animal, and human health. There is accumulating evidence that changes to microbiomes from anthropogenic activities are associated with adverse health outcomes. Despite this evidence and calls for action, almost no oversight mechanisms exist to protect microbiomes or their key functions, in part due to uncertainty about what to protect, and how. We have previously proposed microbiome stewardship as a foundational concept that can act across policy domains to facilitate the ongoing presence of key microbial communities and their functions. The purpose of this article is to provide a working definition of microbiome stewardship and develop guiding principles to support its implementation. The concept of microbiome stewardship is relevant to a wide range of policy domains, such as public health, clinical care, environmental protection, food production, and agriculture. Nonetheless, the implementation of microbiome stewardship will be highly specific, as it needs to be guided by considerations of microbial habitat, objectives of stewardship, and available opportunities for intervention. Accordingly, aligning stewardship responsibility with specific institutions and governance mechanisms will be context-dependent. We conclude with a discussion that situates microbiome stewardship relative to other initiatives.</p>","PeriodicalId":516860,"journal":{"name":"Sustainable microbiology","volume":"3 3","pages":"qvag028"},"PeriodicalIF":0.0,"publicationDate":"2026-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13403186/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148709236","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evidence for microbial-induced transformation of acrylonitrile-butadiene-styrene (ABS) and styrene-acrylonitrile (SAN) polymer blends by plastic-degrading bacteria.","authors":"Franciele Saorin, Tarcisio Camlofski, Jade Oliveira, Anderson Oliveira da Silva, Marcia Porto, Mariana Mattioli, Ricardo Krüger, Julianna Peixoto","doi":"10.1093/sumbio/qvag027","DOIUrl":"10.1093/sumbio/qvag027","url":null,"abstract":"<p><p>Poly(acrylonitrile-butadiene-styrene) (ABS) and styrene-acrylonitrile (SAN) are extensively used in cosmetic and industrial packaging due to their mechanical strength and durability. However, their intrinsic resistance to microbial and enzymatic attack underlies their long-term environmental persistence. To date, there is limited experimental evidence regarding the microbial transformation of ABS/SAN polymers. Here, we investigated whether four previously reported polyethylene-degrading bacterial strains-<i>Comamonas</i> sp., <i>Delftia</i> sp., <i>Stenotrophomonas</i> sp., and <i>Alcaligenes</i> sp.-can grow on an ABS/SAN blend and induce measurable physicochemical modifications. Each strain was incubated for 90 days in a minimal medium containing ABS/SAN as the sole added carbon and energy source. Bacterial growth, viability, and polymer modification were assessed by fluorescence microscopy, gravimetric analysis, and attenuated total reflectance Fourier-transform infrared spectroscopy (ATR-FTIR). All strains sustained active growth and remained viable throughout incubation. <i>Stenotrophomonas</i> sp. and <i>Delftia</i> sp. exhibited the strongest responses, with approximately 6-fold and 2.5-fold increases in viable cell counts and corresponding mass losses of 2.20% and 1.27%, respectively. ATR-FTIR profiles revealed strain-specific chemical changes on the polymer surface, including reductions in nitrile and carbonyl content consistent with partial oxidation and assimilation of ABS/SAN fragments. Comparative genomic analysis further identified genes encoding putative catabolic functions that may facilitate polymer transformation, such as nitrilases, amidases, phenylacetate and aromatic compound degradation pathways, redox-active enzymes, and efflux transporters. Together, these findings provide a novel experimental evidence that select bacterial strains can interact with and induce measurable modifications in ABS/SAN polymer blend, highlighting new perspectives for the biological degradation of recalcitrant synthetic plastics.</p>","PeriodicalId":516860,"journal":{"name":"Sustainable microbiology","volume":"3 3","pages":"qvag027"},"PeriodicalIF":0.0,"publicationDate":"2026-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13375299/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148709119","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The digital bioeconomy: microbiomes as a stress test for global digital sequence information governance.","authors":"Pierre-Mathieu Pélissier, Indré Karciauskaité, Tanja Kostic, Emmanuelle Maguin, Angela Sessitsch, Kosuke Shiraishi","doi":"10.1093/sumbio/qvag026","DOIUrl":"10.1093/sumbio/qvag026","url":null,"abstract":"<p><p>Digital sequence information governance has entered a high-stakes implementation era. The Convention on Biological Diversity's 'Cali Fund' is operationalised as the financial engine of its multilateral mechanism (MLM), with similar frameworks under negotiation across other international ocean and agricultural treaties. However, because microorganisms and their functional clusters transcend national borders, traditional bilateral mechanisms are difficult to implement. This policy briefing uses microbiomes as a stress test for these evolving MLMs, evaluating three primary challenges: the holobiont 'data sandwich', the 'oblivious user' awareness gap, and overlapping jurisdictions. By analysing these friction points, we discuss pathways to ensure global MLMs support both innovation and equitable benefit-sharing.</p>","PeriodicalId":516860,"journal":{"name":"Sustainable microbiology","volume":"3 2","pages":"qvag026"},"PeriodicalIF":0.0,"publicationDate":"2026-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13375339/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148709013","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Harnessing indigenous bacterial defenders to improve disease resistance and plant health in vegetable <i>Brassica</i> crops.","authors":"Ganesh G Madakaripura Rangaswamy, Snehalatha Pasupuleti, Jeanine Umfuyisoni, Toni A Chapman, Jonathan M Plett, Uffe N Nielsen","doi":"10.1093/sumbio/qvag025","DOIUrl":"10.1093/sumbio/qvag025","url":null,"abstract":"<p><p>Vegetable crops in the Brassicaceae family have significant economic and nutritional value, supporting livelihoods worldwide. Despite ongoing efforts to control pathogens, infections continue to degrade crop quality and yield. Rising disease incidence, coupled with restrictions on chemical treatments and limited alternatives, has heightened the need for new, sustainable disease management approaches. The plant microbiome plays a crucial role in sustaining plant health and resilience under stress. Harnessing the microbiome provides an environmentally friendly means to enhance crop production by improving disease resistance. This review summarizes knowledge on how beneficial bacteria could be used to enhance plant health and disease resistance in <i>Brassica</i> crops, highlighting a preference for indigenous bacteria adapted to local growing conditions. We explore the composition and dynamics of the <i>Brassica</i> bacterial microbiome, detailing functional characteristics, biocontrol mechanisms, and potential approaches to optimize the balance between <i>Brassica</i> growth and defence under stress. We discuss methodologies for identifying and characterizing beneficial bacteria, their applications and management, and emphasize challenges hindering broad implementation. This synthesis shows that utilizing indigenous <i>Brassica</i>-associated bacteria through careful isolation, multitraits assessment, and the development of region-specific consortia offers the most reliable path to sustainable disease management. This approach links ecological adaptation with practical agricultural applications.</p>","PeriodicalId":516860,"journal":{"name":"Sustainable microbiology","volume":"3 3","pages":"qvag025"},"PeriodicalIF":0.0,"publicationDate":"2026-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13375344/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148709197","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}