Sustainable microbiology最新文献

{"title":"Bridging research gaps and advancing policy for healthy soils.","authors":"Alex Williams, Jim Lynch","doi":"10.1093/sumbio/qvaf017","DOIUrl":"10.1093/sumbio/qvaf017","url":null,"abstract":"<p><p>The policy framework previously presented by Neale and colleagues in Sustainable Microbiology highlights the central role of soil microorganisms in sustainable agriculture and global food security, offering actionable interventions grounded in emerging scientific advances. However, the translation of soil science and ecology into impactful policy and practice remains limited. This opinion article revisits the longstanding concept of soil biotechnology, and regulatory/societal barriers to progress. We emphasize that the soil microbiome holds untapped potential for improving plant health, reducing agrochemical reliance, and promoting sustainable food systems through continued research. Interkingdom microbial interactions, especially those involving root exudation as a mechanism for microbial recruitment, are proposed as pivotal but underexplored areas of study. Phenotype-driven, trait-based approaches are advocated over traditional phylogenetic methods to better identify functionally relevant microbial consortia and intervention strategies. Furthermore, we stress the need to integrate ecological, agronomic, and economic insights to develop soil-centric food systems. This includes monetizing ecosystem services provided by healthy soils and implementing incentivized conservation schemes. Unlocking the potential of soil microbial ecology requires coordinated, interdisciplinary efforts and a paradigm shift in policy, funding, and public perception.</p>","PeriodicalId":516860,"journal":{"name":"Sustainable microbiology","volume":"2 3","pages":"qvaf017"},"PeriodicalIF":0.0,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13375290/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148709057","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":"Designating river environments as bathing waters: challenges and opportunities at the science-policy interface.","authors":"David M Oliver","doi":"10.1093/sumbio/qvaf015","DOIUrl":"10.1093/sumbio/qvaf015","url":null,"abstract":"<p><p>Regulatory standards for primary contact recreation are used around the world to limit risks to human health from exposure to poor water quality. Prior to 2020, no stretches of river in the UK were designated as bathing water environments. However, growing recreational use of rivers combined with grassroots action by campaign groups to promote a river clean-up agenda has helped to establish, and increase the number of, designated riverine bathing waters in the UK. Nevertheless, since 2020 most newly designated riverine bathing waters have struggled to meet the microbiological standards associated with the Bathing Water Directive due to anthropogenic inputs originating from farming, sewage, and wastewater discharges. This is, in part, due to UK rivers being managed historically for different ecosystem services, with no statutory monitoring for public health. Calls are growing for river water quality improvements, fuelled by frequent media coverage concerning sewage overflows into freshwater environments and widespread recognition of poor delivery on targets for UK waterbody quality. In response, a five-point plan to improve understanding and future management of faecal indicators at riverine bathing water sites is proposed, offering transferability to other regions of the world where microbiological monitoring of river environments is needed to support recreation.</p>","PeriodicalId":516860,"journal":{"name":"Sustainable microbiology","volume":"2 3","pages":"qvaf015"},"PeriodicalIF":0.0,"publicationDate":"2025-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13375313/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148709009","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":"Impact and applications of cyclic di-GMP second messenger signaling in biotechnology and medicine.","authors":"Ute Römling","doi":"10.1093/sumbio/qvaf016","DOIUrl":"10.1093/sumbio/qvaf016","url":null,"abstract":"<p><p>3',3'-cyclic diguanylate (cyclic di-GMP) and alternative cyclic di- and oligonucleotides are ancient highly conserved signaling molecules of bacteria and archaea, which can be present in metazoans up to humans. Their impact in fundamental behavioral modes and physiological and metabolic processes, the modular organization of their signaling cascades and the versatility and flexibility of their components in microbes in combination with their far-reaching effects including stimulation of the innate and adaptive immune response in humans makes these molecules and the respective signaling cascades promising targets in antibiofilm therapy, modulation of multicellularity and tools for treatment strategies and biotechnological applications. This review will thus describe the current state-of-the-art of applications and use as therapeutic targets of cyclic di- and oligonucleotides and the limitations and challenges in the application of those molecules and their use as targets. Future possibilities to successfully exploit those molecules and their signaling cascades equally as potential shortcomings are discussed.</p>","PeriodicalId":516860,"journal":{"name":"Sustainable microbiology","volume":"2 3","pages":"qvaf016"},"PeriodicalIF":0.0,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13375341/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148709001","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":"Monitoring of antimicrobial resistance genes and influenza viruses in avian-populated water bodies.","authors":"Kata Farkas, Margaret E Knight, Nick Woodhall, Rachel C Williams, Wannipa Seerung, Reshma Silvester, Rachel Abbey, Matthew J Wade, Lorenzo Cattarino, Tom White, Davey Jones","doi":"10.1093/sumbio/qvaf013","DOIUrl":"10.1093/sumbio/qvaf013","url":null,"abstract":"<p><p>Monitoring zoonotic and multi-species pathogens is challenging due to the resources required to sample individual animals. In this study, we propose the use of DNA/RNA detection methods to assess the prevalence of bacterial, antimicrobial resistance (AMR), and viral markers in 19 water sites in England and Wales where close contact occurs with avian species. For bacteria and AMR monitoring, we utilized high-throughput quantitative polumerase chain reaction (HT-qPCR), which revealed a consistent abundance of AMR genes and mobile genetic elements, with aminoglycoside-resistance gene <i>aadA7</i> being most prevalent. Elevated levels of multidrug resistance genes were detected at two sites, potentially linked to wildlife rather than anthropogenic factors. The <i>intl3</i> gene was a dominant integron, supporting its use as a marker for AMR prevalence. We also developed a streamlined pipeline (including sampling, sample process and pathogen identification/quantification) for influenza prevalence assessment. The detection of influenza virus coincided with reported avian influenza outbreak in wild birds. The frequent detection of human (crAssphage) and bird-associated (<i>Catellicoccus marimammalium</i>) markers suggested that they provide a robust framework for assessing faecal pollution in water bodies. This study demonstrates how molecular monitoring can track emerging pathogens simultaneously and identify pollution sources, providing a valuable approach for the surveillance of zoonotic threats.</p>","PeriodicalId":516860,"journal":{"name":"Sustainable microbiology","volume":"2 2","pages":"qvaf013"},"PeriodicalIF":0.0,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13375323/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148709289","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":"Allochthonous carbon primarily of marine origin in Irish saltmarshes: novel insights from bacteriohopanepolyol biomarkers.","authors":"Saule Akhmetkaliyeva, Robert B Sparkes, Eliza Fairchild, Ragna Hoogenboom, Grace M Cott","doi":"10.1093/sumbio/qvaf012","DOIUrl":"10.1093/sumbio/qvaf012","url":null,"abstract":"<p><p>Coastal blue carbon ecosystems (BCEs) are among the most effective carbon (C) sinks, yet Irish saltmarshes, covering 4000-6500 hectares, remain understudied in terms of C sources. Understanding saltmarshes' connectivity to marine and terrestrial sources, and the provenance of allochthonous (ex-situ-produced) carbon, is essential for assessing their long-term C sequestration potential and management. This study analysed organic carbon (OC) and bacteriohopanepolyol biomarkers (BHPs), microbial lipids that trace sedimentary OC sources, in sediment cores from Derrymore Island (DI) and North Bull Island (NBI). OC concentrations varied down-core, ranging from 0.26-26.68 wt% at DI, 0.44-12.19 wt% in NBI's North Lagoon, and 0.07-26.45 wt% in its South Lagoon. The <i>R</i> _soil index values (0.02-0.24 at DI, 0.01-0.06 at NBI) indicate a predominantly marine OC origin, though soil-specific BHPs were present, with higher soil marker concentrations in deeper, older DI sediments. This suggests saltmarshes may gradually transition toward terrestrial characteristics over time. This study enhances our understanding of OC sequestration in two Irish saltmarshes, highlighting their dynamic nature. The allochthonous nature of sequestered sedimentary OC further underscores the importance of sustained tidal influence and connectivity with the wider marine environment. Further research into labile OC sources is recommended to enhance carbon assessments in these ecosystems.</p>","PeriodicalId":516860,"journal":{"name":"Sustainable microbiology","volume":"2 3","pages":"qvaf012"},"PeriodicalIF":0.0,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13375332/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148708988","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":"Biological resources driving productivity: bioinputs for sustainable plant agriculture in Brazil.","authors":"Mateus Florentino Barbosa, Rodrigo Maurício Marinsek Sales, Flávia Augusta Dias Galarza, Clarissa Quirino Kruger, Léia Cecília de Lima Fávaro, Betania Ferraz Quirino","doi":"10.1093/sumbio/qvaf011","DOIUrl":"10.1093/sumbio/qvaf011","url":null,"abstract":"<p><p>Brazil is a world leader in agriculture, playing an important role in world food security. Agriculture has changed drastically over the years in Brazil. Different kinds of technology are being developed to increase production, reduce costs, and to decrease environmental impacts of agriculture. In 2020, the Brazilian Ministry of Agriculture, Livestock, and Supply (MAPA) launched the National Bioinputs Program to promote the adoption of sustainable technologies derived from biological resources, bioinputs, many of which are microbial-based. Bioinputs aim at enhancing agricultural productivity, improving soil health, and mitigate environmental impacts. Bioinputs can be classified into three main groups according to functionality: those that promote plant growth and development, those that serve as biological pest control agents, and those that contribute to soil conditioning or restoration. Each of these categories is further subdivided according to their mode of action. In this review, we will focus on bioinputs currently commercialized in Brazil. Details about these products, including the microorganisms involved, their mode of action, and target crops will be discussed. The advantages and challenges for widespread adoption of this new technology will be explored.</p>","PeriodicalId":516860,"journal":{"name":"Sustainable microbiology","volume":"2 3","pages":"qvaf011"},"PeriodicalIF":0.0,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13375378/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148708984","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":"Occurrence and molecular detection of antibiotic-resistant genes in <i>Escherichia coli</i> isolated from drinking water in selected locations in southwestern Nigeria.","authors":"Kehinde Olubunmi Adediran, Mary Adejumoke Adefioye, Saheed Adekunle Akinola, Olugbenga A Olowe","doi":"10.1093/sumbio/qvaf010","DOIUrl":"10.1093/sumbio/qvaf010","url":null,"abstract":"<p><p>The quality of water available for households' use was investigated in some selected locations in Nigeria. A total of 180 water samples were analyzed. The antimicrobial susceptibility testing of the <i>Escherichia coli</i> from the water samples was determined using standard microbiological protocols and detection of extended-spectrum β-lactamase (ESBL) resistance genes. Microbiological mean total coliform count values obtained in both stored and source water in sampling locations were high ranging from 3.10 ± 1.46 to 156.80 ± 42.9 cfu/100 ml for stored water and from 0.50 ± 0.31 to 90.60 ± 38.05 cfu/100 ml for source water. Also, the majority of the source waters were devoid of fecal coliform, whereas the stored water had mean count values between 0.80 ± 0.70 and 64.30 ± 14.15 cfu/100 ml. Twenty-five <i>E. coli</i> isolates obtained from the water samples were resistant to most antibacterial used. However, four of the <i>E. coli</i> isolates were sensitive to cefotaxime. Polymerase chain reaction (PCR) revealed that 11 out of 25 <i>E. coli</i> isolates (44%) screened for ESBL resistance genes had TEM genes, while four of the isolates (16%) had SHV genes. This study concluded that drinking water could be a source of exposure to antibiotic-resistant <i>E. coli</i>, which may pose a threat to human populations and their health in the study area.</p>","PeriodicalId":516860,"journal":{"name":"Sustainable microbiology","volume":"2 3","pages":"qvaf010"},"PeriodicalIF":0.0,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13375381/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148709141","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":"Mycorrhizal symbioses and Arctic shrubification.","authors":"Kevin K Newsham, Peter Convey","doi":"10.1093/sumbio/qvaf009","DOIUrl":"10.1093/sumbio/qvaf009","url":null,"abstract":"<p><p>A unifying feature of the deciduous and evergreen shrubs contributing to the greening of the Arctic landmass-the process known as shrubification-is that their roots consistently form ectomycorrhizal or ericoid mycorrhizal symbioses with soil fungi. Here, we review the potential roles of these symbioses in shrubification, focusing on their effects on shrub nitrogen (N) acquisition from N-limited Arctic tundra soils. Enhanced shrub growth in response to warming or elevated atmospheric CO₂ is attributable to several mycorrhizal-mediated processes associated with N acquisition, including increased frequencies of fungal symbionts on, in, or around shrub roots, elevated activities of extracellular enzymes secreted by mycorrhizal hyphae, or enhanced hyphal access to N at the permafrost thaw front. An analysis of the responses to experimental warming of 11 frequent ectomycorrhizal fungal genera shows no effects on their abundances but a 20% reduction in taxonomic richness in warmed soil, suggesting that elevated temperature selects for specific fungal taxa. The effects of warming on ectomycorrhizas are most pronounced in mesic soils. We conclude that ectomycorrhizal and ericoid mycorrhizal symbioses most probably influence shrubification, but that further research is needed to determine the processes by which they do so.</p>","PeriodicalId":516860,"journal":{"name":"Sustainable microbiology","volume":"2 2","pages":"qvaf009"},"PeriodicalIF":0.0,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13375330/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148709296","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":"Testing eukaryotic routes for heterologous production of ketocarotenoids in cyanobacteria.","authors":"Anika V Mahdi, Dennis N Wittmann, Sayali S Hanamghar, Oskar Zorć, Jialan Cao, G Alexander Groß, Poul Erik Jensen, David A Russo, Julie A Z Zedler","doi":"10.1093/sumbio/qvaf008","DOIUrl":"10.1093/sumbio/qvaf008","url":null,"abstract":"<p><p>Pigments and dyes are widely used in multiple industries. Ketocarotenoids are a highly sought-after group of pigments with a dark-red hue and strong antioxidant properties. Currently, chemical synthesis is the major route for ketocarotenoid production. However, the environmental risks and large demand have led to a call for the development of more sustainable sources. Cyanobacteria have promising properties for sustainable ketocarotenoid production: Some strains show fast growth, are genetically tractable, and natively produce ketocarotenoid precursors. Despite a few promising studies, engineering ketocarotenoid production in cyanobacteria is so far underexplored. Here, we expand the biosynthetic routes for ketocarotenoids by testing the astaxanthin synthase CrtS of <i>Xanthophyllomyces dendrorhous</i> and the β-carotene ketolase CrBKT from <i>Chlamydomonas reinhardtii</i>. While CrtS was successfully produced in <i>Synechocystis</i> sp. PCC 6803, no changes in ketocarotenoid profiles were detected. On the other hand, expression of <i>CrBKT</i> in <i>Synechococcus elongatus</i> UTEX 2973 and <i>Synechocystis</i> sp. PCC 6803 led to the production of both canthaxanthin (0.12% and 0.1% of dry cell weight, respectively) and astaxanthin (0.012% and 0.004% of dry cell weight, respectively). Looking forward, expression of <i>CrBKT</i> is a promising route to produce ketocarotenoids in cyanobacteria. But further work is needed to increase strain stability and product yields.</p>","PeriodicalId":516860,"journal":{"name":"Sustainable microbiology","volume":"2 2","pages":"qvaf008"},"PeriodicalIF":0.0,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13375318/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148709306","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":"Combinatorial characterization of bacterial taxa-driven differences in the microbiome of oyster beds.","authors":"Erika L Cyphert, Sanjiev Nand, Gabriela Franco, Michael Hajkowski, Luzmaria Soto, Danica Marvi Lee, Matthew C Ferner, Chela J Zabin, Jeffrey Blumenthal, Anna K Deck, Katharyn E Boyer, Laura W Burrus, Christopher J Hernandez, Archana Anand","doi":"10.1093/sumbio/qvaf006","DOIUrl":"10.1093/sumbio/qvaf006","url":null,"abstract":"<p><p>Oyster reefs and beds provide crucial ecosystem services, including water filtration, coastal protection, and habitat provision for marine species. However, these habitats face significant threats from climate change and anthropogenic stressors. To address these challenges, numerous oyster restoration initiatives have been undertaken globally. Intertidal microbial communities, comprising diverse bacteria, archaea, and unicellular eukaryotes, drive key biogeochemical processes, but remain poorly understood in ecosystems targeted for oyster restoration. We investigated the microbiome associated with the Olympia oyster (<i>Ostrea lurida)</i>, a key restoration target in the western USA, by characterizing microbial abundance and diversity in sediment, oyster-associated biofilm, and oysters at four sites in San Francisco Bay. Our findings revealed distinct microbial assemblages in oysters and sediment compared to biofilm. Diversity, measured by the Shannon index, was highest at Heron's Head (5.47), followed by Brickyard Park (5.35), Dunphy Park (5.17), and Point Pinole (4.85). Notably, microbes <i>Ruminococcus, Streptococcus, Staphylococcus, Prevotella, Porphyromonas, Parvimonas, Neisseria, Lactococcus, Haemophilus, Fusobacterium, Dorea, Clostridium, Campylobacter, Bacteroides</i>, and <i>Akkermansia</i> were positively associated with biofilm collected from hard surfaces where oysters were attached at most sites. Potential implications of these microbial associations for oyster growth, survival, and interactions with environmental factors remain largely unexplored. Future research is warranted on culturing specific microbes to assess their functions and investigating environmental and ecological drivers of microbial diversity to determine relationships indicative of oyster health and potential for enhancing oyster recruitment.</p>","PeriodicalId":516860,"journal":{"name":"Sustainable microbiology","volume":"2 2","pages":"qvaf006"},"PeriodicalIF":0.0,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12102694/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144145345","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}