ISME communications最新文献

{"title":"Black Sea picocyanobacteria exploit ancestral traits for energy and chlorophyll production in dark anoxia.","authors":"Maciej Bartosiewicz, Pedro J Cabello-Yeves, Ester M Eckert, Andrea Di Cesare, Richard J Puxty, Anna Przytulska, Helena Osterholz, Anders Meibom, Stephane Escrig, Nina Dzhembekova, Jakob Zopfi, Moritz F Lehmann, Cristiana Callieri","doi":"10.1093/ismeco/ycag159","DOIUrl":"10.1093/ismeco/ycag159","url":null,"abstract":"<p><p>Picocyanobacteria, typically associated with oxygenated waters, also thrive in oxygen minimum zones (OMZs) and anoxic environments. The extent to which retention of diverse ancestral anaerobic traits facilitate their metabolic flexibility with regards to transitioning between oxic and anoxic habitats is poorly understood. Here, using Black Sea <i>Cyanobium</i> (BSA11S), we performed ¹³C-glucose and ¹⁵N-ammonium incubations coupled with nanoscale ion mass spectrometry (NanoSIMS) and transcriptomics to characterize the growth mode and gene expression during transition from light-to-dark and oxic-to-anoxic conditions. Incubated picocyanobacteria assimilate ¹³C-glucose and ammonium under anoxic-dark conditions, grow slowly without light, and retain the capability to synthesize photosynthetic pigments. These organisms moderately upregulate genes responsible for chlorophyll-<i>a</i>/bilin biosynthesis, uptake of C sources, debranching of glycogen storage, and the pentose phosphate pathway for ATP, NADH, and NADPH production, as well as genes involved in NAD+ regeneration, including proton-reduction hydrogen-metabolism coupled with lactic acid fermentation. Our results support the remarkable versatility, plasticity, and potential for mixotrophy in photoautotrophs that allow them to dominate diverse aquatic systems worldwide.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag159"},"PeriodicalIF":6.4,"publicationDate":"2026-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13588713/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149009294","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":"Genetic access to the obligate cyanobacterial endosymbiont <i>Nostoc azollae</i> within the <i>Azolla</i> fern host.","authors":"Cristina Sarasa-Buisán, Erbil Güngör, Enrique Flores, Peter Lindblad, Sandra Nierzwicki-Bauer, Henriette Schluepmann","doi":"10.1093/ismeco/ycag209","DOIUrl":"10.1093/ismeco/ycag209","url":null,"abstract":"<p><p>Eukaryote-associated microbes are ubiquitous, but their essential roles in the development and ecology of their host is yet to be fully understood, partly because complex associations cannot be reconstituted and, in many instances, the genetic tools to elucidate those roles are not available. Here, we report the conjugative transfer of DNA into <i>Nostoc azollae</i> within three <i>Azolla</i> fern hosts. <i>N. azollae</i> is a filamentous, N₂-fixing, heterocyst-forming cyanobacterium which is the predominant obligate endosymbiont of the complex microbial community associated with the floating ferns of the genus <i>Azolla</i>. The cyanobiont provides fixed nitrogen to its host, supporting maximum growth rates without any N-fertilizer and making <i>Azolla</i> symbioses both ecologically and agriculturally important. Triparental mating protocols and fluorescent reporter detection were optimized for the cyanobiont isolated from the fern, allowing the further demonstration of heterologous gene expression in <i>N. azollae</i> driven by several promoters, including some of a CRISPR-associated transposon system. <i>Azolla</i> was then treated with a cytokinin hormone to render fern shoot apexes amenable to <i>in planta</i> conjugation, permitting DNA transfer to, and gene expression in two distinct developmental stages of <i>N. azollae</i> within <i>Azolla</i>. These included (i) cells of filaments from the Shoot Apical <i>Nostoc</i> colony, the only cyanobacterial stem-cell population vertically transmitted across fern generations, and (ii) cells from differentiated filaments in early formed <i>Azolla</i> leaf cavities. Our approach represents a technically groundbreaking advance for the genetic engineering of cyanobacterial endosymbioses that may be useful for other symbiotic systems, opening a way to investigate these important biological entities.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag209"},"PeriodicalIF":6.4,"publicationDate":"2026-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13540726/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148889480","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":"Soil aggregate and microbial traits mediate soil organic carbon accumulation in a paddy field under long-term elevated CO₂ and warming.","authors":"Yuan Liu, Mengting Li, Jiayi Xiong, Feng Li, Cheng Liu, Xiaoyu Liu","doi":"10.1093/ismeco/ycag206","DOIUrl":"https://doi.org/10.1093/ismeco/ycag206","url":null,"abstract":"<p><p>Climate change is increasingly impacting ecosystem functions and soil microorganisms, altering the accumulation and stability of soil organic carbon (SOC). However, the effect of climate change on SOC dynamics at the aggregate scale is poorly understood. Here, we conducted a 13-year experiment to investigate how elevated CO₂ (+200 ppm) and warming (+2°C) affect microbial community and necromass, and potential enzyme activities within soil aggregates in a paddy field. Results showed that long-term elevated CO₂ and warming significantly increased SOC and total nitrogen contents but reduced soil pH and total phosphorus (TP) within all three aggregate fractions. The SOC and TP contents were the most closely related to changes in microbial communities in aggregates. Elevated CO₂ and warming significantly increased microbial activities, specially increasing both fungal and bacterial abundances, leading to increases in C- and N-potential enzyme activities in large macroaggregate and microaggregates. In contrast, P-acquiring enzyme activities and the stoichiometry for P:N enzyme ratio significantly decreased with elevated CO₂ and warming. Furthermore, climate change effects on the microbial necromass varied across aggregate sizes. Elevated CO₂ significantly increased fungal necromass C and its contribution to SOC in large macroaggregates, while warming increased bacterial necromass C and its contribution to SOC in microaggregates. The SOC was positively correlated with microbial necromass and fungal necromass C in macroaggregates. The highest microbial necromass C in large macroaggregates may be attributed to higher fungal abundance and lower microbial enzyme activities. These results suggest that climate change may regulate SOC dynamics by affecting microbial growth and activity in soil aggregates. Our study highlights that soil aggregates stratify microbial communities and necromass, which improve our understanding the responses of agricultural ecosystem C cycling to future climate change.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag206"},"PeriodicalIF":6.4,"publicationDate":"2026-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13477214/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148763685","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":"Co-infection with <i>Streptococcus</i> and <i>Rothia</i> spp. drives prophage dynamics in <i>Pseudomonas aeruginosa</i> in an artificial sputum model.","authors":"Laura L Wright, Adrian Cazares, Wendy Figueroa, Laura Chatterley, Thomas Willmott, Siobhan O'Brien, Joanne L Fothergill","doi":"10.1093/ismeco/ycag191","DOIUrl":"https://doi.org/10.1093/ismeco/ycag191","url":null,"abstract":"<p><p>Chronic bacterial lung infections with <i>Pseudomonas aeruginosa</i> are common in people with cystic fibrosis (CF), but interactions with other members of the CF lung community, such as <i>Streptococcus</i> and <i>Rothia</i> spp., are not well understood. The aim of this study was to determine the impact of other species on <i>P. aeruginosa</i> using an artificial sputum medium (ASM) model. <i>P. aeruginosa</i> LESB58, representing a CF strain, was inoculated into ASM either alone or in co-culture with <i>Streptococcus anginosus</i>, <i>Streptococcus vestibularis</i>, <i>Rothia mucilaginosa</i>, or <i>Rothia dentocariosa</i>. Gene expression was assessed using RNAseq at 72 and 96 h timepoints. Free phage numbers assessed by plaque assay and qPCR. Differential expression of <i>P. aeruginosa</i> genes, including those related to virulence factors such as prophage, type III secretion, and exopolysaccharides, was seen in co-culture conditions. At 72 h, there was lower expression of prophage genes under co-culture conditions, and this corresponded with lower free phage. During co-culture, there were reduced levels of a D3112-like transposable phage, previously shown to drive CF-like adaptations in an experimental evolution model, and increased Pf1-like filamentous phage, associated with altered biofilm formation and immune responses. Gene expression changes during co-culture with <i>Streptococcus</i> and <i>Rothia</i> spp. were identified, affecting key <i>P. aeruginosa</i> virulence factors, including phage. Further work indicated changes to free phage levels of two important prophages with potential to affect <i>P. aeruginosa</i> adaptation, antibiotic resistance, and host immune response in the CF lung. This study emphasizes the importance of understanding the influence of lung commensals on focal pathogens.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag191"},"PeriodicalIF":6.4,"publicationDate":"2026-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13600431/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149042348","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":"BileActome reveals community-assembled bile acid metabolism in the rumen microbiome.","authors":"Boyan Zhang, Xianzhe Jiang, Hailong Zhao, Bing Wang","doi":"10.1093/ismeco/ycag205","DOIUrl":"https://doi.org/10.1093/ismeco/ycag205","url":null,"abstract":"<p><p>Microbial bile acid metabolism is an important link between microbiomes and host physiology, but its genetic basis remains difficult to resolve from genome and metagenome data. This is largely because existing annotation resources are not designed for the high sequence diversity and functional complexity of microbial bile acid genes. Here we present BileActome, a reusable annotation resource developed specifically for microbial bile acid metabolism. BileActome defines 27 experimentally supported gene families, including bile salt hydrolases, bile acid-inducible operon genes, and microbial hydroxysteroid dehydrogenases. Its design prioritizes experimentally supported functional sites when available and conserved domain features otherwise, while also distinguishing key functional subtypes. We applied BileActome to 1693 high-quality rumen metagenome-assembled and isolate genomes and validated its performance using controlled <i>in vitro</i> rumen fermentations under three bile acid interventions. In metagenomic gene-catalog analyses, BileActome enabled pathway-level interpretation of microbial responses to bile acid exposure, with the most reproducible responses centered on Bai-associated gene families. At genome scale, it generated a phylogeny-informed map of bile acid metabolic potential that was broader and more informative than Kyoto Encyclopedia of Genes and Genomes (KEGG)-based annotation. Further analyses of genomes, local gene organization, and genome-level guilds showed that bile acid metabolism in the rumen is modular, phylogenetically structured, and distributed across different microbial members. Deconjugation and oxidation/epimerization-related functions were widespread, whereas complete bile acid-inducible systems were less common. Together, these findings support a community-assembled model of bile acid metabolism and establish BileActome as an open and reproducible framework for studying specialized microbial functions in complex ecosystems.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag205"},"PeriodicalIF":6.4,"publicationDate":"2026-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13477222/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148763006","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":"Enhanced <i>Synechococcus</i> export associated with diatom sinking.","authors":"Takehiro Shimonaka, Taketoshi Kodama, Shigeyoshi Otosaka, Taku Wagawa, Takafumi Kataoka, Junya Hirai, Kazutaka Takahashi","doi":"10.1093/ismeco/ycag183","DOIUrl":"10.1093/ismeco/ycag183","url":null,"abstract":"<p><p>Phytoplankton sinking represents a major component of oceanic biological carbon sequestration, commonly referred to as the biological carbon pump (BCP). Despite their small size and lack of mineral ballast, pico-sized cyanobacteria are transported to the deep ocean and contribute to carbon sequestration. However, the mechanisms governing their sinking remain poorly understood. To address this knowledge gap, we investigated sinking eukaryotic and cyanobacterial communities and their DNA-based fluxes in zooplankton fecal pellets and non-fecal particles using metabarcoding and qPCR analyses targeting the 16S and 18S rRNA genes. Cyanobacteria, mainly <i>Synechococcus</i> subcluster 5.1 clade I, accounted for 3.11%-46.2% of phytoplankton reads in sinking particles, with their contribution and flux peaking during the spring diatom bloom. Diatoms were the largest contributors among phytoplankton and a dominant component of the eukaryotic assemblages in sinking particles. A substantial proportion of the sinking cyanobacterial flux was observed in the non-fecal particle fraction. The cyanobacterial sinking flux was not associated with satellite-derived surface cyanobacterial biomass but was significantly and positively correlated with the diatom sinking flux. These results suggest that the incorporation of cyanobacteria into diatom-containing aggregates represents a major pathway by which they contribute to the BCP, especially during the spring bloom. Our findings demonstrate positive feedback of diatom biomass on the BCP and highlight that modulation of interactions among phytoplankton groups regulates cyanobacterial sinking.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag183"},"PeriodicalIF":6.4,"publicationDate":"2026-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13503964/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148820504","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":"A field-based study of phyllosphere mycobiomes in apple orchards under varying agricultural management strategies.","authors":"Sophie Boutin, Jonathan Rondeau-Leclaire, Alexis Roy, Isabelle Laforest-Lapointe","doi":"10.1093/ismeco/ycag203","DOIUrl":"10.1093/ismeco/ycag203","url":null,"abstract":"<p><p>Microbial communities in the phyllosphere are key players in plant health and disease resistance, yet their response to agricultural management strategies remains poorly understood under field conditions. Here, we compare fungal community composition and diversity across conventional and organic apple orchards using ITS amplicon sequencing. Leaf samples were collected from six sites at three distinct time points during the 2023 growing season (in May, July, and August) corresponding approximately to monthly intervals throughout the summer. Flower samples were collected from the same trees in May. Our analyses reveal that agricultural management strategies are significantly associated with fungal community structure, with effects intensifying from May to July. Both types of management strategies showed enrichment for different genera known to include common apple tree pathogens: <i>Alternaria</i> and <i>Podosphaera</i> were associated with conventional sites, while <i>Didymella</i> and <i>Ramularia</i> were associated with organic sites. Although fungal alpha diversity was higher in May at conventional orchards compared to organic orchards, it declined over time at conventional sites while it remained stable at organic sites. Together, these patterns indicate that distinct management interventions impose contrasting selective pressures on the apple tree phyllosphere mycobiome, thus shaping both broad fungal community composition and the dominance dynamics of key fungal taxa. Our findings underscore the ecological relevance and inherent challenges of field-based microbiome research, and provide insights to inform the development of sustainable orchard management strategies grounded in fungal community dynamics.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag203"},"PeriodicalIF":6.4,"publicationDate":"2026-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13494798/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148802356","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":"Twenty-two novel glacier <i>Pseudomonas</i> species expand cultivated representation: nitrogen-cycling potential and temperature-responsive proteomes.","authors":"Chan Zhao, Lei-Lei Yang, Yu-Hua Xin, Qing Liu","doi":"10.1093/ismeco/ycag204","DOIUrl":"https://doi.org/10.1093/ismeco/ycag204","url":null,"abstract":"<p><p>Accelerating glacier retreat exports cryospheric microbiomes into downstream ecosystems, raising questions about their functional roles. However, a persistent gap between genomic predictions and physiologically validated functions exists, largely due to the scarcity of cultivated and taxonomically resolved model organisms from these environments. Here we characterize 23 <i>Pseudomonas</i> strains isolated from ice, cryoconite, and supraglacial meltwater collected across ten glaciers in China. Phylogenomic inference places them within the <i>Pseudomonas mandelii</i> subgroup, and genome metrics delineate 22 strains as distinct novel species (ANI ≤95.71%; dDDH ≤64.6% to their closest type strains). Phenotypic analyses showed broad environmental tolerance, including growth at -2°C, strain-dependent upper growth limits of 30°C-37°C, and growth over an approximate pH range of 5.0-11.0. Genome-based reconstruction predicted heterogeneous nitrogen-transforming potential, including DNRA-related genes in all strains, nitrate-reduction genes in 14 strains, complete denitrification marker sets in 12 strains, and nitrogen-fixation genes in one strain. Phenotypic assays showed broader nitrate-reduction activity than predicted, with all 23 strains reducing nitrate to nitrite and seven showing reduction beyond nitrite, underscoring the value of cultivation-based functional validation in non-model cryospheric bacteria. Comparative proteomics of four representative species at 0°C versus 28°C reveals shared temperature-responsive pathways and a common network backbone involving translation, proteostasis, and carbon economy. Together, these cultured genomes provide valuable models for linking cryospheric <i>Pseudomonas</i> diversity to temperature-responsive physiology and biogeochemical potential.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag204"},"PeriodicalIF":6.4,"publicationDate":"2026-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13600387/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149042361","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":"From CRISPR-Cas to Argonautes: Defense systems of bacteria and archaea in the hydrothermal deep subsurface.","authors":"Lei Su, Paraskevi Mara, Virginia Edgcomb, Andreas Teske","doi":"10.1093/ismeco/ycag200","DOIUrl":"https://doi.org/10.1093/ismeco/ycag200","url":null,"abstract":"<p><p>Microbial defense systems are central to virus-host interactions and thus to microbial survival but remain poorly studied in microbial communities of extreme environments. Here we examine the repertoire and distribution of microbial defense genes in hydrothermally influenced deep subsurface sediments and rocks of the Guaymas Basin (Gulf of California). Restriction-modification and abortive infection systems were broadly distributed across the examined sediment depths, and clustered, regularly interspaced short palindromic repeats-Cas systems were primarily detected within temperate surficial sediments. Prokaryotic Argonaute genes were found mostly in archaeal MAGs at elevated temperatures up to 81.8°C. Overall defense gene repertoire declines downcore, as temperature increases and phylogenetic host range narrows, with phylogeny as the decisive control factor. We suggest that these defense systems, together with DNA repair mechanisms, protein maintenance activities, and RNA modification pathways, constitute a survival toolkit for the hydrothermally influenced subsurface, where energy limitation and temperature extremes select for resilient microbial communities.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag200"},"PeriodicalIF":6.4,"publicationDate":"2026-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13477220/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148763779","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":"Fit for purpose: evaluation and evolution of agricultural bioinoculants across production landscapes.","authors":"Lauren M Hemara, Rebecca T Doyle, George C diCenzo, Matthew G Bakker, Kailey R Hopkins, Jangwoo Lee, Ivan J Oresnik, Terrence H Bell","doi":"10.1093/ismeco/ycag190","DOIUrl":"10.1093/ismeco/ycag190","url":null,"abstract":"<p><p>Microbial inoculants are currently advancing sustainable agriculture by reducing reliance on chemical fertilizers and pesticides, and enhancing soil and plant health in ways that traditional chemical inputs cannot. However, despite over a century of research and development, their in-field establishment and performance remain unreliable, limiting their widespread adoption and impact. Typically, the selection of candidate inoculants centers around performance-based traits (e.g. nitrogen fixation) assessed <i>in vitro</i>; yet, viable and impactful inoculants must express a wide range of traits that promote their fitness across heterogeneous landscapes. Successful inoculants must do well across the industrial production pipeline, which requires rapid growth in nutrient-rich liquid media. They must also tolerate long-term storage and subsequently perform consistently across diverse field conditions. These traits are essential for scalability, economic viability, and impact. To date, commercially available inoculants are mostly based on microbes exhibiting rapid growth under common laboratory conditions, traits which may or may not correlate with in-field delivery of beneficial functions. In this review, we propose a multi-faceted evaluation approach for inoculant performance, considering both biotic and abiotic aspects of inoculant success. We then use this framework to evaluate how adaptive laboratory evolution could enhance inoculant performance at key industrial pipeline steps. This approach is essential to widening the range of taxa that are considered for commercialization, while identifying and potentially mitigating the pitfalls of growing, storing, and applying microbes through traditional industrial production pipelines.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag190"},"PeriodicalIF":6.4,"publicationDate":"2026-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13502203/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148814995","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}