Elisabeth Williamson, Kelly Hill, Katja Hogendoorn, Raphael Eisenhofer
{"title":"The bacterial community associated with the solitary resin bee Megachile tosticauda throughout its life cycle.","authors":"Elisabeth Williamson, Kelly Hill, Katja Hogendoorn, Raphael Eisenhofer","doi":"10.1093/femsec/fiaf023","DOIUrl":"10.1093/femsec/fiaf023","url":null,"abstract":"<p><p>Unlike in eusocial bees where the identity, acquisition, and function of symbiotic microbes are well understood, little is known about the relationships formed between solitary bees and bacteria. Assessing the potential role of microbes in solitary bee health is important, especially in the face of global bee declines. Early evidence suggests solitary bee microbiomes differ between bee species and development stages, but the reported bacteria are often indistinguishable from environmental taxa. Here, we use metabarcoding of the 16S rRNA gene to characterize the bacterial communities associated with solitary resin bee Megachile tosticauda. We describe the microbiome at different life cycle stages, and within pollen provisions, and investigate indirect inheritance from nesting substrate upon eclosion. The microbiome of adult M. tosticauda was consistent between samples, and the bacterial composition of larval pollen supplies changed with progressing larval development. In wild adults and pollen provisions, the genus Acinetobacter-a common nectar associate-dominated the communities. In prepupae and frass, Tyzzerella dominated, a genus that has been found in a number of other immature bee systems. Intriguingly, while wild adults did not harbour Tyzzerella, all bees that had newly emerged from the nest did. The combined observations show that M. tosticauda acquire their bacterial community from the environment, and Tyzzerella may represent a beneficial symbiont for mature brood.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143556166","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Meaghan Castledine, Daniel Padfield, Rai Lewis, Angus Buckling
{"title":"Microbial community structure is affected by phage-resistance associated increases in host density.","authors":"Meaghan Castledine, Daniel Padfield, Rai Lewis, Angus Buckling","doi":"10.1093/femsec/fiaf027","DOIUrl":"https://doi.org/10.1093/femsec/fiaf027","url":null,"abstract":"<p><p>Lytic bacteriophages ('phages') can limit bacterial densities and shape community structure, either directly through lysis or indirectly through costs to resistance. However, phages have also been reported to have no, and in some cases even positive, effects on host densities. Here, we investigate the mechanisms behind an increase in host density in Variovorax sp. populations following a fixation of resistance that was maintained after phage extinction. Our results demonstrate that the density increase was a genetic trait coinciding with resistance emergence. Growth curves showed that phage resistance shifted population growth curves such that density was higher in the death-phase. This density-increasing effect of resistance had important implications for community structure with phage resistant Variovorax decreasing the density of a conspecific. That resistance to lytic phage can increase host densities has implications for wider ecology and phage therapy where lytic phages are presumed to have negative effects on their hosts.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143656603","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Plipastatin is a shared good by Bacillus subtilis during combating Fusarium spp.","authors":"Rune Overlund Stannius, Ákos T Kovács","doi":"10.1093/femsec/fiaf020","DOIUrl":"10.1093/femsec/fiaf020","url":null,"abstract":"<p><p>Bacillus subtilis a Gram-positive soil-dwelling bacterium known for its wide range of bioactive secondary metabolites. The lipopeptide plipastatin produced by most B. subtilis isolates have been shown to exhibit potent antifungal activity against plant pathogenic fungi. While the effect of these antifungal compounds are well studied in the context of biocontrol, much less is known of their role in the environment, which also harbor nonproducing strains of these compounds. Fusarium species produce multiple antibacterial compounds resulting in dysbiosis of the plant-associated microbiome and inhibition of plant beneficial bacteria like B. subtilis. While plipastatin is expected to be important for survival of B. subtilis, not all isolates carry the biosynthetic gene cluster for plipastatin suggesting that the protective effect of plipastatin might be shared. In this study, we investigated the protective effect of plipastatin against Fusarium oxysporum in a coculture using a producer and a nonproducer isolate of plipastatin. We tested the survival of single and cocultured strains under Fusarium challenge in liquid media and solid agar plates to dissect the influence of spatial structure. Our results highlights that plipastatin protects the nonproducer strain in a density-dependent manner.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143499223","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Valentin Barberoux, Adriana Anzil, Loïc Meinertzhagen, Thanh Nguyen-Dinh, Pierre Servais, Isabelle F George
{"title":"Spatio-temporal dynamics of bacterial community composition in a Western European watershed, the Meuse River watershed.","authors":"Valentin Barberoux, Adriana Anzil, Loïc Meinertzhagen, Thanh Nguyen-Dinh, Pierre Servais, Isabelle F George","doi":"10.1093/femsec/fiaf022","DOIUrl":"10.1093/femsec/fiaf022","url":null,"abstract":"<p><p>This study aimed to identify factors influencing bacterial diversity in the Meuse River watershed by analyzing 42 locations sampled in spring and summer 2019, combined with biweekly sampling of one mid-stream location for a year. Bacterial community composition (BCC) was assessed in the small (SF; <5 µm) and large fractions (LF; ≥5 µm,), alongside physico-chemical parameters. LF consistently exhibited greater alpha diversity than SF. During the spatial campaigns, alpha diversity increased downstream in spring with high discharge, and BCC differed significantly between headwaters and the main river. Along this axis, several genera, Flavobacterium, Limnohabitans, and Aquirufa stood out as indicators of good water quality. Rhodoferax, another taxon indicative of good water quality, prevailed in the headwaters and during winter. In contrast, two cyanobacteria genera indicators of poor river quality, Microcystis PCC 7914 and Cyanobium PCC 6307, peaked in summer. BCC in spring and summer temporal samples aligned with spatial ones, while winter and autumn samples had distinct BCC. Finally, season, temperature, and distance from river mouth were the main driving parameters of beta diversity, outweighing the effect of fraction size on the BCC. These findings reinforce the notion that local conditions exert significant influence on bacterial communities in rivers.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143566530","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Andreas Härer, Joshua Dominguez, Jonathan B Shurin, Diana J Rennison
{"title":"Contrasting alpha, beta, and gamma diversity in the littoral zones of mountain lakes: effects of habitat size and within-lake community structuring on bacterial biogeography.","authors":"Andreas Härer, Joshua Dominguez, Jonathan B Shurin, Diana J Rennison","doi":"10.1093/femsec/fiaf026","DOIUrl":"https://doi.org/10.1093/femsec/fiaf026","url":null,"abstract":"<p><p>Research on microbial biogeography has revealed key patterns like the diversity-area relationship and distance-decay of similarity. However, how habitat size affects bacterial diversity in freshwater environments remains largely unclear. Here, we characterize bacterial communities in the littoral zones of ten mountain lakes in the Sierra Nevada, California, ranging in surface area from 0.92 to 71.72 hectares. Despite significant habitat size effects on community composition, dominant bacterial phyla were shared across lakes. We found no evidence for diversity-area relationships, either in single samples (alpha diversity) or cumulative lake-level samples (within-lake gamma diversity), when accounting for environmental variation. Moreover, within-lake beta diversity showed little spatial structuring, with similar bacterial community composition across samples regardless of geographic distance. Gamma diversity did not reach saturation with our sample size, and lake size had no effect on the predicted sample size necessary to reach gamma diversity saturation. Our findings offer new insights into diversity-area dynamics and spatial structuring by investigating alpha, beta, and gamma diversity in freshwater environments. Notably, individual water samples captured much of the bacterial community, with strong correlations between alpha and gamma diversity. These results advance our understanding of microbial biogeography and inform sampling designs for characterizing bacterial diversity in freshwater ecosystems.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647862","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Stefanie Becker, Thu Trang Dang, Ran Wei, Andreas Kappler
{"title":"Evaluation of Thiobacillus denitrificans' sustainability in nitrate-reducing Fe(II) oxidation and the potential significance of Fe(II) as a growth-supporting reductant.","authors":"Stefanie Becker, Thu Trang Dang, Ran Wei, Andreas Kappler","doi":"10.1093/femsec/fiaf024","DOIUrl":"https://doi.org/10.1093/femsec/fiaf024","url":null,"abstract":"<p><p>The Betaproteobacterium Thiobacillus denitrificans (ATCC 25259) oxidizes Fe(II) while reducing nitrate, yet its capacity for autotrophic growth as a nitrate-reducing Fe(II)-oxidizer remains uncertain. This study explored this capacity through cultivation experiments across multiple transfers, using growth medium with Fe(II) and nitrate as sole electron donor and acceptor, respectively. This setup necessitated nitrate reduction coupled to Fe(II) oxidation as the primary energy-yielding mechanism and Fe(II) as the exclusive electron donor for CO2 fixation and biomass production. Thiosulfate/nitrate pre-grown T. denitrificans oxidized 42% of 10 mM Fe(II), reduced 54% of 3.5 mM nitrate, and accumulated 1.6 mM nitrite, but showed no cell growth. Subsequent transfers from this Fe(II)/nitrate culture to fresh medium with Fe(II) and nitrate showed no nitrate-reducing Fe(II) oxidation or population growth. While bacterial activity (Fe(II) oxidation, nitrate reduction) occurred in the first transfer from thiosulfate/nitrate to Fe(II)/nitrate, nitrite was produced, further reacting with Fe(II) abiotically (chemodenitrification). A kinetic model assessed enzymatic versus abiotic Fe(II) oxidation, revealing enzymatic oxidation accounted for twice as much (ca. 70%) as abiotic denitrification (ca. 30%) within 22 days. These findings suggest T. denitrificans performs the first step of denitrification with Fe(II) as an electron donor but does not achieve autotrophic growth under these conditions.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647863","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dominika Klimek, Malte Herold, Inês Rosado Vitorino, Zuzana Dedova, Sebastien Lemaigre, Jimmy Roussel, Xavier Goux, Olga Maria Lage, Magdalena Calusinska
{"title":"Insights into the phylogenetic and metabolic diversity of Planctomycetota in anaerobic digesters and the isolation of novel Thermoguttaceae species.","authors":"Dominika Klimek, Malte Herold, Inês Rosado Vitorino, Zuzana Dedova, Sebastien Lemaigre, Jimmy Roussel, Xavier Goux, Olga Maria Lage, Magdalena Calusinska","doi":"10.1093/femsec/fiaf025","DOIUrl":"https://doi.org/10.1093/femsec/fiaf025","url":null,"abstract":"<p><p>Studying bacteria in anaerobic digestion (AD) is crucial for optimising microbial processes. While abundant taxa are often studied, less abundant groups may harbour novel metabolic potential. This study fills the gap by focusing on the Planctomycetota phylum, known to encode diverse carbohydrate-active enzymes (CAZymes). Despite their common presence in diverse aerobic and anaerobic environments, their role in AD is relatively unexplored. We utilised both culture-dependent and culture-independent techniques to investigate the phylogenetic and metabolic diversity of Planctomycetota within AD reactors. Our findings revealed that among the diverse planctomycetotal operational taxonomic units present, only a few are prevalent and abundant community members. Planctomycetota share functional traits with e.g. Verrucomicrobiota exhibiting distinct CAZyme gene repertoires that indicates specialisation in degrading algal polysaccharides and glycoproteins. To explore the planctomycetotal metabolic capabilities, we monitored their presence in algal-fed digesters. Additionally, we isolated a strain from mucin-based medium, revealing its genetic potential for a mixotrophic lifestyle. Based on the genomic analysis, we propose to introduce the Candidatus Luxemburgiella decessa gen. nov. sp. nov., belonging to the Thermoguttaceae family within the Pirellulales order of the Planctomycetia class. This study enhances our understanding of Planctomycetota in AD by highlighting their phylogenetic diversity and metabolic capabilities.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647864","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Diana Masch, François Buscot, Wolfgang Rohe, Kezia Goldmann
{"title":"Bark beetle infestation alters mycobiomes in wood, litter, and soil associated with Norway spruce.","authors":"Diana Masch, François Buscot, Wolfgang Rohe, Kezia Goldmann","doi":"10.1093/femsec/fiaf015","DOIUrl":"10.1093/femsec/fiaf015","url":null,"abstract":"<p><p>Recent exceptionally hot and dry summers provoked massive bark beetle outbreaks in German forests, which killed many conifers, forcing to clear-cut complete non-mature stands. The importance of fungi in ecosystems in particular in association with trees is widely recognized, but the ecology of how insect infestations of trees affect their mycobiomes remains poorly understood. Using Illumina MiSeq sequencing, we investigated fungal communities in soil, litter, and stem wood at early and late stages of bark beetle infestation in a Norway spruce [Picea abies (L.) Karst] stand in Central Germany. Fungal diversity decreased from soil to wood, with the highest proportion of unknown fungi in stem wood. Lifestyles, particularly of those fungi associated with stem wood, clearly changed depending on the infestation stage. The answer of tree-associated fungi to beetle infestation was characterized by an increasing community dissimilarity among all three habitats, i.e. it concerned not only the above-ground fungal communities directly connected to the tree. Our study, thus, pinpoints the cascading effects of tree infestations by bark beetles and subsequent tree diebacks on the proximate and distant mycobiomes of the plant soil system, which should be entirely considered to tackle the effects of environmental events on tree health.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11840958/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143074435","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Multi-omics analysis of the correlation between surface microbiome and metabolome in Saccharina latissima (Laminariales, Phaeophyceae).","authors":"Emilie Adouane, Cédric Hubas, Catherine Leblanc, Raphaël Lami, Soizic Prado","doi":"10.1093/femsec/fiae160","DOIUrl":"10.1093/femsec/fiae160","url":null,"abstract":"<p><p>The microbiome of Saccharina latissima, an important brown macroalgal species in Europe, significantly influences its health, fitness, and pathogen resistance. Yet, comprehensive studies on the diversity and function of microbial communities (bacteria, eukaryotes, and fungi) associated with this species are lacking. Using metabarcoding, we investigated the epimicrobiota of S. latissima and correlated microbial diversity with metabolomic patterns (liquid chromatography coupled to tandem mass spectrometry). Specific epibacterial and eukaryotic communities inhabit the S. latissima surface, alongside a core microbiota, while fungal communities show lower and more heterogeneous diversity. Metabolomic analysis revealed a large diversity of mass features, including putatively annotated fatty acids, amino derivatives, amino acids, and naphthofurans. Multiple-factor analysis linked microbial diversity with surface metabolome variations, driven mainly by fungi and bacteria. Two taxa groups were identified: one associated with bacterial consortia and the other with fungal consortia, each correlated with specific metabolites. This study demonstrated a core bacterial and eukaryotic microbiota associated with a core metabolome and highlighted interindividual variations. Annotating the surface metabolome using Natural Products databases suggested numerous metabolites potentially involved in interspecies chemical interactions. Our findings establish a link between microbial community structure and function, identifying two microbial consortia potentially involved in the chemical defense of S. latissima.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11879540/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143472357","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gerardo Mejia, Angélica Jara-Servin, Cristóbal Hernández-Álvarez, Luis Romero-Chora, Mariana Peimbert, Rocío Cruz-Ortega, Luis D Alcaraz
{"title":"Rhizosphere microbiome influence on tomato growth under low-nutrient settings.","authors":"Gerardo Mejia, Angélica Jara-Servin, Cristóbal Hernández-Álvarez, Luis Romero-Chora, Mariana Peimbert, Rocío Cruz-Ortega, Luis D Alcaraz","doi":"10.1093/femsec/fiaf019","DOIUrl":"10.1093/femsec/fiaf019","url":null,"abstract":"<p><p>Studies have suggested that reduced nutrient availability enhances microbial diversity around plant roots, positively impacting plant productivity. However, the specific contributions of rhizosphere microbiomes in nutrient-poor environments still need to be better understood. This study investigates tomato (Solanum lycopersicum L.) root microbiome under low-nutrient conditions. Plants were grown in hydroponics with soil-derived microbial community inoculations. We hypothesized that nutrient limitation would increase the selection of beneficial bacterial communities, compensating for nutrient deficiencies. We identified 12 294 operational taxonomic units across treatments and controls using 16S rRNA gene sequencing. Increased plant biomass was observed in treatments compared to controls, suggesting a role for the microbiome in mitigating nutrient limitations. The relative abundance of genera such as Luteolibacter and Sphingopyxis relative abundance correlated with plant phenotypic traits (P ≤ .05), and their presence was further validated using shotgun metagenomics. We annotated 722 677 protein families and calculated a core set of 48 116 protein families shared across all treatments and assigned them into bacteria (93.7%) and eukaryota (6.2%). Within the core bacterial metagenome, we identified protein families associated with pathways involved in positive plant interactions like the nitrogen fixation. Limited nutrient availability enhanced plant productivity under controlled conditions, offering a path to reduce fertilizer use in agriculture.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11879582/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143499416","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}