FEMS microbiology ecology最新文献

{"title":"Vintage and terroir are the strongest determinants of grapevine carposphere microbiome in the viticultural zone of Drama, Greece.","authors":"Fotios Bekris, Elena Papadopoulou, Sotirios Vasileiadis, Nikolaos Karapetsas, Serafeim Theocharis, Thomas K Alexandridis, Stefanos Koundouras, Dimitrios G Karpouzas","doi":"10.1093/femsec/fiaf008","DOIUrl":"10.1093/femsec/fiaf008","url":null,"abstract":"<p><p>The role of microbial terroir for enhancing the geographical origin of wines is well appreciated. Still, we lack a good understanding of the assembly mechanisms driving carposphere grapevine microbiota. We investigated the role of cultivar, vintage, terroir units (TUs), and vineyard geographic location on the composition of the carpospheric microbiota of three important cultivars in the viticultural zone of Drama, Greece using amplicon sequencing. Our strategy to define TUs based on georeferencing analysis allowed us to disentangle the effects of TU and vineyards geographic location, considered as a lumped factor in most studies to date. We hypothesized that (i) these factors contribute differently on the assembly of the carposphere microbiome and that (ii) fungal and bacterial communities follow different assembly mechanisms. Vintage and TU were the stronger determinants of the carposphere fungal and bacterial communities, although the latter showed weaker response. The stronger effect of TU over vineyard geography and cultivar reinforces the role of microbial terroir in viticulture. We identified fungi (Cladosporium, Aureobasidium, Alternaria) and bacteria (Pseudomonas, Methylobacterium, Sphingomonadaceae) as main members of the core microbiome. These microorganisms were associated with specific cultivars and TUs, a feature that could be pursued towards a new microbiome-modulated paradigm of viticulture.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11797032/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143002947","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":"Co-inoculation with Bacillus thuringiensis RZ2MS9 and rhizobia improves the soybean development and modulates soil functional diversity.","authors":"Leandro Fonseca de Souza, Helena Gutierrez Oliveira, Thierry Alexandre Pellegrinetti, Lucas William Mendes, Maria Leticia Bonatelli, Aline Silva Romão Dumaresq, Vanessa V C Sinatti, José Baldin Pinheiro, João Lucio Azevedo, Maria Carolina Quecine","doi":"10.1093/femsec/fiaf013","DOIUrl":"10.1093/femsec/fiaf013","url":null,"abstract":"<p><p>Despite the beneficial effects of plant growth-promoting rhizobacteria on agriculture, understanding the consequences of introducing foreign microbes into soil taxonomic and functional diversity is necessary. This study evaluated the effects co-inoculation of soybean with Bacillus thuringiensis (Bt) RZ2MS9 and commercial rhizobia on the natural microbial community structure and functional potential. Our results indicated that soybean development was positively influenced by co-inoculation, plants exhibited greater height and a higher number of pods, and no reductions in productivity estimates. Soil prokaryotic diversity and community structure remained unchanged by Bt RZMS9 inoculation or co-inoculation with rhizobia 147 days after sowing. However, functional diversity was influenced by sole Bt inoculation, potentially due to community quorum sensing disruption by N-acyl homoserine lactone hydrolases. The genes enriched by co-inoculation were mostly related to soil phosphorus cycling, with gcd showing the most pronounced increase. The nifA genes increased when rhizobia alone were inoculated, suggesting that this pathway could be affected by Bt RZ2MS9 inoculation. This study demonstrates the synergistic activity of rhizobia and Bt RZ2MS9 on soybean development, without significantly interfering with natural microbial community, presenting a promising approach for sustainable crop management.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11796456/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143022786","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":"Oral amoxicillin treatment disrupts the gut microbiome and metabolome without interfering with luminal redox potential in the intestine of Wistar Han rats.","authors":"Sandra Bermúdez-Sánchez, Martin Iain Bahl, Egon Bech Hansen, Tine Rask Licht, Martin Frederik Laursen","doi":"10.1093/femsec/fiaf003","DOIUrl":"10.1093/femsec/fiaf003","url":null,"abstract":"<p><p>Oral antibiotic treatment is well known to be one of the main factors affecting gut microbiota composition by altering bacterial diversity. It decreases the abundance of butyrate-producing bacteria such as Lachnospiraceae and Ruminococcaceae, while increasing abundance of Enterobacteriaceae. The recovery time of commensal bacteria post-antibiotic treatment varies among individuals, and often, complete recovery is not achieved. Recently, gut microbiota disruption has been associated with increased gut oxygen levels and higher redox potential in faecal samples. Given that redox balance is crucial for microbial metabolism and gut health, influencing fermentation processes and maintaining anaerobic conditions, we investigated the impact of oral amoxicillin treatment on the redox potential in the caecum. We used 24 Wistar Han male rats and measured caecal redox potential in situ with a probe, before and after 7 days of amoxicillin treatment, as well as after 7 days of recovery. Additionally, we analysed caecal weight, pH, antioxidant capacity, caecal microbiota, metabolome, and colonic tissue expression of relevant genes involved in the redox potential state. Our findings show that oral amoxicillin treatment significantly reduced archaeal load, and decreased the bacterial alpha diversity and affected bacterial composition of the caecal microbiome. The caecal metabolome was also significantly affected, exemplified by reduced amounts of short chain fatty acids during amoxicillin treatment. While the caecal metabolome fully recovered 7 days post amoxicillin treatment, the microbiome did not fully recover within this time frame. However, amoxicillin did not lead to an increase in luminal redox potential in the cecum during or post amoxicillin treatment. Limited differences were observed for colonic expression of genes involved in intestinal barrier function and generation of reactive oxygen species, except for the catalase gene, which was significantly upregulated post-amoxicillin treatment. Our results suggest that while oral amoxicillin disrupts the gut microbiome and metabolome, it does not directly interfere with gut luminal redox state.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11775830/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142947090","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":"Sea urchin intestinal bacterial communities depend on seaweed diet and contain nitrogen-fixing symbionts.","authors":"Mia M Bengtsson, Marita Helgesen, Haitao Wang, Stein Fredriksen, Kjell Magnus Norderhaug","doi":"10.1093/femsec/fiaf006","DOIUrl":"10.1093/femsec/fiaf006","url":null,"abstract":"<p><p>Kelp deforestation by sea urchin grazing is a widespread phenomenon globally, with vast consequences for coastal ecosystems. The ability of sea urchins to survive on a kelp diet of poor nutritional quality is not well understood and bacterial communities in the sea urchin intestine may play an important role in digestion. A no-choice feeding experiment was conducted with the sea urchin Strongylocentrotus droebachiensis, offering three different seaweeds as diet, including the kelp Saccharina latissima. Starved sea urchins served as experimental control. Amplicons of the 16S rRNA gene were analyzed from fecal pellets. One dominant symbiont (Psychromonas marina) accounted for 44% of all sequence reads and was especially abundant in the sea urchins fed seaweed diets. The starved and field-captured sea urchins consistently displayed higher diversity than the seaweed-fed sea urchins. Cloning and sequencing of the nifH gene revealed diverse nitrogen fixers. We demonstrate that the sea urchin intestinal microbiome is dynamic, with bacterial communities that are plastic, depending on diet and have the capacity for nitrogen fixation. This reflects the dietary flexibility of these sea urchins, and their intestinal microbiota could be a key component in understanding catastrophic kelp forest grazing events.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11797059/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142982960","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":"Distinct bacteria display genus and species-specific associations with mycobionts in paramo lichens in Colombia.","authors":"Maryam Chaib De Mares, Emerson Arciniegas Castro, Maria Alejandra Ulloa, Jean Marc Torres, Maria A Sierra, Daniel J Butler, Christopher E Mason, María Mercedes Zambrano, Bibiana Moncada, Alejandro Reyes Muñoz","doi":"10.1093/femsec/fiaf010","DOIUrl":"10.1093/femsec/fiaf010","url":null,"abstract":"<p><p>Lichens are complex symbiotic systems where fungi interact with an extracellular arrangement of one or more photosynthetic partners and an indeterminate number of other microbes. Recently, specific lichen-microbial community associations have been proposed. In this study, we aimed to characterize the differences in bacteria associated with closely related lichens, under a defined set of environmental conditions in Colombian paramos. Our goal was to determine if there is a correlation between microbiota and host divergence in lichen species belonging to the genus Sticta. We found that specific microbiota are defined by their mycobiont at the genus level. Further, distinct bacterial families show differences among the three studied genera, and specific amplicon sequence variants further discriminate among lichen species within each genus. A geographic component also determines the composition of these microbial communities among lichen species. Our functional analysis revealed that fungal partners play a key role in synthesizing complex polysaccharides, while bacterial-derived antioxidants and photoprotective mechanisms contribute to desiccation tolerance in lichens. These insights highlight the complex interactions within lichen symbioses that could be relevant in environments such as the paramo ecosystem.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11800485/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143064868","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":"Importance, structure, cultivability, and resilience of the bacterial microbiota during infection of laboratory-grown Haematococcus spp. by the blastocladialean pathogen Paraphysoderma sedebokerense: evidence for a domesticated microbiota and its potential for biocontrol.","authors":"Jeanne Miebach, David Green, Martina Strittmatter, Claire Mallinger, Lucie Le Garrec, Qian Yi Zhang, Pierre Foucault, Caroline Kunz, Claire M M Gachon","doi":"10.1093/femsec/fiaf011","DOIUrl":"10.1093/femsec/fiaf011","url":null,"abstract":"<p><p>Industrial production of the unicellular green alga Haematococcus lacustris is compromised by outbreaks of the fungal pathogen Paraphysoderma sedebokerense (Blastocladiomycota). Here, using axenic algal and fungal cultures and antibiotic treatments, we show that the bacterial microbiota of H. lacustris is necessary for the infection by P. sedebokerense and that its modulation affects the outcome of the interaction. We combined metagenomics and laboratory cultivation to investigate the diversity of the bacterial microbiota associated to three Haematococcus species and monitor its change upon P. sedebokerense infection. We unveil three types of distinct, reduced bacterial communities, which likely correspond to keystone taxa in the natural Haematococcus spp. microbiota. Remarkably, the taxonomic composition and functionality of these communities remained stable during infection. The major bacterial taxa identified in this study have been cultivated by us or others, paving the way to developing synthetic communities to experimentally explore interactions within this tripartite system. We discuss our results in the light of emerging evidence concerning the structuring and domestication of plant and animal microbiota, thus providing novel experimental tools and a new conceptual framework necessary to enable the engineering of Haematococcus spp. microbiota toward the biocontrol of P. sedebokerense.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11797010/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143002945","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":"Correction to: FEMSEC-thematic issue \"Rhizosphere-a One Health concept\".","authors":"","doi":"10.1093/femsec/fiae165","DOIUrl":"10.1093/femsec/fiae165","url":null,"abstract":"","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":"101 2","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11774122/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143052106","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":"Spinach seed microbiome characteristics linked to suppressiveness against Globisporangium ultimum damping-off.","authors":"Makrina Diakaki, Beatriz Andreo Jimenez, Ezra de Lange, Patrick Butterbach, Liesbeth van der Heijden, Jürgen Köhl, Wietse de Boer, Joeke Postma","doi":"10.1093/femsec/fiaf004","DOIUrl":"10.1093/femsec/fiaf004","url":null,"abstract":"<p><p>Recently we demonstrated that the seed microbiome of certain spinach (Spinacia oleracea) seed lots can confer disease suppression against Globisporangium ultimum damping-off (previously known as Pythium ultimum). We hypothesized that differences in the microbial community composition of spinach seed lots correlate with the levels of damping-off suppressiveness of each seed lot. Here, we show that a large proportion of variance in seed-associated bacterial (16S) and fungal (Internal Transcribed Spacer 1) amplicon sequences was explained by seed lot identity, while 9.8% of bacterial and 7.1% of fungal community variance correlated with disease suppression. More specifically, a higher relative abundance of basidiomycetous dimorphic yeasts such as Vishniacozyma, Filobasidium, and Papiliotrema and of the bacterial genus Massilia was a key feature of suppressive seed microbiomes. We suggest that the abundance of these genera is indicative of seed lot suppressive potential. Seed processing and treatment can become more targeted with indicator taxa being used to evaluate the presence of beneficial seed-associated microbial functions. This process, in turn, could contribute to the sustainable management of seedling diseases. Finally, this study highlights the ubiquity of yeasts in spinach seed microbiota and their potential beneficial roles for seed health.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11775829/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142947091","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":"Community assembly of gut microbiomes in yolk sac fry of Atlantic salmon: host genetics, environmental microbiomes, and ecological processes.","authors":"Amalie Johanne Horn Mathisen, Sol Gómez de la Torre Canny, Madeleine S Gundersen, Mari-Ann Østensen, Yngvar Olsen, Olav Vadstein, Ingrid Bakke","doi":"10.1093/femsec/fiaf007","DOIUrl":"10.1093/femsec/fiaf007","url":null,"abstract":"<p><p>In this study, we investigated the influence of host genetics and environmental microbiomes on the early gut microbiome of Atlantic salmon. We aimed at rearing the fish in either r- or K-selected environments, where the r-selected environment would be expected to be dominated by fast-growing opportunistic bacteria and thus represent more detrimental microbial environment than the K-selected water. Eggs from both wild and aquaculture strains of Atlantic salmon were hatched under germ-free conditions. One week after hatching, rearing flasks were inoculated with either r- or K-selected water communities. Three weeks after hatching, no effect of host strain on the gut microbiomes were observed. r-selection was found to take place in the rearing water of all flasks, including in the flasks added K-selected water. Still, the water microbiomes differed significantly between the flasks that had been added r- and K-selected water (Add-r and Add-K flasks, respectively). Lower alpha diversity and higher abundances of Pseudomonas were observed for the Add-K flasks, indicating a potential unfavorable microbial environment. Selection in the host structured the gut microbiomes, but an extensive interindividual variation was explained by stochastic processes in community assembly. The gut microbiomes also differed significantly between the Add-r and Add-K flasks. In Add-K flasks, they had higher similarities to the rearing water microbiomes, and the assembly of gut communities was less influenced by stochastic processes. The fish in Add-K flasks had lower growth rates than in Add-r flasks, probably as a result of negative host-microbe interactions. These findings highlight the importance of, but also the challenges related to, managing the microbial environment when cultivating fish.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11797051/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143002941","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":"Microbial changing patterns across lateral and vertical horizons in recently formed permafrost after the outburst of Zonag Lake, Tibetan Plateau.","authors":"Saifei Li, Yang Liu, Wenqiang Wang, Yongqin Liu, Mukan Ji","doi":"10.1093/femsec/fiaf001","DOIUrl":"10.1093/femsec/fiaf001","url":null,"abstract":"<p><p>In polar and alpine regions, global warming and landform changes are draining lakes, transforming them into permafrost with altered microbial communities and element cycling. In this study, we investigated bacterial and archaeal (prokaryotic) community changes in the newly exposed sediment of Zonag Lake (Tibetan Plateau), focusing on prokaryotic diversity, community structure, and genes involved in carbon fixation and nitrogen cycling across lateral (up to 800 m) and vertical (up to 80 cm) horizons. The results showed that prokaryotic richness decreased across the lateral horizons, coinciding with reductions in carbon concentrations. Dramatic changes in community structure were also observed, primarily influenced by the distance from the lake and then by sediment depth, with environmental filtering and dispersal limitations shaping the lateral and vertical distributions, respectively. Based on PICRUSt2 results, the relative abundance of genes related to carbon fixation increased along the lateral horizon, suggesting that microbial carbon fixers are counteracting the carbon loss during permafrost formation. In contrast, the genes related to denitrification also increased, which may lead to nitrogen loss and contribute to global warming by releasing nitric oxide gas. This study highlights the resilience of prokaryotic communities in drained lake basins and their ecological implications under global warming.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11774121/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143055903","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}