FEMS microbiology ecology最新文献

{"title":"From Eggs to Guts: Symbiotic Association of Sodalis nezarae sp. nov. with the Southern Green Shield Bug Nezara viridula.","authors":"Magda A Rogowska-van der Molen, Alejandro Manzano-Marín, Jelle L Postma, Silvia Coolen, Theo van Alen, Robert S Jansen, Cornelia U Welte","doi":"10.1093/femsec/fiaf017","DOIUrl":"https://doi.org/10.1093/femsec/fiaf017","url":null,"abstract":"<p><p>Phytophagous insects engage in symbiotic relationships with bacteria that contribute to digestion, nutrient supplementation, and development of the host. The analysis of shield bug microbiomes has been mainly focused on the gut intestinal tract predominantly colonized by Pantoea symbionts, and other microbial community members in the gut or other organs have hardly been investigated. In this study, we reveal that the Southern green shield bug Nezara viridula harbours a Sodalis symbiont in several organs, with a notable prevalence in salivary glands, and anterior regions of the midgut. Removing external egg microbiota via sterilization profoundly impacted insect viability but did not disrupt the vertical transmission of Sodalis and Pantoea symbionts. Based on the dominance of Sodalis in testes, we deduce that N. viridula males could be involved in symbiont vertical transmission. Genomic analyses comparing Sodalis species revealed that Sodalis sp. Nvir shares characteristics with both free-living and obligate insect-associated Sodalis spp. Sodalis sp. Nvir also displays genome instability typical of endosymbiont lineages, which suggests ongoing speciation to an obligate endosymbiont. Together, our study reveals that shield bugs harbour unrecognized symbionts that might be paternally transmitted.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143406518","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":"Limited similarity in microbial composition among coral reef fishes from the Great Barrier Reef, Australia.","authors":"Vincenzo A Costa, David R Bellwood, Jonathon C O Mifsud, Jemma L Geoghegan, Erin Harvey, Edward C Holmes","doi":"10.1093/femsec/fiaf016","DOIUrl":"https://doi.org/10.1093/femsec/fiaf016","url":null,"abstract":"<p><p>Reef fishes exhibit enormous biodiversity within a highly interactive ecosystem. Relatively little is known about the diversity and evolution of microbial species associated with reef fish, even though this may provide valuable insights into the factors that shape microbial communities. Through metatranscriptomic sequencing we characterised the viruses, bacteria, and single-celled eukaryotes from 126 reef fish species inhabiting Lizard Island and Orpheus Island on the Great Barrier Reef, Australia. We assessed whether microbial communities differed between islands that are separated by 450 kilometres, and to what extent fish viruses emerge in new hosts. Despite strong ecological interactions within the species-rich reef environment, and the presence of the same families of viruses on both islands, there was minimal evidence for the presence of individual viruses shared among fish species, reflecting low levels of cross-species transmission. Among bacteria, we identified the opportunistic bacterial pathogen Photobacterium damselae in apparently healthy cardinalfish species from both islands, indicating that these fish species are natural reservoirs. These data suggest that reef fishes have microbial-host associations that arose prior to the formation of the Great Barrier Reef, likely leading to strong host barriers to cross-species transmission and hence infectious disease emergence.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143364183","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":"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":"https://doi.org/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 affects 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, pin points the cascading effects of tree infestations by bark beetles and subsequent tree dieback 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":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editorial: FEMS EC Thematic Issue \"Aquatic Microbial Ecology\".","authors":"Martin W Hahn, Veljo Kisand","doi":"10.1093/femsec/fiaf005","DOIUrl":"10.1093/femsec/fiaf005","url":null,"abstract":"","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/PMC11775825/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143002943","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":"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":"Delayed feeding disrupts diurnal oscillations in the gut microbiome of a neotropical bat in captivity.","authors":"Dominik W Melville, Magdalena Meyer, Corbinian Kümmerle, Kevin A Alvarado-Barrantes, Kerstin Wilhelm, Simone Sommer, Marco Tschapka, Alice Risely","doi":"10.1093/femsec/fiaf012","DOIUrl":"10.1093/femsec/fiaf012","url":null,"abstract":"<p><p>Diurnal rhythms of the gut microbiota are emerging as an important yet often overlooked facet of microbial ecology. Feeding is thought to stimulate gut microbial rhythmicity, but this has not been explicitly tested. Moreover, the role of the gut environment is entirely unexplored, with rhythmic changes to gut pH rather than feeding per se possibly affecting gut microbial fluctuations. In this study, we experimentally manipulated the feeding schedule of captive lesser long-nosed bats, Leptonycteris yerbabuenae, to dissociate photic and feeding cues, and measured the faecal microbiota and gut pH every 2 h. We detected strong diurnal rhythms in both microbial alpha diversity and beta diversity as well as in pH within the control group. However, a delay in feeding disrupted oscillations of gut microbial diversity and composition, but did not affect rhythms in gut pH. The oscillations of some genera, such as Streptococcus, which aid in metabolizing nutrients, shifted in accordance with the delayed-feeding cue and were correlated with pH. For other bacterial genera, oscillations were disturbed and no connection to pH was found. Our findings suggest that the rhythmic proliferation of bacteria matches peak feeding times, providing evidence that diurnal rhythms of the gut microbiota likely evolved to optimize their metabolic support to the host's circadian phenotype.</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/PMC11783575/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143022788","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":"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":"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}