FEMS microbiology ecology最新文献_第9页

Community assembly of gut microbiomes in yolk sac fry of Atlantic salmon: host genetics, environmental microbiomes, and ecological processes. 大西洋鲑鱼卵黄囊苗肠道微生物群落组装：宿主遗传学、环境微生物群和生态过程。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2025-01-28 DOI: 10.1093/femsec/fiaf007

Amalie Johanne Horn Mathisen, Sol Gómez de la Torre Canny, Madeleine S Gundersen, Mari-Ann Østensen, Yngvar Olsen, Olav Vadstein, Ingrid Bakke

{"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":"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.","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}

引用次数: 0

Microbial changing patterns across lateral and vertical horizons in recently formed permafrost after the outburst of Zonag Lake, Tibetan Plateau. 青藏高原宗若湖溃决后新近形成的多年冻土中微生物横向和纵向变化格局

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2025-01-28 DOI: 10.1093/femsec/fiaf001

Saifei Li, Yang Liu, Wenqiang Wang, Yongqin Liu, Mukan Ji

{"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":"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.","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}

引用次数: 0

The protist community of the oligotrophic waters of the Gulf of Mexico is distinctly shaped by depth-specific physicochemical conditions during the warm season. 墨西哥湾贫营养水域的原生生物群落在温暖季节明显受到深度特定的物理化学条件的影响。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2025-01-28 DOI: 10.1093/femsec/fiaf009

Karla Sidón-Ceseña, Miguel Angel Martínez-Mercado, Jennyfers Chong-Robles, Yamne Ortega-Saad, Victor Froylán Camacho-Ibar, Lorena Linacre, Asunción Lago-Lestón

{"title":"The protist community of the oligotrophic waters of the Gulf of Mexico is distinctly shaped by depth-specific physicochemical conditions during the warm season.","authors":"Karla Sidón-Ceseña, Miguel Angel Martínez-Mercado, Jennyfers Chong-Robles, Yamne Ortega-Saad, Victor Froylán Camacho-Ibar, Lorena Linacre, Asunción Lago-Lestón","doi":"10.1093/femsec/fiaf009","DOIUrl":"10.1093/femsec/fiaf009","url":null,"abstract":"Marine protists are key components of biogeochemical cycles and microbial food webs, which respond quickly to environmental factors. In the Gulf of Mexico (GoM), the Loop Current intensifies in summer and supplies the gulf with warm and oligotrophic waters. However, the cyclonic eddies within the GoM create favorable conditions for biological productivity by bringing nutrient-rich water to the subsurface layer. In this study, we investigated the response of the protist community to the regional physicochemical conditions, its spatial and temporal variability, the influence of mesoscale structures, and its ecological roles in the mixed layer (ML) and deep chlorophyll maximum (DCM). This is the first study to conduct a V9-18S rRNA gene survey for this community in the Mexican Exclusive Economic Zone of the GoM. The regional distribution, temporal changes, and mesoscale structures significantly affected the structure of the protist community in the ML. In contrast, only mesoscale structures significantly affected the protist community in the DCM. Different protist assemblages were also present between the ML and DCM, with the Alveolata representing ∼60% of the community in both layers, followed by haptophytes and MAST (Marine Stramenopiles) in the ML; pelagophytes and radiolarians were the more prevalent taxa in the DCM. Finally, co-occurrence analyses revealed that competition, parasitism, and predation were the potential interactions shaping these communities at both depths.","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/PMC11800482/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143058574","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}

引用次数: 0

Fungal communities in boreal soils are influenced by land use, agricultural soil management, and depth. 北方土壤真菌群落受土地利用、农业土壤管理和土壤深度的影响。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2025-01-28 DOI: 10.1093/femsec/fiaf002

Laura Häkkinen, Igor S Pessi, Anna-Reetta Salonen, Oona Uhlgren, Helena Soinne, Jenni Hultman, Jussi Heinonsalo

{"title":"Fungal communities in boreal soils are influenced by land use, agricultural soil management, and depth.","authors":"Laura Häkkinen, Igor S Pessi, Anna-Reetta Salonen, Oona Uhlgren, Helena Soinne, Jenni Hultman, Jussi Heinonsalo","doi":"10.1093/femsec/fiaf002","DOIUrl":"10.1093/femsec/fiaf002","url":null,"abstract":"Land use and agricultural soil management affect soil fungal communities that ultimately influence soil health. Subsoils harbor nutrient reservoir for plants and can play a significant role in plant growth and soil carbon sequestration. Typically, microbial analyses are restricted to topsoil (0-30 cm) leaving subsoil fungal communities underexplored. To address this knowledge gap, we analyzed fungal communities in the vertical profile of four boreal soil treatments: long-term (24 years) organic and conventional crop rotation, meadow, and forest. Internal transcribed spacer (ITS2) amplicon sequencing revealed soil-layer-specific land use or agricultural soil management effects on fungal communities down to the deepest measured soil layer (40-80 cm). Compared to other treatments, higher proportion of symbiotrophs, saprotrophs, and pathotrophs + plant pathogens were found in forest, meadow and crop rotations, respectively. The proportion of arbuscular mycorrhizal fungi was higher in deeper (>20 cm) soil than in topsoil. Forest soil below 20 cm was dominated by fungal functional groups with proposed interactions with plants or other soil biota, whether symbiotrophic or pathotrophic. Ferrous oxide was an important factor shaping fungal communities throughout the vertical profile of meadow and cropping systems. Our results emphasize the importance of including subsoil in microbial community analyses in differently managed soils.","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/PMC11774123/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142947089","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}

引用次数: 0

Experimental evidence on the impact of climate-induced hydrological and thermal variations on glacier-fed stream biofilms. 气候引起的水文和热量变化对冰川溪流生物膜影响的实验证据。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2025-01-07 DOI: 10.1093/femsec/fiae163

David Touchette, Martina Gonzalez Mateu, Grégoire Michoud, Nicola Deluigi, Ramona Marasco, Daniele Daffonchio, Hannes Peter, Tom Battin

{"title":"Experimental evidence on the impact of climate-induced hydrological and thermal variations on glacier-fed stream biofilms.","authors":"David Touchette, Martina Gonzalez Mateu, Grégoire Michoud, Nicola Deluigi, Ramona Marasco, Daniele Daffonchio, Hannes Peter, Tom Battin","doi":"10.1093/femsec/fiae163","DOIUrl":"10.1093/femsec/fiae163","url":null,"abstract":"Climate change is predicted to alter the hydrological and thermal regimes of high-mountain streams, particularly glacier-fed streams. However, relatively little is known about how these environmental changes impact the microbial communities in glacier-fed streams. Here, we operated streamside flume mesocosms in the Swiss Alps, where benthic biofilms were grown under treatments simulating climate change. Treatments comprised four flow (natural, intermittent, stochastic, and constant) and two temperature (ambient streamwater and warming of +2°C) regimes. We monitored microbial biomass, diversity, community composition, and metabolic diversity in biofilms over 3 months. We found that community composition was largely influenced by successional dynamics independent of the treatments. While stochastic and constant flow regimes did not significantly affect community composition, droughts altered their composition in the intermittent regime, favouring drought-adapted bacteria and decreasing algal biomass. Concomitantly, warming decreased algal biomass and the abundance of some typical glacier-fed stream bacteria and eukaryotes, and stimulated heterotrophic metabolism overall. Our study provides experimental evidence towards potential and hitherto poorly considered impacts of climate change on benthic biofilms in glacier-fed streams.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11705997/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142824131","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}

引用次数: 0

Extensive environmental survey of free-living amoebae and their elusive association with Mycobacterium bovis or Mycobacterium avium subsp. paratuberculosis. 自由生活变形虫的广泛环境调查及其与牛分枝杆菌或鸟分枝杆菌亚种的难以捉摸的联系。副结核。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2025-01-07 DOI: 10.1093/femsec/fiae164

Amélie Jessu, Thierry Cochard, Mélanie Burtin, Stéphanie Crapart, Vincent Delafont, Ascel Samba-Louaka, Franck Biet, Jean-Louis Moyen, Yann Héchard

{"title":"Extensive environmental survey of free-living amoebae and their elusive association with Mycobacterium bovis or Mycobacterium avium subsp. paratuberculosis.","authors":"Amélie Jessu, Thierry Cochard, Mélanie Burtin, Stéphanie Crapart, Vincent Delafont, Ascel Samba-Louaka, Franck Biet, Jean-Louis Moyen, Yann Héchard","doi":"10.1093/femsec/fiae164","DOIUrl":"10.1093/femsec/fiae164","url":null,"abstract":"Free-living amoebae (FLA) are described as environmental reservoirs for some bacteria able to resist their phagocytosis. In the environment, the fate of Mycobacterium bovis (Mbo) and Mycobacterium avium subsp. paratuberculosis (Map) responsible for bovine tuberculosis and paratuberculosis, respectively, remains poorly understood and is considered potentially problematic in the eradication and control of these diseases. We hypothesize that FLA may play a role in the persistence of Mbo and Map in the environment. In this study, 90 samples were collected from herds affected by one or both diseases to investigate the diversity of amoeba and their associated bacteria. Metabarcoding analyses revealed that Acanthamoeba, Copromyxa, Naegleria, and Vermamoeba were the most represented genera of FLA, with Pseudomonadota being the bacteria most commonly found associated with FLA. Although no Mbo and Map DNA were identified by sequencing, traces were detected by ddPCR (digital droplet PCR), specifically targeting these bacteria. In conclusion, we described a wide diversity of FLA and associated bacteria in this environment. It also suggests that Map and Mbo could be associated, even weakly, with FLA in the environment. However, this needs to be confirmed by detecting a highest amount of DNA and, if possible, cultivable Map and/or Mbo associated with these environmental FLA.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11707876/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142846238","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}

引用次数: 0

An interdisciplinary perspective of the built-environment microbiome. 建筑环境微生物组的跨学科视角。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2025-01-07 DOI: 10.1093/femsec/fiae166

John S McAlister, Michael J Blum, Yana Bromberg, Nina H Fefferman, Qiang He, Eric Lofgren, Debra L Miller, Courtney Schreiner, K Selcuk Candan, Heather Szabo-Rogers, J Michael Reed

{"title":"An interdisciplinary perspective of the built-environment microbiome.","authors":"John S McAlister, Michael J Blum, Yana Bromberg, Nina H Fefferman, Qiang He, Eric Lofgren, Debra L Miller, Courtney Schreiner, K Selcuk Candan, Heather Szabo-Rogers, J Michael Reed","doi":"10.1093/femsec/fiae166","DOIUrl":"10.1093/femsec/fiae166","url":null,"abstract":"The built environment provides an excellent setting for interdisciplinary research on the dynamics of microbial communities. The system is simplified compared to many natural settings, and to some extent the entire environment can be manipulated, from architectural design to materials use, air flow, human traffic, and capacity to disrupt microbial communities through cleaning. Here, we provide an overview of the ecology of the microbiome in the built environment. We address niche space and refugia, population, and community (metagenomic) dynamics, spatial ecology within a building, including the major microbial transmission mechanisms, as well as evolution. We also address landscape ecology, connecting microbiomes between physically separated buildings. At each stage, we pay particular attention to the actual and potential interface between disciplines, such as ecology, epidemiology, materials science, and human social behavior. We end by identifying some opportunities for future interdisciplinary research on the microbiome of the built environment.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11715626/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142863690","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}

引用次数: 0

The role of anthropogenic influences on a tropical lake ecosystem and its surrounding catchment: a case study of Lake Sentani. 人为影响对热带湖泊生态系统及其周边集水区的作用：以森塔尼湖为例。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2025-01-07 DOI: 10.1093/femsec/fiae162

Sulung Nomosatryo, Daniel Lipus, Alexander Bartholomäus, Cynthia Henny, Iwan Ridwansyah, Puguh Sujarta, Sizhong Yang, Dirk Wagner, Jens Kallmeyer

{"title":"The role of anthropogenic influences on a tropical lake ecosystem and its surrounding catchment: a case study of Lake Sentani.","authors":"Sulung Nomosatryo, Daniel Lipus, Alexander Bartholomäus, Cynthia Henny, Iwan Ridwansyah, Puguh Sujarta, Sizhong Yang, Dirk Wagner, Jens Kallmeyer","doi":"10.1093/femsec/fiae162","DOIUrl":"10.1093/femsec/fiae162","url":null,"abstract":"Lake Sentani is a tropical lake in Indonesia, consisting of four interconnected sub-basins of different water depths. While previous work has highlighted the impact of catchment composition on biogeochemical processes in Lake Sentani, little is currently known about the microbiological characteristics across this unique ecosystem. With recent population growth in this historically rural area, the anthropogenic impact on Lake Sentani and hence its microbial life is also increasing. Therefore, we aimed to explore the influence of environmental and anthropogenic factors on the microbial diversity of Lake Sentani. Here, we present a detailed microbiological evaluation of Lake Sentani, analyzing 49 different sites across the lake, its tributary rivers and their river mouths to assess diversity and community structure using 16S rRNA gene sequencing. Our results reveal distinct communities in lake and river sediments, supporting the observed geochemical differences. Taxonomic assessment showed the potential impact of anthropogenic pressure along the northern, urbanized shore, as river and river mouth samples revealed high abundances of Bacteroidota, Firmicutes, and Cyanobacteria, which could be attributed to pollution and eutrophication. In contrast, lake sediment communities were dominated by Thermodesulfovibrionia, Methanomethylicia, Bathyarchaeia, and Thermoplasmata, suggesting sulfate reducing, thermophilic, acidophilic bacteria and methanogenic archaea to play an important role in tropical lake systems. This study provides novel insights into ecological functions of tropical lakes and contributes to the optimization of management strategies of Lake Sentani, ensuring its holistic preservation in the future.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11707878/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142846241","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}

引用次数: 0

Dynamics of fungal endophytic communities in bilberry (Vaccinium myrtillus L.) fruits through development is shaped by host phenolic compounds. 越桔果实发育过程中真菌内生群落的动态受寄主酚类化合物的影响。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2025-01-07 DOI: 10.1093/femsec/fiae168

Minh-Phuong Nguyen, Kaisa Lehosmaa, Françoise Martz, Janne J Koskimäki, Katalin Toth, Saija H K Ahonen, Hely Häggman, Anna-Maria Pirttilä

{"title":"Dynamics of fungal endophytic communities in bilberry (Vaccinium myrtillus L.) fruits through development is shaped by host phenolic compounds.","authors":"Minh-Phuong Nguyen, Kaisa Lehosmaa, Françoise Martz, Janne J Koskimäki, Katalin Toth, Saija H K Ahonen, Hely Häggman, Anna-Maria Pirttilä","doi":"10.1093/femsec/fiae168","DOIUrl":"10.1093/femsec/fiae168","url":null,"abstract":"The physical and chemical properties of wild berry fruits change dramatically during development, and the ripe berries host species-specific endophytic communities. However, the development of fungal endophytic communities during berry ripening is unknown. We studied bilberries (Vaccinium myrtillus L.), valuable natural resources in northern Europe and richest sources of phenolic compounds, to characterize dynamics of the fungal communities over fruit developmental stages (raw, veraison, and ripe). Our focus was to examine the changes in the fruit phenolic compounds associated with the fungal community structure using liquid chromatography-mass spectrometry for phenolic compounds and high-throughput sequencing technology targeting the internal transcribed spacer 2 ribosomal DNA region for endophytic fungi. We found that the fungal diversity increased with the ripening stages. The fungal profile changed dramatically through fruit development, and the veraison stage was a transition stage, where the core mycobiome of fruits changed. The fungal community structure and abundance of the most dominant genera in raw and ripe stages, Monilinia and Cladosporium, respectively, were driven by the bilberry phenolic profile. We conclude that sampling time, tissue age, and phenolic compounds play important roles in the development of fruit fungal community. Moreover, phenolic compounds could be the host's strategy to recruit beneficial microbes.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":"101 1","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11730187/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142978112","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}

引用次数: 0

A genome-scale metabolic reconstruction provides insight into the metabolism of the thermophilic bacterium Rhodothermus marinus. 基因组尺度的代谢重建提供了对嗜热细菌海洋红热菌代谢的深入了解。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2025-01-07 DOI: 10.1093/femsec/fiae167

Thordis Kristjansdottir, Gudmundur O Hreggvidsson, Elisabet Eik Gudmundsdottir, Snaedis H Bjornsdottir, Olafur H Fridjonsson, Sigmar Karl Stefansson, Eva Nordberg Karlsson, Justine Vanhalst, Birkir Reynisson, Steinn Gudmundsson

{"title":"A genome-scale metabolic reconstruction provides insight into the metabolism of the thermophilic bacterium Rhodothermus marinus.","authors":"Thordis Kristjansdottir, Gudmundur O Hreggvidsson, Elisabet Eik Gudmundsdottir, Snaedis H Bjornsdottir, Olafur H Fridjonsson, Sigmar Karl Stefansson, Eva Nordberg Karlsson, Justine Vanhalst, Birkir Reynisson, Steinn Gudmundsson","doi":"10.1093/femsec/fiae167","DOIUrl":"10.1093/femsec/fiae167","url":null,"abstract":"The thermophilic bacterium Rhodothermus marinus has mainly been studied for its thermostable enzymes. More recently, the potential of using the species as a cell factory and in biorefinery platforms has been explored, due to the elevated growth temperature, native production of compounds such as carotenoids and exopolysaccharides, the ability to grow on a wide range of carbon sources including polysaccharides, and available genetic tools. A comprehensive understanding of the metabolism of cell factories is important. Here, we report a genome-scale metabolic model of R. marinus DSM 4252T. Moreover, the genome of the genetically amenable R. marinus ISCaR-493 was sequenced and the analysis of the core genome indicated that the model could be used for both strains. Bioreactor growth data were obtained, used for constraining the model and the predicted and experimental growth rates were compared. The model correctly predicted the growth rates of both strains. During the reconstruction process, different aspects of the R. marinus metabolism were reviewed and subsequently, both cell densities and carotenoid production were investigated for strain ISCaR-493 under different growth conditions. Additionally, the dxs gene, which was not found in the R. marinus genomes, from Thermus thermophilus was cloned on a shuttle vector into strain ISCaR-493 resulting in a higher yield of carotenoids.","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11730185/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142880684","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}

引用次数: 0