Ana Paula Rosa, Elena Puerta-Fernández, Cristina Cruz, Juan M Gonzalez, Margarida M Santana
{"title":"Increased survival of Parageobacillus thermoglucosidasius, a thermophilic soil bacterium, in a rhizosphere milieu.","authors":"Ana Paula Rosa, Elena Puerta-Fernández, Cristina Cruz, Juan M Gonzalez, Margarida M Santana","doi":"10.1093/femsec/fiaf059","DOIUrl":"10.1093/femsec/fiaf059","url":null,"abstract":"<p><p>Previous studies have highlighted the widespread presence of thermophilic bacterial genera in upper soil layers, their role in biogeochemical cycles, and their potential application in soil fertilization. However, the mechanisms by which these thermophiles maintain cell viability in temperate soils remain largely unknown. The isolation of thermophilic bacteria from rhizospheric soils has been reported, hence it may be hypothesized that the rhizosphere environment plays a role in their survival. In this study, we developed a hydroponic system to introduce the thermophilic bacterium Parageobacillus thermoglucosidasius into the rhizosphere of tomato plants, demonstrating that this environment increased bacterial survival rates at 20°C-25°C by over 23-fold. The rhizosphere exudates contributed to this increase, as their addition boosted bacterial survival in pure cultures at 25°C by up to twofold. We propose that the rhizosphere and its exudates, characterized through targeted metabolomics, support the persistence of thermophilic bacteria in temperate soils during colder periods, ensuring viable cells that contribute to soil fertilization during warmer seasons.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12166544/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144233679","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}
Tara N Gaire, Jared Young, Thomas Wehri, Mark Schwartz, Randall Singer, Maria Pieters, Noelle R Noyes
{"title":"The impact of pooling on the observed microbiome profile of preweaned piglet feces.","authors":"Tara N Gaire, Jared Young, Thomas Wehri, Mark Schwartz, Randall Singer, Maria Pieters, Noelle R Noyes","doi":"10.1093/femsec/fiaf058","DOIUrl":"10.1093/femsec/fiaf058","url":null,"abstract":"<p><p>Pooling individual samples could be an efficient approach for large-scale population-based microbiome studies. However, it is unknown whether pooled samples accurately reflect the microbiome composition and diversity obtained from individual samples. This study investigated the impact of various pooling methods on the observed fecal microbiome of preweaned piglets. Individual fecal samples were collected from 10 litters of day-old piglets (N = 137) and 10 litters of 20-day-old piglets (N = 121), as well as pen-floor samples from the same litters. The individually collected samples were processed individually and also used to create pools of both raw feces and extracted DNA. Individual samples, raw feces pools, DNA pools, and pen-floor samples were subjected to 16S rRNA gene sequencing. The microbial profile in pen-floor samples from litters of preweaned piglets was very different from individual piglet samples within the pen; thus, they may not be suitable for litter-level piglet microbiome studies. However, overall microbial diversity and composition from DNA and feces pools were comparable to individual samples, despite potentially underestimating some low-abundance or low-prevalence taxa. These results suggest that pooling can be used as an efficient and cost-effective approach to characterize litter-level microbial profiles for current and future population-level microbiome research in preweaned piglet populations.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12166543/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144247231","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":"Deciphering oxidative stress responses in human gut microbes and fecal microbiota: a cultivation-based approach.","authors":"Janina N Zünd, Marina Caflisch, Denisa Mujezinovic, Serafina Plüss, Christophe Lacroix, Benoit Pugin","doi":"10.1093/femsec/fiaf054","DOIUrl":"10.1093/femsec/fiaf054","url":null,"abstract":"<p><p>Chronic inflammation creates an oxidative environment, altering the gut microbiota. However, the mechanisms underlying oxidative stress-induced community changes remain poorly understood, owing to the complexity of the host environment, high inter-individual variability, and a lack of comparative data on stress tolerance across intestinal taxa. To address this, we developed an in vitro cultivation approach to assess the effects of oxidative stress, induced by 12 concentrations each of hydrogen peroxide (H₂O₂) and oxygen (O₂), on 41 intestinal strains and seven adults' fecal microbiota. Fusicatenibacter saccharivorans and Lachnospira eligens emerged as particularly sensitive taxa in both pure cultures and complex communities. Oxidative stress also reduced butyrate-producing taxa, like Agathobacter and Anaerostipes, along with total butyrate levels. In contrast, facultative anaerobes, like Escherichia-Shigella and Enterococcus, were largely unaffected, and Bacteroides showed high resilience. Notably, the impact of oxidative stress varied among individuals, with numerous genera showing taxon-specific changes depending on the host microbiota composition. These findings underscore the importance of considering individual microbiota backgrounds when assessing oxidative stress effects on microbial communities. Our study provides a tolerance profile of gut microbes to oxidative stress, reveals overlooked taxa involved in community restructuring, and introduces a screening tool to characterize individual microbial and metabolic responses.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12105573/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144110442","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":"Catch crop amendments and microbial inoculants differently modulate apple rhizosphere microbiomes and plant responses.","authors":"Kristin Hauschild, Adriana Giongo, Benye Liu, Doreen Babin, Elke Bloem, Ludger Beerhues, Traud Winkelmann, Kornelia Smalla","doi":"10.1093/femsec/fiaf055","DOIUrl":"10.1093/femsec/fiaf055","url":null,"abstract":"<p><p>Plant-soil feedback and soil microbial legacies play crucial roles in replanting success of apple. This study investigated how different soil amendment strategies influence these factors in replant disease-affected soil. Two approaches were tested: (i) the preculture and amendment of catch crops-either a single species, Tagetes patula, or a diverse catch crop mixture (CCM), and (ii) the inoculation of plant-beneficial microbes-bacteria, arbuscular mycorrhizal fungi, or their combination (SynC). Apple rootstock M.26 was grown for seven weeks in a greenhouse, and plant growth, soil nutrients, root phytoalexins, and microbial communities in rhizosphere and root-affected soil were analyzed. Catch crop amendments but not microbial inoculations, significantly altered soil nutrients. Root length increased significantly under CCM, and in tendency in Tagetes and SynC. Phytoalexin contents were lowest in Tagetes and highest in CCM, both differing from the control in specific compounds. Microbiome analysis revealed that catch crops strongly modulated fungal communities in rhizosphere and root-affected soil, favoring potentially beneficial Linnemannia and Mortierella, while microbial inoculations predominantly modulated bacterial/archaeal rhizosphere communities. Our results suggest that catch crops and microbial inoculants induced distinct shifts in soil-plant-microbe interactions under replanting conditions.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12168782/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144132345","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}
Nina Naghshineh, Steve Kutos, J D Lewis, Elle M Barnes
{"title":"Reorganization of bacterial community network structure in the eastern redback salamander (Plethodon cinereus) and its soil reservoir across a gradient of land use.","authors":"Nina Naghshineh, Steve Kutos, J D Lewis, Elle M Barnes","doi":"10.1093/femsec/fiaf057","DOIUrl":"10.1093/femsec/fiaf057","url":null,"abstract":"<p><p>The eastern redback salamander Plethodon cinereus is prevalent in the urbanized northeastern USA and exhibits low susceptibility to the fungal pathogen Batrachochytrium dendrobatidis (Bd). Disease resistance is partially attributed to Bd-inhibitory microbes in the P. cinereus cutaneous microbiome, but less is known regarding the associations that structure these bacterial communities. This is an essential area of study as shifts in microbial associations may influence community stability and function, driving differences in disease tolerance. Here, we analyzed the networks of the soil and salamander skin core bacterial communities along a 65-km urbanization gradient originating in New York City. We leveraged network analysis tools that help account for the biases inherent in 16S rRNA amplicon datasets, finding that soil networks were the most complex and stable, but complexity and stability increased with urbanization intensity in salamander networks. The network of Bd-positive salamanders was also more complex and stable than that of Bd-negative salamanders. While stress and complexity are thought to be destabilizing, our results suggest that prolonged exposure to environmental degradation may promote larger, stable co-occurring populations of microbes on hosts. This network analysis work generated hypotheses with experimental applicability, ultimately having the potential to enhance conservation management efforts.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12166547/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144208103","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":"Custom-made medium approach for effective enrichment and isolation of chemolithotrophic iron-oxidizing bacteria.","authors":"Tomoki Uchijima, Shingo Kato, Kazuya Tanimoto, Fumito Shiraishi, Natsuko Hamamura, Kohei Tokunaga, Hiroko Makita, Momoko Kondo, Moriya Ohkuma, Satoshi Mitsunobu","doi":"10.1093/femsec/fiaf051","DOIUrl":"10.1093/femsec/fiaf051","url":null,"abstract":"<p><p>Chemolithotrophic neutrophilic iron (Fe)-oxidizing bacteria, which mainly belong to the family Gallionellaceae, universally prevail in terrestrial environments changing Fe cycling. However, they are typically recognized as difficult-to-culture microbes. Despite efforts, there are few Fe(II)-oxidizing lithotroph isolates; hence, their physiological and ecological knowledge remains limited. This limitation is largely owing to difficulties in their cultivation, and we hypothesize that the difficulty exists because substrate and mineral concentrations in the cultivation medium are not tuned to a specific environmental condition under which these organisms live. To address this hypothesis, this study proposes a novel custom-made medium approach for chemolithotrophic Fe(II)-oxidizing bacteria; a method that manipulates medium components through diligent analysis of field environment. A new custom-made medium simulating energy substrates and nutrients under the field condition was prepared by modifying both chemical composition and physical setup in the glass-tube medium. In particular, the modification of the physical setup in the tube had a significant effect on adjusting dissolved Fe(II) and O2 concentrations to the field environment. Using the medium, Gallionellaceae members were successfully enriched and a new Gallionellaceae species was isolated from a natural hot spring site. Compared with conventional medium, the custom-made medium has significantly higher ability in enriching Gallionellaceae members.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12089753/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143975834","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}
Danica Kynast, Florian Reverey, Lars Ganzert, Hans-Peter Grossart, Gunnar Lischeid, Steffen Kolb
{"title":"Detectable land use impact on methanotrophs and methanogens in kettle hole sediments but not on net methane production potentials.","authors":"Danica Kynast, Florian Reverey, Lars Ganzert, Hans-Peter Grossart, Gunnar Lischeid, Steffen Kolb","doi":"10.1093/femsec/fiaf050","DOIUrl":"10.1093/femsec/fiaf050","url":null,"abstract":"<p><p>Kettle holes (KHs) are dynamic freshwater systems and potential sources of the greenhouse gas methane. Due to their small size (<1 hectare), KHs are subject to inorganic and organic matter input from their terrestrial surroundings, governed by land use. Matter inputs include inorganic solutes that are alternative electron acceptors and impact on methanotrophs and methanogens. Thus, they might affect methane net production. We sampled 10 kettle hole sediments embedded in landscapes with either agricultural or forest land use and determined their (i) potential net methane production rates, (ii) the composition of their microbial communities, and (iii) physicochemical soil parameters. Potential net methane production did not significantly differ by land use type but between single KHs. However, land use type had a strong impact on methanotroph and methanogen and on total bacterial and archaeal microbiota structure. Relative abundances of methanotrophs and methanogens were significantly higher in agricultural KHs, and their relative abundances were among the most influential variables projecting net methane production potentials along with nutrient status and water content. Land use type was thus identified as a major factor that impacts the structure and biodiversity of general and methane-cycling microbiota, but it did not affect net methane production potentials.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12089754/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144005653","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}
Ivan Sosa Marquez, Karla Griesbaum, Lindsay V Clark, Elizabeth A Ainsworth, Natalie Christian, Katy D Heath
{"title":"Dominant foliar endophytes influence soybean yield and transcriptome.","authors":"Ivan Sosa Marquez, Karla Griesbaum, Lindsay V Clark, Elizabeth A Ainsworth, Natalie Christian, Katy D Heath","doi":"10.1093/femsec/fiaf053","DOIUrl":"10.1093/femsec/fiaf053","url":null,"abstract":"<p><p>Microorganisms associated with plants can affect nutrient and water acquisition, plant defenses, and ecological interactions, with effects on plant growth that range from beneficial to antagonistic. In Glycine max (soybean), many studies have examined the soil microbiome and the legume-rhizobium relationship, but little is known about foliar endophytes, their effects on plant biomass and fitness, and how plants respond to their presence. To address these questions, we inoculated Glycine max with field-collected isolates of previously isolated, dominant strains of Methylobacterium and Colletotrichum in either sterile or non-sterile soil. We then used RNAseq to compare the transcriptomic responses of plants to single- and co-inoculation of endophytes. We found that all endophyte treatments increased soybean growth compared to control, but only in sterile soil. These results suggest context-dependency, with endophytes serving as facultative mutualists under stress or nutrient deprivation. Similarly, transcriptomic analyses revealed that soybean defense and stress responses depended on the interaction of endophytes; Methylobacterium elicited the strongest response but was modulated by the presence of Colletotrichum. Our findings highlight the environmentally dependent effects of co-existing endophytes within soybean leaves.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12089775/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144000767","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}
Mark Swaine, Alessandro Bergna, Ben Oyserman, Sotirios Vasileiadis, Panagiotis A Karas, Claudio Screpanti, Dimitrios G Karpouzas
{"title":"Impact of pesticides on soil health: identification of key soil microbial indicators for ecotoxicological assessment strategies through meta-analysis.","authors":"Mark Swaine, Alessandro Bergna, Ben Oyserman, Sotirios Vasileiadis, Panagiotis A Karas, Claudio Screpanti, Dimitrios G Karpouzas","doi":"10.1093/femsec/fiaf052","DOIUrl":"10.1093/femsec/fiaf052","url":null,"abstract":"<p><p>Pesticides remain a cornerstone of modern agriculture. Despite their key role, it is well documented that pesticides can have considerable off-target effects on a range of organisms. The effects of pesticides on soil health, and more importantly on soil microbiota, are currently not well addressed at the regulatory level, despite cumulative evidence for the pivotal role of the soil microbiota on ecosystem functioning. Here, we use a meta-analysis to assess the effects of pesticides on soil health parameters identifying key biological indicators for environmental risk assessment analysis. We demonstrate that ammonia oxidizing archaeal and bacterial amoA gene abundance were the most consistent indicators for pesticide exposure, with inhibition driven by herbicides and fungicides. Our meta-analysis, combined with their key functional role and the existence of well-standardized, high-resolution methods for monitoring their abundance, highlighted the potential of ammonia-oxidizing microorganisms (AOMs) as indicators of the toxicity of pesticides on soil microbiota. AOM could serve as drivers of chemical innovation in a \"benign and sustainable by design\" approach where new pesticide compounds will have to meet sustainability targets and ensure soil health preservation.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12105574/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143960735","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}