Olivier Nouwen, Francois Rineau, Petr Kohout, Petr Baldrian, Nico Eisenhauer, Natalie Beenaerts, Sofie Thijs, Jaco Vangronsveld, Nadejda A Soudzilovskaia
{"title":"Towards understanding the impact of mycorrhizal fungal environments on the functioning of terrestrial ecosystems.","authors":"Olivier Nouwen, Francois Rineau, Petr Kohout, Petr Baldrian, Nico Eisenhauer, Natalie Beenaerts, Sofie Thijs, Jaco Vangronsveld, Nadejda A Soudzilovskaia","doi":"10.1093/femsec/fiaf062","DOIUrl":"https://doi.org/10.1093/femsec/fiaf062","url":null,"abstract":"<p><p>Mutualistic interactions between plants and soil fungi, mycorrhizas, control carbon and nutrient fluxes in terrestrial ecosystems. Soil of ecosystems featuring a particular type of mycorrhiza exhibit specific properties across multiple dimensions of soil functioning. The knowledge about the impacts of mycorrhizal fungi on soil functioning accumulated so far, indicates that these impacts are of major importance, yet poorly conceptualized. We propose a concept of mycorrhizal fungal environments in soil. Within this concept, we discuss knowledge gaps related to the understanding and quantification of mycorrhizal fungal impacts. We introduce an experimental framework to address these gaps in a quantitative manner, and present the field experiment \"Mycotron\", where we established vegetation series featuring three mycorrhizal types-Ericoid (ERM), Ecto- (ECM) and Arbuscular mycorrhiza (AM), to quantitatively assess mycorrhizal fungal impacts on soil functioning. The experimental treatments entail manipulations in dominance levels of vegetation of three mycorrhizal types (AM, ECM, ERM) in standardized soil conditions. This experiment constitutes a unique testbed to quantitatively evaluate the impacts of distinct mycorrhizal fungal environments on a large variety of ecosystem functions. Our approach aids the quantification of microbiota and plant-microbial interaction impacts on soil biochemical cycles.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144283167","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}
Jesse Ouwehand, Bregje W Brinkmann, Willie J G M Peijnenburg, Martina G Vijver
{"title":"Microbial custody: key microbiome inhabitant Sphingomonas alleviates silver nanoparticle toxicity in Daphnia magna.","authors":"Jesse Ouwehand, Bregje W Brinkmann, Willie J G M Peijnenburg, Martina G Vijver","doi":"10.1093/femsec/fiaf061","DOIUrl":"https://doi.org/10.1093/femsec/fiaf061","url":null,"abstract":"<p><p>Increased usage of nanotechnological applications inevitably leads to exposure of hosts and their associated microbiomes to metallic nanoparticles. Various bacteria within the microbiome harbour mechanisms to protect themselves against metal-related toxicity. These mechanisms have broadly been described in the absence of a host. Here, we studied how silver ion-resistant bacteria isolated from the Daphnia magna microbiome shape the host's exposure to silver nanoparticles. With germfree and mono-associated neonates, the effects of these microbes on the sensitivity of D. magna to silver nanoparticles were studied. By using this approach, a core member of the D. magna microbiome Sphingomonas yanoikuyae was identified to be silver-resistant. Neonates mono-associated with S. yanoikuyae were as sensitive to silver nanoparticles as naturally colonized neonates, whereas mono-association with Microbacterium and germfree neonates had increased sensitivity. Silver ions are the major attribution to toxicity in germfree and Microbacterium-associated neonates, whereas particles contribute more to the toxicity for the naturally- and Sphingomonas-colonized neonates. Sphingomonas accumulated in vivo more silver ions from its local environment than the other D. magna bacterial isolates. The current study shows that bacteria can play a vital role in shaping the speciation of nanomaterials and thereby modifying the toxicity to hosts.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144247230","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}
Jiri Barta, Hana Santruckova, Martin Novak, Bohuslava Cejkova, Ivana Jackova, Frantisek Buzek, Marketa Stepanova, Jan Curik, Frantisek Veselovsky, Eva Prechova
{"title":"Microbial Community Dynamics in Two Central European Peatlands Affected by Different Nitrogen Depositions.","authors":"Jiri Barta, Hana Santruckova, Martin Novak, Bohuslava Cejkova, Ivana Jackova, Frantisek Buzek, Marketa Stepanova, Jan Curik, Frantisek Veselovsky, Eva Prechova","doi":"10.1093/femsec/fiaf056","DOIUrl":"https://doi.org/10.1093/femsec/fiaf056","url":null,"abstract":"<p><p>Changes in organic matter accumulation in wetlands are critical for climate dynamics. Different nitrogen (N) inputs in Sphagnum-dominated peat bogs can lead to varying rates of carbon (C) and N accumulation, influencing greenhouse gas emissions. We investigated how contrasting N deposition shapes microbial communities in two Czech peat bogs, focusing on biological N2 fixation (BNF) as a key N input in pristine wetlands. Higher N deposition resulted in a more active microbial community with increased enzyme activity and C acquisition, potentially accelerating decomposition and reducing C storage. Enhanced denitrification, indicated by active nosZ Clade I genes, suggests that higher N inputs may increase N losses through denitrification. In contrast, the lower N site showed a less active microbial community with slower decomposition, beneficial for C sequestration, though potentially less adaptable to future N increases. Experimental BNF rates were 70 times higher at the high N site, consistent with elevated diazotroph activity indicated by active nifH gene. Phosphorus (P) availability and NH4+/NO3- ratios appeared to drive BNF differences, emphasizing the need for managed N inputs to maintain peatland ecological functions.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144247229","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}
Logan M Peoples, J Joseph Giersch, Tyler H Tappenbeck, Joseph W Vanderwall, John M Ranieri, Trista J Vick-Majors, James J Elser, Matthew J Church
{"title":"Microbial communities in glacial lakes of Glacier National Park, MT, USA.","authors":"Logan M Peoples, J Joseph Giersch, Tyler H Tappenbeck, Joseph W Vanderwall, John M Ranieri, Trista J Vick-Majors, James J Elser, Matthew J Church","doi":"10.1093/femsec/fiaf060","DOIUrl":"https://doi.org/10.1093/femsec/fiaf060","url":null,"abstract":"<p><p>Glaciers are retreating, altering alpine ecosystems and creating new proglacial lakes. Compared to lakes fed by snowpack, glacial lakes are often enriched in nutrients and suspended solids that decrease light penetration. However, the microorganisms and biogeochemical conditions within these newly formed lakes are not well characterized. We describe the microbial communities in 14 glacial lakes in Glacier National Park, MT, USA using 16S rRNA gene amplicon sequencing and measurements of nutrient concentrations, water clarity, and other environmental properties. Microbial communities were distinct between lakes, including those connected to the same glacier, indicating the importance of site-specific biogeochemical and physical dynamics on these systems. Microbial community composition correlated with lake age (formation before or after the Little Ice Age) and conductivity but not with whether a lake was connected to a contemporaneous glacier > 0.1 km2. Heterotrophic lineages found in other glacial systems were abundant and widespread, while cyanobacteria only reached appreciable abundances in shallow lakes where light reached the benthos. Relative abundances of ammonia and nitrite oxidizers correlated with concentrations of nitrate and nitrite, suggesting nitrification may help control nitrogen forms and concentrations in glacial lakes. We show that as glaciers recede, unique glacial lake microbial communities are lost with them.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144233680","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}
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}
{"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}