Liam T Sullivan, Suzanne E Kelly, Alison Ravenscraft, Martha S Hunter
{"title":"Acquisition of an obligate environmental symbiont may be limited in the arboreal environment.","authors":"Liam T Sullivan, Suzanne E Kelly, Alison Ravenscraft, Martha S Hunter","doi":"10.1093/femsec/fiaf045","DOIUrl":"https://doi.org/10.1093/femsec/fiaf045","url":null,"abstract":"<p><p>Many eukaryotic organisms have environmentally acquired microbial symbionts. In animals, microbes commonly occupy the gut and may supply critical nutrients. The leaf-footed bug, Leptoglossus zonatus (Coreidae), is a true bug that is dependent upon ingestion of the free-living, soilborne bacterium Caballeronia early in development for growth and reproduction. In 2019 and 2020, we tested the ability of second instar L. zonatus to acquire Caballeronia in the canopy of pomegranate trees where L. zonatus are often found. We compared the acquisition rate of Caballeronia in nymphs left to forage for the symbiont to bugs fed Caballeronia in advance. Additionally, we aimed to determine whether the microhabitat of potential symbiont sources influenced acquisition success. We hypothesized that the acquisition rate would be heterogeneous among treatments. In 2019, ∼30% of experimental bugs acquired Caballeronia, compared to 75% of those fed the symbiont. In 2020, only about 4% of experimental bugs acquired any symbiont. The symbiont composition of caged bugs differed, and strain diversity was reduced relative to wild bugs. We concluded that Caballeronia is present in the canopy environment, but nymphs may fail to acquire it in the fragments of habitat represented by caged branches, suggesting a cost to host dependency on environmentally acquired symbionts.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":"101 5","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12063585/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143994346","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}
Huimin Zhou, Li Tang, Kristin A Fenton, Xiaobo Song
{"title":"Exploring and evaluating microbiome resilience in the gut.","authors":"Huimin Zhou, Li Tang, Kristin A Fenton, Xiaobo Song","doi":"10.1093/femsec/fiaf046","DOIUrl":"https://doi.org/10.1093/femsec/fiaf046","url":null,"abstract":"<p><p>The gut ecosystem is closely related to human gastrointestinal health and overall wellness. Microbiome resilience refers to the capability of a microbial community to resist or recover from perturbations to its original state of balance. So far, there is no consensus on the criteria for assessing microbiome resilience. This article provides new insights into the metrics and techniques for resilience assessment. We discussed several potential parameters, such as microbiome structure, keystone species, biomarkers, persistence degree, recovery rate, and various research techniques in microbiology, metagenomics, biochemistry, and dynamic modeling. The article further explores the factors that influence the gut microbiome resilience. The microbiome structure (i.e. abundance and diversity), keystone species, and microbe-microbe interplays determine microbiome resilience. Microorganisms employ a variety of mechanisms to achieve the microbiome resilience, including flexible metabolism, quorum sensing, functional redundancy, microbial cooperation, and competition. Host-microbe interactions play a crucial role in maintaining microbiome stability and functionality. Unlike other articles, we focus on the regulation of host immune system on microbiome resilience. The immune system facilitates bacterial preservation and colonization, community construction, probiotic protection, and pathogen elimination through the mechanisms of immunological tolerance, immune-driven microbial compartmentalization, and immune inclusion and exclusion. Microbial immunomodulation indirectly modulates microbiome resilience.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":"101 5","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12065411/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143975744","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":"Particle-size dependent of bacterial diversity associated with suspended particulate matter continuum in Lake Taihu.","authors":"Fangwei Fan, Yichen Ren, Zhendu Mao, Biao Li, Chunyan Yu, Jiawei Gao, Yu Gu, Jianing Ding, Huabing Li, Qinglong L Wu","doi":"10.1093/femsec/fiaf038","DOIUrl":"https://doi.org/10.1093/femsec/fiaf038","url":null,"abstract":"<p><p>Suspended particulate matter (SPM) of varying particle sizes is widespread in aquatic ecosystems, providing crucial habitats for bacteria and serving as hotspots for mineralization and nutrient cycling. However, prior studies have typically treated bacteria associated with these particulates as a homogeneous group, overlooking size-related differences in diversity and composition. In this study, we separated the SPM continuum into five size-fractions (0.2, 2, 20, 200, and 500 µm) and investigated bacterial diversity, community assembly, and environmental drivers across four representative regions of Lake Taihu, China, over 1-year period. Using 16S rRNA gene sequencing, we observed particle-size-dependent variations in bacterial diversity. Alpha diversity decreased significantly with increasing particle size, while beta diversity showed a similar trend. Environmental factors influencing species richness varied by particle size, while bacteria associated with smaller particles (0.2, 2, and 20 µm) were more sensitive to environmental factors compared to those associated with larger ones (200 and 500 µm). The role of deterministic processes in community assembly increased with particle size, indicating stronger selection on larger particles. This study enhances our understanding of bacterial diversity in aquatic ecosystems and highlights the importance of particle size in bacterial community dynamics.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":"101 5","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12005152/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143985639","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}
Gabrielle Scheffer, Jayne Rattray, Paul Evans, Wei Shi, Srijak Bhatnagar, Casey R J Hubert
{"title":"Nitrate-reducing microorganisms prevent souring of an oil field produced water storage pond.","authors":"Gabrielle Scheffer, Jayne Rattray, Paul Evans, Wei Shi, Srijak Bhatnagar, Casey R J Hubert","doi":"10.1093/femsec/fiaf041","DOIUrl":"https://doi.org/10.1093/femsec/fiaf041","url":null,"abstract":"<p><p>Nitrate addition for mitigating sulfide production in oil field systems has been studied in laboratory settings and in some subsurface oil reservoirs. To promote water recycling and reuse associated with oil reservoirs produced by hydraulic fracturing, high-salinity produced waters are temporarily stored in surface ponds prior to subsequent reinjection into the subsurface. In this study, nitrate was added directly to a storage pond to prevent sulfide accumulation. DNA sequencing of pond water over a 4-week period revealed a decrease in the proportion of sulfate-reducing microorganisms following nitrate application. Sulfate levels remained stable during this period, whereas nitrate and nitrite fluctuated in the days following the nitrate addition. Metagenome-assembled genomes (MAGs) reconstructed from the pond water microbiome highlighted different organisms with genes for organoheterotrophic and lithoheterotrophic nitrate reduction, whereas genes associated with sulfide production via sulfate or thiosulfate reduction were barely detected. Within those MAGs, genes for acetate metabolism were observed, consistent with acetate decreasing substantially in the pond water in the presence of nitrate. After nitrate was consumed an increase in relative abundance of putative autotrophic microorganisms was observed (e.g. Arhodomonas, Guyparkeria, and Psychroflexus), corresponding to a drop in total inorganic carbon measurements in the storage pond. This trial offers an overview on microbial processes taking place in storage pond environments in response to nitrate addition.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":"101 5","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12047076/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143988038","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":"Phylogenetic clustering of microbial communities as a biomarker for chemical pollution.","authors":"Thomas P Smith, Rachel Hope, Thomas Bell","doi":"10.1093/femsec/fiaf047","DOIUrl":"https://doi.org/10.1093/femsec/fiaf047","url":null,"abstract":"<p><p>Microbial communities play a critical role in ecosystem functioning and offer promising potential as bioindicators of chemical pollution in aquatic environments. Here we examine the responses of both bacterial isolates and microbial communities to a range of pollutants, focusing on the phylogenetic predictability of their responses. We tested the growth inhibition of environmental bacterial isolates by 168 agricultural pollutants recently shown to have off-purpose antimicrobial activity in human gut bacteria. We also tested the growth responses of whole microbial communities to the same chemical pollutants and quantified changes in the composition of select communities, to link compositional changes to functioning. We found that bacterial isolates exhibited a strong phylogenetic signal in their growth responses, with closely related taxa responding similarly to chemical stress. In microbial communities, pollutants that significantly impacted isolates also reduced community diversity and growth, causing shifts in community structure toward increased phylogenetic clustering, suggesting environmental filtering. The mean phylogenetic distance effectively captured these shifts, indicating its potential as a simple metric for monitoring pollution. Our findings highlight the predictability of microbial responses to pollution and suggest that microbial-based bioindicators, coupled with rapid sequencing technologies, could transform environmental monitoring.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":"101 5","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12067926/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144005050","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}
Muhammad Syamsu Rizaludin, Ana Shein Lee Díaz, Hans Zweers, Jos M Raaijmakers, Paolina Garbeva
{"title":"Foliar infections by Botrytis cinerea modulate the tomato root volatilome and microbiome.","authors":"Muhammad Syamsu Rizaludin, Ana Shein Lee Díaz, Hans Zweers, Jos M Raaijmakers, Paolina Garbeva","doi":"10.1093/femsec/fiaf042","DOIUrl":"https://doi.org/10.1093/femsec/fiaf042","url":null,"abstract":"<p><p>The fungal pathogen Botrytis cinerea causes significant damage to aboveground plant parts, but its impact on root chemistry and microbiome composition is less understood. This study investigated how B. cinerea foliar infection influences the root volatilome and microbiome of two tomato genotypes: wild Solanum pimpinellifolium and domesticated Solanum lycopersicum var. Moneymaker. In the absence of infection, wild tomato roots emitted higher levels of monoterpenes such as α-pinene and terpinene compared to domesticated tomato roots. The fungal infection induced elevated levels of benzyl alcohol and benzofuran in the root headspace and/or rhizosphere of both genotypes, alongside genotype-specific changes. Multivariate analyses revealed that B. cinerea significantly altered bacterial and fungal community compositions in the rhizosphere and rhizoplane, with stronger bacterial community shifts in the rhizoplane. Taxa depletion and enrichment were observed, particularly among Proteobacteria and Ascomycota. Mantel tests showed significant correlations between rhizoplane bacterial community compositions and root-associated volatilome. Notably, enriched bacterial taxa such as Pelomonas and Comamonadaceae positively correlated with benzyl alcohol and benzofuran levels in the root volatilome. These findings demonstrate that B. cinerea foliar infection might induce profound changes in root-associated volatilome and microbiome composition, highlighting its systemic effects on plant root chemistry and microbiome composition.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":"101 5","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12023855/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143960652","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":"Exploring methanogenic archaea and their thermal responses in the glacier-fed stream sediments of Rongbuk River basin, Mt. Everest.","authors":"Wei Ma, Miao Lin, Peihua Shen, Hongfei Chi, Weizhen Zhang, Jingyi Zhu, Shaoyi Tian, Pengfei Liu","doi":"10.1093/femsec/fiaf044","DOIUrl":"https://doi.org/10.1093/femsec/fiaf044","url":null,"abstract":"<p><p>Glacier-fed streams (GFS) are emergent sources of greenhouse gas methane, and methanogenic archaea in sediments contribute largely to stream methane emissions. However, little is known about the methanogenic communities in GFS sediments and their key environmental driving factors. This study analyzed stream sediments from the Rongbuk River basin on Mt. Everest for methanogenic communities and their temperature responses through anaerobic microcosm incubations at 5°C and 15°C. Diverse methanogens were identified, including acetoclastic, hydrogenotrophic, and hydrogen-dependent methylotrophic types. Substantial methane and CO2 production were detected across altitudes and increased significantly at 15°C, with both methane and CO2 production rates negatively correlated with altitude. The temperature sensitivity of CO2 production also showed a negative altitude correlation. Methanogens increased substantially over long-term incubation, dominating the archaeal community. At 15°C, the relative abundance of several methanogenic groups was strongly correlated with altitude, with positive correlations observed for Methanomassiliicoccaceae and Methanoregulaceae, and negative correlations for Methanocellaceae, respectively. Besides altitude, phosphorus, carbon to nitrogen ratio, and pH also affected methanogenic structure, methane and CO2 production, and temperature sensitivities. This study offers new insights into methanogens and methane production in GFS sediments, improving our understanding of GFS carbon cycling and its potential responses to climate change.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":"101 5","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12038898/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143981728","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}
Samantha G Fortin, Kelley Uhlig, Robert C Hale, Bongkeun Song
{"title":"Microplastic biofilms as potential hotspots for plastic biodegradation and nitrogen cycling: a metagenomic perspective.","authors":"Samantha G Fortin, Kelley Uhlig, Robert C Hale, Bongkeun Song","doi":"10.1093/femsec/fiaf035","DOIUrl":"10.1093/femsec/fiaf035","url":null,"abstract":"<p><p>Microplastics are an emerging contaminant worldwide, with the potential to impact organisms and facilitate the sorption and release of chemicals. Additionally, they create a novel habitat for microbial communities, forming biofilms known as the plastisphere. While the plastisphere has been studied in select aquatic environments, those in estuarine ecosystems merit additional attention due to their proximity to plastic debris sources. Additionally, the role plastisphere communities play in nutrient cycling has rarely been examined. This study used metagenomic analysis to investigate the taxonomic composition and functional genes of developing plastisphere communities living on petroleum-based (polyethylene and polyvinyl chloride) and biopolymer-based (polylactic acid) substrates. Isolated metagenome-assembled genomes (MAGs) showed plastisphere communities have the genes necessary to perform nitrification and denitrification and degrade petroleum and biopolymer-based plastics. The functions of these plastispheres have implications for estuarine nitrogen cycling and provide a possible explanation for the plastisphere microbes' competitiveness in biofilm environments. Overall, microplastics in the estuarine system provide a novel habitat for microbial communities and associated nitrogen cycling, facilitating the growth of microbes with plastic-degrading capabilities.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11995698/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143771820","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":"Editorial: celebrating the biogeosphere at the joint meeting of International Societies for Environmental Biogeochemistry and Subsurface Microbiology.","authors":"Lotta Purkamo, Maria Dittrich, Tillmann Lueders","doi":"10.1093/femsec/fiaf049","DOIUrl":"https://doi.org/10.1093/femsec/fiaf049","url":null,"abstract":"","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":"101 5","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12067925/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143958215","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":"Heterotrophic unicellular eukaryotes feeding on the unicellular red alga Cyanidiococcus sp. in moderately hot geothermal sulfuric springs.","authors":"Yuki Sunada, Dai Tsujino, Shota Yamashita, Wei-Hsun Hsieh, Kei Tamashiro, Jin Izumi, Fumi Yagisawa, Baifeng Zhou, Shunsuke Hirooka, Takayuki Fujiwara, Shin-Ya Miyagishima","doi":"10.1093/femsec/fiaf048","DOIUrl":"https://doi.org/10.1093/femsec/fiaf048","url":null,"abstract":"<p><p>Sulfuric acidic hot springs (<pH 4.0, >37°C) are found in volcanic regions worldwide, where various bacteria, archaea, and the unicellular red algae Cyanidiophyceae dominate. Regarding heterotrophic eukaryotes, the only known species was the thermophilic amoeboflagellate Tetramitus thermacidophilus (class Eutetramitea, phylum Heterolobosea), which feeds on surrounding bacteria and archaea. In this study, we investigated three sulfuric hot springs (34.7°C-50°C, ∼pH 2.0) in Japan to determine whether other heterotrophic eukaryotes inhabit these environments. As a result, we isolated and identified cultures of four species capable of surviving at pH 2.0 and 40°C: Allovahlkampfia sp. (Eutetramitea, Heterolobosea); Nuclearia sp. and Parvularia sp. (Nucleariidea, Cristidiscoidea); and Vannella sp. (Discosea, Amoebozoa). Phylogenetic analyses suggest that these four species independently evolved from mesophilic and neutrophilic ancestors, separate from each other. Additionally, Platyophrya sp. (Colpodea, Ciliophora) and two species of Neobodo (Euglenozoa, Kinetoplastea) were also found in the same environment, while their maximum survival temperatures were 35°C and 30°C, respectively. Among these, all species except Neobodo were confirmed to grow exclusively by feeding on Cyanidiococcus sp., a dominant species of Cyanidiophyceae in the environment. Thus, various lineages of heterotrophic unicellular eukaryotes have independently developed acidophilic and thermotolerant traits, allowing them to colonize sulfuric hot springs.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":"101 5","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12063673/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143987344","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}