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Katona BW, Shukla A, Hu W, Nyul T, Dudzik C, Arvanitis A, Clay D, Dungan M, Weber M, Tu V, Hao F, Gan S, Chau L, Buchner AM, Falk GW, Jaffe DL, Ginsberg G, Palmer SN, Zhan X, Patterson AD, Bittinger K, Ni J. Microbiota and metabolite-based prediction tool for colonic polyposis with and without a known genetic driver. Gut Microbes 2025; 17:2474141. [PMID: 40069167 PMCID: PMC11913376 DOI: 10.1080/19490976.2025.2474141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2024] [Revised: 01/22/2025] [Accepted: 02/25/2025] [Indexed: 03/19/2025] Open
Abstract
Despite extensive investigations into the microbiome and metabolome changes associated with colon polyps and colorectal cancer (CRC), the microbiome and metabolome profiles of individuals with colonic polyposis, including those with (Gene-pos) and without (Gene-neg) a known genetic driver, remain comparatively unexplored. Using colon biopsies, polyps, and stool from patients with Gene-pos adenomatous polyposis (N = 9), Gene-neg adenomatous polyposis (N = 18), and serrated polyposis syndrome (SPS, N = 11), we demonstrated through 16S rRNA sequencing that the mucosa-associated microbiota in individuals with colonic polyposis is representative of the microbiota associated with small polyps, and that both Gene-pos and SPS cohorts exhibit differential microbiota populations relative to Gene-neg polyposis cohorts. Furthermore, we used these differential microbiota taxa to perform linear discriminant analysis to differentiate Gene-neg subjects from Gene-pos and from SPS subjects with an accuracy of 89% and 93% respectively. Stool metabolites were quantified via 1H NMR, revealing an increase in alanine in SPS subjects relative to non-polyposis subjects, and Partial Least Squares Discriminant Analysis (PLS-DA) analysis indicated that the proportion of leucine to tyrosine in fecal samples may be predictive of SPS. Use of these microbial and metabolomic signatures may allow for better diagnostric and risk-stratification tools for colonic polyposis patients and their families as well as promote development of microbiome-targeted approaches for polyp prevention.
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Affiliation(s)
- Bryson W. Katona
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ashutosh Shukla
- Division of Digestive & Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Weiming Hu
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Thomas Nyul
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Christina Dudzik
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Alex Arvanitis
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Daniel Clay
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Michaela Dungan
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Marina Weber
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Vincent Tu
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Fuhua Hao
- Department of Veterinary and Biomedical Sciences, Center for Molecular Toxicology and Carcinogenesis, Penn State University, University Park, PA, USA
| | - Shuheng Gan
- Peter O’Donnell Jr. School of Public Health, Quantitative Biomedical Research Center, Center for the Genetics and Host Defense, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lillian Chau
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Anna M. Buchner
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Gary W. Falk
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - David L. Jaffe
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Gregory Ginsberg
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Suzette N. Palmer
- Peter O’Donnell Jr. School of Public Health, Quantitative Biomedical Research Center, Center for the Genetics and Host Defense, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiaowei Zhan
- Peter O’Donnell Jr. School of Public Health, Quantitative Biomedical Research Center, Center for the Genetics and Host Defense, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Andrew D. Patterson
- Department of Veterinary and Biomedical Sciences, Center for Molecular Toxicology and Carcinogenesis, Penn State University, University Park, PA, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Josephine Ni
- Division of Digestive & Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
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2
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Organski AC, Rajwa B, Reddivari A, Jorgensen JS, Cross TWL. Gut microbiome-driven regulation of sex hormone homeostasis: a potential neuroendocrine connection. Gut Microbes 2025; 17:2476562. [PMID: 40071861 PMCID: PMC11913384 DOI: 10.1080/19490976.2025.2476562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2024] [Revised: 12/17/2024] [Accepted: 03/03/2025] [Indexed: 03/19/2025] Open
Abstract
The gut microbiome is known to have a bidirectional relationship with sex hormone homeostasis; however, its role in mediating interactions between the primary regulatory axes of sex hormones and their productions is yet to be fully understood. We utilized both conventionally raised and gnotobiotic mouse models to investigate the regulatory role of the gut microbiome on the hypothalamic-pituitary-gonadal (HPG) axis. Male and female conventionally raised mice underwent surgical modifications as follows: (1) hormonally intact controls; (2) gonadectomized males and females; (3) gonadectomized males and females supplemented with testosterone and estrogen, respectively. Fecal samples from these mice were used to colonize sex-matched, intact, germ-free recipient mice through fecal microbiota transplant (FMT). Serum gonadotropins, gonadal sex hormones, cecal microbiota, and the serum global metabolome were assessed. FMT recipients of gonadectomized-associated microbiota showed lower circulating gonadotropin levels than recipients of intact-associated microbiota, opposite to that of FMT donors. FMT recipients of gonadectomized-associated microbiota also had greater testicular weights compared to recipients of intact-associated microbiota. The gut microbiota composition of recipient mice differed significantly based on the FMT received, with the male microbiota having a more concerted impact in response to changes in the HPG axis. Network analyses showed that multiple metabolically unrelated pathways may be involved in driving differences in serum metabolites due to sex and microbiome received in the recipient mice. In sum, our findings indicate that the gut microbiome responds to the HPG axis and subsequently modulates its feedback mechanisms. A deeper understanding of interactions between the gut microbiota and the neuroendocrine-gonadal system may contribute to the development of therapies for sexually dimorphic diseases.
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Affiliation(s)
| | - Bartek Rajwa
- Bindley Bioscience, Purdue University, West Lafayette, IN, USA
| | - Anjali Reddivari
- Department of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, USA
| | - Joan S. Jorgensen
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Tzu-Wen L. Cross
- Department of Nutrition Science, Purdue University, West Lafayette, IN, USA
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3
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Zhang W, Xiong W, Wang M, Zhao D, Guo X, Zhan A. Vertical exchange versus horizontal dispersal in structuring local planktonic and sedimentary bacterial communities in polluted lotic ecosystems. J Environ Sci (China) 2025; 156:859-870. [PMID: 40412982 DOI: 10.1016/j.jes.2024.10.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 10/22/2024] [Accepted: 10/30/2024] [Indexed: 05/27/2025]
Abstract
Elucidating the mechanisms underlying community assembly remains a central question in community ecology, especially in aquatic ecosystems disrupted by human activities. Understanding the causes and consequences of community responses to changing environment is essential for revealing the ecological effects of anthropogenic disturbances and proposing practical strategies for ecological restoration. While stochastic dispersal and species sorting are known to influence local biological communities, most studies have focused on horizontal dispersal, often neglecting the vertical exchange of organisms between planktonic and sedimentary communities when studying stochastic dispersal. We used a highly disturbed urban river in Beijing as a model system to investigate the relative roles of stochastic dispersal versus species sorting driven by local pollution, as well as two components of stochastic dispersal, vertical exchange and horizontal dispersal, in structuring local bacterial communities. Our integrated analyses of planktonic and sedimentary bacterial communities revealed that, despite different spatial patterns along the river, both types of bacterial communities were primarily shaped by stochastic dispersal processes rather than species sorting influenced by the environmental gradient. Notably, in addition to the effect of horizontal dispersal along the river, the vertical exchange between planktonic and sedimentary bacterial communities significantly contributed to the formation of local communities. These findings suggest that both vertical exchange and horizontal dispersal should be considered when assessing the role of stochastic dispersal in shaping local community structure in microbial communities.
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Affiliation(s)
- Wei Zhang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources Environment and Tourism, Capital Normal University, Beijing 100048, China
| | - Wei Xiong
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Min Wang
- College of Resources Environment and Tourism, Capital Normal University, Beijing 100048, China
| | - Dongliang Zhao
- College of Resources Environment and Tourism, Capital Normal University, Beijing 100048, China
| | - Xiaoyu Guo
- College of Resources Environment and Tourism, Capital Normal University, Beijing 100048, China.
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China; Yunnan Collaborative Innovation Center for Plateau Lake Ecology and Environmental Health, Kunming 650214, China.
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4
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Chang VC, Purandare V, Li S, Andreotti G, Hua X, Wan Y, Dagnall CL, Jones K, Hicks BD, Hutchinson A, Yano Y, Dalton KR, Lee M, Parks CG, London SJ, Sandler DP, Gail MH, Shi J, Hofmann JN, Sinha R, Abnet CC, Vogtmann E, Beane Freeman LE. Animal farming and the oral microbiome in the Agricultural Health Study. ENVIRONMENTAL RESEARCH 2025; 281:121964. [PMID: 40436194 DOI: 10.1016/j.envres.2025.121964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2024] [Revised: 05/08/2025] [Accepted: 05/24/2025] [Indexed: 06/11/2025]
Abstract
BACKGROUND Raising farm animals imparts various exposures that may shape the human microbiome. The oral microbiome has been increasingly implicated in disease development. Animal farming has also been associated with certain chronic diseases such as cancer; however, underlying biological mechanisms are unclear. We investigated associations between raising farm animals and the oral microbiome in the Agricultural Health Study. METHODS This analysis included 1,245 participants (865 farmers and 380 spouses) who provided oral wash specimens and information on types and numbers of specific animals raised on their farms within 2 years before sample collection. The oral microbiome was measured by sequencing the V4 region of the 16S ribosomal RNA gene. We evaluated associations of farm animal exposures with alpha and beta diversity metrics (within- and between-sample diversity, respectively), as well as presence and relative abundance of specific bacterial genera. All analyses adjusted for potential confounders (e.g., age, sex, smoking, alcohol consumption). RESULTS Overall, 63 % of participants raised farm animals, most commonly cattle (46 %) and hogs (20 %). Those who raised a large number of hogs (≥2,000 vs. no hogs) had higher alpha diversity. Conversely, raising sheep/goats and raising larger numbers of poultry were associated with lower alpha diversity. Beta diversity was not significantly different between participants with and without any farm animals. Participants raising any farm animals had higher relative abundance of Porphyromonas and lower relative abundances of Prevotella and Ruminococcaceae UCG-014. Several genera were more likely to be absent with specific animal exposures (e.g., Capnocytophaga for cattle and sheep/goats; Corynebacterium, Dialister, Stomatobaculum, and Solobacterium for sheep/goats and poultry). CONCLUSIONS This was the largest study of farm animal exposures and the human microbiome to date. Findings suggest that raising specific farm animals may influence the oral microbiome, supporting the need to further investigate the potential role of animal farming in disease etiology.
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Affiliation(s)
- Vicky C Chang
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA.
| | - Vaishnavi Purandare
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Shilan Li
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Gabriella Andreotti
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Xing Hua
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Frederick National Laboratory for Cancer Research/Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Yunhu Wan
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Frederick National Laboratory for Cancer Research/Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Casey L Dagnall
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Frederick National Laboratory for Cancer Research/Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Kristine Jones
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Frederick National Laboratory for Cancer Research/Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Belynda D Hicks
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Frederick National Laboratory for Cancer Research/Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Amy Hutchinson
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA; Frederick National Laboratory for Cancer Research/Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Yukiko Yano
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Kathryn R Dalton
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Mikyeong Lee
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Christine G Parks
- Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Stephanie J London
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Mitchell H Gail
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jianxin Shi
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jonathan N Hofmann
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Rashmi Sinha
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Christian C Abnet
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Emily Vogtmann
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Laura E Beane Freeman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
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5
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Peng Q, Zhou H, Zheng H, Xie G. Investigating the role of primary fungi in Huangjiu fermentation: Insights from flavor orientation and synthetic microbiomes. Food Microbiol 2025; 129:104765. [PMID: 40086991 DOI: 10.1016/j.fm.2025.104765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2024] [Revised: 02/16/2025] [Accepted: 03/03/2025] [Indexed: 03/16/2025]
Abstract
Huangjiu, a traditional alcoholic beverage, presents a complex fermentation ecosystem primarily influenced by specific fungal species. This study utilized a culture-dependent approach and amplicon sequencing to explore fungal community succession during Huangjiu fermentation. Key fungi identified include Saccharomyces cerevisiae, Aspergillus species (flavus, oryzae, niger), Saccharomycopsis fibuligera, Thermomyces lanuginosus, Rhizopus arrhizus, Issatchenkia orientalis, Wickerhamomyces anomalus, and Diutina rugosa. Employing a synthetic microbiome, we developed a dual-strain fermentation system to evaluate the impact of these fungi on Huangjiu's organoleptic properties. Introduction of these fungi significantly altered the flavor profile, enhancing 23 volatile organic compounds (VOCs), with S. fibuligera notably increasing nine distinct VOCs. While molds contributed to bitterness by increasing bitter amino acids, S. fibuligera effectively mitigated these components, enhancing the beverage's alcohol body, smoothness, and balance. These findings provide crucial insights for optimizing Huangjiu fermentation to improve its quality and appeal.
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Affiliation(s)
- Qi Peng
- National Engineering Research Center for Chinese CRW (branch center), School of Life and Environmental Sciences, Shaoxing University, Shaoxing, 312000, Zhejiang, China
| | - Huihui Zhou
- National Engineering Research Center for Chinese CRW (branch center), School of Life and Environmental Sciences, Shaoxing University, Shaoxing, 312000, Zhejiang, China
| | - Huajun Zheng
- National Engineering Research Center for Chinese CRW (branch center), School of Life and Environmental Sciences, Shaoxing University, Shaoxing, 312000, Zhejiang, China
| | - Guangfa Xie
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou, 310015, Zhejiang, China.
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6
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Li B, Liang C, Xu B, Song P, Liu D, Zhang J, Gu H, Jiang F, Gao H, Cai Z, Zhang T. Extreme winter environment dominates gut microbiota and metabolome of white-lipped deer. Microbiol Res 2025; 297:128182. [PMID: 40252261 DOI: 10.1016/j.micres.2025.128182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Revised: 03/23/2025] [Accepted: 04/10/2025] [Indexed: 04/21/2025]
Abstract
Qinghai-Tibet Plateau (QTP) is marked by harsh environments that drive the evolution of unique nutrient metabolism mechanism in indigenous animal gut microbiotas. Yet, responses of these microbiotas to different extreme environments remain poorly understood. White-lipped deer (Przewalskium albirostris), a native endangered species in the QTP, serves as an ideal model to study how gut microbiotas adapt to season and human disturbances. Here, a multi-omics integrated analysis of 16S rRNA, metagenomics, and untargeted metabolomics was performed to investigate the composition, function, and metabolic characteristics of gut microbiota in White-lipped deer across different seasons and living environments. Our results revealed that extreme winter environment dominated the composition, function, and metabolism of gut microbiota in white-lipped deer. The white-lipped deer exhibited an enriched gut microbiota associated with producing short-chain fatty acids in winter, with core feature genera including norank_o_Rhodospirillales, Rikenellaceae_RC9_gut_group, and unclassified_c_Clostridia. However, potential pathogenic bacteria and few short-chain fatty acid producers, with core feature genera including norank_f_p-2534-18B5_gut_group, Cellulosilyticum, and Paeniclostridium, showed enrichment in captivity. Pathways associated with carbohydrate metabolism, amino acid metabolism, and immune regulation showed enrichment in winter group as an adaptation to the cold and food scarcity. Among these, Rikenellaceae_RC9_gut_group and unclassified_c_Clostridia contributed significantly to these metabolic pathways. The gut microbiota of white-lipped deer exhibited enrichment in pathways related to intestinal inflammation and enhanced immune regulation to alleviate the stress of captivity. Among these, norank_f_p-2534-18B5_gut_group contributed the most to these pathways. Butyric, valeric, and valproic acids were significantly more abundant in the winter group, while 3-hydroxybutyric and (S)-beta-aminoisobutyric acids were higher in the captive group. Furthermore, enriched metabolites and associated pathways in both groups further supported the inferences on metagenomic functions. This study confirms the key role of specific gut microbiota in adapting to high-altitude winters and anthropogenic disturbances, emphasizing its importance for environmental resilience in wild, high-altitude mammals.
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Affiliation(s)
- Bin Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Chengbo Liang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Bo Xu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Pengfei Song
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | | | | | - Haifeng Gu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China; Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Feng Jiang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China; Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Hongmei Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China; Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China
| | - Zhenyuan Cai
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China; Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China.
| | - Tongzuo Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China; Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, China.
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7
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Smirnova AV, Verbeke TJ, Furgason CC, Albakistani EA, Nwosu FC, Kim JJ, Haupt ES, Sheremet A, Lee ES, Trang E, Richardson E, Dacks JB, Dunfield PF. Microbial community development in an oil sands pit lake. THE SCIENCE OF THE TOTAL ENVIRONMENT 2025; 987:179764. [PMID: 40460542 DOI: 10.1016/j.scitotenv.2025.179764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2025] [Revised: 05/06/2025] [Accepted: 05/24/2025] [Indexed: 06/16/2025]
Abstract
Surface mining and extraction of oil sands in Canada produces fluid tailings that contain several compounds of concern for the environment. One option for mine reclamation is the construction of Pit Lakes (PLs) to contain and remediate these tailings. Ultimately, PLs should support food webs typical of boreal lakes. From 2015 to 2021, we applied 16S/18S rRNA gene amplicon sequencing and metagenomics to monitor prokaryotic and eukaryotic microbes in the only full-scale PL of the oil sands industry (Base Mine Lake or BML), and compared it to two control environments: a freshwater reservoir unaffected by tailings, and active tailings ponds receiving regular industrial input. Microbial communities in BML were always intermediate to the two control environments based on alpha and beta diversity analyses. BML communities were highly variable with year, season, and water depth, and contained fewer core species than the freshwater reservoir. Several hydrocarbon degraders and sulfur cycling bacteria were identified as indicator species of tailings ponds, while several phototrophs were indicative of freshwater. However, all of these species were abundant in BML, suggesting that the PL supports food webs characteristic of each control environment. Over the 6-year study, the relative abundances of some common freshwater phytoplankton (Cryptomonas, Mychonastes, Trebouxiophyceae, Cyanobium) and heterotrophic bacteria (Sporichthyaceae, Ca. Fonsibacter, Ilumatobacteraceae, Microbacteriaceae, Ca. Planktophila) increased in BML. The results suggest that microbial communities and processes in BML represent an intermediate state between a tailings pond and a natural freshwater system, and did not stabilize within 10 years of its creation.
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Affiliation(s)
- Angela V Smirnova
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N 1N4, Canada
| | - Tobin J Verbeke
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N 1N4, Canada
| | - Chantel C Furgason
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N 1N4, Canada
| | - Emad A Albakistani
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N 1N4, Canada
| | - Felix C Nwosu
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N 1N4, Canada
| | - Joong-Jae Kim
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N 1N4, Canada
| | - Evan S Haupt
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N 1N4, Canada
| | - Andriy Sheremet
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N 1N4, Canada
| | - Eun-Suk Lee
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N 1N4, Canada
| | - Esther Trang
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N 1N4, Canada
| | - Elisabeth Richardson
- Division of Infectious Diseases, Department of Medicine, Department of Biological Sciences, 1-001 CCIS, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Joel B Dacks
- Division of Infectious Diseases, Department of Medicine, Department of Biological Sciences, 1-001 CCIS, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N 1N4, Canada.
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8
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Liu J, Xu G, Zhao S, He J. Microbiomes of coastal sediments and plastispheres shaped by microplastics and decabrominated diphenyl ether. WATER RESEARCH 2025; 280:123417. [PMID: 40112457 DOI: 10.1016/j.watres.2025.123417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2024] [Revised: 01/25/2025] [Accepted: 02/28/2025] [Indexed: 03/22/2025]
Abstract
Deciphering the impact of microplastic and persistent organic pollutants (POPs) co-contamination on coastal sediment is critical for developing effective remediation strategies for polluted sites yet remains underexplored. This study investigated the interactions between microplastics, decabrominated diphenyl ether (deca-BDE), and their co-contamination effects on the evolvement of coastal sediment and plastisphere microbiomes for over 2 years. Results showed that deca-BDE was naturally debrominated in sediments via diverse pathways, with microplastic polystyrene stimulating the debromination rate by up to 78.7 ± 10.0 %. The putative OHRB Dehalobacter and uncultured Dehalococcoidia populations were identified responsible for the complete debromination. Co-exposure to microplastics and deca-BDE induced significant shifts in community composition, diversity, and function in the sediment microbiomes, while plastisphere microbiomes exhibited distinct compositions and functional profiles, specializing in pathogenicity, pollutant degradation, and biogeochemical cycling. The type of plastics and the presence of deca-BDE influenced the plastisphere composition. Changes in sediment properties and debromination activity profoundly shaped microbial communities, with deterministic assembly dominating the plastisphere. Co-contamination increased the complexity, modularity, and stability of the plastisphere networks, creating unique niches for OHRB. These findings highlight the intricate interplay between microplastics, deca-BDE, and microbiomes, with significant implications for ecosystem health and remediation efforts.
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Affiliation(s)
- Jinting Liu
- Department of Civil and Environmental Engineering, National University of Singapore, 117576, Singapore
| | - Guofang Xu
- Department of Civil and Environmental Engineering, National University of Singapore, 117576, Singapore
| | - Siyan Zhao
- Department of Civil and Environmental Engineering, National University of Singapore, 117576, Singapore
| | - Jianzhong He
- Department of Civil and Environmental Engineering, National University of Singapore, 117576, Singapore.
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9
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Deng B, Ren Z, Li Q, Zhang Z, Xu C, Wang P, Zhao H, Yuan Q. Black soldier fly larvae mediate Zinc and Chromium transformation through the ZnuCBA and citric acid cycle system. WATER RESEARCH 2025; 280:123483. [PMID: 40090144 DOI: 10.1016/j.watres.2025.123483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2024] [Revised: 03/09/2025] [Accepted: 03/11/2025] [Indexed: 03/18/2025]
Abstract
Intestinal microbiota and metal regulatory proteins (MRPs) underlie the transformation of heavy metals (HMs) by the black soldier fly larvae (BSFL), but the mechanisms involved are still not fully defined. Here, using 16S rRNA and metagenomics-assisted tracing, we found that zinc (Zn) and chromium (Cr) stress led to enrichment of Proteobacteria in the BSFL intestine. Support of Proteobacteria also led to increased levels of the Zn transporter proteins ZnuC/B/A and the Zn efflux proteins zntR/A. Meanwhile, the genes MltE, CitT, and SLT, which mediate the citric acid cycle, were also significantly up-regulated and involved in the cellular uptake of Cr. Although Zn and Cr stress affected the expression of antibiotic resistance genes and pathogenic genes, the BSFL intestine tended to form stable microbial communities (MCs) to transform HMs through a mechanism driven by ZupT and chrA. In addition, the expression of SCARB1 and LdcA was significantly down-regulated by acute HMs stimulation, but BSFL were still able to complete the life cycle. Therefore, we determined the protective role of MCs and MRPs on BSFL during the transformation of HMs.
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Affiliation(s)
- Bo Deng
- Key Laboratory of Smart Farming for Agricultural Animals, College of Engineering, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Zihe Ren
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, PR China
| | - Qiang Li
- Key Laboratory of Smart Farming for Agricultural Animals, College of Engineering, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Zhijian Zhang
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, PR China
| | - Chao Xu
- Hubei Biomass-Resource Chemistry and Environmental Biotechnology Key Laboratory, School of Resource and Environmental Sciences, Wuhan University, Wuhan 430079, PR China
| | - Panpan Wang
- Key Laboratory of Recycling and Eco-Treatment of Waste Biomass of Zhejiang Province, College of Environment and Natural Resources, Zhejiang University of Science and Technology, Hangzhou 310023, PR China
| | - Heping Zhao
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, PR China.
| | - Qiaoxia Yuan
- Key Laboratory of Smart Farming for Agricultural Animals, College of Engineering, Huazhong Agricultural University, Wuhan 430070, PR China.
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10
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Peng H, Zhang Z, Kang X, Zhang Y, Zhang H, Wang Y, Yang D, Zhang J, Wang Y, Cui L, Zhu YG, Ju F. Unveiling gut microbiota and metabolic functions contributed to polyvinyl chloride degradation in Spodoptera frugiperda larvae. JOURNAL OF HAZARDOUS MATERIALS 2025; 492:138209. [PMID: 40222058 DOI: 10.1016/j.jhazmat.2025.138209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2025] [Revised: 04/04/2025] [Accepted: 04/06/2025] [Indexed: 04/15/2025]
Abstract
The accumulation of synthetic plastic waste, particularly polyvinyl chloride (PVC), threatens ecosystems globally. While microbial biodegradation represents a sustainable solution, limited effective PVC-degrading microbial bioresources have been identified. Here, we investigated the gut microbiota of Spodoptera frugiperda larvae, revealing a consistent microbial profile dominated by Enterococcus in both gut contents and tissues. PVC film feeding induced significant microbiota shifts, with functional parallels to PVC powder-fed Tenebrio molitor larvae despite taxonomic divergence. Through enzyme-centric analysis, we found an Enterococcus casseliflavus strain from the gut of S. frugiperda larvae could encode a NAD-dependent oxidoreductase that directly dechlorinates additive-free PVC, representing the first case of enzymatic polymer dechlorination. This enzyme reduced PVC molecular weight (Mn: 12.02 %; Mw: 14.07 %) and notably liberated chloride ions (6.48 mg/L with NADH as a co-factor). Our findings demonstrate the PVC-degrading capacity of S. frugiperda gut microbiota and reveal its dechlorination mechanism, offering an enzymatic candidate for developing novel biocatalysts and engineered microbial strains for enhanced biodegradation. By unravelling insect-associated microbes and enzymes, this work lays a theoretical foundation for their application potentials in sustainable PVC wastes upcycling and microplastic remediation.
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Affiliation(s)
- Haoran Peng
- Research Center for Industries of the Future, School of Engineering, Westlake University, Hangzhou 310030, China; Zhejiang Provincial Key Laboratory of Intelligent Low-Carbon Biosynthesis, Hangzhou 310030, China; Westlake Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China
| | - Zhe Zhang
- Research Center for Industries of the Future, School of Engineering, Westlake University, Hangzhou 310030, China; Zhejiang Provincial Key Laboratory of Intelligent Low-Carbon Biosynthesis, Hangzhou 310030, China; Westlake Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China
| | - Xiaoxi Kang
- Research Center for Industries of the Future, School of Engineering, Westlake University, Hangzhou 310030, China; Zhejiang Provincial Key Laboratory of Intelligent Low-Carbon Biosynthesis, Hangzhou 310030, China
| | - Yunhua Zhang
- Research Center for Industries of the Future, School of Engineering, Westlake University, Hangzhou 310030, China; Zhejiang Provincial Key Laboratory of Intelligent Low-Carbon Biosynthesis, Hangzhou 310030, China; Westlake Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China
| | - Huilin Zhang
- Research Center for Industries of the Future, School of Engineering, Westlake University, Hangzhou 310030, China; Zhejiang Provincial Key Laboratory of Intelligent Low-Carbon Biosynthesis, Hangzhou 310030, China
| | - Yuxuan Wang
- Westlake Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China
| | - Dongchen Yang
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
| | - Jinlin Zhang
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
| | - Yajie Wang
- Westlake Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China
| | - Li Cui
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-environmental Science, Chinese Academy of Sciences, Beijing 100085, China
| | - Yong-Guan Zhu
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-environmental Science, Chinese Academy of Sciences, Beijing 100085, China
| | - Feng Ju
- Research Center for Industries of the Future, School of Engineering, Westlake University, Hangzhou 310030, China; Zhejiang Provincial Key Laboratory of Intelligent Low-Carbon Biosynthesis, Hangzhou 310030, China; Westlake Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China; Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou 310024, China.
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11
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Tao M, Ke X, Ma J, Liu L, Qiu Y, Hu Z, Liu F. Dissolved organic matter (DOM) - Driven variations of cadmium mobility and bioavailability in waterlogged paddy soil. JOURNAL OF HAZARDOUS MATERIALS 2025; 492:138065. [PMID: 40158508 DOI: 10.1016/j.jhazmat.2025.138065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2025] [Revised: 03/20/2025] [Accepted: 03/23/2025] [Indexed: 04/02/2025]
Abstract
Cadmium (Cd) mobility and bioavailability in paddy soils are strongly influenced by dissolved organic matter (DOM), yet the mechanisms remain unclear. This study conducted a 90-day waterlogged soil incubation with DOM / sulfate amendments under varying Cd levels. Key parameters, including dissolved organic carbon (DOC), pe+pH, Fe/S - related parameters, alongside indicators of Cd mobility and bioavailability, were monitored. Results revealed that DOM addition increased Cd mobility on the 3rd day of incubation (DOI), irrespective of sulfate application, due to Cd desorption from iron oxides and DOM-Cd complexation. After the 10th DOI, DOM addition reduced Cd mobility and bioavailability mainly due to facilitation of sulfide-mediated Cd sequestration driven by Fe-S related reducing bacteria. The combined application with sulfate strengthened this effect. However, in low-Cd soils, DOM addition increased Cd bioavailability since the 45th DOI, likely due to the low Cd/DOM ratio, which limited sulfide immobilization. Nevertheless, sulfate application mitigated this effect. Furthermore, DOM supplementation generally decreased Cd mobility, but increased Cd availability at the 45th DOI in high-Cd soils due to competitive adsorption and Fe transformation. This study demonstrates the dual role of DOM in regulating Cd dynamics and its interaction with sulfate, offering insights for Cd contamination management in paddy soils.
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Affiliation(s)
- Mingming Tao
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101408, China; Department of Plant and Environmental Science, Faculty of Science, University of Copenhagen, Taastrup DK-2630, Denmark; Sino-Danish Centre for Education and Research (SDC), Beijing 101408, China
| | - Xianlin Ke
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101408, China; Sino-Danish Centre for Education and Research (SDC), Beijing 101408, China; Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg 1871, Denmark
| | - Jingnan Ma
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101408, China; Sino-Danish Centre for Education and Research (SDC), Beijing 101408, China
| | - Linlin Liu
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101408, China; Department of Plant and Environmental Science, Faculty of Science, University of Copenhagen, Taastrup DK-2630, Denmark; Sino-Danish Centre for Education and Research (SDC), Beijing 101408, China
| | - Yanhua Qiu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Zhengyi Hu
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101408, China; Sino-Danish Centre for Education and Research (SDC), Beijing 101408, China.
| | - Fulai Liu
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101408, China; Department of Plant and Environmental Science, Faculty of Science, University of Copenhagen, Taastrup DK-2630, Denmark; Sino-Danish Centre for Education and Research (SDC), Beijing 101408, China
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12
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Zhao X, Chen A, Gong X, Zhang P, Cui K, Li S, Zhang W, Zhu C, Gang H, Huo J, Xie F, Qin D. Metabolite-mediated responses of phyllosphere microbiota to powdery mildew infection in resistant and susceptible black currant cultivars. HORTICULTURE RESEARCH 2025; 12:uhaf092. [PMID: 40371437 PMCID: PMC12077297 DOI: 10.1093/hr/uhaf092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2024] [Accepted: 03/18/2025] [Indexed: 05/16/2025]
Abstract
Plant-metabolite-microbe interactions play essential roles in disease suppression. Most studies focus on the root exudates and rhizosphere microbiota to fight soil-borne pathogens, but it is poorly understood whether the changes in phyllosphere metabolites can actively recruit beneficial microbes to enhance disease resistance. In this study, the differences of phyllosphere microbial communities and key leaf metabolites were systematically explored in resistant and susceptible black currant cultivars related to powdery mildew (PM) by integrating microbiome and metabolomic analyses. The results showed that the diversity and composition of microbiome changed, as highlighted by a reduction in microbial alpha-diversity and beta-diversity of susceptible cultivars. An increasing fungal network complexity and a decreasing bacterial network complexity occurred in resistant cultivar. Bacillus, Burkholderia (bacteria), and Penicillium (fungi) were identified as keystone microorganisms and resistance effectors in resistant cultivar. Metabolites such as salicylic acid, trans-zeatin, and griseofulvin were more abundant in resistant cultivar, which had a positive regulatory effect on the abundance of bacterial and fungal keystones. These findings unravel that resistant cultivar can enrich beneficial microorganisms by adjusting leaf metabolites, thus showing the external disease-resistant response. Moreover, the reduced stomatal number and increased tissue thickness were observed in resistant cultivar, suggesting inherent physical structure also provides a basic defense against PM pathogens. Therefore, resistant black currant cultivar displayed multilevel defense responses of physical structures, metabolites, and microorganisms to PM pathogens. Collectively, our study highlights the potential for utilizing phyllosphere microbiome dynamics and metabolomic adjustments in agricultural practices, plant breeding, and microbiome engineering to develop disease-resistant crops.
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Affiliation(s)
- Xueying Zhao
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, No 600, Changjiang Road, Xiangfang District, Harbin City, Heilongjiang Province, China
- National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, Northeast Agricultural University, No 600, Changjiang Road, Xiangfang District, Harbin City, Heilongjiang Province, China
| | - Along Chen
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, No 600, Changjiang Road, Xiangfang District, Harbin City, Heilongjiang Province, China
| | - Xiaonan Gong
- Shandong Provincial Forestry Protection and Development Service Center, No.5948, Second Ring East Road, LixiaDistrict, Jinan City, Shandong Province, China
| | - Peng Zhang
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, No 600, Changjiang Road, Xiangfang District, Harbin City, Heilongjiang Province, China
- National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, Northeast Agricultural University, No 600, Changjiang Road, Xiangfang District, Harbin City, Heilongjiang Province, China
| | - Kaojia Cui
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, No 600, Changjiang Road, Xiangfang District, Harbin City, Heilongjiang Province, China
- National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, Northeast Agricultural University, No 600, Changjiang Road, Xiangfang District, Harbin City, Heilongjiang Province, China
| | - Shuxian Li
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, No 600, Changjiang Road, Xiangfang District, Harbin City, Heilongjiang Province, China
- National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, Northeast Agricultural University, No 600, Changjiang Road, Xiangfang District, Harbin City, Heilongjiang Province, China
| | - Weixia Zhang
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, No 600, Changjiang Road, Xiangfang District, Harbin City, Heilongjiang Province, China
- National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, Northeast Agricultural University, No 600, Changjiang Road, Xiangfang District, Harbin City, Heilongjiang Province, China
| | - Chenqiao Zhu
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, No 600, Changjiang Road, Xiangfang District, Harbin City, Heilongjiang Province, China
- National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, Northeast Agricultural University, No 600, Changjiang Road, Xiangfang District, Harbin City, Heilongjiang Province, China
| | - Huixin Gang
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, No 600, Changjiang Road, Xiangfang District, Harbin City, Heilongjiang Province, China
- National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, Northeast Agricultural University, No 600, Changjiang Road, Xiangfang District, Harbin City, Heilongjiang Province, China
| | - Junwei Huo
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, No 600, Changjiang Road, Xiangfang District, Harbin City, Heilongjiang Province, China
- National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, Northeast Agricultural University, No 600, Changjiang Road, Xiangfang District, Harbin City, Heilongjiang Province, China
| | - Fuchun Xie
- College of Animal Science and Technology, Northeast Agricultural University, No 600, Changjiang Road, Xiangfang District, Harbin City, Heilongjiang Province, China
| | - Dong Qin
- College of Horticulture & Landscape Architecture, Northeast Agricultural University, No 600, Changjiang Road, Xiangfang District, Harbin City, Heilongjiang Province, China
- National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, Northeast Agricultural University, No 600, Changjiang Road, Xiangfang District, Harbin City, Heilongjiang Province, China
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13
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Zhang J, Zhang Q, Zhang C, Wang R, Wang H, Zheng P. Vegetation succession enhances microbial diversity, network complexity, and stability in coastal wetlands, underscoring the pivotal role of soil salinity and key microbial species. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2025; 388:125997. [PMID: 40446786 DOI: 10.1016/j.jenvman.2025.125997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2025] [Revised: 05/15/2025] [Accepted: 05/25/2025] [Indexed: 06/16/2025]
Abstract
In coastal wetlands, vegetation succession is primarily driven by changes in hydrology, sedimentation, and soil salinity. This ecological process is known to significantly influence microbial communities. However, its specific effect on microbial interactions and network dynamics in coastal wetlands remains insufficiently understood. This study adopted a spatial ecological sequence approach instead of a temporal succession method to comprehensively analyze the effects of vegetation succession on microbial communities in the Yellow River Delta. The results demonstrated that soil salinity, rather than nutrient levels, was the primary driver of microbial community shifts during succession. Succession increased the relative abundance of dominant phyla, such as Acidobacteria, Actinobacteria, Chloroflexi, and Planctomycetota, whereas key taxa, including salt-tolerant species, functioned as pivotal nodes regulating community interactions. Co-occurrence network analysis revealed that vegetation succession significantly enhanced the complexity and stability of microbial networks by reducing soil salinity and thereby altering the composition of key microbial taxa. These findings reveal the salinity-mediated mechanisms underlying microbial network assembly during vegetation succession in coastal wetlands and identify environmentally responsive microbial taxa that act as critical connectors within microbial communities, providing a mechanistic basis for the ecological restoration and sustainable management of salinized coastal ecosystems.
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Affiliation(s)
- Jilin Zhang
- School of Life Sciences, Shandong University, Qingdao, 266237, PR China; Shandong Provincial Engineering and Technology Research Center for Vegetation Ecology, Shandong University, Qingdao, 266237, PR China; Qingdao Forest Ecology Research Station of National Forestry and Grassland Administration, Shandong University, Qingdao, 266237, PR China; Qingdao Key Laboratory of Forest and Wetland Ecology, Shandong University, Qingdao, 266237, PR China
| | - Qing Zhang
- School of Life Sciences, Shandong University, Qingdao, 266237, PR China; Shandong Provincial Engineering and Technology Research Center for Vegetation Ecology, Shandong University, Qingdao, 266237, PR China; Qingdao Forest Ecology Research Station of National Forestry and Grassland Administration, Shandong University, Qingdao, 266237, PR China; Qingdao Key Laboratory of Forest and Wetland Ecology, Shandong University, Qingdao, 266237, PR China
| | - Chunyu Zhang
- School of Life Sciences, Shandong University, Qingdao, 266237, PR China; Shandong Provincial Engineering and Technology Research Center for Vegetation Ecology, Shandong University, Qingdao, 266237, PR China; Qingdao Forest Ecology Research Station of National Forestry and Grassland Administration, Shandong University, Qingdao, 266237, PR China; Qingdao Key Laboratory of Forest and Wetland Ecology, Shandong University, Qingdao, 266237, PR China
| | - Renqing Wang
- School of Life Sciences, Shandong University, Qingdao, 266237, PR China; Shandong Provincial Engineering and Technology Research Center for Vegetation Ecology, Shandong University, Qingdao, 266237, PR China; Qingdao Forest Ecology Research Station of National Forestry and Grassland Administration, Shandong University, Qingdao, 266237, PR China; Qingdao Key Laboratory of Forest and Wetland Ecology, Shandong University, Qingdao, 266237, PR China
| | - Hui Wang
- School of Life Sciences, Shandong University, Qingdao, 266237, PR China; Shandong Provincial Engineering and Technology Research Center for Vegetation Ecology, Shandong University, Qingdao, 266237, PR China; Qingdao Forest Ecology Research Station of National Forestry and Grassland Administration, Shandong University, Qingdao, 266237, PR China; Qingdao Key Laboratory of Forest and Wetland Ecology, Shandong University, Qingdao, 266237, PR China.
| | - Peiming Zheng
- School of Life Sciences, Shandong University, Qingdao, 266237, PR China; Shandong Provincial Engineering and Technology Research Center for Vegetation Ecology, Shandong University, Qingdao, 266237, PR China; Qingdao Forest Ecology Research Station of National Forestry and Grassland Administration, Shandong University, Qingdao, 266237, PR China; Qingdao Key Laboratory of Forest and Wetland Ecology, Shandong University, Qingdao, 266237, PR China.
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14
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Jiang T, Ren J, Li D, Luo Y, Huang Y, Gao T, Yang J, Yu J, Liu L, Yuan H. Pseudomonas syringae exacerbates apple replant disease caused by Fusarium. Microbiol Res 2025; 296:128124. [PMID: 40054134 DOI: 10.1016/j.micres.2025.128124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2024] [Revised: 02/14/2025] [Accepted: 02/24/2025] [Indexed: 04/10/2025]
Abstract
Apple replant disease (ARD) causes significant economic losses globally, including in China. Analyzing the causes of this replant disease from the perspective of rhizosphere microecology is therefore essential. In this study, we examined rhizosphere soils from apple trees subjected to continuous cropping. The mechanisms underlying ARD were elucidated through high-throughput sequencing of the soil microbiome, co-occurrence network analysis using NetShift, and correlation analyses. Core bacterial microbes were isolated, and their roles in altering the microecological environment were verified through reinoculation experiments. The results indicated that the disease indices for apple seedlings cultivated increased in continuously cropped soils. Bacterial diversity decreased in continuously cropped apple orchards for 10 years (R10) and 15 years (R15), but the relative abundance of Pseudomonas increased. In contrast, fungal diversity increased, with the relative abundance of Fusarium also increasing. As a dominant genus, Pseudomonas exhibited significant network variation after 10 years of consecutive cultivation, suggesting that this microorganism may play a key role in the occurrence of ARD. Moreover, the correlation analysis revealed, for the first time, that Pseudomonas is negatively correlated with bacterial diversity but positively correlated with the relative abundance of Fusarium, indicating a close relationship between Pseudomonas and Fusarium in continuously cropped soil. Four key Pseudomonas amplicon sequence variants (ASVs) strains were isolated from the continuously cropped rhizosphere soil of apple trees, and reinoculation experiments verified that introducing Pseudomonas exacerbated the occurrence of replant diseases in both strawberry and apple, with significantly higher disease indices compared to single Fusarium inoculation. The findings of this study provide new and timely insights into the mechanism underlying the occurrence of ARD.
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Affiliation(s)
- Tingting Jiang
- State Key Laboratory of Animal Biotech Breeding, and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jiaxi Ren
- Hebei Engineering Research Center for Resource Utilization of Agricultural Waste, College of Life Sciences, Hebei Agricultural University, Baoding, Hebei 071000, China
| | - Dongmei Li
- State Key Laboratory of Animal Biotech Breeding, and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Ying Luo
- State Key Laboratory of Animal Biotech Breeding, and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yaru Huang
- State Key Laboratory of Animal Biotech Breeding, and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Tongguo Gao
- Hebei Engineering Research Center for Resource Utilization of Agricultural Waste, College of Life Sciences, Hebei Agricultural University, Baoding, Hebei 071000, China
| | - Jinshui Yang
- State Key Laboratory of Animal Biotech Breeding, and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jiayi Yu
- Beijing Siliang Technology Limited Company, Beijing 100193, China
| | - Liang Liu
- State Key Laboratory of Animal Biotech Breeding, and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| | - Hongli Yuan
- State Key Laboratory of Animal Biotech Breeding, and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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15
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Temovska M, Hegner R, Ortiz-Ardila AE, Usack JG, Angenent LT. Lactate production from lactose-rich wastewater: A comparative study on reactor configurations to maximize conversion rates and efficiencies. WATER RESEARCH 2025; 278:123365. [PMID: 40022799 DOI: 10.1016/j.watres.2025.123365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2024] [Revised: 02/13/2025] [Accepted: 02/21/2025] [Indexed: 03/04/2025]
Abstract
About 90 % of global lactate production is derived from bacterial fermentation of sugars via pure homofermentative cultures in batch mode. Acid whey, which is a lactose-rich wastewater from the yogurt industry, can be used as an alternative substrate for commercial lactate production. Operating reactor microbiomes reduces the lactate production costs by circumventing sterilization, while continuous operation with biomass retention achieves higher productivity at shorter production times. To find the best reactor configuration with biomass retention for lactate production from acid whey, we operated three different reactor configurations: (1) an upflow anaerobic sludge blanket (UASB) reactor; (2) an anaerobic filter reactor (AFR); and (3) an anaerobic continuously stirred tank reactor (CSTR) with a hollow-fiber membrane module. We operated at different hydraulic retention times (HRTs) to find the optimum production parameters at a temperature of 50 °C and a pH of 5.0. We did not use an inoculum but enriched the endogenous D-lactate-producing Lactobacillus spp. that later dominated the reactor microbiomes (> 90 % relative abundance). Undissociated lactic acid concentrations of more than 60 mmol C L-1 inhibited the microbiomes. We alleviated the inhibition effect by shortening the HRT to 0.6 days and using diluted acid-whey substrate (1.67-fold dilution) to achieve almost complete conversion of the acid-whey sugars to lactate. At the 0.6-day HRT, the AFR and CSTR performed better than the UASB reactor due to their better cell retention abilities. During the period between Day 365-384, we experienced an error in the pH control of the CSTR system during which the pH value dropped to 4.3. After this pH-error period, the lactose and galactose-into-lactate (LG-into-LA) conversion efficiency for the CSTR considerably improved and surpassed the AFR. We achieved the highest lactate conversion rate of 1256 ± 46.3 mmol C L-1 d-1 (1.57 ± 0.06 g L-1 h-1) at a LG-into-LA conversion efficiency of 82.2 ± 3.4 % (in mmol C), with a yield of 0.85 ± 0.02 mmol C mmol C-1 (product per consumed substrate) for the CSTR.
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Affiliation(s)
- Monika Temovska
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstr. 94-96, 72076 Tübingen, Germany
| | - Richard Hegner
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstr. 94-96, 72076 Tübingen, Germany
| | - Andrés E Ortiz-Ardila
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstr. 94-96, 72076 Tübingen, Germany
| | - Joseph G Usack
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstr. 94-96, 72076 Tübingen, Germany; Department of Food Science and Technology, University of Georgia, Athens, Georgia
| | - Largus T Angenent
- Environmental Biotechnology Group, Department of Geosciences, University of Tübingen, Schnarrenbergstr. 94-96, 72076 Tübingen, Germany; AG Angenent, Max Planck Institute for Biology, Max Planck Ring 5, 72076 Tübingen, Germany; Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej 10D, 8000 Aarhus C, Denmark; The Novo Nordisk Foundation CO(2) Research Center (CORC), Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark; Cluster of Excellence - Controlling Microbes to Fight Infections, University of Tübingen, Auf der Morgenstelle 28, 72074 Tübingen, Germany.
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Hrabar J, Babić I, Jozić S, Trumbić Ž, Pioppi A, Nielsen LJD, Maravić A, Tomašević T, Kovacs ÁT, Mladineo I. Prospecting microbiota of Adriatic fish: Bacillus velezensis as a potential probiotic candidate. Anim Microbiome 2025; 7:64. [PMID: 40517265 DOI: 10.1186/s42523-025-00429-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2025] [Accepted: 05/24/2025] [Indexed: 06/16/2025] Open
Abstract
BACKGROUND Aquaculture is one of the fastest growing sectors of food production and covers more than half of the market demand for fish and fishery products. However, aquaculture itself faces numerous challenges, such as infectious disease outbreaks, which are one of the limiting factors for the growth and environmental sustainability of modern aquaculture. Understanding the composition and diversity of the gut microbiota of fish is important to elucidate its role in host health and aquaculture management. In addition, the gut microbiota represents a valuable source of bacteria with probiotic potential for farmed fish. RESULTS In this study, we analysed the intestinal microbiota of two economically important fish species, the European seabass (Dicentrarchus labrax) and the gilthead seabream (Sparus aurata), using 16S rRNA gene amplicon sequencing. The taxonomic analysis identified 462 amplicon sequence variants at a similarity level of 99 and showed similar alpha diversity indices between seabass and gilthead seabream. Beta diversity analysis showed no significant differentiation in gut microbiota between fish species or aquaculture sites. Among the culturable isolates, a high proportion of Photobacterium damselae and Bacillus spp. was detected. We selected a single Bacillus velezensis isolate and further characterised its biosynthetic potential by performing whole genome sequencing. Its genome contains biosynthetic gene clusters for most of the common secondary metabolites typical of B. velezensis. Antibiotic susceptibility testing showed the sensitivity of the selected isolates to several antibiotics according to EFSA recommendations. Furthermore, stimulation of peripheral blood leukocytes (PBL) with B. velezensis resulted in a strong pro-inflammatory response, with a pronounced upregulation of cytokines il1b, il6, tnfa and il10 observed over time. CONCLUSIONS Overall, this study provides an insight into the composition of the intestinal microbiota and the diversity of culturable intestinal bacteria of two economically most important fish species from Adriatic cage culture and sheds light on the autochthonous intestinal B. velezensis as a promising probiotic candidate for Mediterranean aquaculture.
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Affiliation(s)
- Jerko Hrabar
- Institute of Oceanography and Fisheries, Split, Croatia.
| | | | - Slaven Jozić
- Institute of Oceanography and Fisheries, Split, Croatia
| | - Željka Trumbić
- Department of Marine Studies, University of Split, Split, Croatia
| | - Adele Pioppi
- Institute of Biology, Leiden University, Leiden, The Netherlands
- DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | | | - Ana Maravić
- Faculty of Science, University of Split, Split, Croatia
| | | | - Ákos T Kovacs
- Institute of Biology, Leiden University, Leiden, The Netherlands
- DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Ivona Mladineo
- Institute of Parasitology, BC CAS, Česke Budêjovice, Czech Republic
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
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17
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Edwin NR, Duff A, Deveautour C, Brennan F, Abram F, O'Sullivan O. Consistent microbial insights across sequencing methods in soil studies: the role of reference taxonomies. mSystems 2025:e0105924. [PMID: 40492742 DOI: 10.1128/msystems.01059-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Accepted: 05/12/2025] [Indexed: 06/12/2025] Open
Abstract
Microbes play an important role in soil functioning, underpinning food production systems and delivering an array of essential ecosystem services. To elucidate how these microbes relate to ecosystem functions, accurate identification and classification of soil microorganisms are important. We evaluated the comparability of shotgun and amplicon sequencing approaches by profiling soil microbiota from 131 diverse temperate grassland soils across Ireland. We assessed method comparability in terms of (i) detection and classification of the most abundant phyla, (ii) their capacity to differentiate samples based on their microbial community, and (iii) their capacity to link microbial communities to measured nitrogen cycle functions. Our findings reveal that both methods offer moderately similar outcomes, providing consistent detection of major phyla, similar microbial community differentiation patterns, and largely identifying the same relationships between the phyla and nitrogen functions. The variations observed between the two methods were mostly associated with differences in the choice of reference taxonomy. Amplicon sequencing represents a cost-effective, less computationally demanding option, while shotgun sequencing provides deeper taxonomic resolution and access to the latest databases, making it suitable for detailed microbial profiling. Our study underscores the need for careful method selection based on project requirements, database availability, and financial resources.IMPORTANCEStudying the microorganisms in soil remains a challenge as soils are one of the most complex and diverse environments. Compounding these challenges is the lack of culturable representatives in soil, with over 99% of soil microorganisms yet to be cultivated in a laboratory setting. Leveraging next-generation sequencing technologies, which bypass traditional culture-dependent methods, scientists are now able to attain low-cost, high-throughput DNA sequencing that can detect even the rarest microorganisms within samples. The present study rigorously compares amplicon and shotgun sequencing techniques in profiling microbial communities across diverse temperate grassland soil samples, focusing on how different databases, classifiers, and sequencing methods influence the results. Our study underscores the crucial need for a harmonized taxonomic database that could greatly enhance comparability and accuracy in the understanding of soil microbiomes.
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Affiliation(s)
- Niranjana Rose Edwin
- Teagasc, Moorepark Food Research Centre, Fermoy, County Cork, Ireland
- Functional Environmental Microbiology, University of Galway, Galway, County Galway, Ireland
- VistaMilk Science Foundation Ireland (SFI) Research Centre, Cork, Ireland
| | - Aoife Duff
- Soils, Environment and Landuse Department, Teagasc, Wexford, Ireland
| | - Coline Deveautour
- AGHYLE Research Unit, Institut Polytechnique UniLaSalle, Mont-Saint-Aignan, France
| | - Fiona Brennan
- VistaMilk Science Foundation Ireland (SFI) Research Centre, Cork, Ireland
- Soils, Environment and Landuse Department, Teagasc, Wexford, Ireland
| | - Florence Abram
- Functional Environmental Microbiology, University of Galway, Galway, County Galway, Ireland
| | - Orla O'Sullivan
- Teagasc, Moorepark Food Research Centre, Fermoy, County Cork, Ireland
- VistaMilk Science Foundation Ireland (SFI) Research Centre, Cork, Ireland
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18
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Nash J, Looney B, Cregger MA, Schadt C, Vilgalys R. Dual-mycorrhizal colonization is determined by plant age and host identity in two species of Populus. MYCORRHIZA 2025; 35:42. [PMID: 40490518 DOI: 10.1007/s00572-025-01215-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2025] [Accepted: 05/28/2025] [Indexed: 06/11/2025]
Abstract
Plants have evolved symbioses with mycorrhizal and endophytic fungi that are essential for their growth and survival. While most plants associate with a single guild of mycorrhizal fungi, a select group termed "dual-mycorrhizal plants" associate with both arbuscular mycorrhizal and ectomycorrhizal fungi. Although a shift from predominance of arbuscular mycorrhizal to ectomycorrhizal colonization with plant development has been demonstrated on other dual-mycorrhizal hosts, it is not known how mycorrhizal colonization shifts with plant age in Populus species. We performed a controlled growth experiment with natural field-sourced inocula to test for age-dependent shifts in fungal colonization rates and for host-specific patterns of colonization in two species of Populus (P. tremuloides and P. trichocarpa). We found that only P. trichocarpa displayed dual-mycorrhizal colonization, while P. tremuloides associated with ectomycorrhizal fungi, but not arbuscular mycorrhizal fungi. Both guilds of mycorrhizal fungi increased in abundance with plant age, while root endophytic fungal colonization decreased. Many of the early-colonizing endophytic fungi that we documented have strong saprotrophic capabilities, which may be an important trait for fast colonization. Dark septate endophytes were more abundant than either guild of mycorrhizal fungi, and are likely to be functionally important members of the Populus root fungal community. Our findings represent a novel pattern in the development of dual-mycorrhizal colonization and illustrate that Populus species vary in their association with arbuscular mycorrhizal fungi. Our results also highlight the importance of dark septate endophyte colonization dynamics on dual-mycorrhizal plants.
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Affiliation(s)
- Jake Nash
- Department of Biology, Duke University, Durham, NC, USA.
| | - Brian Looney
- Department of Biology, Duke University, Durham, NC, USA
| | - Melissa A Cregger
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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Babalola OO, Osuji IE, Akanmu AO. Amplicon-based metagenomic survey of microbes associated with the organic and inorganic rhizosphere soil of Glycine max L. BMC Genom Data 2025; 26:40. [PMID: 40481438 PMCID: PMC12142974 DOI: 10.1186/s12863-025-01333-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2025] [Accepted: 05/23/2025] [Indexed: 06/11/2025] Open
Abstract
Objectives The metagenomic dataset of 16S rRNA and ITS gene amplicons of DNA were obtained from the cultivated soybean rhizosphere of organic and inorganic treatments. The organic treatments consisted of poultry waste, and cow dung treatments while the inorganic consisted of samples from untreated soybean plots and the bulk. Amplicon sequencing was performed on the Illumina platform, and the raw sequence data were processed and analyzed using Quantitative Insights Into Microbial Ecology (QIIME 2 version 2019.1.). Data description The analysis revealed a metagenomic library from soybean rhizospheric soils, providing insights into diversity and distribution of the bacterial and fungal community diversities. The most predominant bacteria phylum taxa across the treatments were Proteobacteria, Firmicutes, Actinobacteriota and Bacteriodota, while those for fungi were Ascomycota, Basidiomycota and Glomeromycota. The dataset provides insights into how different organic fertilization sources affect the structure, composition, and diversity of the microbiome in the soybean rhizosphere. The sequences have been deposited in the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI) with assigned bioproject accession numbers; 16S rRNA (SRP540791) and ITS (SRP541849).
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Affiliation(s)
- Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa.
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK.
| | - Ijeoma Emelda Osuji
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa
| | - Akinlolu Olalekan Akanmu
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa
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Zhou X, Xiao C, Zhang B, Yang X. Depth-dependent response of soil microbial community and greenhouse gas efflux to polylactic acid microplastics and tidal cycles in a mangrove ecosystem. JOURNAL OF HAZARDOUS MATERIALS 2025; 489:137664. [PMID: 39987736 DOI: 10.1016/j.jhazmat.2025.137664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2024] [Revised: 01/28/2025] [Accepted: 02/17/2025] [Indexed: 02/25/2025]
Abstract
The impacts of microplastics (MPs) on greenhouse gas emissions from mangrove soil remain poorly understood. Previous studies mostly focused on the topsoil in stable inundation state, ignoring the effects of natural tidal cycle and deep soil under different soil oxygen conditions. In this study, we analyzed soil microbial communities and greenhouse gas emissions from mangrove soils across various depths and tidal conditions (by adding seawater to create different inundation durations) in response to polylactic acid (PLA) MP exposure. Results indicated that PLA MPs addition enhances CO2 and CH4 release from the continuously anaerobic subsoil (100-120 cm). With increasing submersion duration, PLA MPs facilitate the emission of CH4 from the topsoil (0-5 cm). An elevated C:N ratio may promote microbial nitrogen mining and organic carbon mineralization, indicating the threat of PLA MPs to soil carbon and nitrogen pools. PLA MPs addition significantly altered the bacterial community structure and reduced bacterial diversity in the subsoil. Increases in the abundance and functioning of communities associated with methanogenesis and sulfate reduction contributed to the release of CO2 and CH4. The duration of inundation had no significant impact on the microbial community structure in the topsoil. These findings demonstrate the accelerating effect of PLA MPs on organic carbon mineralization and carbon release, which was critically regulated by the soil depth and tidal inundation.
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Affiliation(s)
- Xu Zhou
- Guangdong Provincial Observation and Research Station for Coupled Human and Natural Systems in Land-ocean Interaction Zone, Beijing Normal University at Zhuhai, Zhuhai 519087, China; State Key Laboratory of Earth Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing 100875, China
| | - Cunde Xiao
- Guangdong Provincial Observation and Research Station for Coupled Human and Natural Systems in Land-ocean Interaction Zone, Beijing Normal University at Zhuhai, Zhuhai 519087, China; State Key Laboratory of Earth Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing 100875, China
| | - Bingwei Zhang
- Guangdong Provincial Observation and Research Station for Coupled Human and Natural Systems in Land-ocean Interaction Zone, Beijing Normal University at Zhuhai, Zhuhai 519087, China; Zhuhai Branch of State Key Laboratory of Earth Surface Processes and Resource Ecology, Beijing Normal University at Zhuhai, Zhuhai 519087, China
| | - Xiaofan Yang
- Guangdong Provincial Observation and Research Station for Coupled Human and Natural Systems in Land-ocean Interaction Zone, Beijing Normal University at Zhuhai, Zhuhai 519087, China; State Key Laboratory of Earth Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing 100875, China.
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21
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Suzuki Y, Ishioka K, Nakamura T, Miyazaki N, Marubashi S, Suzutani T. Function of Yogurt Fermented with the Lactococcus lactis 11/19-B1 Strain in Improving the Lipid Profile and Intestinal Microbiome in Hemodialysis Patients. Nutrients 2025; 17:1931. [PMID: 40507200 PMCID: PMC12157043 DOI: 10.3390/nu17111931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2025] [Revised: 05/23/2025] [Accepted: 05/28/2025] [Indexed: 06/16/2025] Open
Abstract
BACKGROUND/OBJECTIVES The number of chronic kidney disease (CKD) patients is increasing in Japan, and this population is at high risk of death from cardiovascular and cerebrovascular diseases. Therefore, prevention of arteriosclerosis as a common underlying cause of these diseases is required. In this study, we examined whether 11/19-B1 yogurt, which has been proven to reduce serum low-density lipoprotein (LDL) levels, can decrease the serum levels of indoxylsulfate and trimethylamine-N-oxide (TMAO), which are produced by intestinal microbiota and known to cause arteriosclerosis, through improving dysbiosis in hemodialysis patients. METHODS Nineteen dialysis patients consumed 50 g of 11/19-B1 yogurt daily for 8 weeks, and changes in serum lipid profile and uremic toxin levels, intestinal microbiome, as well as the frequency of bowel movement and stool characteristics were observed. RESULTS The results demonstrated that an intake of yogurt decreased serum LDL 99.3 to 88.5 (p = 0.049) and indoxylsulfate in seven of nine subjects with previously high concentrations, and improved stool characteristics as estimated by the Bristle stool score, although decreased HDL and no beneficial effect on serum TMAO was observed. CONCLUSIONS These results may suggest that the ingestion of 11/19-B1 yogurt provides a preventative effect against the progression of atherosclerosis and renal dysfunction.
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Affiliation(s)
- Yoshiki Suzuki
- Department of Microbiology, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima 960-1295, Japan; (Y.S.); (K.I.); (N.M.)
- Department of Hepato-Biliary-Pancreatic and Transplant Surgery, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima 960-1295, Japan;
- Department of Nephrology, Mito Red Cross Hospital, 3-12-48 Sannomaru, Mito 310-0011, Ibaragi, Japan;
| | - Ken Ishioka
- Department of Microbiology, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima 960-1295, Japan; (Y.S.); (K.I.); (N.M.)
| | - Taichi Nakamura
- Department of Nephrology, Mito Red Cross Hospital, 3-12-48 Sannomaru, Mito 310-0011, Ibaragi, Japan;
| | - Nozomu Miyazaki
- Department of Microbiology, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima 960-1295, Japan; (Y.S.); (K.I.); (N.M.)
| | - Shigeru Marubashi
- Department of Hepato-Biliary-Pancreatic and Transplant Surgery, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima 960-1295, Japan;
| | - Tatsuo Suzutani
- Department of Microbiology, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima 960-1295, Japan; (Y.S.); (K.I.); (N.M.)
- Vaccine Center, Ohara General Hospital, 6-1 Agemachi, Fukushima 960-8611, Japan
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Barrena-González J, Lloret E, Zornoza R, Lavado-Contador F, Pulido M. Spatial patterns of soil bacterial communities in grazing areas of Southwest Spain. THE SCIENCE OF THE TOTAL ENVIRONMENT 2025; 979:179516. [PMID: 40280101 DOI: 10.1016/j.scitotenv.2025.179516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2025] [Revised: 03/31/2025] [Accepted: 04/22/2025] [Indexed: 04/29/2025]
Abstract
The spatial distribution of soil bacterial communities in agrosilvopastoral systems remains understudied, despite its fundamental role in ecosystem functioning. This study investigates the spatial dynamics of dominant copiotrophic and oligotrophic bacterial phyla in grazing areas of Southwest Spain, focusing on their interactions with land management, soil properties, and environmental covariates. Five management systems; occasional grazing (OG), holistic management (HM), organic farming (OF), conventional rangeland (CR), and conventional grassland (CG) were analyzed across three topographic positions (hilltop, mid-slope, valley bottom), representing a gradient of grazing intensity. A total of 71 soil samples were collected and analyzed using 16S rRNA metabarcoding. Alpha and beta diversity metrics revealed significant shifts in community composition driven by both management and topography, with HM showing higher richness compared to CR and CG. Among dominant phyla, copiotrophic groups such as Proteobacteria and Actinobacteriota were more abundant in upper slope areas and under higher grazing intensity, whereas oligotrophic Verrucomicrobiota was enriched in valley bottoms and under lower grazing pressure. Spatial prediction models based on Random Forest and recursive feature elimination (RFE) identified key environmental drivers, with vegetation indices being more relevant for Proteobacteria and Verrucomicrobiota, and topographic features for Actinobacteriota. RDA and SEM confirmed that animal stocking rate and soil organic matter were major predictors of β-diversity. This study provides novel insights into microbial spatial heterogeneity in Mediterranean grazing systems, highlighting the interplay of management practices, soil characteristics, and topography. The findings underscore the ecological benefits of holistic management in enhancing bacterial diversity and inform strategies for sustainable land use in agrosilvopastoral ecosystems.
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Affiliation(s)
- Jesús Barrena-González
- Instituto Universitario de Investigación para el Desarrollo Territorial Sostenible, Universidad de Extremadura, Av. de las Letras, s/n, 10071 Cáceres, Spain.
| | - Eva Lloret
- Sustainable Use, Management and Reclamation of Soil and Water Research Group, Department of Agricultural Engineering, Universidad Politécnica de Cartagena, Paseo Alfonso XIII, 48, 30203 Cartagena, Spain; Instituto de Biotecnología Vegetal (IBV), Campus Muralla del Mar, Edificio I+D+I, Universidad Politécnica de Cartagena, 30202 Cartagena, Spain
| | - Raúl Zornoza
- Sustainable Use, Management and Reclamation of Soil and Water Research Group, Department of Agricultural Engineering, Universidad Politécnica de Cartagena, Paseo Alfonso XIII, 48, 30203 Cartagena, Spain; Instituto de Biotecnología Vegetal (IBV), Campus Muralla del Mar, Edificio I+D+I, Universidad Politécnica de Cartagena, 30202 Cartagena, Spain
| | - Francisco Lavado-Contador
- Instituto Universitario de Investigación para el Desarrollo Territorial Sostenible, Universidad de Extremadura, Av. de las Letras, s/n, 10071 Cáceres, Spain
| | - Manuel Pulido
- Instituto Universitario de Investigación para el Desarrollo Territorial Sostenible, Universidad de Extremadura, Av. de las Letras, s/n, 10071 Cáceres, Spain
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Chen B, Zeng Y, Wang J, Lei M, Gan B, Wan Z, Wu L, Luo G, Cao S, An T, Zhang Q, Pan K, Jing B, Ni X, Zeng D. Targeted Screening of Fiber Degrading Bacteria with Probiotic Function in Herbivore Feces. Probiotics Antimicrob Proteins 2025; 17:1473-1497. [PMID: 38300451 DOI: 10.1007/s12602-024-10215-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2024] [Indexed: 02/02/2024]
Abstract
Cellulolytic bacteria with probiotic functions play a crucial role in promoting the intestinal health in herbivores. In this study, we aimed to correlate the 16S rRNA gene amplicon sequencing and fiber-degrading enzyme activity data from six different herbivore feces samples. By utilizing the separation and screening steps of probiotics, we targeted and screened high-efficiency fiber-degrading bacteria with probiotic functions. The animals included Maiwa Yak (MY), Holstein cow (CC), Tibetan sheep (TS), Southern Sichuan black goat (SG), Sichuan white rex rabbit (CR), and New Zealand white rabbit (ZR). The results showed that the enzymes associated with fiber degradation were higher in goat and sheep feces compared to cattle and rabbit's feces. Correlation analysis revealed that Bacillus and Fibrobacter were positively correlated with five types of fiber-degrading related enzymes. Notably, the relative abundance of Bacillus in the feces of Tibetan sheep was significantly higher than that of other five herbivores. A strain TS5 with good cellulose decomposition ability from the feces of Tibetan sheep by Congored staining, filter paper decomposition test, and enzyme activity determination was isolated. The strain was identified as Bacillus velezensis by biological characteristics, biochemical analysis, and 16S rRNA gene sequencing. To test the probiotic properties of Bacillus velezensis TS5, we evaluated its tolerance to acid and bile salt, production of digestive enzymes, antioxidants, antibacterial activity, and adhesion ability. The results showed that the strain had good tolerance to pH 2.0 and 0.3% bile salts, as well as good potential to produce cellulase, protease, amylase, and lipase. This strain also had good antioxidant capacity and the ability to antagonistic Staphylococcus aureus BJ216, Salmonella SC06, Enterotoxigenic Escherichia coli CVCC196, and Escherichia coli ATCC25922. More importantly, the strain had good self-aggregation and Caco-2 cell adhesion rate. In addition, we tested the safety of Bacillus velezensis TS5 by hemolysis test, antimicrobial susceptibility test, and acute toxicity test in mice. The results showed that the strain had no hemolytic phenotype, did not develop resistance to 19 commonly used antibiotics, had no cytotoxicity to Caco-2, and did not have acute toxic harm to mice. In summary, this study targeted isolated and screened a strain of Bacillus velezensis TS5 with high fiber-degrading ability and probiotic potency. This strain can be used as a potential probiotic for feeding microbial preparations for ruminants.
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Affiliation(s)
- Benhao Chen
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yan Zeng
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Jie Wang
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mingxia Lei
- Neijiang Center for Animal and Plant Epidemic Disease Prevention and Control and Agricultural Products Quality Inspection, Neijiang, China
| | - Baoxing Gan
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zhiqiang Wan
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Liqian Wu
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Guangrong Luo
- Sichuan Longri Breeding Stock Farm, Aba Autonomous Prefecture, China
| | - Suizhong Cao
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Tianwu An
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Qibin Zhang
- Agricultural Comprehensive Service Center of Beimu Town, Neijiang, China
| | - Kangcheng Pan
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Bo Jing
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xueqin Ni
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.
| | - Dong Zeng
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.
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Shi Z, Zeng W, Liu Z, Yao F, Guo J, Chen Y, Qin Z, Zhang J. Invasive apple snails with their core microbes are underestimated hotspots for disseminating antibiotic resistance genes and virulence factors in aquatic habitats. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2025; 385:125575. [PMID: 40339249 DOI: 10.1016/j.jenvman.2025.125575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2025] [Revised: 03/19/2025] [Accepted: 04/26/2025] [Indexed: 05/10/2025]
Abstract
Antibiotic resistance in pathogens is a threat to human health. The invasive apple snail (Pomacea canaliculata), widely distributed and linked to human activities, is a potential vector for human pathogens. However, its role in spreading antibiotic resistance genes (ARGs) is poorly understood. This study assessed the microbiological risk of this snail by sampling from five interconnected habitats: feces of invasive apple snails and native snails, ditch water, sediment, and soil. Using metagenomic and 16S rRNA sequencing, we analyzed the microbial communities and quantified the ARGs and virulence factors (VFs). Results showed that invasive apple snails carried significantly higher levels of ARGs and VFs compared with the native snails and environmental samples. ARGs and VFs were primarily found co-occurring in Aeromonas and Citrobacter freundii, with Aeromonas identified as the core microbe selected by invasive apple snails. Furthermore, the abundance and community dissimilarity of Aeromonas positively correlated with those of ARGs and VFs, both directly and indirectly through mobile genetic elements. This suggests Aeromonas may play a key role in disseminating ARGs and VFs across habitats. Overall, this study highlights the invasive apple snail as a significant vector for ARGs and virulent pathogens, providing critical insights for risk assessment and targeted management within the One Health framework.
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Affiliation(s)
- Zhaoji Shi
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Engineering Technology Research Centre of Modern Eco-agriculture and Circular Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Wen Zeng
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Engineering Technology Research Centre of Modern Eco-agriculture and Circular Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Ziqiang Liu
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Engineering Technology Research Centre of Modern Eco-agriculture and Circular Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Fucheng Yao
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Engineering Technology Research Centre of Modern Eco-agriculture and Circular Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Jing Guo
- Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, China
| | - Yongjian Chen
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Engineering Technology Research Centre of Modern Eco-agriculture and Circular Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Zhong Qin
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Engineering Technology Research Centre of Modern Eco-agriculture and Circular Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Jiaen Zhang
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou, 510642, China; Guangdong Engineering Technology Research Centre of Modern Eco-agriculture and Circular Agriculture, South China Agricultural University, Guangzhou, 510642, China.
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25
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Liu H, Xu T, Ye W, Li Y, He K, Zhu Y, Zou X, Ruan H. Urbanisation Affects Millipede Gut Microbiota Communities by Impeding Host Gene Flow. Mol Ecol 2025; 34:e17792. [PMID: 40347019 DOI: 10.1111/mec.17792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Revised: 04/11/2025] [Accepted: 04/28/2025] [Indexed: 05/12/2025]
Abstract
Urbanisation leads to the alteration of the living environment of soil fauna and isolates them, significantly influencing the evolutionary processes of soil fauna. Faunal gut microbiota serves to bridge hosts with changing environments; thus, they are viable indicators of host adaptation. For this study, we investigated how urbanisation affects the gut microbiota and population genetics of Spirobolus bungii. The results revealed that urbanisation did not affect the genetic diversity of S. bungii populations but acted as a barrier, which hindered its gene flow. Genetic differentiation was associated with the compositional similarity of gut microbiota among populations; however, environmental distinctions had no impact. Our findings highlighted that gene flow between populations was a critical factor, which supported the premise that urbanisation influences the gut microbiota compositions of species. This study contributes to a deeper understanding of the mechanisms that underlie changes in faunal gut microbiota driven by gene flow in the context of urbanisation.
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Affiliation(s)
- Hongyi Liu
- College of Life Sciences, Nanjing Forestry University, Nanjing, China
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
| | - Tangjun Xu
- College of Life Sciences, Nanjing Forestry University, Nanjing, China
| | - Wentao Ye
- College of Life Sciences, Nanjing Forestry University, Nanjing, China
| | - Yuanyuan Li
- School of Food Science, Nanjing Xiaozhuang University, Nanjing, China
| | - Ke He
- College of Animal Science and Technology, Zhejiang A&F University, Lin'an, China
| | - Ying Zhu
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Xiaoming Zou
- Department of Environmental Science, College of Natural Sciences, University of Puerto Rico, San Juan, Puerto Rico, USA
| | - Honghua Ruan
- College of Ecology and Environment, Nanjing Forestry University, Nanjing, China
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26
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Liu Y, Niu Y, Zhou Z, Ma Y, Chen M, Xu N, Zhao F, Sun Y, Chen P. Insight into endophytic microbiota-driven geographical and bioactive signatures toward a novel quality assessment model for Codonopsis Radix. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2025; 223:109888. [PMID: 40203555 DOI: 10.1016/j.plaphy.2025.109888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2024] [Revised: 04/02/2025] [Accepted: 04/04/2025] [Indexed: 04/11/2025]
Abstract
Codonopsis Radix, a medicinal and dietary herb in traditional Chinese medicine, largely owes its pharmacological efficacy to both intrinsic phytochemistry and symbiotic interactions with plant-associated microbes. Here, we deciphered the geo-environmental regulation of Codonopsis Radix's endophytic microbiota across four major production regions using 16S rRNA/ITS sequencing and bioactive compound profiling. Results demonstrated that the planting environment significantly shaped the endophytic community of Codonopsis Radix, where Bifidobacteriaceae and Muribaculaceae exhibited the strongest correlations with its bioactive components. Monolobus and Bradyrhizobium not only exhibit distinct associations with Lobetyolin and Atractylenolide III respectively, but also demonstrate significant correlations with the key biosynthetic pathways of these compounds. Leveraging machine learning, we developed the first microbiota-driven quality assessment model, achieving 100.0% and 85.7% prediction accuracies for Lobetyolin and Atractylenolide III respectively, using Random Forest algorithms. This dual-metric framework-integrating microbial signatures with chemical profiles-establishes a novel paradigm for Codonopsis Radix quality control, bridging ecological insights with precision agriculture. Our findings illuminate the microbiota's role as a biosynthetic orchestrator in geoherbalism, offering actionable strategies for sustainable cultivation and standardized production of Codonopsis Radix.
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Affiliation(s)
- Yingjie Liu
- School of Pharmacy, Lanzhou University, No. 199 Donggang West Road, Lanzhou, Gansu, 730000, PR China
| | - Yuqing Niu
- School of Pharmacy, Lanzhou University, No. 199 Donggang West Road, Lanzhou, Gansu, 730000, PR China
| | - Zhongkun Zhou
- School of Pharmacy, Lanzhou University, No. 199 Donggang West Road, Lanzhou, Gansu, 730000, PR China
| | - Yunhao Ma
- School of Pharmacy, Lanzhou University, No. 199 Donggang West Road, Lanzhou, Gansu, 730000, PR China
| | - Min Chen
- School of Pharmacy, Lanzhou University, No. 199 Donggang West Road, Lanzhou, Gansu, 730000, PR China
| | - Ning Xu
- School of Pharmacy, Lanzhou University, No. 199 Donggang West Road, Lanzhou, Gansu, 730000, PR China
| | - Fanting Zhao
- School of Pharmacy, Lanzhou University, No. 199 Donggang West Road, Lanzhou, Gansu, 730000, PR China
| | - Ying Sun
- Gansu Institute for Drug Control, State Drug Administration-Key Laboratory of Quality Control of Chinese Medicinal Materials and Decoction Pieces, No. 7 Yin'an Road, Lanzhou, Gansu, 730030, PR China.
| | - Peng Chen
- School of Pharmacy, Lanzhou University, No. 199 Donggang West Road, Lanzhou, Gansu, 730000, PR China.
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27
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Plokhovska S, García-Villaraco A, Lucas JA, Gutiérrez-Mañero FJ, Ramos-Solano B. Pseudomonas sp. N5.12 Metabolites Formulated in AgNPs Enhance Plant Fitness and Metabolism Without Altering Soil Microbial Communities. PLANTS (BASEL, SWITZERLAND) 2025; 14:1655. [PMID: 40508329 PMCID: PMC12157261 DOI: 10.3390/plants14111655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/26/2025] [Revised: 05/23/2025] [Accepted: 05/26/2025] [Indexed: 06/16/2025]
Abstract
This study investigated the effects of metabolites from the beneficial bacteria Pseudomonas N5.12 formulated as silver nanoparticles (AgNPs) on tomato plants and soil microbial communities to explore the environmental safety of AgNPs for future applications in agriculture. AgNPs coated with bacterial metabolites exhibit biological activity that is dose-dependent, as shown by cytoskeleton alterations in Arabidopsis roots. The results show that N5.12-AgNPs can trigger beneficial effects on tomato plants, either when delivered through the leaves or roots, indicating the effectiveness of the metabolites formulated as NP. These effects consist of lowering oxidative stress metabolism and, therefore, improving plant resilience and increasing chlorophyll a and carotenoid content. The significant reduction in H2O2 content was not associated with ROS-scavenging enzymes but with an increase in total phenolic content. In contrast, AgNPs had a minimal impact on bacterial metabolic activity, irrespective of the application method. The structure of microbial communities was not altered by AgNPs, indicating environmental safety for agronomic applications. These findings suggest that Pseudomonas N5.12 metabolites formulated in AgNPs at physiological concentrations (30 ppm) may offer agricultural benefits by improving plant health and appearing as an environmentally safe alternative for agriculture.
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Affiliation(s)
- Svitlana Plokhovska
- Faculty of Pharmacy, Universidad San Pablo-CEU Universities, 28668 Madrid, Spain; (A.G.-V.); (J.A.L.); (F.J.G.-M.)
- Institute of Food Biotechnology and Genomics NAS of Ukraine, 04123 Kyiv, Ukraine
| | - Ana García-Villaraco
- Faculty of Pharmacy, Universidad San Pablo-CEU Universities, 28668 Madrid, Spain; (A.G.-V.); (J.A.L.); (F.J.G.-M.)
| | - Jose Antonio Lucas
- Faculty of Pharmacy, Universidad San Pablo-CEU Universities, 28668 Madrid, Spain; (A.G.-V.); (J.A.L.); (F.J.G.-M.)
| | | | - Beatriz Ramos-Solano
- Faculty of Pharmacy, Universidad San Pablo-CEU Universities, 28668 Madrid, Spain; (A.G.-V.); (J.A.L.); (F.J.G.-M.)
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28
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Nieves-Morales R, Paez-Diaz JA, Rodriguez-Carrio SM, Melendez Martinez G, Rivera-Lopez EO, Rodríguez-Ramos J, García-Arrarás JE, Rios-Velazquez C. Intestinal microbiome profile of the brown rock sea cucumber ( Holothuria glaberrima) using ITS and 16S rDNA amplicons from direct mechanical, enzymatic, and chemical metagenomic extraction. Microbiol Resour Announc 2025:e0029325. [PMID: 40434086 DOI: 10.1128/mra.00293-25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2025] [Accepted: 05/07/2025] [Indexed: 05/29/2025] Open
Abstract
Using direct mechanical, enzymatic, and chemical extraction methods, the intestinal microbiome of the marine invertebrate Holothuria glaberrima was obtained. ITS and 16S rDNA regions were sequenced to enrich and investigate the prokaryotic and fungal diversity profiles from different anatomical regions within the sea cucumber's intestinal biology.
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Affiliation(s)
- Rene Nieves-Morales
- Microbial Biotechnology and Bioprospecting Laboratory, Biology Department, University of Puerto Rico at Mayagüez, Mayagüez, USA
| | - Jessica Alejandra Paez-Diaz
- Microbial Biotechnology and Bioprospecting Laboratory, Biology Department, University of Puerto Rico at Mayagüez, Mayagüez, USA
| | - Sofia Marie Rodriguez-Carrio
- Microbial Biotechnology and Bioprospecting Laboratory, Biology Department, University of Puerto Rico at Mayagüez, Mayagüez, USA
| | - Gabriela Melendez Martinez
- Microbial Biotechnology and Bioprospecting Laboratory, Biology Department, University of Puerto Rico at Mayagüez, Mayagüez, USA
| | - Edwin Omar Rivera-Lopez
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Josué Rodríguez-Ramos
- Pacific Northwest National Laboratory, Biological Sciences Division, Richland, Washington, USA
| | - José E García-Arrarás
- Department of Biology, University of Puerto Rico, Río Piedras Campus, Río Piedras, Puerto Rico, USA
| | - Carlos Rios-Velazquez
- Microbial Biotechnology and Bioprospecting Laboratory, Biology Department, University of Puerto Rico at Mayagüez, Mayagüez, USA
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29
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Lutsiv T, Fitzgerald VK, Neil ES, McGinley JN, Hussan H, Thompson HJ. Cooked Bean ( Phaseolus vulgaris L.) Consumption Alters Bile Acid Metabolism in a Mouse Model of Diet-Induced Metabolic Dysfunction: Proof-of-Concept Investigation. Nutrients 2025; 17:1827. [PMID: 40507096 PMCID: PMC12157300 DOI: 10.3390/nu17111827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2025] [Revised: 05/22/2025] [Accepted: 05/26/2025] [Indexed: 06/16/2025] Open
Abstract
Background/Objectives: Metabolic dysregulation underlies a myriad of chronic diseases, including metabolic dysfunction-associated steatotic liver disease (MASLD) and obesity, and bile acids emerge as an important mediator in their etiology. Weight control by improving diet quality is the standard of care in prevention and control of these metabolic diseases. Inclusion of pulses, such as common bean, is an affordable yet neglected approach to improving diet quality and metabolic outcomes. Thus, this study evaluated the possibility that common bean alters bile acid metabolism in a health-beneficial manner. Methods: Using biospecimens from several similarly designed studies, cecal content, feces, liver tissue, and plasma samples from C57BL/6 mice fed an obesogenic diet lacking (control) or containing cooked common bean were subjected to total bile acid analysis and untargeted metabolomics. RNA-seq, qPCR, and Western blot assays of liver tissue complemented the bile acid analyses. Microbial composition and predicted function in the cecal contents were evaluated using 16S rRNA gene amplicon and shotgun metagenomic sequencing. Results: Bean-fed mice had increased cecal bile acid content and excreted more bile acids per gram of feces. Consistent with these effects, increased synthesis of bile acids in the liver was observed. Microbial composition and capacity to metabolize bile acids were markedly altered by bean, with greater prominence of secondary bile acid metabolites in bean-fed mice, i.e., microbial metabolites of chenodeoxycholate/lithocholate increased while metabolites of hyocholate were reduced. Conclusions: In rendering mice resistant to obesogenic diet-induced MASLD and obesity, cooked bean consumption sequesters bile acids, increasing their hepatic synthesis and enhancing their diversity through microbial metabolism. Bean-induced changes in bile acid metabolism have potential to improve dyslipidemia.
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Affiliation(s)
- Tymofiy Lutsiv
- Cancer Prevention Laboratory, Colorado State University, Fort Collins, CO 80523, USA; (T.L.); (V.K.F.); (E.S.N.); (J.N.M.)
- Graduate Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Vanessa K. Fitzgerald
- Cancer Prevention Laboratory, Colorado State University, Fort Collins, CO 80523, USA; (T.L.); (V.K.F.); (E.S.N.); (J.N.M.)
| | - Elizabeth S. Neil
- Cancer Prevention Laboratory, Colorado State University, Fort Collins, CO 80523, USA; (T.L.); (V.K.F.); (E.S.N.); (J.N.M.)
| | - John N. McGinley
- Cancer Prevention Laboratory, Colorado State University, Fort Collins, CO 80523, USA; (T.L.); (V.K.F.); (E.S.N.); (J.N.M.)
| | - Hisham Hussan
- Department of Internal Medicine, University of California, Davis, Sacramento, CA 95817, USA;
| | - Henry J. Thompson
- Cancer Prevention Laboratory, Colorado State University, Fort Collins, CO 80523, USA; (T.L.); (V.K.F.); (E.S.N.); (J.N.M.)
- Graduate Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
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30
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Mezhibovsky E, Wu G, Wu Y, Ning Z, Bacalia K, Sadangi S, Patel R, Poulev A, Duran RM, Macor M, Coyle S, Lam YY, Raskin I, Figeys D, Zhao L, Roopchand DE. Grape polyphenols reduce fasting glucose and increase hyocholic acid in healthy humans: a meta-omics study. NPJ Sci Food 2025; 9:87. [PMID: 40425565 PMCID: PMC12116990 DOI: 10.1038/s41538-025-00443-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2024] [Accepted: 05/06/2025] [Indexed: 05/29/2025] Open
Abstract
Grape polyphenols (GPs) are rich in B-type proanthocyanidins, which promote metabolic resilience. Longitudinal metabolomic, metagenomic, and metaproteomic changes were measured in 27 healthy subjects supplemented with soy protein isolate (SPI, 40 g per day) for 5 days followed by GPs complexed to SPI (GP-SPI standardized to 5% GPs, 40 g per day) for 10 days. Fecal, urine, and/or fasting blood samples were collected before supplementation (day -5), after 5 days of SPI (day 0), and after 2, 4 and 10 days of GP-SPI. Most multi-omic changes observed after 2 and/or 4 days of GP-SPI intake were temporary, returning to pre-supplementation profiles by day 10. Shotgun metagenomics sequencing provided insights that could not be captured with 16S rRNA amplicon sequencing. Notably, 10 days of GP-SPI decreased fasting blood glucose and increased serum hyocholic acid (HCA), a glucoregulatory bile acid, which negatively correlated with one gut bacterial guild. In conclusion, GP-induced suppression of a bacterial guild may lead to higher HCA and lower fasting blood glucose.
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Affiliation(s)
- Esther Mezhibovsky
- Department of Food Science and New Jersey Institute for Food, Nutrition and Health (Rutgers Center for Lipid Research), School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Guojun Wu
- Department of Biochemistry and Microbiology and New Jersey Institute for Food, Nutrition, and Health, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Yue Wu
- Department of Food Science and New Jersey Institute for Food, Nutrition and Health (Rutgers Center for Lipid Research), School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Zhibin Ning
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Karen Bacalia
- Department of Food Science and New Jersey Institute for Food, Nutrition and Health (Rutgers Center for Lipid Research), School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Sriya Sadangi
- Department of Food Science and New Jersey Institute for Food, Nutrition and Health (Rutgers Center for Lipid Research), School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Riddhi Patel
- Department of Food Science and New Jersey Institute for Food, Nutrition and Health (Rutgers Center for Lipid Research), School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Alexander Poulev
- Department of Plant Biology, School of Environmental and Biological Sciences, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Rocio M Duran
- Department of Food Science and New Jersey Institute for Food, Nutrition and Health (Rutgers Center for Lipid Research), School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Marie Macor
- Department of Surgery, Rutgers Robert Wood Johnson Medical School (RWJMS), New Brunswick, 08903, NJ, USA
| | - Susette Coyle
- Department of Surgery, Rutgers Robert Wood Johnson Medical School (RWJMS), New Brunswick, 08903, NJ, USA
| | - Yan Y Lam
- Department of Biochemistry and Microbiology and New Jersey Institute for Food, Nutrition, and Health, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Department of Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Ilya Raskin
- Department of Plant Biology, School of Environmental and Biological Sciences, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Daniel Figeys
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Liping Zhao
- Department of Biochemistry and Microbiology and New Jersey Institute for Food, Nutrition, and Health, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Diana E Roopchand
- Department of Food Science and New Jersey Institute for Food, Nutrition and Health (Rutgers Center for Lipid Research), School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA.
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31
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Castaneda A, Indugu N, Lenker K, Narayan K, Rassler S, Bender J, Baker L, Purandare O, Chai D, Zhao X, Pitta D. Host-specific microbiome-rumination interactions shape methane-yield phenotypes in dairy cattle. mSphere 2025; 10:e0009025. [PMID: 40277354 DOI: 10.1128/msphere.00090-25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2025] [Accepted: 03/31/2025] [Indexed: 04/26/2025] Open
Abstract
Enteric methane emissions (EMEs) negatively impact both the environment and livestock efficiency. Given the proposed link between CH4 yield and the rumination time (RT) phenotype, we hypothesize that this connection is mediated by the gut microbiome. This study investigated the RT-microbiome-EME connection using rumination-bolus, fecal, and rumen microbiomes as non-invasive proxies for identifying low-EME cows. High-RT cows ruminated 94 minutes longer per day (20%) and exhibited 26% lower EME than low-RT cows, confirming a strong RT-CH4-yield association. Microbial analysis revealed conserved methanogen diversity across the rumen, bolus, and fecal microbiomes, though functional differences were evident. High-RT cows had a greater abundance of Methanosphaera stadtmanae, suggesting an increased potential for methylotrophic methanogenesis, whereas low-RT cows exhibited higher Methanobrevibacter YE315 abundance, indicative of CO2-utilizing methanogenesis. Additionally, high-RT cows showed increased alternative hydrogen sinks, supported by upregulated genes encoding fumarate reductase, sulfate reductase, nitrate reductase, and ammonia-forming nitrite reductase, thereby reducing hydrogen availability for methanogenesis. Metabolically, high-RT cows had higher propionate concentrations and were enriched with rapid-fermenting bacteria (Prevotella, Sharpea, Veillonellaceae, and Succinivibrionaceae), whereas low-RT cows exhibited higher acetate concentrations with elevated acetate-producing pathways, reflecting differences in energy partitioning mechanisms. This study establishes RT as a microbiome-linked, non-invasive screening tool for identifying low-EME cows. The observed microbial and metabolic shifts in high-RT cows suggest that RT-based selection could enhance methane mitigation, rumen efficiency, and climate-smart livestock production. Leveraging RT-associated microbial profiles offers a scalable and cost-effective approach to reducing EME in cattle. IMPORTANCE Methane emissions from livestock contribute to climate change and reduce animal efficiency. This study reveals that cows with longer rumination times (chewing cud for an extra 94 minutes daily) produce 26% less methane than cows with shorter rumination times. The gut microbiome plays a key role-low-methane cows host microbial communities that produce less methane while efficiently utilizing hydrogen for energy conservation in the rumen. By analyzing rumination sensor data and/or in combination with microbial profiles from rumen or fecal samples, farmers can non-invasively identify and select cows that naturally emit less methane. This scalable, cost-effective strategy offers a practical solution for reducing livestock's environmental footprint while enhancing efficiency and advancing climate-smart agriculture.
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Affiliation(s)
- Alejandro Castaneda
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Nagaraju Indugu
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kathryn Lenker
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kapil Narayan
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sarah Rassler
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Joseph Bender
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Linda Baker
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ojas Purandare
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - David Chai
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Xin Zhao
- Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Dipti Pitta
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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32
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Benbrik B, Reid TE, Nkir D, Chaouki H, Aallam Y, Clark IM, Mauchline TH, Harris J, Pawlett M, Barakat A, Rchiad Z, Bargaz A. Unlocking the agro-physiological potential of wheat rhizoplane fungi under low P conditions using a niche-conserved consortium approach. JOURNAL OF EXPERIMENTAL BOTANY 2025; 76:2320-2337. [PMID: 40000427 DOI: 10.1093/jxb/eraf042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 01/30/2025] [Indexed: 02/27/2025]
Abstract
Plant growth-promoting fungi (PGPF) hold promise for enhancing crop yield. This study delves into the fungal diversity of the wheat rhizoplane across seven Moroccan agricultural regions, employing a niche-conserved strategy to construct fungal consortia (FC) exhibiting higher phosphorus (P) acquisition and plant growth promotion. This study combined culture-independent and culture-dependent methods exploring taxonomic and functional diversity in the rhizoplane of wheat plants obtained from 28 zones. Twenty fungal species from eight genera were isolated and confirmed through internal transcribed spacer (ITS) Sanger sequencing. P solubilization (PS) capacity was assessed for individual species, with Talaromyces sp. (F11) and Rhizopus arrhizus CMRC 585 (F12) exhibiting notable PS rates, potentially due to production of organic acids such as gluconic acid. PGPF traits and antagonism activities were considered when constructing 28 niche-conserved FC (using isolates from the same zone), seven intra-region FC (different zones within a region), and one inter-region FC. Under low P conditions, in planta inoculation with niche-conserved FC (notably FC14 and FC17) enhanced growth, physiological parameters, and P uptake of wheat, in both vegetative and reproductive stages. FC14 and FC17, composed of potent fungi such as F11 and F12, demonstrated superior plant growth benefits compared with intra- and inter-region constructed FC. Our study underscores the efficacy of the niche-conserved strategy in designing synthetic fungal community from isolates within the same niche, proving significant agro-physiological potential to enhance P uptake and plant growth of wheat.
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Affiliation(s)
- Brahim Benbrik
- AgroBiosciences Program, College of Agriculture and Environmental Sciences, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Tessa E Reid
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, UK
| | - Dounia Nkir
- AgroBiosciences Program, College of Agriculture and Environmental Sciences, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Hicham Chaouki
- AgroBiosciences Program, College of Agriculture and Environmental Sciences, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Yassine Aallam
- AgroBiosciences Program, College of Agriculture and Environmental Sciences, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Ian M Clark
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, UK
| | - Tim H Mauchline
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, UK
| | - Jim Harris
- Environment and Agrifood, Faculty of Engineering and Applied Sciences, Cranfield University, Cranfield MK43 0AL, UK
| | - Mark Pawlett
- Environment and Agrifood, Faculty of Engineering and Applied Sciences, Cranfield University, Cranfield MK43 0AL, UK
| | - Abdellatif Barakat
- AgroBiosciences Program, College of Agriculture and Environmental Sciences, Mohammed VI Polytechnic University, Ben Guerir, Morocco
- IATE, Université de Montpellier, INRAE, Agro Institut. 2, Place Pierre Viala, 34060 Montpellier, France
| | - Zineb Rchiad
- Biosciences Division, CoreLabs, Mohammed 6 Polytechnic University, Ben Guerir, Morocco
| | - Adnane Bargaz
- AgroBiosciences Program, College of Agriculture and Environmental Sciences, Mohammed VI Polytechnic University, Ben Guerir, Morocco
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Oz A, Mairesse O, Raikin S, Hanani H, Mor H, Dafny Yelin M, Sharon I. Pear flower and leaf microbiome dynamics during the naturally occurring spread of Erwinia amylovora. mSphere 2025; 10:e0001125. [PMID: 40323108 DOI: 10.1128/msphere.00011-25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2025] [Accepted: 04/08/2025] [Indexed: 05/28/2025] Open
Abstract
Erwinia amylovora is the causal pathogen of fire blight, a contagious disease that affects apple and pear trees and other members of the family Rosaceae. In this study, we investigated the community dynamics of the pear flower microbiome in an agricultural setting during the naturally occurring infection of E. amylovora. Five potential factors were considered: collection date, the flower's phenological stage, location on the tree, location within the orchard, and pear cultivar. The phenological stage and the collection date were identified as the most important factors associated with pear flower microbiome composition, while the location of the tree in the orchard and the flower's location on the tree had a marginal effect. The leaf microbiome reflected that of the abundant phenological stage on each date. The flower microbiome shifted toward E. amylovora dominating the community as time and phenological stages progressed, leading to a decreased community diversity. The E. amylovora population was represented almost exclusively by six amplicon sequence variants (ASVs) with similar proportions throughout the entire collection period. Other taxa, including Pseudomonas, Pantoea, Lactobacillus, and Sphingomonas, were represented by dozens of ASVs, and different succession patterns in their populations were observed. Some of the taxa identified include known antagonists to E. amylovora. Overall, our results suggest that flower physiology and the interaction with the environment are strongly associated with the pear flower microbiome and should be considered separately. Taxon-specific succession patterns under E. amylovora spread should be considered when choosing candidates for antagonist-based treatments for fire blight.IMPORTANCEThe spread of pathogens in plants is an important ecological phenomenon and has a significant economic impact on agriculture. Flowers serve as the entry point for E. amylovora, but members of the flower microbiome can inhibit or slow down the proliferation and penetration of the pathogen. Knowledge about leaf and flower microbiome response to the naturally occurring spread of E. amylovora is still lacking. The current study is the first to describe the Rosaceae flower microbiome dynamics during the naturally occurring infection of E. amylovora. Unlike previous studies, the study design enabled us to evaluate the contribution of five important environmental parameters to community composition. We identified different ASV succession patterns across different taxa in the flower consortia throughout the season. These results contribute to our understanding of plant microbial ecology during pathogen spread and can help improve biological treatments for fire blight.
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Affiliation(s)
- Aia Oz
- Migal-Galilee Technology Center, Kiryat Shmona, Israel
| | - Orly Mairesse
- Northern Agriculture Research & Development, Migal-Galilee Technology Center, Kiryat Shemona, Israel
- Faculty of Sciences and Technology, Tel-Hai Academic College, Upper Galilee, North District, Israel
| | - Shira Raikin
- Northern Agriculture Research & Development, Migal-Galilee Technology Center, Kiryat Shemona, Israel
| | - Hila Hanani
- Migal-Galilee Technology Center, Kiryat Shmona, Israel
| | - Hadar Mor
- Migal-Galilee Technology Center, Kiryat Shmona, Israel
| | - Mery Dafny Yelin
- Northern Agriculture Research & Development, Migal-Galilee Technology Center, Kiryat Shemona, Israel
| | - Itai Sharon
- Migal-Galilee Technology Center, Kiryat Shmona, Israel
- Faculty of Sciences and Technology, Tel-Hai Academic College, Upper Galilee, North District, Israel
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Ávila-Cervantes R, González-Pech P, Sandoval-Castro C, Torres-Acosta F, Ramos-Zapata J, Galicia-Jiménez M, Pacheco-Arjona R. Effects of Grazing in a Low Deciduous Forest on Rumen Microbiota and Volatile Fatty Acid Production in Lambs. Animals (Basel) 2025; 15:1565. [PMID: 40509031 PMCID: PMC12153761 DOI: 10.3390/ani15111565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2025] [Revised: 05/10/2025] [Accepted: 05/13/2025] [Indexed: 06/16/2025] Open
Abstract
The aim of the present study was to evaluate the effect of grazing the low deciduous forest (LDF) vegetation on the diversity of the rumen microbiome in growing lambs and its relationship with volatile fatty acid (VFA) profiles. After a 35-day indoor acclimatization (stabilization period), the lambs were assigned to two groups: housed (CG, n = 4) and grazing (EG, n = 4). The grazing lambs had a 14-day habituation period in the LDF (4 h/day) and a further 30 grazing days when fodder intake was observed. Ruminal samples were collected at the end of the stabilization, on day 14 post-stabilization (14DPS), and on day 44 post-stabilization (44DPS). The ruminal butyrate concentration showed a progressive decrease of approximately 23% over the time (p = 0.0130). The qualitative composition (p = 0.001) and relative proportions of bacteria (p = 0.004) in EG-44DPS exhibited a greater diversity, with 107 total genera and 19 unique, significant abundances in 13 genera with a higher presence of Bacteroidales_RF16_group, Lachnospiraceae_ND3007_group, and WCHB1-41. Moreover, significant functional profiles are associated with key metabolic pathways in bacteria and are interconnected by the need to generate energy and biosynthetic precursors and to manage available nitrogen and carbon. Finally, eight bacterial genera were identified as biomarkers correlated with the increase in VFA in EG-44DPS.
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Affiliation(s)
- Raúl Ávila-Cervantes
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma de Yucatán, Mérida 97000, Yucatán, Mexico; (R.Á.-C.); (P.G.-P.); (C.S.-C.); (F.T.-A.)
| | - Pedro González-Pech
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma de Yucatán, Mérida 97000, Yucatán, Mexico; (R.Á.-C.); (P.G.-P.); (C.S.-C.); (F.T.-A.)
| | - Carlos Sandoval-Castro
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma de Yucatán, Mérida 97000, Yucatán, Mexico; (R.Á.-C.); (P.G.-P.); (C.S.-C.); (F.T.-A.)
| | - Felipe Torres-Acosta
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma de Yucatán, Mérida 97000, Yucatán, Mexico; (R.Á.-C.); (P.G.-P.); (C.S.-C.); (F.T.-A.)
| | - José Ramos-Zapata
- Departamento de Ecología Tropical, Campus de Ciencias Biológicas y Agropecuarias, Universidad Autónoma de Yucatán, Mérida 97000, Yucatán, Mexico;
| | - Mónica Galicia-Jiménez
- Instituto de Investigación de Genética, Universidad del Mar, Ciudad Universitaria, Carretera Vía Sola de Vega, Puerto Escondido, San Pedro Mixtepec, Juquila 71980, Oaxaca, Mexico;
| | - Ramón Pacheco-Arjona
- Secretaría de Ciencias, Humanidades, Tecnología e Innovación-Universidad Autónoma de Yucatán, Mérida 97000, Yucatán, Mexico
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Jimenez NR, Herman CR, Łaniewski P, Cope E, Lee K, Mahnert ND, Chase DM, Caporaso JG, Herbst-Kralovetz MM. Navigating complexities of polymorphic microbiomes in endometrial cancer. NPJ Biofilms Microbiomes 2025; 11:85. [PMID: 40404643 PMCID: PMC12098703 DOI: 10.1038/s41522-025-00690-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Accepted: 04/01/2025] [Indexed: 05/24/2025] Open
Abstract
The microbiome is key to understanding endometrial cancer (EC) etiology and prevention strategies, implicated in the regulation of estrogen in estrogen-driven cancers. Utilizing robust methodologies in the QIIME 2 platform, we examined 16S rRNA vaginal and rectal microbiome data from an EC cohort: 192 women with benign gynecologic conditions, endometrial hyperplasia, or endometrial cancer. Distinct microbial compositions and community networks specific to EC were identified and related to histological grade with adjustments for EC risk factors. Vaginal health-associated Lactobacillus and Limosilactobacillus, and rectal Prevotella and Peptoniphilus, were depleted in EC, while detrimental vaginal Anaerococcus, Porphyromonas, Prevotella, Peptoniphilus, and rectal Buttiaxella were enriched. Significant bacterial features were shared between rectal and vaginal sites in EC, such as Prevotella timonensis and Peptoniphilus A. Vaginal Lactobacillus abundance contributed to less feature sharing from the rectum. Putative microbial metabolic analysis identified dysregulation of amino acid, complex carbohydrate, and hormone metabolism amongst patients with EC.
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Affiliation(s)
- Nicole R Jimenez
- Department of Obstetrics and Gynecology, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA
| | - Chloe R Herman
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
- School of Informatics, Computing and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Paweł Łaniewski
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA
| | - Emily Cope
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Keehoon Lee
- Translational Genomics Research Institute, part of City of Hope, Flagstaff, AZ, USA
| | - Nichole D Mahnert
- Department of Obstetrics and Gynecology, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA
| | - Dana M Chase
- David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - J Gregory Caporaso
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA.
| | - Melissa M Herbst-Kralovetz
- Department of Obstetrics and Gynecology, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA.
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA.
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Nieves-Morales R, Paez-Diaz JA, Rivera-Lopez EO, Pérez-Santos N, Borrero-Villabol SJ, Rodríguez-Ramos J, Nieves-Rivera AM, Rios-Velazquez C. Characterization of fungal communities in Puerto Rican caves using internal transcribed spacer sequencing. Microbiol Resour Announc 2025:e0002225. [PMID: 40401940 DOI: 10.1128/mra.00022-25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2025] [Accepted: 04/22/2025] [Indexed: 05/23/2025] Open
Abstract
Cave ecosystems harbor unique and diverse microbial ecology, with fungal communities playing important roles. This study utilizes internal transcribed spacer across seven caves in the northern limestone karst belt area of Puerto Rico to investigate fungal composition. This enhances scientific understanding of subterranean microbial dynamics and supports conservation efforts.
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Affiliation(s)
- Rene Nieves-Morales
- Department of Biology, Microbial Biotechnology and Bioprospecting Laboratory, University of Puerto Rico, Mayagüez, Puerto Rico, USA
| | - Jessica Alejandra Paez-Diaz
- Department of Biology, Microbial Biotechnology and Bioprospecting Laboratory, University of Puerto Rico, Mayagüez, Puerto Rico, USA
| | - Edwin Omar Rivera-Lopez
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Natalia Pérez-Santos
- Department of Biology, Microbial Biotechnology and Bioprospecting Laboratory, University of Puerto Rico, Mayagüez, Puerto Rico, USA
| | - Sebastián J Borrero-Villabol
- Department of Biology, Microbial Biotechnology and Bioprospecting Laboratory, University of Puerto Rico, Mayagüez, Puerto Rico, USA
| | - Josué Rodríguez-Ramos
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | | | - Carlos Rios-Velazquez
- Department of Biology, Microbial Biotechnology and Bioprospecting Laboratory, University of Puerto Rico, Mayagüez, Puerto Rico, USA
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Olimi E, Duller M, Stangl M, Bickel S, Battisti A, Kusstatscher P, Wicaksono WA, Abdelfattah A, Cernava T, Berg G. Plant microbiome responses to bioinoculants and volatiles. ENVIRONMENTAL MICROBIOME 2025; 20:55. [PMID: 40400031 PMCID: PMC12096642 DOI: 10.1186/s40793-025-00715-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2025] [Accepted: 04/24/2025] [Indexed: 05/23/2025]
Abstract
BACKGROUND There is an increase in the adoption of biological solutions for plant production as a means of attaining sustainable agriculture. A detailed understanding of the influence of specific bioinoculants and their volatile metabolites on native soil and plant microbiomes can improve future microbiome management practices. RESULTS Here, we examined the effect of bacterial inoculants and volatile compounds as individual and combined treatments on apple plant and soil microbiome. The study used specially designed microcosms that facilitated the separation of the different plant compartments. A compartment- and soil-specific effect of treatments on the native soil and plant microbiome was observed. The live bacterial inoculants as compared to their volatiles had a stronger effect on the plant and soil microbiome, particularly the root microbial community. The combined effect of bacterial inoculants was higher compared to volatiles (R2 = 5% vs. 3%). Treatment-specific effects were observed, like the influence of 2-butanone on the phyllosphere bacterial diversity, and an increase in fungal richness in Serratia-treated soils. CONCLUSIONS Among the examined treatments, inoculation with bacteria compared to volatile metabolites induced more significant shifts within the plant and soil microbiome. This observation has implications regarding the merits of applying living microorganisms. The findings highlight the potential of microbiome management approaches for enhancing microbiota functions.
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Affiliation(s)
- Expedito Olimi
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK.
| | - Martina Duller
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Martina Stangl
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Samuel Bickel
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Angelika Battisti
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Peter Kusstatscher
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Ahmed Abdelfattah
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany.
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
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Smahajcsik D, Roager L, Strube ML, Zhang SD, Gram L. Stronger together: harnessing natural algal communities as potential probiotics for inhibition of aquaculture pathogens. Microbiol Spectr 2025:e0042125. [PMID: 40396728 DOI: 10.1128/spectrum.00421-25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2025] [Accepted: 03/22/2025] [Indexed: 05/22/2025] Open
Abstract
Intensive fish rearing in aquaculture is challenged by infectious diseases, and although vaccines have been successfully developed for mature fish, alternative disease control measures are needed for fish larvae and juveniles. Probiotics offer a promising alternative to antibiotics, with the potential to reduce the risk of antibiotic resistance. Probiotics are typically isolated and used as pure cultures; however, in natural environments, it is the concerted effort of the complex microbiome that keeps pathogens at bay. Here, we developed an in vitro assay to evaluate the anti-pathogen efficacy of mixed algal microbiomes from the live feed microalgae Tetraselmis suecica and Isochrysis galbana. The inhibition of a green fluorescent protein (GFP)-tagged Vibrio anguillarum, a key fish pathogen, by microbial communities was measured and quantified as reduction in fluorescence. The Isochrysis galbana microbiome was more inhibitory to V. anguillarum than the Tetraselmis suecica microbiome. During co-culture with the pathogen, the bacterial density of the Isochrysis microbiomes increased, while the diversity was reduced as determined by metataxonomic analyses. Bacteria isolated from the fully inhibitory microbiomes were members of Alteromonadaceae, Halomonadaceae, Rhodobacteraceae, Vibrionaceae, Flavobacteriaceae, and Erythrobacteraceae. Although some strains individually inhibited the pathogen, these were not the key members of the microbiome, and enhanced inhibition was observed when Sulfitobacter pontiacus D3 and Vreelandella alkaliphila D2 were co-cultured, even though neither was inhibitory as monocultures. Thus, this study demonstrates that microbial communities derived from natural algal microbiomes can have anti-pathogen effects, and that bacterial co-cultures may offer synergistic advantages over monocultures as probiotics, highlighting their promise for aquaculture health strategies.IMPORTANCEAquaculture is the fastest-growing food protein-producing sector, and sustainable disease control measures are required. Probiotics have gained interest as a promising solution for combating fish pathogens, and using mixtures of microorganisms rather than pure cultures may represent a more stable pathogen control. We developed an assay using green fluorescent protein (GFP) tagging of a fish pathogen, enabling the quantitative assessment of the anti-pathogen effects of complex microbiomes. We show that the efficiency of pathogen suppression can be increased with co-cultures compared to monocultures, thus emphasizing the potential in using mixtures of bacteria as probiotics.
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Affiliation(s)
- Dóra Smahajcsik
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Line Roager
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Mikael Lenz Strube
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Sheng-Da Zhang
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
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Mori-Bazzano L, Nguyen NHA, Sevcu A, Riha J, Fu T, Slaveykova VI, Ibelings BW. Plastic degradation in Lake Geneva: Influence of depth, seasonal shifts, and bacterial community dynamics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2025; 983:179615. [PMID: 40398166 DOI: 10.1016/j.scitotenv.2025.179615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2025] [Revised: 04/24/2025] [Accepted: 05/05/2025] [Indexed: 05/23/2025]
Abstract
Aquatic ecosystems suffer disproportionately from plastic pollution given that they integrate material from terrestrial watersheds. Most studies on microbial colonisation and degradation of plastics have focused on marine environments, leaving a knowledge gap for freshwaters. Our study explores the possible degradation and the role of bacterial community composition of plastics in Lake Geneva. We exposed polyethylene terephthalate (PET) and low-density polyethylene (LDPE) for 45 weeks to environmental lake gradients that change with depth and season. The substrates were suspended at 2 and 30 m depth, resulting in strikingly different environmental conditions for biofilm development, including light (PAR), temperature, and nutrient availability. We monitored the bacterial colonisation using 16S rRNA sequencing and assessed the abundance of the alkane hydrolase gene (alkB) to evaluate the potential ability of the biofilm to degrade PET and LDPE. Additionally, we analysed plastic surface modifications through spectroscopy, contact angle measurements and microscopy. We found that the PET surface showed no degradation after 45 weeks in the lake, at either depth. The LDPE surface at 2 m exhibited a decrease in hydrophobicity, but no evidence of oxidation or degradation was found. In contrast, the LDPE surface at 30 m displayed oxidation, a decrease in hydrophobicity, and porous cavities. In addition, we observed an increase in the alkane alkB gene abundance in the biofilm, with the development of plastic-degrading taxa in the community. Our results underline the complexity of plastic degradation in aquatic ecosystems; not only does the type of plastic have an effect, so do the spatio-temporal variable environmental lake conditions and the biofilm community. The multifactorial nature of these processes complicates predictions on the fate of plastics in the environment.
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Affiliation(s)
- Laureen Mori-Bazzano
- Department F.-A. Forel for Environmental and Aquatic Sciences, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Nhung H A Nguyen
- Department of Applied Biology, Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Liberec, Czech Republic
| | - Alena Sevcu
- Department of Applied Biology, Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Liberec, Czech Republic
| | - Jakub Riha
- Department of Applied Biology, Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Liberec, Czech Republic
| | - Tingting Fu
- Department of Quantum Matter Physics, Laboratory of Advanced Technology, University of Geneva, Geneva, Switzerland
| | - Vera I Slaveykova
- Department F.-A. Forel for Environmental and Aquatic Sciences, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Bastiaan W Ibelings
- Department F.-A. Forel for Environmental and Aquatic Sciences, Faculty of Science, University of Geneva, Geneva, Switzerland
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40
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Uchijima T, Kato S, Tanimoto K, Shiraishi F, Hamamura N, Tokunaga K, Makita H, Kondo M, Ohkuma M, Mitsunobu S. Custom-made medium approach for effective enrichment and isolation of chemolithotrophic iron-oxidizing bacteria. FEMS Microbiol Ecol 2025; 101:fiaf051. [PMID: 40328454 PMCID: PMC12089753 DOI: 10.1093/femsec/fiaf051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2024] [Revised: 03/29/2025] [Accepted: 05/02/2025] [Indexed: 05/08/2025] Open
Abstract
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.
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Affiliation(s)
- Tomoki Uchijima
- Department of Science and Technology for Biological Resources and Environment, Graduate School of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime 790-8566, Japan
| | - Shingo Kato
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Kazuya Tanimoto
- Department of Science and Technology for Biological Resources and Environment, Graduate School of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime 790-8566, Japan
| | - Fumito Shiraishi
- Earth and Planetary Systems Science Program, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Natsuko Hamamura
- Department of Biology, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kohei Tokunaga
- Ningyo-Toge Environmental Engineering Center, Japan Atomic Energy Agency, Okayama 708-0698, Japan
| | - Hiroko Makita
- Department of Ocean Sciences, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research, (X-star), Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka 237-0061, Japan
| | - Momoko Kondo
- Department of Science and Technology for Biological Resources and Environment, Graduate School of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime 790-8566, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Satoshi Mitsunobu
- Department of Science and Technology for Biological Resources and Environment, Graduate School of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime 790-8566, Japan
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Zhang C, Bosma TNP, Atashgahi S, Smidt H. Genome-resolved transcriptomics reveals novel PCE-dehalogenating bacteria from Aarhus Bay sediments. mSystems 2025; 10:e0150324. [PMID: 40237482 PMCID: PMC12090745 DOI: 10.1128/msystems.01503-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2024] [Accepted: 03/20/2025] [Indexed: 04/18/2025] Open
Abstract
Organohalide-respiring bacteria (OHRB) are keystone microbes in bioremediation of sites contaminated with organohalides and in natural halogen cycling. Known OHRB belong to distinct genera within the phyla Chloroflexota, Proteobacteria, and Firmicutes, whereas information about novel OHRB mediating natural halogen cycling remains scarce. In this study, we applied a genome-resolved transcriptomic approach to characterize the identity and activity of OHRB from tetrachloroethene respiring cultures previously enriched from sediments of Aarhus Bay. Combining short- and long-read sequencing approaches, we assembled 37 medium-quality bins with over 75% completeness and less than 5% contamination. Sixteen bins harbored RDase genes and were affiliated taxonomically to the class of Bacilli and phyla of Bacteroidota, Synergistota, and Spirochaetota, which have not been reported to catalyze reductive dehalogenation. Among the 16 bins, bin.26, phylogenetically close to the genus Vulcanibacillus (phylum Firmicutes), contained an unprecedented 97 reductive dehalogenase (RDase) genes. Of these, 84 RDase genes of bin.26 were transcribed during tetrachloroethene dechlorination in addition to RDase genes from the members of Synergistales (bin.5 and bin.32) and Bacteroidales (bin.18 and bin.24). Moreover, metatranscriptome analysis suggested that the RDase genes were likely under the regulation of transcriptional regulators not previously associated with organohalide respiration, such as HrcA and SigW, which are known to respond to abiotic environmental stresses, such as temperature changes. Combined application of genomic methods enabled us to pinpoint novel OHRB from pristine environments not previously known to mediate reductive dechlorination and to add to the current knowledge of the diversity, activity, and regulation of RDase genes.IMPORTANCEPristine marine environment is the major reservoir for naturally produced organohalides, in which reductive dehalogenation underneath plays an important role in the overall cycling of these compounds. Here, we obtain some novel OHRB genomes from Aarhus Bay marine sediments, which are phylogenetically distant to the well-documented OHRB and widely distributed across the bacterial phyla, such as Bacteroidota, Synergistota, and Spirochaetota. Furthermore, transcriptional profiles unravel that these RDase genes are induced differently, and their activity is controlled by diverse regulatory systems. Accordingly, elucidating the reductive dehalogenation of pristine marine environments substantially advances our understanding of the diversity, phylogeny, and regulatory variety of dehalogenating bacteria contributing to the global halogen cycle.
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Affiliation(s)
- Chen Zhang
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Tom N. P. Bosma
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands
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42
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Wang J, Su X, Zhang C, Han Z, Wang M. Biodegradation of Benzo(a)pyrene in Contaminated Soil: Plant and Microorganism Contributions from Isotope Tracing. TOXICS 2025; 13:405. [PMID: 40423484 DOI: 10.3390/toxics13050405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2025] [Revised: 05/12/2025] [Accepted: 05/13/2025] [Indexed: 05/28/2025]
Abstract
Biological degradation effectively removes benzo(a)pyrene (BaP) from contaminated soil; however, knowledge regarding the contributions of plant absorption, microbial degradation, and volatilization to BaP removal remains limited. In this study, the BaP removal pathway in contaminated soil was investigated. The structural evolution of the microbial community in contaminated soil was revealed using a comparative experimental study. BaP, as a representative of high-molecular-weight polycyclic aromatic hydrocarbons, was removed from freshly contaminated soil by microbial degradation, plant absorption, and volatilization in proportions of 20.955%, 12.771%, and 0.005%, respectively. The proportions of BaP removed by microbial degradation, plant absorption, and volatilization in aged contaminated soil were 29.471%, 16.453%, and 0.004%. Microbial degradation was the most responsible mechanism for BaP removal. Moreover, a higher number of BaP degrading bacteria occurred in the aged contaminated soil. At the genus level, Pseudomonas and Sphingomonas were detected in both types of soils, being the key bacterial species involved in BaP degradation.
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Affiliation(s)
- Jianlong Wang
- Key Laboratory of Urban Storm Water System and Water Environment, Ministry of Education, Beijing University of Civil Engineering and Architecture, Beijing 100044, China
- Beijing Energy Conservation & Sustainable Urban and Rural Development Provincial and Ministry Co-Construction Collaboration Innovation Center, Beijing 100044, China
| | - Xiaobing Su
- Key Laboratory of Urban Storm Water System and Water Environment, Ministry of Education, Beijing University of Civil Engineering and Architecture, Beijing 100044, China
- Beijing Energy Conservation & Sustainable Urban and Rural Development Provincial and Ministry Co-Construction Collaboration Innovation Center, Beijing 100044, China
| | - Changhe Zhang
- Key Laboratory of Urban Storm Water System and Water Environment, Ministry of Education, Beijing University of Civil Engineering and Architecture, Beijing 100044, China
- China Academy of Building Research, Beijing 100013, China
| | - Zhimeng Han
- Key Laboratory of Urban Storm Water System and Water Environment, Ministry of Education, Beijing University of Civil Engineering and Architecture, Beijing 100044, China
| | - Meiqi Wang
- Key Laboratory of Urban Storm Water System and Water Environment, Ministry of Education, Beijing University of Civil Engineering and Architecture, Beijing 100044, China
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Jiang H, Zhou C, Liang Z, Wu W, Ahmed T, Gao Q, Liao M, Cao H. Serratia marcescens Sm85 produces dimethyl disulfide defense against rice sheath blight and effects on phyllosphere bacterial community. PEST MANAGEMENT SCIENCE 2025. [PMID: 40370113 DOI: 10.1002/ps.8853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 02/18/2025] [Accepted: 04/09/2025] [Indexed: 05/16/2025]
Abstract
BACKGROUND Rice sheath blight (RSB), caused by Rhizoctonia solani Kuhn, significantly impacts rice yield and quality. The extensive use of chemical pesticides, while often effective, requires high application rates, causes environmental damage, is expensive, and contributes to the development of pesticide resistance. The lack of reliability and robustness of these conventional techniques necessitates the development of sustainable and environmentally friendly agricultural practices. Identifying novel biological control agents is crucial for developing effective and eco-friendly strategies to manage RSB. RESULTS This study identifies S. marcescens 85 (Sm85), isolated from rice stems, as a potential biocontrol agent against RSB. Sm85 produces the volatile chemical dimethyl disulfide (DMDS), which has antagonistic activity both in vivo (67.4% effective) and in vitro (97.7% effective). DMDS disrupts pathogen cell membrane integrity by increasing reactive oxygen species (ROS) production and reducing ergosterol content. The pot experiments demonstrated that DMDS treatment significantly reduces RSB lesion length, with a control effect comparable to commercial fungicides. The high-throughput data revealed that DMDS application alters the phyllosphere microbial community structure, increasing its richness and diversity. Notably, DMDS treatment enriches potentially beneficial bacteria such as Stenotrophomonas and Burkholderia, known for their roles in plant stress tolerance and pesticide degradation. Functional gene analysis reveals an upregulation of sulfur metabolism-related genes in the phyllosphere microbiome, suggesting adaptive responses to DMDS. CONCLUSION This study highlights the potential of Sm85 and its volatile metabolite DMDS as eco-friendly alternatives for RSB management, while also emphasizing the importance of considering microbial community dynamics in biocontrol strategies. © 2025 Society of Chemical Industry.
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Affiliation(s)
- Hubiao Jiang
- Key Laboratory of Agro-Products Quality and Biosafety (Ministry of Education), Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, Anhui Agricultural University, Hefei, China
- School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Chunhui Zhou
- Anhui Engineering Laboratory for Agro-products Processing, Anhui Agricultural University, Hefei, China
- College of Tea and Food Science & Technology, Anhui Agricultural University, Hefei, China
| | - Zihao Liang
- Key Laboratory of Agro-Products Quality and Biosafety (Ministry of Education), Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, Anhui Agricultural University, Hefei, China
- School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Weifu Wu
- Key Laboratory of Agro-Products Quality and Biosafety (Ministry of Education), Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, Anhui Agricultural University, Hefei, China
- School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Temoor Ahmed
- Department of Life Sciences, Western Caspian University, Baku, Azerbaijan
- Department of Plant Biotechnology, Korea University, Seoul, South Korea
| | - Quan Gao
- Key Laboratory of Agro-Products Quality and Biosafety (Ministry of Education), Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, Anhui Agricultural University, Hefei, China
- School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Min Liao
- Key Laboratory of Agro-Products Quality and Biosafety (Ministry of Education), Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, Anhui Agricultural University, Hefei, China
- School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Hiaqun Cao
- Key Laboratory of Agro-Products Quality and Biosafety (Ministry of Education), Anhui Agricultural University, Hefei, China
- Anhui Province Engineering Laboratory for Green Pesticide Development and Application, Anhui Agricultural University, Hefei, China
- School of Plant Protection, Anhui Agricultural University, Hefei, China
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Castaño-Jiménez PA, Baltazar-Díaz TA, González-Hernández LA, García-Salcido R, Klimov-Kravtchenko K, Andrade-Villanueva JF, Arellano-Arteaga KJ, Padilla-Sánchez MP, Del Toro-Arreola S, Bueno-Topete MR. Deciphering the Language of Intestinal Microbiota Associated with Sepsis, Organ Failure, and Mortality in Patients with Alcohol-Related Acute-on-Chronic Liver Failure (ACLF): A Pioneer Study in Latin America. Microorganisms 2025; 13:1138. [PMID: 40431310 PMCID: PMC12113797 DOI: 10.3390/microorganisms13051138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2025] [Revised: 05/05/2025] [Accepted: 05/10/2025] [Indexed: 05/29/2025] Open
Abstract
ACLF is a severe stage of liver cirrhosis, characterized by multiple organ failure, systemic inflammation, and high short-term mortality. The intestinal microbiota (IM) influences its pathophysiology; however, there are currently no studies in Latin American populations. Therefore, we analyzed IM and its relationships with sepsis, organ failure, and mortality. In parallel, we quantified serum lipopolysaccharides as a marker of bacterial translocation. Fecal samples from 33 patients and 20 healthy controls (HCs) were obtained. The IMs were characterized by 16S-rRNA amplicon sequencing, the metagenomic functional predictive profiles were analyzed by PICRUSt2, and LPS quantification was performed by ELISA. Patients with ACLF showed significant alterations in alpha and beta diversity compared to the HCs. A strong dominance index accurately predicted 28-day and 90-day mortalities. The IMs showed a polarization toward Proteobacteria associated with increased LPS. The LPS correlated with clinical severity, organ dysfunction, and higher pathogenic taxa. The Klebsiella/Faecalibacterium ratio showed good performance in identifying sepsis (AUROC = 0.83). Furthermore, Morganella, Proteus, and Klebsiella were enriched in patients with multiorgan failure. Lactobacillus, Escherichia/Shigella, Veillonella, and Ruminococcus gnavus exhibited potential in predicting 28- and 90-day mortalities. The IM alterations in ACLF may be useful as clinical biomarkers of poor prognosis, primarily for mortality and sepsis. These findings are representative of western Mexico.
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Affiliation(s)
- Paula Alejandra Castaño-Jiménez
- Departamento de Biología Molecular y Genómica, Instituto de Investigación en Enfermedades Crónico-Degenerativas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44350, Mexico; (P.A.C.-J.); (T.A.B.-D.); (K.K.-K.); (M.P.P.-S.); (S.D.T.-A.)
| | - Tonatiuh Abimael Baltazar-Díaz
- Departamento de Biología Molecular y Genómica, Instituto de Investigación en Enfermedades Crónico-Degenerativas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44350, Mexico; (P.A.C.-J.); (T.A.B.-D.); (K.K.-K.); (M.P.P.-S.); (S.D.T.-A.)
| | - Luz Alicia González-Hernández
- Unidad de VIH, Hospital Civil de Guadalajara “Fray Antonio Alcalde”, Guadalajara 44350, Mexico;
- Departamento de Clínicas Médicas, Instituto de Investigación en Inmunodeficiencias y VIH, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44350, Mexico;
| | - Roxana García-Salcido
- Unidad de Urgencias Médicas, Hospital Civil de Guadalajara “Fray Antonio Alcalde”, Guadalajara 44350, Mexico;
| | - Ksenia Klimov-Kravtchenko
- Departamento de Biología Molecular y Genómica, Instituto de Investigación en Enfermedades Crónico-Degenerativas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44350, Mexico; (P.A.C.-J.); (T.A.B.-D.); (K.K.-K.); (M.P.P.-S.); (S.D.T.-A.)
| | - Jaime F. Andrade-Villanueva
- Departamento de Clínicas Médicas, Instituto de Investigación en Inmunodeficiencias y VIH, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44350, Mexico;
- Unidad de Urgencias Médicas, Hospital Civil de Guadalajara “Fray Antonio Alcalde”, Guadalajara 44350, Mexico;
| | | | - Mayra Paola Padilla-Sánchez
- Departamento de Biología Molecular y Genómica, Instituto de Investigación en Enfermedades Crónico-Degenerativas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44350, Mexico; (P.A.C.-J.); (T.A.B.-D.); (K.K.-K.); (M.P.P.-S.); (S.D.T.-A.)
| | - Susana Del Toro-Arreola
- Departamento de Biología Molecular y Genómica, Instituto de Investigación en Enfermedades Crónico-Degenerativas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44350, Mexico; (P.A.C.-J.); (T.A.B.-D.); (K.K.-K.); (M.P.P.-S.); (S.D.T.-A.)
| | - Miriam Ruth Bueno-Topete
- Departamento de Biología Molecular y Genómica, Instituto de Investigación en Enfermedades Crónico-Degenerativas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44350, Mexico; (P.A.C.-J.); (T.A.B.-D.); (K.K.-K.); (M.P.P.-S.); (S.D.T.-A.)
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Bressa C, González-Soltero R, Tabone M, Clemente-Velasco S, Gálvez BG, Larrosa M. Exploring the relationship between APOEε4 allele and gut microbiota composition and function in healthy adults. AMB Express 2025; 15:77. [PMID: 40372527 PMCID: PMC12081816 DOI: 10.1186/s13568-025-01888-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2025] [Accepted: 05/06/2025] [Indexed: 05/16/2025] Open
Abstract
The APOE ε4 allele (APOE4) is a known risk factor for neurodegenerative and cardiovascular diseases, but its link to body composition and metabolism remains debated. The gut microbiota influences host metabolism and immunity, yet its relationship with APOE genotype in healthy individuals is not well understood. The objective of this work was to examine associations between APOE genotype and gut microbiota composition and function in healthy adults, focusing on microbial and metabolic differences related to the APOE4 allele. Seventy-seven healthy Spanish adults were genotyped for APOE. Fecal microbiota profiles were assessed by 16 S rRNA gene sequencing, and predicted functions were inferred using PICRUSt2. Body composition (DEXA) and physical activity (accelerometry) were also measured. APOE4 carriers exhibited subtle shifts in microbiota composition, including a five-fold reduction in Megamonas and lower abundance of the Eubacterium brachy group-both linked to energy harvest and adiposity-compared to APOE3 homozygotes. An uncharacterized Puniceicoccaceae genus was enriched in APOE4 carriers. Although E. brachy group abundance correlated with adiposity, no significant differences in body composition were observed. Functional predictions showed APOE4-associated microbiota enriched in pathways for carotenoid biosynthesis and trehalose metabolism, and depleted in tryptophan biosynthesis, propionate production, and multidrug resistance mechanisms. APOE4 carriers harbor gut microbiota with distinct taxonomic and functional features, potentially reflecting adaptations to metabolic and oxidative challenges. These findings underscore the relevance of the gut microbiome in shaping APOE4-associated phenotypes and warrant further investigation into its mechanistic contributions to health and disease.
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Affiliation(s)
- C Bressa
- Masmicrobiota Research Group, Madrid, Spain
- Facultad de Ciencias Experimentales, Universidad Francisco de Vitoria, Ctra. Pozuelo- Majadahonda km 1,800, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - R González-Soltero
- Masmicrobiota Research Group, Madrid, Spain
- Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Madrid, Spain
| | - M Tabone
- Masmicrobiota Research Group, Madrid, Spain
- Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Madrid, Spain
| | - S Clemente-Velasco
- Masmicrobiota Research Group, Madrid, Spain
- Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Madrid, Spain
- Department of Food Science and Nutrition, Faculty of Pharmacy, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - B G Gálvez
- Masmicrobiota Research Group, Madrid, Spain.
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Universidad Complutense de Madrid, Madrid, Spain.
| | - M Larrosa
- Masmicrobiota Research Group, Madrid, Spain.
- Department of Food Science and Nutrition, Faculty of Pharmacy, Universidad Complutense de Madrid, 28040, Madrid, Spain.
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Argenta N, Clark KF. Shell bacterial community dynamics suggest that American lobster (Homarus americanus) impoundment shell disease is caused by a dysbiosis. J Invertebr Pathol 2025; 211:108355. [PMID: 40379204 DOI: 10.1016/j.jip.2025.108355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2025] [Revised: 05/05/2025] [Accepted: 05/12/2025] [Indexed: 05/19/2025]
Abstract
Impoundment shell disease (ISD) in the American lobster (Homarus americanus) is a distinct pathological condition from the more well-known epizootic shell disease. It is commonly observed at low prevalences in live American lobsters held overwinter in tidal pounds and significantly reduces their economic value. Impoundment shell disease was originally described in 1937; however, its etiology remains unclear. The main goal of this study was to characterize the bacterial community associated with ISD in Canadian lobsters. Lobsters were collected from a pound in southwest Nova Scotia, Canada, and the full 16S rRNA gene of bacterial communities from lesion and healthy shell areas of asymptomatic (As), moderately symptomatic (MS) and severely symptomatic (SS) animals was sequenced. Pielou evenness and Shannon diversity indexes of alpha-diversity were higher in healthy areas compared to lesion areas. Beta-diversity metrics indicate that the bacterial diversity differences are driven mainly by the relative abundance of a small number of bacteria, rather than the specific taxa present in the samples. Taxa were designated as being potentially involved with ISD based on their relative frequency, relative abundance or being core bacteriome in the lesion shell area. Among those found in this study, Tenacibaculum and Vibrio were previously described in ISD lesions; but others, such as Cellvibrionaceae, Polaribacter, Maribacter and Sulfitobacter were not. Altogether, the findings of this study indicate that ISD is driven by dysbiosis. Moreover, the inconsistency of taxa with previous studies may indicate that ISD consists of a combination of specific functional groups of bacteria, rather specific taxa.
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Affiliation(s)
- Nicolas Argenta
- Department of Animal Science and Aquaculture, Faculty of Agriculture, Dalhousie University, Bible Hill, NS, Canada.
| | - K Fraser Clark
- Department of Animal Science and Aquaculture, Faculty of Agriculture, Dalhousie University, Bible Hill, NS, Canada
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Shevchenko AY, Ursalov GI, Eromasova NI, Shelyakin PV, Gelfand MS, Tutukina MN, Abramov AA, Vishnivetskaya TA, Rivkina EM. Microbial diversity of high-elevated fumarole fields, low-biomass communities on the boundary between ice and fire. Sci Rep 2025; 15:16600. [PMID: 40360685 PMCID: PMC12075824 DOI: 10.1038/s41598-025-99782-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2024] [Accepted: 04/22/2025] [Indexed: 05/15/2025] Open
Abstract
Fumarole fields on active volcanoes are habitats that host unique microbial ecosystems. However, DNA extraction from them for further analysis is rather challenging. In this study, we compared two different ways of sample homogenization for DNA extraction to further profile the microbial communities of active fumarolic fields from Elbrus and Ushkovsky volcanoes and the frozen fumarole deposits of Fujiyama. Vertical homogenizer gave significantly higher DNA concentrations for the Elbrus samples, and more archaeal amplicon sequence variants for Elbrus and Ushkovsky samples compared to the horizontal one. This suggests that vertical homogenizer might be preferable for DNA extraction from sandy and rocky soils. Independent of the homogenizer type, the dominant phyla for Elbrus were Acidobacteriota and Pseudomonadota, and Crenarchaeota for Ushkovsky. The bacterial community of Fuji was less diverse, with Actinomycetota, Pseudomonadota and Bacillota being the dominant phyla. Thus, the studied fumaroles showed distinct microbial profiles, revealing unique adaptations to their respective extreme environments. Within the fungal community, Ascomycota, Basidiomycota and Chytridiomycota were the most dominant phyla for all three volcanoes, but their abundance varied. This study offers the first comprehensive analysis of microbial and fungal communities of active and frozen fumarolic fields, and demonstrates that the choice of methodology can significantly influence the understanding of microbial diversity in extreme environments.
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Affiliation(s)
- Alla Yu Shevchenko
- Center for Molecular and Cellular Biology, Moscow, Russia.
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, PSCBR RAS, Pushchino, Russia.
| | | | - Natalya I Eromasova
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, PSCBR RAS, Pushchino, Russia
| | - Pavel V Shelyakin
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | | | - Maria N Tutukina
- Center for Molecular and Cellular Biology, Moscow, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Institute of Cell Biophysics, Russian Academy of Sciences, PSCBR RAS, Pushchino, Russia
| | - Andrey A Abramov
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, PSCBR RAS, Pushchino, Russia
| | | | - Elizaveta M Rivkina
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, PSCBR RAS, Pushchino, Russia
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Wang JQ, Yu T, Qiu HY, Ji SW, Xu ZQ, Cui QC, Li HF, Liang WF, Feng S, Fu CT, Gao X, Han ZZ, Tian WN, Li JX, Xue SJ. Differential impact of spotted fever group rickettsia and anaplasmosis on tick microbial ecology: evidence from multi-species comparative microbiome analysis. Front Microbiol 2025; 16:1589263. [PMID: 40432969 PMCID: PMC12106494 DOI: 10.3389/fmicb.2025.1589263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2025] [Accepted: 04/22/2025] [Indexed: 05/29/2025] Open
Abstract
Tick-borne diseases (TBDs) pose a significant public health challenge, as their incidence is increasing due to the effects of climate change and ecological shifts. The interplay between tick-borne pathogens and the host microbiome is an emerging area of research that may elucidate the mechanisms underlying disease susceptibility and severity. To investigate the diversity of microbial communities in ticks infected with vertebrate pathogens, we analyzed the microbiomes of 142 tick specimens. The presence of Rickettsia and Anaplasma pathogens in individual samples was detected through PCR. Our study aimed to elucidate the composition and variation of microbial communities associated with three tick species, which are known vectors for various pathogens affecting both wildlife and humans. We employed high-throughput sequencing techniques to characterize the microbial diversity and conducted statistical analyses to assess the correlation between the presence of specific pathogens and the overall microbial community structure. Pathogen screening revealed an overall positivity rate of 51.9% for Anaplasma and 44.6% for spotted fever group rickettsia (SFGR). Among the three tick species (Dermacentor silvarum, Haemaphysalis concinna, and Haemaphysalis japonica) analyzed, D. silvarum (the predominant species) exhibited the highest pathogen prevalence. The results indicate significant variation in microbial diversity between tick samples, with the presence of Anaplasma and SFGR associated with distinct changes in the microbial community composition. These findings underscore the complex interactions between ticks and their microbial inhabitants, enriching our understanding of tick-borne diseases.
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Affiliation(s)
- Jin-qi Wang
- Agricultural College of Yanbian University, Yanji, China
| | - Tian Yu
- Agricultural College of Yanbian University, Yanji, China
| | - Hong-yu Qiu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Sheng-wei Ji
- Agricultural College of Yanbian University, Yanji, China
| | - Zhi-qiang Xu
- Agricultural College of Yanbian University, Yanji, China
| | - Qi-chao Cui
- Agricultural College of Yanbian University, Yanji, China
| | - Hai-feng Li
- Agricultural College of Yanbian University, Yanji, China
| | - Wan-feng Liang
- Agricultural College of Yanbian University, Yanji, China
| | - Shuai Feng
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Chen-tao Fu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Xu Gao
- Agricultural College of Yanbian University, Yanji, China
| | - Zhen-zhen Han
- Animal Health and Epidemic Prevention Center, Huludao, China
| | - Wan-nian Tian
- College of Animal Science, Jilin Agricultural Science and Technology College, Jilin, China
| | - Ji-xu Li
- Yanbian Center for Disease Control and Prevention, Yanji, China
| | - Shu-jiang Xue
- Agricultural College of Yanbian University, Yanji, China
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Xie X, Wang JK, Liu JX, Guan LL, Neves ALA. Temporal microbial colonization on different forages is driven by the rumen environmental conditions. Anim Microbiome 2025; 7:46. [PMID: 40355960 PMCID: PMC12067915 DOI: 10.1186/s42523-025-00407-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2025] [Accepted: 04/09/2025] [Indexed: 05/15/2025] Open
Abstract
The rumen is one of the four compartments of the ruminant stomach and houses a diverse array of anaerobic microbes that play a crucial role in feed digestion and volatile fatty acid (VFA) production. The aim of this study was to explore how two different in vivo rumen environmental conditions, AHR (created from sheep-fed alfalfa hay) and CSR (created from sheep-fed corn stover), affect fiber digestion and rumen bacterial colonization in relation to two types of forage, alfalfa hay (AH) and corn stover (CS). Both AH and CS forages were subjected to in-sacco incubation in AHR and CSR conditions for a period of 48 h. The results revealed that CSR exhibited a less variant pH, lower total VFA concentration, and higher acetate-to-propionate ratio than AHR. CSR significantly enhanced the degradation of neutral detergent fiber and acid detergent fiber in both incubated forages (AH and CS). Although CSR did not improve the degradation of dry matter (DM) or crude protein (CP) on AH, it improved the degradation of DM and CP on CS. Both CS and AH incubated under CSR were found to have a greater abundance of fibrolytic bacteria (e.g., Fibrobacter and Butyrivibrio 2) compared to the same forage incubated under AHR, especially during the initial stages of incubation. However, CS and AH incubated under AHR were colonized by bacteria specialized in breaking down soluble carbohydrates (e.g., Prevotella and Succinivibrio). Compared with AHR, CSR enhanced the degradation rates of both incubated forages (CS and AH). These findings underscore the role of the rumen microenvironment in affecting the composition of adherent microbial communities and enhancing the breakdown of forages. Therefore, optimizing the rumen microenvironment to promote the attachment of fibrolytic bacteria during the early fermentation stages while minimizing hydrogen accumulation to stabilize the pH could lead to improved forage fermentation and animal performance.
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Affiliation(s)
- X Xie
- School of Marine Sciences, Ningbo University, 315832, Ningbo, People's Republic of China
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, 310058, Hangzhou, People's Republic of China
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - J K Wang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, 310058, Hangzhou, People's Republic of China
| | - J X Liu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, 310058, Hangzhou, People's Republic of China
| | - L L Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
| | - A L A Neves
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 3, 1870, Frederiksberg C, Denmark.
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Sacharow J, Ratering S, Quiroga S, Geissler-Plaum R, Schneider B, Österreicher Cunha-Dupont A, Schnell S. Composition of cercozoan diversity: Unravelling leaf, root, and soil specificity in crop plants. Eur J Protistol 2025; 99:126152. [PMID: 40513363 DOI: 10.1016/j.ejop.2025.126152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2024] [Revised: 05/09/2025] [Accepted: 05/09/2025] [Indexed: 06/16/2025]
Abstract
Protists are integral components of the plant holobiome, influencing plant growth and pathogenic pressure through their predatory activities. Wheat (Triticum aestivum), one of the most important crops globally, depends on favorable environmental conditions and effective pathogen management to achieve high yields. This study investigates the natural compositions of cercozoan diversity in winter wheat across various developmental stages (before sowing, at flowering, at ripening, and after harvesting) and plant compartments (leaves, roots, rhizosphere, and bulk soil) over two field seasons. The results revealed a pronounced dominance of the families Sandonidae, Allapsidae, Cercomonadidae, and Rhogostomidae across all samples. A strong enrichment of Sandonidae in leaf samples and Allapsidae in root samples was particularly notable. Importantly, no significant differences in cercozoan composition were observed across the different developmental stages of the plant. A comparative analysis between Triticum aestivum and Hordeum vulgare (barley) showed substantial similarity in cercozoan diversity across soil, leaf, and root compartments, with the only notable difference occurring in leaf samples during the ripening stage. The study concludes that cercozoan diversity in winter wheat is compartment-specific and remain stable across developmental stages. Further research is needed to explore cercozoan communities in greater taxonomic depth and to elucidate their ecological roles. Future studies should also assess whether similar patterns of compartmental variation and developmental consistency are observed in other major agricultural crops.
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Affiliation(s)
- Julia Sacharow
- Institute of Applied Microbiology,IFZ, Heinrich-Buff-Ring 26-32, Justus-Liebig-University Giessen, 35392 Giessen, Germany.
| | - Stefan Ratering
- Institute of Applied Microbiology,IFZ, Heinrich-Buff-Ring 26-32, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Santiago Quiroga
- Institute of Applied Microbiology,IFZ, Heinrich-Buff-Ring 26-32, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Rita Geissler-Plaum
- Institute of Applied Microbiology,IFZ, Heinrich-Buff-Ring 26-32, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Bellinda Schneider
- Institute of Applied Microbiology,IFZ, Heinrich-Buff-Ring 26-32, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | | | - Sylvia Schnell
- Institute of Applied Microbiology,IFZ, Heinrich-Buff-Ring 26-32, Justus-Liebig-University Giessen, 35392 Giessen, Germany
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