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Yuan H, Zhang R, Chen J, Wu J, Han Q, Li Q, Lu Q. Phosphorus resource partitioning underpins diversity patterns and assembly processes of microbial communities in plateau karst lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 952:175860. [PMID: 39214351 DOI: 10.1016/j.scitotenv.2024.175860] [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: 07/01/2024] [Revised: 08/09/2024] [Accepted: 08/27/2024] [Indexed: 09/04/2024]
Abstract
Eutrophication triggered by internal phosphorus (P) poses a substantial threat to the biodiversity of organisms in freshwater ecosystems. However, little is known about the linkages between P resource partitioning and microbial succession, especially in karst sediments. Here, we studied the diversity patterns and assembly processes of bacterial and archaeal communities in sediment cores from two historically hyper-eutrophicated karst lakes, Hongfeng Lake and Aha Lake, and investigated the relative contribution of P fractions to them. Our null and neutral models consistently indicated that bacterial and archaeal community assembly was judged to be deterministic rather than stochastic. We found a monotonically decreasing pattern for bacterial Shannon diversity toward deep sediments in Aha Lake, but U- or hump-shaped patterns for archaea in Hongfeng and Aha Lakes. Intriguingly, the community dissimilarity Bray-Curtis of bacteria and archaea consistently increased with increasing depth distance, with slopes of 0.0080 and 0.0069 in Hongfeng Lake and 0.0078 and 0.0087 in Aha Lake, respectively. Such cross-taxon congruence was well-supported by equivalent ecological processes (i.e., environmental selection). For bacteria and archaea, Shannon diversity was primarily affected by the total P (TP) fractions such as the loosely adsorbed TP or calcium-bound TP and sediment TP. Their community composition was significantly (P < 0.05) affected by calcium-bound inorganic P (Pi), loosely adsorbed Pi and reductant-soluble Pi. Although sediment properties were important, bacterial and archaeal diversity or community composition were well-explained by the Pi fractions, with high direct or indirect effects. In particular, Pi fractions exhibited stronger effects on bacterial and archaeal characteristics than organic P fractions. Taken together, our study provides novel insights into the ecological importance of P resource partitioning to microbial succession, which has crucial implications for disentangling the biogeochemical processes of P cycling in aquatic ecosystems.
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Affiliation(s)
- Haijun Yuan
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Runyu Zhang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China.
| | - Jingan Chen
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Jing Wu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiao Han
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiuxing Li
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; College of Earth Science, Chengdu University of Technology, Chengdu 610059, China
| | - Qiping Lu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
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Khiaosa-Ard R, Pacífico C, Mahmood M, Mickdam E, Meixner J, Traintinger LS, Zebeli Q. Changes in the solid-associated bacterial and fungal communities following ruminal in vitro fermentation of winery by-products: aspects of the bioactive compounds and feed safety. Anaerobe 2024; 89:102893. [PMID: 39122139 DOI: 10.1016/j.anaerobe.2024.102893] [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: 03/24/2024] [Revised: 07/11/2024] [Accepted: 08/06/2024] [Indexed: 08/12/2024]
Abstract
OBJECTIVES Feeding winery by-products (WBP) could affect the bovine microbiome because of their phenol compounds and a transfer of WBP-associated microbiota. This work examined changes in the underexplored solid-associated rumen microbiome following the inclusion of WBP. METHODS Using the rumen simulation technique, fermenters were inoculated with the inoculum of donor cows and were fed one of six dietary treatments including a control diet of 70 % hay +30 % concentrate (CON), control diet + 3.7 % commercial grapeseed extract (EXT), 65 % hay + 25 % concentrate + 10 % grape pomace (GP-low), 56 % hay + 24 % concentrate + 20 % grape pomace (GP-high), 70 % hay + 25 % concentrate + 5 % grapeseed meal (GS-low), and 65 % hay + 25 % concentrate + 10 % grapeseed meal (GS-high) (dry matter basis). The compositional changes of bacteria, archaea and fungi in the solid fractions were based on 16S and ITS2 rRNA sequencing. RESULTS The alpha- and beta-diversity of the microbiota were unaffected. However, treatment modified the bacterial composition at low taxonomic levels. Butyrivibrio fibrisolvens, Treponema bryantii, and bacterium MC2010 decreased in EXT, while Treponema berlinense was increased in GP-high and GP-low compared to CON. Concerning fungi, GS-high increased Candida spp., Lachancea spp., Microdochium spp., Mucor spp., Pichia spp., Saturnispora spp., and Zygosaccharomyces spp. compared to CON. Many non-Saccharomyces yeasts were detected in WBP samples but absent in donor cows and CON samples. The genera affected by treatment were not the major contributors to the ruminal degradation of nutrients. CONCLUSIONS The results indicate a sensitivity of rumen solid bacteria to grape phenols when delivered as an extract and a transfer of WBP-associated microbiota into the rumen.
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Affiliation(s)
- Ratchaneewan Khiaosa-Ard
- Centre for Animal Nutrition and Welfare, Clinical Department for Farm Animals and Food System Science, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria.
| | - Cátia Pacífico
- Centre for Animal Nutrition and Welfare, Clinical Department for Farm Animals and Food System Science, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Mubarik Mahmood
- Animal Nutrition Section, Department of Animal Sciences, University of Veterinary and Animal Sciences, Lahore, Subcampus Jhang, 12 Km Chiniot Road, 35200 Jhang, Pakistan
| | - Elsayed Mickdam
- Nutrition and Clinical Nutrition Department, Faculty of Veterinary Medicine, South Valley University, 83523 Qena, Egypt
| | - Julia Meixner
- Centre for Animal Nutrition and Welfare, Clinical Department for Farm Animals and Food System Science, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Laura-Sophie Traintinger
- Centre for Animal Nutrition and Welfare, Clinical Department for Farm Animals and Food System Science, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Qendrim Zebeli
- Centre for Animal Nutrition and Welfare, Clinical Department for Farm Animals and Food System Science, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria
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Wu H, Gao T, Dini-Andreote F, Xiao N, Zhang L, Kimirei IA, Wang J. Biotic and abiotic factors interplay in structuring the dynamics of microbial co-occurrence patterns in tropical mountainsides. ENVIRONMENTAL RESEARCH 2024; 250:118517. [PMID: 38401680 DOI: 10.1016/j.envres.2024.118517] [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: 11/30/2023] [Revised: 02/13/2024] [Accepted: 02/16/2024] [Indexed: 02/26/2024]
Abstract
Ecological interactions are important for maintaining biodiversity and ecosystem functions. Particularly in stream biofilms, little is known about the distributional patterns of different taxonomic groups and their potential interactions along elevational gradients. Here, we investigated the bacterial and fungal community structures of stream biofilms across elevational gradients on Mount Kilimanjaro, and explored patterns of their distribution, diversity, community structures, and taxa co-occurrence. We found that fungal and bacterial richness were more convergent at higher elevations, while their community structures became significantly more divergent. Inferred network complexity and stability significantly decreased with increasing elevation for fungi, while an opposite trend was observed for bacteria. Further quantitative analyses showed that network structures of bacteria and fungi were more divergent as elevation increased. This pattern was strongly associated with shifts in abiotic factors, such as mean annual temperatures, water PO43--P, and stream width. By constructing bipartite networks, we showed the fungal-bacterial network to be less redundant, more clustering, and unstable with increasing elevation. Abiotic factors (e.g., temperatures and stream width) and microbial community properties (i.e., structure and composition) significantly explained the dynamic changes in fungal-bacterial network properties. Taken together, this study provides evidence for the interplay of biotic and abiotic factors structuring potential microbial interactions in stream biofilms along a mountainside elevational gradient.
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Affiliation(s)
- Hao Wu
- College of Oceanography, Hohai University, Nanjing, 210098, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Tianheng Gao
- College of Oceanography, Hohai University, Nanjing, 210098, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; College of Marine Science and Engineering, Nanjing Normal University, Nanjing, Jiangsu Province, 210023, China.
| | - Francisco Dini-Andreote
- Department of Plant Science & Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA; The One Health Microbiome Center, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Nengwen Xiao
- Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Lu Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Ismael Aaron Kimirei
- Tanzania Fisheries Research Institute, Headquarter, Dar Es Salaam, P.O. Box 9750, Tanzania
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.
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Yuan H, Zhang R, Li Q, Han Q, Lu Q, Wu J. Unveiling the ecological significance of phosphorus fractions in shaping bacterial and archaeal beta diversity in mesotrophic lakes. Front Microbiol 2023; 14:1279751. [PMID: 37886062 PMCID: PMC10598868 DOI: 10.3389/fmicb.2023.1279751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 09/27/2023] [Indexed: 10/28/2023] Open
Abstract
Both community variation and phosphorus (P) fractions have been extensively studied in aquatic ecosystems, but how P fractions affect the mechanism underlying microbial beta diversity remains elusive, especially in sediment cores. Here, we obtained two sediment cores to examine bacterial and archaeal beta diversity from mesotrophic lakes Hongfeng Lake and Aha Lake, having historically experienced severe eutrophication. Utilizing the Baselga's framework, we partitioned bacterial and archaeal total beta diversity into two components: species turnover and nestedness, and then examined their sediment-depth patterns and the effects of P fractions on them. We found that total beta diversity, species turnover or nestedness consistently increased with deeper sediment layers regarding bacteria and archaea. Notably, there were parallel patterns between bacteria and archaea for total beta diversity and species turnover, which is largely underlain by equivalent processes such as environmental selection. For both microbial taxa, total beta diversity and species turnover were primarily constrained by metal oxide-bound inorganic P (NaOH-Pi) and sediment total phosphorus (STP) in Hongfeng Lake, while largely affected by reductant-soluble total P or calcium-bound inorganic P in Aha Lake. Moreover, NaOH-Pi and STP could influence bacterial total beta diversity by driving species nestedness in Hongfeng Lake. The joint effects of organic P (Po), inorganic P (Pi) and total P fractions indicated that P fractions are important to bacterial and archaeal beta diversity. Compared to Po fractions, Pi fractions had greater pure effects on bacterial beta diversity. Intriguingly, for total beta diversity and species turnover, archaea rather than bacteria are well-explained by Po fractions in both lakes, implying that the archaeal community may be involved in Po mineralization. Overall, our study reveals the importance of P fractions to the mechanism underlying bacterial and archaeal beta diversity in sediments, and provides theoretical underpinnings for controlling P sources in biodiversity conservation.
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Affiliation(s)
- Haijun Yuan
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Runyu Zhang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, China
| | - Qiuxing Li
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, China
- College of Earth Science, Chengdu University of Technology, Chengdu, China
| | - Qiao Han
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qiping Lu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing Wu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, China
- University of Chinese Academy of Sciences, Beijing, China
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Liu H, Yao J, Liu B, Li M, Liu J, Jiang S, Yu W, Zhao Y, Duran R. Active tailings disturb the surrounding vegetation soil fungal community: Diversity, assembly process and co-occurrence patterns. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 865:161133. [PMID: 36566868 DOI: 10.1016/j.scitotenv.2022.161133] [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: 11/02/2022] [Revised: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Soil fungi play an important role in the soil biogeochemical cycle and are important biological indicators for the ecological remediation of mine tailings contaminated sites, therefore understanding the characteristics of soil fungal communities is a key aspect of pollution remediation. However, the influence of biological factors on the characteristics of fungal community diversity; assembly mechanisms and co-occurrence patterns of fungal community along environmental gradients around tailings are not well understood. In this study, soil samples from forest, agriculture and grass around tailings were collected to reveal the assembly mechanisms and co-occurrence patterns of soil fungal community and to quantify the contribution of abiotic and biotic factors to fungal diversity. The results suggest that vegetation types and Cu concentration together drive the distribution of fungal diversity. We found that Exophiala has potential as a biomarker species indicative of restoration progress. Increased environmental stress accelerates the process of changing fungal community assemblages from stochastic to deterministic, while also allowing fungal communities tend to resist tailings-induced environmental stresses through species coexistence. Together, this study provides new insights into the influence of biological factors on fungal community diversity, as well as revealing mechanisms of fungal community assembly and co-occurrence patterns, which are important for understanding the maintenance mechanisms of fungal community diversity and ecological remediation of tailings-contaminated soils.
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Affiliation(s)
- Houquan Liu
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Jun Yao
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China.
| | - Bang Liu
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China; Université de Pau et des Pays de l'Adour, E2S-UPPA, IPREM UMR CNRS 5254, BP 1155, 64013 Pau Cedex, France
| | - Miaomiao Li
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Jianli Liu
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Shun Jiang
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Wenjing Yu
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Yuhui Zhao
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Robert Duran
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, PR China; Université de Pau et des Pays de l'Adour, E2S-UPPA, IPREM UMR CNRS 5254, BP 1155, 64013 Pau Cedex, France
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