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Yang M, Luo X, Cai Y, Mwangi BN, Khan MS, Haider FU, Huang W, Cheng X, Yang Z, Zhou H, Liu S, Zhang Q, Luo M, Ou J, Xiong S, Li Y. Effect of fire and post-fire management on soil microbial communities in a lower subtropical forest ecosystem after a mountain fire. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 351:119885. [PMID: 38147772 DOI: 10.1016/j.jenvman.2023.119885] [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: 09/20/2023] [Revised: 11/29/2023] [Accepted: 12/17/2023] [Indexed: 12/28/2023]
Abstract
Wildfires and post-fire management exert profound effects on soil properties and microbial communities in forest ecosystems. Understanding microbial community recovery from fire and what the best post-fire management should be is very important but needs to be sufficiently studied. In light of these gaps in our understanding, this study aimed to assess the short-term effects of wildfire and post-fire management on both bacteria and fungi community composition, diversity, structure, and co-occurrence networks, and to identify the principal determinants of soil processes influencing the restoration of these communities. Specifically, we investigated soil bacterial and fungal community composition, diversity, structure, and co-occurrence networks in lower subtropical forests during a short-term (<3 years) post-fire recovery period at four main sites in Guangdong Province, southern China. Our results revealed significant effects of wildfires on fungal community composition, diversity, and co-occurrence patterns. Network analysis indicated reduced bacterial network complexity and connectivity post-fire, while the same features were enhanced in fungal networks. However, post-fire management effects on microbial communities were negligible. Bacterial diversity correlated positively with soil microbial biomass nitrogen, soil organic carbon, and soil total nitrogen. Conversely, based on the best random forest model, fungal community dynamics were negatively linked to nitrate-nitrogen and soil water content. Spearman's correlation analysis suggested positive associations between bacterial networks and soil factors, whereas fungal networks exhibited predominantly negative associations. This study elucidates the pivotal role of post-fire management in shaping ecological outcomes. Additionally, it accentuates the discernible distinctions between bacterial and fungal responses to fire throughout a short-term recovery period. These findings contribute novel insights that bear significance in evaluating the efficacy of environmental management strategies.
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Affiliation(s)
- Mengmeng Yang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Guangzhou, 51650, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xuan Luo
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Guangzhou, 51650, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; Central South University of Forestry and Technology, Changsha, 410004, China.
| | - Ying Cai
- Xiamen University, Xiamen, 361000, China.
| | - Brian N Mwangi
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Guangzhou, 51650, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Muhammad Sadiq Khan
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Guangzhou, 51650, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Fasih Ullah Haider
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Guangzhou, 51650, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Wanxuan Huang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Guangzhou, 51650, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xianli Cheng
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Guangzhou, 51650, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; Hubei University, Wuhan, 430062, China.
| | - Zefan Yang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Guangzhou, 51650, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Hongen Zhou
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Guangzhou, 51650, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; South China University of Technology, Guangzhou, 510641, China.
| | - Shizhong Liu
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Guangzhou, 51650, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Qianmei Zhang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Guangzhou, 51650, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Mingdao Luo
- Forestry Science Research Institute of Gaoming District, Foshan, 528500, China.
| | - Jinwei Ou
- Forestry Science Research Institute of Gaoming District, Foshan, 528500, China.
| | - Shiyang Xiong
- Forestry Science Research Institute of Gaoming District, Foshan, 528500, China.
| | - Yuelin Li
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Guangzhou, 51650, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
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Weigel B, Graco-Roza C, Hultman J, Pajunen V, Teittinen A, Kuzmina M, Zakharov EV, Soininen J, Ovaskainen O. Local eukaryotic and bacterial stream community assembly is shaped by regional land use effects. ISME COMMUNICATIONS 2023; 3:65. [PMID: 37365224 PMCID: PMC10293236 DOI: 10.1038/s43705-023-00272-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 05/30/2023] [Accepted: 06/14/2023] [Indexed: 06/28/2023]
Abstract
With anticipated expansion of agricultural areas for food production and increasing intensity of pressures stemming from land-use, it is critical to better understand how species respond to land-use change. This is particularly true for microbial communities which provide key ecosystem functions and display fastest responses to environmental change. However, regional land-use effects on local environmental conditions are often neglected, and, hence, underestimated when investigating community responses. Here we show that the effects stemming from agricultural and forested land use are strongest reflected in water conductivity, pH and phosphorus concentration, shaping microbial communities and their assembly processes. Using a joint species distribution modelling framework with community data based on metabarcoding, we quantify the contribution of land-use types in determining local environmental variables and uncover the impact of both, land-use, and local environment, on microbial stream communities. We found that community assembly is closely linked to land-use type but that the local environment strongly mediates the effects of land-use, resulting in systematic variation of taxon responses to environmental conditions, depending on their domain (bacteria vs. eukaryote) and trophic mode (autotrophy vs. heterotrophy). Given that regional land-use type strongly shapes local environments, it is paramount to consider its key role in shaping local stream communities.
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Affiliation(s)
- Benjamin Weigel
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. 65, FI-00014, Helsinki, Finland.
- INRAE, EABX, 50 avenue de Verdun, 33612, Cestas, France.
| | - Caio Graco-Roza
- Laboratory of Ecology and Physiology of Phytoplankton, Department of Plant Biology, State University of Rio de Janeiro, Rua São Francisco Xavier 524, PHLC, Sala 511a, Rio de Janeiro, 20550-900, Brazil
- Department of Geosciences and Geography, University of Helsinki, PO, Box 64, FI-00014, Helsinki, Finland
| | - Jenni Hultman
- Soil Ecosystems, Natural Resources Institute Finland, Latokartanonkaari 9, 00790, Helsinki, Finland
| | - Virpi Pajunen
- Department of Geosciences and Geography, University of Helsinki, PO, Box 64, FI-00014, Helsinki, Finland
- Department of Built Environment, Aalto University, PO Box 11000, 00076 AALTO, Espoo, Finland
| | - Anette Teittinen
- Department of Geosciences and Geography, University of Helsinki, PO, Box 64, FI-00014, Helsinki, Finland
| | - Maria Kuzmina
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Evgeny V Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Janne Soininen
- Department of Geosciences and Geography, University of Helsinki, PO, Box 64, FI-00014, Helsinki, Finland
| | - Otso Ovaskainen
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. 65, FI-00014, Helsinki, Finland
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, N-7491, Trondheim, Norway
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Shangguan H, Fu T, Shen C, Mi H, Wei J, Tang J, Zhou S. In situ generated oxygen distribution causes maturity differentiation during electrolytic oxygen aerobic composting. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 850:157939. [PMID: 35952878 DOI: 10.1016/j.scitotenv.2022.157939] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Electrolytic oxygen aerobic composting (EOAC) is an effective treatment with greater technical superiority and cost advantages for organic solid waste using in situ electrolytic oxygen as a feasible strategy to replace conventional aeration. However, the unclear effects of distribution and variation of in situ electrolytic oxygen on compost maturation in different depth zones of EOAC need further exploration. This study demonstrated that the humification of organic matter was faster at the bottom than in the middle and at the top. The main reason was that the higher oxygen content and lower moisture content in the bottom promoted microbial degradation and heat production, resulting in higher temperatures. The microbial analysis showed that the abundance of typical thermophilic bacteria (such as Cerasibacillus, Lactobacillus, and Pseudogracilibacillus) that could promote compost maturation was higher at the bottom than in the middle and at the top. The finding provided in-depth molecular insights into differentiated humification from bottom to top in EOAC and revealed its further practical engineering applications.
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Affiliation(s)
- Huayuan Shangguan
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Fu
- The Key Laboratory of Water and Sediment Sciences (Ministry of Education), College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Chang Shen
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Huan Mi
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Junrong Wei
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiahuan Tang
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Shungui Zhou
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Ben Moussa H, Bertrand C, Rochelle-Newall E, Fiorini S, Pédron J, Barny MA. The Diversity and Abundance of Soft Rot Pectobacteriaceae Along the Durance River Stream in the Southeast of France Revealed by Multiple Seasonal Surveys. PHYTOPATHOLOGY 2022; 112:1676-1685. [PMID: 35224981 DOI: 10.1094/phyto-12-21-0515-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Although irrigation water is frequently assessed for the presence of plant pathogens, large spatial and temporal surveys that provide clues on the diversity and circulation of pathogens are missing. We evaluate the diversity of soft rot Pectobacteriaceae (SRP) of the genera Dickeya and Pectobacterium over 2 years in a temperate, mixed-use watershed. The abundance of isolated strains correlates with the agricultural gradient along the watershed with a positive correlation found with temperature, nitrate, and dissolved organic carbon water concentration. We characterized 582 strains by amplification and sequencing of the gapA gene. Multilocus sequence analysis, performed with three housekeeping genes for 99 strains, and core genome analysis of 38 sequenced strains, confirmed for all the strains but one, the taxonomic assignation obtained with the sole gapA sequence. Pectobacterium spp. (549 isolates) were far more abundant than Dickeya spp. (33 isolates). Dickeya spp. were only observed in the lower part of the river when water temperature was >19°C, and we experimentally confirmed a decreased fitness of several Dickeya spp. at 8°C in river water. D. oryzae dominates the Dickeya spp. and P. versatile and P. aquaticum dominate the Pectobacterium spp., but their repartition along the watershed was different, with P. versatile being the only species regularly recovered all along the watershed. Excepting P. versatile, the Dickeya and Pectobacterium spp. responsible for disease outbreak on crops were less abundant or rarely detected. This work sheds light on the various ecological behaviors of different SRP types in stream water and indicates that SRP occupation is geographically structured.
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Affiliation(s)
- Hajar Ben Moussa
- Sorbonne Université, Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environnement, Institut de Recherche pour le Développement, Centre National de la Recherche Scientifique, Université Paris-Est Créteil, Institut d'Ecologie et des Sciences de l'Environnement de Paris, UMR 7618, F-75252 Paris, France
| | - Claire Bertrand
- Sorbonne Université, Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environnement, Institut de Recherche pour le Développement, Centre National de la Recherche Scientifique, Université Paris-Est Créteil, Institut d'Ecologie et des Sciences de l'Environnement de Paris, UMR 7618, F-75252 Paris, France
| | - Emma Rochelle-Newall
- Sorbonne Université, Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environnement, Institut de Recherche pour le Développement, Centre National de la Recherche Scientifique, Université Paris-Est Créteil, Institut d'Ecologie et des Sciences de l'Environnement de Paris, UMR 7618, F-75252 Paris, France
| | - Sarah Fiorini
- Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Centre de Recherche en Écologie Expérimentale et Prédictive, Paris Sciences & Lettres Research University, UMS 3194, 77140 Saint-Pierre-lès-Nemours, France
| | - Jacques Pédron
- Sorbonne Université, Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environnement, Institut de Recherche pour le Développement, Centre National de la Recherche Scientifique, Université Paris-Est Créteil, Institut d'Ecologie et des Sciences de l'Environnement de Paris, UMR 7618, F-75252 Paris, France
| | - Marie-Anne Barny
- Sorbonne Université, Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environnement, Institut de Recherche pour le Développement, Centre National de la Recherche Scientifique, Université Paris-Est Créteil, Institut d'Ecologie et des Sciences de l'Environnement de Paris, UMR 7618, F-75252 Paris, France
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5
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Ionescu D, Bizic M, Karnatak R, Musseau CL, Onandia G, Kasada M, Berger SA, Nejstgaard JC, Ryo M, Lischeid G, Gessner MO, Wollrab S, Grossart H. From microbes to mammals: Pond biodiversity homogenization across different land‐use types in an agricultural landscape. ECOL MONOGR 2022. [DOI: 10.1002/ecm.1523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- D. Ionescu
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - M. Bizic
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - R. Karnatak
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - C. L. Musseau
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Department of Biology, Chemistry, Pharmacy, Institute of Biology Free University of Berlin Germany
| | - G. Onandia
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Leibniz Centre for Agricultural Landscape Research (ZALF) Müncheberg Germany
| | - M. Kasada
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
| | - S. A. Berger
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - J. C. Nejstgaard
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - M. Ryo
- Leibniz Centre for Agricultural Landscape Research (ZALF) Müncheberg Germany
- Brandenburg University of Technology Cottbus–Senftenberg Cottbus Germany
| | - G. Lischeid
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Leibniz Centre for Agricultural Landscape Research (ZALF) Müncheberg Germany
| | - M. O. Gessner
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Department of Ecology Berlin Institute of Technology (TU Berlin) Berlin Germany
| | - S. Wollrab
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - H.‐P. Grossart
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Institute of Biochemistry and Biology Potsdam University Potsdam Germany
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Wang C, Masoudi A, Wang M, Yang J, Yu Z, Liu J. Land-use types shape soil microbial compositions under rapid urbanization in the Xiong'an New Area, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 777:145976. [PMID: 33677303 DOI: 10.1016/j.scitotenv.2021.145976] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 02/03/2021] [Accepted: 02/14/2021] [Indexed: 06/12/2023]
Abstract
For urban planning and infrastructural projects, considerable attention has been paid to the relationship between soil biota, especially protists, and edaphic conditions in various land-use types having different plant species in the Xiong'an New Area of China. To elucidate this relationship, we assessed edaphic variables and soil biota compositions and compared them among 5 habitat types: human-made forests, crop cultivations, arid rivers, Baiyangdian (BYD) Lake, and around oil wells. In all, 12 experimental plots from terrestrial and aquatic ecosystems were assessed using high-throughput sequencing of environmental DNA, targeting the V3-V4 region of the 16S rRNA gene, internal transcribed spacer 1, and V4 region of the 18S rRNA gene for bacteria, fungi, and protists, respectively. The abundance of bacterial and protist communities was higher than fungi, possibly because fungi prefer acidic soil conditions and likely have greater susceptibility to anthropogenic activities. Across all experimental plots, land-use types contributed the most to the β-diversity of soil biota, followed by soil moisture. Diversity and richness were significantly higher at aquatic habitats than at terrestrial habitats. Predictive metagenomic analysis of trophic groups predicted relatively high frequency of functional genes from bacterial metabolism pathways (carbohydrate and amino acid); contrary to expectation, phototrophic protists, but not fungal symbionts and protistan consumers, were the dominant group at the BYD Lake. Geographical coordinates showed significant (P < 0.05) relationships with all microbiome taxa (nodes at network) from all land-use types. Moreover, soil-microbiome relationships were more complex and more intense at crop habitats. Links between protist and fungal taxa were the highest at the petroleum-contaminated sampling sites, indicating the importance of these two soil microbiomes in polluted soil. Thus, our findings suggest that human manipulation and land-use types are crucial factors for soil biota structure and composition across our sampling sites.
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Affiliation(s)
- Can Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China
| | - Abolfazl Masoudi
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China
| | - Min Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China
| | - Jia Yang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China
| | - Zhijun Yu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China.
| | - Jingze Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, PR China.
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Nakhle P, Ribolzi O, Boithias L, Rattanavong S, Auda Y, Sayavong S, Zimmermann R, Soulileuth B, Pando A, Thammahacksa C, Rochelle-Newall EJ, Santini W, Martinez JM, Gratiot N, Pierret A. Effects of hydrological regime and land use on in-stream Escherichia coli concentration in the Mekong basin, Lao PDR. Sci Rep 2021; 11:3460. [PMID: 33568764 PMCID: PMC7876097 DOI: 10.1038/s41598-021-82891-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 01/11/2021] [Indexed: 01/30/2023] Open
Abstract
In the basin of Mekong, over 70 million people rely on unimproved surface water for their domestic requirements. Surface water is often contaminated with fecal matter and yet little information exists on the underlying mechanisms of fecal contamination in tropical conditions at large watershed scales. Our objectives were to (1) investigate the seasonality of fecal contamination using Escherichia coli as fecal indicator bacteria (FIB), and (2) establish links between the fecal contamination in stream water and its controlling factors (hydrology and land use). We present the results of (1) a sampling campaign at the outlet of 19 catchments across Lao PDR, in both the dry and the rainy seasons of 2016, and (2) a 10-day interval monitoring conducted in 2017 and 2018 at three point locations of three rivers (Nam Ou, Nam Suang, and Mekong) in northern Lao PDR. Our results show the presence of fecal contamination at most of the sampled sites, with a seasonality characterized by higher and extreme E. coli concentrations occurring during the rainy season. The highest E. coli concentrations, strongly correlated with total suspended sediment concentrations, were measured in catchments dominated by unstocked forest areas, especially in mountainous northern Lao PDR and in Vientiane province.
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Affiliation(s)
- Paty Nakhle
- Géosciences Environnement Toulouse (GET), Université de Toulouse, CNRS, IRD, UPS, Toulouse, France
| | - Olivier Ribolzi
- Géosciences Environnement Toulouse (GET), Université de Toulouse, CNRS, IRD, UPS, Toulouse, France
| | - Laurie Boithias
- Géosciences Environnement Toulouse (GET), Université de Toulouse, CNRS, IRD, UPS, Toulouse, France.
| | - Sayaphet Rattanavong
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Yves Auda
- Géosciences Environnement Toulouse (GET), Université de Toulouse, CNRS, IRD, UPS, Toulouse, France
| | - Saysongkham Sayavong
- Lao Department of Agriculture Land Management (DALaM), Ministry of Agriculture and Forestry, Vientiane, Lao PDR
| | - Rosalie Zimmermann
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
- Department of Medical Microbiology, Amsterdam University Medical Centers (UMC), Amsterdam, The Netherlands
| | - Bounsamay Soulileuth
- Institut de Recherche Pour le Développement (IRD), iEES-Paris, UMR 242 (IRD, SU-UPMC, CNRS, INRA, Univ. de Paris, UPEC), PO Box 5992, Vientiane, Lao PDR
| | - Anne Pando
- Institut de Recherche Pour le Développement (IRD), iEES-Paris, UMR 242 (IRD, SU-UPMC, CNRS, INRA, Univ. de Paris, UPEC), PO Box 5992, Vientiane, Lao PDR
| | - Chanthamousone Thammahacksa
- Institut de Recherche Pour le Développement (IRD), iEES-Paris, UMR 242 (IRD, SU-UPMC, CNRS, INRA, Univ. de Paris, UPEC), PO Box 5992, Vientiane, Lao PDR
| | - Emma J Rochelle-Newall
- Institute of Ecology and Environmental Sciences of Paris (iEES-Paris), Sorbonne Université, Univ Paris Est Creteil, IRD, CNRS, INRA, Paris, France
| | - William Santini
- Géosciences Environnement Toulouse (GET), Université de Toulouse, CNRS, IRD, UPS, Toulouse, France
| | - Jean-Michel Martinez
- Géosciences Environnement Toulouse (GET), Université de Toulouse, CNRS, IRD, UPS, Toulouse, France
| | - Nicolas Gratiot
- Univ. Grenoble Alpes, CNRS, IRD, Grenoble INP, IGE, 38000, Grenoble, France
- Asian Research Center on Water (CARE-Rescif), Ho Chi Minh City University of Technology, Block B7, 268 Ly Thuong Kiet Street, District 10, Ho Chi Minh City, Viet Nam
| | - Alain Pierret
- Institut de Recherche Pour le Développement (IRD), iEES-Paris, UMR 242 (IRD, SU-UPMC, CNRS, INRA, Univ. de Paris, UPEC), PO Box 5992, Vientiane, Lao PDR
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Pédron J, Guyon L, Lecomte A, Blottière L, Chandeysson C, Rochelle-Newall E, Raynaud X, Berge O, Barny MA. Comparison of Environmental and Culture-Derived Bacterial Communities through 16S Metabarcoding: A Powerful Tool to Assess Media Selectivity and Detect Rare Taxa. Microorganisms 2020; 8:microorganisms8081129. [PMID: 32727027 PMCID: PMC7464939 DOI: 10.3390/microorganisms8081129] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/16/2020] [Accepted: 07/23/2020] [Indexed: 12/19/2022] Open
Abstract
To compare environmental and culture-derived microbial communities, we performed 16S metabarcoding of uncultured samples and their culture-derived bacterial lawns. Microbial communities were obtained from freshwater river samples representative of an anthropization gradient along a river stream. Their culture-derived bacterial lawns were obtained by growing aliquots of the samples on a broad range medium and on two different semi-selective media. The V3–V4 16S rRNA region was amplified and sequenced. The bacterial diversity of water samples decreased from the upper to lower stream sampling sites and, as expected, these differences were mostly suppressed by the culture step. Overall, the diversity of cultured-derived bacterial communities reflected selectivity of each tested medium. Comparison of treatments indicated that the culture selected both detected and rare undetected environmental species. Accurate detection of rare environmental bacteria of the Pectobacterium genus by 16S metabarcoding of the culture lawn was demonstrated. Interestingly, for abundant taxa, such as those of the Pseudomonas genus, the culture/environment ratio varied between sampled sites, indicating the difficulty of comparing cultured-derived taxa abundance between environmental sites. Finally, our study also highlighted media specificity and complementarity: bacterial communities grown on the two selective media, while selecting a small set of specific species, were mostly a subset of the bacterial community observed on the broad range medium.
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Affiliation(s)
- Jacques Pédron
- INRAE, IRD, Institute of Ecology and Environmental Sciences-Paris, Sorbonne Université, IEES-Paris, F-75231 Paris, France; (J.P.); (L.G.); (A.L.); (L.B.); (E.R.-N.); (X.R.)
| | - Léa Guyon
- INRAE, IRD, Institute of Ecology and Environmental Sciences-Paris, Sorbonne Université, IEES-Paris, F-75231 Paris, France; (J.P.); (L.G.); (A.L.); (L.B.); (E.R.-N.); (X.R.)
| | - Amandine Lecomte
- INRAE, IRD, Institute of Ecology and Environmental Sciences-Paris, Sorbonne Université, IEES-Paris, F-75231 Paris, France; (J.P.); (L.G.); (A.L.); (L.B.); (E.R.-N.); (X.R.)
| | - Lydie Blottière
- INRAE, IRD, Institute of Ecology and Environmental Sciences-Paris, Sorbonne Université, IEES-Paris, F-75231 Paris, France; (J.P.); (L.G.); (A.L.); (L.B.); (E.R.-N.); (X.R.)
| | | | - Emma Rochelle-Newall
- INRAE, IRD, Institute of Ecology and Environmental Sciences-Paris, Sorbonne Université, IEES-Paris, F-75231 Paris, France; (J.P.); (L.G.); (A.L.); (L.B.); (E.R.-N.); (X.R.)
| | - Xavier Raynaud
- INRAE, IRD, Institute of Ecology and Environmental Sciences-Paris, Sorbonne Université, IEES-Paris, F-75231 Paris, France; (J.P.); (L.G.); (A.L.); (L.B.); (E.R.-N.); (X.R.)
| | - Odile Berge
- INRAE, Pathologie Végétale, F-84143 Montfavet, France; (C.C.); (O.B.)
| | - Marie-Anne Barny
- INRAE, IRD, Institute of Ecology and Environmental Sciences-Paris, Sorbonne Université, IEES-Paris, F-75231 Paris, France; (J.P.); (L.G.); (A.L.); (L.B.); (E.R.-N.); (X.R.)
- Correspondence:
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Chen L, Fang K, Dong XF, Yang AL, Li YX, Zhang HB. Characterization of the fungal community in the canopy air of the invasive plant Ageratina adenophora and its potential to cause plant diseases. PLoS One 2020; 15:e0230822. [PMID: 32214396 PMCID: PMC7098561 DOI: 10.1371/journal.pone.0230822] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 03/09/2020] [Indexed: 11/19/2022] Open
Abstract
Airborne fungi and their ecological functions have been largely ignored in plant invasions. In this study, high-throughput sequencing technology was used to characterize the airborne fungi in the canopy air of the invasive weed Ageratina adenophora. Then, representative phytopathogenic strains were isolated from A. adenophora leaf spots and their virulence to A.adenophora as well as common native plants in the invaded range was tested. The fungal alpha diversities were not different between the sampling sites or between the high/low part of the canopy air, but fungal co-occurrences were less common in the high than in the low part of the canopy air. Interestingly, we found that the phytopathogenic Didymellaceae fungi co-occurred more frequently with themselves than with other fungi. Disease experiments indicated that all 5 Didymellaceae strains could infect A. adenophora as well as the 16 tested native plants and that there was large variation in the virulence and host range. Our data suggested that the diverse pathogens in the canopy air might be a disease infection source that weakens the competition of invasive weeds, a novel phenomenon that remains to be explored in other invasive plants.
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Affiliation(s)
- Lin Chen
- School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan Province, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, Yunnan Province, China
- School of Life Sciences, Yunnan University, Kunming, Yunnan Province, China
| | - Kai Fang
- School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan Province, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, Yunnan Province, China
- School of Life Sciences, Yunnan University, Kunming, Yunnan Province, China
| | - Xing-Fan Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, Yunnan Province, China
- School of Life Sciences, Yunnan University, Kunming, Yunnan Province, China
| | - Ai-Ling Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, Yunnan Province, China
- School of Life Sciences, Yunnan University, Kunming, Yunnan Province, China
| | - Yu-Xuan Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, Yunnan Province, China
- School of Life Sciences, Yunnan University, Kunming, Yunnan Province, China
| | - Han-Bo Zhang
- School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan Province, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, Yunnan Province, China
- School of Life Sciences, Yunnan University, Kunming, Yunnan Province, China
- * E-mail:
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