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Liu M, Ye L, Chen L, Korpelainen H, Niinemets Ü, Li C. Sex-specific phosphorus acquisition strategies and cycling in dioecious Populus euphratica forests along a natural water availability gradient. PLANT, CELL & ENVIRONMENT 2024; 47:3266-3281. [PMID: 38742574 DOI: 10.1111/pce.14951] [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: 03/14/2024] [Revised: 04/29/2024] [Accepted: 05/03/2024] [Indexed: 05/16/2024]
Abstract
Soil phosphorus (P) availability affects plant growth and distribution. However, it is still unknown how sex-specific variation in functional traits affects plants' P acquisition and soil P transformation. On wet sites, female poplars had a greater specific root length (SRL), and a higher diversity of arbuscular mycorrhizal fungi (AMF) and phosphate-solubilizing bacteria (PSB). Male poplars living on wet sites increased the abundance of AMF and PSB communities and enhanced moderately labile and highly resistant organic P mineralisation via increased phosphatase activity. In contrast, on the dry site, the abundance and diversity of AMF and PSB communities increased in females, enhancing moderately labile and highly resistant organic P mineralisation via elevating phosphatase activities. Males maintained greater SRL and promoted Ca-P mobilisation via the release of root carboxylic acids and rhizosphere acidification on the dry site. The AMF community diversity followed a similar pattern as that of the PSB community when altering the P availability of different-sex plants. Our results indicated that organic P and Ca-P are the major sources of plant-available P in natural P. euphratica forests. Seasonal shifts and geographic locations affected the share of organic and inorganic P pools, and AMF and PSB diversities, ultimately altering sex-specific P acquisition strategies of plants.
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Affiliation(s)
- Miao Liu
- Department of Ecology, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Department of Landscape Architecture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Liyun Ye
- Department of Ecology, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Liangliang Chen
- Department of Ecology, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Helena Korpelainen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Ülo Niinemets
- Department of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Chunyang Li
- Department of Landscape Architecture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
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2
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Wang Z, Fu X, Kuramae EE. Insight into farming native microbiome by bioinoculant in soil-plant system. Microbiol Res 2024; 285:127776. [PMID: 38820701 DOI: 10.1016/j.micres.2024.127776] [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: 02/12/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 06/02/2024]
Abstract
Applying beneficial microorganisms (BM) as bioinoculants presents a promising soil-amendment strategy while impacting the native microbiome, which jointly alters soil-plant performance. Leveraging the untapped potential of native microbiomes alongside bioinoculants may enable farmers to sustainably regulate soil-plant systems via natural bioresources. This review synthesizes literature on native microbiome responses to BMs and their interactive effects on soil and plant performance. We highlight that native microbiomes harbor both microbial "helpers" that can improve soil fertility and plant productivity, as well as "inhibitors" that hinder these benefits. To harness the full potential of resident microbiome, it is crucial to elucidate their intricate synergistic and antagonistic interplays with introduced BMs and clarify the conditions that facilitate durable BM-microbiome synergies. Hence, we indicate current challenges in predicting these complex microbial interactions and propose corresponding strategies for microbiome breeding via BM bioinoculant. Overall, fully realizing the potential of BMs requires clarifying their interactions with native soil microbiomes and judiciously engineering microbiome to harness helpful microbes already present within agroecosystems.
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Affiliation(s)
- Zhikang Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China; Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen 6708 PB, the Netherlands
| | - Xiangxiang Fu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China.
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen 6708 PB, the Netherlands; Ecology and biodiversity, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, the Netherlands.
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3
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Kang H, Xue Y, Cui Y, Moorhead DL, Lambers H, Wang D. Nutrient limitation mediates soil microbial community structure and stability in forest restoration. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 935:173266. [PMID: 38759924 DOI: 10.1016/j.scitotenv.2024.173266] [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: 02/14/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/19/2024]
Abstract
Soil microorganisms are often limited by nutrients, representing an important control of heterotrophic metabolic processes. However, how nutrient limitations relate to microbial community structure and stability remains unclear, which creates a knowledge gap to understanding microbial biogeography and community changes during forest restoration. Here, we combined an eco-enzymatic stoichiometry model and high-throughput DNA sequencing to assess the potential roles of nutrient limitation on microbial community structure, assembly, and stability along a forest restoration sequence in the Qinling Mountains, China. Results showed that nutrient limitations tended to decrease during the oak forest restoration. Carbon and phosphorus limitations enhanced community dissimilarity and significantly increased bacterial alpha diversity, but not fungal diversity. Stochastic assembly processes primarily structured both bacterial (average contribution of 74.73 % and 74.17 % in bulk and rhizosheath soils, respectively) and fungal (average contribution of 77.23 % and 72.04 % in bulk and rhizosheath soils, respectively) communities during forest restoration, with nutrient limitation also contributing to the importance of stochastic processes in the bacterial communities. The migration rate (m) for bacteria was 0.19 and 0.23, respectively in both bulk soil and rhizosheath soil, and was greater than that for the fungi (m was 1.19 and 1.41, respectively), indicating a stronger dispersal limitation for fungal communities. Finally, nutrient limitations significantly affected bacterial and fungal co-occurrence with more interconnections occurring among weakly nutrient-limited microbial taxa and nutrient limitations reducing community stability when nutrient availability changed during forest restoration. Our findings highlight the fundamental effects of nutrient limitations on microbial communities and their self-regulation under changing environmental resources.
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Affiliation(s)
- Haibin Kang
- College of Forestry, Northwest Agriculture & Forestry University, Yangling 712100, China; School of Biological Sciences, The University of Western Australia, Perth 6009, Australia
| | - Yue Xue
- School of Geography and Oceanography, Nanjing University, Nanjing 210023, China
| | - Yongxing Cui
- Institute of Biology, Freie Universität Berlin, Berlin 14195, Germany
| | - Daryl L Moorhead
- Department of Environmental Sciences, University of Toledo, Toledo 43606, USA
| | - Hans Lambers
- School of Biological Sciences, The University of Western Australia, Perth 6009, Australia
| | - Dexiang Wang
- College of Forestry, Northwest Agriculture & Forestry University, Yangling 712100, China.
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Tang S, Gong J, Song B, Li J, Cao W, Zhao J. Co-influence of biochar-supported effective microorganisms and seasonal changes on dissolved organic matter and microbial activity in eutrophic lake. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 923:171476. [PMID: 38458471 DOI: 10.1016/j.scitotenv.2024.171476] [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: 11/11/2023] [Revised: 02/27/2024] [Accepted: 03/03/2024] [Indexed: 03/10/2024]
Abstract
DOM (dissolved organic matter) play a crucial role in lakes' geochemical and carbon cycles. Eutrophication evolution would influence nutrient status of waters and investigating the DOM variation helps a better understanding of bioremediation on environmental behavior of DOM in eutrophic lakes. In our study, the contents, compositions and characteristics of systematic DOM&SOM (sediment organic matter) were greatly influenced by seasonal changes. But the effective bioremediations obviously reduced the DOM concentration and thus mitigated the eutrophication outbreak risks in water bodies due to the increased MBC (microbial biomass carbon), microbial activity and metabolism. In early summer, the overall DOM in each treatment were readily low levels and derived from both autochthonous and exogenous origins, dominated by fulvic acid-like. In midsummer, the DOM contents and characteristics in each treatment increased significantly as phytoplankton activity improved, and the majority of DOM were humic acid-like and mainly of biological origin. The greatest differences of enzymes, MBC, microbial metabolism and DOM&SOM removal among different treatments were observed in summer months. In autumn, the systematic DOM&SOM slightly reduced due to the deceased microbial activity, in which the microbial humic acids were main component and derived from endogenous sources. Additionally, the gradually decreased SOM with cultivated time in each treatment was a result of microbiological conversion of SOM into DOM. For various treatments, BE, BE.A, BE.C and BE.E increased the MBC, enzymatic and microbial activities due to the application of biochar-supported EMs. Among these, BE and BE.A, especially BE.A with oxygen supplement, achieved the most desirable effect on reducing systematic DOM&SOM levels and increasing enzymatic and microbial activities. The group of EM also reduced the levels of DOM&SOM as improved degradation of EMs for DOM. However, BC, BE.C and BE.E finally did not achieved the desirable effect on reducing DOM&SOM due to the suppression of microbial activities, respectively, from high dose of biochar, weakening of dominant species and additional introduction of EMs in low liveness.
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Affiliation(s)
- Siqun Tang
- College of Environmental Science and Engineering, Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China; Greater Bay Area Institute for Innovation, Hunan University, Guangzhou 511300, Guangdong Province, PR China; Shenzhen Institute, Hunan University, Shenzhen 518000, PR China
| | - Jilai Gong
- College of Environmental Science and Engineering, Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China; Greater Bay Area Institute for Innovation, Hunan University, Guangzhou 511300, Guangdong Province, PR China; Shenzhen Institute, Hunan University, Shenzhen 518000, PR China.
| | - Biao Song
- College of Environmental Science and Engineering, Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China; Greater Bay Area Institute for Innovation, Hunan University, Guangzhou 511300, Guangdong Province, PR China; Shenzhen Institute, Hunan University, Shenzhen 518000, PR China
| | - Juan Li
- College of Environmental Science and Engineering, Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China; Greater Bay Area Institute for Innovation, Hunan University, Guangzhou 511300, Guangdong Province, PR China; Shenzhen Institute, Hunan University, Shenzhen 518000, PR China
| | - Weicheng Cao
- College of Environmental Science and Engineering, Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China; Greater Bay Area Institute for Innovation, Hunan University, Guangzhou 511300, Guangdong Province, PR China; Shenzhen Institute, Hunan University, Shenzhen 518000, PR China
| | - Jun Zhao
- College of Environmental Science and Engineering, Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, PR China; Greater Bay Area Institute for Innovation, Hunan University, Guangzhou 511300, Guangdong Province, PR China; Shenzhen Institute, Hunan University, Shenzhen 518000, PR China
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5
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Wei Z, Zhao L, Wang S, Chang L, Shi J, Kong X, Li M, Lin J, Zhang W, Bao Z, Ding W, Hu X. Paralytic shellfish toxins producing dinoflagellates cause dysbacteriosis in scallop gut microbial biofilms. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 273:116146. [PMID: 38412634 DOI: 10.1016/j.ecoenv.2024.116146] [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: 11/16/2023] [Revised: 02/05/2024] [Accepted: 02/22/2024] [Indexed: 02/29/2024]
Abstract
Filter-feeding bivalves could accumulate paralytic shellfish toxins (PSTs) produced by harmful dinoflagellates through diet. Despite that bivalves are resistant to these neurotoxins due to possessing PST-resistant sodium channel, exposure to PSTs-producing dinoflagellates impair bivalve survival. We hypothesized that ingesting PSTs-producing dinoflagellates may influence the gut microbiota, and then the health of bivalves. To test this idea, we compared the gut microbiota of the scallop Patinopecten yessoensis, after feeding with PST-producing or non-toxic dinoflagellates. Exposure to PSTs-producing dinoflagellates resulted in a decline of gut microbial diversity and a disturbance of community structure, accompanied by a significant increase in the abundance and richness of pathogenic bacteria, represented by Vibrio. Moreover, network analysis demonstrated extensive positive correlations between pathogenic bacteria abundances and PSTs concentrations in the digestive glands of the scallops. Furthermore, isolation of a dominant Vibrio strain and its genomic analysis revealed a variety of virulence factors, including the tolC outer membrane exporter, which were expressed in the gut microbiota. Finally, the infection experiment demonstrated scallop mortality caused by the isolated Vibrio strain; further, the pathogenicity of this Vibrio strain was attenuated by a mutation in the tolC gene. Together, these findings demonstrated that the PSTs may affect gut microbiota via direct and taxa-specific interactions with opportunistic pathogens, which proliferate after transition from seawater to the gut environment. The present study has revealed novel mechanisms towards deciphering the puzzles in environmental disturbances-caused death of an important aquaculture species.
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Affiliation(s)
- Zhongcheng Wei
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Liang Zhao
- Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, China
| | - Shuaitao Wang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Lirong Chang
- Weihai Changqing Ocean Science & Technology Co. Ltd, Rongcheng, China
| | - Jiaoxia Shi
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Xiangfu Kong
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Moli Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Jinshui Lin
- Shaanxi Key Laboratory of Chinese Jujube, College of Life Sciences, Yanan University, Yanan, China
| | - Weipeng Zhang
- Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Wei Ding
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China.
| | - Xiaoli Hu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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6
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Kumar V, Roy S, Parida SN, Bisai K, Dhar S, Jana AK, Das BK. Deciphering the impact of endoparasitic infection on immune response and gut microbial composition of Channa punctata. Front Cell Infect Microbiol 2024; 14:1296769. [PMID: 38476164 PMCID: PMC10927727 DOI: 10.3389/fcimb.2024.1296769] [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: 09/19/2023] [Accepted: 01/19/2024] [Indexed: 03/14/2024] Open
Abstract
Intestinal parasitic infections caused by helminths are globally distributed and are a major cause of morbidity worldwide. Parasites may modulate the virulence, gut microbiota diversity and host responses during infection. Despite numerous works, little is known about the complex interaction between parasites and the gut microbiota. In the present study, the complex interplay between parasites and the gut microbiota was investigated. A total of 12 bacterial strains across four major families, including Enterobacteriaceae, Morganellaceae, Flavobacteriaceae, and Pseudomonadaceae, were isolated from Channa punctata, infected with the nematode species Aporcella sp., Axonchium sp., Tylencholaimus mirabilis, and Dioctophyme renale. The findings revealed that nematode infection shaped the fish gut bacterial microbiota and significantly affected their virulence levels. Nematode-infected fish bacterial isolates are more likely to be pathogenic, with elevated hemolytic activity and biofilm formation, causing high fish mortality. In contrast, isolates recovered further from non-parasitised C. punctata were observed to be non-pathogenic and had negligible hemolytic activity and biofilm formation. Antibiogram analysis of the bacterial isolates revealed a disproportionately high percentage of bacteria that were either marginally or multidrug resistant, suggesting that parasitic infection-induced stress modulates the gut microenvironment and enables colonization by antibiotic-resistant strains. This isolation-based study provides an avenue to unravel the influence of parasitic infection on gut bacterial characteristics, which is valuable for understanding the infection mechanism and designing further studies aimed at optimizing treatment strategies. In addition, the cultured isolates can supplement future gut microbiome studies by providing wet lab specimens to compare (meta)genomic information discovered within the gut microenvironment of fish.
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Affiliation(s)
| | | | | | | | | | | | - Basanta Kumar Das
- Aquatic Environmental Biotechnology and Nanotechnology (AEBN) Division, Indian Council of Agricultural Research (ICAR)-Central Inland Fisheries Research Institute (CIFRI), Barrackpore, India
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7
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Gao N, Shu Y, Wang Y, Sun M, Wei Z, Song C, Zhang W, Sun Y, Hu X, Bao Z, Ding W. Acute Ammonia Causes Pathogenic Dysbiosis of Shrimp Gut Biofilms. Int J Mol Sci 2024; 25:2614. [PMID: 38473861 DOI: 10.3390/ijms25052614] [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: 01/17/2024] [Revised: 02/08/2024] [Accepted: 02/12/2024] [Indexed: 03/14/2024] Open
Abstract
Acute ammonia exposure has detrimental effects on shrimp, but the underlying mechanisms remain to be fully explored. In the present study, we investigated the impact of acute ammonia exposure on the gut microbiota of the white shrimp Litopenaeus vannamei and its association with shrimp mortality. Exposure to a lethal concentration of ammonia for 48 h resulted in increased mortality in L. vannamei, with severe damage to the hepatopancreas. Ammonia exposure led to a significant decrease in gut microbial diversity, along with the loss of beneficial bacterial taxa and the proliferation of pathogenic Vibrio strains. A phenotypic analysis revealed a transition from the dominance of aerobic to facultative anaerobic strains due to ammonia exposure. A functional analysis revealed that ammonia exposure led to an enrichment of genes related to biofilm formation, host colonization, and virulence pathogenicity. A species-level analysis and experiments suggest the key role of a Vibrio harveyi strain in causing shrimp disease and specificity under distinct environments. These findings provide new information on the mechanism of shrimp disease under environmental changes.
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Affiliation(s)
- Ning Gao
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
- Southern Marine Science and Engineer Guangdong Laboratory, Guangzhou 511458, China
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266003, China
| | - Yi Shu
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
- Southern Marine Science and Engineer Guangdong Laboratory, Guangzhou 511458, China
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266003, China
| | - Yongming Wang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
- Southern Marine Science and Engineer Guangdong Laboratory, Guangzhou 511458, China
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266003, China
| | - Meng Sun
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Zhongcheng Wei
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266003, China
| | - Chenxi Song
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266003, China
| | - Weipeng Zhang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Yue Sun
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266003, China
| | - Xiaoli Hu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266003, China
| | - Zhenmin Bao
- Southern Marine Science and Engineer Guangdong Laboratory, Guangzhou 511458, China
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266003, China
| | - Wei Ding
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266003, China
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Yang M, Zhao L, Yu X, Shu W, Cao F, Liu Q, Liu M, Wang J, Jiang Y. Microbial community structure and co-occurrence network stability in seawater and microplastic biofilms under prometryn pollution in marine ecosystems. MARINE POLLUTION BULLETIN 2024; 199:115960. [PMID: 38159383 DOI: 10.1016/j.marpolbul.2023.115960] [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: 10/06/2023] [Revised: 11/20/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024]
Abstract
Prometryn has been extensively detected in marine environment because of its widespread usage in agriculture and aquaculture and has been concerns since its serious effects on aquatic organisms. However, its impact on the microbial community in the marine ecosystem including seawater and biofilm is still unclear. Therefore, a short-term indoor microcosm experiment of prometryn exposure was conducted. This study found that prometryn had a more significant impact on the structure and stability of the microbial community in seawater compared to microplastic biofilms. Additionally, we observed that the assembly of the microbial community in biofilms was more affected by stochastic processes than in seawater under the exposure of prometryn. Our study provided evidence for the increasing impact of the microbial communities under the stress of prometryn and microplastics.
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Affiliation(s)
- Mengyao Yang
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Lingchao Zhao
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Xiaowen Yu
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Wangxinze Shu
- Fisheries College, Ocean University of China, Qingdao 266003, China
| | - Furong Cao
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Qian Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Mingjian Liu
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; MoE Key Laboratory of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Jun Wang
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Yong Jiang
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; MoE Key Laboratory of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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9
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He X, Xiao X, Wei W, Li L, Zhao Y, Zhang N, Wang M. Soil rare microorganisms mediated the plant cadmium uptake: The central role of protists. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168505. [PMID: 37967623 DOI: 10.1016/j.scitotenv.2023.168505] [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: 08/22/2023] [Revised: 10/25/2023] [Accepted: 11/09/2023] [Indexed: 11/17/2023]
Abstract
Plants and microorganisms symbiotically mediate and/or catalyse the turnover of elements in rhizosphere soils, thus directly influencing the effectiveness of phytoremediation in addressing heavy metal contamination. Soil rare microbial communities are diverse but not well understood in terms of their importance for phytoremediation. In this study, we simulated the loss of rare microorganisms through dilution-to-extinction approach, and investigated the effects on integrated rhizosphere microbiome with soil microcosm experiments, including bacteria, fungi, protists, and microfauna. Additionally, we explored the implications for ryegrass (Lolium multiflorum Lam.) growth and its uptake of Cd (cadmium). Compared with the undiluted group, ryegrass exhibited a significant decrease in Cd uptake ranging from 52.34 % to 73.71 % in the rare species-loss soils, indicating a lack of functional redundancy in rhizosphere soil microbial community following rare species loss. Interestingly, these soils displayed a remarkable 1.79-fold increase in plant biomass and a 41.02 % increase in plant height. By sequencing the 16S, 18S, and ITS rRNA gene amplicons of rhizosphere microbes, we found that soil rare species loss decreased the rhizosphere microbial α-diversity, changed the community structures, and shifted the functional potential. Protists were particularly affected. Through the analysis of species co-occurrence networks, along with the partial least squares path modeling, we found that the diversity of protists and bacteria and the co-occurring network connectivity of protists and fungi contributed most to plant Cd uptake and growth. These results highlighted the potential significance of rare microorganisms, particularly protists, in phytoextraction of Cd-contaminated soils, owing to their central role in the microbial food web.
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Affiliation(s)
- Xingguo He
- School of Environmental Science and Engineering, Changzhou University, Changzhou 213164, China
| | - Xian Xiao
- School of Environmental Science and Engineering, Changzhou University, Changzhou 213164, China.
| | - Weiwei Wei
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Environmental Protection Key Laboratory for Lake Pollution Control, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Liangzhong Li
- Chongqing Huanyue Ecological Environment Technology Co., Ltd., Chongqing 400000, China
| | - Yuan Zhao
- School of Environmental Science and Engineering, Changzhou University, Changzhou 213164, China
| | - Na Zhang
- Hunan Soil and Fertilizer Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Mingyu Wang
- School of Environmental Science and Engineering, Changzhou University, Changzhou 213164, China
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10
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Christel A, Chemidlin Prevost-Bouré N, Dequiedt S, Saby N, Mercier F, Tripied J, Comment G, Villerd J, Djemiel C, Hermant A, Blondon M, Bargeot L, Matagne E, Horrigue W, Maron PA, Ranjard L. Differential responses of soil microbial biomass, diversity and interactions to land use intensity at a territorial scale. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167454. [PMID: 37783435 DOI: 10.1016/j.scitotenv.2023.167454] [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: 07/20/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 10/04/2023]
Abstract
Impact of land use intensification on soil microbial communities across a territory remains poorly documented. Yet, it has to be deciphered to validate the results obtained at local and global scales by integrating the variations of environmental conditions and agricultural systems at a territorial scale. We investigated the impact of different land uses (from forest to agricultural systems) and associated soil management practices on soil molecular microbial biomass and diversity across a territory of 3300 km2 in Burgundy (France). Microbial biomass and diversity were determined by quantifying and high-throughput sequencing of soil DNA from 300 soils, respectively. Geostatistics were applied to map the soil macro-ecological patterns and variance partitioning analysis was used to rank the influence of soil physicochemical characteristics, land uses and associated practices on soil microbial communities. Geographical patterns differed between microbial biomass and diversity, emphasizing that distinct environmental drivers shaped these parameters. Soil microbial biomass was mainly driven by the soil organic carbon content and was significantly altered by agricultural land uses, with a loss of about 71 % from natural to agricultural ecosystems. The best predictors of bacterial and fungal richness were soil texture and pH, respectively. Microbial diversity was less sensitive than microbial biomass to land use intensification, and fungal richness appeared more impacted than bacteria. Co-occurrence network analysis of the interactions among microbial communities showed a decline of about 95 % of network complexity with land use intensification, which counterbalanced the weak response of microbial diversity. Grouping of the 147 cropland plots in four clusters according to their agricultural practices confirmed that microbial parameters exhibited different responses to soil management intensification, especially soil tillage and crop protection. Our results altogether allow evaluating the different levels of microbial parameters' vulnerability to land use intensity at a territorial scale.
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Affiliation(s)
- A Christel
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France; AgroParisTech, 75732 Paris, France
| | | | - S Dequiedt
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - N Saby
- INRAE, US1106 Info&Sols, F-45075 Orleans, France
| | - F Mercier
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France; Dijon Céréales, Alliance BFC, 4 Boulevard de Beauregard, 21600 Longvic, France
| | - J Tripied
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - G Comment
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - J Villerd
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - C Djemiel
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - A Hermant
- Chambre d'agriculture de Côte d'Or, 1 rue des Coulots, 21110 Bretenière, France
| | - M Blondon
- Dijon Céréales, Alliance BFC, 4 Boulevard de Beauregard, 21600 Longvic, France
| | - L Bargeot
- AGARIC-IG, 144 Rue Rambuteau, 71000 Macon, France
| | - E Matagne
- AGARIC-IG, 144 Rue Rambuteau, 71000 Macon, France
| | - W Horrigue
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - P A Maron
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - L Ranjard
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France.
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11
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Erhunmwunse AS, Guerra VA, Liu JC, Mackowiak CL, Blount ARS, Dubeux JCB, Liao HL. Soil Bacterial Diversity Responds to Long-Term Establishment of Perennial Legumes in Warm-Season Grassland at Two Soil Depths. Microorganisms 2023; 11:3002. [PMID: 38138146 PMCID: PMC10745480 DOI: 10.3390/microorganisms11123002] [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: 10/31/2023] [Revised: 11/24/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
The introduction of rhizoma peanut (RP Arachis glabrata Benth) into bahiagrass (Paspalum notatum Flüggé) may require time to develop stable plant-soil microbe interactions as the microbial legacy of the previous plant community may be long-lasting. A previous study showed that <2 years of introducing rhizoma peanut into bahiagrass pastures minimally affected soil bacterial diversity and community composition. In this study, we compared the effects of the long-term inclusion of rhizoma peanut (>8 years) into bahiagrass on soil bacterial diversity and community composition against their monocultures at 0 to 15 and 15 to 30 cm soil depths using next-generation sequencing to target bacterial 16S V3-V4 regions. We observed that a well-established RP-bahiagrass mixed stand led to a 36% increase in bacterial alpha diversity compared to the bahiagrass monoculture. There was a shift from a soil bacterial community dominated by Proteobacteria (~26%) reported in other bahiagrass and rhizoma peanut studies to a soil bacterial community dominated by Firmicutes (39%) in our study. The relative abundance of the bacterial genus Crossiella, known for its antimicrobial traits, was enhanced in the presence of RP. Differences in soil bacterial diversity and community composition were substantial between 0 to 15 and 15 to 30 cm soil layers, with N2-fixing bacteria belonging to the phylum Proteobacteria concentrated in 0 to 15 cm. Introducing RP into bahiagrass pastures is a highly sustainable alternative to mineral N fertilizer inputs. Our results provide evidence that this system also promotes greater soil microbial diversity and is associated with unique taxa that require further study to better understand their contributions to healthy pastures.
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Affiliation(s)
- Adesuwa Sylvia Erhunmwunse
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL 32351, USA (H.-L.L.)
- Soil, Water and Ecosystem Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Victor Alonso Guerra
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL 32351, USA (H.-L.L.)
- Soil, Water and Ecosystem Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Jung-Chen Liu
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL 32351, USA (H.-L.L.)
- Soil, Water and Ecosystem Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Cheryl L. Mackowiak
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL 32351, USA (H.-L.L.)
- Soil, Water and Ecosystem Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Ann Rachel Soffes Blount
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL 32351, USA (H.-L.L.)
| | - José Carlos Batista Dubeux
- North Florida Research and Education Center, University of Florida, 3925 Highway 71, Marianna, FL 32446, USA;
| | - Hui-Ling Liao
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL 32351, USA (H.-L.L.)
- Soil, Water and Ecosystem Sciences Department, University of Florida, Gainesville, FL 32611, USA
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12
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Cao L, Garcia SL, Wurzbacher C. Establishment of microbial model communities capable of removing trace organic chemicals for biotransformation mechanisms research. Microb Cell Fact 2023; 22:245. [PMID: 38042813 PMCID: PMC10693053 DOI: 10.1186/s12934-023-02252-6] [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: 07/31/2023] [Accepted: 11/16/2023] [Indexed: 12/04/2023] Open
Abstract
BACKGROUND Removal of trace organic chemicals (TOrCs) in aquatic environments has been intensively studied. Some members of natural microbial communities play a vital role in transforming chemical contaminants, however, complex microbial interactions impede us from gaining adequate understanding of TOrC biotransformation mechanisms. To simplify, in this study, we propose a strategy of establishing reduced-richness model communities capable of removing diverse TOrCs via pre-adaptation and dilution-to-extinction. RESULTS Microbial communities were adapted from tap water, soil, sand, sediment deep and sediment surface to changing concentrations of 27 TOrCs mixture. After adaptation, the communities were further diluted to reduce diversity into 96 deep well plates for high-throughput cultivation. After characterizing microbial structure and TOrC removal performance, thirty taxonomically non-redundant model communities with different removal abilities were obtained. The pre-adaptation process was found to reduce the microbial richness but to increase the evenness and phylogenetic diversity of resulting model communities. Moreover, phylogenetic diversity showed a positive effect on the number of TOrCs that can be transformed simultaneously. Pre-adaptation also improved the overall TOrC removal rates, which was found to be positively correlated with the growth rates of model communities. CONCLUSIONS This is the first study that investigated a wide range of TOrC biotransformation based on different model communities derived from varying natural microbial systems. This study provides a standardized workflow of establishing model communities for different metabolic purposes with changeable inoculum and substrates. The obtained model communities can be further used to find the driving agents of TOrC biotransformation at the enzyme/gene level.
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Affiliation(s)
- Lijia Cao
- Chair of Urban Water Systems Engineering, Technical University of Munich, Garching, Germany
| | - Sarahi L Garcia
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
- Institute for Chemistry and Biology of the Marine environment (ICBM), University of Oldenburg, Oldenburg, Germany
| | - Christian Wurzbacher
- Chair of Urban Water Systems Engineering, Technical University of Munich, Garching, Germany.
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13
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Deshoux M, Sadet-Bourgeteau S, Gentil S, Prévost-Bouré NC. Effects of biochar on soil microbial communities: A meta-analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 902:166079. [PMID: 37553053 DOI: 10.1016/j.scitotenv.2023.166079] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/10/2023]
Abstract
Changes in soil microbial communities may impact soil fertility and stability because microbial communities are key to soil functioning by supporting soil ecological quality and agricultural production. The effects of soil amendment with biochar on soil microbial communities are widely documented but studies highlighted a high degree of variability in their responses following biochar application. The multiple conditions under which they were conducted (experimental designs, application rates, soil types, biochar properties) make it difficult to identify general trends. This supports the need to better determine the conditions of biochar production and application that promote soil microbial communities. In this context, we performed the first ever meta-analysis of the biochar effects on soil microbial biomass and diversity (prokaryotes and fungi) based on high-throughput sequencing data. The majority of the 181 selected publications were conducted in China and evaluated the short-term impact (<3 months) of biochar. We demonstrated that a large panel of variables corresponding to biochar properties, soil characteristics, farming practices or experimental conditions, can affect the effects of biochar on soil microbial characteristics. Using a variance partitioning approach, we showed that responses of soil microbial biomass and prokaryotic diversity were highly dependent on biochar properties. They were influenced by pyrolysis temperature, biochar pH, application rate and feedstock type, as wood-derived biochars have particular physico-chemical properties (high C:N ratio, low nutrient content, large pores size) compared to non-wood-derived biochars. Fungal community data was more heterogenous and scarcer than prokaryote data (30 publications). Fungal diversity indices were rather dependent on soil properties: they were higher in medium-textured soils, with low pH but high soil organic carbon. Altogether, this meta-analysis illustrates the need for long-term field studies in European agricultural context for documenting responses of soil microbial communities to biochar application under diverse conditions combining biochar types, soil properties and conditions of use.
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Affiliation(s)
- Maëlle Deshoux
- INRAE UMR Agroécologie, Institut Agro, University Bourgogne, University Bourgogne Franche-Comté, F-21000 Dijon, France; Groupe Bordet, Froidvent, F-21290 Leuglay, France.
| | - Sophie Sadet-Bourgeteau
- INRAE UMR Agroécologie, Institut Agro, University Bourgogne, University Bourgogne Franche-Comté, F-21000 Dijon, France
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14
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Roth SW, Griffiths NA, Kolka RK, Oleheiser KC, Carrell AA, Klingeman DM, Seibert A, Chanton JP, Hanson PJ, Schadt CW. Elevated temperature alters microbial communities, but not decomposition rates, during 3 years of in situ peat decomposition. mSystems 2023; 8:e0033723. [PMID: 37819069 PMCID: PMC10654087 DOI: 10.1128/msystems.00337-23] [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: 04/10/2023] [Accepted: 08/29/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE Microbial community changes in response to climate change drivers have the potential to alter the trajectory of important ecosystem functions. In this paper, we show that while microbial communities in peatland systems responded to manipulations of temperature and CO2 concentrations, these changes were not associated with similar responses in peat decomposition rates over 3 years. It is unclear however from our current studies whether this functional resiliency over 3 years will continue over the longer time scales relevant to peatland ecosystem functions.
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Affiliation(s)
- Spencer W. Roth
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Natalie A. Griffiths
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Randall K. Kolka
- Northern Research Station, USDA Forest Service, Grand Rapids, Minnesota, USA
| | - Keith C. Oleheiser
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Alyssa A. Carrell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Dawn M. Klingeman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Angela Seibert
- Department of Geosciences, Boise State University, Boise, Idaho, USA
| | - Jeffrey P. Chanton
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, Florida, USA
| | - Paul J. Hanson
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Christopher W. Schadt
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
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15
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Tibihenda C, Zhong H, Liu K, Dai J, Lin X, Motelica-Heino M, Hou S, Zhang M, Lu Y, Xiao L, Zhang C. Ecologically different earthworm species are the driving force of microbial hotspots influencing Pb uptake by the leafy vegetable Brassica campestris. Front Microbiol 2023; 14:1240707. [PMID: 37860140 PMCID: PMC10582336 DOI: 10.3389/fmicb.2023.1240707] [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: 06/20/2023] [Accepted: 09/11/2023] [Indexed: 10/21/2023] Open
Abstract
Food chain contamination by soil lead (Pb), beginning with Pb uptake by leafy vegetables, is a threat to food safety and poses a potential risk to human health. This study highlights the importance of two ecologically different earthworm species (the anecic species Amynthas aspergillum and the epigeic species Eisenia fetida) as the driving force of microbial hotspots to enhance Pb accumulation in the leafy vegetable Brassica campestris at different Pb contamination levels (0, 100, 500, and 1,000 mg·kg-1). The fingerprints of phospholipid fatty acids (PLFAs) were employed to reveal the microbial mechanism of Pb accumulation involving earthworm-plant interaction, as PLFAs provide a general profile of soil microbial biomass and community structure. The results showed that Gram-positive (G+) bacteria dominated the microbial community. At 0 mg·kg-1 Pb, the presence of earthworms significantly reduced the total PLFAs. The maximum total of PLFAs was found at 100 mg·kg-1 Pb with E. fetida inoculation. A significant shift in the bacterial community was observed in the treatments with E. fetida inoculation at 500 and 1,000 mg·kg-1 Pb, where the G+/G- bacteria ratio was significantly decreased compared to no earthworm inoculation. Principal component analysis (PCA) showed that E. fetida had a greater effect on soil microbial hotspots than A. aspergillum, thus having a greater effect on the Pb uptake by B. campestris. Redundancy analysis (RDA) showed that soil microbial biomass and structure explained 43.0% (R2 = 0.53) of the total variation in Pb uptake by B. campestris, compared to 9.51% of microbial activity. G- bacteria explained 23.2% of the total variation in the Pb uptake by B. campestris, significantly higher than the other microbes. The Mantel test showed that microbial properties significantly influenced Pb uptake by B. campestris under the driving force of earthworms. E. fetida inoculation was favorable for the G- bacterial community, whereas A. aspergillum inoculation was favorable for the fungal community. Both microbial communities facilitated the entry of Pb into the vegetable food chain system. This study delivers novel evidence and meaningful insights into how earthworms prime the microbial mechanism of Pb uptake by leafy vegetables by influencing soil microbial biomass and community composition. Comprehensive metagenomics analysis can be employed in future studies to identify the microbial strains promoting Pb migration and develop effective strategies to mitigate Pb contamination in food chains.
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Affiliation(s)
- Cevin Tibihenda
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Tanzania Agricultural Research Institute, Dodoma, Tanzania
| | - Hesen Zhong
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Kexue Liu
- School of Resources and Planning, Guangzhou Xinhua University, Guangzhou, China
| | - Jun Dai
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Xiaoqin Lin
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | | | - Shuyu Hou
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Menghao Zhang
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Ying Lu
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Ling Xiao
- Department of Civil and Environmental Engineering, Shantou University, Shantou, China
| | - Chi Zhang
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
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16
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Hellal J, Barthelmebs L, Bérard A, Cébron A, Cheloni G, Colas S, Cravo-Laureau C, De Clerck C, Gallois N, Hery M, Martin-Laurent F, Martins J, Morin S, Palacios C, Pesce S, Richaume A, Vuilleumier S. Unlocking secrets of microbial ecotoxicology: recent achievements and future challenges. FEMS Microbiol Ecol 2023; 99:fiad102. [PMID: 37669892 PMCID: PMC10516372 DOI: 10.1093/femsec/fiad102] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/21/2023] [Accepted: 09/04/2023] [Indexed: 09/07/2023] Open
Abstract
Environmental pollution is one of the main challenges faced by humanity. By their ubiquity and vast range of metabolic capabilities, microorganisms are affected by pollution with consequences on their host organisms and on the functioning of their environment. They also play key roles in the fate of pollutants through the degradation, transformation, and transfer of organic or inorganic compounds. Thus, they are crucial for the development of nature-based solutions to reduce pollution and of bio-based solutions for environmental risk assessment of chemicals. At the intersection between microbial ecology, toxicology, and biogeochemistry, microbial ecotoxicology is a fast-expanding research area aiming to decipher the interactions between pollutants and microorganisms. This perspective paper gives an overview of the main research challenges identified by the Ecotoxicomic network within the emerging One Health framework and in the light of ongoing interest in biological approaches to environmental remediation and of the current state of the art in microbial ecology. We highlight prevailing knowledge gaps and pitfalls in exploring complex interactions among microorganisms and their environment in the context of chemical pollution and pinpoint areas of research where future efforts are needed.
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Affiliation(s)
| | - Lise Barthelmebs
- Université de Perpignan Via Domitia, Biocapteurs – Analyse-Environnement, Perpignan, France
- Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Annette Bérard
- UMR EMMAH INRAE/AU – équipe SWIFT, 228, route de l'Aérodrome, 84914 Avignon Cedex 9, France
| | | | - Giulia Cheloni
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Sète, France
| | - Simon Colas
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | | | - Caroline De Clerck
- AgricultureIsLife, Gembloux Agro-Bio Tech (Liege University), Passage des Déportés 2, 5030 Gembloux, Belgium
| | | | - Marina Hery
- HydroSciences Montpellier, Université de Montpellier, CNRS, IRD, Montpellier, France
| | - Fabrice Martin-Laurent
- Institut Agro Dijon, INRAE, Université de Bourgogne, Université de Bourgogne Franche-Comté, Agroécologie, 21065 Dijon, France
| | - Jean Martins
- IGE, UMR 5001, Université Grenoble Alpes, CNRS, G-INP, INRAE, IRD Grenoble, France
| | | | - Carmen Palacios
- Université de Perpignan Via Domitia, CEFREM, F-66860 Perpignan, France
- CNRS, CEFREM, UMR5110, F-66860 Perpignan, France
| | | | - Agnès Richaume
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5557, Ecologie Microbienne, Villeurbanne, France
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17
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Osburn ED, Yang G, Rillig MC, Strickland MS. Evaluating the role of bacterial diversity in supporting soil ecosystem functions under anthropogenic stress. ISME COMMUNICATIONS 2023; 3:66. [PMID: 37400524 PMCID: PMC10318037 DOI: 10.1038/s43705-023-00273-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/14/2023] [Accepted: 06/19/2023] [Indexed: 07/05/2023]
Abstract
Ecosystem functions and services are under threat from anthropogenic global change at a planetary scale. Microorganisms are the dominant drivers of nearly all ecosystem functions and therefore ecosystem-scale responses are dependent on responses of resident microbial communities. However, the specific characteristics of microbial communities that contribute to ecosystem stability under anthropogenic stress are unknown. We evaluated bacterial drivers of ecosystem stability by generating wide experimental gradients of bacterial diversity in soils, applying stress to the soils, and measuring responses of several microbial-mediated ecosystem processes, including C and N cycling rates and soil enzyme activities. Some processes (e.g., C mineralization) exhibited positive correlations with bacterial diversity and losses of diversity resulted in reduced stability of nearly all processes. However, comprehensive evaluation of all potential bacterial drivers of the processes revealed that bacterial α diversity per se was never among the most important predictors of ecosystem functions. Instead, key predictors included total microbial biomass, 16S gene abundance, bacterial ASV membership, and abundances of specific prokaryotic taxa and functional groups (e.g., nitrifying taxa). These results suggest that bacterial α diversity may be a useful indicator of soil ecosystem function and stability, but that other characteristics of bacterial communities are stronger statistical predictors of ecosystem function and better reflect the biological mechanisms by which microbial communities influence ecosystems. Overall, our results provide insight into the role of microorganisms in supporting ecosystem function and stability by identifying specific characteristics of bacterial communities that are critical for understanding and predicting ecosystem responses to global change.
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Affiliation(s)
- Ernest D Osburn
- Department of Soil and Water Systems, University of Idaho, Moscow, ID, USA.
| | - Gaowen Yang
- College of Grassland Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Matthias C Rillig
- Institute of Biology, Freie Universität Berlin, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195, Berlin, Germany
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18
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Ma X, Ren B, Yu J, Wang J, Bai L, Li J, Li D, Meng M. Changes in grassland soil types lead to different characteristics of bacterial and fungal communities in Northwest Liaoning, China. Front Microbiol 2023; 14:1205574. [PMID: 37448571 PMCID: PMC10336218 DOI: 10.3389/fmicb.2023.1205574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/09/2023] [Indexed: 07/15/2023] Open
Abstract
Introduction Soil microbial communities are critical in regulating grassland biogeochemical cycles and ecosystem functions, but the mechanisms of how environmental factors affect changes in the structural composition and diversity of soil microbial communities in different grassland soil types is not fully understood in northwest Liaoning, China. Methods We investigated the characteristics and drivers of bacterial and fungal communities in 4 grassland soil types with 11 sites across this region using high-throughput Illumina sequencing. Results and Discussion Actinobacteria and Ascomycota were the dominant phyla of bacterial and fungal communities, respectively, but their relative abundances were not significantly different among different grassland soil types. The abundance, number of OTUs, number of species and diversity of both bacterial and fungal communities in warm and temperate ecotone soil were the highest, while the warm-temperate shrub soil had the lowest microbial diversity. Besides, environmental factors were not significantly correlated with soil bacterial Alpha diversity index. However, there was a highly significant negative correlation between soil pH and Shannon index of fungal communities, and a highly significant positive correlation between plant cover and Chao1 index as well as Observed species of fungal communities. Analysis of similarities showed that the structural composition of microbial communities differed significantly among different grassland soil types. Meanwhile, the microbial community structure of temperate steppe-sandy soil was significantly different from that of other grassland soil types. Redundancy analysis revealed that soil total nitrogen content, pH and conductivity were important influencing factors causing changes in soil bacterial communities, while soil organic carbon, total nitrogen content and conductivity mainly drove the differentiation of soil fungal communities. In addition, the degree of connection in the soil bacterial network of grassland was much higher than that in the fungal network and soil bacterial and fungal communities were inconsistently limited by environmental factors. Our results showed that the microbial community structure, composition and diversity of different grassland soil types in northwest Liaoning differed significantly and were significantly influenced by environmental factors. Microbial community structure and the observation of soil total nitrogen and organic carbon content can predict the health changes of grassland ecosystems to a certain extent.
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19
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Louisson Z, Hermans SM, Buckley HL, Case BS, Taylor M, Curran-Cournane F, Lear G. Land use modification causes slow, but predictable, change in soil microbial community composition and functional potential. ENVIRONMENTAL MICROBIOME 2023; 18:30. [PMID: 37024971 PMCID: PMC10080853 DOI: 10.1186/s40793-023-00485-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/19/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Bacterial communities are critical to ecosystem functioning and sensitive to their surrounding physiochemical environment. However, the impact of land use change on microbial communities remains understudied. We used 16S rRNA gene amplicon sequencing and shotgun metagenomics to assess soil microbial communities' taxonomic and functional responses to land use change. We compared data from long-term grassland, exotic forest and horticulture reference sites to data from sites that transitioned from (i) Grassland to exotic forest or horticulture and from (ii) Exotic forest to grassland. RESULTS Community taxonomic and functional profiles of the transitional sites significantly differed from those within reference sites representing both their historic and current land uses (P < 0.001). The bacterial communities in sites that transitioned more recently were compositionally more similar to those representing their historic land uses. In contrast, the composition of communities from sites exposed to older conversion events had shifted towards the compositions at reference sites representing their current land use. CONCLUSIONS Our study indicates that microbial communities respond in a somewhat predictable way after a land use conversion event by shifting from communities reflecting their former land use towards those reflecting their current land use. Our findings help us to better understand the legacy effects of land use change on soil microbial communities and implications for their role in soil health and ecosystem functioning. Understanding the responsiveness of microbial communities to environmental disturbances will aid us in incorporating biotic variables into soil health monitoring techniques in the future.
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Affiliation(s)
- Z. Louisson
- School of Biological Sciences, University of Auckland, 3a Symonds Street, Auckland, 1010 New Zealand
| | - S. M. Hermans
- School of Science, Auckland University of Technology, 34 St Paul Street, Auckland, 1010 New Zealand
| | - H. L. Buckley
- School of Science, Auckland University of Technology, 34 St Paul Street, Auckland, 1010 New Zealand
| | - B. S. Case
- School of Science, Auckland University of Technology, 34 St Paul Street, Auckland, 1010 New Zealand
| | - M. Taylor
- Waikato Regional Council, 160 Ward St, Hamilton, 3204 New Zealand
| | - F. Curran-Cournane
- Joint Evidence Data and Insights, Ministry for the Environment, 45 Queens Street, Auckland, 1010 New Zealand
| | - G. Lear
- School of Biological Sciences, University of Auckland, 3a Symonds Street, Auckland, 1010 New Zealand
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20
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Gao H, Wang C, Chen J, Wang P, Zhang J, Zhang B, Wang R, Wu C. Enhancement effects of decabromodiphenyl ether on microbial sulfate reduction in eutrophic lake sediments: A study on sulfate-reducing bacteria using dsrA and dsrB amplicon sequencing. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 843:157073. [PMID: 35780888 DOI: 10.1016/j.scitotenv.2022.157073] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/26/2022] [Accepted: 06/26/2022] [Indexed: 06/15/2023]
Abstract
Although sulfate (SO42-) reduction by sulfate-reducing bacteria (SRB) is an important sulfur cycling processes, little is known about how the persistent organic pollutants affect the SO42- reduction process in the eutrophic lake sediments. Here, we carried out a 120-day microcosm experiment to explore the effects of decabromodiphenyl ether (BDE-209) on SO42- reduction mediated by SRB in sediment collected from Taihu Lake, a typical eutrophic lake in China. The results showed that BDE-209 contamination significantly enhanced the activity of dissimilatory sulfite reductase (DSR) (r = 0.83), which led to an increased concentration of sulfide produced by SO42- reduction. This stimulatory effect of BDE-209 on DSR activity was closely related to variations in the dsrA- and dsrB-type SRB communities. The abundances and diversities of the dsrA- and dsrB-containing SRB increased and their community composition varied in response to BDE-209 contamination. The gene copies (r = 0.72), Chao 1 (r = 0.50), Shannon (r = 0.55), and Simpson (r = 0.70) indices of dsrB-containing SRB was positively correlated with BDE-209 contamination. Co-occurrence network analysis revealed that network complexity, connectivity, and the interspecific cooperative relationship in SRB were strengthened by BDE-209 contamination. The keystone species identified in the SRB community mainly belonged to the genera Candidatus Sulfopaludibacter for the dsrA-containing SRB and Desulfatiglans for the dsrB-containing SRB, and their relative abundances were positively correlated with DSR activity in the sediment. The relative abundance of the keystone species and SRB diversity were important microbial factors directly contributing to the variations in DSR activity based on structural equation modeling analysis. Notably, the results of abundance, community structure, and interspecific relationships showed that the dsrB-containing SRB may be more sensitive to the BDE-209 contamination than the dsrA-containing SRB. These results will help us understand the effects of BDE-209 on microbial sulfate reduction in eutrophic lakes.
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Affiliation(s)
- Han Gao
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Chao Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Juan Chen
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China.
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Jingjing Zhang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Bo Zhang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Rong Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Cheng Wu
- Kunming Engineering Corporation Limited, Power China, 115 People's East Road, Kunming 650051, PR China
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21
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Sadet-Bourgeteau S, Djemiel C, Chemidlin Prévost-Bouré N, Feder F. Dynamic of bacterial and archaeal diversity in a tropical soil over 6 years of repeated organic and inorganic fertilization. Front Microbiol 2022; 13:943314. [PMID: 36051761 PMCID: PMC9425033 DOI: 10.3389/fmicb.2022.943314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/08/2022] [Indexed: 11/13/2022] Open
Abstract
The soil microbial community plays important roles in nutrient cycling, plant pathogen suppression, decomposition of residues and degradation of pollutants; as such, it is often regarded as a good indicator of soil quality. Repeated applications of mixed organic and inorganic materials in agriculture improve the soil microbial quality and in turn crop productivity. The soil microbial quality following several years of repeated fertilizer inputs has received considerable attention, but the dynamic of this community over time has never been assessed. We used high-throughput sequencing targeting 16S ribosomal RNA genes to investigate the evolution of the bacterial and archaeal community throughout 6 years of repeated organic and inorganic fertilizer applications. Soils were sampled from a field experiment in La Mare (Reunion Island, France), where different mixed organic-inorganic fertilizer inputs characterized by more or less stable organic matter were applied regularly for 6 years. Soil samples were taken each year, more than 6 months after the latest fertilizer application. The soil molecular biomass significantly increased in some organically fertilized plots (by 35–45% on average), 3–5 years after the first fertilizers application. The significant variations in soil molecular microbial biomass were explained by the fertilization practices (cumulated organic carbon inputs) and sometimes by the soil parameters (sand and soil carbon contents). The structure of the bacterial and archaeal community was more influenced by time than by the fertilization type. However, repeated fertilizer applications over time tended to modify the abundance of the bacterial phyla Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. To conclude, the present study highlights that the soil bacterial and archaeal community is lastingly modified after 6 years of repeated fertilizer inputs. These changes depend on the nature of the organic input and on the fertilization practice (frequency and applied quantity).
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Affiliation(s)
- Sophie Sadet-Bourgeteau
- Agroécologie, INRAE, Institut Agro Dijon, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
- *Correspondence: Sophie Sadet-Bourgeteau,
| | - Christophe Djemiel
- Agroécologie, INRAE, Institut Agro Dijon, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | | | - Frederic Feder
- CIRAD, UPR Recyclage et Risque, Montpellier, France
- Recyclage et risque, Univ Montpellier, CIRAD, Montpellier, France
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22
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Xu R, Tao W, Lin H, Huang D, Su P, Gao P, Sun X, Yang Z, Sun W. Effects of Perfluorooctanoic Acid (PFOA) and Perfluorooctane Sulfonic Acid (PFOS) on Soil Microbial Community. MICROBIAL ECOLOGY 2022; 83:929-941. [PMID: 34283261 DOI: 10.1007/s00248-021-01808-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 06/22/2021] [Indexed: 06/13/2023]
Abstract
The extensive application of perfluoroalkyl and polyfluoroalkyl substances (PFASs) causes their frequent detection in various environments. In this work, two typical PFASs, perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS), are selected to investigate their effects on soil microorganisms. Microbial community structure and microbe-microbe relationships were investigated by high-throughput sequencing and co-occurrence network analysis. Under 90 days of exposure, the alpha-diversity of soil microbial communities was increased with the PFOS treatment, followed by the PFOA treatment. The exposure of PFASs substantially changed the compositions of soil microbial communities, leading to the enrichment of more PFASs-tolerant bacteria, such as Proteobacteria, Burkholderiales, and Rhodocyclales. Comparative co-occurrence networks were constructed to investigate the microbe-microbe interactions under different PFASs treatments. The majority of nodes in the PFOA and PFOS networks were associated with the genus Azospirillum and Hydrogenophaga, respectively. The LEfSe analysis further identified a set of biomarkers in the soil microbial communities, such as Azospirillum, Methyloversatilis, Hydrogenophaga, Pseudoxanthomonas, and Fusibacter. The relative abundances of these biomarkers were also changed by different PFASs treatments. Functional gene prediction suggested that the microbial metabolism processes, such as nucleotide transport and metabolism, cell motility, carbohydrate transport and metabolism, energy production and conversion, and secondary metabolites biosynthesis transport and catabolism, might be inhibited under PFAS exposure, which may further affect soil ecological services.
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Affiliation(s)
- Rui Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Wan Tao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Hanzhi Lin
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Duanyi Huang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, People's Republic of China
| | - Pingzhou Su
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Pin Gao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Zhaohui Yang
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, People's Republic of China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China.
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China.
- School of Environment, Henan Normal University, Xinxiang, China.
- Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, 808 Tianyuan Road, Guangzhou, Guangdong, China.
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23
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Temporal Dynamics of Bacterial Communities along a Gradient of Disturbance in a U.S. Southern Plains Agroecosystem. mBio 2022; 13:e0382921. [PMID: 35420482 PMCID: PMC9239210 DOI: 10.1128/mbio.03829-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Land conversion for intensive agriculture produces unfavorable changes to soil ecosystems, causing global concern. Soil bacterial communities mediate essential terrestrial ecosystem processes, making it imperative to understand their responses to agricultural perturbations. Here, we used high-throughput sequencing coupled with a functional gene array to study temporal dynamics of soil bacterial communities over 1 year under different disturbance intensities across a U.S. Southern Plains agroecosystem, including tallgrass prairie, Old World bluestem pasture, no-tillage (NT) canola, and conventional tillage (CT) wheat. Land use had the greatest impact on bacterial taxonomic diversity, whereas sampling time and its interaction with land use were central to functional diversity differences. The main drivers of taxonomic diversity were tillage > sampling time > temperature, while all measured factors explained similar amounts of variations in functional diversity. Temporal differences had the strongest correlation with total nitrogen > rainfall > nitrate. Within land uses, community variations for CT wheat were attributed to nitrogen levels, whereas soil organic matter and soil water content explained community variations for NT canola. In comparison, all measured factors contributed almost equally to variations in grassland bacterial communities. Finally, functional diversity had a stronger relationship with taxonomic diversity for CT wheat compared to phylogenetic diversity in the prairie. These findings reinforce that tillage management has the greatest impact on bacterial community diversity, with sampling time also critical. Hence, our study highlights the importance of the interaction between temporal dynamics and land use in influencing soil microbiomes, providing support for reducing agricultural disturbance to conserve soil biodiversity.
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24
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Zhou A, Xie S, Tang H, Zhang L, Zhang Y, Zuo Z, Li X, Zhao W, Xu G, Zou J. The dynamic of the potential pathogenic bacteria, antibiotic-resistant bacteria, and antibiotic resistance genes in the water at different growth stages of grass carp pond. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:23806-23822. [PMID: 34817812 DOI: 10.1007/s11356-021-17578-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/12/2021] [Indexed: 06/13/2023]
Abstract
Pond aquaculture has become the most important and broadest breeding model in China, and an extremely important source of aquatic products, but the potential hazard factors of potential pathogenic bacteria (PPB), antibiotic resistance bacteria (ARB), and antibiotic resistance genes (ARGs) in aquaculture environment are largely invisible. In the present study, the bacterial communities in the larvae, juvenile, rearing, and harvesting culture stages of great grass carp (Ctenopharyngodon idellus) ponds were investigated and the structure of microbial flora analysis showed that the larvae culture stage has the highest abundance and the most dominant phyla were Proteobacteria (27.8%). A total of 123 significant Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotations and the relative abundance of nine bacterial phenotypes implied that the larvae culture stage had the most abundance of pathogenic potential and mobile elements. The correlation analyses of environmental factors showed that temperature, stocking density, pH, and transparency showed the significant impacts on both the distribution of microbiome and the PPB. More importantly, a total of 40 ARB were identified, and 16 ARGs have the detection rates of 100%, which revealed that they are widely distributed and highly enriched in the aquaculture production. Notably, this is the first robust report to analyze and understand the PPB, ARB, and ARGs characteristics and dynamic changes in the pond aquaculture.
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Affiliation(s)
- Aiguo Zhou
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
- Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, PEI, C1A 5T1, Canada
| | - Shaolin Xie
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Huijuan Tang
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Li Zhang
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yue Zhang
- Departments of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Zhiheng Zuo
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xiang Li
- Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, PEI, C1A 5T1, Canada
| | - Wenyu Zhao
- Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, School of Hydraulic Engineering, Changsha University of Science & Technology, Changsha, 410114, China
| | - Guohuan Xu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China.
| | - Jixing Zou
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China.
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25
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Wang L. Research trends in Jiang-flavor baijiu fermentation: From fermentation microecology to environmental ecology. J Food Sci 2022; 87:1362-1374. [PMID: 35275413 DOI: 10.1111/1750-3841.16092] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 01/15/2022] [Accepted: 01/30/2022] [Indexed: 12/11/2022]
Abstract
Chinese baijiu is one of the six major distilled spirits worldwide and is widely enjoyed because of its unique flavor. Among typical baijiu, Jiang-flavor baijiu is gaining popularity. However, the fermentation mechanisms of baijiu remain unclear due to its open inoculation environment and complex brewing process. In recent years, advances in high-throughput sequencing and multi-omics technologies have yielded meaningful information regarding fermentation microbiome. Therefore, this paper reviews recent developments in the investigation of the diversity, stability, and metabolism of the Jiang-flavor baijiu microbial community. Furthermore, the importance of protecting the ecology of the production environment is proposed based on the putative contribution of environmental factors to the fermentation microbiome and baijiu characteristics. Finally, this paper discusses current research challenges that need to be addressed, including the limitations of sequencing technologies and difficulties unveiling the mechanisms of microbial interaction between the fermentation microbiome and the environmental ecology. The findings of this review will promote further understanding of the Jiang-flavor baijiu fermentation process and provide valuable information for the research and development of traditional baijiu and other naturally fermented foods. PRACTICAL APPLICATION: Baijiu, a transparent strong alcoholic drink, is the world's largest consumed and the most valuable spirit in the market. However, the fermentation mechanisms of baijiu remain unclear due to its open inoculation environment and complex brewing process. Therefore, if we can summarizes the current advances and research challenges of microbial fermentation in baijiu, it will deepen the reader's understanding of the complex fermentation process and fermentation mechanism in baijiu. Furthermore, based on the putative contribution of environmental factors to the fermentation process, the importance of protecting the ecology of the production environment is proposed in future research trends, which will provide valuable information for the research and development of other traditional naturally fermented foods. This will not only achieve breakthroughs in academic value, but also bring higher practical value to fermented foods.
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Affiliation(s)
- Li Wang
- Kweichow Moutai Distillery Co., Ltd., Zunyi City, China
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26
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Nutrient supply controls the linkage between species abundance and ecological interactions in marine bacterial communities. Nat Commun 2022; 13:175. [PMID: 35013303 PMCID: PMC8748817 DOI: 10.1038/s41467-021-27857-6] [Citation(s) in RCA: 84] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 10/14/2021] [Indexed: 12/14/2022] Open
Abstract
Nutrient scarcity is pervasive for natural microbial communities, affecting species reproduction and co-existence. However, it remains unclear whether there are general rules of how microbial species abundances are shaped by biotic and abiotic factors. Here we show that the ribosomal RNA gene operon (rrn) copy number, a genomic trait related to bacterial growth rate and nutrient demand, decreases from the abundant to the rare biosphere in the nutrient-rich coastal sediment but exhibits the opposite pattern in the nutrient-scarce pelagic zone of the global ocean. Both patterns are underlain by positive correlations between community-level rrn copy number and nutrients. Furthermore, inter-species co-exclusion inferred by negative network associations is observed more in coastal sediment than in ocean water samples. Nutrient manipulation experiments yield effects of nutrient availability on rrn copy numbers and network associations that are consistent with our field observations. Based on these results, we propose a “hunger games” hypothesis to define microbial species abundance rules using the rrn copy number, ecological interaction, and nutrient availability. Environmental and biotic factors control ecological communities. Here, the authors study community ribosomal rRNA gene copy number in coastal sediment and ocean bacterial communities, and in microcosm nutrient addition experiments, to propose a conceptual framework of how nutrient supply and ecological interactions shape the community.
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27
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Tan L, Zeng WA, Xiao Y, Li P, Gu S, Wu S, Zhai Z, Feng K, Deng Y, Hu Q. Fungi-Bacteria Associations in Wilt Diseased Rhizosphere and Endosphere by Interdomain Ecological Network Analysis. Front Microbiol 2021; 12:722626. [PMID: 34552573 PMCID: PMC8450586 DOI: 10.3389/fmicb.2021.722626] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/11/2021] [Indexed: 11/13/2022] Open
Abstract
In the plant rhizosphere and endosphere, some fungal and bacterial species regularly co-exist, however, our knowledge about their co-existence patterns is quite limited, especially during invasion by bacterial wilt pathogens. In this study, the fungal communities from soil to endophytic compartments were surveyed during an outbreak of tobacco wilt disease caused by Ralstonia solanacearum. It was found that the stem endophytic fungal community was significantly altered by pathogen invasion in terms of community diversity, structure, and composition. The associations among fungal species in the rhizosphere and endosphere infected by R. solanacearum showed more complex network structures than those of healthy plants. By integrating the bacterial dataset, associations between fungi and bacteria were inferred by Inter-Domain Ecological Network (IDEN) approach. It also revealed that infected samples, including both the rhizosphere and endosphere, had more complex interdomain networks than the corresponding healthy samples. Additionally, the bacterial wilt pathogenic Ralstonia members were identified as the keystone genus within the IDENs of both root and stem endophytic compartments. Ralstonia members was negatively correlated with the fungal genera Phoma, Gibberella, and Alternaria in infected roots, as well as Phoma, Gibberella, and Diaporthe in infected stems. This suggested that those endophytic fungi may play an important role in resisting the invasion of R. solanacearum.
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Affiliation(s)
- Lin Tan
- Hunan Agricultural University, Changsha, China
| | - Wei-Ai Zeng
- Changsha Tobacco Company of Hunan Province, Changsha, China
| | - Yansong Xiao
- Chenzhou Tobacco Company of Hunan Province, Chenzhou, China
| | - Pengfei Li
- Wenshan Tobacco Company of Yunnan Province, Wenshan, China
| | - Songsong Gu
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,Institute for Marine Science and Technology, Shandong University, Qingdao, China
| | - Shaolong Wu
- Tobacco Company of Hunan Province, Changsha, China
| | | | - Kai Feng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,Institute for Marine Science and Technology, Shandong University, Qingdao, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Qiulong Hu
- Hunan Agricultural University, Changsha, China
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28
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Chemidlin Prévost-Bouré N, Karimi B, Sadet-Bourgeteau S, Djemiel C, Brie M, Dumont J, Campedelli M, Nowak V, Guyot P, Letourneur C, Manneville V, Gillet F, Bouton Y. Microbial transfers from permanent grassland ecosystems to milk in dairy farms in the Comté cheese area. Sci Rep 2021; 11:18144. [PMID: 34518581 PMCID: PMC8438085 DOI: 10.1038/s41598-021-97373-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/17/2021] [Indexed: 01/07/2023] Open
Abstract
The specificity of dairy Protected Designation of Origin (PDO) products is related to their “terroir” of production. This relationship needs better understanding for efficient and sustainable productions preserving the agroecological equilibrium of agroecosystems, especially grasslands. Specificity of PDO Comté cheese was related to the diversity of natural raw milk bacterial communities, but their sources need to be determined. It is hypothesized that raw milk indigenous microbial communities may originate from permanent grazed grasslands by the intermediate of dairy cows according to the sequence soil–phyllosphere–teat–milk. This hypothesis was evaluated on a 44 dairy farms network across PDO Comté cheese area by characterizing prokaryotic and fungal communities of these compartments by metabarcoding analysis (16S rRNA gene: V3–V4 region, 18S rRNA gene: V7–V8 region). Strong and significant links were highlighted between the four compartments through a network analysis (0.34 < r < 0.58), and were modulated by soil pH, plant diversity and elevation; but also by farming practices: organic fertilization levels, cattle intensity and cow-teat care. This causal relationship suggests that microbial diversity of agroecosystems is a key player in relating a PDO product to its “terroir”; this under the dependency of farming practices. Altogether, this makes the “terroir” even more local and needs to be considered for production sustainability.
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Affiliation(s)
- N Chemidlin Prévost-Bouré
- UMR 1347 Agroécologie - AgroSup Dijon - INRAE - Université Bourgogne - Université Bourgogne Franche-Comté, 21000, Dijon, France.
| | - B Karimi
- UMR 1347 Agroécologie - AgroSup Dijon - INRAE - Université Bourgogne - Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - S Sadet-Bourgeteau
- UMR 1347 Agroécologie - AgroSup Dijon - INRAE - Université Bourgogne - Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - C Djemiel
- UMR 1347 Agroécologie - AgroSup Dijon - INRAE - Université Bourgogne - Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - M Brie
- AgroSup Dijon, 26 boulevard du Dr Petitjean, 21000, Dijon, France
| | - J Dumont
- AgroSup Dijon, 26 boulevard du Dr Petitjean, 21000, Dijon, France
| | - M Campedelli
- AgroSup Dijon, 26 boulevard du Dr Petitjean, 21000, Dijon, France
| | - V Nowak
- UMR 1347 Agroécologie - AgroSup Dijon - INRAE - Université Bourgogne - Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - P Guyot
- Comité Interprofessionnel de Gestion du Comté - Unité R&D, Bâtiment INRAE URTAL, 39800, Poligny, France
| | - C Letourneur
- Comité Interprofessionnel de Gestion du Comté - Unité R&D, Bâtiment INRAE URTAL, 39800, Poligny, France
| | | | - F Gillet
- Université Bourgogne Franche-Comté, UMR6249 Chrono-Environnement, 25030, Besançon, France
| | - Y Bouton
- Comité Interprofessionnel de Gestion du Comté - Unité R&D, Bâtiment INRAE URTAL, 39800, Poligny, France
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Wang H, Weil M, Dumack K, Zak D, Münch D, Günther A, Jurasinski G, Blume-Werry G, Kreyling J, Urich T. Eukaryotic rather than prokaryotic microbiomes change over seasons in rewetted fen peatlands. FEMS Microbiol Ecol 2021; 97:6356952. [PMID: 34427631 DOI: 10.1093/femsec/fiab121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 08/20/2021] [Indexed: 12/12/2022] Open
Abstract
In the last decades, rewetting of drained peatlands is on the rise worldwide, to restore their significant carbon sink function. Despite the increasing understanding of peat microbiomes, little is known about the seasonal dynamics and network interactions of the microbial communities in these ecosystems, especially in rewetted fens (groundwater-fed peatlands). Here, we investigated the seasonal dynamics in both prokaryotic and eukaryotic microbiomes in three common fen types in Northern Germany. The eukaryotic microbiomes, including fungi, protists and microbial metazoa, showed significant changes in their community structures across the seasons in contrast to largely unaffected prokaryotic microbiomes. Furthermore, our results proved that the dynamics in eukaryotic microbiomes in the rewetted sites differed between fen types, specifically in terms of saprotrophs, arbuscular mycorrhiza and grazers of bacteria. The co-occurrence networks also exhibited strong seasonal dynamics that differed between rewetted and drained sites, and the correlations involving protists and prokaryotes were the major contributors to these dynamics. Our study provides the insight that microbial eukaryotes mainly define the seasonal dynamics of microbiomes in rewetted fen peatlands. Accordingly, future research should unravel the importance of eukaryotes for biogeochemical processes, especially the under-characterized protists and metazoa, in these poorly understood ecosystems.
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Affiliation(s)
- Haitao Wang
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, 17487 Greifswald, Germany
| | - Micha Weil
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, 17487 Greifswald, Germany
| | - Kenneth Dumack
- Cologne Biocenter, University of Cologne, Zülpicher Strasse 47b, 50674 Cologne, Germany
| | - Dominik Zak
- Department of Bioscience, Aarhus University, Vejlsøvej 25, 8600 Silkeborg, Denmark.,Department of Chemical Analytics and Biogeochemistry, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, 12587 Berlin, Germany
| | - Diana Münch
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, 17487 Greifswald, Germany
| | - Anke Günther
- Faculty of Agriculture and Environmental Sciences, University of Rostock, Justus-von-Liebig-Weg 6, 18059 Rostock, Germany
| | - Gerald Jurasinski
- Faculty of Agriculture and Environmental Sciences, University of Rostock, Justus-von-Liebig-Weg 6, 18059 Rostock, Germany
| | - Gesche Blume-Werry
- Experimental Plant Ecology, University of Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany
| | - Jürgen Kreyling
- Experimental Plant Ecology, University of Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany
| | - Tim Urich
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, 17487 Greifswald, Germany
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Wang C, Gao H, Chen J, Wang P, Zhang J, Hu Y, Pan Y. Long-term effects of decabromodiphenyl ether on denitrification in eutrophic lake sediments: Different sensitivity of six-type denitrifying bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 774:145147. [PMID: 33609823 DOI: 10.1016/j.scitotenv.2021.145147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/07/2021] [Accepted: 01/09/2021] [Indexed: 05/28/2023]
Abstract
The widespread use of polybrominated diphenyl ethers inevitably results in their increased release into natural waters and subsequent deposition in sediments. However, their long-term effects on the bacteria participating in each step of denitrification in eutrophic lake sediments are still unknown. Here, we conducted a one-year microcosm experiment to determine the long-term effects of decabromodiphenyl ether (BDE-209), at low (2 mg kg-1 dry weight) and high (20 mg kg-1 dry weight) contamination levels, on six-type denitrifying bacteria and their activities in sediments collected from Taihu Lake, a typical eutrophic lake in China. At the end of the experiment, sediment denitrifying reductase activities were inhibited by BDE-209 at both levels, with the greatest inhibition seen for nitric oxide reductase activity. The higher nitrate concentration in the contaminated sediments was attributed to the inhibition of nitrate reductase activities. The abundances of six-type denitrifying genes (narG, napA, nirK, nirS, norB, and nosZ) significantly decreased under high BDE-209 treatment, and narG and napA genes were more sensitive to the toxicity of BDE-209. The results from pyrosequencing showed that BDE-209, at either treatment concentration, decreased the six-type denitrifying bacterial diversities and altered their community composition. This shift of six-type denitrifying bacterial communities might also be driven by the debrominated products concentrations of BDE-209 and variations in sediment inorganic nitrogen concentrations. In particular, some genera from phylum Proteobacteria such as Pseudomonas, Cupriavidus, and Azoarcus were decreased significantly because of BDE-209 and its debrominated products.
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Affiliation(s)
- Chao Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Han Gao
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Juan Chen
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China.
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Jingjing Zhang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Yu Hu
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Ying Pan
- School of Ecology, Sun Yat-sen University, Guangzhou 510275, PR China
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Dunn L, Lang C, Marilleau N, Terrat S, Biju-Duval L, Lelièvre M, Perrin S, Chemidlin Prévost-Bouré N. Soil microbial communities in the face of changing farming practices: A case study in an agricultural landscape in France. PLoS One 2021; 16:e0252216. [PMID: 34138883 PMCID: PMC8211295 DOI: 10.1371/journal.pone.0252216] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/12/2021] [Indexed: 11/19/2022] Open
Abstract
According to biogeography studies, the abundance and richness of soil microorganisms vary across multiple spatial scales according to soil properties and farming practices. However, soil microorganisms also exhibit poorly understood temporal variations. This study aimed at better understanding how soil microbial communities respond to changes in farming practices at a landscape scale over time. A regular grid of 269 sites was set up across a 1,200 ha farming landscape, and soil samples were characterized for their molecular microbial biomass and bacterial richness at two dates (2011 and 2016). A mapping approach highlighted that spatial microbial patterns were stable over time, while abundance and richness levels were modified. The drivers of these changes were investigated though a PLS-PM (partial least square path-modeling) approach. Soil properties were stable over time, but farming practices changed. Molecular microbial biomass was mainly driven by soil resources, whereas bacterial richness depended on both farming practices and ecological parameters. Previous-crop and management effects and a temporal dependence of the microbial community on the historical farming management were also highlighted.
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Affiliation(s)
- Laurie Dunn
- UMR 1347 Agroécologie, INRAE, AgrosupDijon, Université Bourgogne Franche-Comté, Dijon, France
| | - Christophe Lang
- Institut de Recherche Femto-ST, CNRS, Université Bourgogne Franche-Comté, Besançon, France
| | | | - Sébastien Terrat
- UMR 1347 Agroécologie, INRAE, AgrosupDijon, Université Bourgogne Franche-Comté, Dijon, France
| | - Luc Biju-Duval
- UMR 1347 Agroécologie, INRAE, AgrosupDijon, Université Bourgogne Franche-Comté, Dijon, France
| | | | - Solène Perrin
- UMR 1347 Agroécologie, Plateforme GenoSol, INRAE, Dijon, France
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Short-Term Effect of Green Waste and Sludge Amendment on Soil Microbial Diversity and Volatile Organic Compound Emissions. Appl Microbiol 2021. [DOI: 10.3390/applmicrobiol1010010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Soil amendments with organic waste products (OWPs) have been widely supported in Europe to improve soil fertility, causing wide changes in the microbial community structure and diversity, especially in the short-term period. Those changes are known to affect the volatile organic compound (VOC) emissions by soil. This work aimed to characterize, in terms of quantity and composition, the effect of green waste and sludge (GWS) application on soil VOC emissions and microbial community 49 h after the last GWS application. Two different soil samples were compared to test the effect of the soil history on VOC emissions and microbial communities. For this reason, we chose a soil that received GWS input for 20 years (GWS sample) and one that did not receive any organic input during the same period (CN sample). Furthermore, samples were manipulated to generate three microbial dilution diversity gradients (low, medium, and high). Results showed that Bacteroidetes phyla took advantage of the GWS application in all samples, increasing their relative abundance by 22% after 49 h, while the Proteobacteria phylum was penalized by the GWS amendment, passing from 58% to 49% relative abundance 49 h after the GWS application. Microbial structure differences between microbial diversity dilution levels remained even after the GWS application. GWS amendment induced a change in the emitted VOC profiles, especially in samples used to receiving GWS. GWS amendment doubled the VOC emissions from samples used to receiving GWS after 49 h. Finally, the microbial community was strongly correlated to the VOC emissions. Firmicutes, Proteobacteria, Actinobacteria, and Crenarchaeota were positively correlated (Pearson coefficient > 0.6), while other phyla, such as Bacteroidetes and Verrucomicrobia, were found to be negatively correlated (Pearson coefficient < −0.6) to the VOC emissions. After the addition of GWS, these correlations shifted from positive to negative and from negative to positive.
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Jiang B, Zhang B, Li L, Zhao Y, Shi Y, Jiang Q, Jia L. Analysis of microbial community structure and diversity in surrounding rock soil of different waste dump sites in fushun western opencast mine. CHEMOSPHERE 2021; 269:128777. [PMID: 33189393 DOI: 10.1016/j.chemosphere.2020.128777] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 09/08/2020] [Accepted: 10/23/2020] [Indexed: 06/11/2023]
Abstract
It is importance to understand the correlation between the physicochemical properties of different surrounding rock soil and microbial communities in Fushun western opencast mining for the ecological restoration of land after mine closure. In this study, two layers of soil samples were collected from four different areas in Fushun western opencast mining: coal gangue area (CGA), green mudstone area (GMA), oil shale area (OSA) and mixed area (MA). Then, the effects of different surrounding rock soil physicochemical properties on the microbial communities were explored using the High-throughput sequencing technique. A wide diversity of taxonomical groups were present in four soil cores, and many were correlated with soil physicochemical properties. The obvious differences in microbial communities between different areas showed the influence of different surrounding rock soil on the microbial communities were significant. Redundancy analysis and the network diagram confirmed that soil physicochemical properties pH (Pondus Hydrogenii)-AN (Available Nitrogen)-EC (Electronic Conductivity)-WC (Water Content)-TK (Total Nitrogen), Cd (Cadmium)-Ni (Nickel) had great influence on the microbial communities. Therefore, this study can provide scientific judgments for the different surrounding rock soil physicochemical properties in coal mining, microbial-mediated rock mineralization and biogeochemical cycles.
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Affiliation(s)
- Binhui Jiang
- Northeastern University, School of Resources and Civil Engineering, Ministry of Education Safety Mining in Deep Metal Mines, Key Laboratory, Shenyang, 110819, China
| | - Bo Zhang
- Northeastern University, School of Resources and Civil Engineering, Ministry of Education Safety Mining in Deep Metal Mines, Key Laboratory, Shenyang, 110819, China
| | - Liang Li
- Northeastern University, School of Resources and Civil Engineering, Ministry of Education Safety Mining in Deep Metal Mines, Key Laboratory, Shenyang, 110819, China
| | - Yan Zhao
- Northeastern University, School of Resources and Civil Engineering, Ministry of Education Safety Mining in Deep Metal Mines, Key Laboratory, Shenyang, 110819, China
| | - Yang Shi
- Northeastern University, School of Resources and Civil Engineering, Ministry of Education Safety Mining in Deep Metal Mines, Key Laboratory, Shenyang, 110819, China
| | - Qi Jiang
- Northeastern University, School of Resources and Civil Engineering, Ministry of Education Safety Mining in Deep Metal Mines, Key Laboratory, Shenyang, 110819, China
| | - Liping Jia
- Northeastern University, School of Resources and Civil Engineering, Ministry of Education Safety Mining in Deep Metal Mines, Key Laboratory, Shenyang, 110819, China; College of Chemistry and Environmental Science, Minnan Normal University, Zhangzhou, 363000, China.
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Kandasamy S, Weerasuriya N, Subramanian G, Thorn RG, Patterson G, Ali S, Lazarovits G. Disentangling the Association of Corn Root Mycobiome With Plant Productivity and the Importance of Soil Physicochemical Balance in Shaping Their Relationship. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.617332] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Soil bacteria and fungi are integral parts of healthy ecosystem functioning in production agriculture. The effects of fungal abundance and diversity on crop productivity is poorly understood. We sampled 10 corn farms at the V10 growth stage across southwestern Ontario, Canada, using aerial infrared imaging to identify zones of low and high productive corn plants. Roots and soils were sampled from low and high yield zones and soil physical and chemical properties were measured in conjunction with assessment of the root mycobiome communities using Illumina MiSeq sequencing of 4 rRNA amplicons. Higher crop yields were associated with sites having greater fungal phylogenetic diversity and Fisher's α diversity. Indicator species associated with high and low yield sites within a farm could be identified but there were no shared fungal indicators of productivity differences across farms. Communities largely varied across locations despite crop genetics, demonstrating a major influence of soil texture and chemistry in shaping the mycobiome in a site-specific manner. Across all 4 primers, roots from high-yielding sites shared 35 major OTUs including Penicillium spp., Trichoderma, Chalara fungorum, and Gibellulopsis. Low-yielding sites shared 31 OTUs including Fusarium spp., Pythium, Setophoma terrestris, and Neonectria. Soil physical and chemical parameters that contributed to broad scale differences in yield and mycobiome diversity included: %clay, %sand, %phosphorus saturation, cation exchange capacity, aluminum, pH, iron, potassium, %moisture, organic matter, and chlorine. The results show the importance of physicochemical balance in shaping the relationship between root mycobiome and plant productivity.
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Haruna A, Yahaya SM. Recent Advances in the Chemistry of Bioactive Compounds from Plants and Soil Microbes: a Review. CHEMISTRY AFRICA 2021. [PMCID: PMC7869076 DOI: 10.1007/s42250-020-00213-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Bioactive compounds derived from plants and microbial sources are required for the survival of the human race and groundbreaking research must continue in this line. Plants and microbes are the major sources of naturally occurring bioactive compounds for numerous biotechnological applications. Recent progress in the fields of bioactive compounds and soil chemistry in agriculture has since given man a lead to the discovery of potent drugs that combat both human and plant diseases. The soil provides the medium for the growth of medicinal plants, but its contamination greatly affects the quality of drugs, food crops, and other essential elements present in the plants which give strength to the body. This area has attracted the attention of scientists and the drug industry toward developing more potent drugs from medicinal plants grown in different soil. The studies of the effect of various parameters and the properties of soil such as; effect of heavy metals, pH, soil organic matter, and phytoremediation process have given a measure of some quality dependence of the soil producing secondary metabolites and soil containing microbes. The information provided will be useful in determine the action of microbes and their interaction with the soil and all true plants producing drugs. Some active compounds in plants and microbes, their properties, and applications have been described in this review. The soil microbes, activities and their interactions, effects of soil particle size, dispersibility and stability of microbes in the soil, and the future outlook for the development of novel active compounds have been reported.
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36
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Haghverdi K, Kooch Y. Soil carbon and nitrogen fractions in response to land use/cover changes. ACTA OECOLOGICA 2020. [DOI: 10.1016/j.actao.2020.103659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Durand A, Maillard F, Foulon J, Chalot M. Interactions between Hg and soil microbes: microbial diversity and mechanisms, with an emphasis on fungal processes. Appl Microbiol Biotechnol 2020; 104:9855-9876. [PMID: 33043392 DOI: 10.1007/s00253-020-10795-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 07/06/2020] [Accepted: 07/21/2020] [Indexed: 11/25/2022]
Abstract
Mercury (Hg) is a highly toxic metal with no known biological function, and it can be highly bioavailable in terrestrial ecosystems. Although fungi are important contributors to a number of soil processes including plant nutrient uptake and decomposition, little is known about the effect of Hg on fungi. Fungi accumulate the largest amount of Hg and are the organisms capable of the highest bioaccumulation of Hg. While referring to detailed mechanisms in bacteria, this mini-review emphasizes the progress made recently on this topic and represents the first step towards a better understanding of the mechanisms underlying Hg tolerance and accumulation in fungal species and hence on the role of fungi within the Hg cycle at Hg-contaminated sites. KEY POINTS: • The fungal communities are more resilient than bacterial communities to Hg exposure. • The exposure to Hg is a threat to microbial soil functions involved in both C and nutrient cycles. • Fungal (hyper)accumulation of Hg may be important for the Hg cycle in terrestrial environments. • Understanding Hg tolerance and accumulation by fungi may lead to new remediation biotechnologies.
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Affiliation(s)
- Alexis Durand
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211, Montbéliard, France
- Laboratoire Sols et Environnement, UMR 1120, Université de Lorraine - INRAE, 2 avenue de la Forêt de Haye BP 20 163, 54505, Vandœuvre-lès-Nancy, France
| | - François Maillard
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211, Montbéliard, France
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Julie Foulon
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211, Montbéliard, France
- Institut des Sciences de la Mer de Rimouski, Université du Québec à Rimouski, 310 Allée des Ursulines, C.P. 3300, Rimouski, QC, G5L 3A1, Canada
| | - Michel Chalot
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211, Montbéliard, France.
- Faculté des Sciences et Technologies, Université de Lorraine, BP 70239, 54506, Vandoeuvre-les-Nancy, France.
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Brunel C, Da Silva AMF, Gros R. Environmental Drivers of Microbial Functioning in Mediterranean Forest Soils. MICROBIAL ECOLOGY 2020; 80:669-681. [PMID: 32399630 DOI: 10.1007/s00248-020-01518-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/24/2020] [Indexed: 06/11/2023]
Abstract
Mediterranean forests own distinct characteristics resulting from climate, soil, and vegetation that affect soil microbial communities' assembly and their associated functions. We initiated a multi-scalar analysis of environmental drivers of soil functioning to (1) identify pertinent factorial scales and (2) determine the relative importance of soil, vegetation, and geoclimate influences in shaping soil microbial functions across the French Mediterranean forests. Soil samples (0-15 cm) were collected from 60 forest sites and soil physicochemical and microbiological properties were assessed across different factorial scales i.e., bioclimates, slope exposures, and forest stands. Patterns in microbial catabolic potential (i.e., extracellular enzymes and microbial respiration) and carbon (C) source utilization (i.e., catabolic-level physiological profiling) were partitioned between vegetation cover, soil characteristics, and geoclimate components. Our results reveal that the catabolic potential of soil microbes was strongly influenced by the forest stands and mainly relied on ammonium and nitrate contents. In contrast, variation in C source utilization was mainly explained by vegetation cover. Soil metabolic capacities of microorganisms and resulting C dynamics were largely constrained by climate parameters, which suggests potentially important consequences for soil C storage. Our study revealed diverse structuration patterns between the catabolic potential and the carbon source utilization of soil microbial communities, and gives insights into the underlying mechanisms of soil microbial functioning in Mediterranean forests.
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Affiliation(s)
- Caroline Brunel
- Mediterranean Institute of Marine and Continental Biodiversity and Ecology, IMBE, Aix Marseille Université, UMR CNRS 7263, IRD, Avignon Université, Campus l'Etoile, Av. Escadrille Normandie Niemen, 13397, Cedex 20, Marseille, France.
- IRD, IPME, 911 Avenue Agropolis, BP 64501, 34394, Montpellier, France.
| | - Anne-Marie Farnet Da Silva
- Mediterranean Institute of Marine and Continental Biodiversity and Ecology, IMBE, Aix Marseille Université, UMR CNRS 7263, IRD, Avignon Université, Campus l'Etoile, Av. Escadrille Normandie Niemen, 13397, Cedex 20, Marseille, France
| | - Raphael Gros
- Mediterranean Institute of Marine and Continental Biodiversity and Ecology, IMBE, Aix Marseille Université, UMR CNRS 7263, IRD, Avignon Université, Campus l'Etoile, Av. Escadrille Normandie Niemen, 13397, Cedex 20, Marseille, France
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Zheng T, Deng Y, Wang Y, Jiang H, Xie X, Gan Y. Microbial sulfate reduction facilitates seasonal variation of arsenic concentration in groundwater of Jianghan Plain, Central China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 735:139327. [PMID: 32473437 DOI: 10.1016/j.scitotenv.2020.139327] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 05/27/2023]
Abstract
Bacterial sulfate reduction (BSR) plays a vital but complex role in regulating groundwater arsenic concentration. A quarterly hydro-biogeochemical investigation was conducted to clarify how BSR participated in arsenic dynamics in the geogenic As-contaminated alluvial aquifers of the Jianghan Plain, central Yangtze River Basin. Anthropogenic input of sulfate was identified in the transitional season with higher Cl concentrations and Cl/Br molar ratios compared to the monsoon season. Seasonal increase of S(-II) and Fe(II) concentrations in monsoon season suggests the co-occurrence of iron and sulfate reduction. Quantitative analysis of dsrB gene abundance revealed the corresponding variations between dsrB gene abundance (up to 1.2 × 107 copies L-1) and Fe(II) in groundwater. High-throughput sequencing of the dsrB gene identified a considerable proportion of sequences in the sulfate-reducing bacterial community was affiliated with Desulfobulbus (22.7 ± 20.8%) and Desulfocapsa (11.5 ± 11.9%). Moreover, the relative abundance of Desulfocapsa increased with the Fe(II) in the groundwater (R = 0.78, P < 0.01). These results suggest that microbially-mediated sulfate reduction facilitated the abiotic reduction of As-bearing Fe-oxides in the monsoon season after anthropogenic input of sulfate in the transitional season under oscillating redox conditions in the groundwater systems. The present research provides new insights into the critical role of BSR in the seasonal redox cycling of iron and variation of As in the aquifer systems, which are not only applicable in the central Yangtze River basin, but also to other similar As-rich alluvial aquifers worldwide.
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Affiliation(s)
- Tianliang Zheng
- Geological Survey, China University of Geosciences, Wuhan 430074, PR China
| | - Yamin Deng
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, PR China.
| | - Yanxin Wang
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, PR China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, PR China.
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, PR China
| | - Xianjun Xie
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, PR China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, PR China
| | - Yiqun Gan
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, PR China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, PR China
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40
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Acid Soil Improvement Enhances Disease Tolerance in Citrus Infected by Candidatus Liberibacter asiaticus. Int J Mol Sci 2020; 21:ijms21103614. [PMID: 32443846 PMCID: PMC7279377 DOI: 10.3390/ijms21103614] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/13/2020] [Accepted: 05/15/2020] [Indexed: 11/20/2022] Open
Abstract
Huanglongbing (HLB) is a devastating citrus disease that has caused massive economic losses to the citrus industry worldwide. The disease is endemic in most citrus-producing areas of southern China, especially in the sweet orange orchards where soil acidification has intensified. In this work, we used lime as soil pH amendment to optimize soil pH and enhance the endurance capacity of citrus against Candidatus Liberibacter asiaticus (CLas). The results showed that regulation of soil acidity is effective to reduce the occurrence of new infections and mitigate disease severity in the presence of HLB disease. We also studied the associated molecular mechanism and found that acid soil improvement can (i) increase the root metabolic activity and up-regulate the expression of ion transporter-related genes in HLB-infected roots, (ii) alleviate the physiological disorders of sieve tube blockage of HLB-infected leaves, (iii) strengthen the citrus immune response by increasing the expression of genes involved in SAR and activating the salicylic acid signal pathway, (iv) up-regulate 55 proteins related to stress/defence response and secondary metabolism. This study contributes to a better understanding of the correlation between environment factors and HLB disease outbreaks and also suggests that acid soil improvement is of potential value for the management of HLB disease in southern China.
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Vallejos MB, Marcos MS, Barrionuevo C, Olivera NL. Fish-processing effluent discharges influenced physicochemical properties and prokaryotic community structure in arid soils from Patagonia. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 714:136882. [PMID: 32018997 DOI: 10.1016/j.scitotenv.2020.136882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 06/10/2023]
Abstract
Along the Patagonian coast, there are processing factories of marine products in land that produce fish-processing effluents. The aim of the present study was to assess the physicochemical properties and the prokaryotic community composition of soils receiving fish-processing effluent discharges (effluent site-ES), and to compare them with those of unaltered soils (control site-CS) in the arid Patagonian steppe. We analyzed soil prokaryotic communities (using amplicon-based sequencing of 16S rRNA genes), soil physicochemical properties and fish-processing effluent characteristics. Soil moisture, electrical conductivity (EC), total and inorganic C were significantly higher in ES than in CS (p < .05). Effluent discharges induced a decrease in the total number of operational taxonomic units (OTUs) and in the Shannon diversity index (p = .0009 and .01, respectively) of soil prokaryotic community. Proteobacteria, Actinobacteria and Acidobacteria were the dominant phyla in CS, while ES soil showed a more heterogeneous composition of phyla. Linear discriminant analysis (LDA) effect size (LEfSe) analysis showed that fish-processing effluent discharges promoted an enrichment of Firmicutes and Bacteroidetes, which are active contributors to organic matter mineralization, along with a decrease of oligotrophic phyla such as Acidobacteria, Chloroflexi, Armatimonadetes and Nitrospirae, commonly found in nutrient-poor arid soils. The concentrations of inorganic C and ammonium, the EC and the soil moisture explained 73% of the total variation within the community composition. Due to its salinity and nutrients, fish-processing effluents have potential mainly for native salt-tolerant plant irrigation, however the impacts of soil prokaryotic community shifts over plant growth remain to be determined.
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Affiliation(s)
- M B Vallejos
- Laboratorio de Microbiología y Biotecnología, Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC, CCT CONICET-CENPAT), Puerto Madryn, Argentina
| | - M S Marcos
- Laboratorio de Microbiología y Biotecnología, Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC, CCT CONICET-CENPAT), Puerto Madryn, Argentina
| | - C Barrionuevo
- Laboratorio de Microbiología y Biotecnología, Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC, CCT CONICET-CENPAT), Puerto Madryn, Argentina
| | - N L Olivera
- Laboratorio de Microbiología y Biotecnología, Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC, CCT CONICET-CENPAT), Puerto Madryn, Argentina.
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Miao Y, Johnson NW, Phan T, Heck K, Gedalanga PB, Zheng X, Adamson D, Newell C, Wong MS, Mahendra S. Monitoring, assessment, and prediction of microbial shifts in coupled catalysis and biodegradation of 1,4-dioxane and co-contaminants. WATER RESEARCH 2020; 173:115540. [PMID: 32018172 DOI: 10.1016/j.watres.2020.115540] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/24/2019] [Accepted: 01/22/2020] [Indexed: 06/10/2023]
Abstract
Microbial community dynamics were characterized following combined catalysis and biodegradation treatment trains for mixtures of 1,4-dioxane and chlorinated volatile organic compounds (CVOCs) in laboratory microcosms. Although a few specific bacterial taxa are capable of removing 1,4-dioxane and individual CVOCs, many microorganisms are inhibited when these contaminants are present in mixtures. Chemical catalysis by tungstated zirconia (WOx/ZrO2) and hydrogen peroxide (H2O2) as a non-selective treatment was designed to achieve nearly 20% 1,4-dioxane and over 60% trichloroethene and 50% dichloroethene removals. Post-catalysis, bioaugmentation with 1,4-dioxane metabolizing bacterial strain,Pseudonocardia dioxanivorans CB1190, removed the remaining 1,4-dioxane. The evolution of the microbial community under different conditions was time-dependent but relatively independent of the concentrations of contaminants. The compositions of microbiomes tended to be similar regardless of complex contaminant mixtures during the biodegradation phase, indicating a r-K strategy transition attributed to the shock experienced during catalysis and the subsequent incubation. The originally dominant genera Pseudomonas and Ralstonia were sensitive to catalytic oxidation, and were overwhelmed by Sphingomonas, Rhodococcus, and other catalyst-tolerant microbes, but microbes capable of biodegradation of organics thrived during the incubation. Methane metabolism, chloroalkane-, and chloroalkene degradation pathways appeared to be responsible for CVOC degradation, based on the identifications of haloacetate dehalogenases, 2-haloacid dehalogenases, and cytochrome P450 family. Network analysis highlighted the potential interspecies competition or commensalism, and dynamics of microbiomes during the biodegradation phase that were in line with shifting predominant genera, confirming the deterministic processes guiding the microbial assembly. Collectively, this study demonstrated that catalysis followed by bioaugmentation is an effective treatment for 1,4-dioxane in the presence of high CVOC concentrations, and it enhanced our understanding of microbial ecological impacts resulting from abiotic-biological treatment trains. These results will be valuable for predicting treatment synergies that lead to cost savings and improve remedial outcomes in short-term active remediation as well as long-term changes to the environmental microbial communities.
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Affiliation(s)
- Yu Miao
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA, 90095, United States
| | - Nicholas W Johnson
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA, 90095, United States
| | - Thien Phan
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA, 90095, United States
| | - Kimberly Heck
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, 77005, United States
| | - Phillip B Gedalanga
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA, 90095, United States; Department of Public Health, California State University, Fullerton, CA, 92834, United States
| | - Xiaoru Zheng
- Department of Statistics, University of California, Los Angeles, CA, 90095, United States
| | - David Adamson
- GSI Environmental Inc., Houston, TX, 77098, United States
| | - Charles Newell
- GSI Environmental Inc., Houston, TX, 77098, United States
| | - Michael S Wong
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, 77005, United States
| | - Shaily Mahendra
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA, 90095, United States.
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Shabanpour M, Daneshyar M, Parhizkar M, Lucas-Borja ME, Antonio Zema D. Influence of crops on soil properties in agricultural lands of northern Iran. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 711:134694. [PMID: 32000321 DOI: 10.1016/j.scitotenv.2019.134694] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/23/2019] [Accepted: 09/26/2019] [Indexed: 06/10/2023]
Abstract
This study evaluates the effects of land use and soil management on a combination of physico-chemical, biological and hydrological properties of soil, in order to assess its quality. Three land uses were selected at the Fuman area, near Masouleh (Iran), grouping soils covered by tea, garden crops and rice. A total of 24 soil samples (3 land uses × 4 replications × 2 soil layers, topsoil and sub-surface soil) was collected; microbial respiration, available water, stability of soil aggregates, pH, organic matter, cation exchange capacity and nutrient content (P, K, N, Mg and Ca) were determined in each land use/soil layer. In comparison with other land uses, garden showed the highest available water, aggregate stability, microbial respiration, nutrient contents and cation exchange capacity, whereas the latter three soil properties had the lowest values in soils covered by tea and rice crops. Based on these results, under the experimental conditions garden had the highest soil quality among the investigated land uses. Conversely, much caution must be paid to some soil properties of tea and rice crops, such as cation exchange capacity, microbial respiration and nutrient contents, which are the lowest among the investigated land uses. Moreover, the differences in the analysed soil properties between the two soil sampling depths were statistically significant (p < 0.05). Finally, a Principal Component Analysis clearly clustered soils covered by garden, tea and rice crops in three differentiated groups according to the sampled soil properties. This study provides a contribution in understanding the variability of soil properties under different land uses, indicating that some of these properties must be considered with caution, in order to avoid a decay of soil health.
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Affiliation(s)
- Mahmood Shabanpour
- Soil Science Department, Faculty of Agricultural Sciences, University of Guilan, Rasht 41635-1314, Iran
| | - Maedeh Daneshyar
- Soil Science Department, Faculty of Agricultural Sciences, University of Guilan, Rasht 41635-1314, Iran
| | - Misagh Parhizkar
- Soil Science Department, Faculty of Agricultural Sciences, University of Guilan, Rasht 41635-1314, Iran
| | - Manuel Esteban Lucas-Borja
- Escuela Técnica Superior Ingenieros Agrónomos y Montes, Universidad de Castilla-La Mancha. Campus Universitario, Albacete E-02071, Spain.
| | - Demetrio Antonio Zema
- Department AGRARIA, Mediterranean University of Reggio Calabria, Loc. Feo di Vito, Reggio Calabria I-89122, Italy
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44
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Muñoz-Arenas LC, Fusaro C, Hernández-Guzmán M, Dendooven L, Estrada-Torres A, Navarro-Noya YE. Soil microbial diversity drops with land-use change in a high mountain temperate forest: a metagenomics survey. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:185-194. [PMID: 31965701 DOI: 10.1111/1758-2229.12822] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 01/12/2020] [Accepted: 01/16/2020] [Indexed: 06/10/2023]
Abstract
Land-use change has been identified as the most severe threat to biodiversity. Soils are important biodiversity reservoirs, but to what extent conversion of high-altitude temperate forest to arable land affects taxonomic and functional soil biodiversity is still largely unknown. Shotgun metagenomics was used to determine the taxonomic and functional diversity of bacteria, archaea and DNA virus in terms of effective number of species in high-altitude temperate oak and pine-oak forest and arable soils from Mexico. Generally, the soil ecosystem maintained its microbial species richness notwithstanding land-use change. Archaea diversity was not affected by land-use change, but the bacterial diversity decreased with 45-55% when the oak forest was converted to arable land and 65-75% when the pine-oak forest was. Loss in bacterial diversity as a result of land-use change was positively correlated (R2 = 0.41) with the 10-25% loss in functional diversity. The archaeal communities were evener than the bacterial ones, which might explain their different response to land-use change. We expected a decrease in DNA viral communities as the bacterial diversity decreased, i.e. their potential hosts. However, a higher viral diversity was found in the arable than in the forest soils. It was found that converting high altitude oak and pine-oak forests to arable land more than halved the bacterial diversity, but did not affect the archaeal and even increased the viral diversity.
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Affiliation(s)
- Ligia C Muñoz-Arenas
- Doctorado en Ciencias Biológicas, Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala, Tlaxcala de Xicohténcatl, Tlaxcala, Mexico
- Facultad de Ingeniería Ambiental, UPAEP Universidad, Puebla, Mexico
| | - Carmine Fusaro
- Doctorado en Ciencias Biológicas, Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala, Tlaxcala de Xicohténcatl, Tlaxcala, Mexico
| | | | - Luc Dendooven
- Laboratory of Soil Ecology, ABACUS-Cinvestav, Ciudad de México, México
| | - Arturo Estrada-Torres
- Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala, Tlaxcala de Xicohténcatl, Tlaxcala, México
| | - Yendi E Navarro-Noya
- Cátedras Conacyt-Universidad Autónoma de Tlaxcala, Tlaxcala de Xicohténcatl, Tlaxcala, México
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Prudent M, Dequiedt S, Sorin C, Girodet S, Nowak V, Duc G, Salon C, Maron PA. The diversity of soil microbial communities matters when legumes face drought. PLANT, CELL & ENVIRONMENT 2020; 43:1023-1035. [PMID: 31884709 DOI: 10.1111/pce.13712] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/20/2019] [Accepted: 12/23/2019] [Indexed: 05/19/2023]
Abstract
The cultivation of legumes shows promise for the development of sustainable agriculture, but yield instability remains one of the main obstacles for its adoption. Here, we tested whether the yield stability (i.e., resistance and resilience) of pea plants subjected to drought could be enhanced by soil microbial diversity. We used a dilution approach to manipulate the microbial diversity, with a genotype approach to distinguish the effect of symbionts from that of microbial diversity as a whole. We investigated the physiology of plants in response to drought when grown on a soil containing high or low level of microbial diversity. Plants grown under high microbial diversity displayed higher productivity and greater resilience after drought. Yield losses were mitigated by 15% on average in the presence of high soil microbial diversity at sowing. Our study provides proof of concept that the soil microbial community as a whole plays a key role for yield stability after drought even in plant species living in relationships with microbial symbionts. These results emphasize the need to restore soil biodiversity for sustainable crop management and climate change adaptation.
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Affiliation(s)
- Marion Prudent
- Agroécologie, AgroSup Dijon, INRAE, University Bourgogne Franche-Comté, Dijon, France
| | - Samuel Dequiedt
- Agroécologie, AgroSup Dijon, INRAE, University Bourgogne Franche-Comté, Dijon, France
| | - Camille Sorin
- Agroécologie, AgroSup Dijon, INRAE, University Bourgogne Franche-Comté, Dijon, France
| | - Sylvie Girodet
- Agroécologie, AgroSup Dijon, INRAE, University Bourgogne Franche-Comté, Dijon, France
| | - Virginie Nowak
- Agroécologie, AgroSup Dijon, INRAE, University Bourgogne Franche-Comté, Dijon, France
| | - Gérard Duc
- Agroécologie, AgroSup Dijon, INRAE, University Bourgogne Franche-Comté, Dijon, France
| | - Christophe Salon
- Agroécologie, AgroSup Dijon, INRAE, University Bourgogne Franche-Comté, Dijon, France
| | - Pierre-Alain Maron
- Agroécologie, AgroSup Dijon, INRAE, University Bourgogne Franche-Comté, Dijon, France
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46
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Breitkreuz C, Buscot F, Tarkka M, Reitz T. Shifts Between and Among Populations of Wheat Rhizosphere Pseudomonas, Streptomyces and Phyllobacterium Suggest Consistent Phosphate Mobilization at Different Wheat Growth Stages Under Abiotic Stress. Front Microbiol 2020; 10:3109. [PMID: 32038552 PMCID: PMC6987145 DOI: 10.3389/fmicb.2019.03109] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 12/23/2019] [Indexed: 11/13/2022] Open
Abstract
Climate change models predict more frequent and prolonged drought events in Central Europe, which will exert extraordinary pressure on agroecosystems. One of the consequences is drought-related nutrient limitations for crops negatively affecting agricultural productivity. These effects can be mitigated by beneficial plant growth promoting rhizobacteria. In this study, we investigated the potential of cultivable bacterial species for phosphate solubilization in the rhizosphere of winter wheat at two relevant growth stages - stem elongation and grain filling stages. Rhizosphere samples were collected in the Global Change Experimental Facility in Central Germany, which comprises plots with conventional and organic farming systems under ambient and future climate. Phosphate-solubilizing bacteria were selectively isolated on Pikovskaya medium, phylogenetically classified by 16S rRNA sequencing, and tested for in vitro mineral phosphate solubilization and drought tolerance using plate assays. The culture isolates were dominated by members of the genera Phyllobacterium, Pseudomonas and Streptomyces. Cultivation-derived species richness and abundance of dominant taxa, especially within the genera Phyllobacterium and Pseudomonas, as well as composition of Pseudomonas species were affected by wheat growth stage. Pseudomonas was found to be more abundant at stem elongation than at grain filling, while for Phyllobacterium the opposite pattern was observed. The abundance of Streptomyces isolates remained stable throughout the studied growth stages. The temporal shifts in the cultivable fraction of the community along with considerable P solubilization potentials of Phyllobacterium and Pseudomonas species suggest functional redundancy between and among genera at different wheat growth stages. Phosphate-solubilizing Phyllobacterium species were assigned to Phyllobacterium ifriqiyense and Phyllobacterium sophorae. It is the first time that phosphate solubilization potential is described for these species. Since Phyllobacterium species showed the highest drought tolerance along all isolates, they may play an increasingly important role in phosphate solubilization in a future dryer climate.
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Affiliation(s)
- Claudia Breitkreuz
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Halle/Saale, Germany
| | - François Buscot
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Halle/Saale, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Mika Tarkka
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Halle/Saale, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Thomas Reitz
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, Halle/Saale, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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47
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Konstantinou S, Monokrousos N, Kapagianni P, Menkissoglu‐Spiroudi U, Gwynn‐Jones D, Stamou GP, Papatheodorou EM. Instantaneous responses of microbial communities to stress in soils pretreated with
Mentha spicata
essential oil and/or inoculated with arbuscular mycorrhizal fungus. Ecol Res 2019. [DOI: 10.1111/1440-1703.12030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Sotiris Konstantinou
- Department of Ecology, School of Biology Aristotle University of Thessaloniki Thessaloniki Greece
| | - Nikos Monokrousos
- Department of Soil Science of Athens, Institute of Soil and Water Resources Hellenic Agricultural Organization‐DEMETER Athens Greece
| | - Pantelitsa Kapagianni
- Department of Ecology, School of Biology Aristotle University of Thessaloniki Thessaloniki Greece
| | - Urania Menkissoglu‐Spiroudi
- Laboratory of Pesticide Science School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment Thessaloniki Greece
| | - Dylan Gwynn‐Jones
- Institute of Biological Environmental and Rural Sciences Aberystwyth University Ceredigion UK
| | | | - Efimia M. Papatheodorou
- Department of Ecology, School of Biology Aristotle University of Thessaloniki Thessaloniki Greece
- International Hellenic University Thessaloniki Greece
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Shi W, Li M, Wei G, Tian R, Li C, Wang B, Lin R, Shi C, Chi X, Zhou B, Gao Z. The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome. MICROBIOME 2019; 7:14. [PMID: 30709420 PMCID: PMC6359780 DOI: 10.1186/s40168-019-0629-2] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 01/17/2019] [Indexed: 05/17/2023]
Abstract
BACKGROUND Soil microorganisms can mediate the occurrence of plant diseases. Potato common scab (CS) is a refractory disease caused by pathogenic Streptomyces that occurs worldwide, but little is known about the interactions between CS and the soil microbiome. In this study, four soil-root system compartments (geocaulosphere soil (GS), rhizosphere soil (RS), root-zone soil (ZS), and furrow soil (FS)) were analyzed for potato plants with naturally high (H) and low (L) scab severity levels. We aimed to determine the composition and putative function of the soil microbiome associated with potato CS. RESULTS The copy numbers of the scab phytotoxin biosynthetic gene txtAB and the bacterial 16S rRNA gene as well as the diversity and composition of each of the four soil-root system compartments were examined; GS was the only compartment that exhibited significant differences between the H and L groups. Compared to the H group, the L group exhibited a lower txtAB gene copy number, lower bacterial 16S copy number, higher diversity, higher co-occurrence network complexity, and higher community function similarity within the GS microbiome. The community composition and function of the GS samples were further revealed by shotgun metagenomic sequencing. Variovorax, Stenotrophomonas, and Agrobacterium were the most abundant genera that were significantly and positively correlated with the scab severity level, estimated absolute abundance (EAA) of pathogenic Streptomyces, and txtAB gene copy number. In contrast, Geobacillus, Curtobacterium, and unclassified Geodermatophilaceae were significantly negatively correlated with these three parameters. Compared to the function profiles in the L group, several genes involved in "ABC transporters," the "bacterial secretion system," "quorum sensing (QS)," "nitrogen metabolism," and some metabolism by cytochrome P450 were enriched in the H group. In contrast, some antibiotic biosynthesis pathways were enriched in the L group. Based on the differences in community composition and function, a simple model was proposed to explain the putative relationships between the soil microbiome and CS occurrence. CONCLUSIONS The GS microbiome was closely associated with CS severity in the soil-root system, and the occurrence of CS was accompanied by changes in community composition and function. The differential functions provide new clues to elucidate the mechanism underlying the interaction between CS occurrence and the soil microbiome, and varying community compositions provide novel insights into CS occurrence.
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Affiliation(s)
- Wencong Shi
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Mingcong Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Guangshan Wei
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, 361005, China
- South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Sun Yat-Sen University, Guangzhou, 510275, China
| | - Renmao Tian
- Department of Botany and Microbiology, Institute for Environmental Genomics, University of Oklahoma, Norman, USA
| | - Cuiping Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Bing Wang
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, 271018, China
| | - Rongshan Lin
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, 271018, China
| | - Chunyu Shi
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
- College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
| | - Xiuli Chi
- Plant Protection Station, Jiaozhou Agricultural Bureau, Qingdao, 266300, China
| | - Bo Zhou
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, 271018, China.
| | - Zheng Gao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China.
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.
- Department of Botany and Microbiology, Institute for Environmental Genomics, University of Oklahoma, Norman, USA.
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Zhao Z, Zhang X, Dong S, Wu Y, Liu S, Su X, Wang X, Zhang Y, Tang L. Soil organic carbon and total nitrogen stocks in alpine ecosystems of Altun Mountain National Nature Reserve in dry China. ENVIRONMENTAL MONITORING AND ASSESSMENT 2018; 191:40. [PMID: 30593592 DOI: 10.1007/s10661-018-7138-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 12/03/2018] [Indexed: 06/09/2023]
Abstract
The Altun Mountain National Nature Reserve (AMNNR), characterized by complex topography, is located on the northern edge of the Qinghai-Tibetan Plateau. The stocks of soil organic carbon (SOC) and total nitrogen (TN) are critically important for carbon and nitrogen sequestration in dry alpine ecosystems of the AMNNR, which is a "natural laboratory" for assessing the carbon and nitrogen storage without human disturbance. We explored the stocks of SOC and TN in soils of different dry alpine ecosystems by sampling 23 sites across the AMNNR during 2013. The results showed that the SOC and TN stocks of AMNNR varied significantly with ecosystem types. The SOC stocks of 0-15 cm were highest in the alpine wet meadow (7.96 kg/m2), followed by alpine steppe (2.63 kg/m2). The stocks of SOC and TN in 0-5 and 5-10 cm soils of alpine wet meadow were significantly (P < 0.05) higher than those in the soils of other dry alpine ecosystems. In the whole AMNNR, total storage of SOC and TN were approximately 80.97 and 4.48 Tg, 34.25% of SOC and 24.01% of TN were stored in the alpine steppe, 21.51% of SOC and 26.01% of TN were stored in the alpine scrub, the largest ecosystem in the AMNNR. Our findings suggested it is important to protect the soil and vegetation of the dry alpine ecosystems, particularly the alpine wet meadow and alpine scrub to promote the carbon storage.
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Affiliation(s)
- Zhenzhen Zhao
- School of Environment, Beijing Normal University, No. 19, XinJieKouWai St., HaiDian District, Beijing, 100875, China
- School of Environmental and Chemical Engineering, Shanghai University, No. 99, Shangda Road, Baoshan District, Shanghai, 200444, China
| | - Xiangfeng Zhang
- School of Environment, Beijing Normal University, No. 19, XinJieKouWai St., HaiDian District, Beijing, 100875, China
| | - Shikui Dong
- School of Environment, Beijing Normal University, No. 19, XinJieKouWai St., HaiDian District, Beijing, 100875, China.
| | - Yu Wu
- School of Environment, Beijing Normal University, No. 19, XinJieKouWai St., HaiDian District, Beijing, 100875, China
| | - Shiliang Liu
- School of Environment, Beijing Normal University, No. 19, XinJieKouWai St., HaiDian District, Beijing, 100875, China
| | - Xukun Su
- School of Environment, Beijing Normal University, No. 19, XinJieKouWai St., HaiDian District, Beijing, 100875, China
| | - Xuexia Wang
- School of Environment, Beijing Normal University, No. 19, XinJieKouWai St., HaiDian District, Beijing, 100875, China
| | - Yong Zhang
- School of Environment, Beijing Normal University, No. 19, XinJieKouWai St., HaiDian District, Beijing, 100875, China
| | - Lin Tang
- School of Environment, Beijing Normal University, No. 19, XinJieKouWai St., HaiDian District, Beijing, 100875, China
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50
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Karačić S, Wilén BM, Suarez C, Hagelia P, Persson F. Subsea tunnel reinforced sprayed concrete subjected to deterioration harbours distinct microbial communities. BIOFOULING 2018; 34:1161-1174. [PMID: 30740996 DOI: 10.1080/08927014.2018.1556259] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 11/29/2018] [Accepted: 11/29/2018] [Indexed: 06/09/2023]
Abstract
Deterioration of concrete is a large societal cost. In the Oslofjord subsea tunnel (Norway), deterioration of sprayed concrete and corrosion of reinforcing steel fibres occur under biofilm formed at sites with intrusion of saline groundwater. In this study, the microbial community structure, in situ environmental gradients and chemical composition of the biofilms were examined at three tunnel sites. Ammonia- and nitrite-oxidising microorganisms, in particular Nitrosopumilus sp., and iron-oxidising bacteria within Mariprofundus sp., were omnipresent, together with a diversity of presumably heterotrophic bacteria. Alpha- and beta diversity measures showed significant differences in richness and community structure between the sites as well as over time and null-models suggested that deterministic factors were important for the community assembly. The superficial flow of water over the biofilm had a strong effect on oxygen penetration in the biofilm and was identified as one major environmental gradient that varied between the sites, likely being important for shaping the microbial communities.
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Affiliation(s)
- Sabina Karačić
- a Department of Architecture and Civil Engineering , Chalmers University of Technology , Göteborg , Göteborg , Sweden
| | - Britt-Marie Wilén
- a Department of Architecture and Civil Engineering , Chalmers University of Technology , Göteborg , Göteborg , Sweden
| | - Carolina Suarez
- b Department of Chemistry and Molecular Biology , University of Gothenburg , Göteborg , Göteborg , Sweden
| | - Per Hagelia
- c Tunnel and Concrete Division , The Norwegian Public Roads Administration , Oslo , Norway
| | - Frank Persson
- a Department of Architecture and Civil Engineering , Chalmers University of Technology , Göteborg , Göteborg , Sweden
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