1
|
Yang J, Ouyang L, Chen S, Zhang C, Zheng J, He S. Amendments affect the community assembly and co-occurrence network of microorganisms in Cd and Pb tailings of the Eucalyptus camaldulensis rhizosphere. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 930:172365. [PMID: 38641118 DOI: 10.1016/j.scitotenv.2024.172365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 04/08/2024] [Accepted: 04/08/2024] [Indexed: 04/21/2024]
Abstract
Mining tailings containing large amounts of Pb and Cd cause severe regional ecosystem pollution. Soil microorganisms play a regulatory role in the restoration of degraded ecosystems. The remediation of heavy metal-contaminated tailings with amendments and economically valuable Eucalyptus camaldulensis is a research hotspot due to its cost-effectiveness and sustainability. However, the succession and co-occurrence patterns of these microbial communities in this context remain unclear. Tailing samples of five kinds of Cd and Pb were collected in E. camaldulensis restoration models. Physicochemical properties, the proportions of different Cd and Pb forms, microbial community structure, and the co-occurrence network of rhizosphere tailings during different restoration process (organic bacterial manure, organic manure, inorganic fertilizer, bacterial agent) were considered. Organic and organic bacterial manures significantly increased pH, cation exchange capacity, and the proportion of residual Pb. Still, there was a significant decrease in the proportion of reducible Pb. The changes in microbial communities were related to physicochemical properties and the types of amendments. Organic and organic bacterium manures decreased the relative abundance of oligotrophic groups and increased the relative abundance of syntrophic groups. Inorganic fertilizers and bacterial agents decreased the relative abundance of saprophytic fungi. B. subtilis would play a better role in the environment improved by organic manure, increasing the relative abundance of beneficial microorganism and reducing the relative abundance of pathogenic microorganism. pH, cation exchange capacity, and the proportion of different forms of Pb were the main factors affecting the bacterial and fungi variation. All four amendments transformed the main critical groups of the microbial network structure from acidophilus and pathogenic microorganisms to beneficial microorganisms. Heavy metal-resistant microorganisms, stress-resistant microorganisms, beneficial microorganisms that promote nutrient cycling, and copiotrophic groups have become critical to building stable rhizosphere microbial communities. The topological properties and stability of the rhizosphere co-occurrence network were also enhanced. Adding organic and organic bacterium manures combined with E. camaldulensis to repair Cd and Pb tailings improved (1) pH and cation exchange capacity, (2) reduced the biological toxicity of Pb, (3) enhanced the stability of microbial networks, and (4) improved ecological network relationships. These positive changes are conducive to the restoration of the ecological functions of tailings.
Collapse
Affiliation(s)
- Jiaqi Yang
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, State Key Laboratory of Efficient Production of Forest Resources, Zhanjiang 524022, China
| | - Linnan Ouyang
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, State Key Laboratory of Efficient Production of Forest Resources, Zhanjiang 524022, China.
| | - Shaoxiong Chen
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, State Key Laboratory of Efficient Production of Forest Resources, Zhanjiang 524022, China
| | - Cheng Zhang
- Experimental Forest Farm of Qingyuan County,Qingyuan 323800, China
| | - Jiaqi Zheng
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, State Key Laboratory of Efficient Production of Forest Resources, Zhanjiang 524022, China
| | - Shae He
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, State Key Laboratory of Efficient Production of Forest Resources, Zhanjiang 524022, China
| |
Collapse
|
2
|
Sun QW, Chen JZ, Liao XF, Huang XL, Liu JM. Identification of keystone taxa in rhizosphere microbial communities using different methods and their effects on compounds of the host Cinnamomum migao. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171952. [PMID: 38537823 DOI: 10.1016/j.scitotenv.2024.171952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 03/21/2024] [Accepted: 03/23/2024] [Indexed: 04/02/2024]
Abstract
Exploring keystone taxa affecting microbial community stability and host function is crucial for understanding ecosystem functions. However, identifying keystone taxa from humongous microbial communities remains challenging. We collected 344 rhizosphere and bulk soil samples from the endangered plant C. migao for 2 years consecutively. Used high-throughput sequencing 16S rDNA and ITS to obtain the composition of bacterial and fungal communities. We explored keystone taxa and the applicability and limitations of five methods (SPEC-OCCU, Zi-Pi, Subnetwork, Betweenness, and Module), as well as the impact of microbial community domain, time series, and rhizosphere boundary on the identification of keystone taxa in the communities. Our results showed that the five methods, identified abundant keystone taxa in rhizosphere and bulk soil microbial communities. However, the keystone taxa shared by the rhizosphere and bulk soil microbial communities over time decreased rapidly decrease in the five methods. Among five methods on the identification of keystone taxa in the rhizosphere community, Module identified 113 taxa, SPEC-OCCU identified 17 taxa, Betweenness identified 3 taxa, Subnetwork identified 3 taxa, and Zi-Pi identified 4 taxa. The keystone taxa are mainly conditionally rare taxa, and their ecological functions include chemoheterotrophy, aerobic chemoheterotrophy, nitrate reduction, and anaerobic photoautotrophy. The results of the random forest model and structural equation model predict that keystone taxa Mortierella and Ellin6513 may have an effects on the accumulation of 1, 4, 7, - Cycloundecatriene, 1, 5, 9, 9-tetramethyl-, Z, Z, Z-, beta-copaene, bicyclogermacrene, 1,8-Cineole in C. migao fruits, but their effects still need further evidence. Our study evidence an unstable microbial community in the bulk soil, and the definition of microbial boundary and ecologically functional affected the identification of keystone taxa in the community. Subnetwork and Module are more in line with the definition of keystone taxa in microbial ecosystems in terms of maintaining community stability and hosting function.
Collapse
Affiliation(s)
- Qing-Wen Sun
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China; Guizhou Province Key Laboratory of Chinese Pharmacology and Pharmacognosy, 550025, China
| | - Jing-Zhong Chen
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China; Guizhou Province Key Laboratory of Chinese Pharmacology and Pharmacognosy, 550025, China.
| | | | | | - Ji-Ming Liu
- College of Forestry, Guizhou University, Guiyang 550025, China
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
Liu X, Liu H, Zhang Y, Liu C, Liu Y, Li Z, Zhang M. Organic amendments alter microbiota assembly to stimulate soil metabolism for improving soil quality in wheat-maize rotation system. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 339:117927. [PMID: 37075633 DOI: 10.1016/j.jenvman.2023.117927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 03/20/2023] [Accepted: 04/10/2023] [Indexed: 05/03/2023]
Abstract
Straw retention (SR) and organic fertilizer (OF) application contribute to improve soil quality, but it is unclear how the soil microbial assemblage under organic amendments mediate soil biochemical metabolism pathways to perform it. This study collected soil samples from wheat field under different application of fertilizer (chemical fertilizer, as control; SR, and OF) in North China Plain, and systematically investigated the interlinkages among microbe assemblages, metabolites, and physicochemical properties. Results showed that the soil organic carbon (SOC) and permanganate oxidizable organic carbon (LOC) in soil samples followed the trend as OF > SR > control, and the activity of C-acquiring enzymes presented significantly positive correlation with SOC and LOC. In organic amendments, bacteria and fungi community were respectively dominated by deterministic and stochastic processes, while OF exerted more selective pressure on soil microbe. Compared with SR, OF had greater potential to boost the microbial community robustness through increasing the natural connectivity and stimulating fungal taxa activities in inter-kingdom microbial networks. Altogether 67 soil metabolites were significantly affected by organic amendments, most of them belonged to benzenoids (Ben), lipids and lipid-like molecules (LL), and organic acids and derivatives (OA). These metabolites were mainly derived from lipid and amino acid metabolism pathways. A list of keystone genera such as stachybotrys and phytohabitans were identified as important to soil metabolites, SOC, and C-acquiring enzyme activity. Structural equation modeling showed that soil quality properties were closely associated with LL, OA, and PP drove by microbial community assembly and keystone genera. Overall, these findings suggested that straw and organic fertilizer might drive keystone genera dominated by determinism to mediate soil lipid and amino acid metabolism for improving soil quality, which provided new insights into understanding the microbial-mediated biological process in amending soil quality.
Collapse
Affiliation(s)
- Xueqing Liu
- State Key Laboratory of Plant Environmental Resilience, Ministry of Education, Key Laboratory of Farming System, Ministry of Agriculture of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Hongrun Liu
- State Key Laboratory of Plant Environmental Resilience, Ministry of Education, Key Laboratory of Farming System, Ministry of Agriculture of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yushi Zhang
- State Key Laboratory of Plant Environmental Resilience, Ministry of Education, Key Laboratory of Farming System, Ministry of Agriculture of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
| | - Churong Liu
- State Key Laboratory of Plant Environmental Resilience, Ministry of Education, Key Laboratory of Farming System, Ministry of Agriculture of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yanan Liu
- State Key Laboratory of Plant Environmental Resilience, Ministry of Education, Key Laboratory of Farming System, Ministry of Agriculture of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhaohu Li
- State Key Laboratory of Plant Environmental Resilience, Ministry of Education, Key Laboratory of Farming System, Ministry of Agriculture of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Mingcai Zhang
- State Key Laboratory of Plant Environmental Resilience, Ministry of Education, Key Laboratory of Farming System, Ministry of Agriculture of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
5
|
Kurth JK, Albrecht M, Glaser K, Karsten U, Vestergaard G, Armbruster M, Kublik S, Schmid CAO, Schloter M, Schulz S. Biological soil crusts on agricultural soils of mesic regions promote microbial cross-kingdom co-occurrences and nutrient retention. Front Microbiol 2023; 14:1169958. [PMID: 37520365 PMCID: PMC10382179 DOI: 10.3389/fmicb.2023.1169958] [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: 02/20/2023] [Accepted: 06/21/2023] [Indexed: 08/01/2023] Open
Abstract
Introduction Biological soil crusts (biocrusts) are known as biological hotspots on undisturbed, nutrient-poor bare soil surfaces and until now, are mostly observed in (semi-) arid regions but are currently poorly understood in agricultural systems. This is a crucial knowledge gap because managed sites of mesic regions can quickly cover large areas. Thus, we addressed the questions (i) if biocrusts from agricultural sites of mesic regions also increase nutrients and microbial biomass as their (semi-) arid counterparts, and (ii) how microbial community assemblage in those biocrusts is influenced by disturbances like different fertilization and tillage regimes. Methods We compared phototrophic biomass, nutrient concentrations as well as the abundance, diversity and co-occurrence of Archaea, Bacteria, and Fungi in biocrusts and bare soils at a site with low agricultural soil quality. Results and Discussion Biocrusts built up significant quantities of phototrophic and microbial biomass and stored more nutrients compared to bare soils independent of the fertilizer applied and the tillage management. Surprisingly, particularly low abundant Actinobacteria were highly connected in the networks of biocrusts. In contrast, Cyanobacteria were rarely connected, which indicates reduced importance within the microbial community of the biocrusts. However, in bare soil networks, Cyanobacteria were the most connected bacterial group and, hence, might play a role in early biocrust formation due to their ability to, e.g., fix nitrogen and thus induce hotspot-like properties. The microbial community composition differed and network complexity was reduced by conventional tillage. Mineral and organic fertilizers led to networks that are more complex with a higher percentage of positive correlations favoring microbe-microbe interactions. Our study demonstrates that biocrusts represent a microbial hotspot on soil surfaces under agricultural use, which may have important implications for sustainable management of such soils in the future.
Collapse
Affiliation(s)
- Julia Katharina Kurth
- Chair for Environmental Microbiology, TUM School of Life Science, Technical University Munich, Freising, Germany
- Environmental Health Centre, Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Neuherberg, Germany
| | - Martin Albrecht
- Department of Applied Ecology and Phycology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Karin Glaser
- Department of Applied Ecology and Phycology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Ulf Karsten
- Department of Applied Ecology and Phycology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Gisle Vestergaard
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Martin Armbruster
- Agricultural Analytical and Research Institute Speyer (LUFA Speyer), Speyer, Germany
| | - Susanne Kublik
- Environmental Health Centre, Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Neuherberg, Germany
| | - Christoph A. O. Schmid
- Environmental Health Centre, Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Neuherberg, Germany
| | - Michael Schloter
- Chair for Environmental Microbiology, TUM School of Life Science, Technical University Munich, Freising, Germany
- Environmental Health Centre, Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Neuherberg, Germany
| | - Stefanie Schulz
- Environmental Health Centre, Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Neuherberg, Germany
| |
Collapse
|
6
|
Aguado-Norese C, Cárdenas V, Gaete A, Mandakovic D, Vasquez-Dean J, Hodar C, Pfeiffer M, Gonzalez M. Topsoil and subsoil bacterial community assemblies across different drainage conditions in a mountain environment. Biol Res 2023; 56:35. [PMID: 37355658 DOI: 10.1186/s40659-023-00445-2] [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: 09/15/2022] [Accepted: 06/08/2023] [Indexed: 06/26/2023] Open
Abstract
BACKGROUND High mountainous environments are of particular interest as they play an essential role for life and human societies, while being environments which are highly vulnerable to climate change and land use intensification. Despite this, our knowledge of high mountain soils in South America and their microbial community structure is strikingly scarce, which is of more concern considering the large population that depends on the ecosystem services provided by these areas. Conversely, the Central Andes, located in the Mediterranean region of Chile, has long been studied for its singular flora, whose diversity and endemism has been attributed to the particular geological history and pronounced environmental gradients in short distances. Here, we explore soil properties and microbial community structure depending on drainage class in a well-preserved Andean valley on the lower alpine vegetation belt (~2500 m a.s.l.) at 33.5˚S. This presents an opportunity to determine changes in the overall bacterial community structure across different types of soils and their distinct layers in a soil depth profile of a highly heterogeneous environment. METHODS Five sites closely located (<1.5 km) and distributed in a well preserved Andean valley on the lower alpine vegetation belt (~2500 m a.s.l.) at 33.5˚S were selected based on a pedological approach taking into account soil types, drainage classes and horizons. We analyzed 113 soil samples using high-throughput sequencing of the 16S rRNA gene to describe bacterial abundance, taxonomic composition, and co-occurrence networks. RESULTS Almost 18,427 Amplicon Sequence Variant (ASVs) affiliated to 55 phyla were detected. The bacterial community structure within the same horizons were very similar validating the pedological sampling approach. Bray-Curtis dissimilarity analysis revealed that the structure of bacterial communities in superficial horizons (topsoil) differed from those found in deep horizons (subsoil) in a site-specific manner. However, an overall closer relationship was observed between topsoil as opposed to between subsoil microbial communities. Alpha diversity of soil bacterial communities was higher in topsoil, which also showed more bacterial members interacting and with higher average connectivity compared to subsoils. Finally, abundances of specific taxa could be considered as biological markers in the transition from topsoil to subsoil horizons, like Fibrobacterota, Proteobacteria, Bacteroidota for shallower soils and Chloroflexi, Latescibacterota and Nitrospirota for deeper soils. CONCLUSIONS The results indicate the importance of the soil drainage conditions for the bacterial community composition, suggesting that information of both structure and their possible ecological relationships, might be useful in clarifying the location of the edge of the topsoil-subsoil transition in mountainous environments.
Collapse
Affiliation(s)
- Constanza Aguado-Norese
- Millennium Institute Center for Genome Regulation, Santiago, 7830490, Chile
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Macul, Chile
| | - Valentina Cárdenas
- Departamento de Ingeniería y Suelos, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile
| | - Alexis Gaete
- Millennium Institute Center for Genome Regulation, Santiago, 7830490, Chile
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Macul, Chile
| | - Dinka Mandakovic
- GEMA Center for Genomics, Ecology and Environment, Universidad Mayor, Santiago, Chile
| | - Javiera Vasquez-Dean
- Millennium Institute Center for Genome Regulation, Santiago, 7830490, Chile
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Macul, Chile
| | - Christian Hodar
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Macul, Chile
- Bioinformatic and Biostatistic Laboratory for Functional Genomics, INTA-Universidad de Chile, Macul, Chile
| | - Marco Pfeiffer
- Departamento de Ingeniería y Suelos, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile.
| | - Mauricio Gonzalez
- Millennium Institute Center for Genome Regulation, Santiago, 7830490, Chile.
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Macul, Chile.
| |
Collapse
|
7
|
Qing L, Qigen D, Jian H, Hongjun W, Jingdu C. Profiles of tetracycline resistance genes in paddy soils with three different organic fertilizer applications. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 306:119368. [PMID: 35489540 DOI: 10.1016/j.envpol.2022.119368] [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: 10/07/2021] [Revised: 04/01/2022] [Accepted: 04/24/2022] [Indexed: 06/14/2023]
Abstract
The rapid expansion of organic rice cultivation areas have been accompanied by increased application of organic fertilizers. The high prevalence of soil antibiotic resistance caused by organic fertilizer application poses a severe threat to the agricultural and soil ecosystems. To date, research efforts and understanding of the effects and mechanism of action of the various organic fertilizers on antibiotic resistance in paddy soils remain poorly investigated. Tetracycline resistance genes (TRGs, including tetB, tetC, tetL, tetZ, tetM, tetO, tetT, and tetX), class 1 integron-integrase gene (intI1) and bacterial communities were characterized using quantitative-PCR and Illumina MiSeq sequencing, in paddy soils exposed to inorganic fertilizer (NPK), animal-derived organic fertilizer (AOF, composted swine and/or chicken manure), plant-derived organic fertilizer (POF, rapeseed cake and/or astragalus) and commercial organic fertilizer (COF, composted of animal manure mix with crop residues) applications. Compared with NPK, AOF applications significantly increased the relative abundance of TRGs, which was predominantly expressed in the increase of the relative abundance of tetC, tetM, tetO, tetT, and tetX, while POF and COF had no significant effect on the relative abundance of TRGs. Principal coordinate analysis revealed that AOF and POF significantly altered bacterial communities in paddy soils relative to NPK, while COF had no significant change of bacterial communities. Variation partitioning analysis indicated that soil physicochemical properties were the decisive factors for the changes of TRGs in organic paddy fields. Furthermore, redundancy analysis and the Mantel test showed that TRG profiles in AOF applied paddy soils were strongly influenced by electrical conductivity (EC). Total nitrogen (TN) and organic matter (OM) affected the distribution of TRGs in COF and POF applied paddy soils through a different mechanism. This study provides insights into the impacts of different types of organic fertilizer on the profiles of TRGs in paddy soils.
Collapse
Affiliation(s)
- Li Qing
- Jiangsu Key Laboratory of Crop Genetic and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Research Institute of Rice Industrial Engineering Technology, Yangzhou University, Yangzhou, 225009, China
| | - Dai Qigen
- Jiangsu Key Laboratory of Crop Genetic and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Research Institute of Rice Industrial Engineering Technology, Yangzhou University, Yangzhou, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, China.
| | - Hu Jian
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, China
| | - Wu Hongjun
- Yangzhou Supervision & Inspection Center for Agri-products, Yangzhou, 225101, China
| | - Chen Jingdu
- Yangzhou Municipal Bureau of Agriculture and Rural Affairs, Yangzhou, 225000, China
| |
Collapse
|
8
|
Zhang X, Park H, Park YJ, Lee K, Yu H, Shin JH, Choo KH. Photolytic quorum quenching effects on the microbial communities and functional gene expressions in membrane bioreactors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 819:152017. [PMID: 34852249 DOI: 10.1016/j.scitotenv.2021.152017] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/07/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
Photolytic quorum quenching by ultraviolet A (UVA) irradiation is an effective strategy for controlling membrane bioreactor (MBR) biofouling; however, its effects on MBR microbial communities and functional genes have not yet been explored. Here, we report on the effects of the UVA irradiation, which mitigates membrane biofouling, on the microbial community structures, alpha and beta diversities, and functional gene expressions in the MBR mixed liquor and biocake (membrane fouling layer) for the first time. The results show that the microbial communities become less diversified when alternating UVA is applied to the MBRs. The changes in the community structure are highly influenced by spatiotemporal factors, such as microbial habitats (mixed liquor and biocake) and reactor operation time, although UVA irradiation also has some impacts on the community. The relative abundance of the Sphingomonadaceae family, which can decompose the furan ring of autoinducer-2 (AI-2) signal molecules, becomes greater with continuous UVA irradiation. Xanthomonadaceae, which produces biofilm-degrading enzymes, is also more abundant with UVA photolysis than without it. Copies of monooxygenase and hydroxylase enzyme-related genes increase in the MBR with longer UVA exposures (i.e., continuous UVA). These enzymes seem to be inducible by UVA, enhancing the AI-2 inactivation. In conclusion, UVA irradiation alters the microbial community and the metabolism in the MBR, contributing to the membrane biofouling mitigation.
Collapse
Affiliation(s)
- Xiaolei Zhang
- Advanced Institute of Water Industry, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea; School of Environmental and Chemical Engineering, Shanghai University, 99 Shangda Road, Shanghai 200444, PR China
| | - Hyeona Park
- School of Architectural, Civil, Environmental, and Energy Engineering, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
| | - Yeong-Jun Park
- Department of Agriculture and Life Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
| | - Kibaek Lee
- Advanced Institute of Water Industry, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea; Department of Biotechnology and Bioengineering, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju 61186, Republic of Korea
| | - Huarong Yu
- Advanced Institute of Water Industry, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea; School of Civil Engineering, Guangzhou University, 230 Wai Huan Xi Road, Guangzhou 510006, PR China
| | - Jae-Ho Shin
- Department of Agriculture and Life Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
| | - Kwang-Ho Choo
- Advanced Institute of Water Industry, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea; School of Architectural, Civil, Environmental, and Energy Engineering, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea; Department of Environmental Engineering, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea.
| |
Collapse
|
9
|
Rui Z, Lu X, Li Z, Lin Z, Lu H, Zhang D, Shen S, Liu X, Zheng J, Drosos M, Cheng K, Bian R, Zhang X, Li L, Pan G. Macroaggregates Serve as Micro-Hotspots Enriched With Functional and Networked Microbial Communities and Enhanced Under Organic/Inorganic Fertilization in a Paddy Topsoil From Southeastern China. Front Microbiol 2022; 13:831746. [PMID: 35495701 PMCID: PMC9039729 DOI: 10.3389/fmicb.2022.831746] [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] [Received: 12/08/2021] [Accepted: 02/28/2022] [Indexed: 11/23/2022] Open
Abstract
Microbial communities of soil aggregate-size fractions were explored with molecular and networking assays for topsoil samples from a clayey rice paddy under long-term fertilization treatments. The treatments included no fertilizer (NF) as control, chemical fertilizer only (CF), chemical fertilizer with swine manure (CFM), and chemical fertilizer with rice straw return (CFS). Following a wet-sieving protocol, water-stable aggregates were separated into size fractions of large macroaggregates (L-MacA, >2,000 μm), macroaggregates (MacA, 2,000-250 μm), microaggregates (MicA, 250-53 μm), fine microaggregates (F-MicA, 53-2 μm), and fine clay (F-Clay, <2 μm). Mass proportion was 32.3-38.2% for F-MicA, 23.0-31.5% for MacA, 19.0-23.1% for MicA, 9.1-12.0% for L-MacA, and 4.9-7.5% for F-Clay, respectively. The proportion of MacA was increased, but F-Clay was reduced by fertilization, whereas the mean weight diameter was increased by 8.0-16.2% from 534.8 μm under NF to 621.5 μm under CFM. Fertilization affected bacterial 16S rRNA and fungal 18S rRNA gene abundance in F-MicA and F-Clay but not in aggregates in size larger than 53 μm. However, bacterial and fungal community α-diversities and community structures were quite more divergent among the fertilization treatments in all size fractions. Organic carbon and gene abundance of bacteria and fungi were enriched in both L-MacA and MacA but depleted in F-Clay, whereas microbial Shannon diversity was rarely changed by fraction size under the four treatments. L-MacA and MacA contained more bacteria of r-strategists and copiotrophs, whereas F-MicA and F-Clay were demonstrated with a higher abundance of K-strategists and oligotrophs. Guilds of parasitic and litter saprotrophic fungi were enriched in F-MicA but depleted in L-MacA. Furthermore, most of bacterial and fungal operational taxonomic units were strongly interacted in L-MacA and MacA rather than in MicA and F-Clay. Thus, MacA acted as micro-hotspots enriched with functional and networked microbial communities, which were enhanced with organic/inorganic fertilization in the rice paddy.
Collapse
Affiliation(s)
- Zhipeng Rui
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
- Department of Soil Science, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Xinda Lu
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Zichuan Li
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
- Department of Soil Science, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Zhi Lin
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
- Department of Soil Science, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Haifei Lu
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
- Department of Soil Science, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Dengxiao Zhang
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
- Department of Soil Science, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | | | - Xiaoyu Liu
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
- Department of Soil Science, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Jufeng Zheng
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
- Department of Soil Science, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Marios Drosos
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
- Department of Soil Science, Nanjing Agricultural University, Nanjing, China
| | - Kun Cheng
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
- Department of Soil Science, Nanjing Agricultural University, Nanjing, China
| | - Rongjun Bian
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
- Department of Soil Science, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Xuhui Zhang
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
- Department of Soil Science, Nanjing Agricultural University, Nanjing, China
| | - Lianqing Li
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
- Department of Soil Science, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Genxing Pan
- Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China
- Department of Soil Science, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| |
Collapse
|
10
|
Qin M, Xu H, Zhao D, Zeng J, Wu QL. Aquaculture drives distinct patterns of planktonic and sedimentary bacterial communities: insights into co-occurrence pattern and assembly processes. Environ Microbiol 2022; 24:4079-4093. [PMID: 35099108 DOI: 10.1111/1462-2920.15922] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 12/13/2021] [Accepted: 01/19/2022] [Indexed: 11/03/2022]
Abstract
Aquaculture would change the environmental condition in the lake ecosystem, affecting the structure and function of the aquatic ecosystem. However, little is known about the underlying mechanisms controlling the distribution patterns of bacterial community respond to aquaculture in water column and sediment. Here, we investigated the composition, co-occurrence patterns, and assembly processes of planktonic and sedimentary bacterial communities (PBC vs. SBC) from an aquaculture-influenced zone of the Eastern Lake Taihu, China. We found that aquaculture activity greatly influenced the diversity and composition of SBC by inducing excess nitrogen into the sediments. Meanwhile, network analysis revealed that aquaculture activity strengthened species interactions within the SBC network but weakened the species interactions within the PBC network. Aquaculture activity also increased the importance of deterministic processes governing the assembly of SBC by heightening the importance of environmental filtering, whereas it decreased the relative importance of deterministic processes within the assembly of PBC. In addition, ecological restoration with macrophytes increased the diversity of PBC and formed a more stable PBC network by increasing the number of network keystones. Overall, our results indicated that aquaculture drove distinct co-occurrence patterns and assembly mechanisms of PBC and SBC. This study has fundamental implications in the lake ecosystem for evaluating the microbially mediated ecological consequences of aquaculture.
Collapse
Affiliation(s)
- Mengyu Qin
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China
| | - Huimin Xu
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China.,State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Dayong Zhao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.,Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, 100039, China
| |
Collapse
|
11
|
Schröder P, Mench M, Povilaitis V, Rineau F, Rutkowska B, Schloter M, Szulc W, Žydelis R, Loit E. Relaunch cropping on marginal soils by incorporating amendments and beneficial trace elements in an interdisciplinary approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 803:149844. [PMID: 34525739 DOI: 10.1016/j.scitotenv.2021.149844] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 06/13/2023]
Abstract
In the EU and world-wide, agriculture is in transition. Whilst we just converted conventional farming imprinted by the post-war food demand and heavy agrochemical usage into integrated and sustainable farming with optimized production, we now have to focus on even smarter agricultural management. Enhanced nutrient efficiency and resistance to pests/pathogens combined with a greener footprint will be crucial for future sustainable farming and its wider environment. Future land use must embrace efficient production and utilization of biomass for improved economic, environmental, and social outcomes, as subsumed under the EU Green Deal, including also sites that have so far been considered as marginal and excluded from production. Another frontier is to supply high-quality food and feed to increase the nutrient density of staple crops. In diets of over two-thirds of the world's population, more than one micronutrient (Fe, Zn, I or Se) is lacking. To improve nutritious values of crops, it will be necessary to combine integrated, systems-based approaches of land management with sustainable redevelopment of agriculture, including central ecosystem services, on so far neglected sites: neglected grassland, set aside land, and marginal lands, paying attention to their connectivity with natural areas. Here we need new integrative approaches which allow the application of different instruments to provide us not only with biomass of sufficient quality and quantity in a site specific manner, but also to improve soil ecological services, e.g. soil C sequestration, water quality, habitat and soil resistance to erosion, while keeping fertilization as low as possible. Such instruments may include the application of different forms of high carbon amendments, the application of macro- and microelements to improve crop performance and quality as well as a targeted manipulation of the soil microbiome. Under certain caveats, the potential of such sites can be unlocked by innovative production systems, ready for the sustainable production of crops enriched in micronutrients and providing services within a circular economy.
Collapse
Affiliation(s)
- Peter Schröder
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Research Unit for Comparative Microiome Analysis, D-85764 Neuherberg, Germany.
| | - Michel Mench
- Univ. Bordeaux, INRAE, BIOGECO, UMR 1202, F-33615 Pessac, France
| | - Virmantas Povilaitis
- Lithuanian Research Centre for Agriculture and Forestry, Akademija LT-58344, Kedainiai distr. Lithuania
| | - Francois Rineau
- Hasselt University, Agoralaan Gebouw D, B-3590 Diepenbeek, Belgium
| | - Beata Rutkowska
- Warsaw University of Life Sciences - SGGW, 02-787 Warsaw, Poland
| | - Michael Schloter
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Research Unit for Comparative Microiome Analysis, D-85764 Neuherberg, Germany
| | - Wieslaw Szulc
- Warsaw University of Life Sciences - SGGW, 02-787 Warsaw, Poland
| | - Renaldas Žydelis
- Lithuanian Research Centre for Agriculture and Forestry, Akademija LT-58344, Kedainiai distr. Lithuania
| | - Evelin Loit
- Estonian University of Life Sciences, Chair of Field Crops and Plant Biology, 51006 Tartu, Estonia.
| |
Collapse
|
12
|
Stavridou E, Giannakis I, Karamichali I, Kamou NN, Lagiotis G, Madesis P, Emmanouil C, Kungolos A, Nianiou-Obeidat I, Lagopodi AL. Biosolid-Amended Soil Enhances Defense Responses in Tomato Based on Metagenomic Profile and Expression of Pathogenesis-Related Genes. PLANTS (BASEL, SWITZERLAND) 2021; 10:2789. [PMID: 34961260 PMCID: PMC8709368 DOI: 10.3390/plants10122789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/12/2021] [Accepted: 12/13/2021] [Indexed: 05/28/2023]
Abstract
Biosolid application is an effective strategy, alternative to synthetic chemicals, for enhancing plant growth and performance and improving soil properties. In previous research, biosolid application has shown promising results with respect to tomato resistance against Fusarium oxysporum f. sp. radicis-lycopersici (Forl). Herein, we aimed at elucidating the effect of biosolid application on the plant-microbiome response mechanisms for tomato resistance against Forl at a molecular level. More specifically, plant-microbiome interactions in the presence of biosolid application and the biocontrol mechanism against Forl in tomato were investigated. We examined whether biosolids application in vitro could act as an inhibitor of growth and sporulation of Forl. The effect of biosolid application on the biocontrol of Forl was investigated based on the enhanced plant resistance, measured as expression of pathogen-response genes, and pathogen suppression in the context of soil microbiome diversity, abundance, and predicted functions. The expression of the pathogen-response genes was variably induced in tomato plants in different time points between 12 and 72 h post inoculation in the biosolid-enriched treatments, in the presence or absence of pathogens, indicating activation of defense responses in the plant. This further suggests that biosolid application resulted in a successful priming of tomato plants inducing resistance mechanisms against Forl. Our results have also demonstrated that biosolid application alters microbial diversity and the predicted soil functioning, along with the relative abundance of specific phyla and classes, as a proxy for disease suppression. Overall, the use of biosolid as a sustainable soil amendment had positive effects not only on plant health and protection, but also on growth of non-pathogenic antagonistic microorganisms against Forl in the tomato rhizosphere and thus, on plant-soil microbiome interactions, toward biocontrol of Forl.
Collapse
Affiliation(s)
- Evangelia Stavridou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, 57001 Thessaloniki, Greece; (E.S.); (I.K.); (G.L.); (P.M.)
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Ioannis Giannakis
- School of Civil Engineering, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (I.G.); (A.K.)
| | - Ioanna Karamichali
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, 57001 Thessaloniki, Greece; (E.S.); (I.K.); (G.L.); (P.M.)
| | - Nathalie N. Kamou
- Laboratory of Plant Pathology, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - George Lagiotis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, 57001 Thessaloniki, Greece; (E.S.); (I.K.); (G.L.); (P.M.)
| | - Panagiotis Madesis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, 57001 Thessaloniki, Greece; (E.S.); (I.K.); (G.L.); (P.M.)
- Laboratory of Molecular Biology of Plants, School of Agricultural Sciences, University of Thessaly, 38221 Volos, Greece
| | - Christina Emmanouil
- School of Spatial Planning and Development, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Athanasios Kungolos
- School of Civil Engineering, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (I.G.); (A.K.)
| | - Irini Nianiou-Obeidat
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Anastasia L. Lagopodi
- Laboratory of Plant Pathology, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| |
Collapse
|
13
|
Wang Q, Huang Q, Wang J, Khan MA, Guo G, Liu Y, Hu S, Jin F, Wang J, Yu Y. Dissolved organic carbon drives nutrient cycling via microbial community in paddy soil. CHEMOSPHERE 2021; 285:131472. [PMID: 34265723 DOI: 10.1016/j.chemosphere.2021.131472] [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: 05/07/2021] [Revised: 07/01/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
Microbial mediated iron cycling drives the biogeochemical cycling of carbon, nitrogen, sulfur, and phosphorus. However, the fate of the microbial community and the relative metabolic pathways in paddy soil after the addition of biogas slurry are poorly understood. In this study, the response of functional genes was investigated by growing one-season rice in paddy soils in a pot experiment. Seven treatments were prepared: 1) control (CK); 2) organic carbon (OC); 3) fertilizer (F); 4) 5% of biogas slurry (B05); 5) 10% of biogas slurry (B10); 6) 15% of biogas slurry (B15); 7) 20% of biogas slurry (B20). In the biogas slurry treatments, Geobacter increased more than in the other treatments during rice growth, which were structured by TOC. Particularly, in the B10 treatment, the relative abundance of Geobacter was 1.6 and 14.8 times higher than that of CK at the heading and mature stages, respectively. At the heading stage, the addition of biogas slurry and OC shifted the microbial phosphorus-transformation communities differently. There were no significant differences in the carbon, nitrogen, and sulfur metabolic pathways between the two treatments. At the mature stage, the carbon: nitrogen: phosphorus balance was significantly influenced by the regulation of functional gene expression and metabolic activities. These findings provide insight into the key factors affecting carbon, nitrogen, sulfur, phosphorus, and iron during rice growth after carbon inputs.
Collapse
Affiliation(s)
- Qingqing Wang
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Haikou, 570228, China; Center for Eco-Environmental Restoration Engineering of Hainan Province, Haikou, 570228, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, China; Key Laboratory for Environmental Toxicology of Haikou, Hainan University, Haikou, Hainan, 570228, China
| | - Qing Huang
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Haikou, 570228, China; Center for Eco-Environmental Restoration Engineering of Hainan Province, Haikou, 570228, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, China; Key Laboratory for Environmental Toxicology of Haikou, Hainan University, Haikou, Hainan, 570228, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
| | - Jiaxin Wang
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Haikou, 570228, China; Center for Eco-Environmental Restoration Engineering of Hainan Province, Haikou, 570228, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, China; Key Laboratory for Environmental Toxicology of Haikou, Hainan University, Haikou, Hainan, 570228, China
| | - Muhammad Amjad Khan
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Haikou, 570228, China; Center for Eco-Environmental Restoration Engineering of Hainan Province, Haikou, 570228, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, China; Key Laboratory for Environmental Toxicology of Haikou, Hainan University, Haikou, Hainan, 570228, China
| | - Genmao Guo
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Haikou, 570228, China; Center for Eco-Environmental Restoration Engineering of Hainan Province, Haikou, 570228, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, China; Key Laboratory for Environmental Toxicology of Haikou, Hainan University, Haikou, Hainan, 570228, China
| | - Yin Liu
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Haikou, 570228, China; Center for Eco-Environmental Restoration Engineering of Hainan Province, Haikou, 570228, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, China; Key Laboratory for Environmental Toxicology of Haikou, Hainan University, Haikou, Hainan, 570228, China
| | - Shan Hu
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Haikou, 570228, China; Center for Eco-Environmental Restoration Engineering of Hainan Province, Haikou, 570228, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, China; Key Laboratory for Environmental Toxicology of Haikou, Hainan University, Haikou, Hainan, 570228, China
| | - Fangming Jin
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Haikou, 570228, China; Center for Eco-Environmental Restoration Engineering of Hainan Province, Haikou, 570228, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, China; Key Laboratory for Environmental Toxicology of Haikou, Hainan University, Haikou, Hainan, 570228, China
| | - Junfeng Wang
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Haikou, 570228, China; Center for Eco-Environmental Restoration Engineering of Hainan Province, Haikou, 570228, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, China; Key Laboratory for Environmental Toxicology of Haikou, Hainan University, Haikou, Hainan, 570228, China; College of Civil and Transportation Engineering, Shenzhen University, Shenzhen, Guangdong, 518061, China
| | - Yunbo Yu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 10085, China
| |
Collapse
|
14
|
Wang H, Li X, Li X, Li F, Su Z, Zhang H. Community Composition and Co-Occurrence Patterns of Diazotrophs along a Soil Profile in Paddy Fields of Three Soil Types in China. MICROBIAL ECOLOGY 2021; 82:961-970. [PMID: 33660069 DOI: 10.1007/s00248-021-01716-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 02/07/2021] [Indexed: 06/12/2023]
Abstract
Diazotrophs play a key role in biological nitrogen (N2) fixation. However, we know little about the distribution of the diazotrophic community along the soil profile in paddy fields. Here, we used Illumina MiSeq sequencing, targeting the nitrogenase reductase (nifH) gene, to investigate changes with depth (0-100 cm) in the diazotrophic community in paddy soils of three regions (Changshu, Hailun, and Yingtan) in China. The results indicated that most diazotrophs belonged to the phylum Proteobacteria, accounting for 78.05% of the total number of sequences. The diazotrophic diversity was generally highest in the 10-20 cm layer, and then significantly decreased with soil depth. Principal coordinate analysis and PERMANOVA indicated that the diazotrophic community structure was significantly affected by region and soil depth. There were obvious differences in the composition of the diazotrophic community between the topsoil (0-40 cm) and the subsoil (40-100 cm). Anaeromyxobacter, Sideroxydans, Methylomonas, Nostoc, Methanocella, and Methanosaeta were enriched in the topsoil, while Geobacter, Azoarcus, Bradyrhizobium, and Dechloromonas were concentrated in the subsoil. Furthermore, co-occurrence network analysis showed that the diazotrophic network in the topsoil was more complex than that in the subsoil. Distance-based redundancy analysis indicated that soil total C and N content and pH were the main factors influencing the vertical variation in the diazotrophic community. These results highlighted that depth has a great impact on the diazotrophic diversity, community composition, and co-occurrence patterns in paddy soil.
Collapse
Affiliation(s)
- Huanhuan Wang
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Xu Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, China
| | - Xinyu Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, China.
| | - Fuli Li
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Zhencheng Su
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, China
| | - Huiwen Zhang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, China
| |
Collapse
|
15
|
Yang T, Lupwayi N, Marc SA, Siddique KH, Bainard LD. Anthropogenic drivers of soil microbial communities and impacts on soil biological functions in agroecosystems. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01521] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
|
16
|
Studying Microbial Communities through Co-Occurrence Network Analyses during Processes of Waste Treatment and in Organically Amended Soils: A Review. Microorganisms 2021; 9:microorganisms9061165. [PMID: 34071426 PMCID: PMC8227910 DOI: 10.3390/microorganisms9061165] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/20/2021] [Accepted: 05/27/2021] [Indexed: 11/16/2022] Open
Abstract
Organic wastes have the potential to be used as soil organic amendments after undergoing a process of stabilization such as composting or as a resource of renewable energy by anaerobic digestion (AD). Both composting and AD are well-known, eco-friendly approaches to eliminate and recycle massive amounts of wastes. Likewise, the application of compost amendments and digestate (the by-product resulting from AD) has been proposed as an effective way of improving soil fertility. The study of microbial communities involved in these waste treatment processes, as well as in organically amended soils, is key in promoting waste resource efficiency and deciphering the features that characterize microbial communities under improved soil fertility conditions. To move beyond the classical analyses of metataxonomic data, the application of co-occurrence network approaches has shown to be useful to gain insights into the interactions among the members of a microbial community, to identify its keystone members and modelling the environmental factors that drive microbial network patterns. Here, we provide an overview of essential concepts for the interpretation and construction of co-occurrence networks and review the features of microbial co-occurrence networks during the processes of composting and AD and following the application of the respective end products (compost and digestate) into soil.
Collapse
|
17
|
Chen H, Zheng C, Qiao Y, Du S, Li W, Zhang X, Zhao Z, Cao C, Zhang W. Long-term organic and inorganic fertilization alters the diazotrophic abundance, community structure, and co-occurrence patterns in a vertisol. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 766:142441. [PMID: 33097271 DOI: 10.1016/j.scitotenv.2020.142441] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 09/10/2020] [Accepted: 09/12/2020] [Indexed: 06/11/2023]
Abstract
Diazotrophs play a critical role in converting air-inactive nitrogen to bio-available nitrogen. Assessing the influences of different fertilization regimes on diazotrophs is essential for a better understanding of their maintenance of soil fertility and agricultural sustainability. In this study, we targeted the nifH gene to investigate the effects of different long-term fertilization on the diazotrophic community in a vertisol, using real-time quantitative polymerase chain reaction (PCR) and MiSeq sequencing. Five fertilization regimes were tested: no fertilizer (CK), chemical nitrogen, phosphorus, and potassium fertilizer (NPK), organic fertilizer (O), chemical NPK plus organic fertilizer with an equivalent application rate of nitrogen (NPKO), and chemical NPK plus organic fertilizer with a high application rate of nitrogen (HNPKO). Our results showed that fertilization significantly affected the diazotrophic activity, abundance and composition. NPK tended to reduce the activity, abundance, operational taxonomic units (OTU)-richness and alpha-diversity of the diazotrophs, while O had the opposite effect. The effects of inorganic and organic fertilization on the diazotrophs depended on the N application rate, showing that the diazotrophic activity, abundance, and alpha-diversity in NPKO were higher than that of HNPKO. For the diazotrophic community structure, CK, O, and NPKO were grouped and separated from NPK and HNPKO. The diazotrophic community structure strongly correlated with the soil pH, electrical conductivity (EC), total carbon content (TC), and total nitrogen content (TN), among which pH was the major factor shaping the diazotrophic community structure. Different network patterns were observed between the long-term organic and non-organic fertilizers, suggesting that the organic amendment resulted in a more complicated diazotrophic community than the non-organic amendments. Rhizobium was the most important hub connecting members in the community. These results indicated that organic amendments are beneficial to diazotrophic activity, abundance, OTU richness, alpha-diversity, and the diazotrophic communities' potential interactions, which may enhance biological nitrogen fixation in vertisols.
Collapse
Affiliation(s)
- Huan Chen
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China; Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chengyan Zheng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuqiang Qiao
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Shizhou Du
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Wei Li
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xiangqian Zhang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Zhu Zhao
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Chengfu Cao
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China.
| | - Weijian Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| |
Collapse
|
18
|
Windisch S, Sommermann L, Babin D, Chowdhury SP, Grosch R, Moradtalab N, Walker F, Höglinger B, El-Hasan A, Armbruster W, Nesme J, Sørensen SJ, Schellenberg I, Geistlinger J, Smalla K, Rothballer M, Ludewig U, Neumann G. Impact of Long-Term Organic and Mineral Fertilization on Rhizosphere Metabolites, Root-Microbial Interactions and Plant Health of Lettuce. Front Microbiol 2021; 11:597745. [PMID: 33519736 PMCID: PMC7838544 DOI: 10.3389/fmicb.2020.597745] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/18/2020] [Indexed: 11/13/2022] Open
Abstract
Fertilization management can affect plant performance and soil microbiota, involving still poorly understood rhizosphere interactions. We hypothesized that fertilization practice exerts specific effects on rhizodeposition with consequences for recruitment of rhizosphere microbiota and plant performance. To address this hypothesis, we conducted a minirhizotron experiment using lettuce as model plant and field soils with contrasting properties from two long-term field experiments (HUB-LTE: loamy sand, DOK-LTE: silty loam) with organic and mineral fertilization history. Increased relative abundance of plant-beneficial arbuscular mycorrhizal fungi and fungal pathotrophs were characteristic of the rhizospheres in the organically managed soils (HU-org; BIODYN2). Accordingly, defense-related genes were systemically expressed in shoot tissues of the respective plants. As a site-specific effect, high relative occurrence of the fungal lettuce pathogen Olpidium sp. (76-90%) was recorded in the rhizosphere, both under long-term organic and mineral fertilization at the DOK-LTE site, likely supporting Olpidium infection due to a lower water drainage potential compared to the sandy HUB-LTE soils. However, plant growth depressions and Olpidium infection were exclusively recorded in the BIODYN2 soil with organic fertilization history. This was associated with a drastic (87-97%) reduction in rhizosphere abundance of potentially plant-beneficial microbiota (Pseudomonadaceae, Mortierella elongata) and reduced concentrations of the antifungal root exudate benzoate, known to be increased in presence of Pseudomonas spp. In contrast, high relative abundance of Pseudomonadaceae (Gammaproteobacteria) in the rhizosphere of plants grown in soils with long-term mineral fertilization (61-74%) coincided with high rhizosphere concentrations of chemotactic dicarboxylates (succinate, malate) and a high C (sugar)/N (amino acid) ratio, known to support the growth of Gammaproteobacteria. This was related with generally lower systemic expression of plant defense genes as compared with organic fertilization history. Our results suggest a complex network of belowground interactions among root exudates, site-specific factors and rhizosphere microbiota, modulating the impact of fertilization management with consequences for plant health and performance.
Collapse
Affiliation(s)
- Saskia Windisch
- Department of Nutritional Crop Physiology, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - Loreen Sommermann
- Institute of Bioanalytical Sciences (IBAS), Anhalt University of Applied Sciences, Bernburg, Germany
| | - Doreen Babin
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute – Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | | | - Rita Grosch
- Plant-Microbe Systems, Leibniz Institute of Vegetable and Ornamental Crops, Großbeeren, Germany
| | - Narges Moradtalab
- Department of Nutritional Crop Physiology, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - Frank Walker
- Central Chemical-Analytical Laboratory, Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
| | - Birgit Höglinger
- Central Chemical-Analytical Laboratory, Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
| | - Abbas El-Hasan
- Department of Phytopathology, Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
| | - Wolfgang Armbruster
- Department of Food Chemistry and Analytical Chemistry, Institute of Food Chemistry, University of Hohenheim, Stuttgart, Germany
| | - Joseph Nesme
- Department of Biology, Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Søren Johannes Sørensen
- Department of Biology, Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Ingo Schellenberg
- Institute of Bioanalytical Sciences (IBAS), Anhalt University of Applied Sciences, Bernburg, Germany
| | - Jörg Geistlinger
- Institute of Bioanalytical Sciences (IBAS), Anhalt University of Applied Sciences, Bernburg, Germany
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute – Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Michael Rothballer
- Institute of Network Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Uwe Ludewig
- Department of Nutritional Crop Physiology, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - Günter Neumann
- Department of Nutritional Crop Physiology, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| |
Collapse
|
19
|
Ray P, Lakshmanan V, Labbé JL, Craven KD. Microbe to Microbiome: A Paradigm Shift in the Application of Microorganisms for Sustainable Agriculture. Front Microbiol 2020; 11:622926. [PMID: 33408712 PMCID: PMC7779556 DOI: 10.3389/fmicb.2020.622926] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 12/02/2020] [Indexed: 12/14/2022] Open
Abstract
Light, water and healthy soil are three essential natural resources required for agricultural productivity. Industrialization of agriculture has resulted in intensification of cropping practices using enormous amounts of chemical pesticides and fertilizers that damage these natural resources. Therefore, there is a need to embrace agriculture practices that do not depend on greater use of fertilizers and water to meet the growing demand of global food requirements. Plants and soil harbor millions of microorganisms, which collectively form a microbial community known as the microbiome. An effective microbiome can offer benefits to its host, including plant growth promotion, nutrient use efficiency, and control of pests and phytopathogens. Therefore, there is an immediate need to bring functional potential of plant-associated microbiome and its innovation into crop production. In addition to that, new scientific methodologies that can track the nutrient flux through the plant, its resident microbiome and surrounding soil, will offer new opportunities for the design of more efficient microbial consortia design. It is now increasingly acknowledged that the diversity of a microbial inoculum is as important as its plant growth promoting ability. Not surprisingly, outcomes from such plant and soil microbiome studies have resulted in a paradigm shift away from single, specific soil microbes to a more holistic microbiome approach for enhancing crop productivity and the restoration of soil health. Herein, we have reviewed this paradigm shift and discussed various aspects of benign microbiome-based approaches for sustainable agriculture.
Collapse
Affiliation(s)
- Prasun Ray
- Noble Research Institute, LLC, Ardmore, OK, United States
| | | | - Jessy L. Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | | |
Collapse
|
20
|
Ding GC, Bai M, Han H, Li H, Ding X, Yang H, Xu T, Li J. Microbial taxonomic, nitrogen cycling and phosphorus recycling community composition during long-term organic greenhouse farming. FEMS Microbiol Ecol 2020; 95:5423879. [PMID: 30927421 DOI: 10.1093/femsec/fiz042] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 03/29/2019] [Indexed: 11/14/2022] Open
Abstract
Understanding the interplay between the farming system and soil microbiomes could aid the design of a sustainable and efficient farming system. A comparative greenhouse experiment consisting of organic (ORG), integrated (INT) and conventional (CON) farming systems was established in northern China in 2002. The effects of 12 years of organic farming on soil microbiomes were explored by metagenomic and 16S rRNA gene amplicon sequencing analyses. Long-term ORG shifted the community composition of dominant phyla, especially Acidobacteria, increased the relative abundance of Ignavibacteria and Acidobacteria Gp6 and decreased the relative abundance of Nitrosomonas, Bacillus and Paenibacillus. Metagenomic analysis further revealed that relative abundance of ammonia oxidizing microorganisms (Bacteria and Archaea) and anaerobic ammonium oxidation bacteria decreased during ORG. Conversely, the relative abundance of bacteria-carrying periplasmic nitrate reductases (napA) was slightly higher for ORG. Long-term organic farming also caused significant alterations to the community composition of functional groups associated with ammonia oxidation, denitrification and phosphorus recycling. In summary, this study provides key insights into the composition of soil microbiomes and long-term organic farming under greenhouse conditions.
Collapse
Affiliation(s)
- Guo-Chun Ding
- Beijing Key Laboratory of Biodiversity and Organic Farming, Department of Ecology and Ecological Engineering, College of Resources and Environmental Science, China Agricultural University,100193, Beijing, China.,Organic Recycling Institute(Suzhou) of China Agricultural University,215128, Wuzhong, Jiangsu Province, China
| | - Mohan Bai
- Beijing Key Laboratory of Biodiversity and Organic Farming, Department of Ecology and Ecological Engineering, College of Resources and Environmental Science, China Agricultural University,100193, Beijing, China
| | - Hui Han
- Beijing Key Laboratory of Biodiversity and Organic Farming, Department of Ecology and Ecological Engineering, College of Resources and Environmental Science, China Agricultural University,100193, Beijing, China
| | - Huixiu Li
- Beijing Key Laboratory of Biodiversity and Organic Farming, Department of Ecology and Ecological Engineering, College of Resources and Environmental Science, China Agricultural University,100193, Beijing, China
| | - Xiaoyan Ding
- Beijing Key Laboratory of Biodiversity and Organic Farming, Department of Ecology and Ecological Engineering, College of Resources and Environmental Science, China Agricultural University,100193, Beijing, China
| | - Hefa Yang
- Quzhou Experimental Station of China Agricultural University, 057250, Quzhou County, Hebei Province, China
| | - Ting Xu
- Beijing Key Laboratory of Biodiversity and Organic Farming, Department of Ecology and Ecological Engineering, College of Resources and Environmental Science, China Agricultural University,100193, Beijing, China.,Organic Recycling Institute(Suzhou) of China Agricultural University,215128, Wuzhong, Jiangsu Province, China
| | - Ji Li
- Beijing Key Laboratory of Biodiversity and Organic Farming, Department of Ecology and Ecological Engineering, College of Resources and Environmental Science, China Agricultural University,100193, Beijing, China.,Organic Recycling Institute(Suzhou) of China Agricultural University,215128, Wuzhong, Jiangsu Province, China
| |
Collapse
|
21
|
The Response of the Soil Microbiota to Long-Term Mineral and Organic Nitrogen Fertilization is Stronger in the Bulk Soil than in the Rhizosphere. Genes (Basel) 2020; 11:genes11040456. [PMID: 32331348 PMCID: PMC7230438 DOI: 10.3390/genes11040456] [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: 03/27/2020] [Revised: 04/14/2020] [Accepted: 04/20/2020] [Indexed: 11/19/2022] Open
Abstract
The effects of different agronomic practices, such as fertilization regimes, can be experimentally tested in long-term experiments (LTE). Here, we aimed to evaluate the effect of different nitrogen fertilizations on the bacterial microbiota in both rhizosphere and bulk soil of sugar beet, in the Giessen-LTE (Germany). Fertilization treatments included mineral-N, manure, mineral-N + manure and no N-amendment. Metabarcoding and co-occurrence analysis of 16S rRNA genes, qPCR of amoA, nirK, nirS, nosZ-I and nosZ-II genes and soil physico-chemical analyses were performed. The effect of the fertilization treatments was more evident in the bulk soil, involving 33.1% of the microbiota. Co-occurrence analysis showed a rhizosphere cluster, dominated by Proteobacteria, Actinobacteria and Verrucomicrobia (hub taxa: Betaproteobacteriales), and a bulk soil cluster, dominated by Acidobacteria, Gemmatominadetes and “Latescibacteria” (hub taxa: Acidobacteria). In the bulk soil, mineral N-fertilization reduced nirK, amoA, nosZ-I and nosZ-II genes. Thirteen Operational taxonomic units (OTUs) showed 23 negative correlations with gene relative abundances. These OTUs likely represent opportunistic species that profited from the amended mineral-N and outgrew the species carrying N-cycle genes. Our results indicate trajectories for future research on soil microbiome in LTE and add new experimental evidence that will be helpful for sustainable management of nitrogen fertilizations on arable soils.
Collapse
|
22
|
Schierstaedt J, Grosch R, Schikora A. Agricultural production systems can serve as reservoir for human pathogens. FEMS Microbiol Lett 2020; 366:5715908. [PMID: 31981360 DOI: 10.1093/femsle/fnaa016] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 01/21/2020] [Indexed: 12/31/2022] Open
Abstract
Food-borne diseases are a threat to human health and can cause severe economic losses. Nowadays, in a growing and increasingly interconnected world, food-borne diseases need to be dealt with in a global manner. In order to tackle this issue, it is essential to consider all possible entry routes of human pathogens into the production chain. Besides the post-harvest handling of the fresh produce itself, also the prevention of contamination in livestock and agricultural soils are of particular importance. While the monitoring of human pathogens and intervening measures are relatively easy to apply in livestock and post-harvest, the investigation of the prevention strategies in crop fields is a challenging task. Furthermore, crop fields are interconnected with livestock via fertilizers and feed; therefore, a poor hygiene management can cause cross-contamination. In this review, we highlight the possible contamination of crop plants by bacterial human pathogens via the rhizosphere, their interaction with the plant and possible intervention strategies. Furthermore, we discuss critical issues and questions that are still open.
Collapse
Affiliation(s)
- Jasper Schierstaedt
- Plant-Microbe Systems, Leibniz Institute of Vegetable and Ornamental Crops, 14979 Großbeeren, Germany
| | - Rita Grosch
- Plant-Microbe Systems, Leibniz Institute of Vegetable and Ornamental Crops, 14979 Großbeeren, Germany
| | - Adam Schikora
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, 38104 Braunschweig, Germany
| |
Collapse
|
23
|
Suleiman AKA, Harkes P, van den Elsen S, Holterman M, Korthals GW, Helder J, Kuramae EE. Organic amendment strengthens interkingdom associations in the soil and rhizosphere of barley (Hordeum vulgare). THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 695:133885. [PMID: 31756853 DOI: 10.1016/j.scitotenv.2019.133885] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/25/2019] [Accepted: 08/10/2019] [Indexed: 06/10/2023]
Abstract
Anthropogenic modification of soil systems has diverse impacts on food web interactions and ecosystem functioning. To understand the positive, neutral or adverse effects of agricultural practices on the associations of community members of soil microbes and microfaunal biomes, we characterized the effects of different fertilization types (organic, inorganic and a combination of organic and inorganic) on the food web active communities in the bulk soil and rhizosphere compartments in field conditions. We examined the influence of fertilization on (i) individual groups (bacteria, protozoa and fungi as microbe representatives and metazoans as microfauna representatives) and (ii) inter-kingdom interactions (focusing on the interactions between bacteria and eukaryotic groups) both neglecting and considering environmental factors in our analysis in combination with the microbial compositional data. Our results revealed different patterns of biota communities under organic versus inorganic fertilization, which shaped food web associations in both the bulk and rhizosphere compartments. Overall, organic fertilization increased the complexity of microbial-microfaunal ecological associations with inter- and intra- connections among categories of primary decomposers (bacteria and fungi) and predators (protozoa and microfauna) and differences in potential function in the soil food web in both the bulk and rhizosphere compartments. Furthermore, the inter-connections between primary decomposers and predators in bulk soil were more pronounced when environmental factors were considered. We suggest that organic fertilization selects bacterial orders with different potential ecological functions and interactions as survival, predation and cooperation due to more complex environment than those of inorganic or combined fertilization. Our findings support the importance of a comprehensive understanding of trophic food web patterns for soil management systems.
Collapse
Affiliation(s)
- Afnan K A Suleiman
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Wageningen, the Netherlands.
| | - Paula Harkes
- Wageningen University and Research Centre (WUR), Laboratory of Nematology, Wageningen, the Netherlands.
| | - Sven van den Elsen
- Wageningen University and Research Centre (WUR), Laboratory of Nematology, Wageningen, the Netherlands.
| | - Martijn Holterman
- Wageningen University and Research Centre (WUR), Laboratory of Nematology, Wageningen, the Netherlands.
| | - Gerard W Korthals
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Wageningen, the Netherlands; Wageningen University and Research Centre (WUR), Laboratory of Nematology, Wageningen, the Netherlands.
| | - Johannes Helder
- Wageningen University and Research Centre (WUR), Laboratory of Nematology, Wageningen, the Netherlands
| | - Eiko E Kuramae
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Wageningen, the Netherlands.
| |
Collapse
|
24
|
Paul Chowdhury S, Babin D, Sandmann M, Jacquiod S, Sommermann L, Sørensen SJ, Fliessbach A, Mäder P, Geistlinger J, Smalla K, Rothballer M, Grosch R. Effect of long-term organic and mineral fertilization strategies on rhizosphere microbiota assemblage and performance of lettuce. Environ Microbiol 2019; 21:2426-2439. [PMID: 30990945 PMCID: PMC6849853 DOI: 10.1111/1462-2920.14631] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 04/12/2019] [Accepted: 04/15/2019] [Indexed: 11/30/2022]
Abstract
Long-term agricultural fertilization strategies gradually change soil properties including the associated microbial communities. Cultivated crops recruit beneficial microbes from the surrounding soil environment via root exudates. In this study, we aimed to investigate the effects of long-term fertilization strategies across field sites on the rhizosphere prokaryotic (Bacteria and Archaea) community composition and plant performance. We conducted growth chamber experiments with lettuce (Lactuca sativa L.) cultivated in soils from two long-term field experiments, each of which compared organic versus mineral fertilization strategies. 16S rRNA gene amplicon sequencing revealed the assemblage of a rhizosphere core microbiota shared in all lettuce plants across soils, going beyond differences in community composition depending on field site and fertilization strategies. The enhanced expression of several plant genes with roles in oxidative and biotic stress signalling pathways in lettuce grown in soils with organic indicates an induced physiological status in plants. Lettuce plants grown in soils with different fertilization histories were visibly free of stress symptoms and achieved comparable biomass. This suggests a positive aboveground plant response to belowground plant-microbe interactions in the rhizosphere. Besides effects of fertilization strategy and field site, our results demonstrate the crucial role of the plant in driving rhizosphere microbiota assemblage.
Collapse
Affiliation(s)
- Soumitra Paul Chowdhury
- Helmholtz Zentrum München, German Research Center for Environmental HealthInstitute of Network BiologyGermany
| | - Doreen Babin
- Federal Research Centre for Cultivated Plants, Julius Kühn‐InstitutInstitute for Epidemiology and Pathogen DiagnosticsBraunschweigGermany
| | - Martin Sandmann
- Plant‐Microbe SystemsLeibniz Institute of Vegetable and Ornamental CropsGroßbeerenGermany
| | - Samuel Jacquiod
- Agroécologie, AgroSup Dijon, INRAUniversity Bourgogne Franche‐ComtéFrance
| | - Loreen Sommermann
- Institute of Bioanalytical SciencesAnhalt University of Applied SciencesBernburgGermany
| | | | - Andreas Fliessbach
- Department of Soil SciencesResearch Institute of Organic Agriculture (FiBL)FrickSwitzerland
| | - Paul Mäder
- Department of Soil SciencesResearch Institute of Organic Agriculture (FiBL)FrickSwitzerland
| | - Joerg Geistlinger
- Institute of Bioanalytical SciencesAnhalt University of Applied SciencesBernburgGermany
| | - Kornelia Smalla
- Federal Research Centre for Cultivated Plants, Julius Kühn‐InstitutInstitute for Epidemiology and Pathogen DiagnosticsBraunschweigGermany
| | - Michael Rothballer
- Helmholtz Zentrum München, German Research Center for Environmental HealthInstitute of Network BiologyGermany
| | - Rita Grosch
- Plant‐Microbe SystemsLeibniz Institute of Vegetable and Ornamental CropsGroßbeerenGermany
| |
Collapse
|
25
|
Blubaugh CK, Carpenter-Boggs L, Reganold JP, Schaeffer RN, Snyder WE. Bacteria and Competing Herbivores Weaken Top-Down and Bottom-Up Aphid Suppression. FRONTIERS IN PLANT SCIENCE 2018; 9:1239. [PMID: 30233608 PMCID: PMC6129616 DOI: 10.3389/fpls.2018.01239] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 08/06/2018] [Indexed: 05/30/2023]
Abstract
Herbivore suppression is mediated by both plant defenses and predators. In turn, plant defenses are impacted by soil fertility and interactions with soil bacteria. Measuring the relative importance of nutritional and microbial drivers of herbivore resistance has proven problematic, in part because it is difficult to manipulate soil-bacterial community composition. Here, we exploit variation in soil fertility and microbial biodiversity across 20 farms to untangle suppression of aphids (Brevicoryne brassicae) through bottom-up and top-down channels. We planted Brassica oleracea plants in soil from each farm, manipulated single and dual infestations of aphids alone or with caterpillars (Pieris rapae), and exposed aphids to parasitoid wasps (Diaeretiella rapae) in the open field. We then used multi-model inference to identify the strongest soil-based predictors of herbivore growth and parasitism. We found that densities of Bacillus spp., a genus known to include plant-growth-promoting rhizobacteria, negatively correlated with aphid suppression by specialist parasitoids. Aphid parasitism also was disrupted on plants that had caterpillar damage, compared to plants attacked only by aphids. Relative abundance of Pseudomonas spp. bacteria correlated with higher aphid growth, although this appeared to be a direct effect, as aphid parasitism was not associated with this group of bacteria. Non-pathogenic soil bacteria are often shown to deliver benefits to plants, improving plant nutrition and the deployment of anti-herbivore defenses. However, our results suggest that these plant growth-promoting bacteria may also indirectly weaken top-down aphid suppression by parasitoids and directly improve aphid performance. Against a background of varying soil fertility, microbial biodiversity, competing herbivores, and natural enemies, we found that effects of non-pathogenic soil microbes on aphid growth outweighed those of nutritional factors. Therefore, predictions about the strength of plant defenses along resource gradients must be expanded to include microbial associates.
Collapse
Affiliation(s)
- Carmen K. Blubaugh
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
- Department of Entomology, Washington State University, Pullman, WA, United States
| | - Lynne Carpenter-Boggs
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - John P. Reganold
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Robert N. Schaeffer
- Department of Entomology, Washington State University, Pullman, WA, United States
| | - William E. Snyder
- Department of Entomology, Washington State University, Pullman, WA, United States
| |
Collapse
|
26
|
Kavamura VN, Hayat R, Clark IM, Rossmann M, Mendes R, Hirsch PR, Mauchline TH. Inorganic Nitrogen Application Affects Both Taxonomical and Predicted Functional Structure of Wheat Rhizosphere Bacterial Communities. Front Microbiol 2018; 9:1074. [PMID: 29896167 PMCID: PMC5986887 DOI: 10.3389/fmicb.2018.01074] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/04/2018] [Indexed: 01/21/2023] Open
Abstract
The effects of fertilizer regime on bulk soil microbial communities have been well studied, but this is not the case for the rhizosphere microbiome. The aim of this work was to assess the impact of fertilization regime on wheat rhizosphere microbiome assembly and 16S rRNA gene-predicted functions with soil from the long term Broadbalk experiment at Rothamsted Research. Soil from four N fertilization regimes (organic N, zero N, medium inorganic N and high inorganic N) was sown with seeds of Triticum aestivum cv. Cadenza. 16S rRNA gene amplicon sequencing was performed with the Illumina platform on bulk soil and rhizosphere samples of 4-week-old and flowering plants (10 weeks). Phylogenetic and 16S rRNA gene-predicted functional analyses were performed. Fertilization regime affected the structure and composition of wheat rhizosphere bacterial communities. Acidobacteria and Planctomycetes were significantly depleted in treatments receiving inorganic N, whereas the addition of high levels of inorganic N enriched members of the phylum Bacteroidetes, especially after 10 weeks. Bacterial richness and diversity decreased with inorganic nitrogen inputs and was highest after organic treatment (FYM). In general, high levels of inorganic nitrogen fertilizers negatively affect bacterial richness and diversity, leading to a less stable bacterial community structure over time, whereas, more stable bacterial communities are provided by organic amendments. 16S rRNA gene-predicted functional structure was more affected by growth stage than by fertilizer treatment, although, some functions related to energy metabolism and metabolism of terpenoids and polyketides were enriched in samples not receiving any inorganic N, whereas inorganic N addition enriched predicted functions related to metabolism of other amino acids and carbohydrates. Understanding the impact of different fertilizers on the structure and dynamics of the rhizosphere microbiome is an important step toward developing strategies for production of crops in a sustainable way.
Collapse
Affiliation(s)
- Vanessa N. Kavamura
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, United Kingdom
| | - Rifat Hayat
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, United Kingdom
- PMAS Arid Agriculture University, Rawalpindi, Pakistan
| | - Ian M. Clark
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, United Kingdom
| | - Maike Rossmann
- Laboratory of Environmental Microbiology, Embrapa Meio Ambiente, Jaguariúna, Brazil
| | - Rodrigo Mendes
- Laboratory of Environmental Microbiology, Embrapa Meio Ambiente, Jaguariúna, Brazil
| | - Penny R. Hirsch
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, United Kingdom
| | - Tim H. Mauchline
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, United Kingdom
| |
Collapse
|