51
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Carreras-Sempere M, Biel C, Viñas M, Guivernau M, Caceres R. The use of recovered struvite and ammonium nitrate in fertigation in a horticultural rotation: agronomic and microbiological assessment. ENVIRONMENTAL TECHNOLOGY 2022:1-17. [PMID: 36453585 DOI: 10.1080/09593330.2022.2154172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Phosphorus and nitrogen recovery from wastewater as struvite and ammonium nitrate (AN) may be viable alternative fertilizers to boost circularity in horticulture. A 2-year fertigated crop rotation in soil under greenhouse conditions was evaluated to determine the efficiency of both recovered products as raw materials for a nutrient solution (NS) manufacture. The effects of these treatments versus synthetic fertilizers were compared in terms of crop performance, plant nutrient uptake, soil chemistry and microbiota. This is the first study to implement struvite through fertigation as the sole source of P in soil crops. Results showed that both recovered products can be used as fertilizers in NS, due to the similar response to the control for different parameters and crops (tomato, lettuce, and cauliflower). However, the AN treatment showed lower yield in the first tomato crop, which results may depend on the cultivar ammonium tolerance. Besides, the concentration of heavy metals in fruits/leaves was below the permissible limits. Total and Olsen phosphorus soil analysis revealed no differences among treatments, resulting in a similar performance of P-struvite to commercial phosphate. Bulk soil bacteria structure, richness and relative dominance were increased over time, while archaea only showed lower evenness, both despite the fertilization strategy. Shannon diversity was not significantly affected. A predominance of ammonia-oxidizing bacteria (AOB) versus archaea (AOA) was observed, while nitrite-oxidizing bacteria (NOB), dominated by Nitrospira, increased with fertigation. Our results demonstrate that fertilizer blends for NS containing recovered nutrients are a feasible alternative to synthetic fertilizers.
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Affiliation(s)
- Mar Carreras-Sempere
- Sustainable Plant Protection Program, Institute of Agrifood Research and Technology (IRTA), Cabrils, Spain
- Sustainability in Biosystems Program, Institute of Agrifood Research and Technology (IRTA), Caldes de Montbui, Spain
| | - Carmen Biel
- Sustainable Plant Protection Program, Institute of Agrifood Research and Technology (IRTA), Cabrils, Spain
| | - Marc Viñas
- Sustainability in Biosystems Program, Institute of Agrifood Research and Technology (IRTA), Caldes de Montbui, Spain
| | - Miriam Guivernau
- Sustainability in Biosystems Program, Institute of Agrifood Research and Technology (IRTA), Caldes de Montbui, Spain
| | - Rafaela Caceres
- Sustainable Plant Protection Program, Institute of Agrifood Research and Technology (IRTA), Cabrils, Spain
- Sustainability in Biosystems Program, Institute of Agrifood Research and Technology (IRTA), Caldes de Montbui, Spain
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52
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Ducousso-Détrez A, Raveau R, Fontaine J, Hijri M, Lounès-Hadj Sahraoui A. Glomerales Dominate Arbuscular Mycorrhizal Fungal Communities Associated with Spontaneous Plants in Phosphate-Rich Soils of Former Rock Phosphate Mining Sites. Microorganisms 2022; 10:microorganisms10122406. [PMID: 36557659 PMCID: PMC9782746 DOI: 10.3390/microorganisms10122406] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/25/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) are key drivers of soil functioning. They interact with multiple soil parameters, notably, phosphorus (P). In this work, AMF communities of native plants grown spontaneously on former mining sites either enriched (P sites) or not enriched with P (nP sites) by mining cuttings of rock phosphate (RP) were studied. No significant differences were observed in the root mycorrhizal rates of the plants when comparing P and nP sites. The assessment of AMF diversity and community structure using Illumina MiSeq metabarcoding and targeting 18S rDNA in roots and rhizospheric soils showed a total of 318 Amplicon Sequence Variants (ASVs) of Glomeromycota phylum. No significant difference in the diversity was found between P and nP sites. Glomeraceae species were largely dominant, formed a fungal core of 26 ASVs, and were persistent and abundant in all sites. In the P soils, eight ASVs were identified by indicator species analysis. A trend towards an increase in Diversisporaceae and Claroideoglomeraceae and a reduction in Paraglomeraceae and Glomeraceae were noticed. These results provide new insights into AMF ecology in former RP mining sites; they document that P concentration is a driver of AMF community structures in soils enriched in RP long term but also suggest an influence of land disturbance, ecosystem self-restoration, and AMF life history strategies as drivers of AMF community profiles.
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Affiliation(s)
- Amandine Ducousso-Détrez
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV), Université du Littoral Côte d’Opale, UR 4492, SFR Condorcet FR CNRS 3417, CEDEX, 62228 Calais, France
- Institut de Recherche en Biologie Végétale (IRBV), 3 AgroBioSciences, Université de Montréal, Montréal, QC H1X 2B2, Canada
| | - Robin Raveau
- INRAE, UMR SAVE, Bordeaux Science Agro, ISVV, 33882 Villenave d’Ornon, France
| | - Joël Fontaine
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV), Université du Littoral Côte d’Opale, UR 4492, SFR Condorcet FR CNRS 3417, CEDEX, 62228 Calais, France
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale (IRBV), 3 AgroBioSciences, Université de Montréal, Montréal, QC H1X 2B2, Canada
- African Genome Center, Mohammed VI Polytechnic University (UM6P), Ben Guerir 43150, Morocco
| | - Anissa Lounès-Hadj Sahraoui
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV), Université du Littoral Côte d’Opale, UR 4492, SFR Condorcet FR CNRS 3417, CEDEX, 62228 Calais, France
- Correspondence:
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53
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Sindhu SS, Sehrawat A, Glick BR. The involvement of organic acids in soil fertility, plant health and environment sustainability. Arch Microbiol 2022; 204:720. [DOI: 10.1007/s00203-022-03321-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/22/2022] [Accepted: 11/03/2022] [Indexed: 11/21/2022]
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Moneda APC, de Carvalho LAL, Teheran-Sierra LG, Funnicelli MIG, Pinheiro DG. Sugarcane cultivation practices modulate rhizosphere microbial community composition and structure. Sci Rep 2022; 12:19174. [PMID: 36357461 PMCID: PMC9649670 DOI: 10.1038/s41598-022-23562-6] [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: 09/10/2022] [Accepted: 11/02/2022] [Indexed: 11/12/2022] Open
Abstract
Sugarcane (Saccharum spp.) represents a crop of great economic importance, remarkably relevant in the food industry and energy supply chains from renewable sources. However, its conventional cultivation involves the intensive use of fertilizers, pesticides, and other agrochemical agents whose detrimental effects on the environment are notorious. Alternative systems, such as organic farming, have been presented as an environmentally friendly way of production. Still, the outcomes of different cropping systems on the microbiota associated with sugarcane-whose role in its health and growth is crucial-remain underexplored. Thus, we studied the rhizospheric microbiota of two adjacent sugarcane fields, which differ in terms of the type of farming system. For this, we used the sequencing of taxonomic markers of prokaryotes (gene 16S rRNA, subregions V3-V4) and fungi (Internal transcribed spacer 2) and evaluated the changes caused by the systems. Our results show a well-conserved microbiota composition among farming systems in the highest taxonomic ranks, such as phylum, class, and order. Also, both systems showed very similar alpha diversity indices and shared core taxa with growth-promoting capacities, such as bacteria from the Bacillus and Bradyrhizobium genera and the fungal genus Trichoderma. However, the composition at more specific levels denotes differences, such as the separation of the samples concerning beta diversity and the identification of 74 differentially abundant taxa between the systems. Of these, 60 were fungal taxa, indicating that this microbiota quota is more susceptible to changes caused by farming systems. The analysis of co-occurrence networks also showed the formation of peripheral sub-networks associated with the treatments-especially in fungi-and the presence of keystone taxa in terms of their ability to mediate relationships between other members of microbial communities. Considering that both crop fields used the same cultivar and had almost identical soil properties, we conclude that the observed findings are effects of the activities intrinsic to each system and can contribute to a better understanding of the effects of farming practices on the plant microbiome.
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Affiliation(s)
- Ana Paula Corrêa Moneda
- grid.410543.70000 0001 2188 478XLaboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP 14884-900 Brazil ,grid.410543.70000 0001 2188 478XGraduate Program in Agricultural and Livestock Microbiology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP Brazil
| | - Lucas Amoroso Lopes de Carvalho
- grid.410543.70000 0001 2188 478XLaboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP 14884-900 Brazil ,grid.410543.70000 0001 2188 478XGraduate Program in Agricultural and Livestock Microbiology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP Brazil
| | - Luis Guillermo Teheran-Sierra
- grid.410543.70000 0001 2188 478XLaboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP 14884-900 Brazil ,grid.410543.70000 0001 2188 478XGraduate Program in Agricultural and Livestock Microbiology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP Brazil
| | - Michelli Inácio Gonçalves Funnicelli
- grid.410543.70000 0001 2188 478XLaboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP 14884-900 Brazil ,grid.410543.70000 0001 2188 478XGraduate Program in Agricultural and Livestock Microbiology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP Brazil
| | - Daniel Guariz Pinheiro
- grid.410543.70000 0001 2188 478XLaboratory of Bioinformatics, Department of Agricultural, Livestock and Environmental Biotechnology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP 14884-900 Brazil ,grid.410543.70000 0001 2188 478XGraduate Program in Agricultural and Livestock Microbiology, School of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP Brazil
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55
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Zhang X, Song X, Wang T, Huang L, Ma H, Wang M, Tan D. The responses to long-term nitrogen addition of soil bacterial, fungal, and archaeal communities in a desert ecosystem. Front Microbiol 2022; 13:1015588. [PMID: 36312972 PMCID: PMC9606763 DOI: 10.3389/fmicb.2022.1015588] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 09/26/2022] [Indexed: 10/29/2023] Open
Abstract
Nitrogen (N) deposition is a worldwide issue caused by human activity. Long-term deposition of N strongly influences plant productivity and community composition. However, it is still unclear how the microbial community responds to long-term N addition in a desert ecosystem. Therefore, a long-term experiment was conducted in the Gurbantonggut Desert in northwestern China in 2015. Four N addition rates, 0 (CK), 5 (N1), 20 (N2), and 80 (N3) kg N ha-1 yr.-1, were tested and the soil was sampled after 6 years of N addition. High-throughput sequencing (HTS) was used to analyze the soil microbial composition. The HTS results showed that N addition had no significant effect on the bacterial α-diversity and β-diversity (p > 0.05) but significantly reduced the archaeal β-diversity (p < 0.05). The fungal Chao1 and ACE indexes in the N2 treatment increased by 24.10 and 26.07%, respectively. In addition, N addition affected the bacterial and fungal community structures. For example, compared to CK, the relative abundance of Actinobacteria increased by 17.80%, and the relative abundance of Bacteroidetes was reduced by 44.46% under N3 treatment. Additionally, N addition also changed the bacterial and fungal community functions. The N3 treatment showed increased relative abundance of nitrate-reducing bacteria (27.06% higher than CK). The relative abundance of symbiotrophic fungi was increased in the N1 treatment (253.11% higher than CK). SOC and NH4 +-N could explain 62% of the changes in the fungal community function. N addition can directly affect the bacterial community function or indirectly through NO3 --N. These results suggest that different microbial groups may have various responses to N addition. Compared with bacteria and fungi, the effect of N addition was less on the archaeal community. Meanwhile, N-mediated changes of the soil properties play an essential role in changes in the microbial community. The results in the present study provided a reliable basis for an understanding of how the microbial community in a desert ecosystem adapts to long-term N deposition.
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Affiliation(s)
- Xuan Zhang
- College of Life Sciences, Xinjiang Agricultural University, Ürümqi, China
| | - Xin Song
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Arid Agroecology, College of Ecology, Lanzhou University, Lanzhou, China
| | - Taotao Wang
- College of Life Sciences, Xinjiang Agricultural University, Ürümqi, China
| | - Lei Huang
- College of Life Sciences, Xinjiang Agricultural University, Ürümqi, China
| | - Haiyang Ma
- College of Life Sciences, Xinjiang Agricultural University, Ürümqi, China
| | - Mao Wang
- College of Life Sciences, Xinjiang Agricultural University, Ürümqi, China
| | - Dunyan Tan
- College of Life Sciences, Xinjiang Agricultural University, Ürümqi, China
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56
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Solanki MK, Solanki AC, Rai S, Srivastava S, Kashyap BK, Divvela PK, Kumar S, Yandigeri MS, Kashyap PL, Shrivastava AK, Ali B, Khan S, Jaremko M, Qureshi KA. Functional interplay between antagonistic bacteria and Rhizoctonia solani in the tomato plant rhizosphere. Front Microbiol 2022; 13:990850. [PMID: 36225362 PMCID: PMC9548980 DOI: 10.3389/fmicb.2022.990850] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 08/18/2022] [Indexed: 12/28/2022] Open
Abstract
Microbial interactions with plant roots play an imperial role in tomato plant growth and defense against the Rhizoctonia solani. This study performed a field experiment with two antagonistic bacteria (Pseudomonas and Bacillus) inoculated in healthy and Rhizoctonia solani treated soil in tomato rhizosphere to understand the metabolic pattern and microbial function during plant disease suppression. In the present study, we assessed soil and microbial enzymes, bacterial and fungal cell forming unit (CFU), and carbon utilization profiling through Bio-Eco plates of rhizoplane samples. Antagonist bacteria and pathogen interaction significantly (p < 0.05) influenced the bacterial count, soil enzymes (chitinase and glucanase), and bacterial function (siderophore and chitinase production). These results indicated that these variables had an imperial role in disease suppression during plant development. Furthermore, the metabolic profiling showed that carbon source utilization enhanced under fruit development and ripening stages. These results suggested that carbon sources were essential in plant/pathogen/antagonist interaction. Substrates like β-methyl-D-glucoside, D-mannitol, D-galacturonic acid, N-acetyl-D-glucosamine, and phenylethylamine strongly connect with the suppuration of root rot disease. These carbon sources may help to propagate a healthy microbial community to reduce the pathogen invasion in the plant root system, and these carbon sources can be stimulators of antagonists against pathogens in the future.
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Affiliation(s)
- Manoj Kumar Solanki
- Faculty of Natural Sciences, Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | | | - Shalini Rai
- Department of Biotechnology, Society of Higher Education and Practical Application (SHEPA), Varanasi, UP, India
| | - Supriya Srivastava
- Department of Health Informatics, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah, Saudi Arabia
| | - Brijendra Kumar Kashyap
- Department of Biotechnology Engineering, Institute of Engineering and Technology, Bundelkhand University, Jhansi, UP, India
| | | | - Sudheer Kumar
- Indian Institute of Wheat and Barley Research (ICAR), Karnal, HR, India
| | - Mahesh S. Yandigeri
- National Bureau of Agricultural Insect Resources (ICAR), Bengaluru, KA, India
- *Correspondence: Mahesh S. Yandigeri,
| | - Prem Lal Kashyap
- Indian Institute of Wheat and Barley Research (ICAR), Karnal, HR, India
| | | | - Baber Ali
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shahid Khan
- Department of Agriculture, University of Swabi, Swabi, Pakistan
- Department of Plant Breeding and Genetics, University of Agriculture Swat, Peshawar, Pakistan
| | - Mariusz Jaremko
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Kamal Ahmad Qureshi
- Department of Pharmaceutics, Unaizah College of Pharmacy, Qassim University, Unaizah, Saudi Arabia
- Kamal Ahmad Qureshi,
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57
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Maywald NJ, Mang M, Pahls N, Neumann G, Ludewig U, Francioli D. Ammonium fertilization increases the susceptibility to fungal leaf and root pathogens in winter wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:946584. [PMID: 36160997 PMCID: PMC9500508 DOI: 10.3389/fpls.2022.946584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/11/2022] [Indexed: 06/16/2023]
Abstract
Nitrogen (N) fertilization is indispensable for high yields in agriculture due to its central role in plant growth and fitness. Different N forms affect plant defense against foliar pathogens and may alter soil-plant-microbe interactions. To date, however, the complex relationships between N forms and host defense are poorly understood. For this purpose, nitrate, ammonium, and cyanamide were compared in greenhouse pot trials with the aim to suppress two important fungal wheat pathogens Blumeria graminis f. sp. tritici (Bgt) and Gaeumannomyces graminis f. sp. tritici (Ggt). Wheat inoculated with the foliar pathogen Bgt was comparatively up to 80% less infested when fertilized with nitrate or cyanamide than with ammonium. Likewise, soil inoculation with the fungal pathogen Ggt revealed a 38% higher percentage of take-all infected roots in ammonium-fertilized plants. The bacterial rhizosphere microbiome was little affected by the N form, whereas the fungal community composition and structure were shaped by the different N fertilization, as revealed from metabarcoding data. Importantly, we observed a higher abundance of fungal pathogenic taxa in the ammonium-fertilized treatment compared to the other N treatments. Taken together, our findings demonstrated the critical role of fertilized N forms for host-pathogen interactions and wheat rhizosphere microbiome assemblage, which are relevant for plant fitness and performance.
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58
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Zhang S, Li X, Chen K, Shi J, Wang Y, Luo P, Yang J, Wang Y, Han X. Long-term fertilization altered microbial community structure in an aeolian sandy soil in northeast China. Front Microbiol 2022; 13:979759. [PMID: 36160213 PMCID: PMC9490088 DOI: 10.3389/fmicb.2022.979759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/17/2022] [Indexed: 11/22/2022] Open
Abstract
Soil microorganisms play crucial roles in nutrient cycling and determining soil quality and fertility; thus, they are important for agricultural production. However, the impacts of long-term fertilization on soil microbial community remain ambiguous due to inconsistent results from different studies. The objective of this study was to characterize changes in bacterial and fungal diversity and community structures after 12 years of different fertilization in aeolian sandy soil by analyzing 16S rRNA and ITS rRNA gene sequences and the soil properties to discover the driving factors. Eight different fertilizer treatments have been set up since 2009: no fertilizer (CK), chemical N fertilizer (N), chemical N and P fertilizer (NP), chemical N, P and K fertilizer (NPK), pig manure only (M), pig manure plus chemical N fertilizer (MN), pig manure plus chemical N and P fertilizer (MNP), pig manure plus chemical N, P, and K fertilizer (MNPK). The results indicated that the long-term application of chemical fertilizer reduced soil pH, whereas the addition of pig manure alleviated a decrease in soil pH value. Chemical fertilizer plus pig manure significantly improved soil available nutrients and soil organic carbon. Long-term MNPK fertilization resulted in changes in bacterial diversity due to effects on specific bacterial species; by contrast, all fertilization treatments resulted in changes in fungal diversity due to changes in soil properties. Principal component analysis indicated that fertilization had a significant effect on soil microbial community structure, and the effect of chemical fertilizer combined with pig manure was greater than that of chemical fertilizer alone. Soil available phosphorus, total phosphorus, and pH were the most important factors that influenced bacterial taxa, whereas soil pH, total phosphorus, organic carbon, ammonium nitrogen and nitrate nitrogen were the most important factors influencing fungal taxa after 12 years of fertilization in aeolian sandy soil.
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Affiliation(s)
- Shiyu Zhang
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shenyang, China
- Monitoring and Experimental Station of Corn Nutrition and Fertilization in Northeast Region, Ministry of Agriculture, Shenyang, China
| | - Xue Li
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shenyang, China
- Monitoring and Experimental Station of Corn Nutrition and Fertilization in Northeast Region, Ministry of Agriculture, Shenyang, China
| | - Kun Chen
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shenyang, China
- Monitoring and Experimental Station of Corn Nutrition and Fertilization in Northeast Region, Ministry of Agriculture, Shenyang, China
| | - Junmei Shi
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shenyang, China
- Monitoring and Experimental Station of Corn Nutrition and Fertilization in Northeast Region, Ministry of Agriculture, Shenyang, China
| | - Yan Wang
- Department of Foreign Languages, Shenyang Agricultural University, Shenyang, China
| | - Peiyu Luo
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shenyang, China
- Monitoring and Experimental Station of Corn Nutrition and Fertilization in Northeast Region, Ministry of Agriculture, Shenyang, China
| | - Jinfeng Yang
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shenyang, China
- Monitoring and Experimental Station of Corn Nutrition and Fertilization in Northeast Region, Ministry of Agriculture, Shenyang, China
| | - Yue Wang
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shenyang, China
- Monitoring and Experimental Station of Corn Nutrition and Fertilization in Northeast Region, Ministry of Agriculture, Shenyang, China
- *Correspondence: Yue Wang,
| | - Xiaori Han
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, Shenyang, China
- Monitoring and Experimental Station of Corn Nutrition and Fertilization in Northeast Region, Ministry of Agriculture, Shenyang, China
- Xiaori Han,
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59
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Carrasco-Espinosa K, Avitia M, Barrón-Sandoval A, Abbruzzini TF, Salazar Cabrera UI, Arroyo-Lambaer D, Uscanga A, Campo J, Benítez M, Wegier A, Rosell JA, Reverchon F, Hernández G, Boege K, Escalante AE. Land-Use Change and Management Intensification Is Associated with Shifts in Composition of Soil Microbial Communities and Their Functional Diversity in Coffee Agroecosystems. Microorganisms 2022; 10:microorganisms10091763. [PMID: 36144367 PMCID: PMC9504970 DOI: 10.3390/microorganisms10091763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/12/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022] Open
Abstract
Despite the central role of microorganisms in soil fertility, little understanding exists regarding the impact of management practices and soil microbial diversity on soil processes. Strong correlations among soil microbial composition, management practices, and microbially mediated processes have been previously shown. However, limited integration of the different parameters has hindered our understanding of agroecosystem functioning. Multivariate analyses of these systems allow simultaneous evaluation of the parameters and can lead to hypotheses on the microbial groups involved in specific nutrient transformations. In the present study, using a multivariate approach, we investigated the effect of microbial composition (16SrDNA sequencing) and soil properties in carbon mineralization (CMIN) (BIOLOG™, Hayward, CA, USA) across different management categories on coffee agroecosystems in Mexico. Results showed that (i) changes in soil physicochemical variables were related to management, not to region, (ii) microbial composition was associated with changes in management intensity, (iii) specific bacterial groups were associated with different management categories, and (iv) there was a broader utilization range of carbon sources in non-managed plots. The identification of specific bacterial groups, management practices, and soil parameters, and their correlation with the utilization range of carbon sources, presents the possibility to experimentally test hypotheses on the interplay of all these components and further our understanding of agroecosystem functioning and sustainable management.
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Affiliation(s)
- Karen Carrasco-Espinosa
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
- Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Morena Avitia
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Alberto Barrón-Sandoval
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
| | - Thalita F. Abbruzzini
- Laboratorio de Biogeoquímica Terrestre y Clima, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Ulises Isaac Salazar Cabrera
- Laboratorio de Biogeoquímica Terrestre y Clima, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Denise Arroyo-Lambaer
- Laboratorio de Restauración Ecológica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Adriana Uscanga
- Laboratorio de Restauración Ecológica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Julio Campo
- Laboratorio de Biogeoquímica Terrestre y Clima, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Mariana Benítez
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Ana Wegier
- Laboratorio de Genética de la Conservación, Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Julieta A. Rosell
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Frédérique Reverchon
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., Pátzcuaro 91070, Mexico
| | - Gerardo Hernández
- Centro Agroecológico del Café A.C. Clúster Biomimic-Inecol, Xalapa Enríquez Centro, Veracruz 91000, Mexico
| | - Karina Boege
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Ana E. Escalante
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
- Correspondence:
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Sommermann L, Babin D, Behr JH, Chowdhury SP, Sandmann M, Windisch S, Neumann G, Nesme J, Sørensen SJ, Schellenberg I, Rothballer M, Geistlinger J, Smalla K, Grosch R. Long-Term Fertilization Strategy Impacts Rhizoctonia solani–Microbe Interactions in Soil and Rhizosphere and Defense Responses in Lettuce. Microorganisms 2022; 10:microorganisms10091717. [PMID: 36144319 PMCID: PMC9501836 DOI: 10.3390/microorganisms10091717] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/04/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022] Open
Abstract
The long-term effects of agricultural management such as different fertilization strategies on soil microbiota and soil suppressiveness against plant pathogens are crucial. Therefore, the suppressiveness of soils differing in fertilization history was assessed using two Rhizoctonia solani isolates and their respective host plants (lettuce, sugar beet) in pot experiments. Further, the effects of fertilization history and the pathogen R. solani AG1-IB on the bulk soil, root-associated soil and rhizosphere microbiota of lettuce were analyzed based on amplicon sequencing of the 16S rRNA gene and ITS2 region. Organic fertilization history supported the spread of the soil-borne pathogens compared to long-term mineral fertilization. The fertilization strategy affected bacterial and fungal community composition in the root-associated soil and rhizosphere, respectively, but only the fungal community shifted in response to the inoculated pathogen. The potential plant-beneficial genus Talaromyces was enriched in the rhizosphere by organic fertilization and presence of the pathogen. Moreover, increased expression levels of defense-related genes in shoots of lettuce were observed in the soil with organic fertilization history, both in the absence and presence of the pathogen. This may reflect the enrichment of potential plant-beneficial microorganisms in the rhizosphere, but also pathogen infestation. However, enhanced defense responses resulted in retarded plant growth in the presence of R. solani (plant growth/defense tradeoff).
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Affiliation(s)
- Loreen Sommermann
- Department of Agriculture, Ecotrophology and Landscape Development, Anhalt University of Applied Sciences, 06406 Bernburg, Germany
- Correspondence:
| | - Doreen Babin
- Julius Kühn-Institute (JKI)—Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, 38104 Braunschweig, Germany
| | - Jan Helge Behr
- Plant-Microbe Systems, Leibniz Institute of Vegetable and Ornamental Crops (IGZ), 14979 Großbeeren, Germany
| | - Soumitra Paul Chowdhury
- Institute of Network Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Martin Sandmann
- Plant-Microbe Systems, Leibniz Institute of Vegetable and Ornamental Crops (IGZ), 14979 Großbeeren, Germany
| | - Saskia Windisch
- Institute of Crop Science (340h), University of Hohenheim, 70599 Stuttgart, Germany
| | - Günter Neumann
- Institute of Crop Science (340h), University of Hohenheim, 70599 Stuttgart, Germany
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Søren J. Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Ingo Schellenberg
- Department of Agriculture, Ecotrophology and Landscape Development, Anhalt University of Applied Sciences, 06406 Bernburg, Germany
| | - Michael Rothballer
- Institute of Network Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Joerg Geistlinger
- Department of Agriculture, Ecotrophology and Landscape Development, Anhalt University of Applied Sciences, 06406 Bernburg, Germany
| | - Kornelia Smalla
- Julius Kühn-Institute (JKI)—Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, 38104 Braunschweig, Germany
| | - Rita Grosch
- Plant-Microbe Systems, Leibniz Institute of Vegetable and Ornamental Crops (IGZ), 14979 Großbeeren, Germany
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Sadet-Bourgeteau S, Djemiel C, Chemidlin Prévost-Bouré N, Feder F. Dynamic of bacterial and archaeal diversity in a tropical soil over 6 years of repeated organic and inorganic fertilization. Front Microbiol 2022; 13:943314. [PMID: 36051761 PMCID: PMC9425033 DOI: 10.3389/fmicb.2022.943314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/08/2022] [Indexed: 11/13/2022] Open
Abstract
The soil microbial community plays important roles in nutrient cycling, plant pathogen suppression, decomposition of residues and degradation of pollutants; as such, it is often regarded as a good indicator of soil quality. Repeated applications of mixed organic and inorganic materials in agriculture improve the soil microbial quality and in turn crop productivity. The soil microbial quality following several years of repeated fertilizer inputs has received considerable attention, but the dynamic of this community over time has never been assessed. We used high-throughput sequencing targeting 16S ribosomal RNA genes to investigate the evolution of the bacterial and archaeal community throughout 6 years of repeated organic and inorganic fertilizer applications. Soils were sampled from a field experiment in La Mare (Reunion Island, France), where different mixed organic-inorganic fertilizer inputs characterized by more or less stable organic matter were applied regularly for 6 years. Soil samples were taken each year, more than 6 months after the latest fertilizer application. The soil molecular biomass significantly increased in some organically fertilized plots (by 35–45% on average), 3–5 years after the first fertilizers application. The significant variations in soil molecular microbial biomass were explained by the fertilization practices (cumulated organic carbon inputs) and sometimes by the soil parameters (sand and soil carbon contents). The structure of the bacterial and archaeal community was more influenced by time than by the fertilization type. However, repeated fertilizer applications over time tended to modify the abundance of the bacterial phyla Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. To conclude, the present study highlights that the soil bacterial and archaeal community is lastingly modified after 6 years of repeated fertilizer inputs. These changes depend on the nature of the organic input and on the fertilization practice (frequency and applied quantity).
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Affiliation(s)
- Sophie Sadet-Bourgeteau
- Agroécologie, INRAE, Institut Agro Dijon, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
- *Correspondence: Sophie Sadet-Bourgeteau,
| | - Christophe Djemiel
- Agroécologie, INRAE, Institut Agro Dijon, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | | | - Frederic Feder
- CIRAD, UPR Recyclage et Risque, Montpellier, France
- Recyclage et risque, Univ Montpellier, CIRAD, Montpellier, France
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Lin Y, Ye G, Hu HW, Fan J, He JZ. Manure applications alter the abundance, community structure and assembly process of diazotrophs in an acidic Ultisol. Front Microbiol 2022; 13:965293. [PMID: 36033880 PMCID: PMC9412762 DOI: 10.3389/fmicb.2022.965293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
The excessive usage of nitrogen (N) fertilizers can accelerate the tendency of global climate change. Biological N fixation by diazotrophs contributes substantially to N input and is a viable solution to sustainable agriculture via reducing inorganic N fertilization. However, how manure application influences the abundance, community structure and assembly process of diazotrophs in soil aggregates is not fully understood. Here, we investigated the effect of manure amendment on diazotrophic communities in soil aggregates of an arable soil. Manure application increased soil aggregation, crop yield and the abundance of nifH genes. The abundance of nifH genes increased with aggregate sizes, indicating that diazotrophs prefer to live in larger aggregates. The abundance of nifH genes in large macroaggregates, rather than in microaggregates and silt and clay, was positively associated with plant biomass and crop yield. Both manure application and aggregate size did not alter the Shannon diversity of diazotrophs but significantly changed the diazotrophic community structure. The variation of diazotrophic community structure explained by manure application was greater than that by aggregate size. Manure application promoted the relative abundance of Firmicutes but reduced that of α-Proteobacteria. Stochastic processes played a dominant role in the assembly of diazotrophs in the control treatment. Low-rate manure (9 Mg ha−1) application, rather than medium-rate (18 Mg ha−1) and high-rate (27 Mg ha−1) manure, significantly increased the relative importance of deterministic processes in diazotrophic community assembly. Taken together, our findings demonstrated that long-term manure application increased nifH gene abundance and altered the community structure and assembly process of diazotrophs in soil aggregates, which advanced our understanding of the ecophysiology and functionality of diazotrophs in acidic Ultisols.
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Affiliation(s)
- Yongxin Lin
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Guiping Ye
- Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, China
| | - Hang-Wei Hu
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Jianbo Fan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- *Correspondence: Jianbo Fan
| | - Ji-Zheng He
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
- Ji-Zheng He
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63
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Li X, Chu Y, Jia Y, Yue H, Han Z, Wang Y. Changes to bacterial communities and soil metabolites in an apple orchard as a legacy effect of different intercropping plants and soil management practices. Front Microbiol 2022; 13:956840. [PMID: 36003931 PMCID: PMC9393497 DOI: 10.3389/fmicb.2022.956840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/12/2022] [Indexed: 11/16/2022] Open
Abstract
Intercropping is an important soil management practice for increasing orchard productivity and land-use efficiency because it has beneficial effects on soil microbial communities and soil properties. However, there is relatively little information available regarding the effects of different crops/grasses on soil microbial communities and soil metabolic products in apple orchards in arid and semi-arid regions. In this study, we showed the microbial communities of apple, intercropping plants, and sandy waste soil, using the third-generation PacBio SMRT long-read sequencing technology. Our results also revealed that the microbial communities and soil metabolic properties differed significantly between apple and the sandy waste soil and the intercropping plants. Intercropping could significantly enrich diverse microbial species, microbial nitrogen, and microbial carbon of soil. Moreover, intercropping with licorice showed better effects in recruiting beneficial microbes, compared to grass and pepper, significantly enriching species belonging to some well-known taxa with beneficial effects, including Bacillus, Ensifer, Paenibacillus, Rhizobium, and Sphingomonas. Thus, intercropping with licorice may improve apple tree growth and disease resistance. Furthermore, Bradyrhizobium and Rubrobacter were included among the keystone taxa of apple, whereas Bacillus, Chitinophaga, Stenotrophobacter, Rubrobacter, and Luteimonas were the keystone taxa of the intercropping plants. The results of our study suggest that intercropping with licorice is a viable option for increasing apple orchard productivity.
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Affiliation(s)
- Xiaolong Li
- College of Horticulture, China Agricultural University, Beijing, China
- Institute of Horticulture, Ningxia Academy of Agricultural and forestry Sciences, Yinchuan, China
| | - Yannan Chu
- Institute of Horticulture, Ningxia Academy of Agricultural and forestry Sciences, Yinchuan, China
| | - Yonghua Jia
- Institute of Horticulture, Ningxia Academy of Agricultural and forestry Sciences, Yinchuan, China
| | - Haiying Yue
- Institute of Horticulture, Ningxia Academy of Agricultural and forestry Sciences, Yinchuan, China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing, China
- Zhenhai Han
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing, China
- *Correspondence: Yi Wang
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64
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Li H, Luo N, Ji C, Li J, Zhang L, Xiao L, She X, Liu Z, Li Y, Liu C, Guo Q, Lai H. Liquid Organic Fertilizer Amendment Alters Rhizosphere Microbial Community Structure and Co-occurrence Patterns and Improves Sunflower Yield Under Salinity-Alkalinity Stress. MICROBIAL ECOLOGY 2022; 84:423-438. [PMID: 34535834 DOI: 10.1007/s00248-021-01870-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/10/2021] [Indexed: 06/13/2023]
Abstract
Response of rhizosphere microbial community structure and co-occurrence patterns to liquid organic fertilizer in sunflower cropland was investigated. Moderate and severe saline-alkaline soils were treated with liquid organic fertilizer containing mainly small molecular organic compounds (450 g L-1) at a rate of 4500 L ha-1 year-1 over 2 years. Compared with the untreated soils, organic fertilizer treatment increased soil nutrient concentrations by 13.8-137.1% while reducing soil pH and salinity by 5.6% and 54.7%, respectively. Organic fertilizer treatment also improved sunflower yield, plant number, and plant height by 28.6-67.3%. Following organic fertilizer treatment, fungal α-diversity was increased, and the effects of salinity-alkalinity stress on rhizosphere microbial communities were alleviated. The relative abundances of some halotolerant microbes and phytopathogenic fungi were reduced in organic fertilizer-treated soils, in contrast to increases in the relative abundances of plant growth-promoting microbes and organic matter decomposers, such as Nocardioides, Rhizophagus, and Stachybotrys. Network analysis revealed that severe salinity-alkalinity stress stimulated cooperation among bacteria, while organic fertilizer treatment tended to stimulate the ecosystem functions of fungi with higher proportions of fungi-bacteria and fungi-fungi links. More keystone taxa (e.g., Amycolatopsis, Variovorax, and Gemmatimonas) were positively correlated with soil nutrient concentrations and crop yield-related traits in organic fertilizer-treated soils. Overall, liquid organic fertilizer amendment could attenuate the adverse effects of salinity-alkalinity stress on sunflower yield by improving soil quality and optimizing rhizosphere microbial community structure and co-occurrence patterns.
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Affiliation(s)
- Haiyang Li
- College of Natural Resources and Environment, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China
| | - Nanyan Luo
- Tongchuan Institute of Agricultural Sciences, Tongchuan, 727000, China
| | - Chenglong Ji
- College of Natural Resources and Environment, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China
| | - Jin Li
- College of Natural Resources and Environment, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China
| | - Lan Zhang
- College of Natural Resources and Environment, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China
| | - Li Xiao
- College of Natural Resources and Environment, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China
| | - Xiaolin She
- Tongchuan Institute of Agricultural Sciences, Tongchuan, 727000, China
| | - Zhe Liu
- College of Natural Resources and Environment, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China
| | - Yulong Li
- College of Natural Resources and Environment, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China
| | - Cunshou Liu
- College of Natural Resources and Environment, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China
| | - Qiao Guo
- College of Natural Resources and Environment, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China.
| | - Hangxian Lai
- College of Natural Resources and Environment, Northwest A&F University, 3 Taicheng Road, Yangling, Xianyang, 712100, Shaanxi, People's Republic of China.
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65
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Guo S, Tao C, Jousset A, Xiong W, Wang Z, Shen Z, Wang B, Xu Z, Gao Z, Liu S, Li R, Ruan Y, Shen Q, Kowalchuk GA, Geisen S. Trophic interactions between predatory protists and pathogen-suppressive bacteria impact plant health. THE ISME JOURNAL 2022; 16:1932-1943. [PMID: 35461357 PMCID: PMC9296445 DOI: 10.1038/s41396-022-01244-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 04/07/2022] [Accepted: 04/11/2022] [Indexed: 12/18/2022]
Abstract
Plant health is strongly impacted by beneficial and pathogenic plant microbes, which are themselves structured by resource inputs. Organic fertilizer inputs may thus offer a means of steering soil-borne microbes, thereby affecting plant health. Concurrently, soil microbes are subject to top-down control by predators, particularly protists. However, little is known regarding the impact of microbiome predators on plant health-influencing microbes and the interactive links to plant health. Here, we aimed to decipher the importance of predator-prey interactions in influencing plant health. To achieve this goal, we investigated soil and root-associated microbiomes (bacteria, fungi and protists) over nine years of banana planting under conventional and organic fertilization regimes differing in Fusarium wilt disease incidence. We found that the reduced disease incidence and improved yield associated with organic fertilization could be best explained by higher abundances of protists and pathogen-suppressive bacteria (e.g. Bacillus spp.). The pathogen-suppressive actions of predatory protists and Bacillus spp. were mainly determined by their interactions that increased the relative abundance of secondary metabolite Q genes (e.g. nonribosomal peptide synthetase gene) within the microbiome. In a subsequent microcosm assay, we tested the interactions between predatory protists and pathogen-suppressive Bacillus spp. that showed strong improvements in plant defense. Our study shows how protistan predators stimulate disease-suppressive bacteria in the plant microbiome, ultimately enhancing plant health and yield. Thus, we suggest a new biological model useful for improving sustainable agricultural practices that is based on complex interactions between different domains of life.
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Affiliation(s)
- Sai Guo
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Chengyuan Tao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Alexandre Jousset
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Wu Xiong
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Zhe Wang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Zongzhuan Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Beibei Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bio-resources, College of Tropical Crops, Hainan University, Haikou, 570228, PR China
| | - Zhihui Xu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Zhilei Gao
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Shanshan Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Rong Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
| | - Yunze Ruan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bio-resources, College of Tropical Crops, Hainan University, Haikou, 570228, PR China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
| | - George A Kowalchuk
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University, 6700 AA, Wageningen, The Netherlands
- Netherlands Department of Terrestrial Ecology, Netherlands Institute for Ecology, (NIOO-KNAW), 6708 PB, Wageningen, The Netherlands
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Liebert J, Benner R, Bezner Kerr R, Björkman T, De Master KT, Gennet S, Gómez MI, Hart AK, Kremen C, Power AG, Ryan MR. Farm size affects the use of agroecological practices on organic farms in the United States. NATURE PLANTS 2022; 8:897-905. [PMID: 35864172 DOI: 10.1038/s41477-022-01191-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Organic agriculture outperforms conventional agriculture across several sustainability metrics due, in part, to more widespread use of agroecological practices. However, increased entry of large-scale farms into the organic sector has prompted concerns about 'conventionalization' through input substitution, agroecosystem simplification and other changes. We examined this shift in organic agriculture by estimating the use of agroecological practices across farm size and comparing indicators of conventionalization. Results from our national survey of 542 organic fruit and vegetable farmers show that fewer agroecological practices were used on large farms, which also exhibited the greatest degree of conventionalization. Intercropping, insectary plantings and border plantings were at least 1.4 times more likely to be used on small (0.4-39 cropland ha) compared with large (≥405 cropland ha) farms, whereas reduced tillage was less likely and riparian buffers were more likely on small compared with medium (40-404 cropland ha) farms. Because decisions about management practices can drive environmental sustainability outcomes, policy should support small and medium farms that already use agroecological practices while encouraging increased use of agroecological practices on larger farms.
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Affiliation(s)
- Jeffrey Liebert
- Soil & Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.
| | | | | | - Thomas Björkman
- Horticulture Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
- Cornell Agritech, Cornell University, Geneva, NY, USA
| | - Kathryn Teigen De Master
- Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA
| | | | - Miguel I Gómez
- Charles H. Dyson School of Applied Economics and Management, Cornell University, Ithaca, NY, USA
| | | | - Claire Kremen
- Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA
- Institute for Resources, Environment and Sustainability, Department of Zoology, Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alison G Power
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Matthew R Ryan
- Soil & Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
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Giffard B, Winter S, Guidoni S, Nicolai A, Castaldini M, Cluzeau D, Coll P, Cortet J, Le Cadre E, d’Errico G, Forneck A, Gagnarli E, Griesser M, Guernion M, Lagomarsino A, Landi S, Bissonnais YL, Mania E, Mocali S, Preda C, Priori S, Reineke A, Rusch A, Schroers HJ, Simoni S, Steiner M, Temneanu E, Bacher S, Costantini EAC, Zaller J, Leyer I. Vineyard Management and Its Impacts on Soil Biodiversity, Functions, and Ecosystem Services. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.850272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Healthy soils form the basis of sustainable viticulture, where soil characteristics have a direct impact on wine quantity and quality. Soil not only provides water and nutrients to vines, but is also a living medium containing micro- and macroorganisms that perform many ecological functions and provide ecosystem services. These organisms are involved in many processes, from decomposing organic matter to providing minerals to vine roots. They also control diseases, pests, and weeds, in addition to improving the soil structure in terms of its capacity to retain water and nutrients. Related to decomposition processes, the carbon content of vineyard soils influences fertility, erosion and biogeochemical cycles, with significant implications for the global climate. However, common agricultural practices represent strong threats to biodiversity and associated ecosystem services provided by vineyard soils. As consumers increasingly consider environmental aspects in their purchase decisions, winegrowers have to adapt their vineyard management strategies, raising the demand for sustainable pest- and weed-control methods. This article presents a comprehensive review of the impacts of vineyard practices on the soil ecosystem, biodiversity, and biodiversity-based ecosystem services, and provides future prospects for sustainable viticulture.
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68
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Zhang L, Yi M, Lu P. Effects of pyrene on the structure and metabolic function of soil microbial communities. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 305:119301. [PMID: 35429592 DOI: 10.1016/j.envpol.2022.119301] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/05/2022] [Accepted: 04/10/2022] [Indexed: 06/14/2023]
Abstract
The widely detected pyrene (PYR) is prone to accumulate and pose risks to the soil ecosystem. In this study, an aerobic closed microcosm was constructed to assess the effects of PYR at the environmental concentration (12.09 mg kg-1) on the structure, interactions, and metabolism of carbon sources of soil microbial communities. The results found that half-life of PYR was 37 d and its aerobic biodegradation was mainly implemented by both Gram-negative and Gram-positive bacteria as revealed by the quantitative results. High-throughput sequencing based on 16 S rRNA and ITS genes showed that PYR exposure interfered more significantly with the diversity and abundance of the bacterial community than that of the fungal community. For bacteria, rare species were sensitive to PYR, while Gemmatimonadota, Gaiellales, and Planococcaceae involved in organic pollutants detoxification and degradation were tolerant of PYR stress. Co-occurrence network analysis demonstrated that PYR enhanced the intraspecific cooperation within the bacterial community and altered the patterns of trophic interaction in the fungal community. Furthermore, the keystone taxa and their topological roles were altered, potentially inducing functionality changes. Function annotation suggested PYR inhibited the nitrogen fixation and ammonia oxidation processes but stimulated methylotrophy and methanol oxidation, especially on day 7. For the metabolism, microbial communities accelerated the metabolism of nitrogenous carbon sources (e.g. amine) to meet the physiological needs under PYR stress. This study clarifies the impacts of PYR on the structure, metabolism, and potential N and C cycling functions of soil microbial communities, deepening the knowledge of the environmental risks of PYR.
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Affiliation(s)
- Lilan Zhang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, People's Republic of China; Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China.
| | - Meiling Yi
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, People's Republic of China; Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China
| | - Peili Lu
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, People's Republic of China; Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China
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69
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Iqbal A, Ali I, Yuan P, Khan R, Liang H, Wei S, Jiang L. Combined Application of Manure and Chemical Fertilizers Alters Soil Environmental Variables and Improves Soil Fungal Community Composition and Rice Grain Yield. Front Microbiol 2022; 13:856355. [PMID: 35910624 PMCID: PMC9330912 DOI: 10.3389/fmicb.2022.856355] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 06/14/2022] [Indexed: 11/13/2022] Open
Abstract
Soil microorganisms play vital roles in energy flow and soil nutrient cycling and, thus, are important for crop production. A detailed understanding of the complex responses of microbial communities to diverse organic manure and chemical fertilizers (CFs) is crucial for agroecosystem sustainability. However, little is known about the response of soil fungal communities and soil nutrients to manure and CFs, especially under double-rice cropping systems. In this study, we investigated the effects of the application of combined manure and CFs to various fertilization strategies, such as no N fertilizer (Neg-CF); 100% chemical fertilizer (Pos-CF); 60% cattle manure (CM) + 40% CF (high-CM); 30% CM + 70% CF (low-CM); 60% poultry manure (PM) + 40% CF (high-PM), and 30% PM + 70% CF (low-PM) on soil fungal communities' structure and diversity, soil environmental variables, and rice yield. Results showed that synthetic fertilizer plus manure addition significantly increased the soil fertility and rice grain yield compared to sole CFs' application. Moreover, the addition of manure significantly changed the soil fungal community structure and increased the relative abundance of fungi such as phyla Ascomycota, Basidiomycota, Mortierellomycota, and Rozellomycota. The relative abundances dramatically differed at each taxonomic level, especially between manured and non-manured regimes. Principal coordinates analysis (PCoA) exhibited greater impacts of the addition of manure amendments than CFs on fungal community distributions. Redundancy analysis showed that the dominant fungal phyla were positively correlated with soil pH, soil organic C (SOC), total N, and microbial biomass C, and the fungal community structure was strongly affected by SOC. Network analysis explored positive relationships between microorganisms and could increase their adaptability in relevant environments. In addition, the structural equation model (SEM) shows the relationship between microbial biomass, soil nutrients, and rice grain yield. The SEM showed that soil nutrient contents and their availability directly affect rice grain yield, while soil fungi indirectly affect grain yield through microbial biomass production and nutrient levels. Our results suggest that manure application combined with CFs altered soil biochemical traits and soil fungal community structure and counteracted some of the adverse effects of the synthetic fertilizer. Overall, the findings of this research suggest that the integrated application of CF and manure is a better approach for improving soil health and rice yield.
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Affiliation(s)
- Anas Iqbal
- College of Life Science and Technology, Guangxi University, Nanning, China
- College of Agriculture, Guangxi University, Nanning, China
| | - Izhar Ali
- College of Agriculture, Guangxi University, Nanning, China
| | - Pengli Yuan
- College of Agriculture, Guangxi University, Nanning, China
| | - Rayyan Khan
- Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture and Rural Affairs, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - He Liang
- College of Agriculture, Guangxi University, Nanning, China
| | - Shanqing Wei
- College of Agriculture, Guangxi University, Nanning, China
| | - Ligeng Jiang
- College of Life Science and Technology, Guangxi University, Nanning, China
- College of Agriculture, Guangxi University, Nanning, China
- *Correspondence: Ligeng Jiang
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70
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Francioli D, Cid G, Hajirezaei MR, Kolb S. Leaf bacterial microbiota response to flooding is controlled by plant phenology in wheat (Triticum aestivum L.). Sci Rep 2022; 12:11197. [PMID: 35778470 PMCID: PMC9249782 DOI: 10.1038/s41598-022-15133-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/20/2022] [Indexed: 11/09/2022] Open
Abstract
Leaf microbiota mediates foliar functional traits, influences plant fitness, and contributes to various ecosystem functions, including nutrient and water cycling. Plant phenology and harsh environmental conditions have been described as the main determinants of leaf microbiota assembly. How climate change may modulate the leaf microbiota is unresolved and thus, we have a limited understanding on how environmental stresses associated with climate change driven weather events affect composition and functions of the microbes inhabiting the phyllosphere. Thus, we conducted a pot experiment to determine the effects of flooding stress on the wheat leaf microbiota. Since plant phenology might be an important factor in the response to hydrological stress, flooding was induced at different plant growth stages (tillering, booting and flowering). Using a metabarcoding approach, we monitored the response of leaf bacteria to flooding, while key soil and plant traits were measured to correlate physiological plant and edaphic factor changes with shifts in the bacterial leaf microbiota assembly. In our study, plant growth stage represented the main driver in leaf microbiota composition, as early and late plants showed distinct bacterial communities. Overall, flooding had a differential effect on leaf microbiota dynamics depending at which developmental stage it was induced, as a more pronounced disruption in community assembly was observed in younger plants.
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Affiliation(s)
- Davide Francioli
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research E.V. (ZALF), Müncheberg, Germany.
| | - Geeisy Cid
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Mohammad-Reza Hajirezaei
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Steffen Kolb
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research E.V. (ZALF), Müncheberg, Germany.,Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany
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71
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Qiu L, Li D, Li Z, Zhang J, Zhao B. Biochar-induced variations in crop yield are closely associated with the abundance and diversity of keystone species. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 827:154340. [PMID: 35257759 DOI: 10.1016/j.scitotenv.2022.154340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 12/10/2021] [Accepted: 03/02/2022] [Indexed: 06/14/2023]
Abstract
Biochar application has widely been used to improve crop yield, but its effectiveness is uncertain. Soil microbial communities may play critical roles, but we lack experimental evidences on the relationships between these communities and crop yield following biochar application. Here, we used cooccurrence networks to demonstrate the importance of ecological clusters (cooccurring taxa of soil microbes including bacteria and fungi) and to identify specific keystone species that were closely connected with the variations in crop yield in a pot experiment. The experiment included two soils (i.e., red soil and yellow-cinnamon soil) for wheat growth, with each soil receiving three biochar application rate. The grain yield in the red soil significantly increased while that in the yellow-cinnamon soil significantly decreased with the biochar application rate. Generally, the grain yield from the two soils showed close correlations with the relative abundance as well as with the diversity of keystone species within major clusters rather than with the soil properties and enzyme activities. This contrasting effectiveness was mainly associated with the enrichment of beneficial and suppression of detrimental keystone species in the red soil and the suppression of beneficial and enrichment of detrimental keystone species in the yellow-cinnamon soil. These species together mainly accounted for the variation in the relative abundance of keystone species within major clusters of each soil, suggesting their potential to affect crop yield following biochar application.
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Affiliation(s)
- Lili Qiu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; College of Resource, Environment and Chemistry, Chuxiong Normal University, Chuxiong 675000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dandan Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Zengqiang Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Jiabao Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Bingzi Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
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72
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van Rijssel SQ, Veen GFC, Koorneef GJ, Bakx-Schotman JMTT, Ten Hooven FC, Geisen S, van der Putten WH. Soil microbial diversity and community composition during conversion from conventional to organic agriculture. Mol Ecol 2022; 31:4017-4030. [PMID: 35726521 PMCID: PMC9545909 DOI: 10.1111/mec.16571] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 05/25/2022] [Accepted: 06/06/2022] [Indexed: 11/30/2022]
Abstract
It is generally assumed that the dependence of conventional agriculture on artificial fertilizers and pesticides strongly impacts the environment, while organic agriculture relying more on microbial functioning may mitigate these impacts. However, it is not well known how microbial diversity and community composition change in conventionally managed farmers' fields that are converted to organic management. Here, we sequenced bacterial and fungal communities of 34 organic fields on sand and marine clay soils in a time series (chronosequence) covering 25 years of conversion. Nearby conventional fields were used as references. We found that community composition of bacteria and fungi differed between organic and conventionally managed fields. In the organic fields, fungal diversity increased with time since conversion. However, this effect disappeared when the conventional paired fields were included. There was a relationship between pH and soil organic matter content and the diversity and community composition of bacteria and fungi. In marine clay soils, when time since organic management increased, fungal communities in organic fields became more dissimilar to those in conventional fields. We conclude that conversion to organic management in these Dutch farmers' fields did not increase microbial community diversity. Instead, we observed that in organic fields in marine clay when time since conversion increased soil fungal community composition became progressively dissimilar from that in conventional fields. Our results also showed that the paired sampling approach of organic and conventional fields was essential in order to control for environmental variation that was otherwise unaccounted for.
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Affiliation(s)
- Sophie Q van Rijssel
- Department of Terrestrial Ecology; Netherlands Institute for Ecology (NIOO-KNAW), PO box 50, 6700, AB, Wageningen, The Netherlands
| | - G F Ciska Veen
- Department of Terrestrial Ecology; Netherlands Institute for Ecology (NIOO-KNAW), PO box 50, 6700, AB, Wageningen, The Netherlands
| | - Guusje J Koorneef
- Department of Soil Chemistry and Chemical Soil Quality; Wageningen University & Research, AA, Wageningen, The Netherlands
| | - J M T Tanja Bakx-Schotman
- Department of Terrestrial Ecology; Netherlands Institute for Ecology (NIOO-KNAW), PO box 50, 6700, AB, Wageningen, The Netherlands
| | - Freddy C Ten Hooven
- Department of Terrestrial Ecology; Netherlands Institute for Ecology (NIOO-KNAW), PO box 50, 6700, AB, Wageningen, The Netherlands
| | - Stefan Geisen
- Department of Terrestrial Ecology; Netherlands Institute for Ecology (NIOO-KNAW), PO box 50, 6700, AB, Wageningen, The Netherlands.,Laboratory of Nematology, Wageningen University, AA, Wageningen, The Netherlands
| | - Wim H van der Putten
- Department of Terrestrial Ecology; Netherlands Institute for Ecology (NIOO-KNAW), PO box 50, 6700, AB, Wageningen, The Netherlands.,Laboratory of Nematology, Wageningen University, AA, Wageningen, The Netherlands
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73
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Dang Q, Zhao X, Yang T, Gong T, He X, Tan W, Xi B. Coordination of bacterial biomarkers with the dominant microbes enhances triclosan biodegradation in soil amended with food waste compost and cow dung compost. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 824:153837. [PMID: 35181369 DOI: 10.1016/j.scitotenv.2022.153837] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/08/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
Increasing concerns regarding the micropollutant triclosan (TCS) derive from its potential threats to human health and ecological security. Compost addition have been verified to be effective in soil remediation, however, the biodegradation of TCS under compost amendment in soil remain unclear. This study investigated the removal of TCS in soils amended with food waste compost (FS), cow dung compost (CS) and sludge compost (SS), respectively, explored the key TCS-degraders and biological mechanisms of TCS removal. Compost addition significantly enhanced the removal of TCS (p < 0.05) in the order of FS > CS > SS. The dosage of 20% (w/w) was the most efficient one and the ultimate concentrations of TCS were decreased by 76.67%, 67.90% and 56.79% compared with CK, respectively. The abundance of key dominant bacterial genus (7 in FS and 4 in CS) and fungal genus (3 in FS and CS) was stimulated due to the increase of soil nutrient factors (including dissolved organic carbon, DOC; soil organic matter, SOM; ammonium nitrogen, NH4+; nitrate nitrogen, NO3-) and the decrease of pH. A negative correlation between these dominant microbes and TCS concentration indicated their potential effect on TCS degradation. A total of four bacterial biomarkers, namely Saccharomonospora, Aequorivita, Bacillaceae and Fodinicurvataceae (both at family level) were the key TCS-degraders. Structural equation model (SEM) indicated that the improvement of soil nutrient factors in FS and CS promoted TCS biodegradation by improving the activity of bacterial biomarkers, as while, the key dominant microbes showed good tolerance to TCS stress. However, there were no significant biological effects on TCS in SS group. Network analysis further confirmed that it was the coordination of bacterial biomarkers with the dominant microbes that enhanced TCS biodegradation in soil amended with food waste compost and cow dung compost.
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Affiliation(s)
- Qiuling Dang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Hazardous Waste Identification and Risk Control, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Xinyu Zhao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Hazardous Waste Identification and Risk Control, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Tianxue Yang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Hazardous Waste Identification and Risk Control, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Tiancheng Gong
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Hazardous Waste Identification and Risk Control, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Xiaosong He
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Wenbing Tan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Beidou Xi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
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74
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Responses of Fungal Community Structure and Functional Composition to Short-Term Fertilization and Dry Season Irrigation in Eucalyptus urophylla × Eucalyptus grandis Plantation Soils. FORESTS 2022. [DOI: 10.3390/f13060854] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Plantation forests productivity is severely limited by the seasonal drought and fertilization practices in South China. Soil nutrient and water availability influence soil fungal community, functional group diversity and the variation of plant productivity; however, the effects of irrigation and fertilization on fungal responses have rarely been studied. Here, we investigate the responses of fungal community structure and functional groups in Eucalyptus plantation soils to short-term fertilization (F), dry-season irrigation (W), short-term fertilization combined with dry-season irrigation (FW), and control (CK) treatments for ten months. A higher proportion of Basidiomycota was observed in the irrigation and/or fertilization treatments; conversely, lower proportions of Ascomycota and Mucoromycotina were observed in the only irrigation and fertilization treatments. Higher soil carbon contents and symbiotroph fungi (mainly Ectomycorrhizas) proportion were detected in the FW treatment, while low proportions of saprophytic and pathogenic fungi were observed in the FW treatment when compared with those in other treatments. These results may indicate that Eucalyptus tree growth under irrigation and fertilization condition was better than under fertilization only, irrigation only, or neither management. The results highlight that short-term fertilization and dry-season irrigation can shift fungal community structure and functional groups by regulating available soil moisture and nutrients. They also provide a theoretical basis for the development of more appropriate management approaches in the early stages of forest plantation.
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75
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The Application of Mixed Organic and Inorganic Fertilizers Drives Soil Nutrient and Bacterial Community Changes in Teak Plantations. Microorganisms 2022; 10:microorganisms10050958. [PMID: 35630402 PMCID: PMC9145699 DOI: 10.3390/microorganisms10050958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/21/2022] [Accepted: 04/28/2022] [Indexed: 11/17/2022] Open
Abstract
Appropriate fertilization can enhance forest productivity by maintaining soil fertility and improving the structure of the bacterial community. However, there is still uncertainty surrounding the effects of combined application of organic and inorganic fertilizers on soil nutrient status and bacterial community structure. A fertilization experiment was set up in an eight-year-old teak plantation with five treatments involved: mixed organic and NPK compound fertilizers (OCF), mixed organic and phosphorus fertilizers (OPF), mixed organic, NPK and phosphorus fertilizers (OCPF), mixed NPK and phosphorus fertilizers (CPF) and no fertilization (CK). Soil chemical properties and bacterial communities were investigated, and the co-occurrence pattern of the bacterial community under different fertilization treatments was compared. The results showed that the contents of soil organic matter and nitrate nitrogen, and the soil pH values were the highest after OCPF treatment, which were 20.39%, 90.91% and 8.16% higher than CK, respectively. The richness and diversity of bacteria underwent no obvious changes, but the structure of the soil’s bacterial community was significantly altered by fertilization. Of the dominant bacteria taxa, the relative abundance increased for Gemmatimonadetes, Myxococcota, ADurb.Bin063-13 and Candidatus_Koribacter, and decreased for Chloroflexi, Proteobacteria, JG30-KF-AS9 and Acidothermus under OCPF treatment in comparison to CK. The number of nodes and edges, the average degree and the network density of bacterial community co-occurrence networks were the greatest in OCPF treatment, indicating that application of OCPF could make the network structure of soil bacteria more stable and complex. Moreover, soil pH and organic matter were significantly correlated with bacterial community structure and were considered the main influencing factors. These findings highlight that the combined application of organic, NPK and phosphorus fertilizers is highly beneficial for improving soil quality and optimizing bacterial community structure in teak plantations.
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76
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Xiong X, Liao H, Xing Y, Han X, Wang W, Wan W, Huang Q, Chen W. Soil Aggregates and Fertilizer Treatments Drive Bacterial Interactions via Interspecies Niche Overlap. Microbiol Spectr 2022; 10:e0252421. [PMID: 35234512 PMCID: PMC8941866 DOI: 10.1128/spectrum.02524-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 02/02/2022] [Indexed: 12/23/2022] Open
Abstract
Bacterial interactions play significant roles in ecological functions in responding to anthropogenic interference and soil structure changes. However, it remains largely unknown how fertilizer regimes and soil particle sizes drive bacterial interactions. To evaluate bacterial interaction patterns in soil aggregates under long-term fertilizer treatments, we sampled nine bacterial co-occurrence communities and compared the difference between interspecies resource consumption patterns and network structure. Despite the differences between fertilizer treatments, the negative correlation ratios of interaction networks in soil aggregates were macroaggregates > microaggregates > silt + clays. Likewise, NPK-supplement (chemical fertilizer) had also decreased the number of positive correlations of the interaction network than M-supplement (organic fertilizer), regardless of the size of soil aggregates. Linear model analysis revealed that interspecies trophic patterns, including niche overlap and nestedness, drove bacterial competition in the interaction networks. Most importantly, interspecies niche overlap may be the intrinsic factor in the effects of fertilizer treatments and soil aggregates on bacterial interactions. This study enhances our understanding of the potential for changes in species trophic patterns and might guide the promotion of land management. IMPORTANCE Despite that the influence of soil structure and fertilizer treatments on the bacterial community has been widely studied, how they drive interspecies interactions has not been largely explored. Connectance and nestedness were significantly correlated with bacterial interactions, but no differences were found in different soil aggregates and fertilizer treatments. However, interspecies niche overlap could respond to soil aggregates and fertilizer treatments and ultimately drive the bacterial interactions. This study enhances our understanding of the mechanism of microbial interactions and highlights the importance of trophic patterns in the bacterial community. Our findings extend knowledge for nutrient availability on interspecific interactions.
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Affiliation(s)
- Xiang Xiong
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Hao Liao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Yanfang Xing
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Xukun Han
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Wanle Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Wenjie Wan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
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77
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Responses of CO2 emissions and soil microbial community structures to organic amendment in two contrasting soils in Zambia. Sci Rep 2022; 12:6368. [PMID: 35430624 PMCID: PMC9013351 DOI: 10.1038/s41598-022-10368-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 04/06/2022] [Indexed: 12/05/2022] Open
Abstract
In sub-Saharan Africa, efforts have been made to increase soil carbon (C) content in agricultural ecosystems due to severe soil degradation. The use of organic materials is a feasible method for recovering soil organic C; however, the effects of organic amendments on soil microbial communities and C cycles under C-limited soil conditions are still unknown. In this study, we conducted field experiments in Zambia using organic amendments at two sites with contrasting C content. At both sites, temporal changes in soil carbon dioxide (CO2) emissions and prokaryotic community structures were monitored during the crop growing season (126 days). The organic amendments increased CO2 emissions and prokaryotic abundance at the Kabwe site, whereas no direct impacts were observed at the Lusaka site. We also observed a larger temporal variability in the soil microbial community structure at Kabwe than that at Lusaka. These contrasting results between the two soils may be due to the microbial community stability differences between each site. However, as organic amendments have considerable potential to enhance microbial abundance and consequently sequester C at the Kabwe site, site-specific strategies are required to address the issues of soil C depletion in drylands.
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78
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Zhao N, Zhang X, Hu L, Liu H, Ma L, Xu T, Han X, Kang S, Wang X, Zhao X, Xu S. Cropping practices manipulate soil bacterial structure and functions on the Qinghai-Tibet Plateau. JOURNAL OF PLANT PHYSIOLOGY 2022; 271:153666. [PMID: 35303514 DOI: 10.1016/j.jplph.2022.153666] [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: 09/02/2021] [Revised: 03/06/2022] [Accepted: 03/06/2022] [Indexed: 06/14/2023]
Abstract
There is an increasing awareness of the adverse environmental effects of the intensive practices used in modern crop farming, such as those that cause greenhouse gas emissions and nutrient leaching. Harnessing beneficial microbes by changing planting practices presents a promising strategy for optimizing plant growth and agricultural sustainability. However, the characteristics of soil microorganisms under different planting patterns remain uncertain. We conducted a study of soil bacterial structure and function under monoculture vs. polyculture planting regimes using 16S rRNA gene sequencing on the Qinghai-Tibet Plateau. We observed substantial variations in bacterial richness, diversity, and relative abundances of taxa between gramineous and leguminous monocultures, as well as between gramineae-legume polycultures. The number of operational taxonomic units and alpha and beta diversity were markedly higher in the leguminous monocultures than in the gramineous monocultures; conversely, network analysis revealed that the interactions among the bacterial genera in the gramineous monocultures were more complex than those in the other two planting regimes. Moreover, nitrogen fixation, soil detoxification, and productivity were increased under the gramineous monocultures; more importantly, low soil-borne diseases (e.g., animals parasitic or symbiont) also facilitated strongly suppressive effects toward soil-borne pathogens. Nevertheless, the gramineae-legume polycultures were prone to nitrate seepage contamination, and leguminous monocultures exhibited strong denitrification effects. These results revealed that the gramineous monoculture is a more promising cropping pattern on the Qinghai-Tibetan Plateau. Understanding the bacterial distribution patterns and interactions of crop-sensitive microbes presents a basis for developing microbial management strategies for smart farming.
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Affiliation(s)
- Na Zhao
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Xining, 810001, China; Key Laboratory of Adaptation and Evolution of Plateau Biota, Chinese Academy of Sciences, Xining, China
| | - XiaoLing Zhang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Xining, 810001, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - LinYong Hu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Xining, 810001, China
| | - HongJin Liu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Xining, 810001, China
| | - Li Ma
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - TianWei Xu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Xining, 810001, China
| | - XuePing Han
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - ShengPing Kang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Xining, 810001, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - XunGang Wang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Xining, 810001, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - XinQuan Zhao
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Xining, 810001, China.
| | - ShiXiao Xu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai Xining, 810001, China.
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Kracmarova M, Uhlik O, Strejcek M, Szakova J, Cerny J, Balik J, Tlustos P, Kohout P, Demnerova K, Stiborova H. Soil microbial communities following 20 years of fertilization and crop rotation practices in the Czech Republic. ENVIRONMENTAL MICROBIOME 2022; 17:13. [PMID: 35346385 PMCID: PMC8962459 DOI: 10.1186/s40793-022-00406-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 03/08/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND Although fertilization and crop rotation practices are commonly used worldwide in agriculture to maximize crop yields, their long-term effect on the structures of soil microorganisms is still poorly understood. This study investigated the long-term impact of fertilization and crop rotation on soil microbial diversity and the microbial community structure in four different locations with three soil types. Since 1996, manure (MF; 330 kg N/ha), sewage sludge (SF; 330 and SF3x; 990 kg N/ha), and NPK (NPK; 330 kg N/ha) fertilizers were periodically applied to the soils classified as chernozem, luvisol and cambisol, which are among the most abundant or fertile soils used for agricultural purposes in the world. In these soils, potato (Solanum tuberosum L.), winter wheat (Triticum aestivum L.), and spring barley (Hordeum vulgare L.) were rotated every three years. RESULTS Soil chemistry, which was significantly associated with location, fertilization, crop rotation, and the interaction of fertilization and location, was the dominant driver of soil microbial communities, both prokaryotic and fungal. A direct effect of long-term crop rotation and fertilization on the structure of their communities was confirmed, although there was no evidence of their influence on microbial diversity. Fungal and bacterial communities responded differently to fertilization treatments; prokaryotic communities were only significantly different from the control soil (CF) in soils treated with MF and SF3x, while fungal communities differed across all treatments. Indicator genera were identified for different treatments. These taxa were either specific for their decomposition activities or fungal plant pathogens. Sequential rotation of the three crops restricted the growth of several of the indicator plant pathogens. CONCLUSIONS Long-term fertilization and crop rotation significantly altered microbial community structure in the soil. While fertilization affected soil microorganisms mainly through changes in nutrient profile, crop rotations lead to the attraction and repulsion of specific plant pathogens. Such changes in soil microbial communities need to be considered when planning soil management.
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Affiliation(s)
- Martina Kracmarova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic.
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Michal Strejcek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Jirina Szakova
- Department of Agro-Environmental Chemistry and Plant Nutrition, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 21, Prague - Suchdol, Czech Republic
| | - Jindrich Cerny
- Department of Agro-Environmental Chemistry and Plant Nutrition, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 21, Prague - Suchdol, Czech Republic
| | - Jiri Balik
- Department of Agro-Environmental Chemistry and Plant Nutrition, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 21, Prague - Suchdol, Czech Republic
| | - Pavel Tlustos
- Department of Agro-Environmental Chemistry and Plant Nutrition, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 21, Prague - Suchdol, Czech Republic
| | - Petr Kohout
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Videnska 1083, 142 20, Praha 4, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Vinicna 5, 128 44, Praha 2, Czech Republic
| | - Katerina Demnerova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Hana Stiborova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic.
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80
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Ducousso-Détrez A, Fontaine J, Lounès-Hadj Sahraoui A, Hijri M. Diversity of Phosphate Chemical Forms in Soils and Their Contributions on Soil Microbial Community Structure Changes. Microorganisms 2022; 10:microorganisms10030609. [PMID: 35336184 PMCID: PMC8950675 DOI: 10.3390/microorganisms10030609] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/25/2022] [Accepted: 03/09/2022] [Indexed: 12/10/2022] Open
Abstract
In many soils, the bioavailability of Phosphorus (P), an essential macronutrient is a limiting factor for crop production. Among the mechanisms developed to facilitate the absorption of phosphorus, the plant, as a holobiont, can rely on its rhizospheric microbial partners. Therefore, microbial P-solubilizing inoculants are proposed to improve soil P fertility in agriculture. However, a better understanding of the interactions of the soil-plant-microorganism continuum with the phosphorus cycle is needed to propose efficient inoculants. Before proposing further methods of research, we carried out a critical review of the literature in two parts. First, we focused on the diversity of P-chemical forms. After a review of P forms in soils, we describe multiple factors that shape these forms in soil and their turnover. Second, we provide an analysis of P as a driver of microbial community diversity in soil. Even if no rule enabling to explain the changes in the composition of microbial communities according to phosphorus has been shown, this element has been perfectly targeted as linked to the presence/absence and/or abundance of particular bacterial taxa. In conclusion, we point out the need to link soil phosphorus chemistry with soil microbiology in order to understand the variations in the composition of microbial communities as a function of P bioavailability. This knowledge will make it possible to propose advanced microbial-based inoculant engineering for the improvement of bioavailable P for plants in sustainable agriculture.
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Affiliation(s)
- Amandine Ducousso-Détrez
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV), Université du Littoral Côte d’Opale, UR4492, SFR Condorcet FR CNRS 3417, 62228 Calais, France; (A.D.-D.); (J.F.); (A.L.-H.S.)
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, Montréal, QC H1X 2B2, Canada
| | - Joël Fontaine
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV), Université du Littoral Côte d’Opale, UR4492, SFR Condorcet FR CNRS 3417, 62228 Calais, France; (A.D.-D.); (J.F.); (A.L.-H.S.)
| | - Anissa Lounès-Hadj Sahraoui
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV), Université du Littoral Côte d’Opale, UR4492, SFR Condorcet FR CNRS 3417, 62228 Calais, France; (A.D.-D.); (J.F.); (A.L.-H.S.)
| | - Mohamed Hijri
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, Montréal, QC H1X 2B2, Canada
- African Genome Center, Mohammed VI Polytechnic University (UM6P), Ben Guerir 43150, Morocco
- Correspondence:
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81
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Wang JL, Liu KL, Zhao XQ, Gao GF, Wu YH, Shen RF. Microbial keystone taxa drive crop productivity through shifting aboveground-belowground mineral element flows. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 811:152342. [PMID: 34919922 DOI: 10.1016/j.scitotenv.2021.152342] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/05/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Unbalanced fertilization of nutritional elements is a potential threat to environmental quality and agricultural productivity in acid soil. Harnessing keystone taxa in soil microbiome represents a promising strategy to enhance crop productivity as well as reducing the adverse environmental effects of fertilizers, with the goal of agricultural sustainability. However, there is a lack of information on which and how soil microbial keystone taxa contribute to sustainable crop productivity in acid soil. Here, we examined soil microbial communities (including bacteria, fungi, and archaea) and soil nutrients, and the mineral nutrition and yield of maize subjected to different inorganic and organic fertilization treatments over 35 years in acid soil. The application of organic fertilizer alone or in combination with inorganic fertilizers sustained high maize yield when compared with the other fertilization treatments. Microbial abundances and community structures rather than their alpha diversities explained the main variation in maize yield among different treatments. Sixteen soil keystone taxa (a fungal operational taxonomic unit and 15 bacterial operational taxonomic units) were identified from the microbial co-occurrence network. Among them, five keystone taxa (in Hypocreales, Bryobacter, Solirubrobacterales, Thermomicrobiales, and Roseiflexaceae) contributed to high maize yield through increasing phosphorus flow and inhibiting toxic aluminum and manganese flow from soils to plants. However, the remaining eleven keystone taxa (in Conexibacter, Acidothermus, Ktedonobacteraceae, Deltaproteobacteria, Actinobacteria, Elsterales, Ktedonobacterales, and WPS-2) exerted the opposite effects. As a result, maize productivity varied among different fertilization treatments because of the altered maize mineral element flows by microbial keystone taxa. We conclude that microbial keystone taxa drive crop productivity through shifting aboveground-belowground mineral element flows in acid soil. This study highlights the importance of microbial keystone taxa for sustainable crop productivity in acid soil and provides deep insights into the relationships between soil microbial keystone taxa, crop mineral nutrition, and productivity.
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Affiliation(s)
- Jia Lin Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Kai Lou Liu
- National Engineering and Technology Research Center for Red Soil Improvement, Jiangxi Institute of Red Soil, Nanchang 331717, China.
| | - Xue Qiang Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Gui-Feng Gao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yong Hong Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Ren Fang Shen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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82
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Bhanwaria R, Singh B, Musarella CM. Effect of Organic Manure and Moisture Regimes on Soil Physiochemical Properties, Microbial Biomass C mic:N mic:P mic Turnover and Yield of Mustard Grains in Arid Climate. PLANTS (BASEL, SWITZERLAND) 2022; 11:722. [PMID: 35336604 PMCID: PMC8949599 DOI: 10.3390/plants11060722] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
(1) Background: Arid conditions occur due to climate abnormality in the different biogeography regions of the world. The aim of this research is to investigate the stoichiometry of manure and moisture regimes on soil properties, microbial biomass C:N:P turnover, and the grain yield of mustard crops under stress in arid conditions; (2) Methods: The field experiment was carried out for 2 years at the farms of the agriculture college of SKN, Jobner (SKRAU Bikaner, Rajasthan). The effects of organic manure, moisture regimes, and saline water treatment on soil properties, such as the soil microbial biomass build-up, loss, turnover, and recycling of carbon (Cmic), nitrogen (Nmic), and phosphorus (Pmic) in the mustard crop were investigated. The twenty-seven treatments studied are described as follows: organic manures (control, FYM @ 10 t ha-1 and vermicompost @ 5 t ha-1), moisture regimes (0.4, 0.6, and 0.8 IW/CPE ratio), and saline irrigation water (control, 6, 12 dSm-1); (3) Results: Our findings indicate that vermicompost @ 5 t ha-1 significantly increases moisture retention and the available water in soil at 33 kPa and 1500 kPa. The microbial biomass build-up of Cmic increases by 43.13% over the control and 14.36% over the FYM. Similarly, the soil microbial biomass of Nmic, and Pmic also increase considerably. The SHC of the soil is enhanced by the application of farmyard fertilizer and vermicompost. The BD and pH decrease significantly, while the SHC, OC, CEC, and ECe of the soil increase significantly. The build-up, losses, and fluxes of the soil microbial biomass of Cmic, Nmic, and Pmic increase significantly, and the turnover rate decreases under vermicompost @ 5 t ha-1. A significant increase in grain yield was observed. Irrigation with a 0.8 IW/CPE moisture regime significantly decreases the pH of the SHC; (4) Conclusions: We hypothesized the interactive outcomes of the moisture regime and found that organic manure significantly influenced grain and stover yield. The treatments of quality irrigation water and the addition of organic manure are efficient enough to improve soil properties, water holding capacity, and soil microbial biomass C:N:P in stress climatic conditions.
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Affiliation(s)
- Rajendra Bhanwaria
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India;
- Plant Sciences and Agrotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, Jammu & Kashmir, India
| | - Bikarma Singh
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India;
- Botanic Garden Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, Uttar Pradesh, India
| | - Carmelo Maria Musarella
- Department of Agraria, Mediterranea University of Reggio Calabria, Feo di Vito snc, 89122 Reggio Calabria, Italy;
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83
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Abstract
Plant roots are colonized by microorganisms from the surrounding soil that belong to different kingdoms and form a multikingdom microbial community called the root microbiota. Despite their importance for plant growth, the relationship between soil management, the root microbiota, and plant performance remains unknown. Here, we characterize the maize root-associated bacterial, fungal, and oomycetal communities during the vegetative and reproductive growth stages of four maize inbred lines and the pht1;6 phosphate transporter mutant. These plants were grown in two long-term experimental fields under four contrasting soil managements, including phosphate-deficient and -sufficient conditions. We showed that the maize root-associated microbiota is influenced by soil management and changes during host growth stages. We identified stable bacterial and fungal root-associated taxa that persist throughout the host life cycle. These taxa were accompanied by dynamic members that covary with changes in root metabolites. We observed an inverse stable-to-dynamic ratio between root-associated bacterial and fungal communities. We also found a host footprint on the soil biota, characterized by a convergence between soil, rhizosphere, and root bacterial communities during reproductive maize growth. Our study reveals the spatiotemporal dynamics of the maize root-associated microbiota and suggests that the fungal assemblage is less responsive to changes in root metabolites than the bacterial community.
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84
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Gupta A, Singh UB, Sahu PK, Paul S, Kumar A, Malviya D, Singh S, Kuppusamy P, Singh P, Paul D, Rai JP, Singh HV, Manna MC, Crusberg TC, Kumar A, Saxena AK. Linking Soil Microbial Diversity to Modern Agriculture Practices: A Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19053141. [PMID: 35270832 DOI: 10.3390/ijerph190531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/04/2022] [Accepted: 03/04/2022] [Indexed: 05/28/2023]
Abstract
Agriculture is a multifarious interface between plants and associated microorganisms. In contemporary agriculture, emphasis is being given to environmentally friendly approaches, particularly in developing countries, to enhance sustainability of the system with the least negative effects on produce quality and quantity. Modern agricultural practices such as extensive tillage, the use of harmful agrochemicals, mono-cropping, etc. have been found to influence soil microbial community structure and soil sustainability. On the other hand, the question of feeding the ever-growing global population while ensuring system sustainability largely remains unanswered. Agriculturally important microorganisms are envisaged to play important roles in various measures to raise a healthy and remunerative crop, including integrated nutrient management, as well as disease and pest management to cut down agrochemicals without compromising the agricultural production. These beneficial microorganisms seem to have every potential to provide an alternative opportunity to overcome the ill effects of various components of traditional agriculture being practiced by and large. Despite an increased awareness of the importance of organically produced food, farmers in developing countries still tend to apply inorganic chemical fertilizers and toxic chemical pesticides beyond the recommended doses. Nutrient uptake enhancement, biocontrol of pests and diseases using microbial inoculants may replace/reduce agrochemicals in agricultural production system. The present review aims to examine and discuss the shift in microbial population structure due to current agricultural practices and focuses on the development of a sustainable agricultural system employing the tremendous untapped potential of the microbial world.
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Affiliation(s)
- Amrita Gupta
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Udai B Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Pramod K Sahu
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Surinder Paul
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Adarsh Kumar
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Deepti Malviya
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Shailendra Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Pandiyan Kuppusamy
- ICAR-Central Institute for Research on Cotton Technology, Ginning Training Centre, Nagpur 440023, India
| | - Prakash Singh
- Department of Plant Breeding and Genetics, Veer Kunwar Singh College of Agriculture, Bihar Agricultural University, Dumraon 802136, India
| | - Diby Paul
- Pilgram Marpeck School of Science, Technology, Engineering and Mathematics, Truett McConnel University, 100 Alumni Dr., Cleveland, GA 30528, USA
| | - Jai P Rai
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Harsh V Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
| | - Madhab C Manna
- Soil Biology Division, ICAR-Indian Institute of Soil Science, Nabibagh, Berasia Road, Bhopal 462038, India
| | - Theodore C Crusberg
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01605, USA
| | - Arun Kumar
- Department of Agronomy, Bihar Agricultural University, Sabour, Bhagalpur 813210, India
| | - Anil K Saxena
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India
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85
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Gupta A, Singh UB, Sahu PK, Paul S, Kumar A, Malviya D, Singh S, Kuppusamy P, Singh P, Paul D, Rai JP, Singh HV, Manna MC, Crusberg TC, Kumar A, Saxena AK. Linking Soil Microbial Diversity to Modern Agriculture Practices: A Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:3141. [PMID: 35270832 PMCID: PMC8910389 DOI: 10.3390/ijerph19053141] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/04/2022] [Accepted: 03/04/2022] [Indexed: 12/01/2022]
Abstract
Agriculture is a multifarious interface between plants and associated microorganisms. In contemporary agriculture, emphasis is being given to environmentally friendly approaches, particularly in developing countries, to enhance sustainability of the system with the least negative effects on produce quality and quantity. Modern agricultural practices such as extensive tillage, the use of harmful agrochemicals, mono-cropping, etc. have been found to influence soil microbial community structure and soil sustainability. On the other hand, the question of feeding the ever-growing global population while ensuring system sustainability largely remains unanswered. Agriculturally important microorganisms are envisaged to play important roles in various measures to raise a healthy and remunerative crop, including integrated nutrient management, as well as disease and pest management to cut down agrochemicals without compromising the agricultural production. These beneficial microorganisms seem to have every potential to provide an alternative opportunity to overcome the ill effects of various components of traditional agriculture being practiced by and large. Despite an increased awareness of the importance of organically produced food, farmers in developing countries still tend to apply inorganic chemical fertilizers and toxic chemical pesticides beyond the recommended doses. Nutrient uptake enhancement, biocontrol of pests and diseases using microbial inoculants may replace/reduce agrochemicals in agricultural production system. The present review aims to examine and discuss the shift in microbial population structure due to current agricultural practices and focuses on the development of a sustainable agricultural system employing the tremendous untapped potential of the microbial world.
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Affiliation(s)
- Amrita Gupta
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
| | - Udai B. Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
| | - Pramod K. Sahu
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
| | - Surinder Paul
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
| | - Adarsh Kumar
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
| | - Deepti Malviya
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
| | - Shailendra Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
| | - Pandiyan Kuppusamy
- ICAR-Central Institute for Research on Cotton Technology, Ginning Training Centre, Nagpur 440023, India;
| | - Prakash Singh
- Department of Plant Breeding and Genetics, Veer Kunwar Singh College of Agriculture, Bihar Agricultural University, Dumraon 802136, India;
| | - Diby Paul
- Pilgram Marpeck School of Science, Technology, Engineering and Mathematics, Truett McConnel University, 100 Alumni Dr., Cleveland, GA 30528, USA;
| | - Jai P. Rai
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Harsh V. Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
| | - Madhab C. Manna
- Soil Biology Division, ICAR-Indian Institute of Soil Science, Nabibagh, Berasia Road, Bhopal 462038, India;
| | - Theodore C. Crusberg
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01605, USA;
| | - Arun Kumar
- Department of Agronomy, Bihar Agricultural University, Sabour, Bhagalpur 813210, India;
| | - Anil K. Saxena
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan 275103, India; (A.G.); (U.B.S.); (P.K.S.); (S.P.); (A.K.); (D.M.); (S.S.); (H.V.S.); (A.K.S.)
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86
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Chi Y, Lin Q, Zhuang R, Xiong M, Ye Z. Evaluation of acid mine drainage sludge as soil substitute for the reclamation of mine solid wastes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:21184-21197. [PMID: 34755294 DOI: 10.1007/s11356-021-17290-z] [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: 07/31/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
The reclamation of mine waste deposits is often hindered by the scarcity of natural topsoil. Acid mine drainage sludge (AMDS), as a mass-produced waste in metalliferous mines, is a potential topsoil substitute but had not been validated. In this study, a pot experiment with three plant species was conducted to evaluate the capacity of AMDS to support plant growth, buffer acidification, and immobilize heavy metal(loid)s when reclaiming mine waste rocks. Chemical fertilizer and compost chicken manure were applied to AMDS at different rates to explore their effects on plant growth and the physicochemical properties of AMDS. Results showed that all the plants could survive in AMDS even without fertilization. The contents of heavy metal(loid)s in rhizosphere remained almost unchanged over the experimental period, indicating low leachability of revegetated AMDS. Fertilizers enhanced macronutrients and soil enzyme activities, leading to significant increases in plant biomass. However, owing to manure composting and low richness and diversity of the bacterial community in AMDS, the NH4+-N and bioavailable phosphorus contents were extremely low. Bermuda grass was a suitable pioneer species for reclamation for its better adaptability to nutrient deficiency and heavy metal(loid) stress. Overall, AMDS is a viable soil substitute for mine reclamation due to its capability to support plant growth and environmental safety.
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Affiliation(s)
- Yihan Chi
- State Key Laboratory for Comprehensive Utilization of Low-Grade Refractory Gold Ores, Longyan, 364200, Fujian, China
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Qinru Lin
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Rongchuan Zhuang
- State Key Laboratory for Comprehensive Utilization of Low-Grade Refractory Gold Ores, Longyan, 364200, Fujian, China
| | - Mingyu Xiong
- State Key Laboratory for Comprehensive Utilization of Low-Grade Refractory Gold Ores, Longyan, 364200, Fujian, China
| | - Zhihong Ye
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China.
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87
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Yin Y, Yuan Y, Zhang X, Huhe, Cheng Y, Borjigin S. Comparison of the Responses of Soil Fungal Community to Straw, Inorganic Fertilizer, and Compost in a Farmland in the Loess Plateau. Microbiol Spectr 2022; 10:e0223021. [PMID: 35019779 PMCID: PMC8754151 DOI: 10.1128/spectrum.02230-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/02/2021] [Indexed: 11/24/2022] Open
Abstract
The Loess Plateau is located in the arid and semi-arid regions in northern China. The ecosystem is particularly sensitive to natural and anthropogenic disturbances. Fungi can produce extracellular enzymes, decompose a variety of organic matter, and regulate carbon and nutrient balance. We studied the changes of soil fungal community compositions in response to straw, inorganic fertilizer, and compost in a typical farmland in the Loess Plateau. Our results demonstrated that the addition of straw significantly reduces the Shannon index of the fungal community, in addition, the participation of straw significantly affects the composition of the fungal community. Functional prediction based on FUNGuild showed that straw significantly reduced the relative abundance of saprotrophs, pathotrophs, symbiotrophs, lichenized, ectomycorrhizal, and plant pathogens. Although fertilization practices destroyed the co-occurrence pattern among the fungal species, the addition of straw alleviated this affect. No significant effect of straw, compost, and inorganic fertilizers on the co-occurrence pattern among species in the soil fungal community was observed. Compared with compost and inorganic fertilizer, the addition of straw shaped the community composition by changing the relative abundance of fungal functional taxa. Thus, in the fragile Loess Plateau environment, over-fertilizing or non-order-fertilizing may destroy the co-occurrence pattern of the fungal communities and Loess Plateau ecosystem. IMPORTANCE Determining the response of soil fungi in sensitive ecosystems to external environmental disturbances is an important, yet little-known, topic in microbial ecology. In this study, we evaluated the impact of traditional fertilization management practices on the composition, co-occurrence pattern, and functional groups of fungal communities in loessial soil. Our results show that in the fragile Loess Plateau environment, fertilizer management changed the composition of the fungal community and disrupted the co-occurrence pattern between fungi. The application of straw alleviates the destroying of the co-occurrence pattern. The current research emphasizes the necessity of rational fertilization of farmland in loessial soil.
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Affiliation(s)
- Yalin Yin
- School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Ye Yuan
- School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Xiaowen Zhang
- School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Huhe
- School of Ecology and Environment, Inner Mongolia University, Hohhot, China
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, Ministry of Education of China, Hohhot, China
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Hohhot, China
| | - Yunxiang Cheng
- School of Ecology and Environment, Inner Mongolia University, Hohhot, China
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, Ministry of Education of China, Hohhot, China
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Hohhot, China
| | - Shinchilelt Borjigin
- Biodiversity Division, National Institute for Environmental Studies, Ibaraki, Japan
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88
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Liu X, Shi Y, Kong L, Tong L, Cao H, Zhou H, Lv Y. Long-Term Application of Bio-Compost Increased Soil Microbial Community Diversity and Altered Its Composition and Network. Microorganisms 2022; 10:microorganisms10020462. [PMID: 35208916 PMCID: PMC8878586 DOI: 10.3390/microorganisms10020462] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 02/08/2022] [Indexed: 01/10/2023] Open
Abstract
The influence of bio-compost on the diversity, composition and structure of soil microbial communities is less understood. Here, Illumina MiSeq sequencing and a network analysis were used to comprehensively characterize the effects of 25 years of bio-compost application on the microbial diversity of soil and community composition. High dosages of bio-compost significantly increased the bacterial and fungal richness. The compositions of bacterial and fungal communities were significantly altered by bio-compost addition. Bio-compost addition enriched the relative abundance of beneficial microorganisms (such as Sphingomonas, Acidibacter, Nocardioides, etc.) and reduced the relative abundance of harmful microorganisms (such as Stachybotrys and Aspergillus). Electrical conductivity, soil organic matter and total phosphorus were the key factors in shaping soil microbial community composition. The bacterial network was more complex than fungal network, and bacteria were more sensitive to changes in environmental factors than fungi. Positive interactions dominated both the bacterial and fungal networks, with stronger positive interactions found in the bacterial network. Functional prediction suggested that bio-composts altered the soil bacterial-community metabolic function with respect to carbon, nitrogen and phosphorus cycles and fungal community trophic modes. In conclusion, suitable bio-compost addition is beneficial to the improvement of soil health and crop quality and therefore the sustainability of agriculture.
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Affiliation(s)
- Xiayan Liu
- Department of Soil and Water Sciences, College of Land Science and Technology, China Agricultural University, Beijing 100193, China; (X.L.); (L.K.); (H.C.)
| | - Yu Shi
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China;
| | - Lingyu Kong
- Department of Soil and Water Sciences, College of Land Science and Technology, China Agricultural University, Beijing 100193, China; (X.L.); (L.K.); (H.C.)
| | - Lihong Tong
- State Key Laboratory of Hydroscience and Engineering, Department of Hydraulic Engineering, Tsinghua University, Beijing 100084, China;
| | - Haoxuan Cao
- Department of Soil and Water Sciences, College of Land Science and Technology, China Agricultural University, Beijing 100193, China; (X.L.); (L.K.); (H.C.)
| | - Hu Zhou
- Department of Soil and Water Sciences, College of Land Science and Technology, China Agricultural University, Beijing 100193, China; (X.L.); (L.K.); (H.C.)
- Correspondence: (H.Z.); (Y.L.); Tel.: +86-010-62731890 (H.Z.); +86-010-62731431 (Y.L.)
| | - Yizhong Lv
- Department of Soil and Water Sciences, College of Land Science and Technology, China Agricultural University, Beijing 100193, China; (X.L.); (L.K.); (H.C.)
- Correspondence: (H.Z.); (Y.L.); Tel.: +86-010-62731890 (H.Z.); +86-010-62731431 (Y.L.)
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89
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Cui J, Zhu R, Wang X, Xu X, Ai C, He P, Liang G, Zhou W, Zhu P. Effect of high soil C/N ratio and nitrogen limitation caused by the long-term combined organic-inorganic fertilization on the soil microbial community structure and its dominated SOC decomposition. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 303:114155. [PMID: 34861507 DOI: 10.1016/j.jenvman.2021.114155] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 10/20/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
The application of organic fertilizers, such as straw and manure, is an efficient approach to maintain soil productivity. However, the effect of these organic fertilizers on soil microbial nutrient balance has not yet been established. In this study, the effects of the long-term combined organic-inorganic fertilization on microbial community were investigated by conducting a 30-year-long field test. Overall, the following five fertilizer groups were employed: inorganic NP fertilizer (NP), inorganic NK fertilizer (NK), inorganic NPK fertilizer (NPK), NPK + manure (MNPK), and NPK + straw (SNPK). The results indicated that the mean natural logarithm of the soil C:N:P acquisition enzyme ratio was 1.04:1.11:1.00 under organic-inorganic treatments, which showed a deviation from its overall mean ratio of 1:1:1. This indicates that microbial resources do not have a balance. Vector analysis (vector angle <45°) and threshold elemental ratio analysis (RC:N-TERC:N > 0) further demonstrated that the microbial metabolism was limited by Nitrogen (N) under SNPK and MNPK treatments. N limitation further influenced soil microbial community structure and its dominated SOC decomposition. Specifically, Microbial communities transformed into a more oligotrophic-dominant condition (fungal, Acidobacteria, Chloroflexi) from copiotrophic-dominant (Proteobacteria, Actinobacteria) condition with increasing N limitation. Lysobacter genus and Blastocatellaceae family, in the bacterial communities along with the Mortierella elongata species in fungal communities, were markedly associated with the N limitation, which could be the critical biomarker that represented N limitation. Both correlation analysis and partial least squares path modeling showed significant positive effects of N limitation on the ratio of bacterial functional genes (Cellulase/Amylase), involved in recalcitrant SOC degradation.
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Affiliation(s)
- Jiwen Cui
- Institute of Agricultural Resource and Regional Planning, Chinese Academy of Agricultural Sciences, Key Lab of Plant Nutrition and Fertilizer, Ministry of Agriculture, Beijing, 100081, PR China
| | - Ruili Zhu
- Institute of Agricultural Resource and Regional Planning, Chinese Academy of Agricultural Sciences, Key Lab of Plant Nutrition and Fertilizer, Ministry of Agriculture, Beijing, 100081, PR China
| | - Xiya Wang
- Institute of Agricultural Resource and Regional Planning, Chinese Academy of Agricultural Sciences, Key Lab of Plant Nutrition and Fertilizer, Ministry of Agriculture, Beijing, 100081, PR China
| | - Xinpeng Xu
- Institute of Agricultural Resource and Regional Planning, Chinese Academy of Agricultural Sciences, Key Lab of Plant Nutrition and Fertilizer, Ministry of Agriculture, Beijing, 100081, PR China
| | - Chao Ai
- Institute of Agricultural Resource and Regional Planning, Chinese Academy of Agricultural Sciences, Key Lab of Plant Nutrition and Fertilizer, Ministry of Agriculture, Beijing, 100081, PR China
| | - Ping He
- Institute of Agricultural Resource and Regional Planning, Chinese Academy of Agricultural Sciences, Key Lab of Plant Nutrition and Fertilizer, Ministry of Agriculture, Beijing, 100081, PR China
| | - Guoqing Liang
- Institute of Agricultural Resource and Regional Planning, Chinese Academy of Agricultural Sciences, Key Lab of Plant Nutrition and Fertilizer, Ministry of Agriculture, Beijing, 100081, PR China
| | - Wei Zhou
- Institute of Agricultural Resource and Regional Planning, Chinese Academy of Agricultural Sciences, Key Lab of Plant Nutrition and Fertilizer, Ministry of Agriculture, Beijing, 100081, PR China.
| | - Ping Zhu
- Jilin Academy of Agricultural Sciences, Gongzhuling, 130124, PR China.
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90
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Lim JY, Kang YG, Sohn KM, Kim PJ, Galgo SJC. Creating new value of blast furnace slag as soil amendment to mitigate methane emission and improve rice cropping environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150961. [PMID: 34656598 DOI: 10.1016/j.scitotenv.2021.150961] [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: 03/29/2021] [Revised: 09/06/2021] [Accepted: 10/09/2021] [Indexed: 06/13/2023]
Abstract
Blast furnace slag (BFS), a by-product of iron making, has been utilized as silicate fertilizer in Korean and Japanese rice paddy. Silicate fertilizer, which has high contents of active iron and manganese as electron acceptor, was newly known to suppress methane (CH4) emission in flooded rice paddies, but the effect of its long-term application on rice cropping environment is still debatable. To evaluate the effect of silicate fertilization on suppressing CH4 emissions, the changes of CH4 index, indicating the ratio (%) of seasonal CH4 flux at the silicate fertilization treatment to that at the control, were generalized using the global investigation data (42 observations from 8 fields in Bangladesh, China, and Korea). Seasonal CH4 fluxes significantly decreased with increasing silicate fertilization levels. In CH4 index changes, 1.5 Mg ha-1 of silicate fertilizer application (the recommended level of rice cultivation in Korea) decreased by 15% of seasonal CH4 fluxes. Rice grain yield highly increased with increasing silicate fertilization rates and maximized at approximately 4 Mg ha-1 with 18% higher than no-silicate fertilization due to overall improvement of soil properties. To evaluate the long-term silicate fertilization effect on rice cropping environments, silicate (1.5 Mg ha-1 year-1) and non-silicate fertilization treatments were installed in a typical temperate-monsoon climate paddy field in South Korea in 1990. Periodic silicate fertilization significantly increased rice grain productivity by an average of 14% over the control for the last 28 years. This fertilization evidently improved rice quality without changes in chemical quality. Consecutive silicate fertilization effectively improved soil physical and chemical properties but did not increase any acid extractable heavy metal concentration in soil. In conclusion, BFS as silicate fertilizer could be a beneficial amendment to mitigate CH4 emission in the rice paddy and improve soil properties and rice productivity and quality without hazardous material accumulation.
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Affiliation(s)
- Ji Yeon Lim
- Institute of Agriculture and Life Sciences, Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Republic of Korea
| | - Yeong Gyeong Kang
- Korea Foundation of Korean Foundation for Quality, 13th Fl, Woolim Lion's Valley B, 168, Gasan digital 1-ro, Geumcheon-gu, Gasan dong, Seoul, Republic of Korea
| | - Keon Mok Sohn
- Division of Applied Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Republic of Korea
| | - Pil Joo Kim
- Institute of Agriculture and Life Sciences, Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Republic of Korea; Division of Applied Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Republic of Korea.
| | - Snowie Jane C Galgo
- Division of Applied Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Republic of Korea.
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91
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Abstract
The present paper reviews the most recent advances regarding the effects of chemical and organic fertilizers on soil microbial communities. Based on the results from the articles considered, some details are presented on how the use of various types of fertilizers affects the composition and activity of soil microbial communities. Soil microbes have different responses to fertilization based on differences in the total carbon (C), nitrogen (N) and phosphorus (P) contents in the soil, along with soil moisture and the presence of plant species. These articles show that the use of chemical fertilizers changes the abundance of microbial populations and stimulates their growth thanks to the nutrient supply added. Overall, however, the data revealed that chemical fertilizers have no significant influence on the richness and diversity of the bacteria and fungi. Instead, the abundance of individual bacterial or fungal species was sensitive to fertilization and was mainly attributed to the changes in the soil chemical properties induced by chemical or organic fertilization. Among the negative effects of chemical fertilization, the decrease in enzymatic activity has been highlighted by several papers, especially in soils that have received the largest amounts of fertilizers together with losses in organic matter.
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92
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Abubakar AY, Ibrahim MM, Zhang C, Tayyab M, Fallah N, Yang Z, Pang Z, Zhang H. Filtered mud improves sugarcane growth and modifies the functional abundance and structure of soil microbial populations. PeerJ 2022; 10:e12753. [PMID: 35111397 PMCID: PMC8771795 DOI: 10.7717/peerj.12753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/15/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Exploring high-quality organic amendments has been a focus of sustainable agriculture. Filtered mud (FM), a sugar factory waste derived from sugarcane stems, could be an alternative organic amendment for sugarcane production. However, the effects of its application proportions on soil fertility, nutrient cycling, structure of soil bacterial and fungal communities, and the growth of sugarcane in clay-loam soils remain unexplored. METHODS Three application proportions of FM: (FM1-(FM: Soil at 1:4), FM2-(FM: Soil at 2:3), and FM3-(FM: Soil at 3:2)) were evaluated on sugarcane growth and soil nutrient cycling. High throughput sequencing was also employed to explore soil microbial dynamics. RESULTS We observed that FM generally increased the soil's nutritional properties while improving NO3 - retention compared to the control, resulting in increased growth parameters of sugarcane. Specifically, FM1 increased the concentration of NH4 +-N, the N fraction preferably taken up by sugarcane, which was associated with an increase in the plant height, and more improved growth properties, among other treatments. An increase in the proportion of FM also increased the activity of soil nutrient cycling enzymes; urease, phosphatase, and β-glucosidase. High throughput sequencing revealed that FM reduced the diversity of soil bacteria while having insignificant effects on fungal diversity. Although increasing FM rates reduced the relative abundance of the phyla Proteobacteria, its class members, the Gammaproteobacteria and Betaproteobacteria containing some N-cycling related genera, were stimulated. Also, FM stimulated the abundance of beneficial and lignocellulose degrading organisms. These included the bacterial phyla Actinobacteria, Bacteroidetes, Acidobacteria, Chloroflexi, and the fungal phylum Ascomycota. The distribution of the soil microbial community under FM rates was regulated by the changes in soil pH and the availability of soil nutrients. Since FM1 showed more promise in improving the growth properties of sugarcane, it could be more economical and sustainable for sugarcane production in clay-loam soils.
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Affiliation(s)
- Ahmad Yusuf Abubakar
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China,Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China,Bioresources Development Centre, National Biotechnology Development Agency, Kano, Nigeria
| | - Muhammed Mustapha Ibrahim
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China,Department of Soil Science, University of Agriculture Makurdi, Benue, Nigeria
| | - Caifang Zhang
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China,Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Muhammad Tayyab
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China,Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Nyumah Fallah
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China,Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Ziqi Yang
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China,Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Ziqin Pang
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China,Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Hua Zhang
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China,Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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93
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Vieira CK, Dos Anjos Borges LG, Bortolini JG, Soares CRFS, Giongo A, Stürmer SL. Does a decrease in microbial biomass alter mycorrhizal attributes and soil quality indicators in coal mining areas under revegetation process? THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 802:149843. [PMID: 34455279 DOI: 10.1016/j.scitotenv.2021.149843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 06/13/2023]
Abstract
Losses of microbial diversity in degraded ecosystems still have obscure consequences, especially when considering the interaction between arbuscular mycorrhizal fungi (AMF) and soil bacteria. This study investigates the effect of decreasing microbial biomass on mycorrhizal attributes and soil quality indicators. The dilution-to-extinction approach was applied in microcosms to search for associations among bacterial diversity, mycorrhizal attributes, and soil quality indicators. The experiment was conducted with four soil treatments (undiluted control 100 = D0, 10-3 = D3, 10-6 = D6, and 10-9 = D9) from a short-term (two years = 2Y) and a long-term (15 years = 15Y) coal mine revegetation area. Microcosms were inoculated with 300 spores of Acaulospora colombiana, Gigaspora albida, and Claroideoglomus etunicatum with millet as the host plant. Results included the total number of AMF spores, mycorrhizal colonization, soil aggregation, glomalin, fluorescein diacetate hydrolysis (FDA), basal soil respiration, microbial biomass, and soil bacterial microbiome. Larger differences were observed between areas than between dilution treatments within the sampling area. Attributes that presented differences in the dilutions compared to D0 2Y samples were mycorrhizal colonization (D0 = 85% and D9 = 43.3%), FDA (D0 = 77.2% and D9 = 55.5%), extractable glomalin-related soil protein (D0 = 0.09 and D9 = 0.11) and bacterial diversity (D0 = 7.3 and D6 = 5.3). D0 15Y samples presented differences in microbial biomass nitrogen (D0: 232.0) and bacterial diversity (D0: 7.9, D9: 5.6) compared to the dilutions. Bacterial microbiome present in the D0 samples formed distinct clusters as to other samples and correlated with soil aggregation and basal respiration attributes. Results suggest that AMF inoculation and dilution-to-extinction did not affect soil quality indicators preeminently, but the bacterial community is affected and can influence the process of environmental revegetation. A long-term revegetation period is substantial to improve quality indicators and establish the diversity of microorganisms and consequently revegetation in areas impacted by coal mining.
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Affiliation(s)
- Caroline Krug Vieira
- Universidade Regional de Blumenau (FURB), Programa de Pós-Graduação em Engenharia Ambiental, 89030-903 Blumenau, SC, Brazil
| | - Luiz Gustavo Dos Anjos Borges
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Instituto do Petróleo e dos Recursos Naturais (IPR), 90619-900 Porto Alegre, RS, Brazil
| | | | | | - Adriana Giongo
- Universidade Regional de Blumenau (FURB), Programa de Pós-Graduação em Engenharia Ambiental, 89030-903 Blumenau, SC, Brazil; Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Sidney Luiz Stürmer
- Universidade Regional de Blumenau (FURB), Departamento de Ciências Naturais (DCN), 89030-903 Blumenau, SC, Brazil.
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94
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Nunes I, Hansen V, Bak F, Bonnichsen L, Su J, Hao X, Raymond NS, Nicolaisen MH, Jensen LS, Nybroe O. OUP accepted manuscript. FEMS Microbiol Ecol 2022; 98:6548193. [PMID: 35285907 PMCID: PMC8951222 DOI: 10.1093/femsec/fiac028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/22/2022] [Accepted: 03/10/2022] [Indexed: 11/21/2022] Open
Abstract
During germination, the seed releases nutrient-rich exudates into the spermosphere, thereby fostering competition between resident microorganisms. However, insight into the composition and temporal dynamics of seed-associated bacterial communities under field conditions is currently lacking. This field study determined the temporal changes from 11 to 31 days after sowing in the composition of seed-associated bacterial communities of winter wheat as affected by long-term soil fertilization history, and by introduction of the plant growth-promoting microbial inoculants Penicillium bilaiae and Bacillus simplex. The temporal dynamics were the most important factor affecting the composition of the seed-associated communities. An increase in the relative abundance of genes involved in organic nitrogen metabolism (ureC and gdhA), and in ammonium oxidation (amoA), suggested increased mineralization of plant-derived nitrogen compounds over time. Dynamics of the phosphorus cycling genes ppt, ppx and cphy indicated inorganic phosphorus and polyphosphate cycling, as well as phytate hydrolysis by the seed-associated bacteria early after germination. Later, an increase in genes for utilization of organic phosphorus sources (phoD, phoX and phnK) indicated phosphorus limitation. The results indicate that community temporal dynamics are partly driven by changed availability of major nutrients, and reveal no functional consequences of the added inoculants during seed germination.
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Affiliation(s)
| | | | | | - Lise Bonnichsen
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Jianqiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xiuli Hao
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University; Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Nelly Sophie Raymond
- Plant and Soil Section, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensevej 40, 1871 Frederiksberg C, Denmark
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Mette Haubjerg Nicolaisen
- Corresponding author: Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, Univeristy of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Denmark. Tel: +45 35332649; E-mail:
| | - Lars Stoumann Jensen
- Plant and Soil Section, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensevej 40, 1871 Frederiksberg C, Denmark
| | - Ole Nybroe
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
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95
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Moulton-Brown CE, Feng T, Kumar SS, Xu L, Dytham C, Helgason T, Cooper JM, Moir JWB. Long-term fertilization and tillage regimes have limited effects on structuring bacterial and denitrifier communities in a sandy loam UK soil. Environ Microbiol 2021; 24:298-308. [PMID: 34913554 DOI: 10.1111/1462-2920.15873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 11/30/2021] [Accepted: 12/08/2021] [Indexed: 11/30/2022]
Abstract
Denitrification causes loss of available nitrogen from soil systems, thereby reducing crop productivity and increasing reliance on agrochemicals. The dynamics of denitrification and denitrifying communities are thought to be altered by land management practices, which affect the physicochemical properties of the soil. In this study, we look at the effects of long-term tillage and fertilization regimes on arable soils following 16 years of treatment in a factorial field trial. By studying the bacterial community composition based on 16S rRNA amplicons, absolute bacterial abundance and diversity of denitrification functional genes (nirK, nirS and nosZ), under conditions of minimum/conventional tillage and organic/synthetic mineral fertilizer, we tested how specific land management histories affect the diversity and distribution of both bacteria and denitrification genes. Bacterial and denitrifier communities were largely unaffected by land management history and clustered predominantly by spatial location, indicating that the variability in bacterial community composition in these arable soils is governed by innate environmental differences and Euclidean distance rather than agricultural management intervention.
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Affiliation(s)
| | - Tianer Feng
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Shreiya Shivagni Kumar
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Luxi Xu
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Calvin Dytham
- Department of Biology, University of York, Heslington, York, UK
| | | | - Julia M Cooper
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - James W B Moir
- Department of Biology, University of York, Heslington, York, UK
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96
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Sivojiene D, Kacergius A, Baksiene E, Maseviciene A, Zickiene L. The Influence of Organic Fertilizers on the Abundance of Soil Microorganism Communities, Agrochemical Indicators, and Yield in East Lithuanian Light Soils. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122648. [PMID: 34961119 PMCID: PMC8703430 DOI: 10.3390/plants10122648] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/28/2021] [Accepted: 11/29/2021] [Indexed: 06/02/2023]
Abstract
Soil microorganisms are one of the main indicators used for assessing the stability of the soil ecosystem, the metabolism in the soil, and its fertility. The most important are the active soil microorganisms and the influence of the fertilizer applied to the soil on the abundance of these microorganisms. We aimed to investigate how the applied organic fertilizers affect the most active soil microorganisms, which determine the soil fertility and stability. Fungi, yeast-like fungi abundance, and abundance of three physiological groups of bacteria were analyzed: non-symbiotic diazotrophic, organotrophic, and mineral nitrogen assimilating. This study is valuable because relatively few similar studies have been performed on infertile Lithuanian soils. The first results of a long-term study were obtained. The results show the effect of fertilizers on trends in the changes of microorganism community diversity; however, more analysis is needed to assess the impact of organic fertilizers on the most active soil microorganisms. Therefore, the investigation was continued. The results of the 2020 quantitative analysis of culturable soil microorganisms show that the highest abundance of organotrophic and non-symbiotic diazotrophic bacteria were recorded during the summer season. Meanwhile, the abundance of bacteria assimilating mineral nitrogen and fungi was higher in autumn. Agrochemical parameters were determined at the beginning of the experiment. The highest concentration of Nmin in the soil was determined after fertilizing the plants with the combination of granulated poultry manure (N170) + biological substance Azotobacter spp. The yield of barley was calculated. It was found that the highest yield of spring barley in 2020 was obtained by fertilizing the experimental field with organic in combination with mineral fertilizers.
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Affiliation(s)
- Diana Sivojiene
- Lithuanian Research Centre for Agriculture and Forestry, Vokė Branch of Institute of Agriculture, Žalioji Sq. 2, LT-02232 Vilnius, Lithuania; (A.K.); (E.B.)
| | - Audrius Kacergius
- Lithuanian Research Centre for Agriculture and Forestry, Vokė Branch of Institute of Agriculture, Žalioji Sq. 2, LT-02232 Vilnius, Lithuania; (A.K.); (E.B.)
| | - Eugenija Baksiene
- Lithuanian Research Centre for Agriculture and Forestry, Vokė Branch of Institute of Agriculture, Žalioji Sq. 2, LT-02232 Vilnius, Lithuania; (A.K.); (E.B.)
| | - Aiste Maseviciene
- Agrochemical Research Laboratory of Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Savanoriu Av. 287, LT-50127 Kaunas, Lithuania; (A.M.); (L.Z.)
| | - Lina Zickiene
- Agrochemical Research Laboratory of Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Savanoriu Av. 287, LT-50127 Kaunas, Lithuania; (A.M.); (L.Z.)
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97
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Effects of Seven-Year Fertilization Reclamation on Bacterial Community in a Coal Mining Subsidence Area in Shanxi, China. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph182312504. [PMID: 34886231 PMCID: PMC8656652 DOI: 10.3390/ijerph182312504] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/20/2021] [Accepted: 11/24/2021] [Indexed: 12/26/2022]
Abstract
The restoration of soil fertility and microbial communities is the key to the soil reclamation and ecological reconstruction in coal mine subsidence areas. However, the response of soil bacterial communities to reclamation is still not well understood. Here, we studied the bacterial communities in fertilizer-reclaimed soil (CK, without fertilizer; CF, chemical fertilizer; M, manure) in the Lu’an reclamation mining region and compared them with those in adjacent subsidence soil (SU) and farmland soil (FA). We found that the compositions of dominant phyla in the reclaimed soil differed greatly from those in the subsidence soil and farmland soil (p < 0.05). The related sequences of Acidobacteria, Chloroflexi, and Nitrospirae were mainly from the subsided soil, whereas those of Alphaproteobacteria, Planctomycetes, and Deltaproteobacteria were mainly derived from the farmland soil. Fertilization affected the bacterial community composition in the reclaimed soil, and bacteria richness and diversity increased significantly with the accumulation of soil nutrients after 7 years of reclamation (p < 0.05). Moreover, soil properties, especially SOM and pH, were found to play a key role in the restoration of the bacterial community in the reclaimed soil. The results are helpful to the study of soil fertility improvement and ecological restoration in mining areas.
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98
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Francioli D, Cid G, Kanukollu S, Ulrich A, Hajirezaei MR, Kolb S. Flooding Causes Dramatic Compositional Shifts and Depletion of Putative Beneficial Bacteria on the Spring Wheat Microbiota. Front Microbiol 2021; 12:773116. [PMID: 34803993 PMCID: PMC8602104 DOI: 10.3389/fmicb.2021.773116] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/13/2021] [Indexed: 01/04/2023] Open
Abstract
Flooding affects both above- and below-ground ecosystem processes, and it represents a substantial threat for crop and cereal productivity under climate change. Plant-associated microbiota play a crucial role in plant growth and fitness, but we still have a limited understanding of the response of the crop-microbiota complex under extreme weather events, such as flooding. Soil microbes are highly sensitive to abiotic disturbance, and shifts in microbial community composition, structure and functions are expected when soil conditions are altered due to flooding events (e.g., anoxia, pH alteration, changes in nutrient concentration). Here, we established a pot experiment to determine the effects of flooding stress on the spring wheat-microbiota complex. Since plant phenology could be an important factor in the response to hydrological stress, flooding was induced only once and at different plant growth stages (PGSs), such as tillering, booting and flowering. After each flooding event, we measured in the control and flooded pots several edaphic and plant properties and characterized the bacterial community associated to the rhizosphere and roots of wheat plant using a metabarcoding approach. In our study, flooding caused a significant reduction in plant development and we observed dramatic shifts in bacterial community composition at each PGS in which the hydrological stress was induced. However, a more pronounced disruption in community assembly was always shown in younger plants. Generally, flooding caused a (i) significant increase of bacterial taxa with anaerobic respiratory capabilities, such as members of Firmicutes and Desulfobacterota, (ii) a significant reduction in Actinobacteria and Proteobacteria, (iii) depletion of several putative plant-beneficial taxa, and (iv) increases of the abundance of potential detrimental bacteria. These significant differences in community composition between flooded and control samples were correlated with changes in soil conditions and plant properties caused by the hydrological stress, with pH and total N as the soil, and S, Na, Mn, and Ca concentrations as the root properties most influencing microbial assemblage in the wheat mircobiota under flooding stress. Collectively, our findings demonstrated the role of flooding on restructuring the spring wheat microbiota, and highlighted the detrimental effect of this hydrological stress on plant fitness and performance.
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Affiliation(s)
- Davide Francioli
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany
| | - Geeisy Cid
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Saranya Kanukollu
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany
| | - Andreas Ulrich
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany
| | - Mohammad-Reza Hajirezaei
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Steffen Kolb
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany.,Faculty of Life Sciences, Thaer Institute, Humboldt University of Berlin, Berlin, Germany
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99
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Nwokolo NL, Enebe MC. Shotgun metagenomics evaluation of soil fertilization effect on the rhizosphere viral community of maize plants. Antonie van Leeuwenhoek 2021; 115:69-78. [PMID: 34762236 DOI: 10.1007/s10482-021-01679-4] [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: 04/06/2021] [Accepted: 10/19/2021] [Indexed: 11/30/2022]
Abstract
The need for sustainability in food supply has led to progressive increase in soil nutrient enrichment. Fertilizer application effects both biological and abiotic processes in the soil, of which the bacterial community that support viral multiplication are equally influenced. Nevertheless, little is known on the effect of soil fertilization on the Soil viral community composition and dynamics. In this study, we evaluated the influence of soil fertilization on the maize rhizosphere viral community growing in Luvisolic soil. The highest abundance of bacteriophages were detected in soil treated with 8 tons/ha compost manure (Cp8), 60 kg/ha inorganic fertilizer (N1), 4 tons/ha compost manure (Cp4) and the unfertilized control (Cn0). Our result showed higher relative abundance of Myoviridae, Podoviridae and Siphoviridae in 8 tons/ha organic manure (Cp8) fertilized compared to others. While Inoviridae and Microviridae were the most relative abundant phage families in 4 tons/ha organic manure (Cp4) fertilized soil. This demonstrate that soil fertilization with organic manure increases the abundance and diversity of viruses in the soil due to its soil conditioning effects.
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Affiliation(s)
| | - Matthew Chekwube Enebe
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa.
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100
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Wang X, Sale P, Franks A, Jin J, Krohn C, Armstrong R, Tang C. An Insight Into the Effect of Organic Amendments on the Transpiration Efficiency of Wheat Plant in a Sodic Duplex Soil. FRONTIERS IN PLANT SCIENCE 2021; 12:722000. [PMID: 34745159 PMCID: PMC8563830 DOI: 10.3389/fpls.2021.722000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
Transpiration efficiency, the shoot biomass produced per unit of transpired water, is generally considered to be a constant property for a given crop in a given environment. To determine whether deep-banded organic amendments affect the transpiration efficiency (TE) of wheat plants and to provide a possible explanation for any changes in the TE, two-column experiments were carried out under controlled environment conditions. A Sodosol soil with physically constrained subsoils and a well-structured Vertosol were subjected to treatments including a control, fertilizer nutrients alone, and fertilizer-enriched organic amendments. The addition of fertilizer-enriched organic amendments in Sodosol consistently increased the canopy TE compared to the control and inorganic fertilizer treatments. The instantaneous TE, at the leaf level, was also increased by the organic-based amendments due to greater reductions in stomatal conductance and transpiration rates during periods of moderate water-deficit stress and the subsequent recovery from this stress. Shoot nitrogen (N) status could not explain the increases in TE following the addition of organic amendments relative to inorganic amendments. The increases in canopy TE were directly associated with increases in the absolute abundance of indigenous Bacillus (R 2 = 0.92, p <0), a well-known genus comprising many strains of plant beneficial rhizobacteria, in subsoil below the amendment band. In contrast, there were no differences in the canopy TE and instantaneous leaf TE between the organic and fertilizer amendments in the Vertosol with a well-structured subsoil. The positive effect of organic amendments on TE in the Sodosol should be attributed to their direct or indirect effect on improving the physical structure or biological properties of the subsoil.
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Affiliation(s)
- Xiaojuan Wang
- Department of Animal, Plant and Soil Sciences, AgriBio-Center for the AgriBiosciences, La Trobe University, Bundoora, VIC, Australia
| | - Peter Sale
- Department of Animal, Plant and Soil Sciences, AgriBio-Center for the AgriBiosciences, La Trobe University, Bundoora, VIC, Australia
| | - Ashley Franks
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
- Center for Future Landscapes, La Trobe University, Bundoora, VIC, Australia
| | - Jian Jin
- Department of Animal, Plant and Soil Sciences, AgriBio-Center for the AgriBiosciences, La Trobe University, Bundoora, VIC, Australia
| | - Christian Krohn
- Department of Animal, Plant and Soil Sciences, AgriBio-Center for the AgriBiosciences, La Trobe University, Bundoora, VIC, Australia
| | - Roger Armstrong
- Department of Jobs, Precincts & Regions, Grains Innovation Center, Horsham, VIC, Australia
| | - Caixian Tang
- Department of Animal, Plant and Soil Sciences, AgriBio-Center for the AgriBiosciences, La Trobe University, Bundoora, VIC, Australia
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