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Zhan J, Li Y, Zhao X, Yang H, Ning Z, Zhang R. Effects of nitrogen addition and plant litter manipulation on soil fungal and bacterial communities in a semiarid sandy land. Front Microbiol 2023; 14:1013570. [PMID: 37051518 PMCID: PMC10083410 DOI: 10.3389/fmicb.2023.1013570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 03/07/2023] [Indexed: 03/29/2023] Open
Abstract
The plant and soil microbial communities are influenced by variability in environmental conditions (e.g., nitrogen addition); however, it is unclear how long-term nitrogen addition and litter manipulation affect soil microbial communities in a semiarid sandy grassland. Therefore, we simulated the impact of N addition and litter manipulation (litter removal, litter doubling) on plant and soil microbial communities in Horqin grassland, northern China through an experiment from 2014 to 2019. Our results revealed that in the case of non-nitrogen (N0), litter manipulation significantly reduced vegetation coverage (V) (p < 0.05); soil bacterial communities have higher alpha diversity than that of the fungi, and the beta diversity of soil fungi was higher than that of the bacteria; soil microbial alpha diversity was significantly decreased by nitrogen addition (N10) (p < 0.05); N addition and litter manipulation had significantly interactive influences on soil microbial beta diversity, and litter manipulation (C0 and C2) had significantly decreased soil microbial beta diversity (p < 0.05) in the case of nitrogen addition (N10) (p < 0.05). Moreover, bacteria were mostly dominated by the universal phyla Proteobacteria, Actinobacteria, and Acidobacteria, and fungi were only dominated by Ascomycota. Furthermore, the correlation analysis, redundancy analysis (RDA), and variation partitioning analysis indicated that the soil fungi community was more apt to be influenced by plant community diversity. Our results provide evidence that plant and soil microbial community respond differently to the treatments of the 6-year N addition and litter manipulation in a semiarid sandy land.
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Affiliation(s)
- Jin Zhan
- Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yulin Li
- Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- *Correspondence: Yulin Li,
| | - Xueyong Zhao
- Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Hongling Yang
- Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Zhiying Ning
- Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Rui Zhang
- Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
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2
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Liu J, Zhang X, Tian J, Li Y, Liu Q, Chen X, Feng F, Yu X, Yang C. Multiomics analysis reveals that peach gum colouring reflects plant defense responses against pathogenic fungi. Food Chem 2022; 383:132424. [PMID: 35182869 DOI: 10.1016/j.foodchem.2022.132424] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 12/22/2021] [Accepted: 02/08/2022] [Indexed: 11/29/2022]
Abstract
In the present study, the differences in the antioxidant capability, metabolite composition and fungal diversity in peach gum with various colours were investigated. Metabolomics revealed that peach gum comprised many small-molecule metabolites (including primary and secondary metabolites), and most polyphenols (such as flavonoids and phenolic acids) showed a significantly positive relationship with the colour deepening, total phenol content and antioxidant capability. Using fungal diversity analysis, the abundance of five fungi at the genus level increased with peach gum colour deepening, and these fungi demonstrated a significantly positive relationship with two defense hormones (salicylic acid and abscisic acid) and most polyphenols (particularly flavonoids). The gummosis pathogenic fungus Botryosphaeria was among the five fungi, suggesting that peach gum colouring may reflect plant defense responses against pathogenic fungi. Additionally, the concentrations of 12 flavonoids in peach gum samples were detected based on LC-QQQ/MS, among which hesperetin, naringenin and eriodictyol were the most abundant.
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Affiliation(s)
- Jia Liu
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, 50 Zhongling Street, Nanjing 210014, China; Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China; School of Food and Biological Engineering, Jiangsu University, 301 Zhenjiang City University Road, Zhenjiang 212001, China
| | - Xiping Zhang
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, 50 Zhongling Street, Nanjing 210014, China; Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
| | - Ju Tian
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, 50 Zhongling Street, Nanjing 210014, China; Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
| | - Yong Li
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, 50 Zhongling Street, Nanjing 210014, China; Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China; School of Food and Biological Engineering, Jiangsu University, 301 Zhenjiang City University Road, Zhenjiang 212001, China.
| | - Qiyue Liu
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, 50 Zhongling Street, Nanjing 210014, China; Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
| | - Xiaolong Chen
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, 50 Zhongling Street, Nanjing 210014, China; Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
| | - Fayun Feng
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, 50 Zhongling Street, Nanjing 210014, China; Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
| | - Xiangyang Yu
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, 50 Zhongling Street, Nanjing 210014, China; Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China.
| | - Chenye Yang
- Central Laboratory in Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China
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3
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Naylor D, McClure R, Jansson J. Trends in Microbial Community Composition and Function by Soil Depth. Microorganisms 2022; 10:microorganisms10030540. [PMID: 35336115 PMCID: PMC8954175 DOI: 10.3390/microorganisms10030540] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/22/2022] [Accepted: 02/25/2022] [Indexed: 12/18/2022] Open
Abstract
Microbial communities play important roles in soil health, contributing to processes such as the turnover of organic matter and nutrient cycling. As soil edaphic properties such as chemical composition and physical structure change from surface layers to deeper ones, the soil microbiome similarly exhibits substantial variability with depth, with respect to both community composition and functional profiles. However, soil microbiome studies often neglect deeper soils, instead focusing on the top layer of soil. Here, we provide a synthesis on how the soil and its resident microbiome change with depth. We touch upon soil physicochemical properties, microbial diversity, composition, and functional profiles, with a special emphasis on carbon cycling. In doing so, we seek to highlight the importance of incorporating analyses of deeper soils in soil studies.
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4
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Hao X, Bai L, Liu X, Zhu P, Liu H, Xiao Y, Geng J, Liu Q, Huang L, Jiang H. Cadmium Speciation Distribution Responses to Soil Properties and Soil Microbes of Plow Layer and Plow Pan Soils in Cadmium-Contaminated Paddy Fields. Front Microbiol 2021; 12:774301. [PMID: 34925280 PMCID: PMC8679784 DOI: 10.3389/fmicb.2021.774301] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 11/09/2021] [Indexed: 11/13/2022] Open
Abstract
Cadmium (Cd) speciation ratio in arable land determines the Cd exposure risk and Cd uptake in crops. However, the driving mechanisms of Cd speciation change on the vertical scale of paddy fields remain poorly understood. In this study, the effects of plow layer and plow pan on Cd speciation distribution were investigated in a long-term Cd-contaminated rice ecosystem. The Cd accumulative effect within rice grain was enhanced with high levels of activated Cd speciation ratios in soils. Activated Cd speciation ratios were higher in plow layer soils, while stabilized Cd speciation ratios were elevated in plow pan soils. Soil physicochemical properties and soil microbes synergistically affected the Cd speciation changes in different ways between the two soil layers. Soil pH and organic elements in plow layer environment directly hindered the transformation of stabilized Cd speciation, while in plow pan environment, soil pH and organic elements indirectly decreased activated Cd speciation ratios and resulted in the accumulation of stabilized Cd speciation via regulating the predominant bacterial taxa. This study will improve our understanding of how soil environments regulate Cd speciation distributions in rice ecosystems and help to seek effective remediation methods of Cd-contaminated paddy fields to reduce the Cd accumulation in rice.
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Affiliation(s)
- Xiaodong Hao
- Shandong Provincial Key Laboratory of Water and Soil Conservation and Environmental Protection, College of Resources and Environment, Linyi University, Linyi, China.,Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Lianyang Bai
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Xueduan Liu
- Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Ping Zhu
- Shandong Provincial Key Laboratory of Water and Soil Conservation and Environmental Protection, College of Resources and Environment, Linyi University, Linyi, China.,Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Hongwei Liu
- Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Yunhua Xiao
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Jibiao Geng
- Shandong Provincial Key Laboratory of Water and Soil Conservation and Environmental Protection, College of Resources and Environment, Linyi University, Linyi, China
| | - Qianjin Liu
- Shandong Provincial Key Laboratory of Water and Soil Conservation and Environmental Protection, College of Resources and Environment, Linyi University, Linyi, China
| | - Lihua Huang
- Shandong Provincial Key Laboratory of Water and Soil Conservation and Environmental Protection, College of Resources and Environment, Linyi University, Linyi, China
| | - Huidan Jiang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
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5
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Montgomery DR, Biklé A. Soil Health and Nutrient Density: Beyond Organic vs. Conventional Farming. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.699147] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Controversy has long surrounded the question of nutritional differences between crops grown organically or using now-conventional methods, with studies dating back to the 1940s showing that farming methods can affect the nutrient density of crops. More recent studies have shown how reliance on tillage and synthetic nitrogen fertilizers influence soil life, and thereby soil health, in ways that can reduce mineral micronutrient uptake by and phytochemical production in crops. While organic farming tends to enhance soil health and conventional practices degrade it, relying on tillage for weed control on both organic and conventional farms degrades soil organic matter and can disrupt soil life in ways that reduce crop mineral uptake and phytochemical production. Conversely, microbial inoculants and compost and mulch that build soil organic matter can increase crop micronutrient and phytochemical content on both conventional and organic farms. Hence, agronomic effects on nutritional profiles do not fall out simply along the conventional vs. organic distinction, making the effects of farming practices on soil health a better lens for assessing their influence on nutrient density. A review of previous studies and meta-studies finds little evidence for significant differences in crop macronutrient levels between organic and conventional farming practices, as well as substantial evidence for the influence of different cultivars and farming practices on micronutrient concentrations. More consistent differences between organic and conventional crops include that conventional crops contain greater pesticide levels, whereas organically grown crops contain higher levels of phytochemicals shown to exhibit health-protective antioxidant and anti-inflammatory properties. Thus, part of the long-running controversy over nutritional differences between organic and conventional crops appears to arise from different definitions of what constitutes a nutrient—the conventional definition of dietary constituents necessary for growth and survival, or a broader one that also encompasses compounds beneficial for maintenance of health and prevention of chronic disease. For assessing the effects of farming practices on nutrient density soil health adds a much needed dimension—the provisioning of micronutrients and phytochemicals that support human health.
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Hong Y, Zhao D, Zhang F, Shen G, Yuan Y, Gao Y, Yan L, Wei D, Wang W. Soil water-stable aggregates and microbial community under long-term tillage in black soil of Northern China. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:1754-1768. [PMID: 33432458 DOI: 10.1007/s10646-020-02317-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/13/2020] [Indexed: 06/12/2023]
Abstract
Long-term frequent tillage would cause black soil degradation and serious soil erosion as soil microbial communities and soil structure are extremely sensitive to tillage process. However, there is no unified conclusion on the relationship between the distribution of soil water-stable aggregates (WSAs), and microbial community construction and diversity under long-term tillage in black soil during different seasons. In this study, we used wet-sieving method to evaluate the composition and stability of soil WSAs and employed Illumina MiSeq high-throughput sequencing technology to study the diversity, taxonomic composition and co-occurrence network properties of microbial community, comparing outcomes between uncultivated soil and long-term cultivated soil for 60 years in Keshan farm of Heilongjiang Province. The results showed that after long-term tillage, the proportion of larger than 1 mm WSAs reduced by 34.17-51.37%, and the stability of WSAs, soil pH, organic matter (OM), total nitrogen (TN) contents decreased significantly in all seasons (P < 0.05), while soil available phosphorus (AP) and available potassium (AK) contents increased remarkably (P < 0.05). The diversity of bacteria increased, while that of fungi decreased. Soil fungal communities were more susceptible to long-term tillage than bacterial and archaeal communities. Actinobacteria mainly exist in large WSAs (˃1 mm), and when their relative abundance is high, it is beneficial to improve the water-stability of black soil; while Proteobacteria and Gemmatimonadetes may exist in small WSAs (˂1 mm), whose high relative abundance will weaken the water-stability of black soil. The experimental results provide a scientific theoretical basis for sustainable utilization of black soil.
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Affiliation(s)
- Yanhua Hong
- College of Agronomy, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Agro- Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Duo Zhao
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Agro- Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
- Engineering Research Center of Processing and Utilization of Grain By-products, Ministry of Education, Daqing, 163319, China
| | - Fangzheng Zhang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Agro- Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
- Engineering Research Center of Processing and Utilization of Grain By-products, Ministry of Education, Daqing, 163319, China
| | - Guinan Shen
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Agro- Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
- Engineering Research Center of Processing and Utilization of Grain By-products, Ministry of Education, Daqing, 163319, China
| | - Yuan Yuan
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Agro- Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
- Engineering Research Center of Processing and Utilization of Grain By-products, Ministry of Education, Daqing, 163319, China
| | - Yamei Gao
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Agro- Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
- Engineering Research Center of Processing and Utilization of Grain By-products, Ministry of Education, Daqing, 163319, China
| | - Lei Yan
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Agro- Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
- Engineering Research Center of Processing and Utilization of Grain By-products, Ministry of Education, Daqing, 163319, China
| | - Dan Wei
- Institute of Plant Nutrition and Resources, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100081, China
| | - Weidong Wang
- College of Agronomy, Heilongjiang Bayi Agricultural University, Daqing, 163319, China.
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Agro- Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, China.
- Engineering Research Center of Processing and Utilization of Grain By-products, Ministry of Education, Daqing, 163319, China.
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7
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Wu J, Buckley HL, Curry L, Stevenson BA, Schipper LA, Lear G. Livestock exclusion reduces the spillover effects of pastoral agriculture on soil bacterial communities in adjacent forest fragments. Environ Microbiol 2021; 23:2919-2936. [PMID: 33734554 DOI: 10.1111/1462-2920.15473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 03/16/2021] [Indexed: 11/29/2022]
Abstract
Forest-to-pasture conversion is known to cause global losses in plant and animal diversity, yet impacts of livestock management after such conversion on vital microbial communities in adjoining natural ecosystems remain poorly understood. We examined how pastoral land management practices impact soil microorganisms in adjacent native forest fragments, by comparing bacterial communities sampled along 21 transects bisecting pasture-forest boundaries. Our results revealed greater bacterial taxon richness in grazed pasture soils and the reduced dispersal of pasture-associated taxa into adjacent forest soils when land uses were separated by a boundary fence. Relative abundance distributions of forest-associated taxa (i.e., Proteobacteria and Nitrospirae) and a pasture-associated taxon (i.e., Firmicutes) also suggest a greater impact of pastoral land uses on forest fragment soil bacterial communities when no fence is present. Bacterial community richness and composition were most related to changes in soil physicochemical variables commonly associated with agricultural fertilization, including concentrations of Olsen P, total P, total Cd, delta 15 N and the ratio of C:P and N:P. Overall, our findings demonstrate clear, and potentially detrimental effects of agricultural disturbance on bacterial communities in forest soils adjacent to pastoral land. We provide evidence that simple land management decisions, such as livestock exclusion, can mitigate the effects of agriculture on adjacent soil microbial communities.
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Affiliation(s)
- Jieyun Wu
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1010, New Zealand.,Plant Health & Environment Laboratory, Ministry for Primary Industries, PO Box 2095, Auckland, 1140, New Zealand
| | - Hannah L Buckley
- School of Science, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
| | - Liz Curry
- Tonkin and Taylor, 711 Victoria Street, Hamilton, 3204, New Zealand
| | - Bryan A Stevenson
- Manaaki Whenua-Landcare Research, Private Bag 3127, Hamilton, 3240, New Zealand
| | - Louis A Schipper
- Environmental Research Institute, School of Science, The University of Waikato, Hamilton, 3240, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1010, New Zealand
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8
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Kane JL, Morrissey EM, Skousen JG, Freedman ZB. Soil microbial succession following surface mining is governed primarily by deterministic factors. FEMS Microbiol Ecol 2021; 96:5854527. [PMID: 32510564 DOI: 10.1093/femsec/fiaa114] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/05/2020] [Indexed: 11/13/2022] Open
Abstract
Understanding the successional dynamics governing soil microbial community assembly following disturbance can aid in developing remediation strategies for disturbed land. However, the influences shaping microbial communities during succession following soil disturbance remain only partially understood. One example of a severe disturbance to soil is surface mining for natural resources, which displaces communities and changes the physical and chemical soil environment. These changes may alter community composition through selective pressure on microbial taxa (i.e. deterministic processes). Dispersal and ecological drift may also shape communities following disturbance (i.e. stochastic processes). Here, the relative influence of stochastic and deterministic processes on microbial community succession was investigated using a chronosequence of reclaimed surface mines ranging from 2-32 years post-reclamation. Sequencing of bacterial and fungal ribosomal gene amplicons coupled with a linear modeling approach revealed that following mine reclamation, while bacterial communities are modestly influenced by stochastic factors, the influence of deterministic factors was ∼7 × greater. Fungal communities were influenced only by deterministic factors. Soil organic matter, texture, and pH emerged as the most influential environmental factors on both bacterial and fungal communities. Our results suggest that management of deterministic soil characteristics over a sufficient time period could increase the microbial diversity and productivity of mine soils.
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Affiliation(s)
- Jennifer L Kane
- West Virginia University, Division of Plant and Soil Sciences, 1206 Evansdale Drive, Morgantown, WV 26506, USA
| | - Ember M Morrissey
- West Virginia University, Division of Plant and Soil Sciences, 1206 Evansdale Drive, Morgantown, WV 26506, USA
| | - Jeffrey G Skousen
- West Virginia University, Division of Plant and Soil Sciences, 1206 Evansdale Drive, Morgantown, WV 26506, USA
| | - Zachary B Freedman
- West Virginia University, Division of Plant and Soil Sciences, 1206 Evansdale Drive, Morgantown, WV 26506, USA.,Current Address: University of Wisconsin-Madison, Department of Soil Science, 1525 Observatory Drive, Madison, WI 53706, USA
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9
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Fernandez-Gnecco G, Smalla K, Maccario L, Sørensen SJ, Barbieri P, Consolo VF, Covacevich F, Babin D. Microbial community analysis of soils under different soybean cropping regimes in the Argentinean south-eastern Humid Pampas. FEMS Microbiol Ecol 2021; 97:fiab007. [PMID: 33444447 DOI: 10.1093/femsec/fiab007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/12/2021] [Indexed: 12/13/2022] Open
Abstract
Soil microbial communities are key players of ecosystem processes and important for crop and soil health. The Humid Pampas region in Argentina concentrates 75% of the national soybean production, which is based on intensive use of agrochemicals, monocropping and no-till. A long-term field experiment under no-till management in the southeast of the Argentinean Pampas provides a unique opportunity to compare soybean under monocropping with cultivation including alternating cover crops or in a three-phase rotation. We hypothesized that cropping regimes and season affect soil microbial community composition and diversity. Amplicon sequencing of 16S rRNA genes and internal transcribed spacer fragments showed a stronger microbial seasonal dynamic in conservation regimes compared to monocropping. In addition, several bacterial (e.g. Catenulispora, Streptomyces and Bacillus) and fungal genera (e.g. Exophiala) with cropping regime-dependent differential relative abundances were identified. Despite a temporal shift in microbial and chemical parameters, this study shows that long-term cropping regimes shaped the soil microbiota. This might have important implications for soil quality and soybean performance and should therefore be considered in the development of sustainable agricultural managements.
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Affiliation(s)
- Gabriela Fernandez-Gnecco
- Instituto de Investigaciones en Biodiversidad y Biotecnología, CONICET- Fundación para Investigaciones Biológicas Aplicadas (INBIOTEC, CONICET-FIBA), Vieytes 3103, B7602FCK Mar del Plata, Buenos Aires, Argentina
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
- Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria Balcarce - CONICET (INTA, EEA Balcarce - CONICET), Ruta 226 Km 73.5, 7620 Balcarce, Buenos Aires, Argentina
| | - Kornelia Smalla
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Lorrie Maccario
- Department of Biology, University of Copenhagen, Section of Microbiology, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Søren J Sørensen
- Department of Biology, University of Copenhagen, Section of Microbiology, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Pablo Barbieri
- National Scientific and Technical Research Council (CONICET), Argentina
- Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria Balcarce - CONICET (INTA, EEA Balcarce - CONICET), Ruta 226 Km 73.5, 7620 Balcarce, Buenos Aires, Argentina
| | - Veronica F Consolo
- Instituto de Investigaciones en Biodiversidad y Biotecnología, CONICET- Fundación para Investigaciones Biológicas Aplicadas (INBIOTEC, CONICET-FIBA), Vieytes 3103, B7602FCK Mar del Plata, Buenos Aires, Argentina
- National Scientific and Technical Research Council (CONICET), Argentina
| | - Fernanda Covacevich
- Instituto de Investigaciones en Biodiversidad y Biotecnología, CONICET- Fundación para Investigaciones Biológicas Aplicadas (INBIOTEC, CONICET-FIBA), Vieytes 3103, B7602FCK Mar del Plata, Buenos Aires, Argentina
- National Scientific and Technical Research Council (CONICET), Argentina
- Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria Balcarce - CONICET (INTA, EEA Balcarce - CONICET), Ruta 226 Km 73.5, 7620 Balcarce, Buenos Aires, Argentina
| | - Doreen Babin
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
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10
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Agricultural Soil Management Practices Differentially Shape the Bacterial and Fungal Microbiome of Sorghum bicolor. Appl Environ Microbiol 2021; 87:AEM.02345-20. [PMID: 33310712 PMCID: PMC8090879 DOI: 10.1128/aem.02345-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Soils play important roles in biological productivity. While past work suggests that microbes affect soil health and respond to agricultural practices, it is not well known how soil management shapes crop host microbiomes. To elucidate the impact of management on microbial composition and function in the sorghum microbiome, we performed 16S rRNA gene and ITS2 amplicon sequencing and metatranscriptomics on soil and root samples collected from a site in California's San Joaquin Valley that is under long-term cultivation with 1) standard (ST) or no tilling (NT) and 2) cover-cropping (CC) or leaving the field fallow (NO). Our results revealed that microbial diversity, composition, and function change across tillage and cover type, with a heightened response in fungal communities, versus bacterial. Surprisingly, ST harbored greater microbial alpha diversity than NT, indicating that tillage may open niche spaces for broad colonization. Across management regimes, we observed class-level taxonomic level shifts. Additionally, we found significant functional restructuring across treatments, including enrichment for microbial lipid and carbohydrate transport and metabolism and cell motility with NT. Differences in carbon cycling were also observed, with increased prevalence of glycosyltransferase and glycoside hydrolase carbohydrate active enzyme families with CC. Lastly, treatment significantly influenced arbuscular mycorrhizal fungi, which had the greatest prevalence and activity under ST, suggesting that soil practices mediate known beneficial plant-microbe relationships. Collectively, our results demonstrate how agronomic practices impact critical interactions within the plant microbiome and inform future efforts to configure trait-associated microbiomes in crops.Importance While numerous studies show that farming practices can influence the soil microbiome, there are often conflicting results on how microbial diversity and activity respond to treatment. In addition, there is very little work published on how the corresponding crop plant microbiome is impacted. With bacteria and fungi known to critically affect soil health and plant growth, we concurrently compared how the practices of no and standard tillage, in combination with either cover-cropping or fallow fields, shape soil and plant-associated microbiomes between the two classifications. In determining not only the response to treatment in microbial diversity and composition, but for activity as well, this work demonstrates the significance of agronomic practice in modulating plant-microbe interactions, as well as encourages future work on the mechanisms involved in community assemblages supporting similar crop outcomes.
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Taskin E, Misci C, Bandini F, Fiorini A, Pacini N, Obiero C, Sila DN, Tabaglio V, Puglisi E. Smallholder Farmers' Practices and African Indigenous Vegetables Affect Soil Microbial Biodiversity and Enzyme Activities in Lake Naivasha Basin, Kenya. BIOLOGY 2021; 10:biology10010044. [PMID: 33440642 PMCID: PMC7826984 DOI: 10.3390/biology10010044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/08/2021] [Accepted: 01/08/2021] [Indexed: 01/03/2023]
Abstract
Simple Summary Smallholder farmers in Sub-Saharan Africa (SSA) are food insecure. Underexploited African indigenous vegetables (AIVs) are consumed locally without being considered a primary source of food and income. However, AIVs hold great potential for the future challenges of food security and climate change. We investigated the effects of different cropping systems and inclusion of AIVs in farming on the soil biodiversity and fertility status of smallholder farmers in Naivasha, Kenya. Compared to mainstream farming approaches, soil microorganisms under AIV cultivations differed significantly. Tillage, fertilization, soil amendments, and traditional homemade plant protection were singled out as the most important factors. The soil alteration index based on enzyme activity offered a reliable way to determine the alteration status for the first time in SSA. These findings could be useful for farmers to integrate AIVs with correct sustainable practices for a sustainable future and may contribute to the mitigation of food insecurity. Abstract Loss of soil biodiversity and fertility in Sub-Saharan Africa (SSA) may put the food security of smallholder farmers in peril. Food systems in SSA are seeing the rise of African indigenous vegetables (AIVs) that are underexploited but locally consumed without being considered a primary source of food and income. Here we present a field study, a first of its kind, in which we investigated the effects of different cropping systems and inclusion of AIVs in the farming approach on bacterial and fungal biodiversity and community structures, enzymatic activity, and the alteration status of soils of the smallholder farmers in Kenya. When compared to mainstream farming approaches, the composition and biodiversity of bacteria and fungi under AIV cultivations was significantly different. Tillage had a significant impact only on the fungal communities. Fertilization and soil amendments caused shifts in microbial communities towards specialized degraders and revealed the introduction of specific microorganisms from amendments. Traditional homemade plant protection products did not cause any disturbance to either of soil bacteria or fungi. The soil alteration index based on enzyme activity successfully differentiated the alteration status for the first time in SSA. These findings could be useful for farmers to integrate AIVs with correct sustainable practices for a sustainable future.
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Affiliation(s)
- Eren Taskin
- Dipartimento di Scienze e Tecnologie Alimentari per la Sostenibilità della Filiera Agro-Alimentare (DISTAS), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy; (E.T.); (C.M.); (F.B.); (E.P.)
| | - Chiara Misci
- Dipartimento di Scienze e Tecnologie Alimentari per la Sostenibilità della Filiera Agro-Alimentare (DISTAS), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy; (E.T.); (C.M.); (F.B.); (E.P.)
| | - Francesca Bandini
- Dipartimento di Scienze e Tecnologie Alimentari per la Sostenibilità della Filiera Agro-Alimentare (DISTAS), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy; (E.T.); (C.M.); (F.B.); (E.P.)
| | - Andrea Fiorini
- Dipartimento di Scienze delle Produzioni Vegetali Sostenibili (DI.PRO.VE.S.), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy;
| | - Nic Pacini
- Dipartimento di Ingegneria dell’Ambiente (DIAm), Università della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, Italy;
- School of Geography, Geology and Environment, University of Leicester, Leicester LE1 7RH, UK
| | - Clifford Obiero
- Land Resource Planning and Management, College of Agriculture and Natural Resources, Jomo Kenyatta University of Agriculture and Technology, Nairobi P.O. Box 62000, Kenya;
| | - Daniel Ndaka Sila
- School of Food and Nutritional Sciences, College of Agriculture and Natural Resources, Jomo Kenyatta University of Agriculture and Technology, Nairobi P.O. Box 62000, Kenya;
| | - Vincenzo Tabaglio
- Dipartimento di Scienze delle Produzioni Vegetali Sostenibili (DI.PRO.VE.S.), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy;
- Correspondence: ; Tel.: +39-0523-599-222
| | - Edoardo Puglisi
- Dipartimento di Scienze e Tecnologie Alimentari per la Sostenibilità della Filiera Agro-Alimentare (DISTAS), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy; (E.T.); (C.M.); (F.B.); (E.P.)
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Zhuang Q, Wu S, Yan Y, Niu Y, Yang F, Xie C. Monitoring land surface thermal environments under the background of landscape patterns in arid regions: A case study in Aksu river basin. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 710:136336. [PMID: 31926416 DOI: 10.1016/j.scitotenv.2019.136336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/23/2019] [Accepted: 12/23/2019] [Indexed: 06/10/2023]
Abstract
Land surface temperature (LST) is defined as an important indicator in the formation and evolution of climate. In some cases, changes in landscape patterns affect LST, even more than the contribution of greenhouse gases. Although much work has been done with respect to the correlations between urban development and thermal environment dynamics, the related questions regarding relationships between LST and landscape patterns in arid regions are not thoroughly considered. Understanding these questions is important in climate change and land planning. The objective of this study was to explore the spatiotemporal variations of LST by distribution index (DI) and Mann-Kendall mutation analysis method and to quantify the relationships between landscape patterns, climatic factors, topographic factors, and the land surface thermal environment (LSTE) by the ordinary linear regressions (OLS) model. The landscape patterns dataset, which was validated by a field trip, was extracted from the Land satellite (Landsat) TM/OLI images by the Random Forest methodology in ArcGIS software. The MODIS/LST product was validated by the "Monthly dataset of China's surface climate" and a field trip. Annual LST increased by 0.54 °C (23.15 °C in 2000 and 23.79 °C in 2015). In different landscape patterns, the percentage of areas with a high level of LST showed a significant difference. In barren land, the highest area proportion for the high LST level was larger than in other landscape patterns. Meanwhile, the area of low LST was mainly concentrated in water bodies. Considerable changes have occurred in landscape patterns, in which the most noteworthy was cultivated land encroaching on grass land (3708.44 km2). The composition of landscape patterns was more important than distribution in determining the region's LST. These findings provide valuable information for land planners dealing with climate change and ecosystem conservation in arid regions.
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Affiliation(s)
- Qingwei Zhuang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shixin Wu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China.
| | - Yuyan Yan
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaxuan Niu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fan Yang
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Conghui Xie
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; University of Chinese Academy of Sciences, Beijing 100049, China
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Garcia-Lemos AM, Gobbi A, Nicolaisen MH, Hansen LH, Roitsch T, Veierskov B, Nybroe O. Under the Christmas Tree: Belowground Bacterial Associations With Abies nordmanniana Across Production Systems and Plant Development. Front Microbiol 2020; 11:198. [PMID: 32194515 PMCID: PMC7064441 DOI: 10.3389/fmicb.2020.00198] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 01/28/2020] [Indexed: 01/01/2023] Open
Abstract
Abies nordmanniana is an economically important tree crop widely used for Christmas tree production. After initial growth in nurseries, seedlings are transplanted to the field. Rhizosphere bacterial communities generally impact the growth and health of the host plant. However, the dynamics of these communities during A. nordmanniana growth in nurseries, and during transplanting, has not previously been addressed. By a 16S rRNA gene amplicon sequencing approach, we characterized the composition and dynamics of bacterial communities in the rhizosphere during early plant growth in field and greenhouse nurseries and for plants transplanted from the greenhouse to the field. Moreover, the N-cycling potential of rhizosphere bacteria across plant age was addressed in both nurseries. Overall, a rhizosphere core microbiome of A. nordmanniana, comprising 19.9% of the taxa at genus level, was maintained across plant age, nursery production systems, and even during the transplantation of plants from the greenhouse to the field. The core microbiome included the bacterial genera Bradyrhizobium, Burkholderia, Flavobacterium, Pseudomonas, Rhizobium, Rhodanobacter, and Sphingomonas, which harbor several N-fixing and plant growth–promoting taxa. Nevertheless, both plant age and production system caused significant changes in the rhizosphere bacterial communities. Concerning community composition, the relative abundance of Rhizobiales (genera Rhizobium, Bradyrhizobium, and Devosia) was higher in the rhizosphere of field-grown A. nordmanniana, whereas the relative abundance of Enterobacteriales and Pseudomonadales (genus Pseudomonas) was higher in the greenhouse. Analysis of community dynamics across plant age showed that in the field nursery, the most abundant bacterial orders showed more dynamic changes in their relative abundance in the rhizosphere than in the bulk soil. In the greenhouse, age-dependent dynamics even occurred but affected different taxa than for the field-grown plants. The N-cycling potential of rhizosphere bacterial communities showed an increase of the relative abundance of genes involved in nitrogen fixation and denitrification by plant age. Similarly, the relative abundance of reported nitrogen-fixing or denitrifying bacteria increased by plant age. However, different community structures seemed to lead to an increased potential for nitrogen fixation and denitrification in the field versus greenhouse nurseries.
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Affiliation(s)
- Adriana M Garcia-Lemos
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Alex Gobbi
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Mette Haubjerg Nicolaisen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Lars H Hansen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Thomas Roitsch
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark.,Department of Adaptive Biotechnologies, Global Change Research Institute, CAS, Brno, Czechia
| | - Bjarke Veierskov
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Ole Nybroe
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
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The Structure and Diversity of Bacterial Communities in Differently Managed Soils Studied by Molecular Fingerprinting Methods. SUSTAINABILITY 2018. [DOI: 10.3390/su10041095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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