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Yang Z, Cui X, Fan X, Ruan Y, Xiang Z, Ji L, Gao H, Zhang M, Shan S, Liu W. "Active carbon" is more advantageous to the bacterial community in the rice rhizosphere than "stable carbon". Comput Struct Biotechnol J 2024; 23:1288-1297. [PMID: 38560279 PMCID: PMC10978811 DOI: 10.1016/j.csbj.2024.03.012] [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: 10/30/2023] [Revised: 03/01/2024] [Accepted: 03/12/2024] [Indexed: 04/04/2024] Open
Abstract
Carbon materials are commonly used for soil carbon sequestration and fertilization, which can also affect crop growth by manipulating the rhizosphere bacterial community. However, the comparison of the differences between active carbon (e.g., organic fertilizers) and stable carbon (e.g., biochar) on rhizosphere microdomains is still unclear. Hence, a trial was implemented to explore the influence of control (CK, no fertilizer; NPK, chemical fertilizer), organic fertilizer (CF-O, organic fertilizer; CF-BO, biochar-based organic fertilizer) and biochar material (CF-B, perishable garbage biochar; CF-PMB, pig manure biochar) on the diversity, composition, and interaction of rice rhizosphere bacterial community through 16 S rRNA gene high-throughput sequencing. Our results demonstrate that organic fertilizer increases bacterial alpha-diversity compared to no-carbon supply treatment to the extend, whereas biochar has the opposite effect. The rhizosphere bacterial community composition showed pronounced variations among the various fertilization treatments. The relative abundance in Firmicutes decreased with organic fertilizer application, whereas that in Chloroflexi and Actinobacteria decreased with biochar application. Bacterial network analysis demonstrate that organic fertilizer enhances the complexity and key taxa of bacterial interactions, while biochar exhibits an opposing trend. The findings of our study indicate that organic fertilizer may contribute to a positive and advantageous impact on bacterial diversity and interaction in rice rhizosphere, whereas the influence of biochar is not as favorable and constructive. This study lays the foundation for elucidating the fate of the rhizosphere bacterial community following different carbon material inputs in the context of sustainable agricultural development.
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Affiliation(s)
- Zongkun Yang
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
| | - Xin Cui
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
| | - Xiaoge Fan
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
| | - Yefeng Ruan
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
| | - Zhennan Xiang
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
| | - Lingfei Ji
- Department of Biology, University of York, York, UK
| | - Han Gao
- State Environmental Protection Key Laboratory of Soil Environmental Management and Pollution Control, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing, China
| | - Min Zhang
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
| | - Shengdao Shan
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
| | - Wenbo Liu
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, School of Environmental and Natural Resources, Zhejiang University of Science and Technology, Hangzhou, China
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Li YL, Xie LN, Li SH, Zhang D, Ge ZM. Photosynthetic carbon allocation in native and invasive salt marshes undergoing hydrological change. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 935:173232. [PMID: 38761926 DOI: 10.1016/j.scitotenv.2024.173232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 05/11/2024] [Accepted: 05/12/2024] [Indexed: 05/20/2024]
Abstract
Biogeochemical processes mediated by plants and soil in coastal marshes are vulnerable to environmental changes and biological invasion. In particular, tidal inundation and salinity stress will intensify under future rising sea level scenarios. In this study, the interactive effects of flooding regimes (non-waterlogging vs. waterlogging) and salinity (0, 5, 15, and 30 parts per thousand (ppt)) on photosynthetic carbon allocation in plant, rhizodeposition, and microbial communities in native (Phragmites australis) and invasive (Spartina alterniflora) marshes were investigated using mesocosm experiments and 13CO2 pulse-labeling techniques. The results showed that waterlogging and elevated salinity treatments decreased specific root allocation (SRA) of 13C, rhizodeposition allocation (RA) 13C, soil 13C content, grouped microbial PLFAs, and the fungal 13C proportion relative to total PLFAs-13C. The lowest SRA, RA, and fungal 13C proportion occurred under the combined waterlogging and high (30 ppt) salinity treatments. Relative to S. alterniflora, P. australis displayed greater sensitivity to hydrological changes, with a greater reduction in rhizodeposition, soil 13C content, and fungal PLFAs. S. alterniflora showed an earlier peak SRA but a lower root/shoot 13C ratio than P. australis. This suggests that S. alterniflora may transfer more photosynthetic carbon to the shoot and rhizosphere to facilitate invasion under stress. Waterlogging and high salinity treatments shifted C allocation towards bacteria over fungi for both plant species, with a higher allocation shift in S. alterniflora soil, revealing the species-specific microbial response to hydrological stresses. Potential shifts towards less efficient bacterial pathways might result in accelerated carbon loss. Over the study period, salinity was the primary driver for both species, explaining 33.2-50.8 % of 13C allocation in the plant-soil-microbe system. We propose that future carbon dynamics in coastal salt marshes under sea-level rise conditions depend on species-specific adaptive strategies and carbon allocation patterns of native and invasive plant-soil systems.
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Affiliation(s)
- Ya-Lei Li
- College of Ecology, Lishui University, 323000 Lishui, China; State Key Laboratory of Estuarine and Coastal Research, Institute of Eco-Chongming, Center for Blue Carbon Science and Technology, East China Normal University, 200241 Shanghai, China
| | - Li-Na Xie
- College of Ecology, Lishui University, 323000 Lishui, China; State Key Laboratory of Estuarine and Coastal Research, Institute of Eco-Chongming, Center for Blue Carbon Science and Technology, East China Normal University, 200241 Shanghai, China
| | - Shi-Hua Li
- School of Advanced Manufacturing, Fuzhou University, 362251 Jinjiang, China
| | - Dan Zhang
- State Key Laboratory of Estuarine and Coastal Research, Institute of Eco-Chongming, Center for Blue Carbon Science and Technology, East China Normal University, 200241 Shanghai, China
| | - Zhen-Ming Ge
- State Key Laboratory of Estuarine and Coastal Research, Institute of Eco-Chongming, Center for Blue Carbon Science and Technology, East China Normal University, 200241 Shanghai, China.
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Monaco P, Baldoni A, Naclerio G, Scippa GS, Bucci A. Impact of Plant-Microbe Interactions with a Focus on Poorly Investigated Urban Ecosystems-A Review. Microorganisms 2024; 12:1276. [PMID: 39065045 PMCID: PMC11279295 DOI: 10.3390/microorganisms12071276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
The urbanization process, which began with the Industrial Revolution, has undergone a considerable increase over the past few decades. Urbanization strongly affects ecological processes, often deleteriously, because it is associated with a decrease in green spaces (areas of land covered by vegetation), loss of natural habitats, increased rates of species extinction, a greater prevalence of invasive and exotic species, and anthropogenic pollutant accumulation. In urban environments, green spaces play a key role by providing many ecological benefits and contributing to human psychophysical well-being. It is known that interactions between plants and microorganisms that occur in the rhizosphere are of paramount importance for plant health, soil fertility, and the correct functioning of plant ecosystems. The growing diffusion of DNA sequencing technologies and "omics" analyses has provided increasing information about the composition, structure, and function of the rhizomicrobiota. However, despite the considerable amount of data on rhizosphere communities and their interactions with plants in natural/rural contexts, current knowledge on microbial communities associated with plant roots in urban soils is still very scarce. The present review discusses both plant-microbe dynamics and factors that drive the composition of the rhizomicrobiota in poorly investigated urban settings and the potential use of beneficial microbes as an innovative biological tool to face the challenges that anthropized environments and climate change impose. Unravelling urban biodiversity will contribute to green space management, preservation, and development and, ultimately, to public health and safety.
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Affiliation(s)
- Pamela Monaco
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy; (A.B.); (G.N.); (G.S.S.)
| | | | | | | | - Antonio Bucci
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy; (A.B.); (G.N.); (G.S.S.)
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Berrios L, Bogar GD, Bogar LM, Venturini AM, Willing CE, Del Rio A, Ansell TB, Zemaitis K, Velickovic M, Velickovic D, Pellitier PT, Yeam J, Hutchinson C, Bloodsworth K, Lipton MS, Peay KG. Ectomycorrhizal fungi alter soil food webs and the functional potential of bacterial communities. mSystems 2024; 9:e0036924. [PMID: 38717159 PMCID: PMC11237468 DOI: 10.1128/msystems.00369-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 04/11/2024] [Indexed: 06/19/2024] Open
Abstract
Most of Earth's trees rely on critical soil nutrients that ectomycorrhizal fungi (EcMF) liberate and provide, and all of Earth's land plants associate with bacteria that help them survive in nature. Yet, our understanding of how the presence of EcMF modifies soil bacterial communities, soil food webs, and root chemistry requires direct experimental evidence to comprehend the effects that EcMF may generate in the belowground plant microbiome. To this end, we grew Pinus muricata plants in soils that were either inoculated with EcMF and native forest bacterial communities or only native bacterial communities. We then profiled the soil bacterial communities, applied metabolomics and lipidomics, and linked omics data sets to understand how the presence of EcMF modifies belowground biogeochemistry, bacterial community structure, and their functional potential. We found that the presence of EcMF (i) enriches soil bacteria linked to enhanced plant growth in nature, (ii) alters the quantity and composition of lipid and non-lipid soil metabolites, and (iii) modifies plant root chemistry toward pathogen suppression, enzymatic conservation, and reactive oxygen species scavenging. Using this multi-omic approach, we therefore show that this widespread fungal symbiosis may be a common factor for structuring soil food webs.IMPORTANCEUnderstanding how soil microbes interact with one another and their host plant will help us combat the negative effects that climate change has on terrestrial ecosystems. Unfortunately, we lack a clear understanding of how the presence of ectomycorrhizal fungi (EcMF)-one of the most dominant soil microbial groups on Earth-shapes belowground organic resources and the composition of bacterial communities. To address this knowledge gap, we profiled lipid and non-lipid metabolites in soils and plant roots, characterized soil bacterial communities, and compared soils amended either with or without EcMF. Our results show that the presence of EcMF changes soil organic resource availability, impacts the proliferation of different bacterial communities (in terms of both type and potential function), and primes plant root chemistry for pathogen suppression and energy conservation. Our findings therefore provide much-needed insight into how two of the most dominant soil microbial groups interact with one another and with their host plant.
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Affiliation(s)
- Louis Berrios
- Department of Biology, Stanford University, Stanford, California, USA
| | - Glade D. Bogar
- Kellogg Biological Station, Michigan State University, Hickory Corners, Michigan, USA
| | - Laura M. Bogar
- Department of Plant Biology, University of California, Davis, Davis, California, USA
| | | | - Claire E. Willing
- Department of Biology, Stanford University, Stanford, California, USA
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
| | - Anastacia Del Rio
- Department of Biology, Stanford University, Stanford, California, USA
| | - T. Bertie Ansell
- Department of Biology, Stanford University, Stanford, California, USA
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Kevin Zemaitis
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Marija Velickovic
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Dusan Velickovic
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | | | - Jay Yeam
- Department of Biology, Stanford University, Stanford, California, USA
| | - Chelsea Hutchinson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kent Bloodsworth
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Mary S. Lipton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kabir G. Peay
- Department of Biology, Stanford University, Stanford, California, USA
- Department of Earth System Science, Stanford University, Stanford, California, USA
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Kaplan DI, Boyanov MI, Losey NA, Lin P, Xu C, O’Loughlin EJ, Santschi PH, Xing W, Kuhne WW, Kemner KM. Uranium Biogeochemistry in the Rhizosphere of a Contaminated Wetland. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:6381-6390. [PMID: 38547454 PMCID: PMC11008245 DOI: 10.1021/acs.est.3c10481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 04/10/2024]
Abstract
The objective of this study was to determine if U sediment concentrations in a U-contaminated wetland located within the Savannah River Site, South Carolina, were greater in the rhizosphere than in the nonrhizosphere. U concentrations were as much as 1100% greater in the rhizosphere than in the nonrhizosphere fractions; however and importantly, not all paired samples followed this trend. Iron (but not C, N, or S) concentrations were significantly enriched in the rhizosphere. XAS analyses showed that in both sediment fractions, U existed as UO22+ coordinated with iron(III)-oxides and organic matter. A key difference between the two sediment fractions was that a larger proportion of U was adsorbed to Fe(III)-oxides, not organic matter, in the rhizosphere, where significantly greater total Fe concentrations and greater proportions of ferrihydrite and goethite existed. Based on 16S rRNA analyses, most bacterial sequences in both paired samples were heterotrophs, and population differences were consistent with the generally more oxidizing conditions in the rhizosphere. Finally, U was very strongly bound to the whole (unfractionated) sediments, with an average desorption Kd value (Usediment/Uaqueous) of 3972 ± 1370 (mg-U/kg)/(mg-U/L). Together, these results indicate that the rhizosphere can greatly enrich U especially in wetland areas, where roots promote the formation of reactive Fe(III)-oxides.
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Affiliation(s)
- Daniel I. Kaplan
- Savannah
River Ecology Laboratory, University of
Georgia, Aiken, South Carolina 29802, United States
| | - Maxim I. Boyanov
- Argonne
National Laboratory, Lemont, Illinois 60439, United States
- Chemical
Engineering, Bulgarian Academy of Sciences, Sofia 1040, Bulgaria
| | - Nathaniel A. Losey
- Savannah
River National Laboratory, Aiken, South Carolina 29808, United States
| | - Peng Lin
- Savannah
River Ecology Laboratory, University of
Georgia, Aiken, South Carolina 29802, United States
| | - Chen Xu
- Marine
& Coastal Environmental Science, Texas
A&M University − Galveston, Galveston, Texas 77553, United States
| | | | - Peter H. Santschi
- Marine
& Coastal Environmental Science, Texas
A&M University − Galveston, Galveston, Texas 77553, United States
| | - Wei Xing
- Savannah
River Ecology Laboratory, University of
Georgia, Aiken, South Carolina 29802, United States
| | - Wendy W. Kuhne
- Savannah
River National Laboratory, Aiken, South Carolina 29808, United States
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Zhao M, Sun Y, Dong M, Zhang K, Zhang J, Qin X, Yao Y. Hexose/pentose ratio in rhizosphere exudates-mediated soil eutrophic/oligotrophic bacteria regulates the growth pattern of host plant in young apple-aromatic plant intercropping systems. Front Microbiol 2024; 15:1364355. [PMID: 38591033 PMCID: PMC11000693 DOI: 10.3389/fmicb.2024.1364355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 02/21/2024] [Indexed: 04/10/2024] Open
Abstract
Introduction The positive effect of intercropping on host plant growth through plant-soil feedback has been established. However, the mechanisms through which intercropping induces interspecific competition remain unclear. Methods In this study, we selected young apple trees for intercropping with two companion plants: medium growth-potential Mentha haplocalyx Briq. (TM) and high growth-potential Ageratum conyzoides L. (TA) and conducted mixed intercropping treatment with both types (TMA) and a control treatment of monocropping apples (CT). Results Our findings revealed that TM increased the under-ground biomass of apple trees and TA and TMA decreased the above-ground biomass of apple trees, with the lowest above-ground biomass of apple trees in TA. The above- and under-ground biomass of intercrops in TA and TMA were higher than those in TM, with the highest in TA, suggesting that the interspecific competition was the most pronounced in TA. TA had a detrimental effect on the photosynthesis ability and antioxidant capacity of apple leaves, resulting in a decrease in above-ground apple biomass. Furthermore, TA led to a reduction in organic acids, alcohols, carbohydrates, and hydrocarbons in the apple rhizosphere soil (FRS) compared to those in both soil bulk (BS) and aromatic plant rhizosphere soil (ARS). Notably, TA caused an increase in pentose content and a decrease in the hexose/pentose (C6/C5) ratio in FRS, while ARS exhibited higher hexose content and a higher C6/C5 ratio. The changes in exudates induced by TA favored an increase in taxon members of Actinobacteria while reducing Proteobacteria in FRS compared to that in ARS. This led to a higher eutrophic/oligotrophic bacteria ratio relative to TM. Discussion This novel perspective sheds light on how interspecific competition, mediated by root exudates and microbial community feedback, influences plant growth and development.
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Affiliation(s)
- Mengnan Zhao
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, China
| | - Yue Sun
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, China
| | - Meilin Dong
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, China
| | - Kui Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, China
| | - Jie Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, China
| | - Xiaoxiao Qin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, China
| | - Yuncong Yao
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, China
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Xin Y, Liu L, Yang XR, Yang LY, Guang SB, Zheng YM, Zhao QB. Adaptive shifts in plant traits associated with nitrogen removal driven by phytoremediation strategies in subtropical river restoration. WATER RESEARCH 2024; 249:121008. [PMID: 38096729 DOI: 10.1016/j.watres.2023.121008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/29/2023] [Accepted: 12/09/2023] [Indexed: 01/03/2024]
Abstract
Phytoremediation, which is commonly carried out through hydroponics and substrate-based strategies, is essential for the effectiveness of nature-based engineered solutions aimed at addressing excess nitrogen in aquatic ecosystems. However, the performance and mechanisms of plants involving nitrogen removal between different strategies need to be deeply understood. Here, this study employed in-situ cultivation coupled with static nitrogen tracing experiments to elucidate the influence of both strategies on plant traits associated with nitrogen removal. The results indicated that removal efficiencies in plants with substrate-based strategies for ammonium nitrogen and nitrate nitrogen were 30.51-71.11 % and 16.82-99.95 %, respectively, which were significantly higher than those with hydroponics strategies (25.98-58.18 % and 7.29-79.19 %, respectively). Similarly, the plant nitrogen uptake rates in the substrate-based strategy also generally showed higher levels compared to hydroponics strategies (P < 0.05). Meanwhile, the microorganisms-mediated nitrous oxide emission rates in the substrate-based strategy during summer (unamended: 0.00-0.58 μg/g/d; potential: 3.35-7.65 μg/g/d) were obviously lower than those in the hydroponics strategy (unamended: 2.23-11.70 μg/g/d; potential: 9.72-43.09 μg/g/d) (P < 0.05). Notably, analysis of similarity tests indicated that the influences of strategy on the above parameters generally surpass the effects attributable to interspecies plant differences, particularly during summer (R > 0, P < 0.05). Based on statistical and metagenomic analyses, this study revealed that these differences were driven by the stabilizing influence of substrate-based strategy on plant roots and enhancing synergistic interplay among biochemical factors within plant-root systems. Even so, phytoremediation strategies did not significantly alter the characteristics of plants with regards to their tendency towards ammonium nitrogen uptake (up to 87.68 %) and dissimilatory nitrate reduction to ammonium as primary biological pathway for nitrogen transformation which accounted for 53.66-96.47 % nitrate removal. In summary, this study suggested that the substrate-based strategy should be a more effective strategy for enhancing the nitrogen removal ability of plants in subtropical river restoration practices.
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Affiliation(s)
- Yu Xin
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lin Liu
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xiao-Ru Yang
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Le-Yang Yang
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shan-Bin Guang
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Yu-Ming Zheng
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Quan-Bao Zhao
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
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Aqeel M, Khalid N, Noman A, Ran J, Manan A, Hou Q, Dong L, Sun Y, Deng Y, Lee SS, Hu W, Deng J. Interplay between edaphic and climatic factors unravels plant and microbial diversity along an altitudinal gradient. ENVIRONMENTAL RESEARCH 2024; 242:117711. [PMID: 37995997 DOI: 10.1016/j.envres.2023.117711] [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: 08/19/2023] [Revised: 11/03/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023]
Abstract
Altitude influences biodiversity and physiochemical soil attributes in terrestrial ecosystems. It is of immense importance to know the patterns of how interactions among climatic and edaphic factors influence plant and microbial diversity in various ecosystems, particularly along the gradients. We hypothesize that altitudinal variation determines the distribution of plant and microbial species as well as their interactions. To test the hypothesis, different sites with variable altitudes were selected. Analyses of edaphic factors revealed significant (p < 0.001) effects of the altitude. Soil ammonium and nitrate were strongly affected by it contrary to potassium (K), soil organic matter and carbon. The response patterns of individual taxonomic groups differed across the altitudinal gradient. Plant species and soil fungal diversity increased with increasing altitude, while soil archaeal and bacterial diversity decreased with increasing altitude. Plant species richness showed significant positive and negative interactions with edaphic and climatic factors. Fungal species richness was also significantly influenced by the soil ammonium, nitrate, available phosphorus, available potassium, electrical conductivity, and the pH of the soil, but showed non-significant interactions with other edaphic factors. Similarly, soil variables had limited impact on soil bacterial and archaeal species richness along the altitude gradient. Proteobacteria, Ascomycota, and Thaumarchaeota dominate soil bacterial, fungal, and archaeal communities, with relative abundance of 27.4%, 70.56%, and 81.55%, respectively. Additionally, Cynodon dactylon is most abundant plant species, comprising 22.33% of the recorded plant taxa in various study sites. RDA revealed that these communities influenced by certain edaphic and climatic factors, e.g., Actinobacteria strongly respond to MAT, EC, and C/N ratio, Ascomycota and Basidiomycota show strong associations with EC and MAP, respectively. Thaumarcheota are linked to pH, and OM, while Cyperus rotundus are sensitive to AI and EC. In conclusion, the observed variations in microbial as well as plant species richness and changes in soil properties at different elevations provide valuable insights into the factors determining ecosystem stability and multifunctionality in different regions.
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Affiliation(s)
- Muhammad Aqeel
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems (SKLHIGA), College of Ecology, Lanzhou University, 730000, Lanzhou, PR China
| | - Noreen Khalid
- Department of Botany, Government College Women University Sialkot, Pakistan
| | - Ali Noman
- Department of Botany, Government College University Faisalabad, Pakistan
| | - Jinzhi Ran
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems (SKLHIGA), College of Ecology, Lanzhou University, 730000, Lanzhou, PR China
| | - Abdul Manan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems (SKLHIGA), College of Ecology, Lanzhou University, 730000, Lanzhou, PR China
| | - Qingqing Hou
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems (SKLHIGA), College of Ecology, Lanzhou University, 730000, Lanzhou, PR China
| | - Longwei Dong
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems (SKLHIGA), College of Ecology, Lanzhou University, 730000, Lanzhou, PR China
| | - Ying Sun
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems (SKLHIGA), College of Ecology, Lanzhou University, 730000, Lanzhou, PR China
| | - Yan Deng
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems (SKLHIGA), College of Ecology, Lanzhou University, 730000, Lanzhou, PR China
| | - Sang Soo Lee
- Department of Environmental and Energy Engineering, Yonsei University, Wonju, 26493, Republic of Korea
| | - Weigang Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems (SKLHIGA), College of Ecology, Lanzhou University, 730000, Lanzhou, PR China.
| | - Jianming Deng
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems (SKLHIGA), College of Ecology, Lanzhou University, 730000, Lanzhou, PR China.
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Cho G, Kim DR, Kwak YS. Transition from Ginseng Root Rot Disease-Conducive Soil to -Suppressive Soil Mediated by Pseudomonadaceae. Microbiol Spectr 2023; 11:e0115023. [PMID: 37404179 PMCID: PMC10433981 DOI: 10.1128/spectrum.01150-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/07/2023] [Indexed: 07/06/2023] Open
Abstract
Ginseng is a popular medicinal herb with established therapeutic effects such as cardiovascular disease prevention, anticancer effects, and anti-inflammatory effects. However, the slow growth of ginseng due to soilborne pathogens has been a challenge for establishing new plantations. In this study, we investigated root rot disease associated with the microbiota in a ginseng monoculture model system. Our results showed that a collapse of the early microbiota community inhibiting root rot disease was observed before the disease became severe, and nitrogen fixation was necessary to support the initial microbiota community structure. Furthermore, changes in the nitrogen composition were essential for the suppression of pathogen activity in early monoculture soils. We hypothesize that Pseudomonadaceae, a population built up by aspartic acid, can inhibit the occurrence of root rot disease in ginseng and that specific management practices that maintain a healthy microbiome can be implemented to prevent and mitigate the disease. Our findings provide insights into the potential use of specific members of the microbiota for controlling root rot disease in ginseng cultivation. IMPORTANCE Understanding the initial soil microbiota and community shifts in a monoculture system is critical for developing disease-suppressive soils for crop production. The lack of resistance genes against soilborne pathogens in plants highlights the need for effective management strategies. Our investigation of root rot disease and initial microbiota community shifts in a ginseng monoculture model system provides valuable insight into the development of conducive soil into specific suppressive soil. With a thorough understanding of the microbiota in disease-conducive soil, we can work toward the development of disease-suppressive soil to prevent outbreaks and ensure sustainable crop production.
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Affiliation(s)
- Gyeongjun Cho
- Division of Agricultural Microbiology, Department of Agricultural Biology, National Institute of Agriculture Science, Rural Development Administration, Wanju, Republic of Korea
| | - Da-Ran Kim
- Division of Applied Life Science and RILS, Gyeongsang National University, Jinju, Republic of Korea
| | - Youn-Sig Kwak
- Division of Applied Life Science and RILS, Gyeongsang National University, Jinju, Republic of Korea
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10
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Morales-Manzo II, Ribes-Moya AM, Pallotti C, Jimenez-Belenguer A, Moro CP, Raigón MD, Rodríguez-Burruezo A, Fita A. Root-Soil Interactions for Pepper Accessions Grown under Organic and Conventional Farming. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091873. [PMID: 37176931 PMCID: PMC10180822 DOI: 10.3390/plants12091873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/12/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023]
Abstract
Modern agriculture has boosted the production of food based on the use of pesticides and fertilizers and improved plant varieties. However, the impact of some such technologies is high and not sustainable in the long term. Although the importance of rhizospheres in final plant performance, nutrient cycling, and ecosystems is well recognized, there is still a lack of information on the interactions of their main players. In this paper, four accessions of pepper are studied at the rhizosphere and root level under two farming systems: organic and conventional. Variations in soil traits, such as induced respiration, enzymatic activities, microbial counts, and metabolism of nitrogen at the rhizosphere and bulk soil, as well as measures of root morphology and plant production, are presented. The results showed differences for the evaluated traits between organic and conventional management, both at the rhizosphere and bulk soil levels. Organic farming showed higher microbial counts, enzymatic activities, and nitrogen mobilization. Our results also showed how some genotypes, such as Serrano or Piquillo, modified the properties of the rhizospheres in a very genotype-dependent way. This specificity of the soil-plant interaction should be considered for future breeding programs for soil-tailored agriculture.
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Affiliation(s)
- Ivan I Morales-Manzo
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Edificio 8E Escalera J, CPI, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Ana M Ribes-Moya
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Edificio 8E Escalera J, CPI, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Claudia Pallotti
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Edificio 8E Escalera J, CPI, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Ana Jimenez-Belenguer
- Centro Avanzado de Microbiología Aplicada, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Clara Pérez Moro
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Edificio 8E Escalera J, CPI, Universitat Politècnica de València, 46022 Valencia, Spain
| | - María Dolores Raigón
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Edificio 8E Escalera J, CPI, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Adrián Rodríguez-Burruezo
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Edificio 8E Escalera J, CPI, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Ana Fita
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Edificio 8E Escalera J, CPI, Universitat Politècnica de València, 46022 Valencia, Spain
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11
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Chen Y, Zhen Z, Li G, Li H, Wei T, Huang F, Li T, Yang C, Ren L, Liang Y, Lin Z, Zhang D. Di-2-ethylhexyl phthalate (DEHP) degradation and microbial community change in mangrove rhizosphere gradients. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 871:162022. [PMID: 36775151 DOI: 10.1016/j.scitotenv.2023.162022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/17/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Di-2-ethylhexyl phthalate (DEHP) is a widespread persistent organic pollutant in the environment. As an ultimate barrier preventing pollutant entry into the ocean, mangrove plays an important role in coastal ecosystem. However, little information is known about DEHP degradation in mangrove rhizosphere. In this study, a rhizobox was used to separate four consecutive rhizosphere compartments with distance of 0-2, 2-4, 4-6, and > 6 mm to the rhizoplane of Kandelia obovata and investigate DEHP gradient degradation behavior in rhizosphere. Sediments closer to the rhizoplane exhibited higher DEHP degradation efficiencies (74.4 % in 0-2 mm layer). More precisely, mangrove rhizosphere promoted the benzoic acid pathway and non-selectively accelerated the production of mono(2-ethylhexyl) phthalate, phthalic acid and benzoic acid. Higher sediment organic matter content, lower pH and less humus in rhizosphere benefited DEHP hydrolysis. In addition, rhizosphere significantly increased microbial biomass and activities comparing to bulk sediments. Some bacterial lineages with potential DEHP degradation capability exhibited a distance-dependent pattern that decreased with the distance to the rhizoplane, including Bacillales, Acidothermaceae, Gammaproteobacteria, and Sphingobacteriales. Our findings suggested that mangrove rhizosphere could accelerate DEHP degradation by altering sediment physicochemical properties and microbial composition, showing positive effects on coastal ecosystem services for eliminating phthalate acid ester contamination.
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Affiliation(s)
- Yijie Chen
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, PR China
| | - Zhen Zhen
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, PR China
| | - Gaoyang Li
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, PR China
| | - Huijun Li
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, PR China
| | - Ting Wei
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, PR China
| | - Fengcheng Huang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, PR China
| | - Tao Li
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, PR China
| | - Changhong Yang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, PR China
| | - Lei Ren
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, PR China
| | - Yanqiu Liang
- Faculty of Chemistry and Environmental Science, Guangdong Ocean University, Zhanjiang 524088, PR China
| | - Zhong Lin
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, PR China; Shenzhen Research Institute of Guangdong Ocean University, Shenzhen 518108, PR China.
| | - Dayi Zhang
- College of New Energy and Environment, Jilin University, Changchun 130021, PR China; Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130012, PR China.
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12
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Mock community as an in situ positive control for amplicon sequencing of microbiotas from the same ecosystem. Sci Rep 2023; 13:4056. [PMID: 36906688 PMCID: PMC10008532 DOI: 10.1038/s41598-023-30916-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 03/03/2023] [Indexed: 03/13/2023] Open
Abstract
Metataxonomy has become the standard for characterizing the diversity and composition of microbial communities associated with multicellular organisms and their environment. Currently available protocols for metataxonomy assume a uniform DNA extraction, amplification and sequencing efficiency for all sample types and taxa. It has been suggested that the addition of a mock community (MC) to biological samples before the DNA extraction step could aid identification of technical biases during processing and support direct comparisons of microbiota composition, but the impact of MC on diversity estimates of samples is unknown. Here, large and small aliquots of pulverized bovine fecal samples were extracted with no, low or high doses of MC, characterized using standard Illumina technology for metataxonomics, and analysed with custom bioinformatic pipelines. We demonstrated that sample diversity estimates were distorted only if MC dose was high compared to sample mass (i.e. when MC > 10% of sample reads). We also showed that MC was an informative in situ positive control, permitting an estimation of the sample 16S copy number, and detecting sample outliers. We tested this approach on a range of sample types from a terrestrial ecosystem, including rhizosphere soil, whole invertebrates, and wild vertebrate fecal samples, and discuss possible clinical applications.
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13
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Li Z, Guo W, Mo C, Tang R, He L, Du L, Li M, Wu H, Tang X, Huang Z, Wu X. Root Metabolism and Effects of Root Exudates on the Growth of Ralstonia solanacearum and Fusarium moniliforme Were Significantly Different between the Two Genotypes of Peanuts. Genes (Basel) 2023; 14:528. [PMID: 36833455 PMCID: PMC9956333 DOI: 10.3390/genes14020528] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Wild peanut species Arachis correntina (A. correntina) had a higher continuous cropping tolerance than peanut cultivars, closely correlating with the regulatory effects of its root exudates on soil microorganisms. To reveal the resistance mechanism of A. correntina to pathogens, we adopted transcriptomic and metabolomics approaches to analyze differentially expressed genes (DEGs) and differentially expressed metabolites (DEMs) between A. correntina and peanut cultivar Guihua85 (GH85) under hydroponic conditions. Interaction experiments of peanut root exudates with Ralstonia solanacearum (R. solanacearum) and Fusarium moniliforme (F. moniliforme) were carried out in this study. The result of transcriptome and metabolomics association analysis showed that there were fewer up-regulated DEGs and DEMs in A. correntina compared with GH85, which were closely associated with the metabolism of amino acids and phenolic acids. Root exudates of GH85 had stronger effects on promoting the growth of R. solanacearum and F. moniliforme than those of A. correntina under 1 and 5 percent volume (1% and 5%) of root exudates treatments. Thirty percent volume (30%) of A. correntina and GH85 root exudates significantly inhibited the growth of two pathogens. The exogenous amino acids and phenolic acids influenced R. solanacearum and F. moniliforme showing concentration effects from growth promotion to inhibition as with the root exudates. In conclusion, the greater resilience of A. correntina) to changes in metabolic pathways for amino acids and phenolic acids might aid in the repression of pathogenic bacteria and fungi.
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Affiliation(s)
- Zhong Li
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530004, China
| | - Wenfeng Guo
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530004, China
| | - Changming Mo
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530004, China
| | - Ronghua Tang
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530004, China
| | - Liangqiong He
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530004, China
| | - Lin Du
- Guangxi Science and Technology Museum, Nanning 530016, China
| | - Ming Li
- Guangxi Science and Technology Museum, Nanning 530016, China
| | - Haining Wu
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530004, China
| | - Xiumei Tang
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530004, China
| | - Zhipeng Huang
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530004, China
| | - Xingjian Wu
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530004, China
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14
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Anguita-Maeso M, Navas-Cortés JA, Landa BB. Insights into the Methodological, Biotic and Abiotic Factors Influencing the Characterization of Xylem-Inhabiting Microbial Communities of Olive Trees. PLANTS (BASEL, SWITZERLAND) 2023; 12:912. [PMID: 36840260 PMCID: PMC9967459 DOI: 10.3390/plants12040912] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 02/08/2023] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
Vascular pathogens are the causal agents of some of the most devastating plant diseases in the world, which can cause, under specific conditions, the destruction of entire crops. These plant pathogens activate a range of physiological and immune reactions in the host plant following infection, which may trigger the proliferation of a specific microbiome to combat them by, among others, inhibiting their growth and/or competing for space. Nowadays, it has been demonstrated that the plant microbiome can be modified by transplanting specific members of the microbiome, with exciting results for the control of plant diseases. However, its practical application in agriculture for the control of vascular plant pathogens is hampered by the limited knowledge of the plant endosphere, and, in particular, of the xylem niche. In this review, we present a comprehensive overview of how research on the plant microbiome has evolved during the last decades to unravel the factors and complex interactions that affect the associated microbial communities and their surrounding environment, focusing on the microbial communities inhabiting the xylem vessels of olive trees (Olea europaea subsp. europaea), the most ancient and important woody crop in the Mediterranean Basin. For that purpose, we have highlighted the role of xylem composition and its associated microorganisms in plants by describing the methodological approaches explored to study xylem microbiota, starting from the methods used to extract xylem microbial communities to their assessment by culture-dependent and next-generation sequencing approaches. Additionally, we have categorized some of the key biotic and abiotic factors, such as the host plant niche and genotype, the environment and the infection with vascular pathogens, that can be potential determinants to critically affect olive physiology and health status in a holobiont context (host and its associated organisms). Finally, we have outlined future directions and challenges for xylem microbiome studies based on the recent advances in molecular biology, focusing on metagenomics and culturomics, and bioinformatics network analysis. A better understanding of the xylem olive microbiome will contribute to facilitate the exploration and selection of specific keystone microorganisms that can live in close association with olives under a range of environmental/agronomic conditions. These microorganisms could be ideal targets for the design of microbial consortia that can be applied by endotherapy treatments to prevent or control diseases caused by vascular pathogens or modify the physiology and growth of olive trees.
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15
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Lu B, Qian J, Hu J, Huang Y, Wang P, Shen J, He Y, Tang S, Liu Y, Zhang Y. Plant rhizosphere defense system respond differently to emerging polyfluoroalkyl substances F-53B and PFOS stress. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130119. [PMID: 36265386 DOI: 10.1016/j.jhazmat.2022.130119] [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: 05/07/2022] [Revised: 09/30/2022] [Accepted: 10/01/2022] [Indexed: 06/16/2023]
Abstract
Chlorinated polyfluoroalkyl ether sulfonate (F-53B) and perfluorooctanesulfonate (PFOS) are used and emitted as fog inhibitors in the chromium plating industry, and they are widely detected worldwide. To study the effects of F-53B and PFOS on the rhizosphere defense system, they were added at two levels (0.1 and 50 mg L-1) to the soil where different plants (Lythrum salicaria and Phragmites communis) were grown. In bulk soils, high concentrations of F-53B/PFOS resulted in significant increases in soil pH, NH4+-N, and NO3--N (the effect of PFOS on NO3--N was not significant). Moreover, the extent of the effects of PFOS and F-53B on the physicochemical properties of bulk soils were different (e.g., PFOS caused an increase of NH4+-N by 8.94%-45.97% compared to 1.63%-25.20% for F-53B). Root exudates and PFASs together influenced the physicochemical properties of rhizosphere soils (e.g., TOC increased significantly in contaminated rhizosphere soils but did not change in non-bulk soils). Under the influence of F-53B/PFOS, the root exudates regulated by plants were changed and weakened the effect of F-53B/PFOS on microbial community of rhizosphere soil. The rhizosphere defense systems of different plants have both similarities and differences in response to different substances and concentrations.
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Affiliation(s)
- Bianhe Lu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Jin Qian
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China.
| | - Jing Hu
- Geosystems Research Institute, Mississippi State University, MS 39759, USA
| | | | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China.
| | - Junwei Shen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Yuxuan He
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Sijing Tang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Yin Liu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Yuhang Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, People's Republic of China; College of Environment, Hohai University, Nanjing 210098, People's Republic of China
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16
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Impacts of Binary Oxide Nanoparticles on the Soybean Plant and Its Rhizosphere, Associated Phytohormones, and Enzymes. Molecules 2023; 28:molecules28031326. [PMID: 36770994 PMCID: PMC9919940 DOI: 10.3390/molecules28031326] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 01/25/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
The utilization of binary oxide nanoparticles is geometrically increasing due to their numerous applications. Their intentional or accidental release after usage has led to their omnipresence in the environment. The usage of sludge or fertilizer containing binary oxide nanoparticles is likely to increase the chance of the plants being exposed to these binary oxide nanoparticles. The aim of the present review is to assess the detailed positive and negative impacts of these oxide nanoparticles on the soybean plants and its rhizosphere. In this study, methods of synthesizing binary oxide nanoparticles, as well as the merits and demerits of these methods, are discussed. Furthermore, various methods of characterizing the binary oxide nanoparticles in the tissues of soybean are highlighted. These characterization techniques help to track the nanoparticles inside the soybean plant. In addition, the assessment of rhizosphere microbial communities of soybean that have been exposed to these binary oxide nanoparticles is discussed. The impacts of binary oxide nanoparticles on the leaf, stem, root, seeds, and rhizosphere of soybean plant are comprehensively discussed. The impacts of binary oxides on the bioactive compounds such as phytohormones are also highlighted. Overall, it was observed that the impacts of the oxide nanoparticles on the soybean, rhizosphere, and bioactive compounds were dose-dependent. Lastly, the way forward on research involving the interactions of binary oxide nanoparticles and soybean plants is suggested.
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17
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Li P, Ye S, Chen J, Wang L, Li Y, Ge L, Wu G, Song L, Wang C, Sun Y, Wang J, Pan A, Quan Z, Wu Y. Combined metagenomic and metabolomic analyses reveal that Bt rice planting alters soil C-N metabolism. ISME COMMUNICATIONS 2023; 3:4. [PMID: 36690796 PMCID: PMC9870860 DOI: 10.1038/s43705-023-00217-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 01/04/2023] [Accepted: 01/13/2023] [Indexed: 01/25/2023]
Abstract
The environmental impacts of genetically modified (GM) plants remain a controversial global issue. To address these issues, comprehensive environmental risk assessments of GM plants is critical for the sustainable development and application of transgenic technology. In this paper, significant differences were not observed between microbial metagenomic and metabolomic profiles in surface waters of the Bt rice (T1C-1, the transgenic line) and non-Bt cultivars (Minghui 63 (the isogenic line) and Zhonghua 11 (the conventional japonica cultivar)). In contrast, differences in these profiles were apparent in the rhizospheres. T1C-1 planting increased soil microbiome diversity and network stability, but did not significantly alter the abundances of potential probiotic or phytopathogenic microorganisms compared with Minghui 63 and Zhonghua 11, which revealed no adverse effects of T1C-1 on soil microbial communities. T1C-1 planting could significantly alter soil C and N, probably via the regulation of the abundances of enzymes related to soil C and N cycling. In addition, integrated multi-omic analysis of root exudate metabolomes and soil microbiomes showed that the abundances of various metabolites released as root exudates were significantly correlated with subsets of microbial populations including the Acidobacteria, Actinobacteria, Chloroflexi, and Gemmatimonadetes that were differentially abundant in T1C-1 and Mnghui 63 soils. Finally, the potential for T1C-1-associated root metabolites to exert growth effects on T1C-1-associated species was experimentally validated by analysis of bacterial cultures, revealing that Bt rice planting could selectively modulate specific root microbiota. Overall, this study indicate that Bt rice can directly modulate rhizosphere microbiome assemblages by altering the metabolic compositions of root exudates that then alters soil metabolite profiles and physiochemical properties. This study unveils the mechanistic associations of Bt plant-microorganism-environment, which provides comprehensive insights into the potential ecological impacts of GM plants.
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Affiliation(s)
- Peng Li
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China.
- Shanghai Co-Elite Agricultural Sci-Tech (Group) Co., Ltd, 201106, Shanghai, China.
| | - Shuifeng Ye
- College of Life Sciences, Shangrao Normal University, 334001, Shangrao, China
| | - Jun Chen
- East China University of Technology, 330013, Nanchang, China
| | - Luyao Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Yujie Li
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Lei Ge
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Guogan Wu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Lili Song
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Cui Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Yu Sun
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Jinbin Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Aihu Pan
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Zhexue Quan
- School of Life Sciences, Fudan University, 200433, Shanghai, China.
| | - Yunfei Wu
- The College of Bioscience and Biotechnology, Yangzhou University, 225009, Yangzhou, China.
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18
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Shaffique S, Imran M, Kang SM, Khan MA, Asaf S, Kim WC, Lee IJ. Seed Bio-priming of wheat with a novel bacterial strain to modulate drought stress in Daegu, South Korea. FRONTIERS IN PLANT SCIENCE 2023; 14:1118941. [PMID: 37180396 PMCID: PMC10173886 DOI: 10.3389/fpls.2023.1118941] [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: 12/09/2022] [Accepted: 03/09/2023] [Indexed: 05/16/2023]
Abstract
Wheat is one of the major cereal crop grown food worldwide and, therefore, plays has a key role in alleviating the global hunger crisis. The effects of drought stress can reduces crop yields by up to 50% globally. The use of drought-tolerant bacteria for biopriming can improve crop yields by countering the negative effects of drought stress on crop plants. Seed biopriming can reinforce the cellular defense responses to stresses via the stress memory mechanism, that its activates the antioxidant system and induces phytohormone production. In the present study, bacterial strains were isolated from rhizospheric soil taken from around the Artemisia plant at Pohang Beach, located near Daegu, in the South Korea Republic of Korea. Seventy-three isolates were screened for their growth-promoting attributes and biochemical characteristics. Among them, the bacterial strain SH-8 was selected preferred based on its plant growth-promoting bacterial traits, which are as follows: abscisic acid (ABA) concentration = 1.08 ± 0.05 ng/mL, phosphate-solubilizing index = 4.14 ± 0.30, and sucrose production = 0.61 ± 0.13 mg/mL. The novel strain SH-8 demonstrated high tolerance oxidative stress. The antioxidant analysis also showed that SH-8 contained significantly higher levels of catalase (CAT), superoxide dismutase (SOD), and ascorbic peroxidase (APX). The present study also quantified and determined the effects of biopriming wheat (Triticum aestivum) seeds with the novel strain SH-8. SH-8 was highly effective in enhancing the drought tolerance of bioprimed seeds; their drought tolerance and germination potential (GP) were increased by up to 20% and 60%, respectively, compared with those in the control group. The lowest level of impact caused by drought stress and the highest germination potential, seed vigor index (SVI), and germination energy (GE) (90%, 2160, and 80%, respectively), were recorded for seeds bioprimed with with SH-8. These results show that SH-8 enhances drought stress tolerance by up to 20%. Our study suggests that the novel rhizospheric bacterium SH-8 (gene accession number OM535901) is a valuable biostimulant that improves drought stress tolerance in wheat plants and has the potential to be used as a biofertilizer under drought conditions.
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Affiliation(s)
- Shifa Shaffique
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Muhammad Imran
- Biosafety Division, National Institute of Agriculture Science, Rural Development Administration, Jeonju, Republic of Korea
| | - Sang-Mo Kang
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Muhammad Aaqil Khan
- Department of Chemical and Life Sciences, Qurtuba University of Science and Information Technology, Peshawar, Pakistan
| | - Sajjad Asaf
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Won-Chan Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
- *Correspondence: Won-Chan Kim, ; In-Jung Lee,
| | - In-Jung Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
- *Correspondence: Won-Chan Kim, ; In-Jung Lee,
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19
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Qu Y, Liu Q, Zhao W, Cheng H, Chen H, Tian Y, Ma S, Chen Y, Ma J. Characters and environmental driving factors of bacterial community in soil of Beijing urban parks. ENVIRONMENTAL RESEARCH 2022; 215:114178. [PMID: 36087773 DOI: 10.1016/j.envres.2022.114178] [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: 06/30/2022] [Revised: 08/06/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
In an era of unprecedented human influence, different human activities have different degrees of impact on specific bacteria, resulting in the regional biological homogenization of soil bacteria. However, the contribution of the impact that a large number of anthropogenic activities on bacteria remains unknown. Here, by high-throughput amplicon sequencing, we characterized the composition, diversity and influencing factors of soil microbes in Beijing urban parks at geographic space and park management aspect. It is the first time to quantify and compare the importance of the impact of up to 15 human activities on soil bacterial communities. The results show that the dominant bacterial phyla in Beijing urban parks were Actinobacteria, Proteobacteria, Acidobacteria and Chloroflexi. The environmental management of different park types, as well as the land use history and development conditions of different regions, had significant differences in soil bacterial community structure. Soil bacteria in urban parks were disturbed by direct human interference far more than natural causes. The most important factors were related to the number of tourists and residents, industrial production and land use patterns. These factors may also be related to the abundance of unknown bacteria in urban parks. This also directly shows that human activities have a non-negligible impact on soil bacteria. The ways in which different human activities brought by global urbanization and their impacting mechanisms are used should be the starting point of future research.
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Affiliation(s)
- Yajing Qu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Qiyuan Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Wenhao Zhao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Hongguang Cheng
- College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Haiyan Chen
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Yuxin Tian
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Saiyan Ma
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Ying Chen
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Jin Ma
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
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20
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Yang Y, Chen X, Liu L, Li T, Dou Y, Qiao J, Wang Y, An S, Chang SX. Nitrogen fertilization weakens the linkage between soil carbon and microbial diversity: A global meta-analysis. GLOBAL CHANGE BIOLOGY 2022; 28:6446-6461. [PMID: 35971768 DOI: 10.1111/gcb.16361] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 07/18/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Soil microbes make up a significant portion of the genetic diversity and play a critical role in belowground carbon (C) cycling in terrestrial ecosystems. Soil microbial diversity and organic C are often tightly coupled in C cycling processes; however, this coupling can be weakened or broken by rapid global change. A global meta-analysis was performed with 1148 paired comparisons extracted from 229 articles published between January 1998 and December 2021 to determine how nitrogen (N) fertilization affects the relationship between soil C content and microbial diversity in terrestrial ecosystems. We found that N fertilization decreased soil bacterial (-11%) and fungal diversity (-17%), but increased soil organic C (SOC) (+19%), microbial biomass C (MBC) (+17%), and dissolved organic C (DOC) (+25%) across different ecosystems. Organic N (urea) fertilization had a greater effect on SOC, MBC, DOC, and bacterial and fungal diversity than inorganic N fertilization. Most importantly, soil microbial diversity decreased with increasing SOC, MBC, and DOC, and the absolute values of the correlation coefficients decreased with increasing N fertilization rate and duration, suggesting that N fertilization weakened the linkage between soil C and microbial diversity. The weakened linkage might negatively impact essential ecosystem services under high rates of N fertilization; this understanding is important for mitigating the negative impact of global N enrichment on soil C cycling.
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Affiliation(s)
- Yang Yang
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
- CAS Center for Excellence in Quaternary Science and Global Change, Xi'an, China
- National Observation and Research Station of Earth Critical Zone on the Loess Plateau, Xi'an, China
| | - Xinli Chen
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada
| | - Liangxu Liu
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
- Urat Desert-Grassland Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Science, Lanzhou, China
| | - Ting Li
- Guangzhou Academy of Forestry and Landscape Architecture, Guangzhou, China
| | - Yanxing Dou
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, China
| | - Jiangbo Qiao
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, China
| | - Yunqiang Wang
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
- CAS Center for Excellence in Quaternary Science and Global Change, Xi'an, China
- National Observation and Research Station of Earth Critical Zone on the Loess Plateau, Xi'an, China
| | - Shaoshan An
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, China
| | - Scott X Chang
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada
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21
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Yuan Z, Liu Q, Pang Z, Fallah N, Liu Y, Hu C, Lin W. Sugarcane Rhizosphere Bacteria Community Migration Correlates with Growth Stages and Soil Nutrient. Int J Mol Sci 2022; 23:ijms231810303. [PMID: 36142216 PMCID: PMC9499485 DOI: 10.3390/ijms231810303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 11/25/2022] Open
Abstract
Plants and rhizosphere bacterial microbiota have intimate relationships. As neighbors of the plant root system, rhizosphere microorganisms have a crucial impact on plant growth and health. In this study, we sampled rhizosphere soil of sugarcane in May (seedling), July (tillering), September (elongation) and November (maturity), respectively. We employ 16S rRNA amplicon sequencing to investigate seasonal variations in rhizosphere bacteria community structure and abundance, as well as their association with soil edaphic factors. The results demonstrate that soil pH, total nitrogen (TN) and available nitrogen (AN) decrease substantially with time. Rhizosphere bacteria diversity (Shannon) and the total enriched OTUs are also significantly higher in July relative to other months. Bacteria OTUs and functional composition exhibit a strong and significant correlation with soil temperature (Tem), suggesting that Tem was the potential determinant controlling rhizosphere bacteria diversity, enriched OTUs as well as functional composition. Redundancy analysis (RDA) point toward soil total potassium (TK), pH, TN, Tem and AN as principal determinant altering shifting bacteria community structure. Variation partitioning analysis (VPA) analysis further validate that a substantial proportion of variation (70.79%) detected in the rhizosphere bacteria community structure was attributed to edaphic factors. Mfuzz analysis classified the bacterial genera into four distinct clusters, with cluster two exhibiting a distinct and dramatic increase in July, predominantly occupied by Allocatelliglobosispora. The stochastic forest model found the key characteristic bacterial populations that can distinguish the four key growth periods of sugarcane. It may help us to answer some pending questions about the interaction of rhizosphere microorganisms with plants in the future.
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Affiliation(s)
- Zhaonian Yuan
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Province and Ministry Co-Sponsored Collaborative Innovation Center of Sugar Industry, Nanning 530000, China
- Correspondence:
| | - Qiang Liu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ziqin Pang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Agro-Ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Nyumah Fallah
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Agro-Ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yueming Liu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chaohua Hu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenxiong Lin
- Fujian Provincial Key Laboratory of Agro-Ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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22
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Liao LB, Chen XX, Xiang J, Zhang NN, Wang ET, Shi FS. Zanthoxylum bungeanum root-rot associated shifts in microbiomes of root endosphere, rhizosphere, and soil. PeerJ 2022; 10:e13808. [PMID: 35945942 PMCID: PMC9357373 DOI: 10.7717/peerj.13808] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 07/07/2022] [Indexed: 01/18/2023] Open
Abstract
Root-rot disease has lead to serious reduction in yields and jeopardized the survival of the economically and ecologically important Zanthoxylum bungeanum trees cultured in Sichuan Province. In order to investigate the interaction between the microbiome and the root-rot disease, a metagenomic analysis was performed to characterize the microbial communities and functions in Z. bungeanum root endosphere, rhizosphere and bulk soil with/without root-rot disease. Soil physicochemical properties, microbial population size and enzyme activities were also analyzed for finding their interactions with the root-rot disease. As results, lower total nitrogen (TN) and available phosphorus (AP) contents but higher pH in rhizosphere and bulk soil, as well as lower substrate-induced respiration (SIR) and higher protease activity in bulk soil of diseased trees were found, in comparison with that of healthy trees. Microbial diversity and community composition were changed by root-rot disease in the endosphere, but not in rhizosphere and bulk soils. The endophytic microbiome of diseased trees presented higher Proteobacteria abundance and lower abundances of Bacteroidetes, Firmicutes and dominant fungal phyla. The relative abundances of nitrogen cycle- and carbon cycle-related genes in endophytic microbiomes were different between the diseased and healthy trees. Based on ANOSIM and PCoA, functional profiles (KEGG and CAZy) of microbiomes in rhizosphere and bulk soil shifted significantly between the diseased and healthy trees. In addition, soil pH, TN, AP, SIR, invertase and protease were estimated as the main factors influencing the shifts of taxonomic and functional groups in microbiomes of rhizosphere and bulk soil. Conclusively, the imbalance of root and soil microbial function groups might lead to shifts in the root endosphere-rhizosphere microenvironment, which in turn resulted in Z. bungeanum root-rot.
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Affiliation(s)
- Li Bin Liao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China,University of Chinese Academy of Sciences, Beijing, China,CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chendu, China
| | - Xiao Xia Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China,University of Chinese Academy of Sciences, Beijing, China,CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chendu, China
| | - Jun Xiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Nan Nan Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China,CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chendu, China
| | - En Tao Wang
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Fu Sun Shi
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China,CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chendu, China
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23
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Impact of Moso Bamboo (Phyllostachys edulis) Expansion into Japanese Cedar Plantations on Soil Fungal and Bacterial Community Compositions. FORESTS 2022. [DOI: 10.3390/f13081190] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Moso bamboo expansion is common across the world. The expansion of moso bamboo into adjacent forests altered plant and soil characteristics. While the community structure of soil fungi and bacteria plays an important role in maintaining the function of forest ecosystems, changes in microbial community compositions remain unclear, limiting our understanding of ecological process changes following moso bamboo expansion. To explore changes in the community structure of soil fungi and bacteria in Japanese cedar plantations experiencing expansion of moso bamboo, Illumina NovaSeq high-throughput sequencing technology was used to elucidate changes in soil microbial communities as well as alteration in litter and soil chemical characteristics. The results showed that moso bamboo expansion decreased content of soil organic carbon, total nitrogen, litter carbon, and the carbon to nitrogen ratio as well as the number of bacterial operational taxonomic units (OTUs) at the genus level, the α-diversity Simple index, and the abundance of Acidobacteria, Chloroflexi, and Gemmatimonadetes. Moso bamboo expansion also increased soil NH4+-N, pH, while it decreased fungi OTUs at the phyla, class, order, family, and genus level. The expansion of moso bamboo into Japanese cedar substantially altered soil fungal and bacterial community structure, which might have implications for changes in the ecosystem element-cycling process. In the forest ecosystem and expansion management of moso bamboo, the types and different expansion stages of moso bamboo should be paid attention to, in the assessment of ecological effects and soil microbial structure.
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24
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Li Q, Xing Y, Huang B, Chen X, Ji L, Fu X, Li T, Wang J, Chen G, Zhang Q. Rhizospheric mechanisms of Bacillus subtilis bioaugmentation-assisted phytostabilization of cadmium-contaminated soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 825:154136. [PMID: 35218830 DOI: 10.1016/j.scitotenv.2022.154136] [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: 08/18/2021] [Revised: 01/24/2022] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
Plant growth promoting (PGP) traits of inoculation in bioaugmentation assisted phytostabilization of heavy metal-contaminated soil have been well documented. The property of inoculation to immobilize heavy metals is another major contributor to phytostabilization efficiency. This study investigated the effects of inoculation with different concentrations of rhizobacteria Bacillus subtilis on the cadmium (Cd) bioavailability and distribution, enzyme activities, and bacterial community structure in soil planted with ryegrass (Lolium multiflorum L.). Addition of a high dosage of Bacillus subtilis decreased plant malondialdehyde (MDA) amount, increased plant antioxidant enzyme and soil nutrient cycling-involved enzyme activities, and subsequently enhanced biomass by 20.9%. In particular, the inoculation reduced the Cd bioavailability in soil, bioaccumulation coefficient (BCF), translocation factors (TF), and accumulation in ryegrass by 39.1%, 36.5%, 24.2%, and 27.9%, respectively. Furthermore, 16S rRNA gene sequencing analysis of rhizosphere soil revealed microbial community structure alterations (e.g., enrichment of Proteobacteria), eight phenotype regulations, and seventeen Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway transformations accounted for the stress mitigation and Cd immobilization in the presence of inocula. Besides, intracellular accumulation and biofilm sequestration were proposed as primary immobilization mechanisms induced by bioaugmentation.
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Affiliation(s)
- Qi Li
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250013, China.
| | - Yingna Xing
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250013, China.
| | - Bin Huang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Xin Chen
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Lei Ji
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250013, China
| | - Xiaowen Fu
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250013, China
| | - Tianyuan Li
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250013, China
| | - Jianing Wang
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250013, China
| | - Guanhong Chen
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250013, China
| | - Qiang Zhang
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250013, China.
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25
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Fu Q, Shao Y, Wang S, Liu F, Tian G, Chen Y, Yuan Z, Ye Y. Soil Microbial Distribution Depends on Different Types of Landscape Vegetation in Temperate Urban Forest Ecosystems. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.858254] [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
Although soil microbes play an important role in the functioning of the forest ecosystem, our understanding of the spatial distribution characteristics of soil microbes among different vegetation types in urban forest ecosystems is poor. In this study, with the help of high-throughput sequencing, we examined the vegetation type preferences of soil microbes (fungi and bacteria) and then analyzed the microbe–environment (plant community, light availability, soil properties) relations in a temperate urban forest in China. Our results showed that the soil microbial (bacterial and fungal) richness of deciduous forest was higher than that of evergreen, and mixed forests. The spatial distribution of fungi was more specialized than that of bacteria among different vegetation types. The driving forces of environmental factors on soil bacteria and fungi were different. Our findings suggest that different vegetation types favor the occurrence of different microbes, and the relationships between soil microbes and environmental factors depend on different vegetation types in this temperate urban forest. These findings shed new light on the biodiversity conservation of microbes in temperate urban forests and point to the potential importance of vegetation types for microbe formation.
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26
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Mushtaq S, Shafiq M, Ashraf T, Haider MS, Atta S, Almaary KS, Elshikh MS. Enumeration of citrus endophytic bacterial communities based on illumine metagenomics technique. PLoS One 2022; 17:e0263144. [PMID: 35417473 PMCID: PMC9007379 DOI: 10.1371/journal.pone.0263144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/03/2022] [Indexed: 02/01/2023] Open
Abstract
Citrus is a valuable crop in Pakistan. It is rich in vitamin C, other nutrients and antioxidants. Huanglongbing (HLB) caused by a bacterium “Candidatus liberibacter asiaticus” (CLas), africanus and americanus has an influence on citrus production around the world. Beside HLB there exist several other bacterial species in citrus groves in Pakistan. The structure and diversity of bacterial species in various ecosystems can be quickly examined using NGS. This approach is considerably quicker and more precise than outdated methods. Healthy or citrus greening infected leaf samples of Grapefruit (Citrus paradisi), C. aurantifolia, and C. reticulata Blanco were used for diversity analysis. In this study high throughput, NGS technique was used to access the population of both cultivable and non-cultivable bacterial endophytes from citrus leaves, by using PCR amplicons of 16S rDNA sequences (V5–V7 regions) with Illumina Hi seq. As a result, a total number of 68,722 sequences were produced from the test samples. According to the NGS-based diversity classification, the most common genera of exploited bacterial endophytes were Proteobacteria, Firmicutes, Bacteroides, Cyanobacteria, and Actinobacteria. C. aurantifolia and C. paradisi showed almost equal diversity, whereas C. reticulata Blanco had a higher proportion of Proteobacteria and Cyanobacteria in their leaves. To determine alpha diversity (AD), additional data was analyzed using statistical indices such as Shannon, Chao1, and Simpson. According to the inverse Simpson diversity index, the abundance of the microbial population in six different citrus samples was 0.48, 0.567, and 0.163, respectively. The metagenomics of microbiota in plant tissues was successfully recorded by NGS technology, which can help us learn more about the interactions between plants and microbes. This research is the first step toward a better understanding of 16SrRNA-based metagenomics from citrus in Pakistan using Illumina (Hi seq) Technology.
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Affiliation(s)
- Sehrish Mushtaq
- Faculty of Agricultural Sciences, Department of Plant Pathology, University of the Punjab, Quaid-e-Azam Campus, Lahore, Pakistan
| | - Muhammad Shafiq
- Faculty of Agricultural Sciences, Department of Horticulture Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, Pakistan
| | - Tehseen Ashraf
- Department of Horticulture Sciences University of Sargodha, Sargodha, Pakistan
| | - Muhammad Saleem Haider
- Faculty of Agricultural Sciences, Department of Plant Pathology, University of the Punjab, Quaid-e-Azam Campus, Lahore, Pakistan
| | - Sagheer Atta
- Department of Plant Protection, Faculty of Agricultural Sciences, Ghazi University Dera Ghazhi Khan, Punjab, Pakistan
- Molecular Plant Pathology Laboratory, USDA-ARS, Beltsville, MD, United States of America
- * E-mail:
| | - Khalid S. Almaary
- Department of Botany and Microbiology, College of Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Soliman Elshikh
- Department of Botany and Microbiology, College of Sciences, King Saud University, Riyadh, Saudi Arabia
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27
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Aldorfová A, Dostálek T, Münzbergová Z. Effects of soil conditioning, root and shoot litter addition interact to determine the intensity of plant–soil feedback. OIKOS 2022. [DOI: 10.1111/oik.09025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Anna Aldorfová
- Inst. of Botany of the Czech Academy of Sciences Průhonice Czech Republic
- Dept of Botany, Faculty of Science, Charles Univ. in Prague Praha 2 Czech Republic
| | - Tomáš Dostálek
- Inst. of Botany of the Czech Academy of Sciences Průhonice Czech Republic
- Dept of Botany, Faculty of Science, Charles Univ. in Prague Praha 2 Czech Republic
| | - Zuzana Münzbergová
- Inst. of Botany of the Czech Academy of Sciences Průhonice Czech Republic
- Dept of Botany, Faculty of Science, Charles Univ. in Prague Praha 2 Czech Republic
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28
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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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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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Moon YS, Ali S. Isolation and identification of multi-trait plant growth-promoting rhizobacteria from coastal sand dune plant species of Pohang beach. Folia Microbiol (Praha) 2022; 67:523-533. [PMID: 35211835 DOI: 10.1007/s12223-022-00959-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/02/2022] [Indexed: 11/27/2022]
Abstract
Rhizobacteria are root-associated bacteria that influence plant growth by various direct and indirect mechanisms. In quest of efficient plant growth-promoting rhizobacteria (PGPR) with multiple plant growth-promoting traits, a total of 52 rhizobacterial isolates were isolated from the rhizospheric soil collected at Pohang beach, Republic of Korea. The bacterial isolates were evaluated in vitro for their plant growth-promoting traits like production of 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, indole-3-acetic acid (IAA), siderophore, and phosphate solubilization activities. More than 28% of the isolates revealed all of the multi-trait plant growth-promoting activities, whereas 11.54% exhibited robust results for producing IAA, ACC deaminase, siderophore, and phosphate solubilization activities. Similarly, 36% isolates were capable for the production of IAA, siderophore, and ACC deaminase, while 32% revealed phosphate solubilization and siderophore production. The isolates with prominent multi-trait plant growth-promoting activities were identified based on 16S rRNA gene sequences and matched to Pseudomonas koreensis-(S4T10), Pseudomonas fluorescens-(S3B1), Serratia fonticola-(S1T1), Sphingobacterium multivorum-(S1B1), Brevundimonas vesicularis-(S1T13), and Arthrobacter sp.-(S2T9) with 99-100% similarity. Our results confirm that further evaluation of these PGPR (exhibiting multi-traits for plant growth promotion) is required on crop plants to reveal their pragmatic role under normal and abiotic stress conditions and add into the consortium of biofertilizers for sustainable agriculture.
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Affiliation(s)
- Yong-Sun Moon
- Department of Horticulture and Life Science, Yeungnam University, Gyeongsan, Republic of Korea
| | - Sajid Ali
- Department of Horticulture and Life Science, Yeungnam University, Gyeongsan, Republic of Korea.
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Zhang B, Xue K, Zhou S, Wang K, Liu W, Xu C, Cui L, Li L, Ran Q, Wang Z, Hu R, Hao Y, Cui X, Wang Y. Environmental selection overturns the decay relationship of soil prokaryotic community over geographic distance across grassland biotas. eLife 2022; 11:70164. [PMID: 35073255 PMCID: PMC8828049 DOI: 10.7554/elife.70164] [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: 05/07/2021] [Accepted: 01/21/2022] [Indexed: 11/26/2022] Open
Abstract
Though being fundamental to global diversity distribution, little is known about the geographic pattern of soil microorganisms across different biotas on a large scale. Here, we investigated soil prokaryotic communities from Chinese northern grasslands on a scale up to 4000 km in both alpine and temperate biotas. Prokaryotic similarities increased over geographic distance after tipping points of 1760–1920 km, generating a significant U-shape pattern. Such pattern was likely due to decreased disparities in environmental heterogeneity over geographic distance when across biotas, supported by three lines of evidences: (1) prokaryotic similarities still decreased with the environmental distance, (2) environmental selection dominated prokaryotic assembly, and (3) short-term environmental heterogeneity followed the U-shape pattern spatially, especially attributed to dissolved nutrients. In sum, these results demonstrate that environmental selection overwhelmed the geographic ‘distance’ effect when across biotas, overturning the previously well-accepted geographic pattern for microbes on a large scale.
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Affiliation(s)
- Biao Zhang
- College of Resources and Environment, University of Chinese Academy of Sciences
| | - Kai Xue
- College of Resources and Environment, University of Chinese Academy of Sciences
| | - Shutong Zhou
- College of Life Sciences, University of Chinese Academy of Sciences
| | - Kui Wang
- College of Life Sciences, University of Chinese Academy of Sciences
| | - Wenjing Liu
- College of Resources and Environment, University of Chinese Academy of Sciences
| | - Cong Xu
- Aerospace Information Research Institute, University of Chinese Academy of Sciences
| | - Lizhen Cui
- College of Life Sciences, University of Chinese Academy of Sciences
| | - Linfeng Li
- College of Resources and Environment, University of Chinese Academy of Sciences
| | - Qinwei Ran
- College of Life Sciences, University of Chinese Academy of Sciences
| | - Zongsong Wang
- College of Life Sciences, University of Chinese Academy of Sciences
| | - Ronghai Hu
- College of Resources and Environment, University of Chinese Academy of Sciences
| | - Yanbin Hao
- College of Life Sciences, University of Chinese Academy of Sciences
| | - Xiaoyong Cui
- Key Laboratory of Adaptation and Evolution of Plateau Biota, University of Chinese Academy of Sciences
| | - Yanfen Wang
- College of Resources and Environment, University of Chinese Academy of Sciences
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Xue Y, Kang H, Cui Y, Lu S, Yang H, Zhu J, Fu Z, Yan C, Wang D. Consistent Plant and Microbe Nutrient Limitation Patterns During Natural Vegetation Restoration. FRONTIERS IN PLANT SCIENCE 2022; 13:885984. [PMID: 35665177 PMCID: PMC9161215 DOI: 10.3389/fpls.2022.885984] [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: 02/28/2022] [Accepted: 03/23/2022] [Indexed: 05/06/2023]
Abstract
Vegetation restoration is assumed to enhance carbon (C) sequestration in terrestrial ecosystems, where plant producers and microbial decomposers play key roles in soil C cycling. However, it is not clear how the nutrient limitation patterns of plants and soil microbes might change during vegetation restoration. We investigated the nutrient limitations of the plant and microbial communities along a natural vegetation restoration chronosequence (1, 8, 16, 31, and 50 years) following farmland abandonment in Qinling Mountains, China, and assessed their relationships with soil factors. The result showed that following natural vegetation restoration, the nitrogen (N) limitation of plant and microbial communities was alleviated significantly, and thereafter, it began to shift to phosphorus (P) limitation at a later stage. Plants showed P limitation 50 years after restoration, while microbial P limitation appeared 31 years later. The changes in plant nutrient limitation were consistent with those in microbial nutrient limitation, but soil microbes were limited by P earlier than plants. Random forest model and partial least squares path modeling revealed that soil nutrient stoichiometry, especially soil C:N ratio, explained more variations in plant and microbial nutrient limitation. Our study demonstrates that the imbalanced soil C:N ratio may determine the soil microbial metabolic limitation and further mediate the variation in plant nutrient limitation during natural vegetation restoration, which provides important insights into the link between metabolic limitation for microbes and nutrient limitation for plants during vegetation restoration to improve our understanding of soil C turnover in temperate forest ecosystems.
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Affiliation(s)
- Yue Xue
- College of Forestry, Northwest Agriculture & Forestry University, Yangling, China
- Key Laboratory of Forest Cultivation on the Loess Plateau, State Forestry and Grassland Administration, Yangling, China
| | - Haibin Kang
- College of Forestry, Northwest Agriculture & Forestry University, Yangling, China
- Key Laboratory of Forest Cultivation on the Loess Plateau, State Forestry and Grassland Administration, Yangling, China
| | - Yongxing Cui
- College of Urban and Environmental Sciences, Sino-French Institute for Earth System Science, Peking University, Beijing, China
| | - Sheng Lu
- College of Forestry, Northwest Agriculture & Forestry University, Yangling, China
| | - Hang Yang
- College of Forestry, Northwest Agriculture & Forestry University, Yangling, China
| | - Jiaqi Zhu
- College of Forestry, Northwest Agriculture & Forestry University, Yangling, China
| | - Zhenjie Fu
- College of Forestry, Northwest Agriculture & Forestry University, Yangling, China
| | - Chenglong Yan
- College of Forestry, Northwest Agriculture & Forestry University, Yangling, China
| | - Dexiang Wang
- College of Forestry, Northwest Agriculture & Forestry University, Yangling, China
- Key Laboratory of Forest Cultivation on the Loess Plateau, State Forestry and Grassland Administration, Yangling, China
- *Correspondence: Dexiang Wang,
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Abstract
Cropping system diversity provides yield benefits that may result from shifts in the composition of root-associated bacterial and fungal communities, which either enhance nutrient availability or limit nutrient loss. We investigated whether temporal diversity of annual cropping systems (four versus two crops in rotation) influences the composition and metabolic activities of root-associated microbial communities in maize at a developmental stage when the peak rate of nitrogen uptake occurs. We monitored total (DNA-based) and potentially active (RNA-based) bacterial communities and total (DNA-based) fungal communities in the soil, rhizosphere, and endosphere. Cropping system diversity strongly influenced the composition of the soil microbial communities, which influenced the recruitment of the resident microbial communities and, in particular, the potentially active rhizosphere and endosphere bacterial communities. The diversified cropping system rhizosphere recruited a more diverse bacterial community (species richness), even though there was little difference in soil species richness between the two cropping systems. In contrast, fungal species richness was greater in the conventional rhizosphere, which was enriched in fungal pathogens; the diversified rhizosphere, however, was enriched in Glomeromycetes. While cropping system influenced endosphere community composition, greater correspondence between DNA- and RNA-based profiles suggests a higher representation of active bacterial populations. Cropping system diversity influenced the composition of ammonia oxidizers, which coincided with diminished potential nitrification activity and gross nitrate production rates, particularly in the rhizosphere. The results of our study suggest that diversified cropping systems shift the composition of the rhizosphere’s active bacterial and total fungal communities, resulting in tighter coupling between plants and microbial processes that influence nitrogen acquisition and retention. IMPORTANCE Crops in simplified, low-diversity agroecosystems assimilate only a fraction of the inorganic nitrogen (N) fertilizer inputs. Much of this N fertilizer is lost to the environment as N oxides, which degrade water quality and contribute to climate change and loss of biodiversity. Ecologically inspired management may facilitate mutualistic interactions between plant roots and microbes to liberate nutrients when plants need them, while also decreasing nutrient loss and pathogen pressure. In this study, we investigate the effects of a conventional (2-year rotation, inorganic fertilization) and a diversified (4-year rotation, manure amendments) cropping system on the assembly of bacterial and fungal root-associated communities, at a maize developmental stage when nitrogen demand is beginning to increase. Our results indicate that agricultural management influences the recruitment of root-associated microbial communities and that diversified cropping systems have lower rates of nitrification (particularly in the rhizosphere), thereby reducing the potential for loss of nitrate from these systems.
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Sun X, Pei J, Zhao L, Ahmad B, Huang LF. Fighting climate change: soil bacteria communities and topography play a role in plant colonization of desert areas. Environ Microbiol 2021; 23:6876-6894. [PMID: 34693620 DOI: 10.1111/1462-2920.15799] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/15/2022]
Abstract
Global warming has exacerbated desertification in arid regions. Exploring the environmental variables and microbial communities that drive the dynamics of geographic patterns of desert crops is important for large-scale standardization of crops that can control desertification. Here, predictions based on future climate data from CMIP6 show that a steady expand in the suitable production areas for three desert plants (Cistanche deserticola, Cynomorium songaricum and Cistanche salsa) under global warming, demonstrating their high adaptability to future climate change. We examined the biogeography of three desert plant soil bacteria communities and assessed the environmental factors affecting the community assembly process. The α-diversity significantly decreased along elevated latitudes, indicating that the soil bacterial communities of the three species have latitude diversity patterns. The neutral community model evaluated 66.6% of the explained variance of the bacterial community in the soil of desert plants and Modified Stochasticity Ratio <0.5, suggesting that deterministic processes dominate the assembly of bacterial communities in three desert plants. Moreover, topography (longitude, elevation) and precipitation as well as key OTUs (OTU4911: Streptomyces eurythermus and OTU4672: Streptomyces flaveus) drive the colonization of three desert plants. This research offers a promising solution for desert management in arid areas under global warming.
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Affiliation(s)
- Xiao Sun
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Jin Pei
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu, Sichuan, 611137, China.,Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China
| | - Lei Zhao
- Central Medical District of Chinese PLA General Hospital, Beijing, 100193, China
| | - Bashir Ahmad
- Center for Biotechnology & Microbiology, University of Peshawar, Peshawar, 25000, Pakistan
| | - Lin-Fang Huang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
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Zhou Y, Tang Y, Hu C, Zhan T, Zhang S, Cai M, Zhao X. Soil applied Ca, Mg and B altered phyllosphere and rhizosphere bacterial microbiome and reduced Huanglongbing incidence in Gannan Navel Orange. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 791:148046. [PMID: 34118675 DOI: 10.1016/j.scitotenv.2021.148046] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 05/27/2023]
Abstract
Huanglongbing (HLB) caused by 'Ca. Liberibacter. Asiaticus (Clas)' is one of the destructive diseases for citrus, threatening the development of citrus industry. Adopting a proper fertilization method instead of using pesticides seems particularly important, which would contribute to a sustainable development of orchard. In this study, the impact of soil application of nutrients combined with foliar spray of macro- and micro-nutrients on the incidence of HLB and the phyllosphere and rhizosphere bacterial microbiome was investigated in Gannan Navel Orange orchard from 2015 to 2018. Compared with the control (T1), the yield of Gannan Navel Orange in all other treatments applied with macro- and micro-nutrients increased significantly in 2018 (by 20.5%-45.8%), but not in the first two years (2016-17). Among treatments, Ca + Mg + B application in soil (T2) showed the highest yield and lowest HLB incidence. According to the PCR results, CLas was negative in T2 but positive in the control, which directly proved HLB incidence was reduced with Ca + Mg + B application in soil. Moreover, 16S rRNA sequencing was used to characterize rhizosphere and phyllosphere microbial communities. Results showed that microbial biodiversity was increased and microbial community structure was altered in T2 treatment, of which the beneficial bacteria were enriched in phyllosphere and rhizosphere. The results of PICRUSt showed that in T2 treatment, rhizosphere microbe contained more membrane transport (ABC transporters) genes, while, carbohydrate metabolism genes were enriched in the control rhizosphere due to HLB obstruct the photosynthetic metabolite transport. In summary, results indicated that macro- and micro-nutrients application improved the yield of Gannan Navel Orange and soil application of Ca + Mg + B reduced HLB incidence by altering microbial community structure and increasing microbial biodiversity. This study developed an environment-friendly way to reduce HLB incidence and improve the yield of citrus.
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Affiliation(s)
- Yingjie Zhou
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China; Hubei Provincial Engineering Laboratory for New-Type Fertilizer, Wuhan 430070, China; Research Center of Trace Elements, Wuhan 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Wuhan 430070, China
| | - Yanni Tang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China; Hubei Provincial Engineering Laboratory for New-Type Fertilizer, Wuhan 430070, China; Research Center of Trace Elements, Wuhan 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Wuhan 430070, China
| | - Chengxiao Hu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China; Hubei Provincial Engineering Laboratory for New-Type Fertilizer, Wuhan 430070, China; Research Center of Trace Elements, Wuhan 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Wuhan 430070, China
| | - Ting Zhan
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China; Hubei Provincial Engineering Laboratory for New-Type Fertilizer, Wuhan 430070, China; Research Center of Trace Elements, Wuhan 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Wuhan 430070, China
| | - Simin Zhang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China; Hubei Provincial Engineering Laboratory for New-Type Fertilizer, Wuhan 430070, China; Research Center of Trace Elements, Wuhan 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Wuhan 430070, China
| | - Miaomiao Cai
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China; Hubei Provincial Engineering Laboratory for New-Type Fertilizer, Wuhan 430070, China; Research Center of Trace Elements, Wuhan 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Wuhan 430070, China
| | - Xiaohu Zhao
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China; Hubei Provincial Engineering Laboratory for New-Type Fertilizer, Wuhan 430070, China; Research Center of Trace Elements, Wuhan 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Wuhan 430070, China.
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You C, Qin D, Wang Y, Lan W, Li Y, Yu B, Peng Y, Xu J, Dong J. Plant Triterpenoids Regulate Endophyte Community to Promote Medicinal Plant Schisandra sphenanthera Growth and Metabolites Accumulation. J Fungi (Basel) 2021; 7:jof7100788. [PMID: 34682210 PMCID: PMC8539763 DOI: 10.3390/jof7100788] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 11/16/2022] Open
Abstract
Beneficial interactions between endophytes and plants are critical for plant growth and metabolite accumulation. Nevertheless, the secondary metabolites controlling the feedback between the host plant and the endophytic microbial community remain elusive in medicinal plants. In this report, we demonstrate that plant-derived triterpenoids predominantly promote the growth of endophytic bacteria and fungi, which in turn promote host plant growth and secondary metabolite productions. From culturable bacterial and fungal microbial strains isolated from the medicinal plant Schisandra sphenanthera, through triterpenoid-mediated screens, we constructed six synthetic communities (SynComs). By using a binary interaction method in plates, we revealed that triterpenoid-promoted bacterial and fungal strains (TPB and TPF) played more positive roles in the microbial community. The functional screening of representative strains suggested that TPB and TPF provide more beneficial abilities to the host. Moreover, pot experiments in a sterilized system further demonstrated that TPB and TPF play important roles in host growth and metabolite accumulation. In summary, these experiments revealed a role of triterpenoids in endophytic microbiome assembly and indicated a strategy for constructing SynComs on the basis of the screening of secondary metabolites, in which bacteria and fungi join forces to promote plant health. These findings may open new avenues towards the breeding of high yielding and high metabolite-accumulating medicinal plants by exploiting their interaction with beneficial endophytes.
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Affiliation(s)
- Chuan You
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing 400715, China; (C.Y.); (D.Q.); (Y.W.); (W.L.); (Y.L.); (B.Y.); (Y.P.); (J.X.)
| | - Dan Qin
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing 400715, China; (C.Y.); (D.Q.); (Y.W.); (W.L.); (Y.L.); (B.Y.); (Y.P.); (J.X.)
- Key Scientific Research Base of Pest and Mold Control of Heritage Collection (Chongqing China Three Gorges Museum), State Administration of Cultural Heritage, Chongqing 400015, China
| | - Yumeng Wang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing 400715, China; (C.Y.); (D.Q.); (Y.W.); (W.L.); (Y.L.); (B.Y.); (Y.P.); (J.X.)
| | - Wenyi Lan
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing 400715, China; (C.Y.); (D.Q.); (Y.W.); (W.L.); (Y.L.); (B.Y.); (Y.P.); (J.X.)
| | - Yehong Li
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing 400715, China; (C.Y.); (D.Q.); (Y.W.); (W.L.); (Y.L.); (B.Y.); (Y.P.); (J.X.)
| | - Baohong Yu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing 400715, China; (C.Y.); (D.Q.); (Y.W.); (W.L.); (Y.L.); (B.Y.); (Y.P.); (J.X.)
| | - Yajun Peng
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing 400715, China; (C.Y.); (D.Q.); (Y.W.); (W.L.); (Y.L.); (B.Y.); (Y.P.); (J.X.)
| | - Jieru Xu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing 400715, China; (C.Y.); (D.Q.); (Y.W.); (W.L.); (Y.L.); (B.Y.); (Y.P.); (J.X.)
| | - Jinyan Dong
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing 400715, China; (C.Y.); (D.Q.); (Y.W.); (W.L.); (Y.L.); (B.Y.); (Y.P.); (J.X.)
- Correspondence:
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Wang J, Wang J, He JZ, Zhu YG, Qiao NH, Ge Y. Arbuscular mycorrhizal fungi and plant diversity drive restoration of nitrogen-cycling microbial communities. Mol Ecol 2021; 30:4133-4146. [PMID: 34146429 DOI: 10.1111/mec.16030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 06/06/2021] [Accepted: 06/16/2021] [Indexed: 11/30/2022]
Abstract
Soil microbial communities, key players of many crucial ecosystem functions, are susceptible to environmental disturbances, which might cause the loss of microbial diversity and functions. However, few ecological concepts and practices have been developed for rescuing stressed soil microbial communities. Here, we manipulated an experiment with or without arbuscular mycorrhizal fungi (AMF) inoculation and at three levels (one, three and six species) of plant diversity to disentangle how the AMF and vegetation rescue soil nitrogen (N) -cycling microbial loop from simulated degraded soil ecosystem. Our results showed that AMF inoculation improved the restoration of soil N-cycling microbial communities. This improved restoration was related to the role of AMF in enhancing interactions within the N-cycling microbial loop. Furthermore, increased plant diversity strengthened the role of AMF in rescuing N-cycling microbial communities. Our findings provide novel insights into the roles of AMF and plant diversity in facilitating the rescue of microbial communities in degraded terrestrial ecosystems.
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Affiliation(s)
- Jichen Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jiang Wang
- School of Life Sciences, Taizhou University, Taizhou, China
| | - Ji-Zheng He
- School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Neng-Hu Qiao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuan Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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Qu Q, Li Y, Zhang Z, Cui H, Zhao Q, Liu W, Lu T, Qian H. Effects of S-metolachlor on wheat (Triticum aestivum L.) seedling root exudates and the rhizosphere microbiome. JOURNAL OF HAZARDOUS MATERIALS 2021; 411:125137. [PMID: 33858101 DOI: 10.1016/j.jhazmat.2021.125137] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/09/2021] [Accepted: 01/09/2021] [Indexed: 06/12/2023]
Abstract
S-metolachlor (S-ME) is a common chloroacetanilide herbicide. Here, we investigated the effects of S-ME on wheat seedling growth and explored via metabolomics the driver through which S-ME changes the rhizosphere microbiome. The results indicated that 4 mg/kg S-ME had a strong inhibitory effect on plant growth by inducing hydrogen peroxide (H2O2) levels. The richness of the rhizosphere microbiome markedly decreased after S-ME treatment, although the abundance of some potential beneficial rhizobacteria, such as Rhizobiaceae and Burkholderiaceae, increased suggesting that plants recruited potential beneficial microorganisms to resist S-ME-induced stress. Spearman correlation analysis revealed that Rhizobiaceae and Burkholderiaceae were positively correlated with organic acids secreted by plants after S-ME treatment, implying that potential beneficial microorganisms may be attracted mainly by organic acids. Our results demonstrated the phytotoxicity of S-ME on crop growth and indicated both that S-ME could influence rhizosphere microorganism abundance and that recruitment of potential beneficial microorganisms could be the result of root exudate regulation.
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Affiliation(s)
- Qian Qu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Yan Li
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Hengzheng Cui
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Qianqiu Zhao
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
| | - Wanyue Liu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China; Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China.
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39
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Acharya M, Ashworth AJ, Yang Y, Burke JM, Lee JA, Sharma Acharya R. Soil microbial diversity in organic and non-organic pasture systems. PeerJ 2021; 9:e11184. [PMID: 33981494 PMCID: PMC8071071 DOI: 10.7717/peerj.11184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 03/08/2021] [Indexed: 11/29/2022] Open
Abstract
Understanding the effects of organic pasture management on the soil microbiome is important for sustainable forage production since soil microbiome diversity contributes to improved nutrient cycling, soil structure, plant growth, and environmental resiliency; however, the soil microbiome response to pasture management is largely unknown. This study assessed the soil microbial diversity, richness, and community structure following 10 years of pasture management (organic or non-organic) of the V4 region of the 16S rRNA using the Illumina MiSeq platform. Soil samples were collected from 0–15 cm in July and August from 2017–2018 and soil nutrient properties (nutrients, carbon, nitrogen, and pH) quantified and correlated with soil microbial diversity. Overall, greater soil bacterial species richness (P ≤ 0.05) occurred in organic relative to non-organic (conventional) systems. Management affected bacterial species richness (Chao1), with greater richness occurring in organic pasture soils and less richness occurring in non-organic systems (P ≤ 0.05). Similarly, management affected bacterial evenness (Simpson’s index), with a more diverse community occurring in organically managed soils relative to non-organic pastures (P ≤ 0.05). Linear discriminant analysis effect size analysis showed statistically significant and biologically consistent differences in bacterial taxa in organic compared with non-organic soils. Therefore, there was a shift in bacterial community structure in organic relative to non-organic soils (P ≤ 0.05). Additionally, soil nutrients (Fe, Mg, Ni, S, Al, K, Cd, and Cu), pH, C, and N were correlated with one or more dominant bacterial phyla (Gemmatimonadetes, Planctomycetes, Firmicutes, Chloroflexi, Actinobacteria, and Acidobacteria). Overall, pasture management affected soil microbial diversity, with greater diversity occurring in organic than non-organic systems, likely owing to applications of organic poultry litter in organic systems compared to non-organic management (use of inorganic-fertilizers and herbicides). Results indicate that when pastures are converted to organic production systems, soil microbial richness and diversity may increase, thereby resulting in enhanced soil microbiome diversity and overall ecosystem services.
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Affiliation(s)
- Mohan Acharya
- Department of Animal Science, University of Arkansas at Fayetteville, Fayetteville, AR, United States of America
| | - Amanda J Ashworth
- Poultry Production and Product Safety Research Unit, United States Department of Agriculture, Agricultural Research Service, Fayetteville, AR, United States of America
| | - Yichao Yang
- Department of Crop, Soil, and Environmental Science, University of Arkansas at Fayetteville, Fayetteville, AR, United States of America
| | - Joan M Burke
- United States Department of Agriculture, Agriculture Research Service, Dale Bumpers Small Farms Research Center, Booneville, AR, United States of America
| | - Jung Ae Lee
- Agriculture Statistics Lab, University of Arkansas at Fayetteville, Fayetteville, AR, United States of America
| | - Roshani Sharma Acharya
- Entomology and Plant Pathology, University of Arkansas at Fayetteville, Fayetteville, AR, United States of America
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40
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Priya P, Aneesh B, Harikrishnan K. Genomics as a potential tool to unravel the rhizosphere microbiome interactions on plant health. J Microbiol Methods 2021; 185:106215. [PMID: 33839214 DOI: 10.1016/j.mimet.2021.106215] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 04/05/2021] [Accepted: 04/06/2021] [Indexed: 12/12/2022]
Abstract
Intense agricultural practices to meet rising food demands have caused ecosystem perturbations. For sustainable crop production, biological agents are gaining attention, but exploring their functional potential on a multi-layered complex ecosystem like the rhizosphere is challenging. This review explains the significance of genomics as a culture-independent molecular tool to understand the diversity and functional significance of the rhizosphere microbiome for sustainable agriculture. It discusses the recent significant studies in the rhizosphere environment carried out using evolving techniques like metagenomics, metatranscriptomics, and metaproteomics, their challenges, constraints infield application, and prospective solutions. The recent advances in techniques such as nanotechnology for the development of bioformulations and visualization techniques contemplating environmental safety were also discussed. The need for development of metagenomic data sets of regionally important crops, their plant microbial interactions and agricultural practices for narrowing down significant data from huge databases have been suggested. The role of taxonomical and functional diversity of soil microbiota in understanding soil suppression and part played by the microbial metabolites in the process have been analyzed and discussed in the context of 'omics' approach. 'Omics' studies have revealed important information about microbial diversity, their responses to various biotic and abiotic stimuli, and the physiology of disease suppression. This can be translated to crop sustainability and combinational approaches with advancing visualization and analysis methodologies fix the existing knowledge gap to a huge extend. With improved data processing and standardization of the methods, details of plant-microbe interactions can be successfully decoded to develop sustainable agricultural practices.
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Affiliation(s)
- P Priya
- Environmental Biology Lab, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India.
| | - B Aneesh
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences Cochin University of Science and Technology, Cochin, Kerala, India.
| | - K Harikrishnan
- Environmental Biology Lab, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India.
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41
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Dang H, Zhang T, Wang Z, Li G, Zhao W, Lv X, Zhuang L. Succession of endophytic fungi and arbuscular mycorrhizal fungi associated with the growth of plant and their correlation with secondary metabolites in the roots of plants. BMC PLANT BIOLOGY 2021; 21:165. [PMID: 33820543 PMCID: PMC8022407 DOI: 10.1186/s12870-021-02942-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/23/2021] [Indexed: 05/03/2023]
Abstract
BACKGROUND To decipher the root and microbial interaction, secondary metabolite accumulation in roots and the microbial community's succession model during the plant's growth period demands an in-depth investigation. However, till now, no comprehensive study is available on the succession of endophytic fungi and arbuscular mycorrhizal fungi (AMF) with roots of medicinal licorice plants and the effects of endophytic fungi and AMF on the secondary metabolite accumulation in licorice plant's root. RESULTS In the current study, interaction between root and microbes in 1-3 years old medicinal licorice plant's root and rhizospheric soil was investigated. Secondary metabolites content in licorice root was determined using high-performance liquid chromatography (HPLC). The composition and diversity of endophytic and AMF in the root and soil were deciphered using high-throughput sequencing technology. During the plant's growth period, as compared to AMF, time and species significantly affected the diversity and richness of endophytic fungi, such as Ascomycota, Basidiomycota, Fusarium, Cladosporium, Sarocladium. The growth period also influenced the AMF diversity, evident by the significant increase in the relative abundance of Glomus and the significant decrease in the relative abundance of Diversispora. It indicated a different succession pattern between the endophytic fungal and AMF communities. Meanwhile, distance-based redundancy analysis and Mantel tests revealed root's water content and secondary metabolites (glycyrrhizic acid, liquiritin, and total flavonoids), which conferred endophytic fungi and AMF diversity. Additionally, plant growth significantly altered soil's physicochemical properties, which influenced the distribution of endophytic fungal and AMF communities. CONCLUSIONS This study indicated a different succession pattern between the endophytic fungal and AMF communities. During the plant's growth period, the contents of three secondary metabolites in roots increased per year, which contributed to the overall differences in composition and distribution of endophytic fungal and AMF communities. The endophytic fungal communities were more sensitive to secondary metabolites than AMF communities. The current study provides novel insights into the interaction between rhizospheric microbes and root exudates.
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Affiliation(s)
- Hanli Dang
- College of life Sciences, Shihezi University, Shihezi City, 832003, Xinjiang, China
| | - Tao Zhang
- College of life Sciences, Shihezi University, Shihezi City, 832003, Xinjiang, China
| | - Zhongke Wang
- College of life Sciences, Shihezi University, Shihezi City, 832003, Xinjiang, China
| | - Guifang Li
- College of life Sciences, Shihezi University, Shihezi City, 832003, Xinjiang, China
| | - Wenqin Zhao
- College of life Sciences, Shihezi University, Shihezi City, 832003, Xinjiang, China
| | - Xinhua Lv
- College of life Sciences, Shihezi University, Shihezi City, 832003, Xinjiang, China
| | - Li Zhuang
- College of life Sciences, Shihezi University, Shihezi City, 832003, Xinjiang, China.
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42
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Liang Y, Pan F, Ma J, Yang Z, Yan P. Long-term forest restoration influences succession patterns of soil bacterial communities. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:20598-20607. [PMID: 33405107 DOI: 10.1007/s11356-020-11849-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 11/25/2020] [Indexed: 06/12/2023]
Abstract
Microorganisms have a major influence on soil biogeochemical processes and vegetation establishment. However, their long-term succession patterns and short-term turnover are not well-understood in artificial forest ecosystems. The aim of the present study was to investigate the effects of stand ages and seasons on soil bacterial community in a chronosequence of Chinese Pinus massoniana plantations, in 3, 19, and 58-year-old plots. Soil physicochemical properties were measured in three stand ages between two seasons (dry-rainy). The soil bacterial community composition was determined by 16S rRNA Illumina HiSeq sequencing. The results showed that soil bacterial community diversity and structure significantly differed among three stand ages, but was not different between two seasons. The diversity of soil bacterial community increased with an increase in stand age. Proteobacteria, Acidobacteria, and Actinobacteria were the dominant phyla in the three stands. The soil bacterial community structure in all the stands was influenced by soil pH, available phosphorus content, and litter phosphorus content. With the accumulation of available phosphorus, the relative abundance of Acidobacteria decreased, while that of Proteobacteria increased. These shifts suggested that dominant microbial communities transitioned from oligotrophic to copiotrophic with increasing stand age. Extending rotation periods could increase soil bacterial diversity, and in turn help improving soil quality of P. massoniana plantations.
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Affiliation(s)
- Yueming Liang
- Key Laboratory of Karst Dynamics, Ministry of Natural and Resources & Guangxi Zhuangzu Autonomy Region, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, 541000, China
| | - Fujing Pan
- College of Environmental and Engineering, Guangxi Key Laboratory of Theory and Technology for Environmental Pollution Control, Guilin University of Technology, Guilin, 541000, China.
| | - Jiangming Ma
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Normal University, Guilin, 541000, China
| | - Zhangqi Yang
- Guangxi Forestry Research Institute, Nanning, 530000, China
| | - Peidong Yan
- Guangxi Forestry Research Institute, Nanning, 530000, China
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43
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Biofuels from Micro-Organisms: Thermodynamic Considerations on the Role of Electrochemical Potential on Micro-Organisms Growth. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11062591] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Biofuels from micro-organisms represents a possible response to the carbon dioxide mitigation. One open problem is to improve their productivity, in terms of biofuels production. To do so, an improvement of the present model of growth and production is required. However, this implies an understanding of the growth spontaneous conditions of the bacteria. In this paper, a thermodynamic approach is developed in order to highlight the fundamental role of the electrochemical potential in bacteria proliferation. Temperature effect on the biosystem behaviour has been pointed out. The results link together the electrochemical potential, the membrane electric potential, the pH gradient through the membrane, and the temperature, with the result of improving the thermodynamic approaches, usually introduced in this topic of research.
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44
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Sweeney CJ, de Vries FT, van Dongen BE, Bardgett RD. Root traits explain rhizosphere fungal community composition among temperate grassland plant species. THE NEW PHYTOLOGIST 2021; 229:1492-1507. [PMID: 33006139 DOI: 10.1111/nph.16976] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 09/17/2020] [Indexed: 05/04/2023]
Abstract
While it is known that interactions between plants and soil fungi drive many essential ecosystem functions, considerable uncertainty exists over the drivers of fungal community composition in the rhizosphere. Here, we examined the roles of plant species identity, phylogeny and functional traits in shaping rhizosphere fungal communities and tested the robustness of these relationships to environmental change. We conducted a glasshouse experiment consisting of 21 temperate grassland species grown under three different environmental treatments and characterised the fungal communities within the rhizosphere of these plants. We found that plant species identity, plant phylogenetic relatedness and plant traits all affected rhizosphere fungal community composition. Trait relationships with fungal communities were primarily driven by interactions with arbuscular mycorrhizal fungi, and root traits were stronger predictors of fungal communities than leaf traits. These patterns were independent of the environmental treatments the plants were grown under. Our results showcase the key role of plant root traits, especially root diameter, root nitrogen and specific root length, in driving rhizosphere fungal community composition, demonstrating the potential for root traits to be used within predictive frameworks of plant-fungal relationships. Furthermore, we highlight how key limitations in our understanding of fungal function may obscure previously unmeasured plant-fungal interactions.
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Affiliation(s)
- Christopher J Sweeney
- Department of Earth and Environmental Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Franciska T de Vries
- Department of Earth and Environmental Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, PO 7 Box 94240, Amsterdam, 1090 GE, the Netherlands
| | - Bart E van Dongen
- Department of Earth and Environmental Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Richard D Bardgett
- Department of Earth and Environmental Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
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45
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Wahdan SFM, Heintz-Buschart A, Sansupa C, Tanunchai B, Wu YT, Schädler M, Noll M, Purahong W, Buscot F. Targeting the Active Rhizosphere Microbiome of Trifolium pratense in Grassland Evidences a Stronger-Than-Expected Belowground Biodiversity-Ecosystem Functioning Link. Front Microbiol 2021; 12:629169. [PMID: 33597941 PMCID: PMC7882529 DOI: 10.3389/fmicb.2021.629169] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/08/2021] [Indexed: 12/14/2022] Open
Abstract
The relationship between biodiversity and ecosystem functioning (BEF) is a central issue in soil and microbial ecology. To date, most belowground BEF studies focus on the diversity of microbes analyzed by barcoding on total DNA, which targets both active and inactive microbes. This approach creates a bias as it mixes the part of the microbiome currently steering processes that provide actual ecosystem functions with the part not directly involved. Using experimental extensive grasslands under current and future climate, we used the bromodeoxyuridine (BrdU) immunocapture technique combined with pair-end Illumina sequencing to characterize both total and active microbiomes (including both bacteria and fungi) in the rhizosphere of Trifolium pratense. Rhizosphere function was assessed by measuring the activity of three microbial extracellular enzymes (β-glucosidase, N-acetyl-glucosaminidase, and acid phosphatase), which play central roles in the C, N, and P acquisition. We showed that the richness of overall and specific functional groups of active microbes in rhizosphere soil significantly correlated with the measured enzyme activities, while total microbial richness did not. Active microbes of the rhizosphere represented 42.8 and 32.1% of the total bacterial and fungal taxa, respectively, and were taxonomically and functionally diverse. Nitrogen fixing bacteria were highly active in this system with 71% of the total operational taxonomic units (OTUs) assigned to this group detected as active. We found the total and active microbiomes to display different responses to variations in soil physicochemical factors in the grassland, but with some degree of resistance to a manipulation mimicking future climate. Our findings provide critical insights into the role of active microbes in defining soil ecosystem functions in a grassland ecosystem. We demonstrate that the relationship between biodiversity-ecosystem functioning in soil may be stronger than previously thought.
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Affiliation(s)
- Sara Fareed Mohamed Wahdan
- Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany.,Department of Biology, Leipzig University, Leipzig, Germany.,Department of Botany, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Anna Heintz-Buschart
- Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Chakriya Sansupa
- Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany
| | - Benjawan Tanunchai
- Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany
| | - Yu-Ting Wu
- Department of Forestry, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Martin Schädler
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Department of Community Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany
| | - Matthias Noll
- Institute for Bioanalysis, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Witoon Purahong
- Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany
| | - François Buscot
- Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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Vermeulen M, Cason ED, Swart WJ. The rhizobiome of herbaceous plants in Clovelly and Sterkspruit soils of the Stevenson–Hamilton supersite. KOEDOE: AFRICAN PROTECTED AREA CONSERVATION AND SCIENCE 2020. [DOI: 10.4102/koedoe.v62i2.1596] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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47
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Shen N, Jing Y, Tu G, Fu A, Lan W. Danger-Associated Peptide Regulates Root Growth by Promoting Protons Extrusion in an AHA2-Dependent Manner in Arabidopsis. Int J Mol Sci 2020; 21:ijms21217963. [PMID: 33120933 PMCID: PMC7663391 DOI: 10.3390/ijms21217963] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/02/2020] [Accepted: 10/12/2020] [Indexed: 11/16/2022] Open
Abstract
Plant elicitor peptides (Peps) are damage/danger-associated molecular patterns (DAMPs) that are derived from precursor proteins PROPEPs and perceived by a pair of leucine-rich repeat receptor-like kinases (LRR-RLKs), PEPR1 and PEPR2, to enhance innate immunity and to inhibit root growth in Arabidopsis thaliana. In this study, we show that Arabidopsis Pep1 inhibits the root growth by interfering with pH signaling, as acidic condition increased, but neutral and alkaline conditions decreased the Pep1 effect on inhibiting the root growth. The perception of Pep1 to PEPRs activated the plasma membrane-localized H+-ATPases (PM H+-ATPases) -the pump proton in plant cell-to extrude the protons into apoplast, and induced an overly acidic environment in apoplastic space, which further promoted the cell swelling in root apex and inhibited root growth. Furthermore, we revealed that pump proton AUTOINHIBITED H+-ATPase 2 (AHA2) physically interacted with PEPR2 and served downstream of the Pep1-PEPRs signaling pathway to regulate Pep1-induced protons extrusion and root growth inhibition. In conclusion, this study demonstrates a previously unrecognized signaling crosstalk between Pep1 and pH signaling to regulate root growth.
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Affiliation(s)
- Nuo Shen
- State Key Laboratory for Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing 210093, China; (N.S.); (G.T.)
| | - Yanping Jing
- College of Life Sciences, Northwest University, Xi’an 710069, China;
| | - Guoqing Tu
- State Key Laboratory for Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing 210093, China; (N.S.); (G.T.)
| | - Aigen Fu
- College of Life Sciences, Northwest University, Xi’an 710069, China;
- Correspondence: (A.F.); (W.L.)
| | - Wenzhi Lan
- State Key Laboratory for Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing 210093, China; (N.S.); (G.T.)
- Correspondence: (A.F.); (W.L.)
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48
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Vaidya BP, Hagmann DF, Balacco J, Passchier S, Krumins JA, Goodey NM. Plants mitigate restrictions to phosphatase activity in metal contaminated soils. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 265:114801. [PMID: 32806404 DOI: 10.1016/j.envpol.2020.114801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 05/09/2020] [Accepted: 05/10/2020] [Indexed: 06/11/2023]
Abstract
Soil anthropogenic contaminants can limit enzymatic nutrient mineralization, either by direct regulation or via impacts on the microbial community, thus affecting plant growth in agricultural and non-agricultural soils. The impact on phosphatase activity of mixing two contaminated, post-industrial rail yard soils was investigated; one was vegetated and had high phosphatase function, the other was barren and had low enzymatic function. The two soils had different abiotic properties, including contaminant load, vegetation cover, soil aggregate size distribution, and phosphatase potential. An experimental gradient was established between the two soils to systematically vary the abiotic properties and microbial community composition of the two soils, creating a gradient of novel ecosystems. The time dependence of extracellular phosphatase activity, soil moisture, and organic matter content was assessed along this gradient in the presence and absence of plants. Initially, mixtures with higher percentages of functional, vegetated soil had higher phosphatase activities. Phosphatase activity remained unchanged through time (65 days) in all soil mixtures in unplanted pots, but it increased in planted pots. For example, in the presence of plants, phosphatase activity increased from 0.6 ± 0.1 to 2.4 ± 0.3 μmol•h-1•gdry soil-1 from day one to day 65 in the 1:1 functional:barren soil mixture. The presence of plants also promoted moisture retention. Inoculation of poorly functioning soil with 10% of the functional soil with its microbial community did not, over 65 days, revitalize the poorly functioning soil. The findings showed that abiotic limitations to enzymatic activity in barren brownfield soils could be mitigated by establishing primary production but not by the addition of enzymatically active microbial communities alone.
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Affiliation(s)
- Bhagyashree P Vaidya
- Department of Earth and Environmental Science, Montclair State University, Montclair, NJ, USA, 07043.
| | - Diane F Hagmann
- Department of Earth and Environmental Science, Montclair State University, Montclair, NJ, USA, 07043.
| | - Jennifer Balacco
- Department of Biology, Montclair State University, Montclair, NJ, USA, 07043.
| | - Sandra Passchier
- Department of Earth and Environmental Science, Montclair State University, Montclair, NJ, USA, 07043.
| | | | - Nina M Goodey
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, NJ, 07043, USA; PSEG Institute of Sustainability Studies, Montclair State University, Montclair, NJ, 07043, USA.
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Lupascu M, Akhtar H, Smith TEL, Sukri RS. Post-fire carbon dynamics in the tropical peat swamp forests of Brunei reveal long-term elevated CH 4 flux. GLOBAL CHANGE BIOLOGY 2020; 26:5125-5145. [PMID: 32475055 DOI: 10.1111/gcb.15195] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 05/19/2020] [Accepted: 05/19/2020] [Indexed: 06/11/2023]
Abstract
Tropical peatlands hold about 15%-19% of the global peat carbon (C) pool of which 77% is stored in the peat swamp forests (PSFs) of Southeast Asia. Nonetheless, these PSFs have been drained, exploited for timber and land for agriculture, leading to frequent fires in the region. The physico-chemical characteristics of peat, as well as the hydrology of PSFs are affected after a fire, during which the ecosystem can act as a C source for decades, as C emissions to the atmosphere exceed photosynthesis. In this work, we studied the longer-term impact of fires on C cycling in tropical PSFs, hence we quantified the magnitude and patterns of C loss (CO2 , CH4 and dissolved organic carbon) and soil-water quality characteristics in an intact and a degraded burnt PSF in Brunei Darussalam affected by seven fires over the last 40 years. We used natural tracers such as 14 C to investigate the age and sources of C contributing to ecosystem respiration (Reco ) and CH4 , while we continuously monitored soil temperature and water table (WT) level from June 2017 to January 2019. Our results showed a major difference in the physico-chemical parameters, which in turn affected C dynamics, especially CH4 . Methane effluxes were higher in fire-affected areas (7.8 ± 2.2 mg CH4 m-2 hr-1 ) compared to the intact PSF (4.0 ± 2.0 mg CH4 m-2 hr-1 ) due to prolonged higher WT and more optimal methanogenesis conditions. On the other hand, we did not find significant differences in Reco between burnt (432 ± 83 mg CO2 m-2 hr-1 ) and intact PSF (359 ± 76 mg CO2 m-2 hr-1 ). Radiocarbon analysis showed overall no significant difference between intact and burnt PSF with a modern signature for both CO2 and CH4 fluxes implying a microbial preference for the more labile C fraction in the peat matrix.
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Affiliation(s)
- Massimo Lupascu
- Department of Geography, National University of Singapore, Singapore, Singapore
- Integrated Tropical Peatland Research Program, NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
| | - Hasan Akhtar
- Department of Geography, National University of Singapore, Singapore, Singapore
| | - Thomas E L Smith
- Department of Geography and Environment, The London School of Economics and Political Science, London, UK
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50
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Cao Y, Zhou B, Wang X, Meng H, Zhang J, Li L, Hong J. Different fertilization treatments in coal mining-affected soils change bacterial populations and enable soil reclamation. ANN MICROBIOL 2020. [DOI: 10.1186/s13213-020-01589-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Purpose
Coal mining activities result in large-scale soil degradation and ecosystem imbalances in many countries. Fertilization is an effective way to improve soil fertility and microbial activity. However, the effect of different fertilizers and remediation time on the subsided soil is not clear. The aim of this study is to explore the effects on soil fertility and the bacterial community.
Methods
In this study, we compared three fertilization regimes (inorganic, organic, and combined) applied over a 5-year period for the purpose of rehabilitating subsoil through measurement of soil’s chemical properties and microbial biomass. Bacterial diversity was evaluated in different reclaimed soils via high-throughput 16S rDNA sequencing; 1,938,561 total sequences were obtained.
Results
The results showed that fertilization improved various soil properties, including the concentrations of available phosphorus, available potassium, and alkali-hydrolysable nitrogen, therefore, increasing microbial biomass. A significant increase in soil microbial diversity was observed in fertilized soils compared to the initial conditions. A positive correlation between microbial diversity and soil properties was observed. Regarding an improvement in soil properties and crop yields, the organic fertilizer demonstrated significantly more effectiveness compared to the inorganic fertilizer. Meanwhile, the relative abundance of Proteobacteria, Bacteroidetes, and Verrucomicrobia increased, but the relative abundance of Chloroflexi and Nitrospirae decreased. More specifically, we found that several Proteobacteria subgroups, such as Rhizobiales, Myxococcales, Sphingomonadales, Rhodospirillales, Xanthomonadales, and Burkholderiales, increased after the restoration. Additionally, the composition of the bacterial community in the 5-year groups (M5, O5, and MO5) was similar to the composition of the FS group, and the yield of the maize test crop following the 5-year restoration period was close to the average in China.
Conclusion
This result indicates that soil reclamation via fertilization can contribute to soil recovery over time. Therefore, we concluded that fertilization is an effective strategy for the restoration of soil properties and bacterial communities in mining soil.
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