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Wu Y, He H, Ren J, Shen H, Sahito ZA, Li B, Tang X, Tao Q, Huang R, Wang C. Assembly patterns and key taxa of bacterial communities in the rhizosphere soil of moso bamboo ( Phyllostachys pubescens) under different Cd and Pb pollution. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2024; 26:1776-1786. [PMID: 38780520 DOI: 10.1080/15226514.2024.2356204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Moso bamboo is excellent candidate for cadmium (Cd)/lead (Pb) phytoremediation, while rhizosphere microbiome has significant impact on phytoremediation efficiency of host plant. However, little is known about the rhizosphere bacterial communities of moso bamboo in Cd/Pb contaminated soils. Therefore, this study investigated the assembly patterns and key taxa of rhizosphere bacterial communities of moso bamboo in Cd/Pb polluted and unpolluted soils, by field sampling, chemical analysis, and 16S rRNA gene sequencing. The results indicated α-diversity between Cd/Pb polluted and unpolluted soils showed a similar pattern (p > 0.05), while β-diversity was significantly different (p < 0.05). The relative abundance analysis indicated α-proteobacteria (37%) and actinobacteria (31%) were dominant in Cd/Pb polluted soils, while γ-proteobacteria (40%) and α-proteobacteria (22%) were dominant in unpolluted soils. Co-occurrence network analysis indicated microbial networks were less complex and more negative in polluted soils than in unpolluted soils. Mantel analysis indicated soil available phosphorus, organic matter, and available Pb were the most important environmental factors affecting microbial community structure. Correlation analysis showed 11 bacterial genera were significantly positively related to Cd/Pb. Overall, this study identified the bacterial community composition of bamboo rhizosphere in responding to Cd/Pb contamination and provides a theoretical basis for microbe-assistant phytoremediation in the future.
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Affiliation(s)
- Yingjie Wu
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Hua He
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Jiayi Ren
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Hongchi Shen
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Zulfiqar Ali Sahito
- College of Environmental and Resource Sciences, Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, Zhejiang University, Hangzhou, China
| | - Bing Li
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Xiaoyan Tang
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Qi Tao
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Rong Huang
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Changquan Wang
- College of Resources, Sichuan Agricultural University, Chengdu, China
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Lai X, Duan W, Zhang W, Peng Z, Wang X, Wang H, Qi X, Pi H, Chen K, Yan L. Integrative analysis of microbiome and metabolome revealed the effect of microbial inoculant on microbial community diversity and function in rhizospheric soil under tobacco monoculture. Microbiol Spectr 2024; 12:e0404623. [PMID: 38989997 PMCID: PMC11302352 DOI: 10.1128/spectrum.04046-23] [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: 11/27/2023] [Accepted: 03/28/2024] [Indexed: 07/12/2024] Open
Abstract
Over-application of chemical fertilizers and continuous cropping obstacles seriously restrict the sustainable development of tobacco production. Localized fertilization of beneficial microbes has potential advantages in achieving higher productivity, but the underlying biological mechanisms of interactions between rhizospheric microorganisms and the related metabolic cycle remain poorly characterized. Here, an integrative analysis of microbiomes with non-targeted metabolomics was performed on 30 soil samples of rhizosphere, root surrounding, and bulk soils from flue-cured tobacco under continuous and non-continuous monocropping systems. The analysis was conducted using UPLC-MS/MS platforms and high-throughput amplicon sequencing targeting the bacterial 16S rRNA gene and fungal ITS gene. The microbial inoculant consisted of Bacillus subtilis, B. velezensis, and B. licheniformis at the ratio of 1:1:1 in effective microbial counts, improved the cured leaf yield and disease resistance of tobacco, and enhanced nicotine and nitrogen contents of tobacco leaves. The bacterial taxa Rhizobium, Pseudomonas, Sphingomonadaceae, and Burkholderiaceae of the phylum Proteobacteria accumulated in high relative abundance and were identified as biomarkers following the application of the microbial inoculant. Under continuous monocropping, metabolomics demonstrated that the application of the microbial inoculant significantly affected the soil metabolite spectrum, and the differential metabolites were significantly enriched to the synthesis and degradation of nicotine (nicotinate and nicotinamide metabolism and biosynthesis of alkaloids derived from nicotinic acid). In addition, microbes were closely related to the accumulation of metabolites through correlation analysis. The interactions between plant roots and rhizospheric microorganisms provide valuable information for understanding how these beneficial microbes affect complex biological processes and the adaption capacity of plants to environments.IMPORTANCEThis study elaborated on how the microbial fertilizer significantly changed overall community structures and metabolite spectrum of rhizospheric microbes, which provide insights into the process of rhizosphere microbial remolding in response to continuous monocropping. we verified the hypothesis that the application of the microbial inoculant in continuous cropping would lead to the selection of distinct microbiota communities by establishing models to correlate biomarkers. Through correlation analysis of the microbiome and metabolome, we proved that rhizospheric microbes were closely related to the accumulation of metabolites, including the synthesis and degradation of nicotine. The interactions between plant roots and rhizospheric microorganisms provide valuable information for understanding how these beneficial microbes affect complex biological processes and the adaption capacity of plants to environments.
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Affiliation(s)
- Xianjun Lai
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, Xichang University, Liangshan, China
| | - Wangjun Duan
- China Tobacco Sichuan Industrial Co. Ltd, Chengdu, China
| | - Wenyou Zhang
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, Xichang University, Liangshan, China
| | - Zhengsong Peng
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, Xichang University, Liangshan, China
| | - Xianjun Wang
- China Tobacco Sichuan Industrial Co. Ltd, Chengdu, China
| | - Haiyan Wang
- Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiaobo Qi
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, Xichang University, Liangshan, China
| | - Huaqiang Pi
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, Xichang University, Liangshan, China
| | - Kailu Chen
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, Xichang University, Liangshan, China
| | - Lang Yan
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, Xichang University, Liangshan, China
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Un Jan Contreras S, Redfern LK, Maguire LW, Promi SI, Gardner CM. Small Interfering RNAs (siRNAs) Negatively Impact Growth and Gene Expression of Environmentally Relevant Bacteria in In Vitro Conditions. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:13856-13865. [PMID: 39066708 DOI: 10.1021/acs.est.4c01685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Rising global populations have amplified food scarcity and ushered in the development of genetically modified (GM) crops containing small interference RNAs (siRNAs) that control gene expression to overcome these challenges. The use of RNA interference (RNAi) in agriculture remains controversial due to uncertainty regarding the unintended release of genetic material and downstream nontarget effects, which have not been assessed in environmental bacteria to date. To evaluate the impacts of siRNAs used in agriculture on environmental bacteria, this study assessed microbial growth and viability as well as transcription activity with and without the presence of environmental stressors. Results showed a statistically significant reduction in growth capacity and maximum biomass achieved when bacteria are exposed to siRNAs alone and with additional external stress (p < 0.05). Further transcriptomic analysis demonstrated that nutrient cycling gene activities were found to be consistently and significantly altered following siRNA exposure, particularly among carbon (xylA, FBPase, limEH, Chitinase, rgl, rgh, rgaE, mannanase, ara) and nitrogen (ureC, nasA, narB, narG, nirK) cycling genes (p < 0.05). Decreases in carbon cycling gene transcription profiles were generally significantly enhanced when siRNA exposure was coupled with nutrient or antimicrobial stress. Collectively, findings suggest that certain conditions facilitate the uptake of siRNAs from their surrounding environments that can negatively affect bacterial growth and gene expression activity, with uncertain downstream impacts on ecosystem homeostasis.
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Affiliation(s)
- S Un Jan Contreras
- Department of Civil and Environmental Engineering, Washington State University, 405 Spokane St., Pullman, Washington 99164, United States
| | - L K Redfern
- Department of Bioengineering, Civil Engineering, and Environmental Engineering, Florida Gulf Coast University, 10501 FGCU Blvd., Fort Myers, Florida 33965, United States
| | - L W Maguire
- Maseeh Department of Civil, Architectural, and Environmental Engineering, University of Texas at Austin, 301E E Dean Keeton St c1700, Austin, Texas 78712, United States
| | - S I Promi
- Maseeh Department of Civil, Architectural, and Environmental Engineering, University of Texas at Austin, 301E E Dean Keeton St c1700, Austin, Texas 78712, United States
| | - C M Gardner
- Department of Civil and Environmental Engineering, Washington State University, 405 Spokane St., Pullman, Washington 99164, United States
- Maseeh Department of Civil, Architectural, and Environmental Engineering, University of Texas at Austin, 301E E Dean Keeton St c1700, Austin, Texas 78712, United States
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Tian K, Chen S, Ye R, Xie Y, Yao L, Lin H. Initial microbiome and tree root status structured the soil microbial community discrepancy of the subtropical pine-oak forest in a large urban forest park. Front Microbiol 2024; 15:1391863. [PMID: 38881652 PMCID: PMC11176443 DOI: 10.3389/fmicb.2024.1391863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 05/06/2024] [Indexed: 06/18/2024] Open
Abstract
Plant-microbe-soil interactions control over the forest biogeochemical cycling. Adaptive plant-soil interactions can shape specific microbial taxa in determining the ecosystem functioning. Different trees produce heterogeneous soil properties and can alter the composition of soil microbial community, which is relevant to the forest internal succession containing contrasting stand types such as the pine-oak forests. Considering representative microbial community characteristics are recorded in the original soil where they had adapted and resided, we constructed a soil transplant incubation experiment in a series of in situ root-ingrowth cores in a subtropical pine-oak forest, to simulate the vegetational pine-oak replacement under environmental succession. The responsive bacterial and fungal community discrepancies were studied to determine whether and how they would be changed. The pine and oak forest stands had greater heterogeneity in fungi composition than bacteria. Original soil and specific tree root status were the main factors that determined microbial community structure. Internal association network characters and intergroup variations of fungi among soil samples were more affected by original soil, while bacteria were more affected by receiving forest. Specifically, dominant tree roots had strong influence in accelerating the fungi community succession to adapt with the surrounding forest. We concluded that soil microbial responses to forest stand alternation differed between microbiome groups, with fungi from their original forest possessing higher resistance to encounter a new vegetation stand, while the bacteria community have faster resilience. The data would advance our insight into local soil microbial community dynamics during ecosystem succession and be helpful to enlighten forest management.
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Affiliation(s)
- Kai Tian
- Henan Field Observation and Research Station of Headwork Wetland Ecosystem of the Central Route of South-to-North Water Diversion Project, School of Life Sciences and Agricultural Engineering, Nanyang Normal University, Nanyang, China
| | - Shaoming Chen
- Henan Field Observation and Research Station of Headwork Wetland Ecosystem of the Central Route of South-to-North Water Diversion Project, School of Life Sciences and Agricultural Engineering, Nanyang Normal University, Nanyang, China
| | - Rumeng Ye
- Henan Field Observation and Research Station of Headwork Wetland Ecosystem of the Central Route of South-to-North Water Diversion Project, School of Life Sciences and Agricultural Engineering, Nanyang Normal University, Nanyang, China
| | - Yanghe Xie
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Lunguang Yao
- Henan Field Observation and Research Station of Headwork Wetland Ecosystem of the Central Route of South-to-North Water Diversion Project, School of Life Sciences and Agricultural Engineering, Nanyang Normal University, Nanyang, China
| | - Hong Lin
- School of Food Science, Institute of Applied Ecology, Nanjing Xiaozhuang University, Nanjing, China
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Kural-Rendon C, Ford NE, Wagner MR. Interactions with fungi vary among Tripsacum dactyloides genotypes from across a precipitation gradient. AOB PLANTS 2023; 15:plad072. [PMID: 38028745 PMCID: PMC10667659 DOI: 10.1093/aobpla/plad072] [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: 04/18/2023] [Accepted: 11/01/2023] [Indexed: 12/01/2023]
Abstract
Plant-associated microbes, specifically fungal endophytes, augment the ability of many grasses to adapt to extreme environmental conditions. Tripsacum dactyloides (Eastern gamagrass) is a perennial, drought-tolerant grass native to the tallgrass prairies of the central USA. The extent to which the microbiome of T. dactyloides contributes to its drought tolerance is unknown. Ninety-seven genotypes of T. dactyloides were collected from native populations across an east-west precipitation gradient in Kansas, Oklahoma and Texas, and then grown together in a common garden for over 20 years. Root and leaf samples were visually examined for fungal density. Because fungal endophytes confer drought-tolerant capabilities to their host plants, we expected to find higher densities of fungal endophytes in plants from western, drier regions, compared to plants from eastern, wetter regions. Results confirmed a negative correlation between endophyte densities in roots and precipitation at the genotype's original location (r = -0.21 P = 0.04). Our analyses reveal that the host genotype's origin along the precipitation gradient predicts the absolute abundance of symbionts in the root, but not the relative abundances of particular organisms or the overall community composition. Overall, these results demonstrate that genetic variation for plant-microbe interactions can reflect historical environment, and reinforce the importance of considering plant genotype in conservation and restoration work in tallgrass prairie ecosystems.
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Affiliation(s)
- Ceyda Kural-Rendon
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
| | - Natalie E Ford
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, KS 66045, USA
| | - Maggie R Wagner
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
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Yuan M, Zhang D, Wang Z, Zhu Z, Sun H, Wang W, Han D, Qu Z, Ma B, Wang J, Wang L, Han D. Salt altered rhizosphere fungal community and induced soybean recruit specific species to ameliorate salt stress. Front Microbiol 2023; 14:1142780. [PMID: 37260678 PMCID: PMC10227517 DOI: 10.3389/fmicb.2023.1142780] [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: 01/12/2023] [Accepted: 01/26/2023] [Indexed: 06/02/2023] Open
Abstract
Different crop genotypes showed different adaptability to salt stress, which is partly attributable to the microorganisms in the rhizosphere. Yet, knowledge about how fungal communities of different genotypes in soybean respond to salt stress is limited. Here, qPCR and ITS sequencing were used to assess the response of rhizobial fungal communities of resistant and susceptible soybean to salt stress. Moreover, we isolated two fungal species recruited by resistant soybeans for validation. The assembly of fungal community structure might be strongly linked to alterations in fungal abundance and soil physicochemical properties. Salt stress derived structural differences in fungal communities of resistant and susceptible genotypes. The salt-resistant genotype appeared to recruit some fungal taxa to the rhizosphere to help mitigating salt stress. An increase of fungal taxa with predicted saprotrophic lifestyles might help promoting plant growth by increasing nutrient availability to the plants. Compared with the susceptible genotypes, the resistant genotypes had more stronger network structure of fungi. Lastly, we verified that recruited fungi, such as Penicillium and Aspergillus, can soybean adapt to salt stress. This study provided a promising approach for rhizospheric fungal community to enhance salt tolerance of soybean from the perspective of microbiology and ecology.
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Affiliation(s)
- Ming Yuan
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Di Zhang
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Zhen Wang
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Zhijia Zhu
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Haoyue Sun
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Wei Wang
- Institute of Soil Fertilizer and Environmental Resources, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Dezhi Han
- Heihe Branch of Heilongjiang Academy of Agricultural Sciences, Heihe, China
| | - Zhongcheng Qu
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Bo Ma
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Junqiang Wang
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Lianxia Wang
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Dongwei Han
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
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Mandakovic D, Aguado-Norese C, García-Jiménez B, Hodar C, Maldonado JE, Gaete A, Latorre M, Wilkinson MD, Gutiérrez RA, Cavieres LA, Medina J, Cambiazo V, Gonzalez M. Testing the stress gradient hypothesis in soil bacterial communities associated with vegetation belts in the Andean Atacama Desert. ENVIRONMENTAL MICROBIOME 2023; 18:24. [PMID: 36978149 PMCID: PMC10052861 DOI: 10.1186/s40793-023-00486-w] [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: 11/15/2022] [Accepted: 03/20/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Soil microorganisms are in constant interaction with plants, and these interactions shape the composition of soil bacterial communities by modifying their environment. However, little is known about the relationship between microorganisms and native plants present in extreme environments that are not affected by human intervention. Using high-throughput sequencing in combination with random forest and co-occurrence network analyses, we compared soil bacterial communities inhabiting the rhizosphere surrounding soil (RSS) and the corresponding bulk soil (BS) of 21 native plant species organized into three vegetation belts along the altitudinal gradient (2400-4500 m a.s.l.) of the Talabre-Lejía transect (TLT) in the slopes of the Andes in the Atacama Desert. We assessed how each plant community influenced the taxa, potential functions, and ecological interactions of the soil bacterial communities in this extreme natural ecosystem. We tested the ability of the stress gradient hypothesis, which predicts that positive species interactions become increasingly important as stressful conditions increase, to explain the interactions among members of TLT soil microbial communities. RESULTS Our comparison of RSS and BS compartments along the TLT provided evidence of plant-specific microbial community composition in the RSS and showed that bacterial communities modify their ecological interactions, in particular, their positive:negative connection ratios in the presence of plant roots at each vegetation belt. We also identified the taxa driving the transition of the BS to the RSS, which appear to be indicators of key host-microbial relationships in the rhizosphere of plants in response to different abiotic conditions. Finally, the potential functions of the bacterial communities also diverge between the BS and the RSS compartments, particularly in the extreme and harshest belts of the TLT. CONCLUSIONS In this study, we identified taxa of bacterial communities that establish species-specific relationships with native plants and showed that over a gradient of changing abiotic conditions, these relationships may also be plant community specific. These findings also reveal that the interactions among members of the soil microbial communities do not support the stress gradient hypothesis. However, through the RSS compartment, each plant community appears to moderate the abiotic stress gradient and increase the efficiency of the soil microbial community, suggesting that positive interactions may be context dependent.
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Affiliation(s)
- Dinka Mandakovic
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Santiago, Chile
- GEMA Center for Genomics, Ecology and Environment, Universidad Mayor, Santiago, Chile
| | - Constanza Aguado-Norese
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Santiago, Chile
| | - Beatriz García-Jiménez
- Center for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid (UPM)/Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)-CSIC, Madrid, Spain
- Present Address: Biome Makers Inc., West Sacramento, CA USA
| | - Christian Hodar
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Santiago, Chile
| | - Jonathan E. Maldonado
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Santiago, Chile
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, 9170022 Santiago, Chile
| | - Alexis Gaete
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Santiago, Chile
| | - Mauricio Latorre
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Laboratorio de Bioingeniería, Instituto de Ciencias de La Ingeniería, Universidad de O’Higgins, Rancagua, Chile
| | - Mark D. Wilkinson
- Center for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid (UPM)/Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)-CSIC, Madrid, Spain
| | - Rodrigo A. Gutiérrez
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Instituto de Biología Integrativa, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Lohengrin A. Cavieres
- Instituto de Ecología y Biodiversidad (IEB), 4070386 Concepción, Chile
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, 4070386 Concepción, Chile
| | - Joaquín Medina
- Center for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid (UPM)/Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)-CSIC, Madrid, Spain
| | - Verónica Cambiazo
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Santiago, Chile
| | - Mauricio Gonzalez
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Santiago, Chile
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Pham DN, Wu Q, Li M. Global profiling of antibiotic resistomes in maize rhizospheres. Arch Microbiol 2023; 205:89. [PMID: 36781495 DOI: 10.1007/s00203-023-03424-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/13/2023] [Accepted: 01/24/2023] [Indexed: 02/15/2023]
Abstract
The spreading of antimicrobial resistance (AMR) in crops and food products represents a global concern. In this study, we conducted a survey of resistomes in maize rhizosphere from Michigan, California, the Netherlands, and South Africa, and investigated potential associations with host bacteria and soil management practices in the crop field. For comparison, relative abundance of antibiotic resistance genes (ARGs) is normalized to the size of individual metagenomes. Michigan maize rhizosphere metagenomes showed the highest abundance and diversity of ARGs, with the detection of blaTEM-116, blaACT-4/-6, and FosA2, exhibiting high similarity (≥ 99.0%) to those in animal and human pathogens. This was probably related to the decade-long application of manure/composted manure from antibiotic-treated animals. Moreover, RbpA, vanRO, mtrA, and dfrB were prevalently found across most studied regions, implying their intrinsic origins. Further analysis revealed that RbpA, vanRO, and mtrA are mainly harbored by native Actinobacteria with low mobility since mobile genetic elements were rarely found in their flanking regions. Notably, a group of dfrB genes are adjacent to the recombination binding sites (attC), which together constitute mobile gene cassettes, promoting the transmission from soil bacteria to human pathogens. These results suggest that maize rhizosphere resistomes can be distinctive and affected by many factors, particularly those relevant to agricultural practices.
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Affiliation(s)
- Dung Ngoc Pham
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Qiong Wu
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Mengyan Li
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ, 07102, USA.
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May-Mutul CG, López-Garrido MA, O’Connor-Sánchez A, Peña-Ramírez YJ, Labrín-Sotomayor NY, Estrada-Medina H, Ferrer MM. Hidden Tenants: Microbiota of the Rhizosphere and Phyllosphere of Cordia dodecandra Trees in Mayan Forests and Homegardens. PLANTS (BASEL, SWITZERLAND) 2022; 11:3098. [PMID: 36432829 PMCID: PMC9699097 DOI: 10.3390/plants11223098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/01/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
During domestication, the selection of cultivated plants often reduces microbiota diversity compared with their wild ancestors. Microbiota in compartments such as the phyllosphere or rhizosphere can promote fruit tree health, growth, and development. Cordia dodecandra is a deciduous tree used by Maya people for its fruit and wood, growing, to date, in remnant forest fragments and homegardens (traditional agroforestry systems) in Yucatán. In this work, we evaluated the microbiota's alpha and beta diversity per compartment (phyllosphere and rhizosphere) and per population (forest and homegarden) in the Northeast and Southwest Yucatán regions. Eight composite DNA samples (per compartment/population/region combination) were amplified for 16S-RNA (bacteria) and ITS1-2 (fungi) and sequenced by Illumina MiSeq. Bioinformatic analyses were performed with QIIME and phyloseq. For bacteria and fungi, from 107,947 and 128,786 assembled sequences, 618 and 1092 operating taxonomic units (OTUs) were assigned, respectively. The alpha diversity of bacteria and fungi was highly variable among samples and was similar among compartments and populations. A significant species turnover among populations and regions was observed in the rhizosphere. The core microbiota from the phyllosphere was similar among populations and regions. Forests and homegarden populations are reservoirs of the C. dodecandra phyllosphere core microbiome and significant rhizosphere biodiversity.
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Affiliation(s)
- Carla G. May-Mutul
- Departamento de Manejo y Conservación de Recursos Naturales Tropicales, Universidad Autónoma de Yucatán, Mérida 97313, Mexico
| | - Miguel A. López-Garrido
- Departamento de Manejo y Conservación de Recursos Naturales Tropicales, Universidad Autónoma de Yucatán, Mérida 97313, Mexico
| | - Aileen O’Connor-Sánchez
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida 97205, Mexico
| | - Yuri J. Peña-Ramírez
- Departamento de Ciencias de la Sustentabilidad, El Colegio de la Frontera Sur Unidad Campeche, Lerma 24500, Mexico
| | - Natalia Y. Labrín-Sotomayor
- Departamento de Ciencias de la Sustentabilidad, El Colegio de la Frontera Sur Unidad Campeche, Lerma 24500, Mexico
| | - Héctor Estrada-Medina
- Departamento de Manejo y Conservación de Recursos Naturales Tropicales, Universidad Autónoma de Yucatán, Mérida 97313, Mexico
| | - Miriam M. Ferrer
- Departamento de Manejo y Conservación de Recursos Naturales Tropicales, Universidad Autónoma de Yucatán, Mérida 97313, Mexico
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Chen J, Li F, Zhao X, Wang Y, Zhang L, Yan L, Yu L. Change in composition and potential functional genes of microbial communities on carbonatite rinds with different weathering times. Front Microbiol 2022; 13:1024672. [PMID: 36386643 PMCID: PMC9663929 DOI: 10.3389/fmicb.2022.1024672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/04/2022] [Indexed: 11/26/2022] Open
Abstract
Organisms and time are important factors for rock weathering to form soils. However, weathering time is usually difficult to quantitatively study, and the potential microorganisms involved in rock weathering are difficult to identify qualitatively. Currently, there is no clear conclusion on how ecological strategies of carbonatite weathering rind microorganisms change with weathering time, and how the microbial composition and functional genes involved in element cycling change over two century-scale weathering time. In this study, we selected abandoned carbonate tombstones as the subject and used the date when the tombstones were erected by humans as the onset of weathering. Using metagenome sequencing methods, we investigated the trends in the composition of fungal, bacterial and archaeal communities of carbonate weathering rind and related elemental cycle functional genes during a weathering time of 19 to 213 years. The results showed that: (1) with the increase in weathering time, at the phylum level, microbial taxa gradually shifted from r-strategists (faster turnover rates, higher mortality rates, higher reproduction, lower competition rate) to K-strategists (slower turnover rates, lower mortality rates, lower reproduction, higher competition rate), which correspondingly increased the abundance of functional genes related to C and N cycles. (2) The properties of the parent rock layer determines the colonization and distribution of weathering rind microorganisms (especially prokaryotic microorganisms) and the corresponding functional gene abundance. Our study provides new insights into the weathering process of carbonate rocks.
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Affiliation(s)
- Jin Chen
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences and Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou,China
| | - Fangbing Li
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences and Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou,China
| | - Xiangwei Zhao
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences and Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou,China
| | - Yang Wang
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences and Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou,China
| | - Limin Zhang
- Institute of Guizhou Mountain Resources, Guizhou Academy of Sciences, Guiyang, Guizhou, China
| | - Lingbin Yan
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences and Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou,China
| | - Lifei Yu
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences and Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou,China
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11
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Wang Y, Zhang M, Li S, Li P, Lang Z. Effects of Insect-Resistant Maize HGK60 on Community Diversity of Bacteria and Fungi in Rhizosphere Soil. PLANTS (BASEL, SWITZERLAND) 2022; 11:2824. [PMID: 36365278 PMCID: PMC9653938 DOI: 10.3390/plants11212824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/08/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
The influence of biotech crops on microbial communities in rhizosphere soil is an important issue in biosafety assessments. The transgenic maize HGK60 harboring the Bt cry1Ah gene enhanced the resistance to lepidopteran pests, while the ecological risk of HGK60 maize on rhizosphere microorganisms is unclear. In this study, we comprehensively analyzed the diversity and composition of bacterial and fungal communities in the rhizosphere soil around Bt maize HGK60 and the near-isogenic non-Bt maize ZD958 at four growth stages via a high-throughput sequencing technique. The results showed that HGK60 maize unleashed temporary effects on the bacterial and fungal diversity and richness during the study plant's development, which would be restored after one cycle of plant cultivation due to the application of the same agricultural management. The differences of bacterial and fungal communities were marked by seasonality, while the different growth stage was the important factor as opposed to the cultivar contributing to the shifts in the bacterial and fungal communities' structure. This study will provide useful information regarding the impact of Bt transgenic maize on the soil microbiome and a theoretical basis for the development of a safety assessment approach for Bt maize in China.
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Affiliation(s)
| | | | | | | | - Zhihong Lang
- Correspondence: ; Tel.: +86-10-82109842; Fax: +86-10-82106142
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12
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Wang Y, He Y, Ding M, Wang Z, Zhou S. Influence of Rosaceous Species and Driving Factors on Differentiation of Rhizospheric Bacteria in a Deciduous Broad-Leaved Forest. Curr Microbiol 2022; 79:368. [PMID: 36253615 DOI: 10.1007/s00284-022-03049-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 09/20/2022] [Indexed: 11/26/2022]
Abstract
Understanding plant-microbe interactions could provide the basis for improved phytoremediation, microbial resource utilization, and secondary metabolite production. Rhizosphere bacterial communities are strongly influenced by abiotic factors such as soil nutrient availability and the composition of such communities exhibits differentiation under different host plants. In a deciduous broad-leaved forest in Anhui Province, eastern China, the rhizospheric bacteria of three different tree species of the Rosaceae family (Sorbus alnifolia, Cerasus serrulata, and Photinia beauverdiana) were studied, with the bacteria of the bulk soil as controls. Bacterial community composition was determined using the Illumina platform for high-throughput sequencing of 16S rRNA genes. The results showed that the bacterial community composition varied between rhizospheric and bulk soils, and dominant bacterial phyla as Proteobacteria, Actinobacteria, and Acidobacteria were found in both soils. Information on predicted functional genes and pathways revealed significant differences between rhizospheric and bulk soil bacteria. It provided ample evidence for the different metabolic characteristics of the rhizosphere bacterial communities of the three tree species. Electrical conductivity (22.72%), total phosphorus concentration (21.89%), and urease activity (22%) were the main drivers for changes in the composition of the rhizosphere bacterial communities from the three tree species.
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Affiliation(s)
- Yukun Wang
- School of Ecology and Environment, Anhui Normal University, 189# South Jiuhua Road, Yijiang District, Wuhu, 241002, China
| | - Yuran He
- School of Ecology and Environment, Anhui Normal University, 189# South Jiuhua Road, Yijiang District, Wuhu, 241002, China
| | - Mao Ding
- School of Ecology and Environment, Anhui Normal University, 189# South Jiuhua Road, Yijiang District, Wuhu, 241002, China
| | - Zhi Wang
- Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection of the People's Republic of China, Nanjing, 210042, China
| | - Shoubiao Zhou
- School of Ecology and Environment, Anhui Normal University, 189# South Jiuhua Road, Yijiang District, Wuhu, 241002, China.
- Anhui Provincial Engineering Laboratory of Water and Soil Pollution Control and Remediation, Anhui Normal University, Wuhu, 241002, China.
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13
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Tao L, Zhang C, Ying Z, Xiong Z, Vaisman HS, Wang C, Shi Z, Shi R. Long-term continuous mono-cropping of Macadamia integrifolia greatly affects soil physicochemical properties, rhizospheric bacterial diversity, and metabolite contents. Front Microbiol 2022; 13:952092. [PMID: 36274682 PMCID: PMC9582743 DOI: 10.3389/fmicb.2022.952092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
Macadamia integrifolia is the most economically important Proteaceae crop known for its edible nuts. The present study was conducted to examine the effect of continuous cultivation (for 1, 5, and 20 years) of M. integrifolia on soil quality, bacterial diversity, and metabolites. Soil rhizospheres from three different Macadamia rhizosphere orchards, 1-year monoculture orchard (CK), 5-year monoculture orchard (Y5), and 20-year monoculture orchard (Y20), were analyzed through metagenomic and metabolomic profiling. The soil physicochemical properties, including organic matter, and available nutrients (P, N, and K) were first increased significantly (p < 0.05) from the CK to the Y5 group and then decreased (p < 0.05) from the Y5 to the Y20 group. The soil pH continuously decreased (p < 0.05) over time from CK to Y20. Metagenomic profiling revealed that Actinobacteria, Acidobacteria, and Proteobacteria were the top three abundant phyla with their inconsistent relative abundance patterns from CK to Y20 (CK: 23.76%, Y5: 34. 06%, and Y20: 31.55%), (CK: 13.59%, Y5: 18.59%, and Y20: 21.35%), and (CK: 27.59%, Y5: 15.98%, and Y20: 17.08%), respectively. Furthermore, the Y5 rhizospheres had a higher number of beneficial bacterial genera belonging to Proteobacteria and Actinobacteria than the Y20 rhizospheres. The KEGG annotation analysis revealed that cellular processes, organism systems, metabolism, and genetic information were the most enriched functional categories. CAZy database screening indicated the highest enrichment of glycoside hydrolases following the glycoside transferases and carbohydrate-binding modules. Differential metabolite analysis revealed the highest number of metabolites (11) in the Y5 group than in the Y20 group (6). It is concluded that continuous monoculture of M. integrifolia improves the soil physicochemical properties, bacterial diversity, and metabolite contents in short-term planted orchards which, however, are deteriorated in long-term planted orchards.
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Affiliation(s)
- Liang Tao
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Landscape Architecture Engineering Research Center of National Forestry and Grassland Administration, Southwest Forestry University, Kunming, Yunnan, China
| | - Chunsheng Zhang
- Office of Academic Affairs, Yunnan University of Finance and Economics, Kunming, Yunnan, China
| | - Zhiping Ying
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Landscape Architecture Engineering Research Center of National Forestry and Grassland Administration, Southwest Forestry University, Kunming, Yunnan, China
| | - Zhi Xiong
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Landscape Architecture Engineering Research Center of National Forestry and Grassland Administration, Southwest Forestry University, Kunming, Yunnan, China
| | | | - Changming Wang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Landscape Architecture Engineering Research Center of National Forestry and Grassland Administration, Southwest Forestry University, Kunming, Yunnan, China
- *Correspondence: Changming Wang,
| | - Zhuogong Shi
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Landscape Architecture Engineering Research Center of National Forestry and Grassland Administration, Southwest Forestry University, Kunming, Yunnan, China
- Zhuogong Shi,
| | - Rui Shi
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Landscape Architecture Engineering Research Center of National Forestry and Grassland Administration, Southwest Forestry University, Kunming, Yunnan, China
- Rui Shi,
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Drinkwater LE, Snapp SS. Advancing the science and practice of ecological nutrient management for smallholder farmers. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.921216] [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
Soil degradation is widespread in smallholder agrarian communities across the globe where limited resource farmers struggle to overcome poverty and malnutrition. This review lays out the scientific basis and practical management options for an ecologically based approach to sustainably managing soil fertility, with particular attention to smallholder subsistence systems. We seek to change the trajectory of development programs that continue to promote inorganic fertilizers and other high input strategies to resource constrained smallholders, despite ample evidence that this approach is falling short of food security goals and contributing to resource degradation. Ecological nutrient management (ENM) is an agroecological approach to managing the biogeochemical cycles that govern soil ecosystem services and soil fertility. The portfolio of ENM strategies extends beyond reliance on inorganic fertilizers and is guided by the following five principles: (1) Build soil organic matter and other nutrient reserves. (2) Minimize the size of N and P pools that are the most susceptible to loss. (3) Maximize agroecosystem capacity to use soluble, inorganic N and P. (4) Use functional and phylogenetic biodiversity to minimize bare fallows and maximize presence of growing plants. (5) Construct agroecosystem and field scale mass balances to track net nutrient flows over multiple growing seasons. Strategic increases in spatial and temporal plant species diversity is a core ENM tactic that expands agroecosystem multifunctionality to meet smallholder priorities beyond soil restoration and crop yields. Examples of ENM practices include the use of functionally designed polycultures, diversified rotations, reduced fallow periods, increased reliance on legumes, integrated crop-livestock production, and use of variety of soil amendments. These practices foster soil organic matter accrual and restoration of soil function, both of which underpin agroecosystem resilience. When ENM is first implemented, short-term yield outcomes are variable; however, over the long-term, management systems that employ ENM can increase yields, yield stability, profitability and food security. ENM rests on a solid foundation of ecosystem and biogeochemical science, and despite the many barriers imposed by current agricultural policies, successful ENM systems are being promoted by some development actors and used by smallholder farmers, with promising results.
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15
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Finn DR, App M, Hertzog L, Tebbe CC. Reconciling concepts of black queen and tragedy of the commons in simulated bulk soil and rhizosphere prokaryote communities. Front Microbiol 2022; 13:969784. [PMID: 36187971 PMCID: PMC9520196 DOI: 10.3389/fmicb.2022.969784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
The Black Queen hypothesis describes the evolutionary strategy to lose costly functions in favour of improving growth efficiency. This results in mutants (cheaters) becoming obligately dependent upon a provider (black queen) to produce a necessary resource. Previous analyses demonstrate black queens and cheaters reach a state of equilibrium in pair-wise systems. However, in complex communities, accumulation of cheaters likely poses a serious burden on shared resources. This should result in a Tragedy of the Commons (ToC), whereby over-utilisation of public resources risks making them growth-limiting. With a collection of differential equations, microbial communities composed of twenty prokaryote ‘species’ either from rhizosphere, characterised by abundant carbon and energy sources, or bulk soil, with limited carbon and energy supply, were simulated. Functional trait groups differed based on combinations of cellulase and amino acid production, growth and resource uptake. Randomly generated communities were thus composed of species that acted as cellulolytic prototrophic black queens, groups that were either cellulolytic or prototrophic, or non-cellulolytic auxotrophic cheaters. Groups could evolve to lose functions over time. Biomass production and biodiversity were tracked in 8,000 Monte Carlo simulations over 500 generations. Bulk soil favoured oligotrophic co-operative communities where biodiversity was positively associated with growth. Rhizosphere favoured copiotrophic cheaters. The most successful functional group across both environments was neither black queens nor cheaters, but those that balanced providing an essential growth-limiting function at a relatively low maintenance cost. Accumulation of loss of function mutants in bulk soil risked resulting in loss of cumulative growth by ToC, while cumulative growth increased in the rhizosphere. In the bulk soil, oligotrophic adaptations assisted species in avoiding extinction. This demonstrated that loss of function by mutation is a successful evolutionary strategy in host-associated and/or resource-rich environments, but poses a risk to communities that must co-operate with each other for mutual co-existence. It was concluded that microbial communities must follow different evolutionary and community assembly strategies in bulk soil versus rhizosphere, with bulk soil communities more dependent on traits that promote co-operative interactions between microbial species.
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16
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Dubey A, Malla MA, Kumar A. Taxonomical and functional bacterial community profiling in disease-resistant and disease-susceptible soybean cultivars. Braz J Microbiol 2022; 53:1355-1370. [PMID: 35415800 PMCID: PMC9433584 DOI: 10.1007/s42770-022-00746-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 03/28/2022] [Indexed: 12/13/2022] Open
Abstract
Highly varied bacterial communities inhabiting the soybean rhizosphere perform important roles in its growth and production; nevertheless, little is known about the changes that occur in these communities under disease-stress conditions. The present study investigated the bacterial diversity and their metabolic profile in the rhizosphere of disease-resistant (JS-20-34) and disease-susceptible (JS-335) soybean (Glycine max (L.) Merr.) cultivars using 16S rRNA amplicon sequencing and community-level physiological profiling (CLPP). In disease-resistant soybean (AKADR) samples, the most dominating phyla were Actinobacteria (40%) followed by Chloroflexi (24%), Proteobacteria (20%), and Firmicutes (12%), while in the disease-susceptible (AKADS) sample, the most dominating phyla were Proteobacteria (35%) followed by Actinobacteria (27%) and Bacteroidetes (17%). Functional profiling of bacterial communities was done using the METAGENassist, and PICRUSt2 software, which shows that AKADR samples have more ammonifying, chitin degrading, nitrogen-fixing, and nitrite reducing bacteria compared to AKADS rhizosphere samples. The bacterial communities present in disease-resistant samples were significantly enriched with genes involved in nitrogen fixation, carbon fixation, ammonification, denitrification, and antibiotic production. Furthermore, the CLPP results show that carbohydrates and carboxylic acids were the most frequently utilized nutrients by the microbes. The principal component analysis (PCA) revealed that the AKADR soils had higher functional activity (strong association with the Shannon-Wiener index, richness index, and hydrocarbon consumption) than AKADS rhizospheric soils. Overall, our findings suggested that the rhizosphere of resistant varieties of soybean comprises of beneficial bacterial population over susceptible varieties.
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Affiliation(s)
- Anamika Dubey
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar, 470003, Madhya Pradesh, India
| | - Muneer Ahmad Malla
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar, 470003, Madhya Pradesh, India
- Department of Zoology, Dr. Harisingh Gour University (A Central University), Sagar, 470003, Madhya Pradesh, India
| | - Ashwani Kumar
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar, 470003, Madhya Pradesh, India.
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17
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Zhao YH, Wang N, Yu MK, Yu JG, Xue LH. Rhizosphere and Straw Return Interactively Shape Rhizosphere Bacterial Community Composition and Nitrogen Cycling in Paddy Soil. Front Microbiol 2022; 13:945927. [PMID: 35875526 PMCID: PMC9301285 DOI: 10.3389/fmicb.2022.945927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/13/2022] [Indexed: 11/17/2022] Open
Abstract
Currently, how rice roots interact with straw return in structuring rhizosphere communities and nitrogen (N) cycling functions is relatively unexplored. In this study, paddy soil was amended with wheat straw at 1 and 2% w/w and used for rice growth. The effects of the rhizosphere, straw, and their interaction on soil bacterial community composition and N-cycling gene abundances were assessed at the rice maturity stage. For the soil without straw addition, rice growth, i.e., the rhizosphere effect, significantly altered the bacterial community composition and abundances of N-cycling genes, such as archaeal and bacterial amoA (AOA and AOB), nirK, and nosZ. The comparison of bulk soils between control and straw treatments showed a shift in bacterial community composition and decreased abundance of AOA, AOB, nirS, and nosZ, which were attributed to sole straw effects. The comparison of rhizosphere soils between control and straw treatments showed an increase in the nifH gene and a decrease in the nirK gene, which were attributed to the interaction of straw and the rhizosphere. The number of differentially abundant genera in bulk soils between control and straw treatments was 13-23, similar to the number of 16-22 genera in rhizosphere soil between control and straw treatment. However, the number of genera affected by the rhizosphere effect was much lower in soil amended with straw (3-4) than in soil without straw addition (9). Results suggest possibly more pronounced impacts of straw amendments in shaping soil bacterial community composition.
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Affiliation(s)
- Ya-Hui Zhao
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture, P.R. China, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Ning Wang
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture, P.R. China, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
- Jiangsu Key Laboratory for Food Quality and Safety, State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
| | - Meng-Kang Yu
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture, P.R. China, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Henan Institute of Science and Technology, Xinxiang, China
| | - Jian-Guang Yu
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture, P.R. China, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
- Jiangsu Key Laboratory for Food Quality and Safety, State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
| | - Li-Hong Xue
- Key Laboratory of Agro-Environment in Downstream of Yangtze Plain, Ministry of Agriculture, P.R. China, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
- Jiangsu Key Laboratory for Food Quality and Safety, State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
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18
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Xu X, Luo Q, Wei Q, Jiang S, Dong C, Faruque MO, Huang Z, Xu Z, Yin C, Zhu Z, Hu X. The Deterioration of Agronomical Traits of the Continuous Cropping of Stevia Is Associated With the Dynamics of Soil Bacterial Community. Front Microbiol 2022; 13:917000. [PMID: 35847059 PMCID: PMC9277660 DOI: 10.3389/fmicb.2022.917000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 05/12/2022] [Indexed: 11/25/2022] Open
Abstract
Stevia rebaudiana Bertoni is grown worldwide as an important, natural sweetener resource plant. The yield of steviol glycosides (SVglys) is greatly influenced by continuous cropping. In this study, we collected the roots, rhizosphere soils, and bulk soils from 2 years of continuous cropping (Y2) and 8 years of continuous cropping (Y8). A high-throughput sequencing technology based on Illumina Hiseq 2500 platform was used to study the structure and diversity of bacterial communities in the roots and soils of stevia with different years of continuous cropping. The results demonstrated that although the content of a group of SVglys was significantly increased in stevia of long-term continuous cropping, it inhibited the growth of plants and lowered the leaf dry weight; as a result, the total amount of SVglys was significantly decreased. Meanwhile, continuous cropping changed the physicochemical properties and the bacterial composition communities of soil. The different sampling sources of the root, rhizosphere soil, and bulk soil had no impact on the richness of bacterial communities, while it exhibited obvious effects on the diversity of bacterial communities. Continuous cropping had a stronger effect on the bacterial community composition in rhizosphere soil than in root and bulk soil. Based on linear discriminant analysis effect size (LEfSe), in the rhizosphere soil of Y8, the relative abundance of some beneficial bacterial genera of Sphingomonas, Devosia, Streptomyces, and Flavobacterium decreased significantly, while the relative abundance of Polycyclovorans, Haliangium, and Nitrospira greatly increased. Moreover, the soil pH and nutrient content, especially the soil organic matter, were correlated with the relative abundance of predominant bacteria at the genus level. This study provides a theoretical basis for uncovering the mechanism of obstacles in continuous stevia cropping and provides guidance for the sustainable development of stevia.
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Affiliation(s)
- Xinjuan Xu
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, China
- Medicinal Plant Engineering Research Center of Hubei Province, Huazhong Agricultural University, Wuhan, China
- Innovation Academy of International Traditional Chinese Medicinal Materials, Huazhong Agricultural University, Wuhan, China
| | - Qingyun Luo
- Department of Traditional Chinese Medicinal Materials, College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Qingyun Luo
| | - Qichao Wei
- Innovation Academy of International Traditional Chinese Medicinal Materials, Huazhong Agricultural University, Wuhan, China
| | - Shangtao Jiang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization/Educational Ministry Engineering Center of Resource-Saving Fertilizers/Jiangsu Collaborative Innovation Center of Solid Organic Waste, Nanjing Agricultural University, Nanjing, China
| | - Caixia Dong
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization/Educational Ministry Engineering Center of Resource-Saving Fertilizers/Jiangsu Collaborative Innovation Center of Solid Organic Waste, Nanjing Agricultural University, Nanjing, China
| | - Mohammad Omar Faruque
- Ethnobotany and Pharmacognosy Lab, Department of Botany, University of Chittagong, Chittagong, Bangladesh
| | - Zhongwen Huang
- Innovation Academy of International Traditional Chinese Medicinal Materials, Huazhong Agricultural University, Wuhan, China
| | - Zhenghua Xu
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, China
- Medicinal Plant Engineering Research Center of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Changxi Yin
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, China
- Medicinal Plant Engineering Research Center of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Zaibiao Zhu
- Department of Traditional Chinese Medicinal Materials, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xuebo Hu
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, China
- Medicinal Plant Engineering Research Center of Hubei Province, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Xuebo Hu
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Zeng Q, Ding X, Wang J, Han X, Iqbal HMN, Bilal M. Insight into soil nitrogen and phosphorus availability and agricultural sustainability by plant growth-promoting rhizobacteria. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:45089-45106. [PMID: 35474421 DOI: 10.1007/s11356-022-20399-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 04/19/2022] [Indexed: 02/08/2023]
Abstract
Nitrogen and phosphorus are critical for the vegetation ecosystem and two of the most insufficient nutrients in the soil. In agriculture practice, many chemical fertilizers are being applied to soil to improve soil nutrients and yield. This farming procedure poses considerable environmental risks which affect agricultural sustainability. As robust soil microorganisms, plant growth-promoting rhizobacteria (PGPR) have emerged as an environmentally friendly way of maintaining and improving the soil's available nitrogen and phosphorus. As a special PGPR, rhizospheric diazotrophs can fix nitrogen in the rhizosphere and promote plant growth. However, the mechanisms and influences of rhizospheric nitrogen fixation (NF) are not well researched as symbiotic NF lacks summarizing. Phosphate-solubilizing bacteria (PSB) are important members of PGPR. They can dissolve both insoluble mineral and organic phosphate in soil and enhance the phosphorus uptake of plants. The application of PSB can significantly increase plant biomass and yield. Co-inoculating PSB with other PGPR shows better performance in plant growth promotion, and the mechanisms are more complicated. Here, we provide a comprehensive review of rhizospheric NF and phosphate solubilization by PGPR. Deeper genetic insights would provide a better understanding of the NF mechanisms of PGPR, and co-inoculation with rhizospheric diazotrophs and PSB strains would be a strategy in enhancing the sustainability of soil nutrients.
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Affiliation(s)
- Qingwei Zeng
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China.
| | - Xiaolei Ding
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Jiangchuan Wang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Xuejiao Han
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, 64849, Monterrey, Mexico
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
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Miranda-Carrazco A, Chávez-López C, Ramírez-Villanueva DA, Dendooven L. Bacteria in (vermi)composted organic wastes mostly survive when applied to an arable soil cultivated with wheat (Triticum sp. L.). ENVIRONMENTAL MONITORING AND ASSESSMENT 2022; 194:363. [PMID: 35419663 DOI: 10.1007/s10661-022-09996-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Composting and vermicomposting are an environmentally friendly way to reduce pathogens in organic wastes and generate a valuable product that provides nutrients for crops. However, how the bacterial community structure changes during these different processes and if the bacteria applied with the (vermi)composted products survive in an arable cultivated soil is still largely unknown. In this study, we monitored how the bacterial community structure changed during conditioning, composting with and without Eisenia fetida, and when the end-product was applied to arable soil cultivated with wheat Triticum sp. L. The organic wastes used were biosolid, cow manure, and a mixture of both. Large changes occurred in the relative abundance of some of the most abundant bacterial genera during conditioning, but the changes were much smaller during composting or vermicomposting. The bacterial community structure was significantly different in the organic wastes during conditioning and (vermi)composting but adding E. fetida had no significant effect on it. Changes in the relative abundance of the bacterial groups in the (vermi)composted waste applied to the arable soil cultivated with wheat were small, suggesting that most survived even after 140 days. As such, applying (vermi)composted organic wastes not only adds nutrients to a crop but also contributes to the survival of plant growth-promoting bacteria found in the (vermi)compost. However, putative human pathogens found in the biosolid also survived in the arable soil, and their relative abundance remained high but mixing the biosolid with cow manure reduced that risk. It was found that applying (vermi)composted organic wastes to an arable soil not only provides plant nutrients and adds bacteria with plant growth-promoting capacities, but some putative pathogens also survived.
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Affiliation(s)
- Alejandra Miranda-Carrazco
- Laboratory of Soil Ecology, Department of Biotechnology and Bioengineering, Cinvestav, Mexico City, Mexico
| | - Claudia Chávez-López
- Laboratory of Soil Ecology, Department of Biotechnology and Bioengineering, Cinvestav, Mexico City, Mexico
| | | | - Luc Dendooven
- Laboratory of Soil Ecology, Department of Biotechnology and Bioengineering, Cinvestav, Mexico City, Mexico.
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21
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Hernández-Guzmán M, Pérez-Hernández V, Navarro-Noya YE, Luna-Guido ML, Verhulst N, Govaerts B, Dendooven L. Application of ammonium to a N limited arable soil enriches a succession of bacteria typically found in the rhizosphere. Sci Rep 2022; 12:4110. [PMID: 35260645 PMCID: PMC8904580 DOI: 10.1038/s41598-022-07623-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 02/01/2022] [Indexed: 12/30/2022] Open
Abstract
Crop residue management and tillage are known to affect the soil bacterial community, but when and which bacterial groups are enriched by application of ammonium in soil under different agricultural practices from a semi-arid ecosystem is still poorly understood. Soil was sampled from a long-term agronomic experiment with conventional tilled beds and crop residue retention (CT treatment), permanent beds with crop residue burned (PBB treatment) or retained (PBC) left unfertilized or fertilized with 300 kg urea-N ha−1 and cultivated with wheat (Triticum durum L.)/maize (Zea mays L.) rotation. Soil samples, fertilized or unfertilized, were amended or not (control) with a solution of (NH4)2SO4 (300 kg N ha−1) and were incubated aerobically at 25 ± 2 °C for 56 days, while CO2 emission, mineral N and the bacterial community were monitored. Application of NH4+ significantly increased the C mineralization independent of tillage-residue management or N fertilizer. Oxidation of NH4+ and NO2− was faster in the fertilized soil than in the unfertilized soil. The relative abundance of Nitrosovibrio, the sole ammonium oxidizer detected, was higher in the fertilized than in the unfertilized soil; and similarly, that of Nitrospira, the sole nitrite oxidizer. Application of NH4+ enriched Pseudomonas, Flavisolibacter, Enterobacter and Pseudoxanthomonas in the first week and Rheinheimera, Acinetobacter and Achromobacter between day 7 and 28. The application of ammonium to a soil cultivated with wheat and maize enriched a sequence of bacterial genera characterized as rhizospheric and/or endophytic independent of the application of urea, retention or burning of the crop residue, or tillage.
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Affiliation(s)
- Mario Hernández-Guzmán
- Laboratory of Soil Ecology, CINVESTAV, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Alcaldía Gustavo A Madero, Mexico City, Mexico
| | - Valentín Pérez-Hernández
- Laboratory of Soil Ecology, CINVESTAV, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Alcaldía Gustavo A Madero, Mexico City, Mexico.,Department of Chemistry and Biochemistry, Instituto Tecnológico de Tuxtla-Gutiérrez, Tuxtla Gutiérrez, Mexico
| | - Yendi E Navarro-Noya
- Centro de Investigación en Ciencias Biológicas, Universidad Autónoma de Tlaxcala, Tlaxcala, México
| | - Marco L Luna-Guido
- Laboratory of Soil Ecology, CINVESTAV, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Alcaldía Gustavo A Madero, Mexico City, Mexico
| | - Nele Verhulst
- International Maize and Wheat Improvement Center (CIMMYT), El Batán, Texcoco, Mexico
| | - Bram Govaerts
- International Maize and Wheat Improvement Center (CIMMYT), El Batán, Texcoco, Mexico.,Cornell University, Ithaca, USA
| | - Luc Dendooven
- Laboratory of Soil Ecology, CINVESTAV, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Alcaldía Gustavo A Madero, Mexico City, Mexico.
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Bi W, Weng B, Yan D, Wang H, Wang M, Yan S, Jing L, Liu T, Chang W. Responses of Phosphate-Solubilizing Microorganisms Mediated Phosphorus Cycling to Drought-Flood Abrupt Alternation in Summer Maize Field Soil. Front Microbiol 2022; 12:768921. [PMID: 35111138 PMCID: PMC8802831 DOI: 10.3389/fmicb.2021.768921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/02/2021] [Indexed: 11/13/2022] Open
Abstract
Soil microbial communities are essential to phosphorus (P) cycling, especially in the process of insoluble phosphorus solubilization for plant P uptake. Phosphate-solubilizing microorganisms (PSM) are the dominant driving forces. The PSM mediated soil P cycling is easily affected by water condition changes due to extreme hydrological events. Previous studies basically focused on the effects of droughts, floods, or drying-rewetting on P cycling, while few focused on drought-flood abrupt alternation (DFAA), especially through microbial activities. This study explored the DFAA effects on P cycling mediated by PSM and P metabolism-related genes in summer maize field soil. Field control experiments were conducted to simulate two levels of DFAA (light drought-moderate flood, moderate drought-moderate flood) during two summer maize growing periods (seeding-jointing stage, tasseling-grain filling stage). Results showed that the relative abundance of phosphate-solubilizing bacteria (PSB) and phosphate-solubilizing fungi (PSF) increased after DFAA compared to the control system (CS), and PSF has lower resistance but higher resilience to DFAA than PSB. Significant differences can be found on the genera Pseudomonas, Arthrobacter, and Penicillium, and the P metabolism-related gene K21195 under DFAA. The DFAA also led to unstable and dispersed structure of the farmland ecosystem network related to P cycling, with persistent influences until the mature stage of summer maize. This study provides references for understanding the micro process on P cycling under DFAA in topsoil, which could further guide the DFAA regulations.
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Affiliation(s)
- Wuxia Bi
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China
| | - Baisha Weng
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China
- Yinshanbeilu Grassland Eco-Hydrology National Observation and Research Station, China Institute of Water Resources and Hydropower Research, Beijing, China
- *Correspondence: Baisha Weng, ,
| | - Denghua Yan
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China
- Yinshanbeilu Grassland Eco-Hydrology National Observation and Research Station, China Institute of Water Resources and Hydropower Research, Beijing, China
| | - Hao Wang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China
| | - Mengke Wang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China
| | - Siying Yan
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China
- College of Resource Environment and Tourism, Capital Normal University, Beijing, China
| | - Lanshu Jing
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China
- College of Hydrology and Water Resources, Hohai University, Nanjing, China
| | - Tiejun Liu
- Yinshanbeilu Grassland Eco-Hydrology National Observation and Research Station, China Institute of Water Resources and Hydropower Research, Beijing, China
- Collaborative Innovation Center for Grassland Ecological Security (Jointly Supported by the Ministry of Education of China and Inner Mongolia Autonomous Region), Hohhot, China
| | - Wenjuan Chang
- College of Hydraulic and Environmental Engineering, China Three Gorges University, Yichang, China
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Nunes I, Hansen V, Bak F, Bonnichsen L, Su J, Hao X, Raymond NS, Nicolaisen MH, Jensen LS, Nybroe O. OUP accepted manuscript. FEMS Microbiol Ecol 2022; 98:6548193. [PMID: 35285907 PMCID: PMC8951222 DOI: 10.1093/femsec/fiac028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/22/2022] [Accepted: 03/10/2022] [Indexed: 11/21/2022] Open
Abstract
During germination, the seed releases nutrient-rich exudates into the spermosphere, thereby fostering competition between resident microorganisms. However, insight into the composition and temporal dynamics of seed-associated bacterial communities under field conditions is currently lacking. This field study determined the temporal changes from 11 to 31 days after sowing in the composition of seed-associated bacterial communities of winter wheat as affected by long-term soil fertilization history, and by introduction of the plant growth-promoting microbial inoculants Penicillium bilaiae and Bacillus simplex. The temporal dynamics were the most important factor affecting the composition of the seed-associated communities. An increase in the relative abundance of genes involved in organic nitrogen metabolism (ureC and gdhA), and in ammonium oxidation (amoA), suggested increased mineralization of plant-derived nitrogen compounds over time. Dynamics of the phosphorus cycling genes ppt, ppx and cphy indicated inorganic phosphorus and polyphosphate cycling, as well as phytate hydrolysis by the seed-associated bacteria early after germination. Later, an increase in genes for utilization of organic phosphorus sources (phoD, phoX and phnK) indicated phosphorus limitation. The results indicate that community temporal dynamics are partly driven by changed availability of major nutrients, and reveal no functional consequences of the added inoculants during seed germination.
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Affiliation(s)
| | | | | | - Lise Bonnichsen
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Jianqiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xiuli Hao
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University; Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Nelly Sophie Raymond
- Plant and Soil Section, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensevej 40, 1871 Frederiksberg C, Denmark
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Mette Haubjerg Nicolaisen
- Corresponding author: Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, Univeristy of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Denmark. Tel: +45 35332649; E-mail:
| | - Lars Stoumann Jensen
- Plant and Soil Section, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensevej 40, 1871 Frederiksberg C, Denmark
| | - Ole Nybroe
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
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24
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Liu Y, Sun J, Dai X, Zhao Z, Wang X, Zhang G. Response of soil bacterial community structure and function under two salt-tolerant plants in a coastal saline soil area of eastern Hebei province of China. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2021; 24:842-854. [PMID: 34651532 DOI: 10.1080/15226514.2021.1982862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The plants Feicai (Sedum aizoon L.) and dandelion(Taraxacum mongolicum Hand.-Mazz.) have good salt tolerance, and can improve soil quality and the micro-ecological environment. Coastal saline-soil plots planted with S. aizoon and T. mongolicum and bare plots were used to explore their effects on the microbial community structure of coastal saline soil. The diversity and function of soil bacterial communities were analyzed using Illumina MiSeq high-throughput sequencing technology. The results showed that the α-diversity of soil bacterial communities were higher in planted than in bare plots, in the following order: T. mongolicum plot > S. aizoon plot > bare plot. The soil bacterial communities also changed after planting S. aizoon and T. mongolicum. The LDA effect size analysis showed that there were 37 indicator species among the three plot types. Correlation analysis of environmental factors showed that EC, AP, and OM were the main factors influencing bacterial community composition in this coastal saline soil. The PICRUSt functional prediction showed that the numbers of metabolic functions of bacterial communities were in the following order: T. mongolicum plot > S. aizoon plot > bare plot. The results provide a theoretical basis and plant species for developing salt-tolerant bacterial resources and phytoremediation of coastal saline soil.
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Affiliation(s)
- Yahui Liu
- Institute of Coastal Agriculture, Hebei Academy of Agriculture and Forestry Sciences, Innovation Center for Saline and Alkali Land Greening Technology of Hebei Province, Caofeidian, Tangshan, China
| | - Jianping Sun
- Institute of Coastal Agriculture, Hebei Academy of Agriculture and Forestry Sciences, Innovation Center for Saline and Alkali Land Greening Technology of Hebei Province, Caofeidian, Tangshan, China
| | - Xianglin Dai
- Institute of Coastal Agriculture, Hebei Academy of Agriculture and Forestry Sciences, Innovation Center for Saline and Alkali Land Greening Technology of Hebei Province, Caofeidian, Tangshan, China
| | - Zijing Zhao
- Institute of Coastal Agriculture, Hebei Academy of Agriculture and Forestry Sciences, Innovation Center for Saline and Alkali Land Greening Technology of Hebei Province, Caofeidian, Tangshan, China
| | - Xiuping Wang
- Institute of Coastal Agriculture, Hebei Academy of Agriculture and Forestry Sciences, Innovation Center for Saline and Alkali Land Greening Technology of Hebei Province, Caofeidian, Tangshan, China
| | - Guoxin Zhang
- Institute of Coastal Agriculture, Hebei Academy of Agriculture and Forestry Sciences, Innovation Center for Saline and Alkali Land Greening Technology of Hebei Province, Caofeidian, Tangshan, China
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Liu TY, Ye N, Wang X, Das D, Tan Y, You X, Long M, Hu T, Dai L, Zhang J, Chen MX. Drought stress and plant ecotype drive microbiome recruitment in switchgrass rhizosheath. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1753-1774. [PMID: 34288433 DOI: 10.1111/jipb.13154] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 07/18/2021] [Indexed: 05/27/2023]
Abstract
The rhizosheath, a layer of soil grains that adheres firmly to roots, is beneficial for plant growth and adaptation to drought environments. Switchgrass is a perennial C4 grass which can form contact rhizosheath under drought conditions. In this study, we characterized the microbiomes of four different rhizocompartments of two switchgrass ecotypes (Alamo and Kanlow) grown under drought or well-watered conditions via 16S ribosomal RNA amplicon sequencing. These four rhizocompartments, the bulk soil, rhizosheath soil, rhizoplane, and root endosphere, harbored both distinct and overlapping microbial communities. The root compartments (rhizoplane and root endosphere) displayed low-complexity communities dominated by Proteobacteria and Firmicutes. Compared to bulk soil, Cyanobacteria and Bacteroidetes were selectively enriched, while Proteobacteria and Firmicutes were selectively depleted, in rhizosheath soil. Taxa from Proteobacteria or Firmicutes were specifically selected in Alamo or Kanlow rhizosheath soil. Following drought stress, Citrobacter and Acinetobacter were further enriched in rhizosheath soil, suggesting that rhizosheath microbiome assembly is driven by drought stress. Additionally, the ecotype-specific recruitment of rhizosheath microbiome reveals their differences in drought stress responses. Collectively, these results shed light on rhizosheath microbiome recruitment in switchgrass and lay the foundation for the improvement of drought tolerance in switchgrass by regulating the rhizosheath microbiome.
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Affiliation(s)
- Tie-Yuan Liu
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, China
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, 999077, China
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong, 999077, China
| | - Nenghui Ye
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Xinyu Wang
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, China
| | - Debatosh Das
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, 999077, China
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong, 999077, China
| | - Yuxiang Tan
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Xiangkai You
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, China
| | - Mingxiu Long
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, China
| | - Tianming Hu
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, China
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Jianhua Zhang
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, 999077, China
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong, 999077, China
| | - Mo-Xian Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
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Sun H, Jiang S, Jiang C, Wu C, Gao M, Wang Q. A review of root exudates and rhizosphere microbiome for crop production. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:54497-54510. [PMID: 34431053 DOI: 10.1007/s11356-021-15838-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/02/2021] [Indexed: 05/04/2023]
Abstract
Increasing crop yields and ensuring food security is a major global challenge. In order to increase crop production, chemical fertilizers and pesticides are excessively used. However, the significance of root exudates is understudied. Beneficial interactions between plant and rhizosphere microbiome are critical for plant fitness and health. In this review, we discuss the application and progress of current research methods and technologies in terms of root exudates and rhizosphere microbiome. We summarize how root exudates promote plant access to nitrogen, phosphorus, and iron, and how root exudates strengthen plant immunity to cope with biotic stress by regulating the rhizosphere microbiome, and thereby reducing dependence on fertilizers and pesticides. Optimizing these interactions to increase plant nutrient uptake and resistance to biotic stresses offers one of the few untapped opportunities to confront sustainability issues in food security. To overcome the limitations of current research, combination of multi-omics, imaging technology together with synthetic communities has the potential to uncover the interaction mechanisms and to fill the knowledge gap for their applications in agriculture to achieve sustainable development.
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Affiliation(s)
- Haishu Sun
- Department of Environmental Engineering, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Shanxue Jiang
- School of Ecology and Environment, Beijing Technology and Business University, Beijing, 100048, China
- State Environmental Protection Key Laboratory of Food Chain Pollution Control, Beijing Technology and Business University, Beijing, 100048, China
| | - Cancan Jiang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Chuanfu Wu
- Department of Environmental Engineering, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Beijing Key Laboratory on Resource-oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, Beijing, 10083, China
| | - Ming Gao
- Department of Environmental Engineering, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Beijing Key Laboratory on Resource-oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, Beijing, 10083, China
| | - Qunhui Wang
- Department of Environmental Engineering, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
- Beijing Key Laboratory on Resource-oriented Treatment of Industrial Pollutants, University of Science and Technology Beijing, Beijing, 10083, China.
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27
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Wu N, Li Z, Tang M. Impact of salt and exogenous AM inoculation on indigenous microbial community structure in the rhizosphere of dioecious plant, Populus cathayana. Sci Rep 2021; 11:18403. [PMID: 34526541 PMCID: PMC8443550 DOI: 10.1038/s41598-021-97674-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 08/27/2021] [Indexed: 12/03/2022] Open
Abstract
The sex-specific physical and biochemical responses in dioecious plants to abiotic stresses could result in gender imbalance, and how to ease the current situation by microorganisms is still unclear. Using native soil where poplars were grown, growth parameters, soil physicochemical properties in the rhizosphere soil of different sexes of Populus cathayana exposed to salt stress and exogenous arbuscular mycorrhizal (AM) inoculation were tested. Besides, the sex-specific microbial community structures in the rhizosphere soil of different sexes of Populus cathayana were compared under salt stress. To identify the sex-specific microbial community characteristics related to salinity and AM symbiosis, a combined qPCR and DGGE method was used to monitor microbial community diversity. Seedlings suffered severe pressure by salt stress, reflected in limited growth, biomass, and nutrient element accumulation, especially on females. Exogenous AM inoculation treatment alleviated these negative effects, especially under salt treatment of 75 mM. Compared with salt effect, exogenous AM inoculation treatment showed a greater effect on soil physical-chemical properties of both sexes. Based on DGGE results, salt stress negatively affected fungal richness but positively affected fungal Simpson diversity index, while exogenous AM inoculation treatment showed the opposite effect. Structural equation modeling (SEM) was performed to show the causal relationships between salt and exogenous AM inoculation treatments with biomass accumulation and microbial community: salt and exogenous AM inoculation treatment showed complicated effects on elementary concentrations, soil properties, which resulted in different relationship with biomass accumulation and microbial community. Salt stress had a negative effect on soil properties and microbial community structure in the rhizosphere soil of P. cathayana, whereas exogenous AM inoculation showed positive impacts on most of the soil physical-chemical properties and microbial community status.
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Affiliation(s)
- Na Wu
- Institute of Applied Biotechnology, School of Life Science, Shanxi Datong University, Datong, 037009, Shanxi, China
| | - Zhen Li
- Institute of Applied Biotechnology, School of Life Science, Shanxi Datong University, Datong, 037009, Shanxi, China
| | - Ming Tang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Lingnan Guangdong Laboratory of Modern Agriculture, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
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Abdulsada Z, Kibbee R, Princz J, DeRosa M, Örmeci B. Transformation of Silver Nanoparticles (AgNPs) during Lime Treatment of Wastewater Sludge and Their Impact on Soil Bacteria. NANOMATERIALS 2021; 11:nano11092330. [PMID: 34578645 PMCID: PMC8465233 DOI: 10.3390/nano11092330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 11/16/2022]
Abstract
This study investigated the impact of lime stabilization on the fate and transformation of AgNPs. It also evaluated the changes in the population and diversity of the five most relevant bacterial phyla in soil after applying lime-stabilized sludge containing AgNPs. The study was performed by spiking an environmentally relevant concentration of AgNPs (2 mg AgNPs/g TS) in sludge, applying lime stabilization to increase pH to above 12 for two hours, and applying lime-treated sludge to soil samples. Transmission electron microscopy (TEM) and energy-dispersive X-ray spectroscopy (EDS) were used to investigate the morphological and compositional changes of AgNPs during lime stabilization. After the application of lime stabilized sludge to the soil, soil samples were periodically analyzed for total genomic DNA and changes in bacterial phyla diversity using quantitative polymerase chain reaction (qPCR). The results showed that lime treatment effectively removed AgNPs from the aqueous phase, and AgNPs were deposited on the lime molecules. The results revealed that AgNPs did not significantly impact the presence and diversity of the assessed phyla in the soil. However, lime stabilized sludge with AgNPs affected the abundance of each phylum over time. No significant effects on the soil total organic carbon (TOC), heterotrophic plate count (HPC), and percentage of the live cells were observed.
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Affiliation(s)
- Zainab Abdulsada
- Department of Civil and Environmental Engineering, Carleton University, Ottawa, ON K1S 5B6, Canada; (Z.A.); (R.K.)
- Department of Environmental Engineering, University of Baghdad, Karrada, Al-Jadriya, Baghdad, Iraq
| | - Richard Kibbee
- Department of Civil and Environmental Engineering, Carleton University, Ottawa, ON K1S 5B6, Canada; (Z.A.); (R.K.)
| | - Juliska Princz
- Environment and Climate Change Canada, 335 River Road South, Ottawa, ON K1V 1C7, Canada;
| | - Maria DeRosa
- Department of Chemistry, Carleton University, Ottawa, ON K1S 5B6, Canada;
| | - Banu Örmeci
- Department of Civil and Environmental Engineering, Carleton University, Ottawa, ON K1S 5B6, Canada; (Z.A.); (R.K.)
- Correspondence: ; Tel.: +1-613-520-2600 (ext. 4144)
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Metagenomic Study of the Community Structure and Functional Potentials in Maize Rhizosphere Microbiome: Elucidation of Mechanisms behind the Improvement in Plants under Normal and Stress Conditions. SUSTAINABILITY 2021. [DOI: 10.3390/su13148079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The community of microbes in the rhizosphere region is diverse and contributes significantly to plant growth and crop production. Being an important staple and economic crop, the maize rhizosphere microbiota has been studied in the past using culture-dependent techniques. However, these limited culturing methods often do not help in understanding the complex community of microbes in the rhizosphere. Moreover, the vital biogeochemical processes carried out by these organisms are yet to be fully characterized. Herein, shotgun metagenomics, which enables the holistic study of several microbial environments, was employed to examine the community structure and functional potentials of microbes in the maize rhizosphere and to assess the influence of environmental variables on these. The dominant microbial phyla found in the soil environments include Actinobacteria, Microsporidia, Bacteroidetes, Thaumarchaeota, Proteobacteria and Firmicutes. Carbohydrate metabolism, protein metabolism and stress metabolism constitute the major functional categories in the environments. The beta diversity analysis indicated significant differences (p = 0.01) in the community structure and functional categories across the samples. A correlation was seen between the physical and chemical properties of the soil, and the structural and functional diversities. The canonical correspondence analysis carried out showed that phosphorus, N-NO3, potassium and organic matter were the soil properties that best influenced the structural and functional diversities of the soil microbes. It can be inferred from this study that the maize rhizosphere is a hotspot for microorganisms of agricultural and biotechnological importance which can be used as bioinoculants for sustainable agriculture.
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Yoshiura CA, Venturini AM, Braga LPP, da França AG, de Lyra MDCCP, Tsai SM, Rodrigues JLM. Responses of Low-Cost Input Combinations on the Microbial Structure of the Maize Rhizosphere for Greenhouse Gas Mitigation and Plant Biomass Production. FRONTIERS IN PLANT SCIENCE 2021; 12:683658. [PMID: 34276734 PMCID: PMC8278312 DOI: 10.3389/fpls.2021.683658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 05/18/2021] [Indexed: 06/13/2023]
Abstract
The microbial composition of the rhizosphere and greenhouse gas (GHG) emissions under the most common input combinations in maize (Zea mays L.) cultivated in Brazil have not been characterized yet. In this study, we evaluated the influence of maize stover coverage (S), urea-topdressing fertilization (F), and the microbial inoculant Azospirillum brasilense (I) on soil GHG emissions and rhizosphere microbial communities during maize development. We conducted a greenhouse experiment and measured methane (CH4), carbon dioxide (CO2), and nitrous oxide (N2O) fluxes from soil cultivated with maize plants under factorial combinations of the inputs and a control treatment (F, I, S, FI, FS, IS, FIS, and control). Plant biomass was evaluated, and rhizosphere soil samples were collected at V5 and V15 stages and DNA was extracted. The abundance of functional genes (mcrA, pmoA, nifH, and nosZ) was determined by quantitative PCR (qPCR) and the structure of the microbial community was assessed through 16S rRNA amplicon sequencing. Our results corroborate with previous studies which used fewer input combinations and revealed different responses for the following three inputs: F increased N2O emissions around 1 week after application; I tended to reduce CH4 and CO2 emissions, acting as a plant growth stimulator through phytohormones; S showed an increment for CO2 emissions by increasing carbon-use efficiency. IS and FIS treatments presented significant gains in biomass that could be related to Actinobacteria (19.0%) and Bacilli (10.0%) in IS, and Bacilli (9.7%) in FIS, which are the microbial taxa commonly associated with lignocellulose degradation. Comparing all factors, the IS (inoculant + maize stover) treatment was considered the best option for plant biomass production and GHG mitigation since FIS provides small gains toward the management effort of F application.
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Affiliation(s)
- Caio Augusto Yoshiura
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Andressa Monteiro Venturini
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Lucas Palma Perez Braga
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Aline Giovana da França
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | - Siu Mui Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
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L Neal A, McLaren T, Lourenço Campolino M, Hughes D, Marcos Coelho A, Gomes de Paula Lana U, Aparecida Gomes E, Morais de Sousa S. Crop type exerts greater influence upon rhizosphere phosphohydrolase gene abundance and phylogenetic diversity than phosphorus fertilization. FEMS Microbiol Ecol 2021; 97:6145522. [PMID: 33609137 DOI: 10.1093/femsec/fiab033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 02/18/2021] [Indexed: 02/04/2023] Open
Abstract
Rock phosphate is an alternative form of phosphorus (P) fertilizer; however, there is no information regarding the influence of P fertilizer sources in Brazilian Cerrado soils upon microbial genes coding for phosphohydrolase enzymes in crop rhizospheres. Here, we analyze a field experiment comparing maize and sorghum grown under different P fertilization (rock phosphate and triple superphosphate) upon crop performance, phosphatase activity and rhizosphere microbiomes at three levels of diversity: small subunit rRNA marker genes of bacteria, archaea and fungi; a suite of alkaline and acid phosphatase and phytase genes; and ecotypes of individual genes. We found no significant difference in crop performance between the fertilizer sources, but the accumulation of fertilizer P into pools of organic soil P differed. Phosphatase activity was the only biological parameter influenced by P fertilization. Differences in rhizosphere microbiomes were observed at all levels of biodiversity due to crop type, but not fertilization. Inspection of phosphohydrolase gene ecotypes responsible for differences between the crops suggests a role for lateral genetic transfer in establishing ecotype distributions. Moreover, they were not reflected in microbial community composition, suggesting that they confer competitive advantage to individual cells rather than species in the sorghum rhizosphere.
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Affiliation(s)
- Andrew L Neal
- Department of Sustainable Agricultural Sciences, Rothamsted Research, North Wyke, Devon EX20 2SB, UK
| | - Timothy McLaren
- Department of Environmental Systems Science, Swiss Federal Institute of Technology (ETH) Zürich, Eschikon 33, 8315 Lindau, Switzerland
| | - Mariana Lourenço Campolino
- Universidade Federal de São João del-Rei, Bioengineering, R. Padre João Pimentel, 80 - Dom Bosco, São João del-Rei, Minas Gerais, 36301-158, Brazil.,Empresa Brasileira de Pesquisa Agropecuária, Embrapa Milho e Sorgo, Rod MG 424 Km 65, Sete Lagoas, Minas Gerais, 35701-970, Brazil
| | - David Hughes
- Department of Computational and Analytical Sciences, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Antônio Marcos Coelho
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Milho e Sorgo, Rod MG 424 Km 65, Sete Lagoas, Minas Gerais, 35701-970, Brazil
| | - Ubiraci Gomes de Paula Lana
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Milho e Sorgo, Rod MG 424 Km 65, Sete Lagoas, Minas Gerais, 35701-970, Brazil
| | - Eliane Aparecida Gomes
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Milho e Sorgo, Rod MG 424 Km 65, Sete Lagoas, Minas Gerais, 35701-970, Brazil
| | - Sylvia Morais de Sousa
- Universidade Federal de São João del-Rei, Bioengineering, R. Padre João Pimentel, 80 - Dom Bosco, São João del-Rei, Minas Gerais, 36301-158, Brazil.,Empresa Brasileira de Pesquisa Agropecuária, Embrapa Milho e Sorgo, Rod MG 424 Km 65, Sete Lagoas, Minas Gerais, 35701-970, Brazil
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Enebe MC, Babalola OO. Soil fertilization affects the abundance and distribution of carbon and nitrogen cycling genes in the maize rhizosphere. AMB Express 2021; 11:24. [PMID: 33555438 PMCID: PMC7870749 DOI: 10.1186/s13568-021-01182-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 01/11/2021] [Indexed: 12/11/2022] Open
Abstract
Soil microbes perform important functions in nitrogen and carbon cycling in the biosphere. Microbial communities in the rhizosphere enhance plants' health and promote nutrient turnover and cycling in the soil. In this study, we evaluated the effects of soil fertilization with organic and inorganic fertilizers on the abundances and distribution of carbon and nitrogen cycling genes within the rhizosphere of maize plants. Our result showed that maize plants through rhizosphere effects selected and enriched the same functional genes glnA, gltB, gudB involved in nitrogen cycle as do high compost and low inorganic fertilizer treatments. This observation was significantly different from those of high doses of inorganic fertilizer and low compost manure treated soil. Only alpha amylase encoding genes were selectively enriched by low compost and high inorganic fertilized soil. The other treatments only selected xynB (in Cp8), lacZ (Cp4), bglA, pldB, trpA (N2), uidA (N1) and glgC, vanA (Cn0) carbon cycling genes in the rhizosphere of maize. Also Actinomycetales are selected by high compost, low inorganic fertilizer and control. The control was without any fertilization and the soil was planted with maize. Bacillales are also promoted by low compost and high inorganic fertilizer. This indicated that only microbes capable of tolerating the stress of high dose of inorganic fertilizer will thrive under such condition. Therefore, soil fertilization lowers nitrogen gas emission as seen with the high abundance of nitrogen assimilation genes or microbial anabolic genes, but increases carbon dioxide evolution in the agricultural soil by promoting the abundance of catabolic genes involve in carbon cycling.
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Tan B, Li Y, Liu T, Tan X, He Y, You X, Leong KH, Liu C, Li L. Response of Plant Rhizosphere Microenvironment to Water Management in Soil- and Substrate-Based Controlled Environment Agriculture (CEA) Systems: A Review. FRONTIERS IN PLANT SCIENCE 2021; 12:691651. [PMID: 34456936 PMCID: PMC8385539 DOI: 10.3389/fpls.2021.691651] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/16/2021] [Indexed: 05/06/2023]
Abstract
As natural agroecology deteriorates, controlled environment agriculture (CEA) systems become the backup support for coping with future resource consumption and potential food crises. Compared with natural agroecology, most of the environmental parameters of the CEA system rely on manual management. Such a system is dependent and fragile and prone to degradation, which includes harmful bacteria proliferation and productivity decline. Proper water management is significant for constructing a stabilized rhizosphere microenvironment. It has been proved that water is an efficient tool for changing the availability of nutrients, plant physiological processes, and microbial communities within. However, for CEA issues, relevant research is lacking at present. The article reviews the interactive mechanism between water management and rhizosphere microenvironments from the perspectives of physicochemical properties, physiological processes, and microbiology in CEA systems. We presented a synthesis of relevant research on water-root-microbes interplay, which aimed to provide detailed references to the conceptualization, research, diagnosis, and troubleshooting for CEA systems, and attempted to give suggestions for the construction of a high-tech artificial agricultural ecology.
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Affiliation(s)
- Bo Tan
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
| | - Yihan Li
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
| | - Tiegang Liu
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
| | - Xiao Tan
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
| | - Yuxin He
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
| | - Xueji You
- Department of Hydraulic Engineering, College of Civil Engineering, Tongji University, Shanghai, China
- Department of Civil, Architectural and Environmental Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Kah Hon Leong
- Department of Environmental Engineering, Faculty of Engineering and Green Technology, Universiti Tunku Abdul Rahman, Kampar, Malaysia
| | - Chao Liu
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
- *Correspondence: Chao Liu,
| | - Longguo Li
- State Key Laboratory of Hydraulics and Mountain River Engineering, College of Water Resource and Hydropower, Sichuan University, Chengdu, China
- Longguo Li,
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Akbari A, Wang Z, He P, Wang D, Lee J, Han IL, Li G, Gu AZ. Unrevealed roles of polyphosphate-accumulating microorganisms. Microb Biotechnol 2021; 14:82-87. [PMID: 33404187 PMCID: PMC7888455 DOI: 10.1111/1751-7915.13730] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 12/29/2022] Open
Abstract
We first review current knowledge on PAOs, with a focus on bacteria, in terms of their phylogenetic identities, metabolic pathways and detection methods. We further discuss the evidence that suggests the ubiquitous presence of PAOs in nature and point out the unrevealed roles of the PAOs that warrant future investigation.
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Affiliation(s)
- Ali Akbari
- School of Civil and Environmental EngineeringCornell UniversityIthacaNY14853USA
| | - ZiJian Wang
- School of Civil and Environmental EngineeringCornell UniversityIthacaNY14853USA
| | - Peisheng He
- School of Civil and Environmental EngineeringCornell UniversityIthacaNY14853USA
| | - Dongqi Wang
- State Key Laboratory of Eco‐hydraulics in Northwest Arid RegionXi’an University of TechnologyXi’anShaanxi710048China
| | - Jangho Lee
- School of Civil and Environmental EngineeringCornell UniversityIthacaNY14853USA
| | - IL Han
- School of Civil and Environmental EngineeringCornell UniversityIthacaNY14853USA
| | - Guangyu Li
- Department of Civil and Environmental EngineeringNortheastern University360 Huntington AvenueBostonMA02115USA
| | - April Z. Gu
- School of Civil and Environmental EngineeringCornell UniversityIthacaNY14853USA
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Rice SST Variation Shapes the Rhizosphere Bacterial Community, Conferring Tolerance to Salt Stress through Regulating Soil Metabolites. mSystems 2020; 5:5/6/e00721-20. [PMID: 33234605 PMCID: PMC7687028 DOI: 10.1128/msystems.00721-20] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Soil salinization is one of the major environmental stresses limiting crop productivity. Crops in agricultural ecosystems have developed various strategies to adapt to salt stress. We used rice mutant and CRISPR-edited lines to investigate the relationships among the Squamosa promoter Binding Protein box (SBP box) family gene (SST/OsSPL10), soil metabolites, and the rhizosphere bacterial community. We found that during salt stress, there are significant differences in the rhizosphere bacterial community and soil metabolites between the plants with the SST gene and those without it. Our findings provide a useful paradigm for revealing the roles of key genes of plants in shaping rhizosphere microbiomes and their relationships with soil metabolites and offer new insights into strategies to enhance rice tolerance to high salt levels from microbial and ecological perspectives. Some plant-specific resistance genes could affect rhizosphere microorganisms by regulating the release of root exudates. In a previous study, the SST (seedling salt tolerant) gene in rice (Oryza sativa) was identified, and loss of SST function resulted in better plant adaptation to salt stress. However, whether the rice SST variation could alleviate salt stress via regulating soil metabolites and microbiota in the rhizosphere is still unknown. Here, we used transgenic plants with SST edited in the Huanghuazhan (HHZ) and Zhonghua 11 (ZH11) cultivars by the CRISPR/Cas9 system and found that loss of SST function increased the accumulation of potassium and reduced the accumulation of sodium ions in rice plants. Using 16S rRNA gene amplicon high-throughput sequencing, we found that the mutant material shifted the rhizobacterial assembly under salt-free stress. Importantly, under salt stress, the sst, HHZcas, and ZH11cas plants significantly changed the assembly of the rhizobacteria. Furthermore, the rice SST gene also affected the soil metabolites, which were closely related to the dynamics of rhizosphere microbial communities, and we further determined the relationship between the rhizosphere microbiota and soil metabolites. Overall, our results show the effects of the rice SST gene on the response to salt stress associated with the soil microbiota and metabolites in the rhizosphere. This study reveals a helpful linkage among the rice SST gene, soil metabolites, and rhizobacterial community assembly and also provides a theoretical basis for improving crop adaptation through soil microbial management practices. IMPORTANCE Soil salinization is one of the major environmental stresses limiting crop productivity. Crops in agricultural ecosystems have developed various strategies to adapt to salt stress. We used rice mutant and CRISPR-edited lines to investigate the relationships among the Squamosa promoter Binding Protein box (SBP box) family gene (SST/OsSPL10), soil metabolites, and the rhizosphere bacterial community. We found that during salt stress, there are significant differences in the rhizosphere bacterial community and soil metabolites between the plants with the SST gene and those without it. Our findings provide a useful paradigm for revealing the roles of key genes of plants in shaping rhizosphere microbiomes and their relationships with soil metabolites and offer new insights into strategies to enhance rice tolerance to high salt levels from microbial and ecological perspectives.
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36
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Fan K, Delgado-Baquerizo M, Guo X, Wang D, Zhu YG, Chu H. Biodiversity of key-stone phylotypes determines crop production in a 4-decade fertilization experiment. ISME JOURNAL 2020; 15:550-561. [PMID: 33028975 DOI: 10.1038/s41396-020-00796-8] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 09/18/2020] [Accepted: 09/24/2020] [Indexed: 12/13/2022]
Abstract
Cropping systems have fertilized soils for decades with undetermined consequences for the productivity and functioning of terrestrial ecosystems. One of the critical unknowns is the role of soil biodiversity in controlling crop production after decades of fertilization. This knowledge gap limits our capacity to assess how changes in soil biodiversity could alter crop production and soil health in changing environments. Here, we used multitrophic ecological networks to investigate the importance of soil biodiversity, in particular, the biodiversity of key-stone taxa in controlling soil functioning and wheat production in a 35-year field fertilization experiment. We found strong and positive associations between soil functional genes, crop production and the biodiversity of key-stone phylotypes; soils supporting a larger number of key-stone nematode, bacteria and fungi phylotypes yielded the highest wheat production. These key-stone phylotypes were also positively associated with plant growth (phototrophic bacteria, nitrogen fixers) and multiple functional genes related to nutrient cycling. The retrieved information on the genomes clustered with key-stone bacterial phylotypes indicated that the key-stone taxa had higher gene copies of oxidoreductases (participating most biogeochemical cycles of ecosystems and linking to microbial energetics) and 71 essential functional genes associated with carbon, nitrogen, phosphorus, and sulfur cycling. Altogether, our work highlights the fundamental role of the biodiversity of key-stone phylotypes in maintaining soil functioning and crop production after several decades of fertilization, and provides a list of key-stone phylotypes linking to crop production and soil nutrient cycling, which could give science-based guidance for sustainable food production.
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Affiliation(s)
- Kunkun Fan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Manuel Delgado-Baquerizo
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - Xisheng Guo
- Institute of Soil and Fertilizer Research, Anhui Academy of Agricultural Sciences, South Nongke Road 40, Hefei, 230031, China
| | - Daozhong Wang
- Institute of Soil and Fertilizer Research, Anhui Academy of Agricultural Sciences, South Nongke Road 40, Hefei, 230031, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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Al-Quwaie DAH. Bacterial community dynamics with rhizosphere of Calotropis procera and Senna alexandrina desert plants in Saudi Arabia. Bioinformation 2020; 16:567-578. [PMID: 33214744 PMCID: PMC7649021 DOI: 10.6026/97320630016567] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 06/12/2020] [Indexed: 12/30/2022] Open
Abstract
It is of interest to study the rhizobacteria associated with two different desert wild plants, e.g., Calotropis procera and Senna alexandrina compared with bulk soil sample in order to identify signatures of microbes in rhizospheres of the two plants and detect influence of soil microbiome in drawing soil architecture. Analysis of deep sequencing microbial dataset indicated occurrence of 296,642 sequence tags assigned 5,210 OTUs (operational taxonomic units). Species richness in control sample was higher than those of either plant's rhizosphere, while microbial abundance was lower. Principal coordinate analysis (PCoA) plot indicated complete separation of microbiome diversity among groups. Abundances of Pseudomonas stutzeri and Virgibacillus koreensis increased in the rhizosphere of C. procera compared with that of S. alexandrina, while those of Streptococcus sobrinus, Veillonella parvula and unassigned species of Sphingomonas genus increased in rhizosphere of S. alexandrina. Unassigned species of genera Marinobacter, Porticoccus and Alcanivorax only exist in rhizosphere microbiome of C. procera, while unassigned species of genus Pseudomonas only exists in rhizosphere microbiome of Senna alexandrina. High abundances of the two microbes Pseudomonas stutzeri and Virgibacillus koreensis in rhizosphere of C. procera allow the plant to grow well under both normal and saline condition. Also, Marinobacter, Porticoccus and Alcanivorax genera only exist in rhizosphere microbiome of C. procera. These microbes produce siderophores that protect plant from pathogens. Data shows that C. procera might be more protected from microbial pathogens compared with S. alexandrina. The differential abundances or exclusive presence of soil microbes reflect the ability of plant species to survive under biotic and abiotic stresses. Results imply that rhizospheric microbes can be used as biomarkers of plant growth rate and the ability to survive under harsh conditions.
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Affiliation(s)
- Diana AH Al-Quwaie
- Department of Biological Sciences, Rabigh College of Science and Arts, King Abdulaziz University (KAU), Rabigh, Saudi Arabia
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Shi Q, Jin J, Liu Y, Zhang Y, Cai Z, Ma Q, Cheng Y, Wen R, Nian H, Lian T. High Aluminum Drives Different Rhizobacterial Communities Between Aluminum-Tolerant and Aluminum-Sensitive Wild Soybean. Front Microbiol 2020; 11:1996. [PMID: 32973720 PMCID: PMC7466775 DOI: 10.3389/fmicb.2020.01996] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 07/28/2020] [Indexed: 11/18/2022] Open
Abstract
Aluminum (Al)-resistant plant cultivars can recruit beneficial microbes to alleviate the stresses. However, the mechanism of how rhizobacterial communities strengthen Al tolerance of wild soybean has not been addressed. The aim of this study was to investigate the bacterial community structure in the rhizosphere of Al-tolerant (BW69) and Al-sensitive (W270) wild soybean germplasm subjected to three Al concentrations. We analyzed the rhizobacterial communities of the two genotypes by high-throughput sequencing of 16S rRNA genes. The results showed that high Al stress recruited different rhizobacterial communities between two genotypes. In total, 49 OTUs, such as OTU15 (Gammaproteobacteria_KF-JG30-C25_norank), OTU23 (Mizugakiibacter), and OTU93 (Alkanibacter), were enriched in the rhizosphere of BW69 at the low and high Al concentrations. Moreover, bacterial community in the rhizosphere of BW69 had a more complex co-occurrence network than did W270 at the high Al concentration. Overall, our findings highlighted that high Al concentration magnified the difference in rhizobacterial community structure between two genotypes. However, the lower modularity of the co-occurrence network in rhizosphere of BW69 than W270 under Al stress may cause the rhizobacterial community to be less resistant and more influenced by disturbance. This study emphasizes the possibility of using rhizobacteria as an improved crop breeding or gene to produce crops that are more resistant to the toxicity of heavy metal.
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Affiliation(s)
- Qihan Shi
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Jing Jin
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Yuantai Liu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Yafeng Zhang
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Zhandong Cai
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Qibin Ma
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Yanbo Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Ronghui Wen
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Tengxiang Lian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
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Wang L, Gan Y, Bainard LD, Hamel C, St-Arnaud M, Hijri M. Expression of N-cycling genes of root microbiomes provides insights for sustaining oilseed crop production. Environ Microbiol 2020; 22:4545-4556. [PMID: 32656968 DOI: 10.1111/1462-2920.15161] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 07/07/2020] [Accepted: 07/09/2020] [Indexed: 11/28/2022]
Abstract
Agricultural production is dependent on inputs of nitrogen (N) whose cycle relies on soil and crop microbiomes. Crop diversification has increased productivity; however, its impact on the expression of microbial genes involved in N-cycling pathways remains unknown. Here, we assessed N-cycling gene expression patterns in the root and rhizosphere microbiomes of five oilseed crops as influenced by three 2-year crop rotations. The first phase consisted of fallow, lentil or wheat, and the second phase consisted of one of five oilseed crops. Expression of bacterial amoA, nirK and nirS genes showed that the microbiome of Ethiopian mustard had the lowest and that of camelina the highest potential for N loss. A preceding rotation phase of lentil significantly increased the expression of nifH gene by 23% compared with wheat and improved nxrA gene expression by 51% with chemical fallow in the following oilseed crops respectively. Lentil substantially increased biological N2 fixation and reduced denitrification in the following oilseed crops. Our results also revealed that most N-cycling gene transcripts are more abundant in the microbiomes associated with roots than with the rhizosphere. The outcome of our investigation brings a new level of understanding on how crop diversification and rotation sequences are related to N-cycling in annual cropping systems.
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Affiliation(s)
- Li Wang
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin Botanique de Montréal, Montréal, QC, H1X 2B2, Canada
| | - Yantai Gan
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, S9H 3X2, Canada
| | - Luke D Bainard
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, S9H 3X2, Canada
| | - Chantal Hamel
- Quebec Research and Development Centre, Agriculture and Agri-Food Canada, Quebec City, QC, G1V 2J3, Canada
| | - Marc St-Arnaud
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin Botanique de Montréal, Montréal, QC, H1X 2B2, Canada
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin Botanique de Montréal, Montréal, QC, H1X 2B2, Canada.,AgroBiosciences, Mohammed VI Polytechnic University (UM6P), Lot 660 - Hay Moulay Rachid, Ben Guerir, 43150, Morocco
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40
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Lisuma JB, Zuberi Z, Ndakidemi PA, Mbega ER. Linking rhizosphere bacterial diversity and soil fertility in tobacco plants under different soil types and cropping pattern in Tanzania: A pilot study. Heliyon 2020; 6:e04278. [PMID: 32671244 PMCID: PMC7347649 DOI: 10.1016/j.heliyon.2020.e04278] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/02/2020] [Accepted: 06/18/2020] [Indexed: 12/14/2022] Open
Abstract
Tobacco (Nicotiana tabacum L.), one of the major crop plants in Tanzania, cropping affects the level of soil fertility, but the reason has not been known. Plant rhizosphere plays an important role in affecting soil fertility through changing microbial composition. We planned a pilot study to understand the changes in microbial composition and soil nutrients in the rhizosphere soils of tobacco in three agro-ecological zone, namely Sikonge, Tabora and Urambo in Tanzania. This study assessed bacteriota composition using 16S rRNA sequencing and soil fertility in the rhizosphere of tobacco plants. The results showed that bacterial diversity in tobacco rhizosphere soils belonged to Proteobacteria phyla, associated significantly (p < 0.05) with solubilization of insoluble P, K and S. The solubilization of P, K and S in soils facilitates the availability of these nutrients to the tobacco plants (a heavy feeder crop) allows low levels of these nutrients in the soils for the subsequent crop. The Proteobacteria phyla also associated with an increase in soil N content through fixation. Therefore, bacteria diversity in tobacco rhizosphere influence solubilities of macronutrients (P, K, S) and quickly up taken by the tobacco plant and reduces their levels in soils, some bacteria involved in fixing N and increases total N in the soil.
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Affiliation(s)
- Jacob Bulenga Lisuma
- Department of Sustainable Agriculture and Biodiversity Ecosystems Management, School of Life Sciences and Bio-engineering, The Nelson Mandela African Institution of Science and Technology (NM-AIST), P.O Box 447, Arusha, Tanzania.,Department of Research, Tobacco Research Institute of Tanzania (TORITA), P.O Box 431, Tabora, Tanzania
| | - Zavuga Zuberi
- Department of Global Health and Biomedical Sciences, School of Life Sciences and Bio-engineering, The Nelson Mandela African Institution of Science and Technology (NM-AIST), P.O Box 447, Arusha, Tanzania.,Department of Science and Laboratory Technology, Dar es Salaam Institute of Technology (DIT), P.O Box 2958, Dar es Salaam, Tanzania
| | - Patrick Alois Ndakidemi
- Department of Sustainable Agriculture and Biodiversity Ecosystems Management, School of Life Sciences and Bio-engineering, The Nelson Mandela African Institution of Science and Technology (NM-AIST), P.O Box 447, Arusha, Tanzania
| | - Ernest Rashid Mbega
- Department of Sustainable Agriculture and Biodiversity Ecosystems Management, School of Life Sciences and Bio-engineering, The Nelson Mandela African Institution of Science and Technology (NM-AIST), P.O Box 447, Arusha, Tanzania
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41
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Richter-Heitmann T, Hofner B, Krah FS, Sikorski J, Wüst PK, Bunk B, Huang S, Regan KM, Berner D, Boeddinghaus RS, Marhan S, Prati D, Kandeler E, Overmann J, Friedrich MW. Stochastic Dispersal Rather Than Deterministic Selection Explains the Spatio-Temporal Distribution of Soil Bacteria in a Temperate Grassland. Front Microbiol 2020; 11:1391. [PMID: 32695081 PMCID: PMC7338559 DOI: 10.3389/fmicb.2020.01391] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 05/29/2020] [Indexed: 01/15/2023] Open
Abstract
Spatial and temporal processes shaping microbial communities are inseparably linked but rarely studied together. By Illumina 16S rRNA sequencing, we monitored soil bacteria in 360 stations on a 100 square meter plot distributed across six intra-annual samplings in a rarely managed, temperate grassland. Using a multi-tiered approach, we tested the extent to which stochastic or deterministic processes influenced the composition of local communities. A combination of phylogenetic turnover analysis and null modeling demonstrated that either homogenization by unlimited stochastic dispersal or scenarios, in which neither stochastic processes nor deterministic forces dominated, explained local assembly processes. Thus, the majority of all sampled communities (82%) was rather homogeneous with no significant changes in abundance-weighted composition. However, we detected strong and uniform taxonomic shifts within just nine samples in early summer. Thus, community snapshots sampled from single points in time or space do not necessarily reflect a representative community state. The potential for change despite the overall homogeneity was further demonstrated when the focus shifted to the rare biosphere. Rare OTU turnover, rather than nestedness, characterized abundance-independent β-diversity. Accordingly, boosted generalized additive models encompassing spatial, temporal and environmental variables revealed strong and highly diverse effects of space on OTU abundance, even within the same genus. This pure spatial effect increased with decreasing OTU abundance and frequency, whereas soil moisture – the most important environmental variable – had an opposite effect by impacting abundant OTUs more than the rare ones. These results indicate that – despite considerable oscillation in space and time – the abundant and resident OTUs provide a community backbone that supports much higher β-diversity of a dynamic rare biosphere. Our findings reveal complex interactions among space, time, and environmental filters within bacterial communities in a long-established temperate grassland.
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Affiliation(s)
- Tim Richter-Heitmann
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.,International Max Planck Research School of Marine Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Benjamin Hofner
- Institut für Medizininformatik, Biometrie und Epidemiologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Franz-Sebastian Krah
- Biodiversity Conservation, Institute for Ecology, Evolution and Diversity, Biologicum, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Johannes Sikorski
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Pia K Wüst
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sixing Huang
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Kathleen M Regan
- Institute of Soil Science and Land Evaluation, Soil Biology Department, University of Hohenheim, Stuttgart, Germany
| | - Doreen Berner
- Institute of Soil Science and Land Evaluation, Soil Biology Department, University of Hohenheim, Stuttgart, Germany
| | - Runa S Boeddinghaus
- Institute of Soil Science and Land Evaluation, Soil Biology Department, University of Hohenheim, Stuttgart, Germany
| | - Sven Marhan
- Institute of Soil Science and Land Evaluation, Soil Biology Department, University of Hohenheim, Stuttgart, Germany
| | - Daniel Prati
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Ellen Kandeler
- Institute of Soil Science and Land Evaluation, Soil Biology Department, University of Hohenheim, Stuttgart, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Michael W Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
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42
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Shi Q, Liu Y, Shi A, Cai Z, Nian H, Hartmann M, Lian T. Rhizosphere Soil Fungal Communities of Aluminum-Tolerant and -Sensitive Soybean Genotypes Respond Differently to Aluminum Stress in an Acid Soil. Front Microbiol 2020; 11:1177. [PMID: 32547532 PMCID: PMC7270577 DOI: 10.3389/fmicb.2020.01177] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Accepted: 05/08/2020] [Indexed: 01/22/2023] Open
Abstract
Different soybean genotypes can differ in their tolerance toward aluminum stress depending on their rhizosphere-inhabiting microorganisms. However, there is limited understanding of the response of fungal communities to different aluminum concentrations across different genotypes. Here, we used metabarcoding of fungal ribosomal markers to assess the effects of aluminum stress on the rhizosphere fungal community of aluminum-tolerant and aluminum-sensitive soybean genotypes. Shifts in fungal community structure were related to changes in plant biomass, fungal abundance and soil chemical properties. Aluminum stress increased the difference in fungal community structure between tolerant and sensitive genotypes. Penicillium, Cladosporium and Talaromyces increased with increasing aluminum concentration. These taxa associated with the aluminum-tolerant genotypes were enriched at the highest aluminum concentration. Moreover, complexity of the co-occurrence network associated with the tolerant genotypes increased at the highest aluminum concentration. Collectively, increasing aluminum concentrations magnified the differences in fungal community structure between the two studied tolerant and sensitive soybean genotypes. This study highlights the possibility to focus on rhizosphere fungal communities as potential breeding target to produce crops that are more tolerant toward heavy metal stress or toxicity in general.
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Affiliation(s)
- Qihan Shi
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China.,The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yuantai Liu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China.,The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Aoqing Shi
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China.,The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zhandong Cai
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China.,The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China.,The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Martin Hartmann
- Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Tengxiang Lian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China.,The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
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43
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Structure, Diversity, and Composition of Bacterial Communities in Rhizospheric Soil of Coptis chinensis Franch under Continuously Cropped Fields. DIVERSITY-BASEL 2020. [DOI: 10.3390/d12020057] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Soil microorganisms are critical factors of plant productivity in terrestrial ecosystems. Coptis chinensis Franch is one of the most important medicinal plants in China. Soil types and cropping systems influence the diversity and composition of the rhizospheric microbial communities. In the current study, we provide detailed information regarding the diversity and composition of the rhizospheric bacterial communities of the C. chinensis plants in continuously cropped fields and fallow fields in two seasons (i.e., winter and summer) using next-generation sequencing. The alpha diversity was higher in the five-year cultivated C. chinensis field (CyS5) and lower in fallow fields (NCS). Significant differences analysis confirmed more biomarkers in the cultivated field soil than in fallow fields. Additionally, the principal coordinate analysis (PcoA) of the beta diversity indices revealed that samples associated with the cultivated fields and fallow fields in different seasons were separated. Besides, Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria, Bacteroidetes, Gemmatimonadetes were the top bacterial phyla. Among these phyla, Proteobacteria were found predominantly and showed a decreasing trend with the continuous cropping of C. chinensis. A phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) revealed that the abundance of C and N functional genes had a significant difference between the soil samples from cultivated (CyS1, CyS3, and CyS5) and fallow (NCS) fields in two seasons (winter and summer). The principal coordinate analysis (PCoA) based on UniFrac distances (i.e., unweighted and weighted) revealed the variations in bacterial community structures in the soil samples. This study could provide a reference for solving the increasingly severe cropping obstacles and promote the sustainable development of the C. chinensis industry.
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44
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Abstract
Climate change, especially precipitation change, will significantly change soil moisture, which then influences root growth, further affecting yield and grain quality. Previous studies focused on the drought or flood effects on summer maize growth. However, few studied the effects of drought-flood abrupt alternation (DFAA) on the growth of summer maize. We explored the DFAA impacts on the roots, leaf area index (LAI), yield, and grain quality in field. The main results show that DFAA had different impacts on the summer maize growth in the seeding-jointing stage (SJS) and tasseling-grain filling stage (TGS). In general, the DFAA reduced the yield. Roots at the depth of 40 cm had obviously positive impacts on the yield. The DFAA reduced the LAI and promoted the maximum LAI achieving in advance. The grain crude protein augmented under DFAA. The drought had evidently negative impacts on the grain crude fat in the TGS, while it had no obvious influence in the SJS. DFAA had no apparent impact on the grain crude starch. These results could provide some references for the effects and adaptation-strategies study of extreme climate events and their impacts on growth of summer maize.
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45
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Ali W, Nadeem M, Ashiq W, Zaeem M, Gilani SSM, Rajabi-Khamseh S, Pham TH, Kavanagh V, Thomas R, Cheema M. The effects of organic and inorganic phosphorus amendments on the biochemical attributes and active microbial population of agriculture podzols following silage corn cultivation in boreal climate. Sci Rep 2019; 9:17297. [PMID: 31754161 PMCID: PMC6872752 DOI: 10.1038/s41598-019-53906-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 10/30/2019] [Indexed: 01/01/2023] Open
Abstract
Phosphorus (P) is the second most important macronutrient that limits the plant growth, development and productivity. Inorganic P fertilization in podzol soils predominantly bound with aluminum and iron, thereby reducing its availability to crop plants. Dairy manure (DM) amendment to agricultural soils can improve physiochemical properties, nutrient cycling through enhanced enzyme and soil microbial activities leading to improved P bioavailability to crops. We hypothesized that DM amendment in podzol soil will improve biochemical attributes and microbial community and abundance in silage corn cropping system under boreal climate. We evaluated the effects of organic and inorganic P amendments on soil biochemical attributes and abundance in podzol soil under boreal climate. Additionally, biochemical attributes and microbial population and abundance under short-term silage corn monocropping system was also investigated. Experimental treatments were [P0 (control); P1: DM with high P2O5; P2: DM with low P2O5; P3: inorganic P and five silage-corn genotypes (Fusion RR, Yukon R, A4177G3RIB, DKC 23-17RIB and DKC 26-28RIB) were laid out in a randomized complete block design in factorial settings with three replications. Results showed that P1 treatment increased acid phosphatase (AP-ase) activity (29% and 44%), and soil available P (SAP) (60% and 39%) compared to control treatment, during 2016 and 2017, respectively. Additionally, P1 treatments significantly increased total bacterial phospholipids fatty acids (ΣB-PLFA), total phospholipids fatty acids (ΣPLFA), fungi, and eukaryotes compared to control and inorganic P. Yukon R and DKC 26-28RIB genotypes exhibited higher total bacterial PLFA, fungi, and total PLFA in their rhizospheres compared to the other genotypes. Redundancy analyses showed promising association between P1 and P2 amendment, biochemical attributes and active microbial population and Yukon R and DKC 26-28RIB genotypes. Pearson correlation also demonstrated significant and positive correlation between AP-ase, SAP and gram negative bacteria (G-), fungi, ΣB-PLFA, and total PLFA. Study results demonstrated that P1 treatment enhanced biochemical attributes, active microbial community composition and abundance and forage production of silage corn. Results further demonstrated higher active microbial population and abundance in rhizosphere of Yukon R and DKC 26-28RIB genotypes. Therefore, we argue that dairy manure amendment with high P2O5 in podzol soils could be a sustainable nutrient source to enhance soil quality, health and forage production of silage corn. Yukon R and DKC 26-28RIB genotypes showed superior agronomic performance, therefore, could be good fit under boreal climatic conditions.
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Affiliation(s)
- Waqas Ali
- School of Science and the Environment, Grenfell Campus Memorial University of Newfoundland, Corner Brook, Newfoundland and Labrador, A2H 5G4, Canada
| | - Muhammad Nadeem
- School of Science and the Environment, Grenfell Campus Memorial University of Newfoundland, Corner Brook, Newfoundland and Labrador, A2H 5G4, Canada
| | - Waqar Ashiq
- School of Science and the Environment, Grenfell Campus Memorial University of Newfoundland, Corner Brook, Newfoundland and Labrador, A2H 5G4, Canada
| | - Muhammad Zaeem
- School of Science and the Environment, Grenfell Campus Memorial University of Newfoundland, Corner Brook, Newfoundland and Labrador, A2H 5G4, Canada
| | - Syed Shah Mohioudin Gilani
- School of Science and the Environment, Grenfell Campus Memorial University of Newfoundland, Corner Brook, Newfoundland and Labrador, A2H 5G4, Canada
| | - Sanaz Rajabi-Khamseh
- Shahrekord University, Rahbr Blvd, Shahrekord Chaharmahal and Bakhtiari, Shahrekord, Iran
| | - Thu Huong Pham
- School of Science and the Environment, Grenfell Campus Memorial University of Newfoundland, Corner Brook, Newfoundland and Labrador, A2H 5G4, Canada
| | - Vanessa Kavanagh
- Department of Fisheries and Land Resources, Government of Newfoundland and Labrador, Pasadena, A0L 1K0, Canada
| | - Raymond Thomas
- School of Science and the Environment, Grenfell Campus Memorial University of Newfoundland, Corner Brook, Newfoundland and Labrador, A2H 5G4, Canada
| | - Mumtaz Cheema
- School of Science and the Environment, Grenfell Campus Memorial University of Newfoundland, Corner Brook, Newfoundland and Labrador, A2H 5G4, Canada.
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46
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Schmidt JE, Kent AD, Brisson VL, Gaudin ACM. Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling. MICROBIOME 2019; 7:146. [PMID: 31699148 PMCID: PMC6839119 DOI: 10.1186/s40168-019-0756-9] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 10/02/2019] [Indexed: 05/11/2023]
Abstract
BACKGROUND Rhizosphere microbial communities are key regulators of plant performance, yet few studies have assessed the impact of different management approaches on the rhizosphere microbiomes of major crops. Rhizosphere microbial communities are shaped by interactions between agricultural management and host selection processes, but studies often consider these factors individually rather than in combination. We tested the impacts of management (M) and rhizosphere effects (R) on microbial community structure and co-occurrence networks of maize roots collected from long-term conventionally and organically managed maize-tomato agroecosystems. We also explored the interaction between these factors (M × R) and how it impacts rhizosphere microbial diversity and composition, differential abundance, indicator taxa, co-occurrence network structure, and microbial nitrogen-cycling processes. RESULTS Host selection processes moderate the influence of agricultural management on rhizosphere microbial communities, although bacteria and fungi respond differently to plant selection and agricultural management. We found that plants recruit management-system-specific taxa and shift N-cycling pathways in the rhizosphere, distinguishing this soil compartment from bulk soil. Rhizosphere microbiomes from conventional and organic systems were more similar in diversity and network structure than communities from their respective bulk soils, and community composition was affected by both M and R effects. In contrast, fungal community composition was affected only by management, and network structure only by plant selection. Quantification of six nitrogen-cycling genes (nifH, amoA [bacterial and archaeal], nirK, nrfA, and nosZ) revealed that only nosZ abundance was affected by management and was higher in the organic system. CONCLUSIONS Plant selection interacts with conventional and organic management practices to shape rhizosphere microbial community composition, co-occurrence patterns, and at least one nitrogen-cycling process. Reframing research priorities to better understand adaptive plant-microbe feedbacks and include roots as a significant moderating influence of management outcomes could help guide plant-oriented strategies to improve productivity and agroecosystem sustainability.
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Affiliation(s)
- Jennifer E. Schmidt
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616 USA
| | - Angela D. Kent
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, N-215 Turner Hall, MC-047, 1102 S. Goodwin Avenue, Urbana, IL USA
| | - Vanessa L. Brisson
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
- The DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Amélie C. M. Gaudin
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616 USA
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47
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Galindo-Castañeda T, Brown KM, Kuldau GA, Roth GW, Wenner NG, Ray S, Schneider H, Lynch JP. Root cortical anatomy is associated with differential pathogenic and symbiotic fungal colonization in maize. PLANT, CELL & ENVIRONMENT 2019; 42:2999-3014. [PMID: 31314912 DOI: 10.1111/pce.13615] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 05/06/2023]
Abstract
Root anatomical phenotypes vary among maize (Zea mays) cultivars and may have adaptive value by modifying the metabolic cost of soil exploration. However, the microbial trade-offs of these phenotypes are unknown. We hypothesized that nodal roots of maize with contrasting cortical anatomy have different patterns of mutualistic and pathogenic fungal colonization. Arbuscular mycorrhizal colonization in the field and mesocosms, root rots in the field, and Fusarium verticillioides colonization in mesocosms were evaluated in maize genotypes with contrasting root cortical anatomy. Increased aerenchyma and decreased living cortical area were associated with decreased mycorrhizal colonization in mesocosm and field experiments with inbred genotypes. In contrast, mycorrhizal colonization of hybrids increased with larger aerenchyma lacunae; this increase coincided with larger root diameters of hybrid roots. F. verticillioides colonization was inversely correlated with living cortical area in mesocosm-grown inbreds, and no relation was found between root rots and living cortical area or aerenchyma in field-grown hybrids. Root rots were positively correlated with cortical cell file number and inversely correlated with cortical cell size. Mycorrhizae and root rots were inversely correlated in field-grown hybrids. We conclude that root anatomy is associated with differential effects on pathogens and mycorrhizal colonization of nodal roots in maize.
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Affiliation(s)
- Tania Galindo-Castañeda
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Kathleen M Brown
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Gretchen A Kuldau
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Gregory W Roth
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Nancy G Wenner
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Swayamjit Ray
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Hannah Schneider
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Jonathan P Lynch
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
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48
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Lablab Purpureus Influences Soil Fertility and Microbial Diversity in a Tropical Maize-Based No-Tillage System. SOIL SYSTEMS 2019. [DOI: 10.3390/soilsystems3030050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
There are multiple mechanisms by which enhanced diversity of plant communities improves soil structure and function. One critical pathway mediating this relationship is through changes to soil prokaryotic communities. Here, nine different cropping systems were studied to evaluate how legume and grass cover crops influence soil fertility and microbial communities in a maize-based no tillage system. The soil’s bacterial and archaeal communities were sequenced (Illumina GAIIx, 12 replicates for treatment) and correlated with eight different soil features. The microbial community composition differed widely between planting treatments, with three primary “community types” emerging in multivariate space: (1) A community type associated with bare soil linked with low P, low pH, and high aluminum [Al]; (2) a community type associated with Lablab beans linked with high soil N, total organic carbon and other base cation concentrations, and high pH; and (3) a community type of all other non-lablab planting arrangements linked with higher soil P (relative to bare soil), but lower soil fertility (N and base cations). Lablab-based arrangements also expressed the highest microbial richness and alpha diversity. The inclusion of Lablab in maize-based cropping systems represents a potential alternative to reduce the use of chemical fertilizers and increase the chemical and biological quality in agricultural soils under the no-tillage system.
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Ali A, Imran Ghani M, Li Y, Ding H, Meng H, Cheng Z. Hiseq Base Molecular Characterization of Soil Microbial Community, Diversity Structure, and Predictive Functional Profiling in Continuous Cucumber Planted Soil Affected by Diverse Cropping Systems in an Intensive Greenhouse Region of Northern China. Int J Mol Sci 2019; 20:ijms20112619. [PMID: 31141960 PMCID: PMC6600451 DOI: 10.3390/ijms20112619] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 05/16/2019] [Accepted: 05/21/2019] [Indexed: 02/05/2023] Open
Abstract
Cover crops are key determinants of the ecological stability and sustainability of continuous cropping soils. However, their agro-ecological role in differentially reshaping the microbiome structure and functioning under a degraded agroecosystem remains poorly investigated. Therefore, structural and metabolic changes in soil bacterial community composition in response to diverse plant species were assessed. Winter catch leafy vegetables crops were introduced as cover plants in a cucumber-fallow period. The results indicate that cover crop diversification promoted beneficial changes in soil chemical and biological attributes, which increased crop yields in a cucumber double-cropping system. Illumina high-throughput sequencing of 16S rRNA genes indicated that the bacterial community composition and diversity changed through changes in the soil properties. Principal component analysis (PCA) coupled with non-metric multidimensional scaling (NMDS) analysis reveals that the cover planting shaped the soil microbiome more than the fallow planting (FC). Among different cropping systems, spinach–cucumber (SC) and non-heading Chinese cabbage–cucumber (NCCC) planting systems greatly induced higher soil nutrient function, biological activity, and bacterial diversity, thus resulting in higher cucumber yield. Quantitative analysis of linear discriminant analysis effect size (LEfSe) indicated that Proteobacteria, Actinobacteria, Bacteroidetes, and Acidobacteria were the potentially functional and active soil microbial taxa. Rhizospheres of NCCC, leaf lettuce–cucumber (LLC), coriander–cucumber (CC), and SC planting systems created hotspots for metabolic capabilities of abundant functional genes, compared to FC. In addition, the predictive metabolic characteristics (metabolism and detoxification) associated with host–plant symbiosis could be an important ecological signal that provides direct evidence of mediation of soil structure stability. Interestingly, the plant density of non–heading Chinese cabbage and spinach species was capable of reducing the adverse effect of arsenic (As) accumulation by increasing the function of the arsenate reductase pathway. Redundancy analysis (RDA) indicated that the relative abundance of the core microbiome can be directly and indirectly influenced by certain environmental determinants. These short-term findings stress the importance of studying cover cropping systems as an efficient biological tool to protect the ecological environment. Therefore, we can speculate that leafy crop diversification is socially acceptable, economically justifiable, and ecologically adaptable to meet the urgent demand for intensive cropping systems to promote positive feedback between crop–soil sustainable intensification.
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Affiliation(s)
- Ahmad Ali
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | | | - Yuhong Li
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Haiyan Ding
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Huanwen Meng
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Zhihui Cheng
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
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Moreau D, Bardgett RD, Finlay RD, Jones DL, Philippot L. A plant perspective on nitrogen cycling in the rhizosphere. Funct Ecol 2019. [DOI: 10.1111/1365-2435.13303] [Citation(s) in RCA: 159] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Delphine Moreau
- Agroécologie, AgroSup Dijon INRA, Université Bourgogne Franche‐Comté Dijon France
| | - Richard D. Bardgett
- School of Earth and Environmental Sciences The University of Manchester Manchester UK
| | - Roger D. Finlay
- Department of Forest Mycology and Plant Pathology Uppsala Biocenter, Swedish University of Agricultural Sciences Uppsala Sweden
| | - David L. Jones
- Environment Centre Wales Bangor University Gwynedd UK
- UWA School of Agriculture and Environment University of Western Australia Crawley Western Australia Australia
| | - Laurent Philippot
- Agroécologie, AgroSup Dijon INRA, Université Bourgogne Franche‐Comté Dijon France
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