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Dietrich M, Panhölzl C, Angel R, Giguere AT, Randi D, Hausmann B, Herbold CW, Pötsch EM, Schaumberger A, Eichorst SA, Woebken D. Plant roots affect free-living diazotroph communities in temperate grassland soils despite decades of fertilization. Commun Biol 2024; 7:846. [PMID: 38987659 PMCID: PMC11237082 DOI: 10.1038/s42003-024-06522-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
Fixation of atmospheric N2 by free-living diazotrophs accounts for an important proportion of nitrogen naturally introduced to temperate grasslands. The effect of plants or fertilization on the general microbial community has been extensively studied, yet an understanding of the potential combinatorial effects on the community structure and activity of free-living diazotrophs is lacking. In this study we provide a multilevel assessment of the single and interactive effects of different long-term fertilization treatments, plant species and vicinity to roots on the free-living diazotroph community in relation to the general microbial community in grassland soils. We sequenced the dinitrogenase reductase (nifH) and the 16S rRNA genes of bulk soil and root-associated compartments (rhizosphere soil, rhizoplane and root) of two grass species (Arrhenatherum elatius and Anthoxanthum odoratum) and two herb species (Galium album and Plantago lanceolata) growing in Austrian grassland soils treated with different fertilizers (N, P, NPK) since 1960. Overall, fertilization has the strongest effect on the diazotroph and general microbial community structure, however with vicinity to the root, the plant effect increases. Despite the long-term fertilization, plants strongly influence the diazotroph communities emphasizing the complexity of soil microbial communities' responses to changing nutrient conditions in temperate grasslands.
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Affiliation(s)
- Marlies Dietrich
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Christopher Panhölzl
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Roey Angel
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, České Budějovice, Czechia
| | - Andrew T Giguere
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Dania Randi
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Craig W Herbold
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Te Kura Pūtaiao Koiora, School of Biological Sciences, Te Whare Wānanga o Waitaha, University of Canterbury, Christchurch, New Zealand
| | - Erich M Pötsch
- Institute of Plant Production and Cultural Landscape, Agricultural Research and Education Centre, Raumberg-Gumpenstein, Austria
| | - Andreas Schaumberger
- Institute of Plant Production and Cultural Landscape, Agricultural Research and Education Centre, Raumberg-Gumpenstein, Austria
| | - Stephanie A Eichorst
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Dagmar Woebken
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
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Sun M, Xiao D, Zhang W, Wang K. Impacts of Managed Vegetation Restoration on Arbuscular Mycorrhizal Fungi and Diazotrophs in Karst Ecosystems. J Fungi (Basel) 2024; 10:280. [PMID: 38667951 PMCID: PMC11051020 DOI: 10.3390/jof10040280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/02/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
The crucial functional arbuscular mycorrhizal fungi (AMF) and diazotrophs play pivotal roles in nutrient cycling during vegetation restoration. However, the impact of managed vegetation restoration strategies on AMF and diazotroph communities remains unclear. In this study, we investigated the community structure and diversity of AMF and diazotrophs in a karst region undergoing managed vegetation restoration from cropland. Soil samples were collected from soils under three vegetation restoration strategies, plantation forest (PF), forage grass (FG), and a mixture of plantation forest and forage grass (FF), along with a control for cropland rotation (CR). The diversity of both AMF and diazotrophs was impacted by managed vegetation restoration. Specifically, the AMF Shannon index was higher in CR and PF compared to FF. Conversely, diazotroph richness was lower in CR, PF, and FG than in FF. Furthermore, both AMF and diazotroph community compositions differed between CR and FF. The relative abundance of AMF taxa, such as Glomus, was lower in FF compared to the other three land-use types, while Racocetra showed the opposite trend. Among diazotroph taxa, the relative abundance of Anabaena, Nostoc, and Rhizobium was higher in FF than in CR. Soil properties such as total potassium, available potassium, pH, and total nitrogen were identified as the main factors influencing AMF and diazotroph diversity. These findings suggest that AMF and diazotroph communities were more sensitive to FF rather than PF and FG after managed vegetation restoration from cropland, despite similar levels of soil nutrients among PF, FG, and FF. Consequently, the integration of diverse economic tree species and forage grasses in mixed plantations notably altered the diversity and species composition of AMF and diazotrophs, primarily through the promotion of biocrust formation and root establishment.
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Affiliation(s)
- Mingming Sun
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (M.S.); (W.Z.)
- Huanjiang Agriculture Ecosystem Observation and Research Station of Guangxi, Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, China
- University of Chinese Academy of Sciences, Beijing 100039, China
- Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, China
| | - Dan Xiao
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (M.S.); (W.Z.)
| | - Wei Zhang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China; (M.S.); (W.Z.)
- Huanjiang Agriculture Ecosystem Observation and Research Station of Guangxi, Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, China
- Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, China
| | - Kelin Wang
- Huanjiang Agriculture Ecosystem Observation and Research Station of Guangxi, Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, China
- Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, China
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Ben Zineb A, Lamine M, Khallef A, Hamdi H, Ahmed T, Al-Jabri H, Alsafran M, Mliki A, Sayadi S, Gargouri M. Harnessing rhizospheric core microbiomes from arid regions for enhancing date palm resilience to climate change effects. Front Microbiol 2024; 15:1362722. [PMID: 38646634 PMCID: PMC11027745 DOI: 10.3389/fmicb.2024.1362722] [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: 12/28/2023] [Accepted: 03/11/2024] [Indexed: 04/23/2024] Open
Abstract
Date palm cultivation has thrived in the Gulf Cooperation Council region since ancient times, where it represents a vital sector in agricultural and socio-economic development. However, climate change conditions prevailing for decades in this area, next to rarefication of rain, hot temperatures, intense evapotranspiration, rise of sea level, salinization of groundwater, and intensification of cultivation, contributed to increase salinity in the soil as well as in irrigation water and to seriously threaten date palm cultivation sustainability. There are also growing concerns about soil erosion and its repercussions on date palm oases. While several reviews have reported on solutions to sustain date productivity, including genetic selection of suitable cultivars for the local harsh environmental conditions and the implementation of efficient management practices, no systematic review of the desertic plants' below-ground microbial communities and their potential contributions to date palm adaptation to climate change has been reported yet. Indeed, desert microorganisms are expected to address critical agricultural challenges and economic issues. Therefore, the primary objectives of the present critical review are to (1) analyze and synthesize current knowledge and scientific advances on desert plant-associated microorganisms, (2) review and summarize the impacts of their application on date palm, and (3) identify possible gaps and suggest relevant guidance for desert plant microbes' inoculation approach to sustain date palm cultivation within the Gulf Cooperation Council in general and in Qatar in particular.
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Affiliation(s)
- Ameni Ben Zineb
- Center for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Mariem Lamine
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
| | - Ahlem Khallef
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
- Higher Institute of Biotechnology of Monastir, University of Monastir, Monastir, Tunisia
| | - Helmi Hamdi
- Center for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Talaat Ahmed
- Environmental Science Center, Qatar University, Doha, Qatar
| | - Hareb Al-Jabri
- Center for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Mohammed Alsafran
- Agricultural Research Station, Office of VP for Research and Graduate Studies, Qatar University, Doha, Qatar
| | - Ahmed Mliki
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
| | - Sami Sayadi
- Center for Sustainable Development, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Mahmoud Gargouri
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
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Bullergahn VB, Menezes KMS, Veloso TGR, da Luz JMR, Castanheira LF, Pereira LL, da Silva MDCS. Diversity of potential nitrogen-fixing bacteria from rhizosphere of the Coffea arabica L. and Coffea canephora L. 3 Biotech 2024; 14:27. [PMID: 38173824 PMCID: PMC10758376 DOI: 10.1007/s13205-023-03875-7] [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: 03/25/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024] Open
Abstract
Coffea arabica L. and Coffea canephora L. are coffee species most consumed and marketed in the world. The coffee crop requires a large amount of nitrogen, which shows the importance of knowledge of the population of nitrogen-fixing bacteria (NFB) from the rhizosphere of these crops. These microorganisms may help the reduction of nitrogen fertilizing. However, there is no production of NFB inoculum in the coffee. Therefore, our objective was to evaluate the diversity of potential nitrogen-fixing bacteria (PNFB) in the rhizosphere of C. arabica and C. canephora. The microbial DNA of the soil was extracted, amplified through PCR, and sequenced at the Illumina Miseq. platform. The PNFB prediction was performed using the program PICRUSt2. Three hundred and thirty-seven amplicon sequence variants (ASVs) were identified as PNFB in two coffee species. Xanthobacteraceae, Rhizobium multhospitiium, Rhizobium mesosinicum, and Bradyrhizobium sp. were detected in all samples and main components of the core microbiota of the coffee plant rhizosphere. Some ASVs are exclusive from one of the coffee farms, showing that the coffee specie cultivated may influence the PNFB communities. However, edaphoclimatic factors and soil chemical attributes can also influence the distribution of ASVs in coffee soil. In the C. canephora, the PNFB diversity was influenced by the altitude and the soil chemical attributes, while the altitude and the phosphorus content influenced the PNFB population in C. arabica. Our results are important to the understanding of the PNFB dynamic in coffee soil and for the agricultural inputs bioprospecting to coffee.
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Affiliation(s)
| | | | | | | | | | - Lucas Louzada Pereira
- Federal Institute of Espírito Santo, Venda Nova do Imigrante, Espírito Santo, Brazil
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Guo B, Zhang H, Liu Y, Chen J, Li J. Drought-resistant trait of different crop genotypes determines assembly patterns of soil and phyllosphere microbial communities. Microbiol Spectr 2023; 11:e0006823. [PMID: 37754752 PMCID: PMC10581042 DOI: 10.1128/spectrum.00068-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 08/04/2023] [Indexed: 09/28/2023] Open
Abstract
Crop microbiomes are widely recognized to play a role in crop stress resistance, but the ecological processes that shape crop microbiomes under water stress are unclear. Therefore, we investigated the bacterial communities of two oat (Avena sativa) and two wheat (Triticum aestivum) genotypes under different water stress conditions. Our results show that the microbial assemblage was determined by the crop compartment niche. Host selection pressure on the bacterial community increased progressively from soil to epiphyte to endophyte pathways, leading to a decrease in bacterial community diversity and network complexity. Source tracing shows that soil is the primary source of crop microbial communities and that bulk soil is the main potential source of crop microbiota. It filters gradually through the different compartment niches of the crop. We found that the phyla Actinobacteria, Proteobacteria, Gemmatimonadota, and Myxococcota were significantly enriched in bacterial communities associated with crop-resistance enzyme activity. Crop genotype influenced the composition of the rhizosphere soil microbial community, and the composition of the phylloplane microbial community was affected by water stress. IMPORTANCE In this paper, we investigated the assembly of the plant microbiome in response to water stress. We found that the determinant of microbiome assembly under water stress was the host type and that microbial communities were progressively filtered and enriched as they moved from soil to epiphyte to endophyte communities, with the main potential source being bulk soil. We also screened for bacterial communities that were significantly associated with crop enzyme activity. Our research provides insights into the manipulation of microbes in response to crop resistance to water stress.
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Affiliation(s)
- Baobei Guo
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
- Pomology Institute, Shanxi Agricultural University, Taiyuan, Shanxi, China
| | - Hong Zhang
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
| | - Yong Liu
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
| | - Jianwen Chen
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
| | - Junjian Li
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
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Gen-Jiménez A, Flores-Félix JD, Rincón-Molina CI, Manzano-Gomez LA, Rogel MA, Ruíz-Valdiviezo VM, Rincón-Molina FA, Rincón-Rosales R. Enhance of tomato production and induction of changes on the organic profile mediated by Rhizobium biofortification. Front Microbiol 2023; 14:1235930. [PMID: 37601341 PMCID: PMC10433389 DOI: 10.3389/fmicb.2023.1235930] [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: 06/07/2023] [Accepted: 07/18/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction The extensive use of chemical fertilizers has served as a response to the increasing need for crop production in recent decades. While it addresses the demand for food, it has resulted in a decline in crop productivity and a heightened negative environmental impact. In contrast, plant probiotic bacteria (PPB) offer a promising alternative to mitigate the negative consequences of chemical fertilizers. PPB can enhance nutrient availability, promote plant growth, and improve nutrient uptake efficiency, thereby reducing the reliance on chemical fertilizers. Methods This study aimed to evaluate the impact of native Rhizobium strains, specifically Rhizobium calliandrae LBP2-1, Rhizobium mayense NSJP1-1, and Rhizobium jaguaris SJP1- 2, on the growth, quality, and rhizobacterial community of tomato crops. Various mechanisms promoting plant growth were investigated, including phosphate solubilization, siderophore production, indole acetic acid synthesis, and cellulose and cellulase production. Additionally, the study involved the assessment of biofilm formation and root colonization by GFP-tagged strains, conducted a microcosm experiment, and analyzed the microbial community using metagenomics of rhizospheric soil. Results The results showed that the rhizobial strains LBP2-1, NSJP1-1 and SJP1-2 had the ability to solubilize dicalcium phosphate, produce siderophores, synthesize indole acetic acid, cellulose production, biofilm production, and root colonization. Inoculation of tomato plants with native Rhizobium strains influenced growth, fruit quality, and plant microbiome composition. Metagenomic analysis showed increased Proteobacteria abundance and altered alpha diversity indices, indicating changes in rhizospheric bacterial community. Discussion Our findings demonstrate the potential that native Rhizobium strains have to be used as a plant probiotic in agricultural crops for the generation of safe food and high nutritional value.
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Affiliation(s)
- Adriana Gen-Jiménez
- Laboratorio de Ecología Genómica, Tecnológico Nacional de México, Instituto Tecnológico de Tuxtla Gutiérrez, Tuxtla Gutiérrez, Chiapas, Mexico
| | | | - Clara Ivette Rincón-Molina
- Laboratorio de Ecología Genómica, Tecnológico Nacional de México, Instituto Tecnológico de Tuxtla Gutiérrez, Tuxtla Gutiérrez, Chiapas, Mexico
| | - Luis Alberto Manzano-Gomez
- Laboratorio de Ecología Genómica, Tecnológico Nacional de México, Instituto Tecnológico de Tuxtla Gutiérrez, Tuxtla Gutiérrez, Chiapas, Mexico
- Departamento de Investigación y Desarrollo, 3R Biotec SA de CV, Tuxtla Gutiérrez, Chiapas, Mexico
| | - Marco Antonio Rogel
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Víctor Manuel Ruíz-Valdiviezo
- Laboratorio de Ecología Genómica, Tecnológico Nacional de México, Instituto Tecnológico de Tuxtla Gutiérrez, Tuxtla Gutiérrez, Chiapas, Mexico
| | - Francisco Alexander Rincón-Molina
- Laboratorio de Ecología Genómica, Tecnológico Nacional de México, Instituto Tecnológico de Tuxtla Gutiérrez, Tuxtla Gutiérrez, Chiapas, Mexico
| | - Reiner Rincón-Rosales
- Laboratorio de Ecología Genómica, Tecnológico Nacional de México, Instituto Tecnológico de Tuxtla Gutiérrez, Tuxtla Gutiérrez, Chiapas, Mexico
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Papatheodorou EM, Papakostas S, Stamou GP. Fire and Rhizosphere Effects on Bacterial Co-Occurrence Patterns. Microorganisms 2023; 11:microorganisms11030790. [PMID: 36985363 PMCID: PMC10052084 DOI: 10.3390/microorganisms11030790] [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: 02/06/2023] [Revised: 03/10/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Fires are common in Mediterranean soils and constitute an important driver of their evolution. Although fire effects on vegetation dynamics are widely studied, their influence on the assembly rules of soil prokaryotes in a small-scale environment has attracted limited attention. In the present study, we reanalyzed the data from Aponte et al. (2022) to test whether the direct and/or indirect effects of fire are reflected in the network of relationships among soil prokaryotes in a Chilean sclerophyllous ecosystem. We focused on bacterial (genus and species level) co-occurrence patterns in the rhizospheres and bulk soils in burned and unburned plots. Four soils were considered: bulk-burnt (BB), bulk-unburnt (BU), rhizosphere-burnt (RB), and rhizosphere-unburnt (RU). The largest differences in network parameters were recorded between RU and BB soils, while RB and BU networks exhibited similar values. The network in the BB soil was the most compact and centralized, while the RU network was the least connected, with no central nodes. The robustness of bacterial communities was enhanced in burnt soils, but this was more pronounced in BB soil. The mechanisms mainly responsible for bacterial community structure were stochastic in all soils, whether burnt or unburnt; however, communities in RB were much more stochastic than in RU.
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Affiliation(s)
| | - Spiros Papakostas
- Department of Science and Technology, School of Science and Technology, University Center of International Programmes of Studies, International Hellenic University, 57001 Thessaloniki, Greece
| | - George P Stamou
- Department of Ecology, School of Biology, AUTH, 54124 Thessaloniki, Greece
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Zhou Y, Shao T, Men G, Chen J, Li N, Gao X, Long X, Rengel Z, Zhu M. Application of malrstone-based conditioner and plantation of Jerusalem artichoke improved properties of saline-alkaline soil in Inner Mongolia. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 329:117083. [PMID: 36566724 DOI: 10.1016/j.jenvman.2022.117083] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 12/15/2022] [Accepted: 12/17/2022] [Indexed: 06/17/2023]
Abstract
Soil salinization is a critical environmental issue restricting agricultural production. Inner Mongolia is one of the areas with severe land salinization in China. This study aimed to investigate the effects of conditioning agent (containing marlstone and a range of enzymes) and cultivating Jerusalem artichoke on saline soils in Inner Mongolia. The effects of conditioner (0, 0.06 and 0.18 kg/m2) on soil physical, chemical and biological properties, including soil carbon fractions and microbiota in saline soils planted with Jerusalem artichoke, were characterized. The results showed that soil salinity was reduced significantly after cultivating Jerusalem artichoke and declined also after the conditioner addition. The application of conditioner increased the content of DOC (dissolved organic carbon), HFOC (heavy fraction organic carbon) and the content of aggregates >0.25 mm compared to the soil planted with Jerusalem artichoke alone. The relative abundance of halophilic bacteria such as Thioalkalivibrio and Thiohalobacter was greater in the CK (non-treated control). By contrast, the relative abundance of microorganisms with the carbon assimilation and nitrogen fixation capacities, such as Cyanobacteria and Rhodovulum, was greater in the conditioner-treated and Jerusalem artichoke-planted treatments. The planting of Jerusalem artichoke reduced soil salinity, increased soil organic carbon fractions, improved soil structure, and altered the soil microbial community, with the application of the conditioning agent enhancing these positive changes. The co-occurrence network structure of "Jerusalem artichoke-conditioner-saline soil-soil microorganism" was established, which provided scientific basis for Jerusalem artichoke-conditioner to improve saline soil.
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Affiliation(s)
- Yujie Zhou
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tianyun Shao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guotao Men
- Institute of Crop Sciences, Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Inner Mongolia, 010031, China
| | - Jiahao Chen
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Liangyungang, China
| | - Na Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiumei Gao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaohua Long
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Zed Rengel
- Soil Science and Plant Nutrition, UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Perth WA, 6009, Australia; Institute for Adriatic Crops and Karst Reclamation, Put Duilova 11, Split, Croatia
| | - Ming Zhu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Liangyungang, China
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Shamim A, Sanka Loganathachetti D, Chandran S, Masmoudi K, Mundra S. Salinity of irrigation water selects distinct bacterial communities associated with date palm (Phoenix dactylifera L.) root. Sci Rep 2022; 12:12733. [PMID: 35882908 PMCID: PMC9325759 DOI: 10.1038/s41598-022-16869-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 07/18/2022] [Indexed: 01/18/2023] Open
Abstract
Saline water irrigation has been used in date palm (Phoenix dactylifera L.) agriculture as an alternative to non-saline water due to water scarcity in hyper-arid environments. However, the knowledge pertaining to saline water irrigation impact on the root-associated bacterial communities of arid agroecosystems is scarce. In this study, we investigated the effect of irrigation sources (non-saline freshwater vs saline groundwater) on date palm root-associated bacterial communities using 16S rDNA metabarcoding. The bacterial richness, Shannon diversity and evenness didn't differ significantly between the irrigation sources. Soil electrical conductivity (EC) and irrigation water pH were negatively related to Shannon diversity and evenness respectively, while soil organic matter displayed a positive correlation with Shannon diversity. 40.5% of total Operational Taxonomic Units were unique to non-saline freshwater irrigation, while 26% were unique to saline groundwater irrigation. The multivariate analyses displayed strong structuring of bacterial communities according to irrigation sources, and both soil EC and irrigation water pH were the major factors affecting bacterial communities. The genera Bacillus, Micromonospora and Mycobacterium were dominated while saline water irrigation whereas contrasting pattern was observed for Rhizobium, Streptomyces and Acidibacter. Taken together, we suggest that date-palm roots select specific bacterial taxa under saline groundwater irrigation, which possibly help in alleviating salinity stress and promote growth of the host plant.
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Affiliation(s)
- Azra Shamim
- Department of Integrative Agriculture, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al-Ain, Abu-Dhabi, UAE
| | | | - Subha Chandran
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain, Abu-Dhabi, UAE
| | - Khaled Masmoudi
- Department of Integrative Agriculture, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al-Ain, Abu-Dhabi, UAE.
| | - Sunil Mundra
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain, Abu-Dhabi, UAE.
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, United Arab Emirates.
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Liu J, Wang C, Guo Z, Xu A, Pan K, Pan X. The effects of climate on soil microbial diversity shift after intensive agriculture in arid and semiarid regions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 821:153075. [PMID: 35038533 DOI: 10.1016/j.scitotenv.2022.153075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 12/14/2021] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
Abstract
In arid and semiarid desert areas, climate factors distinctly impact soil microbial community, which can also be greatly altered after agricultural practices at multiple spatial scales. However, it is still poorly unknown whether the effects of climate on soil microbial diversity change after intensive agriculture at a large spatial scale. To uncover this concern, we used time-interval archived soils, taken from paired desert and agricultural experiments at five field stations of the Chinese Ecosystem Research Network across northern China, and performed high-throughput sequencing. Herein, we discovered that the clustering pattern of soil microbial communities was influenced by precipitation at some extent in desert ecosystem, while not impacted by climate factors in agricultural ecosystem. In addition, the analyses on microbial communities presented that the effects of climate factors on the communities decreased after agricultural practices. Soil microbial richness was significantly correlated with environmental temperature in deserts (R = -0.39, P < 0.001) and croplands (R = 0.34, P = 0.004), while the coefficients were opposite; the richness-precipitation relationship was significant in deserts (R = 0.63, P < 0.001) while nonsignificant in croplands (R = -0.03, P = 0.815). Moreover, for the dominant microbial groups (the top 10 phyla), the relationships between their richness and climate factors differed in two land use types, and fewer significant correlations were observed in croplands. In summary, it can be indicated that the influences of climate on soil microbial communities are shifted after intensive agriculture, and the relations of the richness with climate factors are also weakened for both the total and dominant microbial groups. These results improve our comprehension about the effects of climate on soil microbial diversity after intensive agriculture in desert areas, which can help to project microbial diversity in varied land uses under the context of global climate changes.
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Affiliation(s)
- Jie Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Changkun Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiying Guo
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Aiai Xu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Pan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China; National Earth System Science Data Center, Nanjing 210008, China
| | - Xianzhang Pan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Abstract
Arid ecosystems cover ∼40% of the Earth's terrestrial surface and store a high proportion of the global nitrogen (N) pool. They are low-productivity, low-biomass, and polyextreme ecosystems, i.e., with (hyper)arid and (hyper)oligotrophic conditions and high surface UV irradiation and evapotranspiration. These polyextreme conditions severely limit the presence of macrofauna and -flora and, particularly, the growth and productivity of plant species. Therefore, it is generally recognized that much of the primary production (including N-input processes) and nutrient biogeochemical cycling (particularly N cycling) in these ecosystems are microbially mediated. Consequently, we present a comprehensive survey of the current state of knowledge of biotic and abiotic N-cycling processes of edaphic (i.e., open soil, biological soil crust, or plant-associated rhizosphere and rhizosheath) and hypo/endolithic refuge niches from drylands in general, including hot, cold, and polar desert ecosystems. We particularly focused on the microbially mediated biological nitrogen fixation, N mineralization, assimilatory and dissimilatory nitrate reduction, and nitrification N-input processes and the denitrification and anaerobic ammonium oxidation (anammox) N-loss processes. We note that the application of modern meta-omics and related methods has generated comprehensive data sets on the abundance, diversity, and ecology of the different N-cycling microbial guilds. However, it is worth mentioning that microbial N-cycling data from important deserts (e.g., Sahara) and quantitative rate data on N transformation processes from various desert niches are lacking or sparse. Filling this knowledge gap is particularly important, as climate change models often lack data on microbial activity and environmental microbial N-cycling communities can be key actors of climate change by producing or consuming nitrous oxide (N2O), a potent greenhouse gas.
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Renoud S, Abrouk D, Prigent-Combaret C, Wisniewski-Dyé F, Legendre L, Moënne-Loccoz Y, Muller D. Effect of Inoculation Level on the Impact of the PGPR Azospirillum lipoferum CRT1 on Selected Microbial Functional Groups in the Rhizosphere of Field Maize. Microorganisms 2022; 10:microorganisms10020325. [PMID: 35208780 PMCID: PMC8877547 DOI: 10.3390/microorganisms10020325] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 02/01/2023] Open
Abstract
The impact of inoculated plant growth-promoting rhizobacteria (PGPR) on its host physiology and nutrition depends on inoculum level. Whether the impact of the inoculated PGPR on the indigenous rhizosphere microbiota also varies with the PGPR inoculum level is unclear. Here, we tested this issue using the PGPR Azospirillum lipoferum CRT1—maize model system, where the initial seed inoculation is known to enhance maize growth and germination, and impacts the maize rhizomicrobiota, including microbial functional groups modulating plant growth. A. lipoferum CRT1 was added to the seeds at standard (105–6 cells.seed−1) or reduced (104–5 cells.seed−1) inoculation levels, in three fields. The effect of the two PGPR formulations was assessed on maize growth and on the nifH (nitrogen fixation), acdS (ACC deaminase activity) and phlD (2,4-diacetylphloroglucinol production) microbial functional groups. The size of the three functional groups was monitored by qPCR at the six-leaf stage and the flowering stage, and the diversity of the nifH and acdS functional groups (as well as the bacterial community) were estimated by MiSeq metabarcoding at the six-leaf stage. The results showed that the benefits of the reduced inoculant formulation were significant in two out of three fields, but different (often lower) than those of the standard formulation. The effects of formulations on the size of the three functional groups differed, and depended on field site and functional group. The reduced formulation had an impact on the diversity of nifH and acdS groups at one site, whereas the standard formulation had an impact at the two other sites. Inoculation significantly impacted the total bacterial community in the three fields, but only with the reduced formulation. In conclusion, the reduced inoculant formulation impacted the indigenous rhizosphere microbiota differently, but not less efficiently, than the standard formulation.
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Affiliation(s)
- Sébastien Renoud
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAe, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 Novembre 1918, F-69622 Villeurbanne, France; (S.R.); (D.A.); (C.P.-C.); (F.W.-D.); (L.L.); (Y.M.-L.)
| | - Danis Abrouk
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAe, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 Novembre 1918, F-69622 Villeurbanne, France; (S.R.); (D.A.); (C.P.-C.); (F.W.-D.); (L.L.); (Y.M.-L.)
| | - Claire Prigent-Combaret
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAe, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 Novembre 1918, F-69622 Villeurbanne, France; (S.R.); (D.A.); (C.P.-C.); (F.W.-D.); (L.L.); (Y.M.-L.)
| | - Florence Wisniewski-Dyé
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAe, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 Novembre 1918, F-69622 Villeurbanne, France; (S.R.); (D.A.); (C.P.-C.); (F.W.-D.); (L.L.); (Y.M.-L.)
| | - Laurent Legendre
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAe, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 Novembre 1918, F-69622 Villeurbanne, France; (S.R.); (D.A.); (C.P.-C.); (F.W.-D.); (L.L.); (Y.M.-L.)
- Département de Biologie Biochimie, Univ Lyon, Université Jean Monnet, UFR des Sciences et Techniques, F-42000 Saint-Etienne, France
| | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAe, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 Novembre 1918, F-69622 Villeurbanne, France; (S.R.); (D.A.); (C.P.-C.); (F.W.-D.); (L.L.); (Y.M.-L.)
| | - Daniel Muller
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAe, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 Novembre 1918, F-69622 Villeurbanne, France; (S.R.); (D.A.); (C.P.-C.); (F.W.-D.); (L.L.); (Y.M.-L.)
- Correspondence: ; Tel.: +33-4-72-43-27-14
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Chen C, Han H, Xu T, Lv Y, Hu K, Li XX, Qiao Y, Ding GC, Li J. Comparison of the Total, Diazotrophic and Ammonia-Oxidizing Bacterial Communities Between Under Organic and Conventional Greenhouse Farming. Front Microbiol 2020; 11:1861. [PMID: 32903338 PMCID: PMC7434936 DOI: 10.3389/fmicb.2020.01861] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 07/15/2020] [Indexed: 12/15/2022] Open
Abstract
Organic greenhouse farming is an innovative system that may maintain a high yield and healthy agroecosystem. There have been no rigorous studies on the comparison of total and nitrogen-cycling bacterial community in vegetable soils between organic and conventional farming management at large scale. A survey of bacterial community and nitrogen cycles from soils under organic and conventional greenhouse farming was performed at 30 sites, covering seven soil types with 4 to 18 years of organic farming history. Communities of the total, diazotrophs and ammonia-oxidizing bacteria were studied with high-throughput sequencing of the 16S rRNA, nifH and amoA genes, respectively. Organic greenhouse farming did not influence alpha diversities. Beta diversities among the total (26/30) and diazotrophic (17/19) bacteria differed between farming systems, but compositional differences in ammonia-oxidizing bacteria between the two farming systems were only detected at 6 sites. Despite the effects of farming system on most bacterial genera were varied across different sites, organic greenhouse farming persistently selected for a few genera, possibly for the biodegradation of organic carbon with high molecular weight (Hyphomicrobium, Rubinisphaera, Aciditerrimonas, Planifilum, Phaselicystis, and Ohtaekwangia), but against putative ammonia oxidizing (Nitrosospira, Nitrosopumilus) and diazotrophic (Bradyrhizobium) bacterial genera, as determined by 16S rRNA analysis. Diazotrophic bacteria affiliated with nifH cluster 1J were preferentially associated with organic greenhouse farming, in contrast to Paenibacillus borealis. In summary, this study provides insights into the complex effects of organic greenhouse farming on the total, diazotrophic and ammonia oxidizing bacterial communities across different environmental context.
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Affiliation(s)
- Chen Chen
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Hui Han
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Ting Xu
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China.,Organic Recycling Institute (Suzhou) of China Agricultural University, Suzhou ViCheck Biotechnology Co., Ltd., Suzhou, China
| | - Yizhong Lv
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Kelin Hu
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Xue Xian Li
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Yuhui Qiao
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Guo-Chun Ding
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China.,Organic Recycling Institute (Suzhou) of China Agricultural University, Suzhou ViCheck Biotechnology Co., Ltd., Suzhou, China
| | - Ji Li
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China.,Organic Recycling Institute (Suzhou) of China Agricultural University, Suzhou ViCheck Biotechnology Co., Ltd., Suzhou, China
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Tian Y, Ma X, Li Y, Cheng C, Ge F, An D. Relationship between microbial diversity and nitrogenase activity of Stipagrostis pennata rhizosheath. J Cell Biochem 2019; 120:13501-13508. [PMID: 30938883 DOI: 10.1002/jcb.28625] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/09/2019] [Accepted: 02/14/2019] [Indexed: 11/09/2022]
Abstract
Nitrogen is the key factor for plant survival and growth, especially in the desert. Stipagrostis pennata, a sand born drought-resistant plant, could colonize pioneerly in Gurbantunggut Desert during revegetation. One strategy for their environment adaptation was the rhizosheath formatted by root-hair, mucilaginous exudates, microbial components, and soil particles, for which not only provides a favorable living microenvironment but also supplies essential nutrients. To understand the relationship between microorganisms living in rhizosheaths and the nitrogen nutrition supply, the microbial diversity and nitrogenase activity was estimated during the growth of S. pennata. Five samples of the rhizosheath, which based on the development periods of the plant, regreen, flowering, filling, seed maturating, and withering period, were collected. The nitrogenase activity was estimated by acetylene reduction and the microbial diversity was analyzed by 16S rRNA high-throughput sequencing. The results showed that the nitrogenase activity was increased slowly during regreen to flowering, while reached a peak rapidly at filling sample and then decreased gradually. A total of 274 operational taxonomic units (OTUs) were identified and significant differences in community structure and composition at each growth period. Among them, the main phyla included Actinobacteria and Proteus, which were the most abundant phyla in all periods. In addition, the microbial diversity in the grain filling period was higher than other periods in view of the analysis of alpha diversity and beta diversity. Furthermore, principal component analysis (PCA) analysis showed that the microbial communities in the filling period was low in similarity with other periods. Most importantly, the OTUs associated with nitrogen fixation is the most during the filling period, involving Phagecidae and Fucoraceae. Overall, the study not only revealed the differences in nitrogenase activity among different developmental periods in S. pennata, but also explored the potential bridges between it and community structure and diversity of bacteria.
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Affiliation(s)
- Yongzhi Tian
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, China
| | - Xiaolin Ma
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, China
| | - Yuanting Li
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, China
| | - Cong Cheng
- Jiangsu Key Laboratory of Microbiology and Functional Genomics, College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Fengwei Ge
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, China
| | - Dengdi An
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, China
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15
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Long-term application of nitrogen, not phosphate or potassium, significantly alters the diazotrophic community compositions and structures in a Mollisol in northeast China. Res Microbiol 2019; 170:147-155. [DOI: 10.1016/j.resmic.2019.02.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 02/16/2019] [Accepted: 02/19/2019] [Indexed: 11/20/2022]
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Mosqueira MJ, Marasco R, Fusi M, Michoud G, Merlino G, Cherif A, Daffonchio D. Consistent bacterial selection by date palm root system across heterogeneous desert oasis agroecosystems. Sci Rep 2019; 9:4033. [PMID: 30858421 PMCID: PMC6412053 DOI: 10.1038/s41598-019-40551-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 02/18/2019] [Indexed: 12/20/2022] Open
Abstract
Highly productive conventional agroecosystems are spatially embedded in resource-homogeneous systems and count on generally nutrient-rich soils. On the contrary, desert oases are isolated, the soil is relatively poor, but yet productivity is similar to conventional agroecosystems. Soil dominates over plant as the main factor shaping root-associated microbiomes in conventional agroecosystems. We hypothesize that in desert oasis, the environmental discontinuity, the resource paucity and limited microbial diversity of the soil make the plant a prevailing factor. We have examined the bacterial communities in the root system of date palm (Phoenix dactylifera), the iconic keystone species of the oases, grown in heterogeneous soils across a broad geographic range (22,200 km2 surface area) of the Sahara Desert in Tunisia. We showed that, regardless of the edaphic conditions and geographic location, the plant invariably selects similar Gammaproteobacteria- and Alphaproteobacteria-dominated bacterial communities. The phylogeny, networking properties and predicted functionalities of the bacterial communities indicate that these two phyla are performing the ecological services of biopromotion and biofertilization. We conclude that in a desert agroecosystem, regardless of the soil microbial diversity baseline, the plant, rather than soil type, is responsible of the bacterial community assembly in its root systems, reversing the pattern observed in conventional agroecosystem.
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Affiliation(s)
- Maria J Mosqueira
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Ramona Marasco
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia.
| | - Marco Fusi
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Grégoire Michoud
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Giuseppe Merlino
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Ameur Cherif
- University of Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, Ariana, 2020, Tunisia
| | - Daniele Daffonchio
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia.
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Sheng R, Li K, Zhang W, Wang H, Liu H, Zhu X, Wu H, Zhang X, Lin Q, Sun X, Tang Y, A L, Wei W. Differentiations of determinants for the community compositions of bacteria, fungi, and nitrogen fixers in various steppes. Ecol Evol 2019; 9:3239-3250. [PMID: 30962889 PMCID: PMC6434564 DOI: 10.1002/ece3.4940] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/01/2019] [Accepted: 01/07/2019] [Indexed: 11/07/2022] Open
Abstract
Different types of steppes could provide heterogeneous habitat environments for underground microorganisms, but much less is known about how soil microbes fit the distinct habitats and what are the underlying mechanisms in shaping their community patterns.We simultaneously examined the community compositions and structures of soil bacteria, fungi, and diazotrophs across desert, typical, and meadow steppes in Inner Mongolia using high-throughput sequencing.The results showed that soil bacteria, fungi, and diazotrophs exhibited different distribution patterns across steppe types. Although different steppes displayed obvious differences in climate conditions, plant traits, and soil properties, most of bacterial species were shared by all the steppes while only a few species were unique, indicating that the soil bacterial compositions were hardly influenced by the steppe types. Nevertheless, the habitat heterogeneity could cause shifts in the relative abundance of some bacterial groups, which resulted in significant changes in the community structure of soil bacteria across steppes. However, the fungal community compositions and structures were similar in typical and meadow steppes but that in desert steppe were significantly different. Whereas, the community compositions and structures of diazotrophs were strongly related to the steppe types. In this study, the similar parent material backgrounds of the steppe soils might be the important factor in shaping the homologous bacterial compositions. However, the variations in soil fertility, soil water repellency, and plant species across steppes would be the major driving forces in regulating the compositions and structures of fungal communities, while the diazotrophic communities would be more closely related to the changes in plant traits and soil fertility among steppes.Our results provided evidence of habitat specificity for different microbial groups and their underlying drivers.
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Affiliation(s)
- Rong Sheng
- Key Laboratory of Agro‐ecological Processes in Subtropical Regions and Taoyuan Agro‐ecosystem Research Station, Soil Molecular Ecology Section, Institute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
| | - Ke Li
- Key Laboratory of Agro‐ecological Processes in Subtropical Regions and Taoyuan Agro‐ecosystem Research Station, Soil Molecular Ecology Section, Institute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
| | - Wenzhao Zhang
- Key Laboratory of Agro‐ecological Processes in Subtropical Regions and Taoyuan Agro‐ecosystem Research Station, Soil Molecular Ecology Section, Institute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
| | - Hai Wang
- Institute of Grassland ScienceChinese Academy of Agricultural SciencesHuhehaoteChina
| | - Honglin Liu
- Institute of Grassland ScienceChinese Academy of Agricultural SciencesHuhehaoteChina
| | - Xiaoya Zhu
- College of Resources and Environmental SciencesChina Agricultural UniversityBeijingChina
| | - Hongxin Wu
- Institute of Grassland ScienceChinese Academy of Agricultural SciencesHuhehaoteChina
| | - Xiaoqing Zhang
- Institute of Grassland ScienceChinese Academy of Agricultural SciencesHuhehaoteChina
| | - Qimei Lin
- College of Resources and Environmental SciencesChina Agricultural UniversityBeijingChina
| | - Xuecheng Sun
- College of Resources and Environmental SciencesHuazhong Agricultural UniversityWuhanChina
| | - Yafang Tang
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, College of Life Science and TechnologyHubei Engineering UniversityXiaoganChina
| | - Lamus A
- Institute of Grassland ScienceChinese Academy of Agricultural SciencesHuhehaoteChina
| | - Wenxue Wei
- Key Laboratory of Agro‐ecological Processes in Subtropical Regions and Taoyuan Agro‐ecosystem Research Station, Soil Molecular Ecology Section, Institute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
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Marasco R, Mosqueira MJ, Fusi M, Ramond JB, Merlino G, Booth JM, Maggs-Kölling G, Cowan DA, Daffonchio D. Rhizosheath microbial community assembly of sympatric desert speargrasses is independent of the plant host. MICROBIOME 2018; 6:215. [PMID: 30514367 PMCID: PMC6280439 DOI: 10.1186/s40168-018-0597-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 11/16/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND The rhizosheath-root system is an adaptive trait of sandy-desert speargrasses in response to unfavourable moisture and nutritional conditions. Under the deserts' polyextreme conditions, plants interact with edaphic microorganisms that positively affect their fitness and resistance. However, the trophic simplicity and environmental harshness of desert ecosystems have previously been shown to strongly influence soil microbial community assembly. We hypothesize that sand-driven ecological filtering constrains the microbial recruitment processes in the speargrass rhizosheath-root niche, prevailing over the plant-induced selection. METHODS Bacterial and fungal communities from the rhizosheath-root compartments (endosphere root tissues, rhizosheath and rhizosphere) of three Namib Desert speargrass species (Stipagrostis sabulicola, S. seelyae and Cladoraphis spinosa) along with bulk sand have been studied to test our hypothesis. To minimize the variability determined by edaphic and climatic factors, plants living in a single dune were studied. We assessed the role of plant species vs the sandy substrate on the recruitment and selection, phylogenetic diversity and co-occurrence microbial networks of the rhizosheath-root system microbial communities. RESULTS Microorganisms associated with the speargrass rhizosheath-root system were recruited from the surrounding bulk sand population and were significantly enriched in the rhizosheath compartments (105 and 104 of bacterial 16S rRNA and fungal ITS copies per gram of sand to up to 108 and 107 copies per gram, respectively). Furthermore, each rhizosheath-root system compartment hosted a specific microbial community demonstrating strong niche-partitioning. The rhizosheath-root systems of the three speargrass species studied were dominated by desert-adapted Actinobacteria and Alphaproteobacteria (e.g. Lechevalieria, Streptomyces and Microvirga) as well as saprophytic Ascomycota fungi (e.g. Curvularia, Aspergillus and Thielavia). Our results clearly showed a random phylogenetic turnover of rhizosheath-root system associated microbial communities, independent of the plant species, where stochastic factors drive neutral assembly. Co-occurrence network analyses also indicated that the bacterial and fungal community members of the rhizosheath-root systems established a higher number of interactions than those in the barren bulk sand, suggesting that the former are more stable and functional than the latter. CONCLUSION Our study demonstrates that the rhizosheath-root system microbial communities of desert dune speargrasses are stochastically assembled and host-independent. This finding supports the concept that the selection determined by the desert sand prevails over that imposed by the genotype of the different plant species.
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Affiliation(s)
- Ramona Marasco
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia.
| | - María J Mosqueira
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Marco Fusi
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Jean-Baptiste Ramond
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Giuseppe Merlino
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Jenny M Booth
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | | | - Don A Cowan
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Daniele Daffonchio
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia.
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19
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Kunda P, Dhal PK, Mukherjee A. Endophytic bacterial community of rice (Oryza sativa L.) from coastal saline zone of West Bengal: 16S rRNA gene based metagenomics approach. Meta Gene 2018. [DOI: 10.1016/j.mgene.2018.08.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Bouffaud ML, Renoud S, Dubost A, Moënne-Loccoz Y, Muller D. 1-Aminocyclopropane-1-carboxylate deaminase producers associated to maize and other Poaceae species. MICROBIOME 2018; 6:114. [PMID: 29925415 PMCID: PMC6011333 DOI: 10.1186/s40168-018-0503-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 06/14/2018] [Indexed: 05/16/2023]
Abstract
BACKGROUND Complex plant-microbe interactions have been established throughout evolutionary time, many of them with beneficial effects on the host in terms of plant growth, nutrition, or health. Some of the corresponding modes of action involve a modulation of plant hormonal balance, such as the deamination of the ethylene precursor 1-aminocyclopropane-1-carboxylate (ACC). Despite its ecological importance, our understanding of ACC deamination is impaired by a lack of direct molecular tools. Here, we developed PCR primers to quantify the ACC deaminase gene acdS and its mRNA in soil communities and assessed acdS+ microorganisms colonizing maize and other Poaceae species. RESULTS Effective acdS primers suitable for soil microbial communities were obtained, enabling recovery of bona fida acdS genes and transcripts of diverse genetic backgrounds. High numbers of acdS genes and transcripts were evidenced in the rhizosphere of Poaceae, and numbers fluctuated according to plant genotype. Illumina sequencing revealed taxonomic specificities of acdS+ microorganisms according to plant host. The phylogenetic distance between Poaceae genotypes correlated with acdS transcript numbers, but not with acdS gene numbers or the genetic distance between acdS functional groups. CONCLUSION The development of acdS primers enabled the first direct analysis of ACC deaminase functional group in soil and showed that plant ability to interact with soil-inhabiting acdS+ microorganisms could also involve particular plant traits unrelated to the evolutionary history of Poaceae species.
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Affiliation(s)
- Marie-Lara Bouffaud
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, VetAgro Sup, UMR5557 Ecologie Microbienne, F-69622, Villeurbanne, France
- Helmholtz Center for Environmental Research UFZ, Theodor-Lieser-Straβe 4, 06120, Halle, Germany
| | - Sébastien Renoud
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, VetAgro Sup, UMR5557 Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Audrey Dubost
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, VetAgro Sup, UMR5557 Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, VetAgro Sup, UMR5557 Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Daniel Muller
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, VetAgro Sup, UMR5557 Ecologie Microbienne, F-69622, Villeurbanne, France.
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Srivastava M, Mishra AK. Comparative responses of diazotrophic abundance and community structure to the chemical composition of paddy soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:399-412. [PMID: 29039042 DOI: 10.1007/s11356-017-0375-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Accepted: 09/28/2017] [Indexed: 06/07/2023]
Abstract
Diazotrophy is considered as one of the most crucial and dynamic phenomena in the rice field and also a major source of nitrogen input. The objective of this study was to elucidate possible interactions between diverse and dominant diazotrophic bacterial community and organic carbon composition of the paddy soil. Our results suggest that most abundantly found diazotrophs belong to a proteobacteria group and uncultured bacterial forms. A gene abundance study clearly showed significantly higher diazotrophic abundance (P < 0.01) at Chandauli (CHN) as compared to Varanasi (VNS) and Ghazipur (GHJ) districts of Eastern Uttar Pradesh, India, with nitrogenase reductase (nifH) copy number between 1.44 × 103 and 3.34 × 103 copy g-1 soil. Fourier-transform infrared (FT-IR) spectroscopy data identified -CO-, C=O ([Formula: see text] and -NH-), [Formula: see text], and OH- as dominant organic functional groups in the paddy soil. Multivariate analysis was performed to get a clear and more accurate picture of interactions between free-living diazotrophs and abiotic soil factors. Regression analysis suggested a similar trend of distribution of different functional groups along each site. Relative abundance and diversity of diazotrophic population increased in response to FT-IR-based soil organic fractions. Maximum number of FT-IR spectral peak at sites in the Chandauli district augmented its bacterial diazotrophic diversity and abundance. Taken together, the present study sheds light on the substrate-driven composition of the microbial population of selected paddy areas.
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Affiliation(s)
- Meenakshi Srivastava
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, 221005, India
| | - Arun Kumar Mishra
- Laboratory of Microbial Genetics, Department of Botany, Banaras Hindu University, Varanasi, 221005, India.
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Hao DC, Xiao PG. Rhizosphere Microbiota and Microbiome of Medicinal Plants: From Molecular Biology to Omics Approaches. CHINESE HERBAL MEDICINES 2017. [DOI: 10.1016/s1674-6384(17)60097-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Sessitsch A, Smalla K, Johnson L, Mitter B. Editorial: Special thematic issue on microbe-assisted crop production. FEMS Microbiol Ecol 2016; 92:fiw167. [PMID: 27495243 DOI: 10.1093/femsec/fiw167] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Angela Sessitsch
- AIT Austrian Institute of Technology GmbH, Health & Environment Department, Bioresources Unit, Konrad-Lorenz-Straße 24, 3430 Tulln, Austria
| | - Kornelia Smalla
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, Braunschweig 38104, Germany
| | - Linda Johnson
- Agresearch Grasslands Research Centre, Forage Improvement, Tennent Drive, Palmerston North 4442, New Zealand
| | - Birgit Mitter
- AIT Austrian Institute of Technology GmbH, Health & Environment Department, Bioresources Unit, Konrad-Lorenz-Straße 24, 3430 Tulln, Austria
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