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Novello G, Bona E, Nasuelli M, Massa N, Sudiro C, Campana DC, Gorrasi S, Hochart ML, Altissimo A, Vuolo F, Gamalero E. The Impact of Nitrogen-Fixing Bacteria-Based Biostimulant Alone or in Combination with Commercial Inoculum on Tomato Native Rhizosphere Microbiota and Production: An Open-Field Trial. BIOLOGY 2024; 13:400. [PMID: 38927280 PMCID: PMC11200462 DOI: 10.3390/biology13060400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 05/28/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024]
Abstract
The agricultural sector is currently encountering significant challenges due to the effects of climate change, leading to negative consequences for crop productivity and global food security. In this context, traditional agricultural practices have been inadequate in addressing the fast-evolving challenges while maintaining environmental sustainability. A possible alternative to traditional agricultural management is represented by using beneficial micro-organisms that, once applied as bioinoculants, may enhance crop resilience and adaptability, thereby mitigating the adverse effects of environmental stressors and boosting productivity. Tomato is one of the most important crops worldwide, playing a central role in the human diet. The aim of this study was to evaluate the impact of a nitrogen-fixing bacterial-based biostimulant (Azospirillum sp., Azotobacter sp., and Rhizobium sp.) in combination or not with a commercial inoculum Micomix (Rhizoglomus irregulare, Funnelliformis mosseae, Funnelliformis caledonium, Bacillus licheniformis, and Bacillus mucilaginosus) (MYC) on the native rhizosphere communities and tomato production. Bacterial populations in the different samples were characterized using an environmental metabarcoding approach. The bioinocula effect on the native rhizosphere microbiota resulted in significant variation both in alpha and beta diversity and in a specific signature associated with the presence of biostimulants.
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Affiliation(s)
- Giorgia Novello
- Dipartimento di Scienze e Innovazione Tecnologica (DISIT), Università del Piemonte Orientale, 15121 Alessandria, Italy; (G.N.); (N.M.); (D.C.C.); (E.G.)
| | - Elisa Bona
- Dipartimento per lo Sviluppo Sostenibile e la Transizione Ecologica (DISSTE), Università del Piemonte Orientale, 13100 Vercelli, Italy;
- Center on Autoimmune and Allergic Diseases (CAAD), Università del Piemonte Orientale, 28100 Novara, Italy
| | - Martina Nasuelli
- Dipartimento per lo Sviluppo Sostenibile e la Transizione Ecologica (DISSTE), Università del Piemonte Orientale, 13100 Vercelli, Italy;
| | - Nadia Massa
- Dipartimento di Scienze e Innovazione Tecnologica (DISIT), Università del Piemonte Orientale, 15121 Alessandria, Italy; (G.N.); (N.M.); (D.C.C.); (E.G.)
| | - Cristina Sudiro
- Landlab S.r.l., 36050 Quinto Vicentino, Italy; (C.S.); (M.L.H.); (A.A.)
| | - Daniela Cristina Campana
- Dipartimento di Scienze e Innovazione Tecnologica (DISIT), Università del Piemonte Orientale, 15121 Alessandria, Italy; (G.N.); (N.M.); (D.C.C.); (E.G.)
| | - Susanna Gorrasi
- Dipartimento di Scienze Ecologiche e Biologiche, Università degli Studi della Tuscia, 01100 Viterbo, Italy;
| | | | - Adriano Altissimo
- Landlab S.r.l., 36050 Quinto Vicentino, Italy; (C.S.); (M.L.H.); (A.A.)
| | | | - Elisa Gamalero
- Dipartimento di Scienze e Innovazione Tecnologica (DISIT), Università del Piemonte Orientale, 15121 Alessandria, Italy; (G.N.); (N.M.); (D.C.C.); (E.G.)
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Kumar A, Solanki MK, Wang Z, Solanki AC, Singh VK, Divvela PK. Revealing the seed microbiome: Navigating sequencing tools, microbial assembly, and functions to amplify plant fitness. Microbiol Res 2024; 279:127549. [PMID: 38056172 DOI: 10.1016/j.micres.2023.127549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 12/08/2023]
Abstract
Microbial communities within seeds play a vital role in transmitting themselves to the next generation of plants. These microorganisms significantly impact seed vigor and early seedling growth, for successful crop establishment. Previous studies reported on seed-associated microbial communities and their influence on processes like dormancy release, germination, and disease protection. Modern sequencing and conventional methods reveal microbial community structures and environmental impacts, these information helps in microbial selection and manipulation. These studies form the foundation for using seed microbiomes to enhance crop resilience and productivity. While existing research has primarily focused on characterizing microbiota in dried mature seeds, a significant gap exists in understanding how these microbial communities assemble during seed development. The review also discusses applying seed-associated microorganisms to improve crops in the context of climate change. However, limited knowledge is available about the microbial assembly pattern on seeds, and their impact on plant growth. The review provides insight into microbial composition, functions, and significance for plant health, particularly regarding growth promotion and pest control.
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Affiliation(s)
- Ajay Kumar
- Amity Institute of Biotechnology, Amity University, Sector-125, Noida, Uttar Pradesh 201313, India
| | - Manoj Kumar Solanki
- Department of Life Sciences and Biological Sciences, IES University, Bhopal, Madhya Pradesh, India; Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland.
| | - Zhen Wang
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Agricultural College, Yulin Normal University, Yulin 537000, China
| | - Anjali Chandrol Solanki
- Department of Agriculture, Mansarover Global University, Bhopal, Madhya Pradesh 462042, India
| | - Vipin Kumar Singh
- Department of Botany, K.S. Saket P.G. College, Ayodhya 224123, Uttar Pradesh, India
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Ansari WA, Kumar M, Krishna R, Singh A, Zeyad MT, Tiwari P, Kumar SC, Chakdar H, Srivastava AK. Influence of rice-wheat and sugarcane-wheat rotations on microbial diversity and plant growth promoting bacteria: Insights from high-throughput sequencing and soil analysis. Microbiol Res 2024; 278:127533. [PMID: 37924641 DOI: 10.1016/j.micres.2023.127533] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 11/06/2023]
Abstract
Wheat is a staple food crop, primarily grown in India's Indo-Gangetic plains, crucial for sustaining the region. Soil quality, vitality, and microbial inhabitants' interplay are pivotal. However, very little information is available on the impacts of agricultural practices, such as crop rotation and cropping systems, on the diversity of both bulk soil (BS) and rhizospheric soil (RS) microbiota. The impact of two different cropping systems, rice-wheat (RW) and sugarcane-wheat (SW) on soil properties, microbial diversity, and plant growth-promoting bacteria (PGPB) in wheat cultivation was investigated in the Indo-Gangetic plains of India. Microbial richness and diversity were analyzed using 16S rRNA sequencing, which reveals distinct clustering patterns between RS and BS, with higher diversity in BS of RW and higher richness in RS of SW. Notably, Proteobacteria dominated across all samples, along with Chloroflexi, Actinobacteria, Bacteroidetes, Acidobacteria, Gemmatimonadetes, Verrucomicrobia, Firmicutes, Planctomycetes, candidate division TM7, Cyanobacteria, and Nitrospirae. Intriguingly, the RS associated with the SW system exhibited the presence of 67 distinct genera, whereas the RS under the RW system showed 48 such genera. Within the realm of specific microbial genera exhibiting plant growth-promoting (PGP) activity, a higher abundance was noted in the RS (17.48%), as opposed to the BS (15.21%). Moreover, certain genera such as Haliangium, Iamia, Bacillus, Gaiella, Candidatus_Entotheonella, Anaerolinea, and Anaeromyxobacter, were found to be positively correlated with the availability of nitrogen, phosphorus, potassium, iron, and sulfur. The study sheds light on the intricate relationships between cropping practices, soil properties, and microbial dynamics, contributing to the development of sustainable agricultural practices for wheat cultivation.
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Affiliation(s)
- Waquar Akhter Ansari
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau 275103, Uttar Pradesh, India
| | - Murugan Kumar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau 275103, Uttar Pradesh, India.
| | - Ram Krishna
- ICAR-Indian Institute of Vegetable Research, Varanasi 221305, Uttar Pradesh, India
| | - Arjun Singh
- ICAR-Central Soil Salinity Research Institute, Regional Research Station, Lucknow 226002, Uttar Pradesh, India
| | - Mohammad Tarique Zeyad
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau 275103, Uttar Pradesh, India
| | - Pushpendra Tiwari
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau 275103, Uttar Pradesh, India
| | - Shiv Charan Kumar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau 275103, Uttar Pradesh, India
| | - Hillol Chakdar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau 275103, Uttar Pradesh, India
| | - Alok Kumar Srivastava
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau 275103, Uttar Pradesh, India
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Adu MO, Zigah N, Yawson DO, Amoah KK, Afutu E, Atiah K, Darkwa AA, Asare PA. Plasticity of root hair and rhizosheath traits and their relationship to phosphorus uptake in sorghum. PLANT DIRECT 2023; 7:e521. [PMID: 37638231 PMCID: PMC10447916 DOI: 10.1002/pld3.521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 06/09/2023] [Accepted: 07/30/2023] [Indexed: 08/29/2023]
Abstract
Sorghum is an essential crop for resilient and adaptive responses to climate change. The root systems of crop plants significantly contribute to the tolerance of abiotic stresses. There is little information on sorghum genotypes' root systems and plasticity to external P supply. In this paper, we investigated the variations in root systems, as well as the responses, trait relationships, and plasticity of two sorghum genotypes (Naga Red and Naga White), popularly grown in Ghana, to five external P concentrations ([P]ext): 0, 100, 200, 300, and 400 mg P kg-1 soil. Sorghum plants were grown in greenhouse pots and harvested for root trait measurements at the five-leaf and growing point differentiation (GPD) developmental stages. The plants were responsive to [P]ext and formed rhizosheaths. The two genotypes showed similar characteristics for most of the traits measured but differed significantly in total and lateral root lengths in favor of the red genotype. For example, at the five-leaf growth stage, the lateral root length of the red and white genotypes was 22.8 and 16.2 cm, respectively, but 124 and 88.9 cm, at the GPD stage. The responses and plasticity of the root system traits, including rhizosheath, to [P]ext were more prominent, positive, and linear at the five-leaf stage than at the GPD growth stage. At the five-leaf growth stage, total root length increased by about 2.5-fold with increasing [P]ext compared to the unamended soil. At the GPD stage, however, total root length decreased by about 1.83-fold as [P]ext increased compared to the unamended soil. Specific rhizosheath weight correlated with RHD, albeit weakly, and together explained up to 59% of the variation in tissue P. Root hair density was more responsive to P supply than root hair length and showed a similar total and lateral root length pattern. Most desirable responses to P occurred at a rate of 200-300 mg P kg-1 soil. It is concluded that sorghum would form rhizosheath, and [P]ext could be critical for the early vigorous growth of sorghum's responsive root and shoot traits. Beyond the early days of development, additional P application might be necessary to sustain the responses and plasticity observed during the early growth period, but this requires further investigation, potentially under field conditions.
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Affiliation(s)
- Michael O. Adu
- Department of Crop Science, School of Agriculture, College of Agriculture and Natural SciencesUniversity of Cape CoastCape CoastGhana
| | - Nathaniel Zigah
- Department of Crop Science, School of Agriculture, College of Agriculture and Natural SciencesUniversity of Cape CoastCape CoastGhana
| | - David O. Yawson
- Centre for Resource Management and Environmental Studies (CERMES)The University of the West IndiesBridgetownBarbados
| | - Kwadwo K. Amoah
- Department of Crop Science, School of Agriculture, College of Agriculture and Natural SciencesUniversity of Cape CoastCape CoastGhana
| | - Emmanuel Afutu
- Department of Crop Science, School of Agriculture, College of Agriculture and Natural SciencesUniversity of Cape CoastCape CoastGhana
| | - Kofi Atiah
- Department of Soil Science, School of Agriculture, College of Agriculture and Natural SciencesUniversity of Cape CoastCape CoastGhana
| | - Alfred A. Darkwa
- Department of Crop Science, School of Agriculture, College of Agriculture and Natural SciencesUniversity of Cape CoastCape CoastGhana
| | - Paul A. Asare
- Department of Crop Science, School of Agriculture, College of Agriculture and Natural SciencesUniversity of Cape CoastCape CoastGhana
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Adebayo AA, Faleye TOC, Adeosun OM, Alhaji IA, Egbe NE. Plant growth promoting potentials of novel phosphate-solubilizing bacteria isolated from rumen content of White Fulani cattle, indigenous to Nigeria. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01227-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Aslam MM, Karanja JK, Dodd IC, Waseem M, Weifeng X. Rhizosheath: An adaptive root trait to improve plant tolerance to phosphorus and water deficits? PLANT, CELL & ENVIRONMENT 2022; 45:2861-2874. [PMID: 35822342 PMCID: PMC9544408 DOI: 10.1111/pce.14395] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 07/07/2022] [Accepted: 07/11/2022] [Indexed: 06/09/2023]
Abstract
Drought and nutrient limitations adversely affect crop yields, with below-ground traits enhancing crop production in these resource-poor environments. This review explores the interacting biological, chemical and physical factors that determine rhizosheath (soil adhering to the root system) development, and its influence on plant water uptake and phosphorus acquisition in dry soils. Identification of quantitative trait loci for rhizosheath development indicate it is genetically determined, but the microbial community also directly (polysaccharide exudation) and indirectly (altered root hair development) affect its extent. Plants with longer and denser root hairs had greater rhizosheath development and increased P uptake efficiency. Moreover, enhanced rhizosheath formation maintains contact at the root-soil interface thereby assisting water uptake from drying soil, consequently improving plant survival in droughted environments. Nevertheless, it can be difficult to determine if rhizosheath development is a cause or consequence of improved plant adaptation to dry and nutrient-depleted soils. Does rhizosheath development directly enhance plant water and phosphorus use, or do other tolerance mechanisms allow plants to invest more resources in rhizosheath development? Much more work is required on the interacting genetic, physical, biochemical and microbial mechanisms that determine rhizosheath development, to demonstrate that selection for rhizosheath development is a viable crop improvement strategy.
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Affiliation(s)
- Mehtab Muhammad Aslam
- Center for Plant Water‐Use and Nutrition Regulation, College of Resource and EnvironmentFujian Agriculture and Forestry UniversityFuzhouFujianChina
- College of AgricultureYangzhou UniversityYangzhouJiangsuChina
- State Key Laboratory of Agrobiotechnology, School of Life SciencesThe Chinese University of Hong KongShatinHong Kong
| | - Joseph K. Karanja
- Center for Plant Water‐Use and Nutrition Regulation, College of Resource and EnvironmentFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Ian C. Dodd
- The Lancaster Environment CentreLancaster UniversityLancasterUK
| | | | - Xu Weifeng
- Center for Plant Water‐Use and Nutrition Regulation, College of Resource and EnvironmentFujian Agriculture and Forestry UniversityFuzhouFujianChina
- College of AgricultureYangzhou UniversityYangzhouJiangsuChina
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Li Y, He X, Yuan H, Lv G. Differed Growth Stage Dynamics of Root-Associated Bacterial and Fungal Community Structure Associated with Halophytic Plant Lycium ruthenicum. Microorganisms 2022; 10:microorganisms10081644. [PMID: 36014066 PMCID: PMC9414475 DOI: 10.3390/microorganisms10081644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/12/2022] [Accepted: 08/12/2022] [Indexed: 01/02/2023] Open
Abstract
Lycium ruthenicum, a halophytic shrub, has been used to remediate saline soils in northwest China. However, little is known about its root-associated microbial community and how it may be affected by the plant’s growth cycle. In this study, we investigate the microbial community structure of L. ruthenicum by examining three root compartments (rhizosphere, rhizoplane, and endosphere) during four growth stages (vegetative, flowering, fruiting, and senescence). The microbial community diversity and composition were determined by Illumina MiSeq sequencing of the 16S V3–V4 and 18S ITS regions. Proteobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, and Acidobacteria were the dominant bacterial phyla, while Ascomycota, Basidiomycota, and Mortierellomycota were the most dominant fungal phyla. The alpha diversity of the bacterial communities was highest in the rhizosphere and decreased from the rhizosphere to the endosphere compartments; the fungal communities did not show a consistent trend. The rhizosphere, rhizoplane, and endosphere had distinct bacterial community structures among the three root compartments and from the bulk soil. Additionally, PERMANOVA indicated that the effect of rhizocompartments explained a large proportion of the total community variation. Differential and biomarker analysis not only revealed that each compartment had unique biomarkers and was enriched for specific bacteria, but also that the biomarkers changed with the plant growth cycle. Fungi were also affected by the rhizocompartment, but to a much less so than bacteria, with significant differences in the community composition along the root compartments observed only during the vegetative and flowering stages. Instead, the growth stages appear to account for most of the fungal community variation as demonstrated by PCoA and NMDS, and supported by differential and biomarker analysis, which revealed that the fungal community composition in the rhizosphere and endosphere were dynamic in response to the growth stage. Many enriched OTUs or biomarkers that were identified in the root compartments were potentially beneficial to the plant, meanwhile, some harmful OTUs were excluded from the root, implying that the host plant can select for beneficial bacteria and fungi, which can promote plant growth or increase salt tolerance. In conclusion, the root compartment and growth stage were both determinant factors in structuring the microbial communities of L. ruthenicum, but the effects were different in bacteria and fungi, suggesting that bacterial and fungal community structures respond differently to these growth factors.
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Affiliation(s)
- Yan Li
- College of Ecology and Environment, Xinjiang University, Urumqi 830046, China
- Key Laboratory of Oasis Ecology, Ministry of Education, Urumqi 830046, China
- Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Urumqi 830046, China
| | - Xuemin He
- College of Ecology and Environment, Xinjiang University, Urumqi 830046, China
- Key Laboratory of Oasis Ecology, Ministry of Education, Urumqi 830046, China
- Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Urumqi 830046, China
| | - Hongfei Yuan
- College of Ecology and Environment, Xinjiang University, Urumqi 830046, China
| | - Guanghui Lv
- College of Ecology and Environment, Xinjiang University, Urumqi 830046, China
- Key Laboratory of Oasis Ecology, Ministry of Education, Urumqi 830046, China
- Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Urumqi 830046, China
- Correspondence:
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Arshad M, Naqqash T, Tahir M, Leveau JH, Zaheer A, Tahira SA, Saeed NA, Asad S, Sajjad M. Comparison of bacterial diversity, root exudates and soil enzymatic activities in the rhizosphere of AVP1-transgenic and non-transgenic wheat (Triticum aestivum L.). J Appl Microbiol 2022; 133:3094-3112. [PMID: 35908279 DOI: 10.1111/jam.15751] [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: 05/08/2022] [Revised: 06/30/2022] [Accepted: 07/07/2022] [Indexed: 11/26/2022]
Abstract
AIMS Soil microbial communities are among the most diverse communities that might be affected due to transgenic crops. Therefore, risk assessment studies on transgenes are essentially required as any adverse effects may depend not only on the specific gene and crop involved but also on soil conditions. METHODS AND RESULTS The present study deals with the comparison of bacterial populations, root exudates, and activities of soil enzymes in non-transgenic and AVP1-transgenic wheat rhizosphere, overexpressing vacuolar H+pyrophosphatase for salinity and drought stress tolerance. Amounts of organic acids and sugars produced as root exudates and activities of dehydrogenase, phosphatase, and protease enzymes in soil solution showed no significant differences in AVP1-transgenic and non-transgenic wheat rhizosphere, except for urease and phenol oxidase activities. The higher copy number of nifH gene showed the abundance of nitrogen-fixing bacteria in the rhizosphere of AVP1-transgenic wheat compared with non-transgenic wheat. nifH gene sequence analysis indicated the common diazotrophic genera Azospirillum, Bradyrhizobium, Rhizobium, and Pseudomonas in AVP1-transgenic and non-transgenic wheat except for Zoogloea detected only in non-transgenic wheat. Using 454-pyrosequencing of 16S rRNA gene from soil DNA, a total of 156, 282 sequences of 18 phyla were obtained, which represented bacterial (128,006), Archeal (7,928), and unclassified (21,568) sequences. Proteobacteria, Crenarchaeota, and Firmicutes were the most abundant phyla in transgenic and non-transgenic wheat rhizosphere. Further comparison of different taxonomic units at the genus level showed similar distribution in transgenic and non-transgenic wheat rhizosphere. CONCLUSION We conclude that AVP1 gene in transgenic wheat has no apparent adverse effects on the soil environment and different bacterial communities. However, bacterial community depends on several other factors not only genetic composition of the host plants. SIGNIFICANCE OF THE STUDY The present research supports introduction and cultivation of transgenic plants in agricultural systems without any adverse effects on indigenous bacterial communities and soil ecosystem.
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Affiliation(s)
- Muhammad Arshad
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Jhang Road, Faisalabad and Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
| | - Tahir Naqqash
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Muhammad Tahir
- Department of Environmental Science, COMSATS University Islamabad, Vehari
| | - Johan H Leveau
- Department of Plant Pathology, One Shield's Avenue, University of California Davis, CA, USA
| | - Ahmad Zaheer
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | | | - Nasir Ahmad Saeed
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Jhang Road, Faisalabad and Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
| | - Shaheen Asad
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Jhang Road, Faisalabad and Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
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Tahir M, Khan MB, Shahid M, Ahmad I, Khalid U, Akram M, Dawood A, Kamran M. Metal-tolerant Pantoea sp. WP-5 and organic manures enhanced root exudation and phytostabilization of cadmium in the rhizosphere of maize. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:6026-6039. [PMID: 34431061 DOI: 10.1007/s11356-021-16018-3] [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: 02/17/2021] [Accepted: 08/13/2021] [Indexed: 05/15/2023]
Abstract
This study investigated the phytoremediation potential of maize (Zea mays L.) in Cd-contaminated soil through co-inoculation of metal-tolerant plant beneficial rhizobacteria (MtPBR: Pantoea sp. strain WP-5) with organic manures (PM, poultry manure, and BGR, biogas residues). The objectives of this study were to (i) examine comparative efficiency of MtPBR, PM and BGR alone or in combined form to improve maize biomass and physiology and (ii) understand the role of organic acid production in root exudates of maize for Cd accumulation and translocation. Pantoea sp. WP-5 showed organic acid production and tolerance to high Cd concentration (1000 mg L-1), thereby inoculated to maize seeds sown in soil spiked with 75 mg Cd kg-1 soil and 500 g each of the organic manures per pot. The co-inoculation of MtPBR + BGR significantly (P<0.05) increased chlorophyll contents, root/shoot dry weight, photosynthetic rate, stomatal conductance, and relative water contents and decreased electrolyte leakage, malondialdehyde contents, ascorbate peroxidase, and catalase activity in maize over the control treatment. The co-inoculation of MtPBR + BGR produced significantly (P<0.05) higher concentrations of acetic and citric acid (52.7±0.5 and 22.8±0.08 μg g-1 root fwt, respectively) in root exudates of maize, which immobilized Cd within plant roots inferred by the positive relation (root Cd vs. organic acids; R2 = 0.80-0.92) and reduced Cd translocation to shoots inferred by the negative relation (shoot Cd vs. organic acids; R2 = 0.81-0.90). It is concluded that the application of MtPBR + BGR enhanced organic acid induced phytostabilization and accumulation of Cd in roots and restricted its translocation to shoots.
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Affiliation(s)
- Muhammad Tahir
- Department of Environmental Sciences, COMSATS University Islamabad, Campus, Vehari, Pakistan.
| | - Muhammad Bismillah Khan
- Department of Agronomy, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Multan, Pakistan
| | - Muhammad Shahid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, 38000, Pakistan
| | - Iftikhar Ahmad
- Department of Environmental Sciences, COMSATS University Islamabad, Campus, Vehari, Pakistan.
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, Shanghai, 200240, China.
| | - Umaira Khalid
- Department of Agronomy, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Multan, Pakistan
| | - Muhammad Akram
- Department of Environmental Sciences, COMSATS University Islamabad, Campus, Vehari, Pakistan
| | - Ahmad Dawood
- Department of Agronomy, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Multan, Pakistan
| | - Muhammad Kamran
- Department of Environmental Sciences, COMSATS University Islamabad, Campus, Vehari, Pakistan
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Fariq A, Yasmin A, Blazier JC, Jannat S. Identification of bacterial communities in extreme sites of Pakistan using high throughput barcoded amplicon sequencing. Biodivers Data J 2021; 9:e68929. [PMID: 34744475 PMCID: PMC8551136 DOI: 10.3897/bdj.9.e68929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/19/2021] [Indexed: 11/12/2022] Open
Abstract
Microorganisms thrive nearly everywhere including extreme environments where few other forms of life can exist. Geochemistry of extreme sites plays a major role in shaping these microbial communities and microbes thriving in such harsh conditions are untapped sources of novel biomolecules. To understand the structure and composition of such microbial communities, culture-independent bacterial diversity was characterised for two extreme sites in Pakistan, Khewra salt range and Murtazaabad hot spring. Barcoded amplicon sequencing technique was used to study the microbial communities. Physicochemical analysis of these sites was also conducted to study the dynamics of microbial communities under stressed conditions. Metagenomic sequencing of salt range soil samples yielded of 40,433 16S rRNA sequences, while hot spring sediments produced 76,449 16S rRNA sequence reads. Proteobacteria were predominant in saline soil while Firmicutes were most abundant in hot spring sediment. The taxonomic analysis of saline samples revealed 914 operational taxonomic units (OTUs) while that of hot spring sequences were clustered into 726 distinct OTUs. OTUs from genus Alkalibacillus were most abundant in hot spring sediments, whereas Haloarcula were more prevalent in saline soil. Some unidentified sequences were also present at each taxonomic level. Multivariate analysis indicated that electrical conductivity and pH are the major environmental factors involved in modelling microbial communities. This study revealed a poly-extremophilic microbial community in the Murtazaabad hot spring and characterised the unexplored halophilic microbial diversity of saline soil of Pakistan.
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Affiliation(s)
- Anila Fariq
- Department of Biotechnology, Fatima Jinnah Women University, Rawalpindi, Pakistan Department of Biotechnology, Fatima Jinnah Women University Rawalpindi Pakistan.,Department of Biotechnology, University of Kotli, AJK, Kotli, Pakistan Department of Biotechnology, University of Kotli, AJK Kotli Pakistan
| | - Azra Yasmin
- Department of Biotechnology, Fatima Jinnah Women University, Rawalpindi, Pakistan Department of Biotechnology, Fatima Jinnah Women University Rawalpindi Pakistan
| | - John C Blazier
- Texas A&M Institute of Genome Sciences and SocietyTexas A&M University,, College Station, Texas, United States of America Texas A&M Institute of Genome Sciences and SocietyTexas A&M University, College Station, Texas United States of America
| | - Sammyia Jannat
- Department of Biotechnology, University of Kotli, AJK, Kotli, Pakistan Department of Biotechnology, University of Kotli, AJK Kotli Pakistan
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11
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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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12
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Wang J, Ding Y, Cao Y, Xu W, Zhang Y. Rhizosheath microbes induce root immune response under soil drying. PLANT SIGNALING & BEHAVIOR 2021; 16:1920752. [PMID: 33906570 PMCID: PMC8244757 DOI: 10.1080/15592324.2021.1920752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/17/2021] [Accepted: 04/19/2021] [Indexed: 06/12/2023]
Abstract
The rhizosheath is an important drought-adaptive trait in roots of many angiosperms and has been regarded as a potential trait for future agricultural sustainability. In recent studies, we found that rice roots could form a pronounced rhizosheath under moderate soil drying (MSD) but not under continuous flooding irrigation (CF). The formation of rhizosheaths substantially changes the microbial community structure in endosphere root tissues and the rhizosphere in rice, which may induce a plant immune response. However, the manner by which the formation of rhizosheaths regulates the immune system of roots remains largely unknown. Here, we have analyzed the root transcriptomes of drought-tolerant rice and drought-sensitive rice under both MSD (rhizosheath-root) and CF (root without rhizosheath) conditions. Our results suggest that rhizosheath-associated microbes may trigger plant immune pathways in root under MSD, including the first line of defense component pattern-triggered immunity and the second line of defense component effector-triggered immunity. These data expand our understanding of rhizosheath-associated microbes and plant interactions.
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Affiliation(s)
- Jiahao Wang
- Institute of Oceanography, Minjiang University, Fuzhou, China
- Center for Plant Water–use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Agriculture, Yangzhou University, Yangzhou, China
| | - Yexin Ding
- Center for Plant Water–use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yiying Cao
- Center for Plant Water–use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weifeng Xu
- Center for Plant Water–use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yingjiao Zhang
- Institute of Oceanography, Minjiang University, Fuzhou, China
- Center for Plant Water–use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, China
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13
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Alsharif W, Saad MM, Hirt H. Desert Microbes for Boosting Sustainable Agriculture in Extreme Environments. Front Microbiol 2020; 11:1666. [PMID: 32793155 PMCID: PMC7387410 DOI: 10.3389/fmicb.2020.01666] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 06/25/2020] [Indexed: 11/13/2022] Open
Abstract
A large portion of the earth's surface consists of arid, semi-arid and hyper-arid lands. Life in these regions is profoundly challenged by harsh environmental conditions of water limitation, high levels of solar radiation and temperature fluctuations, along with soil salinity and nutrient deficiency, which have serious consequences on plant growth and survival. In recent years, plants that grow in such extreme environments and their naturally associated beneficial microbes have attracted increased interest. The rhizosphere, rhizosheath, endosphere, and phyllosphere of desert plants display a perfect niche for isolating novel microbes. They are well adapted to extreme environments and offer an unexploited reservoir for bio-fertilizers and bio-control agents against a wide range of abiotic and biotic stresses that endanger diverse agricultural ecosystems. Their properties can be used to improve soil fertility, increase plant tolerance to various environmental stresses and crop productivity as well as benefit human health and provide enough food for a growing human population in an environment-friendly manner. Several initiatives were launched to discover the possibility of using beneficial microbes. In this review, we will be describing the efforts to explore the bacterial diversity associated with desert plants in the arid, semi-arid, and hyper-arid regions, highlighting the latest discoveries and applications of plant growth promoting bacteria from the most studied deserts around the world.
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Affiliation(s)
- Wiam Alsharif
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Maged M. Saad
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Heribert Hirt
- DARWIN21, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Max Perutz Laboratories, University of Vienna, Vienna, Austria
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14
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Tahir M, Naeem M, Shahid M, Khalid U, Farooq A, Ahmad N, Ahmad I, Arshad M, Waqar A. Inoculation of
pqq
E gene inhabiting
Pantoea
and
Pseudomonas
strains improves the growth and grain yield of wheat with a reduced amount of chemical fertilizer. J Appl Microbiol 2020; 129:575-589. [DOI: 10.1111/jam.14630] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 01/14/2020] [Accepted: 02/28/2020] [Indexed: 02/05/2023]
Affiliation(s)
- M. Tahir
- Department of Environmental Sciences COMSATS University Islamabad Vehari Campus Pakistan
| | - M.A. Naeem
- Department of Environmental Sciences COMSATS University Islamabad Vehari Campus Pakistan
| | - M. Shahid
- Department of Bioinformatics and Biotechnology Government College University Faisalabad Pakistan
| | - U. Khalid
- Department of Agronomy Bahauddin Zakariya University Multan Punjab Pakistan
| | - A.B.U. Farooq
- Department of Environmental Sciences COMSATS University Islamabad Vehari Campus Pakistan
| | - N. Ahmad
- Department of Environmental Sciences COMSATS University Islamabad Vehari Campus Pakistan
| | - I. Ahmad
- Department of Environmental Sciences COMSATS University Islamabad Vehari Campus Pakistan
| | - M. Arshad
- Department of Biotechnology University of Okara Punjab Pakistan
| | - A. Waqar
- Department of Environmental Sciences COMSATS University Islamabad Vehari Campus Pakistan
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15
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Tahir M, Ahmad I, Shahid M, Shah GM, Farooq ABU, Akram M, Tabassum SA, Naeem MA, Khalid U, Ahmad S, Zakir A. Regulation of antioxidant production, ion uptake and productivity in potato (Solanum tuberosum L.) plant inoculated with growth promoting salt tolerant Bacillus strains. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 178:33-42. [PMID: 30991245 DOI: 10.1016/j.ecoenv.2019.04.027] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 04/01/2019] [Accepted: 04/08/2019] [Indexed: 05/21/2023]
Abstract
The exchangeable sodium (Na+) in salt affected soils is a major constraint in potassium (K+) availability to plants that disturb ion transport and inhibit plant growth, adversely. Salt tolerant plant growth promoting rhizobacteria (PGPR) may regulate the Na+/K+ efflux and increase K+ uptake by the plant from the soil. Therefore, a pot study was performed to examine the effect of salt tolerant PGPR Bacillus sp. alone and in consortium, on antioxidant enzyme activity, ion uptake and potato (Solanum tuberosum L.) tuber yield in normal and salt affected soils. We observed that Bacillus sp. (strains SR-2-1 and SR-2-1/1) solubilized insoluble phosphorous and produced indole-3-acetic acid while only SR-2-1/1 produced ACC deaminase in culture medium supplemented with various concentrations of NaCl (0-6%). In the pot experiment, the consortium treatment of strains was found to increase relative leaf water contents whereas decreased the electrolyte leakage and antioxidant enzyme activity both in normal and salt affected soils. Similarly, consortium treatment decreased Na+ whereas increased K+, Ca+2, K+/Na+ and Ca+2/Na+ in plant dry matter in both soils. It has been investigated that inoculation of PGPR significantly (p < 0.05) increased plant biomass, number of tubers per plant and tuber weight as compared to un-inoculated plants in both soils. In addition, PGPR inoculation enhanced auxin production in root exudates of young potato plants and bacterial population dynamics in both soils. Na+ ion regulation (R2 = 0.95) and tuber weight (R2 = 0.90) in salt affected soil were significantly correlated with auxin production in the rhizosphere. Results of this study conferred that consortium of Bacillus strains (SR-2-1, SR-2-1/1) enhanced auxin production in the rhizosphere of potato plants and that ultimately regulated antioxidant enzyme production and uptake of Na+, K+ and Ca+2 in potato plants resulted into a higher tuber yield in both normal and salt affected soils.
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Affiliation(s)
- Muhammad Tahir
- Department of Environmental Sciences, COMSATS University Islamabad, Vehari-Campus, Vehari, 61100, Pakistan
| | - Iftikhar Ahmad
- Department of Environmental Sciences, COMSATS University Islamabad, Vehari-Campus, Vehari, 61100, Pakistan.
| | - Muhammad Shahid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, 38040, Pakistan
| | - Ghulam Mustafa Shah
- Department of Environmental Sciences, COMSATS University Islamabad, Vehari-Campus, Vehari, 61100, Pakistan
| | - Abu Bakr Umer Farooq
- Department of Environmental Sciences, COMSATS University Islamabad, Vehari-Campus, Vehari, 61100, Pakistan
| | - Muhammad Akram
- Department of Environmental Sciences, COMSATS University Islamabad, Vehari-Campus, Vehari, 61100, Pakistan
| | - Sohail Akhtar Tabassum
- Department of Environmental Sciences, COMSATS University Islamabad, Vehari-Campus, Vehari, 61100, Pakistan
| | - Muhammad Asif Naeem
- Department of Environmental Sciences, COMSATS University Islamabad, Vehari-Campus, Vehari, 61100, Pakistan
| | - Umaira Khalid
- Department of Agronomy, Bahauddin Zakarrya University, Multan, 60000, Pakistan
| | - Sajjad Ahmad
- Department of Environmental Sciences, COMSATS University Islamabad, Vehari-Campus, Vehari, 61100, Pakistan
| | - Ali Zakir
- Department of Environmental Sciences, COMSATS University Islamabad, Vehari-Campus, Vehari, 61100, Pakistan.
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16
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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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17
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He Z, Mao R, Dong JE, Liang Z, Zhang H, Liu L. Remediation of deterioration in microbial structure in continuous Pinellia ternata cropping soil by crop rotation. Can J Microbiol 2019; 65:282-295. [DOI: 10.1139/cjm-2018-0409] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Pinellia ternata is a traditional Chinese herb that suffers from continuous cropping (CC), which significantly decreases both yield and quality. The influence of CC on the microbiome in P. ternata rhizosphere and the effects of remediation on microbiota by rotational cropping (CR) were assessed by Illumina high-throughput sequencing technology. CC tends to decrease the α-diversities as a function of cultivation time, whereas CR tends to increase them. Differentially abundant analysis showed that microbial structure was important in maintaining the health status of P. ternata rhizosphere. Results suggested that CC soils were mainly enriched for Pseudomonas, Rhizobium, and Streptophyta operational taxonomic units (OTUs), while the CR soils were mainly enriched for Rhizobium, Pseudomonas, Flavobacterium, Sphingomonas, Rhizobacter, and Arthrobacter OTUs. On the basis of the community dissimilarities, we grouped all sample replicates into three post hoc clusters in which soils were defined as healthy, health-suppressed, and health-depressed soils. The three soil types represented different soil physicochemical properties. The activities of the microbiome features, including ammonia oxidizer, sulfate reducer, nitrite reducer, dehalogenation, xylan degrader, sulfide oxidizer, nitrogen fixation, atrazine metabolism, chitin degradation, degraded aromatic hydrocarbons, and chlorophenol degradation, were also considerably different among the three soils.
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Affiliation(s)
- Zhigui He
- College of Life Sciences, Northwest A & F University, Yangling 712100, P.R. China
- Institute of Food Science and Biological Engineering, Guilin Tourism University, Guilin 541006, P.R. China
| | - Renjun Mao
- College of Life Sciences, Northwest A & F University, Yangling 712100, P.R. China
| | - Juan e Dong
- College of Life Sciences, Northwest A & F University, Yangling 712100, P.R. China
| | - Zongsuo Liang
- College of Life Sciences, Northwest A & F University, Yangling 712100, P.R. China
- School of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, P.R. China
| | - Haihua Zhang
- College of Life Sciences, Northwest A & F University, Yangling 712100, P.R. China
- School of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, P.R. China
| | - Lin Liu
- College of Life Sciences, Northwest A & F University, Yangling 712100, P.R. China
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18
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Liu TY, Ye N, Song T, Cao Y, Gao B, Zhang D, Zhu F, Chen M, Zhang Y, Xu W, Zhang J. Rhizosheath formation and involvement in foxtail millet (Setaria italica) root growth under drought stress. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:449-462. [PMID: 30183129 DOI: 10.1111/jipb.12716] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 09/03/2018] [Indexed: 06/08/2023]
Abstract
The rhizosheath, a layer of soil particles that adheres firmly to the root surface by a combination of root hairs and mucilage, may improve tolerance to drought stress. Setaria italica (L.) P. Beauv. (foxtail millet), a member of the Poaceae family, is an important food and fodder crop in arid regions and forms a larger rhizosheath under drought conditions. Rhizosheath formation under drought conditions has been studied, but the regulation of root hair growth and rhizosheath size in response to soil moisture remains unclear. To address this question, in this study we monitored root hair growth and rhizosheath development in response to a gradual decline in soil moisture. Here, we determined that a soil moisture level of 10%-14% (w/w) stimulated greater rhizosheath production compared to other soil moisture levels. Root hair density and length also increased at this soil moisture level, which was validated by measurement of the expression of root hair-related genes. These findings contribute to our understanding of rhizosheath formation in response to soil water stress.
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Affiliation(s)
- Tie-Yuan Liu
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Nenghui Ye
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha 410128, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Tao Song
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Yunying Cao
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
- College of Life Sciences, Nantong University, Nantong 226019, China
| | - Bei Gao
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Di Zhang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Fuyuan Zhu
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Moxian Chen
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Yingjiao Zhang
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Weifeng Xu
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jianhua Zhang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
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19
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Combined application of biochar and PGPR consortia for sustainable production of wheat under semiarid conditions with a reduced dose of synthetic fertilizer. Braz J Microbiol 2019; 50:449-458. [PMID: 30671922 DOI: 10.1007/s42770-019-00043-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/20/2018] [Indexed: 10/27/2022] Open
Abstract
This study investigates the combined effect of locally adopted plant growth promoting rhizobacteria (PGPR), biochar, and synthetic fertilizer on the wheat crop for the production and economic returns. A total of 20 PGPR strains were isolated from three different ecological zones of Pakistan and were evaluated. Of them, three isolates were selected for further studies. The treatments included (i) control with a full dose of the recommended fertilizer, (ii) control with half a dose of the fertilizer, (iii) PGPR consortia with half a dose of the fertilizer, (iv) biochar with half a dose of the fertilizer, and (v) PGPR + biochar with half a dose of the fertilizer. The study was repeated at three different locations. The data collected for leaf area index (LAI), grain yield, biological yield, straw yield, and harvest index (HI) revealed significant differences (P ≤ 0.05) for the locations and treatments, but the interaction of location and treatments was not significant. Based on the productivity and economic returns, the treatment with PGPR + biochar with half a dose of the fertilizer proved to be the best. Thus, the use of the PGPR consortia and biochar can improve the yield and profit of wheat crop with reduced synthetic fertilization. Graphical abstract ᅟ.
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20
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Galbieri R, Davis RF, Kobayasti L, Albuquerque MCF, Bélot JL, Echer FR, Boldt AS. Influence of Cotton Root System Size on Tolerance to Rotylenchulus reniformis. PLANT DISEASE 2018; 102:2473-2479. [PMID: 30281421 DOI: 10.1094/pdis-09-17-1424-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The factors that influence the ability of cotton to minimize yield loss despite parasitism by Rotylenchulus reniformis (i.e., tolerance) were evaluated for 12 cotton genotypes. Reproduction of R. reniformis and total length of the root system were measured under greenhouse conditions, and the relationship of those variables to yield loss caused by R. reniformis in infested fields was evaluated. Values for nematodes per gram of root and root length were standardized by setting the genotype with greatest value as 100% and then calculating a percentage for each genotype. There was significant variability among genotypes in yield loss, resistance, and root length. Average yield loss for the genotypes ranged from 10.4% for IAC 26RMD to 43.2% for IMACD 5675B2RF. The least nematode reproduction was on IAC 26RMD, which had 49.6% of the reproduction on the susceptible check, Deltapine 16. The genotype with the shortest total root length was 34% less than the genotype with the greatest length. There was a significant linear relationship between percentage yield loss caused by R. reniformis and root length and nematodes per gram of root, both expressed as a percentage of the maximum, represented by the following equation: Yield loss (%) = 16.1258 - 0.1918*(% maximum root length) + 0.3728*(% maximum eggs + vermiform/g of roots). We conclude that tolerance to R. reniformis in cotton is influenced by the size of the root system and the parasitic load on the plant (nematodes per gram of root). Management approaches that increase root growth may lower the parasitic load, thereby reducing losses in cotton to R. reniformis.
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Affiliation(s)
- Rafael Galbieri
- Programa de Pós-Graduação em Agricultura Tropical, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil
| | - Richard F Davis
- USDA Agricultural Research Service, Crop Protection and Management Research Unit, P.O. Box 748, Tifton, GA 31793
| | - Leimi Kobayasti
- Universidade Federal de Mato Grosso - UFMT, Cuiabá - MT, Brazil
| | | | - Jean-Louis Bélot
- Instituto Mato-grossense do Algodão - IMAmt, Primavera do Leste - MT, Brazil
| | - Fabio R Echer
- Instituto Mato-grossense do Algodão - IMAmt, Primavera do Leste - MT, Brazil
| | - Alberto S Boldt
- Instituto Mato-grossense do Algodão - IMAmt, Primavera do Leste - MT, Brazil
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21
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Suleman M, Yasmin S, Rasul M, Yahya M, Atta BM, Mirza MS. Phosphate solubilizing bacteria with glucose dehydrogenase gene for phosphorus uptake and beneficial effects on wheat. PLoS One 2018; 13:e0204408. [PMID: 30240432 PMCID: PMC6150522 DOI: 10.1371/journal.pone.0204408] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 09/04/2018] [Indexed: 11/18/2022] Open
Abstract
The aim of this study was to isolate, characterize and use phosphate solubilizing bacteria to enhance the bioavailability of insoluble Ca-phosphate for wheat plants. For this purpose, 15 phosphorus solubilizing bacteria (PSB) were isolated from wheat rhizospheric soils of Peshawar and southern Punjab region, Pakistan. These isolates were identified using light microscopy and 16S rRNA gene. Among the isolated bacteria, two strains (Pseudomonas sp. MS16 and Enterobacter sp. MS32) were the efficient P solubilizers based on their P solubilization activity determined qualitatively (solubilization index 3.2-5.8) as well as quantitatively (136-280 μg mL-1). These two strains produced indole-3-acetic acid (25.6-28.1 μg mL-1), gibberellic acid (2.5-11.8), solubilized zinc compounds (SI 2.8-3.3) and showed nitrogenase and 1-Aminocyclopropane-1-carboxylic acid deaminase activity in vitro. Phosphate solubilization activity of Pseudomonas sp. MS16 was further validated by amplification, sequencing and phylogenetic analysis of glucose dehydrogenase (gcd) gene (LT908484) responsible for P solubilization. Response Surface Methodology for large-scale production was used to find optimal conditions (Temperature 22.5°C, pH 7) for P solubilization. Glucose was found to support higher P solubilization in vitro. In an in vitro experiment, PSB treated wheat seedlings improved germination and seedling vigor (11% increases) as compared to un-inoculated control. Rhizoscanning of these seedlings showed an increase in various root growth parameters. Wheat inoculation with selected strain MS16 showed pronounced effect on grain yield in pot (38.5% increase) and field (17-18% increase) experiments compared to non-inoculated control. Root colonization by PSB through Florescent in situ Hybridization and Confocal Laser Scanning Microscopy confirmed their rhizosphere competence in soil. BOX-PCR confirmed the re-isolated colonies of Pseudomonas sp. MS16. The results indicated that gluconic acid producing Pseudomonas sp. MS16 from un-explored soils may be cost effective and environment friendly candidate to improve plant growth and phosphorous uptake by wheat plants.
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Affiliation(s)
- Muhammad Suleman
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Sumera Yasmin
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Maria Rasul
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Mahreen Yahya
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Babar Manzoor Atta
- Plant Breeding and Genetics Division, Nuclear Institute for Food and Agriculture (NIFA), Peshawar, Pakistan
| | - Muhammad Sajjad Mirza
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
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22
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Tahir M, Khalid U, Ijaz M, Shah GM, Naeem MA, Shahid M, Mahmood K, Ahmad N, Kareem F. Combined application of bio-organic phosphate and phosphorus solubilizing bacteria (Bacillus strain MWT 14) improve the performance of bread wheat with low fertilizer input under an arid climate. Braz J Microbiol 2018; 49 Suppl 1:15-24. [PMID: 29728340 PMCID: PMC6328723 DOI: 10.1016/j.bjm.2017.11.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 10/17/2017] [Accepted: 11/12/2017] [Indexed: 11/25/2022] Open
Abstract
This study was aimed to investigate the effect of bio-organic phosphate either alone or in combination with phosphorus solubilizing bacteria strain (Bacillus MWT-14) on the growth and productivity of two wheat cultivars (Galaxy-2013 and Punjab-2011) along with recommended (150–100 NP kg ha−1) and half dose (75–50 NP kg ha−1) of fertilizers. The combined application of bio-organic phosphate and the phosphorous solubilizing bacteria strain at either fertilizer level significantly improved the growth, yield parameters and productivity of both wheat cultivars compared to non-inoculated control treatments. The cultivar Punjab-2011 produced the higher chlorophyll contents, crop growth rate, and the straw yield at half dose of NP fertilizer; while Galaxy-2013, with the combined application of bio-organic phosphate and phosphorous solubilizing bacteria under recommended NP fertilizer dose. Combined over both NP fertilizer levels, the combined use of bio-organic phosphate and phosphorous solubilizing bacteria enhanced the grain yield of cultivar Galaxy-2013 by 54.3% and that of cultivar Punjab-2011 by 83.3%. The combined application of bio-organic phosphate and phosphorous solubilizing bacteria also increased the population of phosphorous solubilizing bacteria, the soil organic matter and phosphorous contents in the soil. In conclusion, the combined application of bio-organic phosphate and phosphorous solubilizing bacteria offers an eco-friendly option to harvest the better wheat yield with low fertilizer input under arid climate.
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Affiliation(s)
- Muhammad Tahir
- COMSATS Institute of Information Technology, Department of Environmental Sciences, Vehari, Pakistan
| | - Umaira Khalid
- Bahauddin Zakariya University, Department of Agronomy, Multan, Pakistan
| | - Muhammad Ijaz
- Bahauddin Zakariya University, Bahadur Sub-Campus, College of Agriculture, Layyah, Pakistan.
| | - Ghulam Mustafa Shah
- COMSATS Institute of Information Technology, Department of Environmental Sciences, Vehari, Pakistan
| | - Muhammad Asif Naeem
- COMSATS Institute of Information Technology, Department of Environmental Sciences, Vehari, Pakistan
| | - Muhammad Shahid
- Government College University, Department of Bioinformatics and Biotechnology, Faisalabad, Pakistan
| | - Khalid Mahmood
- Aarhus University, Faculty of Science and Technology, Department of Agro-ecology, Aarhus, Denmark
| | - Naveed Ahmad
- COMSATS Institute of Information Technology, Department of Environmental Sciences, Vehari, Pakistan
| | - Fazal Kareem
- Bahauddin Zakariya University, Department of Agronomy, Multan, Pakistan
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23
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Zhou J, Jiang X, Wei D, Zhao B, Ma M, Chen S, Cao F, Shen D, Guan D, Li J. Consistent effects of nitrogen fertilization on soil bacterial communities in black soils for two crop seasons in China. Sci Rep 2017; 7:3267. [PMID: 28607352 PMCID: PMC5468298 DOI: 10.1038/s41598-017-03539-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 05/01/2017] [Indexed: 01/08/2023] Open
Abstract
Long-term use of inorganic nitrogen (N) fertilization has greatly influenced the bacterial community in black soil of northeast China. It is unclear how N affects the bacterial community in two successive crop seasons in the same field for this soil type. We sampled soils from a long-term fertilizer experimental field in Harbin city with three N gradients. We applied sequencing and quantitative PCR targeting at the 16S rRNA gene to examine shifts in bacterial communities and test consistent shifts and driving-factors bacterial responses to elevated N additions. N addition decreased soil pH and bacterial 16S rDNA copy numbers, and increased soil N and crop yield. N addition consistently decreased bacterial diversity and altered bacterial community composition, by increasing the relative abundance of Proteobacteria, and decreasing that of Acidobacteria and Nitrospirae in both seasons. Consistent changes in the abundant classes and genera, and the structure of the bacterial communities across both seasons were observed. Our results suggest that increases in N inputs had consistent effects on the richness, diversity and composition of soil bacterial communities across the crop seasons in two continuous years, and the N addition and the subsequent edaphic changes were important factors in shaping bacterial community structures.
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Affiliation(s)
- Jing Zhou
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China.,College of Biological Sciences, China Agricultural University, Beijing, 100094, PR China
| | - Xin Jiang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China. .,Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, PR China.
| | - Dan Wei
- The Institute of Soil Fertility and Environmental Sources, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, PR China
| | - Baisuo Zhao
- Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, PR China
| | - Mingchao Ma
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China.,Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, PR China
| | - Sanfeng Chen
- College of Biological Sciences, China Agricultural University, Beijing, 100094, PR China
| | - Fengming Cao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China.,Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, PR China
| | - Delong Shen
- Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, PR China
| | - Dawei Guan
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Jun Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China. .,Laboratory of Quality & Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing, 100081, PR China.
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24
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Dimitrov MR, Veraart AJ, de Hollander M, Smidt H, van Veen JA, Kuramae EE. Successive DNA extractions improve characterization of soil microbial communities. PeerJ 2017; 5:e2915. [PMID: 28168105 PMCID: PMC5291099 DOI: 10.7717/peerj.2915] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 12/15/2016] [Indexed: 01/21/2023] Open
Abstract
Currently, characterization of soil microbial communities relies heavily on the use of molecular approaches. Independently of the approach used, soil DNA extraction is a crucial step, and success of downstream procedures will depend on how well DNA extraction was performed. Often, studies describing and comparing soil microbial communities are based on a single DNA extraction, which may not lead to a representative recovery of DNA from all organisms present in the soil. The use of successive DNA extractions might improve soil microbial characterization, but the benefit of this approach has only been limitedly studied. To determine whether successive DNA extractions of the same soil sample would lead to different observations in terms of microbial abundance and community composition, we performed three successive extractions, with two widely used commercial kits, on a range of clay and sandy soils. Successive extractions increased DNA yield considerably (1-374%), as well as total bacterial and fungal abundances in most of the soil samples. Analysis of the 16S and 18S ribosomal RNA genes using 454-pyrosequencing, revealed that microbial community composition (taxonomic groups) observed in the successive DNA extractions were similar. However, successive DNA extractions did reveal several additional microbial groups. For some soil samples, shifts in microbial community composition were observed, mainly due to shifts in relative abundance of a number of microbial groups. Our results highlight that performing successive DNA extractions optimize DNA yield, and can lead to a better picture of overall community composition.
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Affiliation(s)
- Mauricio R Dimitrov
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands; Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - Annelies J Veraart
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) , Wageningen , Netherlands
| | - Mattias de Hollander
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) , Wageningen , Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University , Wageningen , Netherlands
| | - Johannes A van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) , Wageningen , Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) , Wageningen , Netherlands
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25
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Yasmin S, Zaka A, Imran A, Zahid MA, Yousaf S, Rasul G, Arif M, Mirza MS. Plant Growth Promotion and Suppression of Bacterial Leaf Blight in Rice by Inoculated Bacteria. PLoS One 2016; 11:e0160688. [PMID: 27532545 PMCID: PMC4988697 DOI: 10.1371/journal.pone.0160688] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 07/23/2016] [Indexed: 11/19/2022] Open
Abstract
The present study was conducted to evaluate the potential of rice rhizosphere associated antagonistic bacteria for growth promotion and disease suppression of bacterial leaf blight (BLB). A total of 811 rhizospheric bacteria were isolated and screened against 3 prevalent strains of BLB pathogen Xanthomonas oryzae pv. oryzae (Xoo) of which five antagonistic bacteria, i.e., Pseudomonas spp. E227, E233, Rh323, Serratia sp. Rh269 and Bacillus sp. Rh219 showed antagonistic potential (zone of inhibition 1-19 mm). Production of siderophores was found to be the common biocontrol determinant and all the strains solubilized inorganic phosphate (82-116 μg mL-1) and produced indole acetic acid (0.48-1.85 mg L-1) in vitro. All antagonistic bacteria were non-pathogenic to rice, and their co-inoculation significantly improved plant health in terms of reduced diseased leaf area (80%), improved shoot length (31%), root length (41%) and plant dry weight (60%) as compared to infected control plants. Furthermore, under pathogen pressure, bacterial inoculation resulted in increased activity of defense related enzymes including phenylalanine ammonia-lyase and polyphenol oxidase, along with 86% increase in peroxidase and 53% increase in catalase enzyme activities in plants inoculated with Pseudomonas sp. Rh323 as well as co-inoculated plants. Bacterial strains showed good colonization potential in the rice rhizosphere up to 21 days after seed inoculation. Application of bacterial consortia in the field resulted in an increase of 31% in grain yield and 10% in straw yield over non-inoculated plots. Although, yield increase was statistically non-significant but was accomplished with overall saving of 20% chemical fertilizers. The study showed that Pseudomonas sp. Rh323 can be used to develop dual-purpose inoculum which can serve not only to suppress BLB but also to promote plant growth in rice.
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Affiliation(s)
- Sumera Yasmin
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- * E-mail:
| | - Abha Zaka
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Asma Imran
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Muhammad Awais Zahid
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Department of Plant Pathology, University College of Agriculture, University of Sargodha, Sargodha, Pakistan
| | - Sumaira Yousaf
- Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, Pakistan
| | - Ghulam Rasul
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Muhammad Arif
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Muhammad Sajjad Mirza
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
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