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Ferrando L, Rariz G, Martínez-Pereyra A, Fernández-Scavino A. Endophytic diazotrophic communities from rice roots are diverse and weakly associated with soil diazotrophic community composition and soil properties. J Appl Microbiol 2024; 135:lxae157. [PMID: 38925647 DOI: 10.1093/jambio/lxae157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/14/2024] [Accepted: 06/25/2024] [Indexed: 06/28/2024]
Abstract
AIM Bacteria that promote plant growth, such as diazotrophs, are valuable tools for achieving a more sustainable production of important non-legume crops like rice. Different strategies have been used to discover new bacteria capable of promoting plant growth. This work evaluated the contribution of soil diazotrophs to the endophytic communities established in the roots of rice seedlings cultivated on seven representative soils from Uruguay. METHODS AND RESULTS The soils were classified into two groups according to the C and clay content. qPCR, terminal restriction fragment length polymorphism (T-RFLP), and 454-pyrosequencing of the nifH gene were used for analyzing diazotrophs in soil and plantlets' roots grown from seeds of the same genotype for 25 days under controlled conditions. A similar nifH abundance was found among the seven soils, roots, or leaves. The distribution of diazotrophs was more uneven in roots than in soils, with dominance indices significantly higher than in soils (nifH T-RFLP). Dominant soils' diazotrophs were mainly affiliated to Alphaproteobacteria and Planctomycetota. Conversely, Alpha, Beta, Gammaproteobacteria, and Bacillota were predominant in different roots, though undetectable in soils. Almost no nifH sequences were shared between soils and roots. CONCLUSIONS Root endophytic diazotrophs comprised a broader taxonomic range of microorganisms than diazotrophs found in soils from which the plantlets were grown and showed strong colonization patterns.
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Affiliation(s)
- Lucía Ferrando
- Laboratorio de Ecología Microbiana Medioambiental, Área Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, General Flores 2124, Montevideo, Uruguay
| | - Gastón Rariz
- Laboratorio de Ecología Microbiana Medioambiental, Área Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, General Flores 2124, Montevideo, Uruguay
| | - Andrea Martínez-Pereyra
- Laboratorio de Ecología Microbiana Medioambiental, Área Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, General Flores 2124, Montevideo, Uruguay
| | - Ana Fernández-Scavino
- Laboratorio de Ecología Microbiana Medioambiental, Área Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, General Flores 2124, Montevideo, Uruguay
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Li M, Gao L, White JC, Haynes CL, O'Keefe TL, Rui Y, Ullah S, Guo Z, Lynch I, Zhang P. Nano-enabled strategies to enhance biological nitrogen fixation. NATURE NANOTECHNOLOGY 2023; 18:688-691. [PMID: 37165029 DOI: 10.1038/s41565-023-01392-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Affiliation(s)
- Mingshu Li
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, China
| | - Li Gao
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jason C White
- Department of Analytical Chemistry, The Connecticut Agricultural Experiment Station, New Haven, CT, USA.
| | - Christy L Haynes
- Department of Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Tana L O'Keefe
- Department of Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Yukui Rui
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China.
| | - Sami Ullah
- School of Geography, Earth and Environmental Sciences, Edgbaston, Birmingham, UK
| | - Zhiling Guo
- School of Geography, Earth and Environmental Sciences, Edgbaston, Birmingham, UK
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, Edgbaston, Birmingham, UK
| | - Peng Zhang
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, China.
- School of Geography, Earth and Environmental Sciences, Edgbaston, Birmingham, UK.
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Zhang W, Yu C, Yin S, Chang X, Chen K, Xing Y, Yang Y. Transmission and retention of antibiotic resistance genes (ARGs) in chicken and sheep manure composting. BIORESOURCE TECHNOLOGY 2023; 382:129190. [PMID: 37196739 DOI: 10.1016/j.biortech.2023.129190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 05/04/2023] [Accepted: 05/14/2023] [Indexed: 05/19/2023]
Abstract
Transmission of ARGs during composting with different feedstocks (i.e., sheep manure (SM), chicken manure (CM) and mixed manure (MM, SM:CM= 3:1 ratio) was studied by metagenomic sequencing. 53 subtypes of ARGs for 22 types of antibiotics were identified as commonly present in these compost mixes; among them, CM had higher abundance of ARGs, 1.69 times than that in SM, while the whole elimination rate of CM, MM and SM were 55.2%, 54.7% and 42.9%, respectively. More than 50 subtypes of ARGs (with 8.6%, 11.4% and 20.9% abundance in the initial stage in CM, MM and SM composting) were "diehard" ARGs, and their abundance grew significantly to 56.5%, 63.2% and 69.9% at the mature stage. These "diehard" ARGs were transferred from initial hosts of pathogenic and/or probiotic bacteria to final hosts of thermophilic bacteria, by horizontal gene transfer (HGT) via mobile gene elements (MGEs), and became rooted in composting products.
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Affiliation(s)
- Wenming Zhang
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, PR China.
| | - Chenxu Yu
- Department of Agriculture and Biosystem Engineering, Iowa State University, Ames 50010, US
| | - Siqian Yin
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Xinyi Chang
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Kaishan Chen
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Yanhong Xing
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Yingxiang Yang
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, PR China
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Tariq M, Hasnain N, Rasul I, Asad MA, Javed A, Rashid K, Shafique J, Iram W, Hameed A, Zafar M. Reconnoitering the capabilities of nodule endophytic Pantoea dispersa for improved nodulation and grain yield of chickpea (Cicer arietinum L.). World J Microbiol Biotechnol 2023; 39:85. [PMID: 36705812 DOI: 10.1007/s11274-023-03525-3] [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: 08/02/2022] [Accepted: 01/11/2023] [Indexed: 01/28/2023]
Abstract
Microorganisms belonging to root and soil provide a wide range of services and benefits to the plant by promoting plant growth and controlling phytopathogens. This study aimed to isolate endophytic bacteria from the root nodules of chickpea (Cicer arietinum L.) and determine their potential in improving plant growth. A total of nineteen different bacterial morphotypes were isolated from root nodules of chickpea and characterized in vitro for plant growth promotion abilities. All bacterial isolates were able to produce indole acetic acid at varying levels, out of which MCA19 was screened as the most efficient indole acetic acid producer (10.25 µg mL-1). MCA8, MCA9, MCA10, MCA11, MCA16, MCA17 and MCA19 were positive for phosphate solubilization, out of which MCA9 was best phosphate solubilizer (18.8 µg mL-1). All bacterial strains showed varying ability to grow on nitrogen-free media. Hydrogen cyanide, pectinase, and cellulase production ability were also observed in isolates, in which MCA9, MCA12, MCA17 and MCA19 were found best. Based on in vitro testing, five isolates MCA2, MCA9, MCA11, MCA17 and MCA19 were selected for further studies. Bacterial isolates MCA9, MCA11, MCA17 and MCA19 were identified by 16S rRNA gene sequence analysis as Pantoea dispersa while MCA2 as Rhizobium pusense. This is the first report on the existence of Pantoea dispersa in the root nodules of chickpea. In pot experiment, a maximum increase of 30% was recorded in plant dry weight upon the application of MCA19. Under field conditions, bacterial isolates, MCA2, MCA11 and MCA19 significantly enhanced nodulation and yield parameters of chickpea, compared to control. Pantoea dispersa MCA19 displayed the highest plant growth-promoting potential by increasing 38% grain yield. Our results indicate that Pantoea dispersa MCA19 is a promising biofertilizer for future applications.
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Affiliation(s)
- Mohsin Tariq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan.
| | - Nayab Hasnain
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Ijaz Rasul
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | | | - Aqsa Javed
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Kamran Rashid
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Javeria Shafique
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Wajeeha Iram
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Amir Hameed
- Plant Breeding and Acclimatization Institute, National Research Institute, 05-870, Radzikow, Blonie, Poland
| | - Marriam Zafar
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
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Saini MR, Chandran LP, Barbadikar KM, Sevanthi AMV, Chawla G, Kaushik M, Mulani E, Phule AS, Govindannagari R, Sonth B, Sinha SK, Sundaram RM, Mandal PK. Understanding plant-microbe interaction of rice and soybean with two contrasting diazotrophic bacteria through comparative transcriptome analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:939395. [PMID: 36483966 PMCID: PMC9724235 DOI: 10.3389/fpls.2022.939395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 10/25/2022] [Indexed: 06/17/2023]
Abstract
Understanding the beneficial plant-microbe interactions is becoming extremely critical for deploying microbes imparting plant fitness and achieving sustainability in agriculture. Diazotrophic bacteria have the unique ability to survive without external sources of nitrogen and simultaneously promote host plant growth, but the mechanisms of endophytic interaction in cereals and legumes have not been studied extensively. We have studied the early interaction of two diazotrophic bacteria, Gluconacetobacter diazotrophicus (GAB) and Bradyrhizobium japonicum (BRH), in 15-day-old seedlings of rice and soybean up to 120 h after inoculation (hai) under low-nitrogen medium. Root colonization of GAB in rice was higher than that of BRH, and BRH colonization was higher in soybean roots as observed from the scanning electron microscopy at 120 hai. Peroxidase enzyme was significantly higher at 24 hai but thereafter was reduced sharply in soybean and gradually in rice. The roots of rice and soybean inoculated with GAB and BRH harvested from five time points were pooled, and transcriptome analysis was executed along with control. Two pathways, "Plant pathogen interaction" and "MAPK signaling," were specific to Rice-Gluconacetobacter (RG), whereas the pathways related to nitrogen metabolism and plant hormone signaling were specific to Rice-Bradyrhizobium (RB) in rice. Comparative transcriptome analysis of the root tissues revealed that several plant-diazotroph-specific differentially expressed genes (DEGs) and metabolic pathways of plant-diazotroph-specific transcripts, viz., chitinase, brassinosteroid, auxin, Myeloblastosis (MYB), nodulin, and nitrate transporter (NRT), were common in all plant-diazotroph combinations; three transcripts, viz., nitrate transport accessory protein (NAR), thaumatin, and thionin, were exclusive in rice and another three transcripts, viz., NAC (NAM: no apical meristem, ATAF: Arabidopsis thaliana activating factor, and CUC: cup-shaped cotyledon), ABA (abscisic acid), and ammonium transporter, were exclusive in soybean. Differential expression of these transcripts and reduction in pathogenesis-related (PR) protein expression show the early interaction. Based on the interaction, it can be inferred that the compatibility of rice and soybean is more with GAB and BRH, respectively. We propose that rice is unable to identify the diazotroph as a beneficial microorganism or a pathogen from an early response. So, it expressed the hypersensitivity-related transcripts along with PR proteins. The molecular mechanism of diazotrophic associations of GAB and BRH with rice vis-à-vis soybean will shed light on the basic understanding of host responses to beneficial microorganisms.
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Affiliation(s)
- Manish Ranjan Saini
- Indian Council of Agricultural Research (ICAR) National Institute for Plant Biotechnology, New Delhi, India
- Kalinga Institute of Industrial Technology (KIIT) School of Biotechnology, KIIT University, Bhubaneswar, India
| | | | | | - Amitha Mithra V. Sevanthi
- Indian Council of Agricultural Research (ICAR) National Institute for Plant Biotechnology, New Delhi, India
| | - Gautam Chawla
- Division of Nematology, ICAR- Indian Agriculture Research Institute, New Delhi, India
| | - Megha Kaushik
- Indian Council of Agricultural Research (ICAR) National Institute for Plant Biotechnology, New Delhi, India
| | - Ekta Mulani
- Indian Council of Agricultural Research (ICAR) National Institute for Plant Biotechnology, New Delhi, India
| | | | | | - Bandeppa Sonth
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Subodh Kumar Sinha
- Indian Council of Agricultural Research (ICAR) National Institute for Plant Biotechnology, New Delhi, India
| | | | - Pranab Kumar Mandal
- Indian Council of Agricultural Research (ICAR) National Institute for Plant Biotechnology, New Delhi, India
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Qin Y, Xie XQ, Khan Q, Wei JL, Sun AN, Su YM, Guo DJ, Li YR, Xing YX. Endophytic nitrogen-fixing bacteria DX120E inoculation altered the carbon and nitrogen metabolism in sugarcane. Front Microbiol 2022; 13:1000033. [DOI: 10.3389/fmicb.2022.1000033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 10/19/2022] [Indexed: 11/09/2022] Open
Abstract
Endophytic nitrogen-fixing bacteria are versatile and widely distributed in plants. Numerous strains of endophytic nitrogen-fixing bacteria are used as biofertilizers to minimize the utilization of chemical fertilizers, improve nutrient use efficiency, increase crop productivity, and reduce environmental pollution. However, the mechanism underlying the interaction between nitrogen-fixing bacteria and plants is still unclear. So, the present study was planned to assess the effects of endophytic nitrogen-fixing bacteria on sugarcane by analyzing the changes in physiological and biochemical activities. In the current study, Klebsiella variicola DX120E, an endophytic nitrogen-fixing bacterium, was inoculated on sugarcane varieties B8 and ROC22 to evaluate the effects on nitrogen and carbon metabolism-related enzymatic activity and biomass. Results showed that DX120E inoculation improved the enzymatic activities related to gluconeogenesis and nitrogen metabolism increased the sugarcane plant’s height, cane juice Brix, biomass, chlorophyll, and soluble sugar content in sugarcane. Metabolomics analysis revealed that the metabolome modules were highly enriched in carbon and nitrogen metabolic pathways of strain-affected sugarcane than uninoculated control. The identified carbohydrates were associated with the glycolysis or gluconeogenesis and tricarboxylic acid (TCA) cycle in plants. Metabolomic profiling in the present investigation showed that carbohydrate metabolism is coordinated with nitrogen metabolism to provide carbon skeletons and energy to amino acid synthesis, and amino acid degradation results in several metabolites used by the citric acid cycle as an energy source. Moreover, differentially expressed metabolites of non-proteinogenic amino acids have a further complementary role to the action of endophytic nitrogen-fixing bacteria. Meanwhile, a significant difference in metabolites and metabolic pathways present in stems and leaves of B8 and ROC22 varieties was found. This study discovered the potential benefits of DX120E in sugarcane and suggested candidate regulatory elements to enhance interactions between nitrogen-fixing microbes and sugarcane.
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Chaudhary P, Agri U, Chaudhary A, Kumar A, Kumar G. Endophytes and their potential in biotic stress management and crop production. Front Microbiol 2022; 13:933017. [PMID: 36325026 PMCID: PMC9618965 DOI: 10.3389/fmicb.2022.933017] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 09/12/2022] [Indexed: 11/21/2022] Open
Abstract
Biotic stress is caused by harmful microbes that prevent plants from growing normally and also having numerous negative effects on agriculture crops globally. Many biotic factors such as bacteria, fungi, virus, weeds, insects, and nematodes are the major constrains of stress that tends to increase the reactive oxygen species that affect the physiological and molecular functioning of plants and also led to the decrease in crop productivity. Bacterial and fungal endophytes are the solution to overcome the tasks faced with conventional farming, and these are environment friendly microbial commodities that colonize in plant tissues without causing any damage. Endophytes play an important role in host fitness, uptake of nutrients, synthesis of phytohormone and diminish the injury triggered by pathogens via antibiosis, production of lytic enzymes, secondary metabolites, and hormone activation. They are also reported to help plants in coping with biotic stress, improving crops and soil health, respectively. Therefore, usage of endophytes as biofertilizers and biocontrol agent have developed an eco-friendly substitute to destructive chemicals for plant development and also in mitigation of biotic stress. Thus, this review highlighted the potential role of endophytes as biofertilizers, biocontrol agent, and in mitigation of biotic stress for maintenance of plant development and soil health for sustainable agriculture.
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Affiliation(s)
- Parul Chaudhary
- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - Upasana Agri
- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | | | - Ashish Kumar
- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - Govind Kumar
- Indian Council of Agricultural Research (ICAR)-Central Institute for Subtropical Horticulture, Lucknow, India
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Chaudhary P, Singh S, Chaudhary A, Sharma A, Kumar G. Overview of biofertilizers in crop production and stress management for sustainable agriculture. FRONTIERS IN PLANT SCIENCE 2022; 13:930340. [PMID: 36082294 PMCID: PMC9445558 DOI: 10.3389/fpls.2022.930340] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/21/2022] [Indexed: 05/09/2023]
Abstract
With the increase in world population, the demography of humans is estimated to be exceeded and it has become a major challenge to provide an adequate amount of food, feed, and agricultural products majorly in developing countries. The use of chemical fertilizers causes the plant to grow efficiently and rapidly to meet the food demand. The drawbacks of using a higher quantity of chemical or synthetic fertilizers are environmental pollution, persistent changes in the soil ecology, physiochemical composition, decreasing agricultural productivity and cause several health hazards. Climatic factors are responsible for enhancing abiotic stress on crops, resulting in reduced agricultural productivity. There are various types of abiotic and biotic stress factors like soil salinity, drought, wind, improper temperature, heavy metals, waterlogging, and different weeds and phytopathogens like bacteria, viruses, fungi, and nematodes which attack plants, reducing crop productivity and quality. There is a shift toward the use of biofertilizers due to all these facts, which provide nutrition through natural processes like zinc, potassium and phosphorus solubilization, nitrogen fixation, production of hormones, siderophore, various hydrolytic enzymes and protect the plant from different plant pathogens and stress conditions. They provide the nutrition in adequate amount that is sufficient for healthy crop development to fulfill the demand of the increasing population worldwide, eco-friendly and economically convenient. This review will focus on biofertilizers and their mechanisms of action, role in crop productivity and in biotic/abiotic stress tolerance.
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Affiliation(s)
- Parul Chaudhary
- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, India
| | - Shivani Singh
- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, India
| | - Anuj Chaudhary
- School of Agriculture and Environmental Science, Shobhit University, Gangoh, India
| | - Anita Sharma
- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, India
| | - Govind Kumar
- Department of Crop Production, Central Institute for Subtropical Horticulture, Lucknow, India
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