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Sadikiel Mmbando G, Ngongolo K. The recent genetic modification techniques for improve soil conservation, nutrient uptake and utilization. GM CROPS & FOOD 2024; 15:233-247. [PMID: 39008437 PMCID: PMC11253881 DOI: 10.1080/21645698.2024.2377408] [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: 04/25/2024] [Accepted: 07/03/2024] [Indexed: 07/17/2024]
Abstract
Advances in genetic modification (GM) techniques have generated huge interest in improving nutrient utilization, maximizing nutrient uptake, and conserving soil in the pursuit of sustainable agriculture. Unfortunately, little is still known about the recent advancements in the application of GM tactics to enhance each of these areas. This review explores the latest GM strategies intended to support soil conservation, maximize nutrient uptake, and improve nutrient utilization in farming, highlighting the critical roles that soil health and nutrient management play in sustainable farming. GM strategies such as improving the efficiency of nutrient uptake through enhanced root systems and increased nutrient transport mechanisms are well discussed. This study suggests that addressing potential obstacles, such as ethical and regulatory concerns, is a necessity for long-term sustainability applications of GM technologies to raise agricultural yields.
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Affiliation(s)
- Gideon Sadikiel Mmbando
- Department of Biology, College of Natural and Mathematical Sciences, The University of Dodoma, Dodoma, United Republic of Tanzania
| | - Kelvin Ngongolo
- Department of Biology, College of Natural and Mathematical Sciences, The University of Dodoma, Dodoma, United Republic of Tanzania
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Bellanger M, Figueroa JL, Tiemann L, Friesen ML, III RW. NF ixDB (Nitrogen Fixation DataBase)-a comprehensive integrated database for robust 'omics analysis of diazotrophs. NAR Genom Bioinform 2024; 6:lqae063. [PMID: 38846350 PMCID: PMC11155484 DOI: 10.1093/nargab/lqae063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/16/2024] [Accepted: 05/23/2024] [Indexed: 06/09/2024] Open
Abstract
Biological nitrogen fixation is a fundamental biogeochemical process that transforms molecular nitrogen into biologically available nitrogen via diazotrophic microbes. Diazotrophs anaerobically fix nitrogen using the nitrogenase enzyme which is arranged in three different gene clusters: (i) molybdenum nitrogenase (nifHDK) is the most abundant, followed by it's alternatives, (ii) vanadium nitrogenase (vnfHDK) and (iii) iron nitrogenase (anfHDK). Multiple databases have been constructed as resources for diazotrophic 'omics analysis; however, an integrated database based on whole genome references does not exist. Here, we present NFixDB (Nitrogen Fixation DataBase), a comprehensive integrated whole genome based database for diazotrophs, which includes all nitrogenases (nifHDK, vnfHDK, anfHDK) and nitrogenase-like enzymes (e.g. nflHD) linked to ribosomal RNA operons (16S-5S-23S). NFixDB was computed using Hidden Markov Models (HMMs) against the entire whole genome based Genome Taxonomy Database (GTDB R214), providing searchable reference HMMs for all nitrogenase and nitrogenase-like genes, complete ribosomal RNA operons, both GTDB and NCBI/RefSeq taxonomy, and an SQL database for querying matches. We compared NFixDB to nifH databases from Buckley, Zehr, Mise and FunGene finding extensive evidence of nifH, in addition to vnfH and nflH. NFixDB contains >4000 verified nifHDK sequences contained on 50 unique phyla of bacteria and archaea. NFixDB provides the first comprehensive nitrogenase database available to researchers unlocking diazotrophic microbial potential.
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Affiliation(s)
- Madeline Bellanger
- North Carolina Research Campus (NCRC), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 150 N Research Campus Dr, Kannapolis, NC 28081, USA
- Computational Intelligence to Predict Health and Environmental Risks (CIPHER), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, USA
| | - Jose L Figueroa
- North Carolina Research Campus (NCRC), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 150 N Research Campus Dr, Kannapolis, NC 28081, USA
- Computational Intelligence to Predict Health and Environmental Risks (CIPHER), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, USA
| | - Lisa Tiemann
- Department of Plant, Soil and Microbial Sciences, Michigan State University, Plant and Soil Sciences Building, 1066 Bogue St Room A286, East Lansing, MI 48824, USA
| | - Maren L Friesen
- Department of Plant Pathology, Washington State University, Clark Hall, 2040 Ellis Way, Pullman, WA 99163, USA
| | - Richard Allen White III
- North Carolina Research Campus (NCRC), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 150 N Research Campus Dr, Kannapolis, NC 28081, USA
- Computational Intelligence to Predict Health and Environmental Risks (CIPHER), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, USA
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Hong L, Wei L, Fanglan G, Jiao L, Shiheng T, Hong Y, Yao R, Xinyue G, Can Y. Unveiling the regulatory mechanism of poly-γ-glutamic acid on soil characteristics under drought stress through integrated metagenomics and metabolomics analysis. Front Microbiol 2024; 15:1387223. [PMID: 38751715 PMCID: PMC11094619 DOI: 10.3389/fmicb.2024.1387223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/17/2024] [Indexed: 05/18/2024] Open
Abstract
It is of utmost importance to understand the characteristics and regulatory mechanisms of soil in order to optimize soil management and enhance crop yield. Poly-γ-glutamic acid (γ-PGA), a stress-resistant amino acid polymer, plays a crucial role in plant drought stress resistance. However, little is known about the effects of γ-PGA on soil characteristics during drought treatments. In this study, the effects of different forms of γ-PGA on soil texture and basic physical and chemical properties under short-term drought conditions were investigated. Furthermore, the impact of γ-PGA on the microbial community and metabolic function of maize was analyzed. Under drought conditions, the introduction of γ-PGA into the soil resulted in notable improvements in the mechanical composition ratio and infiltration capacity of the soil. Concurrently, this led to a reduction in soil bulk density and improved soil organic matter content and fertility. Additionally, metagenomic analysis revealed that under drought conditions, the incorporation of γ-PGA into the soil enhanced the soil microbiota structure. This shift led to the predominance of bacteria that are crucial for carbon, nitrogen, and phosphorus cycles in the soil. Metabolomics analysis revealed that under drought treatment, γ-PGA affected soil metabolic patterns, with a particular focus on alterations in amino acid and vitamin metabolism pathways. Correlation analysis between the soil metagenome and metabolites showed that microorganisms played a significant role in metabolite accumulation. These results demonstrated that γ-PGA could improve soil characteristics under drought conditions and play an important role in soil microorganisms and microbial metabolism, providing further insights into the changes in soil characteristics under drought conditions.
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Affiliation(s)
- Li Hong
- Key Laboratory of the Evaluation and Monitoring of Southwest Land Resources (Ministry of Education), Sichuan Normal University, Chengdu, China
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Li Wei
- Key Laboratory of the Evaluation and Monitoring of Southwest Land Resources (Ministry of Education), Sichuan Normal University, Chengdu, China
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Ge Fanglan
- Key Laboratory of the Evaluation and Monitoring of Southwest Land Resources (Ministry of Education), Sichuan Normal University, Chengdu, China
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Li Jiao
- Key Laboratory of the Evaluation and Monitoring of Southwest Land Resources (Ministry of Education), Sichuan Normal University, Chengdu, China
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Tu Shiheng
- Key Laboratory of the Evaluation and Monitoring of Southwest Land Resources (Ministry of Education), Sichuan Normal University, Chengdu, China
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Yang Hong
- Key Laboratory of the Evaluation and Monitoring of Southwest Land Resources (Ministry of Education), Sichuan Normal University, Chengdu, China
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Ren Yao
- Key Laboratory of the Evaluation and Monitoring of Southwest Land Resources (Ministry of Education), Sichuan Normal University, Chengdu, China
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Gong Xinyue
- Key Laboratory of the Evaluation and Monitoring of Southwest Land Resources (Ministry of Education), Sichuan Normal University, Chengdu, China
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Yao Can
- Key Laboratory of the Evaluation and Monitoring of Southwest Land Resources (Ministry of Education), Sichuan Normal University, Chengdu, China
- College of Life Sciences, Sichuan Normal University, Chengdu, China
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Wang T, Xu J, Chen J, Liu P, Hou X, Yang L, Zhang L. Progress in Microbial Fertilizer Regulation of Crop Growth and Soil Remediation Research. PLANTS (BASEL, SWITZERLAND) 2024; 13:346. [PMID: 38337881 PMCID: PMC10856823 DOI: 10.3390/plants13030346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024]
Abstract
More food is needed to meet the demand of the global population, which is growing continuously. Chemical fertilizers have been used for a long time to increase crop yields, and may have negative effect on human health and the agricultural environment. In order to make ongoing agricultural development more sustainable, the use of chemical fertilizers will likely have to be reduced. Microbial fertilizer is a kind of nutrient-rich and environmentally friendly biological fertilizer made from plant growth-promoting bacteria (PGPR). Microbial fertilizers can regulate soil nutrient dynamics and promote soil nutrient cycling by improving soil microbial community changes. This process helps restore the soil ecosystem, which in turn promotes nutrient uptake, regulates crop growth, and enhances crop resistance to biotic and abiotic stresses. This paper reviews the classification of microbial fertilizers and their function in regulating crop growth, nitrogen fixation, phosphorus, potassium solubilization, and the production of phytohormones. We also summarize the role of PGPR in helping crops against biotic and abiotic stresses. Finally, we discuss the function and the mechanism of applying microbial fertilizers in soil remediation. This review helps us understand the research progress of microbial fertilizer and provides new perspectives regarding the future development of microbial agent in sustainable agriculture.
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Affiliation(s)
- Tingting Wang
- College of Plant Protection, Shandong Agricultural University, Tai’an 271002, China; (T.W.); (J.X.); (P.L.); (X.H.)
| | - Jiaxin Xu
- College of Plant Protection, Shandong Agricultural University, Tai’an 271002, China; (T.W.); (J.X.); (P.L.); (X.H.)
| | - Jian Chen
- Institute of Food Quality and Safety, Jiangsu Academy of Agricultural Sciences, Nanjing 221122, China;
| | - Peng Liu
- College of Plant Protection, Shandong Agricultural University, Tai’an 271002, China; (T.W.); (J.X.); (P.L.); (X.H.)
| | - Xin Hou
- College of Plant Protection, Shandong Agricultural University, Tai’an 271002, China; (T.W.); (J.X.); (P.L.); (X.H.)
| | - Long Yang
- College of Plant Protection, Shandong Agricultural University, Tai’an 271002, China; (T.W.); (J.X.); (P.L.); (X.H.)
| | - Li Zhang
- College of Plant Protection, Shandong Agricultural University, Tai’an 271002, China; (T.W.); (J.X.); (P.L.); (X.H.)
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Rashad YM, Hafez M, Rashad M. Diazotrophic Azotobacter salinestris YRNF3: a probable calcite-solubilizing bio-agent for improving the calcareous soil properties. Sci Rep 2023; 13:20621. [PMID: 37996572 PMCID: PMC10667278 DOI: 10.1038/s41598-023-47924-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 11/20/2023] [Indexed: 11/25/2023] Open
Abstract
Calcareous soils are characterized by a high calcium carbonate content (calcite), which plays a crucial role in the soil structure, plant growth, and nutrient availability. The high content of CaCO3 leads to the increment of the soil alkalinity, which results in a lowering of the nutrient availability causing a challenge for the agriculture in these soils. In this study, the calcite-solubilizing potential of the diazotrophic Azotobacter salinestris YRNF3 was investigated in vitro as a probable bio-agent for enhancing the calcareous soils properties such as soil pH and nutrient availability. Twelve diazotrophic bacterial strains were isolated from wheat rhizosphere collected from different wheat-cultivated fields in five Egyptian governorates. Using Nessler's reagent, all isolated bacterial strains were found to have the ability to produce ammonia. By amplification of nifH gene, a PCR product of 450 bp was obtained for all isolated bacterial strains. For each isolate, three biological and three technical replicates were applied. All isolated diazotrophic bacteria were qualitatively screened for their calcite-solubilizing ability. To quantitatively investigate the calcite-solubilizing potential of A. salinestris YRNF3 in vitro, changes in the contents of soluble calcium (Ca2+), bicarbonate (HCO3-), total nitrogen (TN), total protein (TP), and pH were daily measured in its culture filtrate along 10 days of incubation. The results showed that the pH values in the culture filtrate ranged from 5.73 to 7.32. Concentration of Ca2+ and HCO3- in the culture filtrate significantly decreased with the increment in the incubation time, while concentration of TN increased along the time. The highest TN concentration (0.0807 gL-1) was observed on days 4 and 5, compared to that of the day 0 (0.0014 gL-1). Content of TP in the culture filtrate also significantly increased along the incubation period. The highest TP content was recorded in day 4 (0.0505%), while no TP content was recorded on day 0. Furthermore, data obtained revealed that A. salinestris YRNF3 produced acid phosphatase at low activity (5.4 U mL-1). HPLC analysis of the culture filtrate indicated production of different organic acids, namely lactic acid (82.57 mg mL-1), formic acid (46.8 mg mL-1), while acetic acid was detected in a low quantity (3.11 mg mL-1). For each analysis, three replicates of each treatment were analyzed. Means of the tested treatments were compared using Tukey's HSD test at p ≤ 0.05. In conclusion, findings of this work suggested that A. salinestris YRNF3 has the potential to be a probable bioagent to be used for the reclamation of the calcareous soils by solubilizing CaCO3, improving soil fertility, and promoting plant growth. However, further studies are needed to investigate its field application and their long-term effects on the soil properties and plant productivity. To the best of the author's knowledge, this is the first study reporting the calcite-solubilizing ability of a nitrogen-fixing bacteria. Having these two abilities by one microorganism is a unique feature, which qualifies it as a promising bioagent for reclamation of the calcareous soils.
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Affiliation(s)
- Younes M Rashad
- Plant Protection and Biomolecular Diagnosis Department, Arid Lands Cultivation Research Institute (ALCRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab, 21934, Egypt.
| | - Mohamed Hafez
- Land and Water Technologies Department, Arid Lands Cultivation Research Institute (ALCRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab, 21934, Egypt.
| | - Mohamed Rashad
- Land and Water Technologies Department, Arid Lands Cultivation Research Institute (ALCRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab, 21934, Egypt
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Nagpal S, Sirari A, Sharma P, Singh S, Mandahal KS, Singh H, Singh S. Marker trait association for biological nitrogen fixation traits in an interspecific cross of chickpea ( Cicer arietinum × Cicer reticulatum). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:1005-1018. [PMID: 37649881 PMCID: PMC10462594 DOI: 10.1007/s12298-023-01335-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 07/14/2023] [Accepted: 07/20/2023] [Indexed: 09/01/2023]
Abstract
A set of 165 Recombinant inbred lines (RILs) derived from an interspecific cross of chickpea was used to identify QTLs for key biological nitrogen fixation (BNF) traits. The phenotyping of BNF and related traits was done at two different agroclimatic zones viz., Central plain zone (Ludhiana) and Sub-Mountainous undulating zone (Gurdaspur) for 2 consecutive rabi seasons (2018-2020). Wild parent C. reticulatum ILWC292 showed significantly high performance in terms of biological nitrogen fixation (BNF) traits over the cultivated C. arietinum GPF-2. The triple interaction of genotypes × locations × years was significant (p 0.05) for all BNF traits in parental lines. Highly significant positive correlation was obtained between grain yield and key growth and symbiotic parameters at both the sites. Phenotypic analysis revealed nodule dry weight and leghaemoglobin content as key traits for BNF efficiency and contrasting DNA bulks were constituted on the basis of these traits. Out of 535 SSR markers, 139 exhibited polymorphism between the parental lines on polyacrylamide gel electrophoresis. A total of 30 SSR markers showed polymorphism between the higher and lower bulks for nodule dry weight and leghaemoglobin content. Out of these, 20 SSRs did not show any segregation distortion in RIL population as determined by chi square analysis (p < 0.05) and were used for quantitative trait loci (QTL) analysis. Using QTL cartographer, markers- CAGM02697, CAGM09835, CAGM09777, CAGM09227, CAGM09021, CAGM08679 were found linked with QTLs for BNF. These markers can be validated further for identification of genes for BNF traits and marker assisted selection in chickpea. To the best of our knowledge this is the first report on identification of genomic regions associated with key BNF traits in chickpea across different agro-climatic zones. Supplementary information The online version contains supplementary material available at 10.1007/s12298-023-01335-3.
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Affiliation(s)
- Sharon Nagpal
- Department of Microbiology, Punjab Agricultural University, Ludhiana, 141004 India
| | - Asmita Sirari
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
| | - Poonam Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
| | - Satinder Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
| | | | - Harpreet Singh
- Regional Research Station, Punjab Agricultural University, Gurdaspur, 143521 India
| | - Sarvjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
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Resendiz-Nava CN, Alonso-Onofre F, Silva-Rojas HV, Rebollar-Alviter A, Rivera-Pastrana DM, Stasiewicz MJ, Nava GM, Mercado-Silva EM. Tomato Plant Microbiota under Conventional and Organic Fertilization Regimes in a Soilless Culture System. Microorganisms 2023; 11:1633. [PMID: 37512805 PMCID: PMC10383152 DOI: 10.3390/microorganisms11071633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/15/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
Tomato is the main vegetable cultivated under soilless culture systems (SCSs); production of organic tomato under SCSs has increased due to consumer demands for healthier and environmentally friendly vegetables. However, organic tomato production under SCSs has been associated with low crop performance and fruit quality defects. These agricultural deficiencies could be linked to alterations in tomato plant microbiota; nonetheless, this issue has not been sufficiently addressed. Thus, the main goal of the present study was to characterize the rhizosphere and phyllosphere of tomato plants cultivated under conventional and organic SCSs. To accomplish this goal, tomato plants grown in commercial greenhouses under conventional or organic SCSs were tested at 8, 26, and 44 weeks after seedling transplantation. Substrate (n = 24), root (n = 24), and fruit (n = 24) composite samples were subjected to DNA extraction and high-throughput 16S rRNA gene sequencing. The present study revealed that the tomato core microbiota was predominantly constituted by Proteobacteria, Actinobacteria, and Firmicutes. Remarkably, six bacterial families, Bacillaceae, Microbacteriaceae, Nocardioidaceae, Pseudomonadaceae, Rhodobacteraceae, and Sphingomonadaceae, were shared among all substrate, rhizosphere, and fruit samples. Importantly, it was shown that plants under organic SCSs undergo a dysbiosis characterized by significant changes in the relative abundance of Bradyrhizobiaceae, Caulobacteraceae, Chitinophagaceae, Enterobacteriaceae, Erythrobacteraceae, Flavobacteriaceae, Nocardioidaceae, Rhodobacteraceae, and Streptomycetaceae. These results suggest that microbial alterations in substrates, roots, and fruits could be potential factors in contributing to the crop performance and fruit quality deficiencies observed in organic SCSs.
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Affiliation(s)
- Carolina N Resendiz-Nava
- Facultad de Quimica, Universidad Autonoma de Queretaro, Cerro de las Campanas S/N, Queretaro 76010, Queretaro, Mexico
| | | | - Hilda V Silva-Rojas
- Posgrado en Recursos Geneticos y Productividad, Produccion de Semillas, Colegio de Postgraduados, Km 36.5 Carretera Mexico-Texcoco, Texcoco 56264, Mexico
| | - Angel Rebollar-Alviter
- Centro Regional Morelia, Universidad Autonoma de Chapingo, Morelia 58170, Michoacan, Mexico
| | - Dulce M Rivera-Pastrana
- Facultad de Quimica, Universidad Autonoma de Queretaro, Cerro de las Campanas S/N, Queretaro 76010, Queretaro, Mexico
| | - Matthew J Stasiewicz
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, 1302W Pennsylvania Ave, Urbana, IL 61801, USA
| | - Gerardo M Nava
- Facultad de Quimica, Universidad Autonoma de Queretaro, Cerro de las Campanas S/N, Queretaro 76010, Queretaro, Mexico
| | - Edmundo M Mercado-Silva
- Facultad de Quimica, Universidad Autonoma de Queretaro, Cerro de las Campanas S/N, Queretaro 76010, Queretaro, Mexico
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Nadarajah K, Abdul Rahman NSN. The Microbial Connection to Sustainable Agriculture. PLANTS (BASEL, SWITZERLAND) 2023; 12:2307. [PMID: 37375932 DOI: 10.3390/plants12122307] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/01/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023]
Abstract
Microorganisms are an important element in modeling sustainable agriculture. Their role in soil fertility and health is crucial in maintaining plants' growth, development, and yield. Further, microorganisms impact agriculture negatively through disease and emerging diseases. Deciphering the extensive functionality and structural diversity within the plant-soil microbiome is necessary to effectively deploy these organisms in sustainable agriculture. Although both the plant and soil microbiome have been studied over the decades, the efficiency of translating the laboratory and greenhouse findings to the field is largely dependent on the ability of the inoculants or beneficial microorganisms to colonize the soil and maintain stability in the ecosystem. Further, the plant and its environment are two variables that influence the plant and soil microbiome's diversity and structure. Thus, in recent years, researchers have looked into microbiome engineering that would enable them to modify the microbial communities in order to increase the efficiency and effectiveness of the inoculants. The engineering of environments is believed to support resistance to biotic and abiotic stressors, plant fitness, and productivity. Population characterization is crucial in microbiome manipulation, as well as in the identification of potential biofertilizers and biocontrol agents. Next-generation sequencing approaches that identify both culturable and non-culturable microbes associated with the soil and plant microbiome have expanded our knowledge in this area. Additionally, genome editing and multidisciplinary omics methods have provided scientists with a framework to engineer dependable and sustainable microbial communities that support high yield, disease resistance, nutrient cycling, and management of stressors. In this review, we present an overview of the role of beneficial microbes in sustainable agriculture, microbiome engineering, translation of this technology to the field, and the main approaches used by laboratories worldwide to study the plant-soil microbiome. These initiatives are important to the advancement of green technologies in agriculture.
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Affiliation(s)
- Kalaivani Nadarajah
- Department of Biological Sciences and Biotechnology, Faculty of Sciences and Technology, University Kebangsaan Malaysia, Bangi 43600, Malaysia
| | - Nur Sabrina Natasha Abdul Rahman
- Department of Biological Sciences and Biotechnology, Faculty of Sciences and Technology, University Kebangsaan Malaysia, Bangi 43600, Malaysia
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Goyal RK, Habtewold JZ. Evaluation of Legume-Rhizobial Symbiotic Interactions Beyond Nitrogen Fixation That Help the Host Survival and Diversification in Hostile Environments. Microorganisms 2023; 11:1454. [PMID: 37374957 PMCID: PMC10302611 DOI: 10.3390/microorganisms11061454] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Plants often experience unfavorable conditions during their life cycle that impact their growth and sometimes their survival. A temporary phase of such stress, which can result from heavy metals, drought, salinity, or extremes of temperature or pH, can cause mild to enormous damage to the plant depending on its duration and intensity. Besides environmental stress, plants are the target of many microbial pathogens, causing diseases of varying severity. In plants that harbor mutualistic bacteria, stress can affect the symbiotic interaction and its outcome. To achieve the full potential of a symbiotic relationship between the host and rhizobia, it is important that the host plant maintains good growth characteristics and stay healthy under challenging environmental conditions. The host plant cannot provide good accommodation for the symbiont if it is infested with diseases and prone to other predators. Because the bacterium relies on metabolites for survival and multiplication, it is in its best interests to keep the host plant as stress-free as possible and to keep the supply stable. Although plants have developed many mitigation strategies to cope with stress, the symbiotic bacterium has developed the capability to augment the plant's defense mechanisms against environmental stress. They also provide the host with protection against certain diseases. The protective features of rhizobial-host interaction along with nitrogen fixation appear to have played a significant role in legume diversification. When considering a legume-rhizobial symbiosis, extra benefits to the host are sometimes overlooked in favor of the symbionts' nitrogen fixation efficiency. This review examines all of those additional considerations of a symbiotic interaction that enable the host to withstand a wide range of stresses, enabling plant survival under hostile regimes. In addition, the review focuses on the rhizosphere microbiome, which has emerged as a strong pillar of evolutionary reserve to equip the symbiotic interaction in the interests of both the rhizobia and host. The evaluation would draw the researchers' attention to the symbiotic relationship as being advantageous to the host plant as a whole and the role it plays in the plant's adaptation to unfavorable environmental conditions.
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Affiliation(s)
- Ravinder K. Goyal
- Agriculture and Agri-Food Canada, Lacombe Research and Development Center, Lacombe, AB T4L 1W1, Canada
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10
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Kour D, Kour H, Khan SS, Khan RT, Bhardwaj M, Kailoo S, Kumari C, Rasool S, Yadav AN, Sharma YP. Biodiversity and Functional Attributes of Rhizospheric Microbiomes: Potential Tools for Sustainable Agriculture. Curr Microbiol 2023; 80:192. [PMID: 37101055 DOI: 10.1007/s00284-023-03300-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 04/11/2023] [Indexed: 04/28/2023]
Abstract
The quest for increasing agricultural yield due to increasing population pressure and demands for healthy food has inevitably led to the indiscriminate use of chemical fertilizers. On the contrary, the exposure of the crops to abiotic stress and biotic stress interferes with crop growth further hindering the productivity. Sustainable agricultural practices are of major importance to enhance production and feed the rising population. The use of plant growth promoting (PGP) rhizospheric microbes is emerging as an efficient approach to ameliorate global dependence on chemicals, improve stress tolerance of plants, boost up growth and ensure food security. Rhizosphere associated microbiomes promote the growth by enhancing the uptake of the nutrients, producing plant growth regulators, iron chelating complexes, shaping the root system under stress conditions and decreasing the levels of inhibitory ethylene concentrations and protecting plants from oxidative stress. Plant growth-promoting rhizospheric microbes belong to diverse range of genera including Acinetobacter, Achromobacter, Aspergillus, Bacillus, Burkholderia, Flavobacterium, Klebsiella, Micrococcus, Penicillium, Pseudomonas, Serratia and Trichoderma. Plant growth promoting microbes are an interesting aspect of research for scientific community and a number of formulations of beneficial microbes are also commercially available. Thus, recent progress in our understanding on rhizospheric microbiomes along with their major roles and mechanisms of action under natural and stressful conditions should facilitate their application as a reliable component in the management of sustainable agricultural system. This review highlights the diversity of plant growth promoting rhizospheric microbes, their mechanisms of plant growth promotion, their role under biotic and abiotic stress and status of biofertilizers. The article further focuses on the role of omics approaches in plant growth promoting rhizospheric microbes and draft genome of PGP microbes.
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Affiliation(s)
- Divjot Kour
- Department of Microbiology, Akal College of Basic Sciences, Eternal University, Baru Sahib, Sirmaur, 173101, Himachal Pradesh, India
| | - Harpreet Kour
- Department of Botany, University of Jammu, Jammu, 180006, Jammu and Kashmir, India
| | - Sofia Shareif Khan
- Department of Biotechnology, Shri Mata Vaishno Devi University, Katra, 182320, Jammu and Kashmir, India
| | - Rabiya Tabbassum Khan
- Department of Biotechnology, Shri Mata Vaishno Devi University, Katra, 182320, Jammu and Kashmir, India
| | - Mansavi Bhardwaj
- Department of Biotechnology, Shri Mata Vaishno Devi University, Katra, 182320, Jammu and Kashmir, India
| | - Swadha Kailoo
- Department of Biotechnology, Shri Mata Vaishno Devi University, Katra, 182320, Jammu and Kashmir, India
| | - Chandresh Kumari
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Vill-Bhajhol Solan, 173229, Himachal Pradesh, India
| | - Shafaq Rasool
- Department of Biotechnology, Shri Mata Vaishno Devi University, Katra, 182320, Jammu and Kashmir, India
| | - Ajar Nath Yadav
- Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmaur, 173101, Himachal Pradesh, India.
- INTI International University, Persiaran Perdana BBN Putra Nilai, 71800, Nilai, Negeri Sembilan, Malaysia.
| | - Yash Pal Sharma
- Department of Botany, University of Jammu, Jammu, 180006, Jammu and Kashmir, India
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11
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Elmore JR, Dexter GN, Baldino H, Huenemann JD, Francis R, Peabody GL, Martinez-Baird J, Riley LA, Simmons T, Coleman-Derr D, Guss AM, Egbert RG. High-throughput genetic engineering of nonmodel and undomesticated bacteria via iterative site-specific genome integration. SCIENCE ADVANCES 2023; 9:eade1285. [PMID: 36897939 PMCID: PMC10005180 DOI: 10.1126/sciadv.ade1285] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 02/01/2023] [Indexed: 05/31/2023]
Abstract
Efficient genome engineering is critical to understand and use microbial functions. Despite recent development of tools such as CRISPR-Cas gene editing, efficient integration of exogenous DNA with well-characterized functions remains limited to model bacteria. Here, we describe serine recombinase-assisted genome engineering, or SAGE, an easy-to-use, highly efficient, and extensible technology that enables selection marker-free, site-specific genome integration of up to 10 DNA constructs, often with efficiency on par with or superior to replicating plasmids. SAGE uses no replicating plasmids and thus lacks the host range limitations of other genome engineering technologies. We demonstrate the value of SAGE by characterizing genome integration efficiency in five bacteria that span multiple taxonomy groups and biotechnology applications and by identifying more than 95 heterologous promoters in each host with consistent transcription across environmental and genetic contexts. We anticipate that SAGE will rapidly expand the number of industrial and environmental bacteria compatible with high-throughput genetics and synthetic biology.
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Affiliation(s)
- Joshua R. Elmore
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Gara N. Dexter
- Biosciences Division, Oak Ridge National Laboratory, One Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Henri Baldino
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Jay D. Huenemann
- Biosciences Division, Oak Ridge National Laboratory, One Bethel Valley Road, Oak Ridge, TN 37831, USA
- Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, TN 37996,USA
| | - Ryan Francis
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - George L. Peabody
- Biosciences Division, Oak Ridge National Laboratory, One Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Jessica Martinez-Baird
- Biosciences Division, Oak Ridge National Laboratory, One Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Lauren A. Riley
- Biosciences Division, Oak Ridge National Laboratory, One Bethel Valley Road, Oak Ridge, TN 37831, USA
- Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, TN 37996,USA
| | - Tuesday Simmons
- Plant and Microbial Biology Department, University of California, Berkeley, CA 94701, USA
| | - Devin Coleman-Derr
- Plant and Microbial Biology Department, University of California, Berkeley, CA 94701, USA
- Plant Gene Expression Center, USDA-ARS, Albany, CA 94710, USA
| | - Adam M. Guss
- Biosciences Division, Oak Ridge National Laboratory, One Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Robert G. Egbert
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
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12
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Harerimana B, Zhou M, Zhu B, Xu P. Regional estimates of nitrogen budgets for agricultural systems in the East African Community over the last five decades. AGRONOMY FOR SUSTAINABLE DEVELOPMENT 2023; 43:27. [PMID: 36909277 PMCID: PMC9993390 DOI: 10.1007/s13593-023-00881-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
The great challenge of reducing soil nutrient depletion and assuring agricultural system productivity in low-income countries caused by limited synthetic fertilizer use necessitates local and cost-effective nutrient sources. We estimated the changes of the nitrogen budget of agricultural systems in the East African Community from 1961 to 2018 to address the challenges of insufficient nitrogen inputs and serious soil nitrogen depletion in agricultural systems of the East African Community region. Results showed that total nitrogen input increased from 12.5 kg N ha-1yr-1 in the 1960s to 21.8 kg N ha-1yr-1 in the 2000s and 27 kg N ha-1yr-1 in the 2010s. Total nitrogen crop uptake increased from 12.8 kg N ha-1yr-1 in the 1960s to 18.2 kg N ha-1yr-1 in the 2000s and 21.8 kg N ha-1yr-1 in the 2010s. Soil nitrogen stock increased from -2.0 kg N ha-1yr-1 in the 1960s to -0.5 kg N ha-1yr-1 in the 2000s and 0.3 kg N ha-1yr-1 in the 2010s. Our results allow us to substantiate for the first time that soil nitrogen depletion decreases with increasing input of nitrogen in agricultural systems of the East African Community region. This suggests that increases in nitrogen inputs through biological nitrogen fixation and animal manure are the critical nitrogen management practices to curb soil nitrogen depletion and sustain agricultural production systems in the East African Community region in order to meet food demand for a growing population. Supplementary Information The online version contains supplementary material available at 10.1007/s13593-023-00881-0.
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Affiliation(s)
- Barthelemy Harerimana
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, No.189, QunXianNan Street, Tianfu New Area, Chengdu, 610041 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Minghua Zhou
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, No.189, QunXianNan Street, Tianfu New Area, Chengdu, 610041 China
| | - Bo Zhu
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, No.189, QunXianNan Street, Tianfu New Area, Chengdu, 610041 China
| | - Peng Xu
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, No.189, QunXianNan Street, Tianfu New Area, Chengdu, 610041 China
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13
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Morris DS, Chowdhury NB, Kathol M, Saha R. Opening the door to nitrogen fixation in oxygenic phototrophs. Trends Biotechnol 2023; 41:283-285. [PMID: 36646524 DOI: 10.1016/j.tibtech.2023.01.005] [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: 12/29/2022] [Revised: 01/07/2023] [Accepted: 01/09/2023] [Indexed: 01/16/2023]
Abstract
Conveying biological nitrogen fixation (BNF) to photosynthetic species may be the next agricultural revolution, yet poses major engineering challenges. Liu et al. created a diazotrophic strain of a previously non-nitrogen-fixing species, the cyanobacterium Synechocystis sp. PCC 6803, and uncovered critical aspects of nitrogen fixation in an oxygenic species.
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Affiliation(s)
- Dianna S Morris
- Complex Biosystems Program, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Niaz Bahar Chowdhury
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Mark Kathol
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Rajib Saha
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
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14
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Barquero M, Poveda J, Laureano-Marín AM, Ortiz-Liébana N, Brañas J, González-Andrés F. Mechanisms involved in drought stress tolerance triggered by rhizobia strains in wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:1036973. [PMID: 36438093 PMCID: PMC9686006 DOI: 10.3389/fpls.2022.1036973] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/06/2022] [Indexed: 05/29/2023]
Abstract
Rhizobium spp. is a well-known microbial plant biostimulant in non-legume crops, but little is known about the mechanisms by which rhizobia enhance crop productivity under drought stress. This work analyzed the mechanisms involved in drought stress alleviation exerted by Rhizobium leguminosarum strains in wheat plants under water shortage conditions. Two (LBM1210 and LET4910) of the four R. leguminosarum strains significantly improved the growth parameters (fresh and dry aerial weight, FW and DW, respectively), chlorophyll content, and relative water content (RWC) compared to a non-inoculated control under water stress, providing values similar to or even higher for FW (+4%) and RWC (+2.3%) than the non-inoculated and non-stressed control. Some other biochemical parameters and gene expression explain the observed drought stress alleviation, namely the reduction of MDA, H2O2 (stronger when inoculating with LET4910), and ABA content (stronger when inoculating with LBM1210). In agreement with these results, inoculation with LET4910 downregulated DREB2 and CAT1 genes in plants under water deficiency and upregulated the CYP707A1 gene, while inoculation with LBM1210 strongly upregulated the CYP707A1 gene, which encodes an ABA catabolic enzyme. Conversely, from our results, ethylene metabolism did not seem to be involved in the alleviation of drought stress exerted by the two strains, as the expression of the CTR1 gene was very similar in all treatments and controls. The obtained results regarding the effect of the analyzed strains in alleviating drought stress are very relevant in the present situation of climate change, which negatively influences agricultural production.
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Affiliation(s)
- Marcia Barquero
- Institute of Environment, Natural Resources and Biodiversity, University of León, León, Spain
| | - Jorge Poveda
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Universidad Pública de Navarra, Pamplona, Spain
| | - Ana M. Laureano-Marín
- Centro de Tecnologías Agroambientales (CTA) Fertiberia - Edificio CITIUS (Centro de Investigación, Tecnología e Innovación) 1, Sevilla, Spain
| | - Noemí Ortiz-Liébana
- Institute of Environment, Natural Resources and Biodiversity, University of León, León, Spain
| | - Javier Brañas
- Centro de Tecnologías Agroambientales (CTA) Fertiberia - Edificio CITIUS (Centro de Investigación, Tecnología e Innovación) 1, Sevilla, Spain
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Abdul Hamid NW, Nadarajah K. Microbe Related Chemical Signalling and Its Application in Agriculture. Int J Mol Sci 2022; 23:ijms23168998. [PMID: 36012261 PMCID: PMC9409198 DOI: 10.3390/ijms23168998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 07/31/2022] [Accepted: 08/04/2022] [Indexed: 11/17/2022] Open
Abstract
The agriculture sector has been put under tremendous strain by the world’s growing population. The use of fertilizers and pesticides in conventional farming has had a negative impact on the environment and human health. Sustainable agriculture attempts to maintain productivity, while protecting the environment and feeding the global population. The importance of soil-dwelling microbial populations in overcoming these issues cannot be overstated. Various processes such as rhizospheric competence, antibiosis, release of enzymes, and induction of systemic resistance in host plants are all used by microbes to influence plant-microbe interactions. These processes are largely founded on chemical signalling. Producing, releasing, detecting, and responding to chemicals are all part of chemical signalling. Different microbes released distinct sorts of chemical signal molecules which interacts with the environment and hosts. Microbial chemicals affect symbiosis, virulence, competence, conjugation, antibiotic production, motility, sporulation, and biofilm growth, to name a few. We present an in-depth overview of chemical signalling between bacteria-bacteria, bacteria-fungi, and plant-microbe and the diverse roles played by these compounds in plant microbe interactions. These compounds’ current and potential uses and significance in agriculture have been highlighted.
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16
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Shaffique S, Khan MA, Wani SH, Pande A, Imran M, Kang SM, Rahim W, Khan SA, Bhatta D, Kwon EH, Lee IJ. A Review on the Role of Endophytes and Plant Growth Promoting Rhizobacteria in Mitigating Heat Stress in Plants. Microorganisms 2022; 10:microorganisms10071286. [PMID: 35889005 PMCID: PMC9319882 DOI: 10.3390/microorganisms10071286] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/17/2022] [Accepted: 06/20/2022] [Indexed: 02/04/2023] Open
Abstract
Among abiotic stresses, heat stress is described as one of the major limiting factors of crop growth worldwide, as high temperatures elicit a series of physiological, molecular, and biochemical cascade events that ultimately result in reduced crop yield. There is growing interest among researchers in the use of beneficial microorganisms. Intricate and highly complex interactions between plants and microbes result in the alleviation of heat stress. Plant–microbe interactions are mediated by the production of phytohormones, siderophores, gene expression, osmolytes, and volatile compounds in plants. Their interaction improves antioxidant activity and accumulation of compatible osmolytes such as proline, glycine betaine, soluble sugar, and trehalose, and enriches the nutrient status of stressed plants. Therefore, this review aims to discuss the heat response of plants and to understand the mechanisms of microbe-mediated stress alleviation on a physio-molecular basis. This review indicates that microbes have a great potential to enhance the protection of plants from heat stress and enhance plant growth and yield. Owing to the metabolic diversity of microorganisms, they can be useful in mitigating heat stress in crop plants. In this regard, microorganisms do not present new threats to ecological systems. Overall, it is expected that continued research on microbe-mediated heat stress tolerance in plants will enable this technology to be used as an ecofriendly tool for sustainable agronomy.
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Affiliation(s)
- Shifa Shaffique
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (S.S.); (M.A.K.); (M.I.); (S.-M.K.); (D.B.); (E.-H.K.)
| | - Muhammad Aaqil Khan
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (S.S.); (M.A.K.); (M.I.); (S.-M.K.); (D.B.); (E.-H.K.)
| | - Shabir Hussain Wani
- Mountain Research Center for Field Crops Khudwani, Shere-e-Kashmir University of Agriculture Sciences and Technology Srinagar, Anantnag 190025, Jammu and Kashmir, India;
| | - Anjali Pande
- Laboratory of Plant Molecular Pathology and Functional Genomics, Department of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu 41944, Korea; (A.P.); (W.R.)
| | - Muhammad Imran
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (S.S.); (M.A.K.); (M.I.); (S.-M.K.); (D.B.); (E.-H.K.)
| | - Sang-Mo Kang
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (S.S.); (M.A.K.); (M.I.); (S.-M.K.); (D.B.); (E.-H.K.)
| | - Waqas Rahim
- Laboratory of Plant Molecular Pathology and Functional Genomics, Department of Plant Biosciences, School of Applied Biosciences, College of Agriculture and Life Science, Kyungpook National University, Daegu 41944, Korea; (A.P.); (W.R.)
| | - Sumera Afzal Khan
- Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar 45000, Pakistan;
| | - Dibya Bhatta
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (S.S.); (M.A.K.); (M.I.); (S.-M.K.); (D.B.); (E.-H.K.)
| | - Eun-Hae Kwon
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (S.S.); (M.A.K.); (M.I.); (S.-M.K.); (D.B.); (E.-H.K.)
| | - In-Jung Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (S.S.); (M.A.K.); (M.I.); (S.-M.K.); (D.B.); (E.-H.K.)
- Correspondence: ; Tel.: +82-53-950-5708
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17
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Micci A, Zhang Q, Chang X, Kingsley K, Park L, Chiaranunt P, Strickland R, Velazquez F, Lindert S, Elmore M, Vines PL, Crane S, Irizarry I, Kowalski KP, Johnston-Monje D, White JF. Histochemical Evidence for Nitrogen-Transfer Endosymbiosis in Non-Photosynthetic Cells of Leaves and Inflorescence Bracts of Angiosperms. BIOLOGY 2022; 11:biology11060876. [PMID: 35741397 PMCID: PMC9220352 DOI: 10.3390/biology11060876] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/15/2022] [Accepted: 06/01/2022] [Indexed: 12/13/2022]
Abstract
Simple Summary We used light and confocal microscopy to visualize bacteria in leaf and bract cells of more than 30 species in 18 families of seed plants. We detected chemical exchanges between intracellular bacteria and plant cells. We found that endophytic bacteria that show evidence of the transfer of nitrogen to plants are present in non-photosynthetic cells of leaves and bracts of diverse plant species. Nitrogen transfer from bacteria was observed in epidermal cells, various filamentous and glandular trichomes, and other non-photosynthetic cells. The most efficient of the nitrogen-transfer endosymbioses were seen to involve glandular trichomes, as seen in hops (Humulus lupulus) and hemp (Cannabis sativa). Trichome chemistry is hypothesized to function to scavenge oxygen around bacteria to facilitate nitrogen fixation. Abstract We used light and confocal microscopy to visualize bacteria in leaf and bract cells of more than 30 species in 18 families of seed plants. Through histochemical analysis, we detected hormones (including ethylene and nitric oxide), superoxide, and nitrogenous chemicals (including nitric oxide and nitrate) around bacteria within plant cells. Bacteria were observed in epidermal cells, various filamentous and glandular trichomes, and other non-photosynthetic cells. Most notably, bacteria showing nitrate formation based on histochemical staining were present in glandular trichomes of some dicots (e.g., Humulus lupulus and Cannabis sativa). Glandular trichome chemistry is hypothesized to function to scavenge oxygen around bacteria and reduce oxidative damage to intracellular bacterial cells. Experiments to assess the differential absorption of isotopic nitrogen into plants suggest the assimilation of nitrogen into actively growing tissues of plants, where bacteria are most active and carbohydrates are more available. The leaf and bract cell endosymbiosis types outlined in this paper have not been previously reported and may be important in facilitating plant growth, development, oxidative stress resistance, and nutrient absorption into plants. It is unknown whether leaf and bract cell endosymbioses are significant in increasing the nitrogen content of plants. From the experiments that we conducted, it is impossible to know whether plant trichomes evolved specifically as organs for nitrogen fixation or if, instead, trichomes are structures in which bacteria easily colonize and where some casual nitrogen transfer may occur between bacteria and plant cells. It is likely that the endosymbioses seen in leaves and bracts are less efficient than those of root nodules of legumes in similar plants. However, the presence of endosymbioses that yield nitrate in plants could confer a reduced need for soil nitrogen and constitute increased nitrogen-use efficiency, even if the actual amount of nitrogen transferred to plant cells is small. More research is needed to evaluate the importance of nitrogen transfer within leaf and bract cells of plants.
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Affiliation(s)
- April Micci
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (Q.Z.); (X.C.); (K.K.); (L.P.); (P.C.); (R.S.); (F.V.); (S.L.); (M.E.); (P.L.V.)
- Correspondence: (A.M.); (J.F.W.); Tel.: +848-932-6286 (J.F.W.)
| | - Qiuwei Zhang
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (Q.Z.); (X.C.); (K.K.); (L.P.); (P.C.); (R.S.); (F.V.); (S.L.); (M.E.); (P.L.V.)
| | - Xiaoqian Chang
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (Q.Z.); (X.C.); (K.K.); (L.P.); (P.C.); (R.S.); (F.V.); (S.L.); (M.E.); (P.L.V.)
| | - Kathryn Kingsley
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (Q.Z.); (X.C.); (K.K.); (L.P.); (P.C.); (R.S.); (F.V.); (S.L.); (M.E.); (P.L.V.)
| | - Linsey Park
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (Q.Z.); (X.C.); (K.K.); (L.P.); (P.C.); (R.S.); (F.V.); (S.L.); (M.E.); (P.L.V.)
| | - Peerapol Chiaranunt
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (Q.Z.); (X.C.); (K.K.); (L.P.); (P.C.); (R.S.); (F.V.); (S.L.); (M.E.); (P.L.V.)
| | - Raquele Strickland
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (Q.Z.); (X.C.); (K.K.); (L.P.); (P.C.); (R.S.); (F.V.); (S.L.); (M.E.); (P.L.V.)
| | - Fernando Velazquez
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (Q.Z.); (X.C.); (K.K.); (L.P.); (P.C.); (R.S.); (F.V.); (S.L.); (M.E.); (P.L.V.)
| | - Sean Lindert
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (Q.Z.); (X.C.); (K.K.); (L.P.); (P.C.); (R.S.); (F.V.); (S.L.); (M.E.); (P.L.V.)
| | - Matthew Elmore
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (Q.Z.); (X.C.); (K.K.); (L.P.); (P.C.); (R.S.); (F.V.); (S.L.); (M.E.); (P.L.V.)
| | - Philip L. Vines
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (Q.Z.); (X.C.); (K.K.); (L.P.); (P.C.); (R.S.); (F.V.); (S.L.); (M.E.); (P.L.V.)
| | - Sharron Crane
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA;
| | - Ivelisse Irizarry
- School of Health and Sciences, Universidad del Sagrado Corazón, San Juan 00914, Puerto Rico;
| | - Kurt P. Kowalski
- US Geological Survey Great Lakes Science Center, Ann Arbor, MI 48105, USA;
| | - David Johnston-Monje
- Max Planck Tandem Group in Plant Microbial Ecology, Universidad del Valle, Cali 760043, Colombia;
| | - James F. White
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (Q.Z.); (X.C.); (K.K.); (L.P.); (P.C.); (R.S.); (F.V.); (S.L.); (M.E.); (P.L.V.)
- Correspondence: (A.M.); (J.F.W.); Tel.: +848-932-6286 (J.F.W.)
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Shamseldin A. Future Outlook of Transferring Biological Nitrogen Fixation (BNF) to Cereals and Challenges to Retard Achieving this Dream. Curr Microbiol 2022; 79:171. [PMID: 35476236 DOI: 10.1007/s00284-022-02852-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 03/21/2022] [Indexed: 11/03/2022]
Abstract
BNF is a fascinating phenomenon which contributes to protect the nature from environmental pollution that can be happened as a result of heavy nitrogen applications. The importance of BNF is due to its supply of the agricultural lands with about 200 million tons of N annually. In this biological process, a specific group of bacteria collectively called rhizobia fix the atmospheric N in symbiosis with legumes called symbiotic nitrogen fixation and others (free living) fix nitrogen gas from the atmosphere termed asymbiotic. Several trials were done by scientists around the world to make cereals more benefited from nitrogen gas through different approaches. The first approach is to engineer cereals to form nodulated roots. Secondly is to transfer nif genes directly to cereals and fix N without Rhizobium partner. The other two approaches are maximizing the inoculation of cereals with both of diazotrophs or endophytes. Recently, scientists solved some challenges that entangle engineering cereals with nif genes directly and they confirmed the suitability of mitochondria and plastids as a suitable place for better biological function of nif genes expression in cereals. Fortunately, this article is confirming the success of scientists not only to transfer synthetic nitrogenase enzyme to Escherichia coli that gave 50% of its activity of expression, but also move it to plants as Nicotiana benthamiana. This mini review aims at explaining the future outlook of BNF and the challenges limiting its transfer to cereals and levels of success to make cereals self nitrogen fixing.
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Affiliation(s)
- Abdelaal Shamseldin
- Environmental Biotechnology Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications, New Borg El Arab, Alexandria, Egypt.
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Kebede E. Contribution, Utilization, and Improvement of Legumes-Driven Biological Nitrogen Fixation in Agricultural Systems. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.767998] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Legumes improve soil fertility through the symbiotic association with microorganisms, such as rhizobia, which fix the atmospheric nitrogen and make nitrogen available to the host and other crops by a process known as biological nitrogen fixation (BNF). Legumes included in the cropping system improve the fertility of the soil and the yield of crops. The advantages of legumes in the cropping system are explained in terms of direct nitrogen transfer, residual fixed nitrogen, nutrient availability and uptake, effect on soil properties, breaking of pests' cycles, and enhancement of other soil microbial activity. The best benefits from the legumes and BNF system can be utilized by integrating them into cropping systems. The most common practices to integrate legumes and their associated BNF into agricultural systems are crop rotation, simultaneous intercropping, improved fallows, green manuring, and alley cropping. However, the level of utilizing nitrogen fixation requires improvement of the systems, such as selecting appropriate legume genotypes, inoculation with effective rhizobia, and the use of appropriate agronomic practices and cropping systems. Therefore, using legumes at their maximum genetic potential, inoculation of legumes with compatible rhizobia, and using appropriate agronomic practices and cropping systems are very important for increasing food production. Importantly, the utilization of legumes as an integral component of agricultural practice in promoting agricultural productivity has gained more traction in meeting the demand of food production of the world populace. Priority should, thus, be given to value the process of BNF through more sustainable technologies and expansion of knowledge to the system.
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Basile LA, Lepek VC. Legume-rhizobium dance: an agricultural tool that could be improved? Microb Biotechnol 2021; 14:1897-1917. [PMID: 34318611 PMCID: PMC8449669 DOI: 10.1111/1751-7915.13906] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 07/15/2021] [Accepted: 07/19/2021] [Indexed: 12/29/2022] Open
Abstract
The specific interaction between rhizobia and legume roots leads to the development of a highly regulated process called nodulation, by which the atmospheric nitrogen is converted into an assimilable plant nutrient. This capacity is the basis for the use of bacterial inoculants for field crop cultivation. Legume plants have acquired tools that allow the entry of compatible bacteria. Likewise, plants can impose sanctions against the maintenance of nodules occupied by rhizobia with low nitrogen-fixing capacity. At the same time, bacteria must overcome different obstacles posed first by the environment and then by the legume. The present review describes the mechanisms involved in the regulation of the entire legume-rhizobium symbiotic process and the strategies and tools of bacteria for reaching the nitrogen-fixing state inside the nodule. Also, we revised different approaches to improve the nodulation process for a better crop yield.
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Affiliation(s)
- Laura A. Basile
- Instituto de Investigaciones Biotecnológicas “Dr. Rodolfo A. Ugalde”Universidad Nacional de San Martín (IIB‐UNSAM‐CONICET)Av. 25 de Mayo y Francia, Gral. San Martín, Provincia de Buenos AiresBuenos AiresB1650HMPArgentina
| | - Viviana C. Lepek
- Instituto de Investigaciones Biotecnológicas “Dr. Rodolfo A. Ugalde”Universidad Nacional de San Martín (IIB‐UNSAM‐CONICET)Av. 25 de Mayo y Francia, Gral. San Martín, Provincia de Buenos AiresBuenos AiresB1650HMPArgentina
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Effects of Abiotic Stress on Soil Microbiome. Int J Mol Sci 2021; 22:ijms22169036. [PMID: 34445742 PMCID: PMC8396473 DOI: 10.3390/ijms22169036] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 02/07/2023] Open
Abstract
Rhizospheric organisms have a unique manner of existence since many factors can influence the shape of the microbiome. As we all know, harnessing the interaction between soil microbes and plants is critical for sustainable agriculture and ecosystems. We can achieve sustainable agricultural practice by incorporating plant-microbiome interaction as a positive technology. The contribution of this interaction has piqued the interest of experts, who plan to do more research using beneficial microorganism in order to accomplish this vision. Plants engage in a wide range of interrelationship with soil microorganism, spanning the entire spectrum of ecological potential which can be mutualistic, commensal, neutral, exploitative, or competitive. Mutualistic microorganism found in plant-associated microbial communities assist their host in a number of ways. Many studies have demonstrated that the soil microbiome may provide significant advantages to the host plant. However, various soil conditions (pH, temperature, oxygen, physics-chemistry and moisture), soil environments (drought, submergence, metal toxicity and salinity), plant types/genotype, and agricultural practices may result in distinct microbial composition and characteristics, as well as its mechanism to promote plant development and defence against all these stressors. In this paper, we provide an in-depth overview of how the above factors are able to affect the soil microbial structure and communities and change above and below ground interactions. Future prospects will also be discussed.
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Goyal RK, Mattoo AK, Schmidt MA. Rhizobial-Host Interactions and Symbiotic Nitrogen Fixation in Legume Crops Toward Agriculture Sustainability. Front Microbiol 2021; 12:669404. [PMID: 34177848 PMCID: PMC8226219 DOI: 10.3389/fmicb.2021.669404] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/29/2021] [Indexed: 11/13/2022] Open
Abstract
Symbiotic nitrogen fixation (SNF) process makes legume crops self-sufficient in nitrogen (N) in sharp contrast to cereal crops that require an external input by N-fertilizers. Since the latter process in cereal crops results in a huge quantity of greenhouse gas emission, the legume production systems are considered efficient and important for sustainable agriculture and climate preservation. Despite benefits of SNF, and the fact that chemical N-fertilizers cause N-pollution of the ecosystems, the focus on improving SNF efficiency in legumes did not become a breeder’s priority. The size and stability of heritable effects under different environment conditions weigh significantly on any trait useful in breeding strategies. Here we review the challenges and progress made toward decoding the heritable components of SNF, which is considerably more complex than other crop allelic traits since the process involves genetic elements of both the host and the symbiotic rhizobial species. SNF-efficient rhizobial species designed based on the genetics of the host and its symbiotic partner face the test of a unique microbiome for its success and productivity. The progress made thus far in commercial legume crops with relevance to the dynamics of host–rhizobia interaction, environmental impact on rhizobial performance challenges, and what collectively determines the SNF efficiency under field conditions are also reviewed here.
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Affiliation(s)
- Ravinder K Goyal
- Agriculture and Agri-Food Canada, Lacombe Research and Development Centre, Lacombe, AB, Canada
| | - Autar K Mattoo
- Sustainable Agricultural Systems Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville Agricultural Research Center, Beltsville, MD, United States
| | - Maria Augusta Schmidt
- Agriculture and Agri-Food Canada, Lacombe Research and Development Centre, Lacombe, AB, Canada
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