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Glockow T, Kaster AK, Rabe KS, Niemeyer CM. Sustainable agriculture: leveraging microorganisms for a circular economy. Appl Microbiol Biotechnol 2024; 108:452. [PMID: 39212740 PMCID: PMC11364797 DOI: 10.1007/s00253-024-13294-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 08/20/2024] [Accepted: 08/21/2024] [Indexed: 09/04/2024]
Abstract
Microorganisms serve as linchpins in agricultural systems. Classic examples include microbial composting for nutrient recovery, using microorganisms in biogas technology for agricultural waste utilization, and employing biofilters to reduce emissions from stables or improve water quality in aquaculture. This mini-review highlights the importance of microbiome analysis in understanding microbial diversity, dynamics, and functions, fostering innovations for a more sustainable agriculture. In this regard, customized microorganisms for soil improvement, replacements for harmful agrochemicals or antibiotics in animal husbandry, and (probiotic) additives in animal nutrition are already in or even beyond the testing phase for a large-scale conventional agriculture. Additionally, as climate change reduces arable land, new strategies based on closed-loop systems and controlled environment agriculture, emphasizing microbial techniques, are being developed for regional food production. These strategies aim to secure the future food supply and pave the way for a sustainable, resilient, and circular agricultural economy. KEY POINTS: • Microbial strategies facilitate the integration of multiple trophic levels, essential for cycling carbon, nitrogen, phosphorus, and micronutrients. • Exploring microorganisms in integrated biological systems is essential for developing practical agricultural solutions. • Technological progress makes sustainable closed-entity re-circulation systems possible, securing resilient future food production.
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Affiliation(s)
- Till Glockow
- Acheron GmbH, Auf Der Muggenburg 30, 28217, Bremen, Germany
| | - Anne-Kristin Kaster
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces 5 (IBG-5), Biotechnology and Microbial Genetics, Hermann-Von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Kersten S Rabe
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces 1 (IBG-1), Biomolecular Micro- and Nanostructures, Hermann-Von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Christof M Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces 1 (IBG-1), Biomolecular Micro- and Nanostructures, Hermann-Von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.
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2
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El-Shazoly RM, Hamed HMA, El-Sayed MM. Individual or successiveseed priming with nitric oxide and calcium toward enhancing salt tolerance of wheat crop through early ROS detoxification and activation of antioxidant defense. BMC PLANT BIOLOGY 2024; 24:730. [PMID: 39085769 PMCID: PMC11290230 DOI: 10.1186/s12870-024-05390-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 07/05/2024] [Indexed: 08/02/2024]
Abstract
Despite the considerable efforts reported so far to enhance seed priming, novel ideas are still needed to be suggested to this sustainable sector of agri-seed industry. This could be the first study addressing the effect of nitric oxide (NO) under open field conditions. The impacts of seed redox-priming using sodium nitroprusside (SNP) and osmo-priming with calcium chloride (CaCl2), both applied individually or successively, were investigated under salinity stress conditions on wheat plants (Triticum aestivum L.). Various parameters, including water relations, growth, yield, photosynthetic pigments, and antioxidant activities (enzymatic and non-enzymatic), were recorded to assess the outcomes of these priming agents on mitigating the negative impacts of salinity stress on wheat plants. Water consumptive use (ETa) and irrigation water applied (IWA) decreased with seeds priming. Successive priming with SNP + CaCl2 induced the greatest values of crop water productivity (CWP), irrigation water productivity (IWP), seed index, grain yield and grain nitrogen content.Under salinity stress, the dry weight of plants was decreased. However, hydro-priming and successive chemical priming agents using combinations of calcium chloride and sodium nitroprusside (CaCl2 + SNP & SNP + CaCl2) preserved growth under salinity stress.Individual priming with sodium nitroprusside (SNP) and calcium chloride (CaCl2) resulted in the lowest recorded content of sodium in the shoot, with a value of 2 ppm. On the other hand, successive priming using CaCl2 + SNP or SNP + CaCl2 induced the contents of potassium in the shoot, with values of 40 ppm and 39 ppm, respectively. Malondialdehyde decreased in shoot significantly withapplicationof priming agents. Successive priming with CaCl2 + SNP induced the highest proline contents in shoot (6 µg/ g FW). The highest value of phenolics and total antioxidants contents in shoot were recorded under successive priming using CaCl2 + SNP and SNP + CaCl2.Priming agents improved the activities of ascorbate peroxidase and catalase enzymes. The successive priming improved water relations (ETa, IWA, CWP and IWP) and wheat growth and productivity under salinity stress more than individual priming treatments.
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Affiliation(s)
- Rasha M El-Shazoly
- Botany and Microbiology Department Faculty of Sciences, New Valley Univ, Al-Kharja, New Valley, 72511, Egypt.
| | - H M A Hamed
- Soils and Water Science Department, Faculty of Agriculture, Al-Azhar Univ, Assiut, Egypt
| | - Mahmoud M El-Sayed
- Soils and Water Science Department, Faculty of Agriculture, Al-Azhar Univ, Assiut, Egypt
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Dias MC, Silva S, Galhano C, Lorenzo P. Olive Tree Belowground Microbiota: Plant Growth-Promoting Bacteria and Fungi. PLANTS (BASEL, SWITZERLAND) 2024; 13:1848. [PMID: 38999688 PMCID: PMC11244348 DOI: 10.3390/plants13131848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/29/2024] [Accepted: 07/02/2024] [Indexed: 07/14/2024]
Abstract
The olive tree is one of the most significant crops in the Mediterranean region. Its remarkable adaptability to various environments has facilitated olive cultivation across diverse regions and agricultural scenarios. The rising global demand for olive products, coupled with climate challenges, is driving changes in cultivation methods. These changes are altering the traditional landscape and may potentially reshape the structure and composition of orchard microbial communities, which can impact productivity and stress tolerance. Bacterial and fungal communities naturally associated with plants have long been recognized as crucial for plant growth and health, serving as a vital component of sustainable agriculture. In this review, we aim to highlight the significance of olive cultivation and the impact of abiotic stresses. We update the current knowledge on the profiles of rhizosphere and root fungal and bacterial communities in olive orchards and examine how (a)biotic factors influence these communities. Additionally, we explore the potential of plant growth-promoting bacteria and fungi in enhancing olive physiological performance and stress tolerance. We identify knowledge gaps and emphasize the need for implementing new strategies. A comprehensive understanding of olive-associated microbiota will aid in developing sustainable agronomic practices to address climatic challenges and meet the growing demand for olive products.
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Affiliation(s)
- Maria Celeste Dias
- Associate Laboratory TERRA, Center for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Sónia Silva
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Cristina Galhano
- Polytechnic Institute of Coimbra, Coimbra Agriculture School, Bencanta, 3045-601 Coimbra, Portugal
| | - Paula Lorenzo
- Associate Laboratory TERRA, Center for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
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Ranjan A, Rajput VD, Chauhan A. Editorial for "Special Abilities of Microbes and Their Application in Agro-Biology". Microorganisms 2024; 12:1179. [PMID: 38930561 PMCID: PMC11206084 DOI: 10.3390/microorganisms12061179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 05/28/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
Currently, climate change-related environmental issues associated with agriculture is alarming and poses a potential risk to global food security, causing significant global concern as a result [...].
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Affiliation(s)
- Anuj Ranjan
- Academy of Biology and Biotechnology, Southern Federal University, Stachki 194/1, 344090 Rostov-on-Don, Russia;
| | - Vishnu D. Rajput
- Academy of Biology and Biotechnology, Southern Federal University, Stachki 194/1, 344090 Rostov-on-Don, Russia;
| | - Abhishek Chauhan
- Amity Institute of Environmental Toxicology, Safety and Management, Amity University, Noida 201301, India;
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Jain A, Sarsaiya S, Singh R, Gong Q, Wu Q, Shi J. Omics approaches in understanding the benefits of plant-microbe interactions. Front Microbiol 2024; 15:1391059. [PMID: 38860224 PMCID: PMC11163067 DOI: 10.3389/fmicb.2024.1391059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 04/29/2024] [Indexed: 06/12/2024] Open
Abstract
Plant-microbe interactions are pivotal for ecosystem dynamics and sustainable agriculture, and are influenced by various factors, such as host characteristics, environmental conditions, and human activities. Omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, have revolutionized our understanding of these interactions. Genomics elucidates key genes, transcriptomics reveals gene expression dynamics, proteomics identifies essential proteins, and metabolomics profiles small molecules, thereby offering a holistic perspective. This review synthesizes diverse microbial-plant interactions, showcasing the application of omics in understanding mechanisms, such as nitrogen fixation, systemic resistance induction, mycorrhizal association, and pathogen-host interactions. Despite the challenges of data integration and ethical considerations, omics approaches promise advancements in precision intervention and resilient agricultural practices. Future research should address data integration challenges, enhance omics technology resolution, explore epigenomics, and understand plant-microbe dynamics under diverse conditions. In conclusion, omics technologies hold immense promise for optimizing agricultural strategies and fortifying resilient plant-microbe alliances, paving the way for sustainable agriculture and environmental stewardship.
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Affiliation(s)
- Archana Jain
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Surendra Sarsaiya
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
- Bioresource Institute for Healthy Utilization, Zunyi Medical University, Zunyi, China
| | - Ranjan Singh
- Department of Microbiology, Faculty of Science, Dr. Rammanohar Lohia Avadh University, Ayodhya, Uttar Pradesh, India
| | - Qihai Gong
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Qin Wu
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Jingshan Shi
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
- Bioresource Institute for Healthy Utilization, Zunyi Medical University, Zunyi, China
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Yang Z, Qu J, Qiao L, Jiang M, Zou X, Cao W. Tea and Pleurotus ostreatus intercropping modulates structure of soil and root microbial communities. Sci Rep 2024; 14:11295. [PMID: 38760401 PMCID: PMC11101613 DOI: 10.1038/s41598-024-61883-w] [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: 02/23/2024] [Accepted: 05/10/2024] [Indexed: 05/19/2024] Open
Abstract
Intercropping with Pleurotus ostreatus has been demonstrated to increase the tea yield and alleviate soil acidification in tea gardens. However, the underlying mechanisms remain elusive. Here, high-throughput sequencing and Biolog Eco analysis were performed to identify changes in the community structure and abundance of soil microorganisms in the P. ostreatus intercropped tea garden at different seasons (April and September). The results showed that the soil microbial diversity of rhizosphere decreased in April, while rhizosphere and non-rhizosphere soil microbial diversity increased in September in the P. ostreatus intercropped tea garden. The diversity of tea tree root microorganisms increased in both periods. In addition, the number of fungi associated with organic matter decomposition and nutrient cycling, such as Penicillium, Trichoderma, and Trechispora, was significantly higher in the intercropped group than in the control group. Intercropping with P. ostreatus increased the levels of total nitrogen (TN), total phosphorus (TP), and available phosphorus (AP) in the soil. It also improved the content of secondary metabolites, such as tea catechins, and polysaccharides in tea buds. Microbial network analysis showed that Unclassified_o__Helotiales, and Devosia were positively correlated with soil TN and pH, while Lactobacillus, Acidothermus, and Monascus were positively correlated with flavone, AE, and catechins in tea trees. In conclusion, intercropping with P. ostreatus can improve the physical and chemical properties of soil and the composition and structure of microbial communities in tea gardens, which has significant potential for application in monoculture tea gardens with acidic soils.
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Affiliation(s)
- Zhengkai Yang
- College of Tea Sciences, Guizhou University, Guiyang, 550025, China
| | - Jiaojiao Qu
- College of Tea Sciences, Guizhou University, Guiyang, 550025, China.
| | - Lu Qiao
- Institute of Fungus Resources, College of Life Sciences, Guizhou University, Guiyang, 550025, China
| | - Meiling Jiang
- College of Tea Sciences, Guizhou University, Guiyang, 550025, China
| | - Xiao Zou
- Institute of Fungus Resources, College of Life Sciences, Guizhou University, Guiyang, 550025, China
| | - Wei Cao
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025, China.
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Jiménez-Ríos L, Torrado A, González-Pimentel JL, Iniesta-Pallarés M, Molina-Heredia FP, Mariscal V, Álvarez C. Emerging nitrogen-fixing cyanobacteria for sustainable cotton cultivation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171533. [PMID: 38458446 DOI: 10.1016/j.scitotenv.2024.171533] [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: 01/15/2024] [Revised: 03/04/2024] [Accepted: 03/04/2024] [Indexed: 03/10/2024]
Abstract
Amid growing environmental concerns and the imperative for sustainable agricultural practices, this study examines the potential of nitrogen-fixing cyanobacteria as biofertilizers, particularly in cotton cultivation. The reliance on synthetic nitrogen fertilizers (SNFs), prevalent in modern agriculture, poses significant environmental challenges, including greenhouse gas emissions and water system contamination. This research aims to shift this paradigm by exploring the capacity of cyanobacteria as a natural and sustainable alternative. Utilizing advanced metabarcoding methods to analyze the 16S rRNA gene, we conducted a comprehensive assessment of soil bacterial communities within cotton fields. This study focused on evaluating the diversity, structure, taxonomic composition, and potential functional characteristics of these communities. Emphasis was placed on the isolation of native N2-fixing cyanobacteria strains rom cotton soils, and their subsequent effects on cotton growth. Results from our study demonstrate significant plant growth-promoting (PGP) activities, measured as N2 fixation, production of Phytohormones, Fe solubilization and biofertilization potential of five isolated cyanobacterial strains, underscoring their efficacy in cotton. These findings suggest a viable pathway for replacing chemical-synthetic nitrogen fertilizers with natural, organic alternatives. The reintegration of these beneficial species into agricultural ecosystems can enhance crop growth while fostering a balanced microbial environment, thus contributing to the broader goals of global sustainable agriculture.
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Affiliation(s)
- Lucía Jiménez-Ríos
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Américo Vespucio 49, 41092 Sevilla, Spain
| | - Alejandro Torrado
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Américo Vespucio 49, 41092 Sevilla, Spain
| | - José Luis González-Pimentel
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Américo Vespucio 49, 41092 Sevilla, Spain
| | - Macarena Iniesta-Pallarés
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Américo Vespucio 49, 41092 Sevilla, Spain
| | - Fernando P Molina-Heredia
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Américo Vespucio 49, 41092 Sevilla, Spain
| | - Vicente Mariscal
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Américo Vespucio 49, 41092 Sevilla, Spain.
| | - Consolación Álvarez
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Américo Vespucio 49, 41092 Sevilla, Spain.
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Jing T, Li J, He Y, Shankar A, Saxena A, Tiwari A, Maturi KC, Solanki MK, Singh V, Eissa MA, Ding Z, Xie J, Awasthi MK. Role of calcium nutrition in plant Physiology: Advances in research and insights into acidic soil conditions - A comprehensive review. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108602. [PMID: 38608506 DOI: 10.1016/j.plaphy.2024.108602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 03/20/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024]
Abstract
Plant mineral nutrition has immense significance for crop productivity and human well-being. Soil acidity plays a major role in determining the nutrient availability that influences plant growth. The importance of calcium (Ca) in biological processes, such as signaling, metabolism, and cell growth, underlines its critical role in plant growth and development. This review focuses on soil acidification, a gradual process resulting from cation leaching, fertilizer utilization, and drainage issues. Soil acidification significantly hampers global crop production by modifying nutrient accessibility. In acidic soils, essential nutrients, such as nitrogen (N), phosphorus (P), potassium (K), magnesium (Mg), and Ca become less accessible, establishing a correlation between soil pH and plant nutrition. Cutting-edge Ca nutrition technologies, including nanotechnology, genetic engineering, and genome sequencing, offer the potential to deliver Ca and reduce the reliance on conventional soluble fertilizers. These fertilizers not only contribute to environmental contamination but also impose economic burdens on farmers. Nanotechnology can enhance nutrient uptake, and Ca nanoparticles improve nutrient absorption and release. Genetic engineering enables the cultivation of acid-tolerant crop varieties by manipulating Ca-related genes. High-throughput technologies such as next-generation sequencing and microarrays aid in identifying the microbial structures, functions, and biosynthetic pathways involved in managing plant nutritional stress. The ultimate goal is to shed light on the importance of Ca, problems associated with soil acidity, and potential of emerging technologies to enhance crop production while minimizing the environmental impact and economic burden on farmers.
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Affiliation(s)
- Tao Jing
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Genetic Improvement of Bananas, Sanya Research Institute, State Key Laboratory of Biological Breeding for Tropical Crops, Hainan Province, China
| | - Jingyang Li
- Tropical Crops Genetic and Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, China
| | - Yingdui He
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Genetic Improvement of Bananas, Sanya Research Institute, State Key Laboratory of Biological Breeding for Tropical Crops, Hainan Province, China
| | - Alka Shankar
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, 382715, Gujarat, India
| | - Abhishek Saxena
- Diatom Research Laboratory, Amity Institute of Biotechnology, Amity University, Noida, India
| | - Archana Tiwari
- Diatom Research Laboratory, Amity Institute of Biotechnology, Amity University, Noida, India
| | - Krishna Chaitanya Maturi
- Department of Civil Engineering, Indian Institute of Technology Guwahati, Guwahati, 781039, India; Department of Biology, Hong Kong Baptist University, Hong Kong, Hong Kong SAR
| | - Manoj Kumar Solanki
- Department of Life Sciences and Biological Sciences, IES University, Bhopal, Madhya Pradesh, India
| | - Vijai Singh
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, 382715, Gujarat, India
| | - Mamdouh A Eissa
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Genetic Improvement of Bananas, Sanya Research Institute, State Key Laboratory of Biological Breeding for Tropical Crops, Hainan Province, China; Department of Soils and Water, Faculty of Agriculture, Assiut University, Assiut, 71526, Egypt
| | - Zheli Ding
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Genetic Improvement of Bananas, Sanya Research Institute, State Key Laboratory of Biological Breeding for Tropical Crops, Hainan Province, China
| | - Jianghui Xie
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Genetic Improvement of Bananas, Sanya Research Institute, State Key Laboratory of Biological Breeding for Tropical Crops, Hainan Province, China.
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
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Liu Z, Zhang C, Ma J, Peng Q, Du X, Sun S, Cheng J, Peng W, Chen L, Gu Z, Zhang W, Su P, Zhang D. Extraction Methods Determine the Quality of Soil Microbiota Acquisition. Microorganisms 2024; 12:403. [PMID: 38399807 PMCID: PMC10891820 DOI: 10.3390/microorganisms12020403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
The soil microbiome plays a key role in plant health. Native soil microbiome inoculation, metagenomic profiling, and high-throughput cultivation require efficient microbe extraction. Sonication and oscillation are the most common methods used to extract soil microbiomes. However, the extraction efficiency of these methods has not been investigated in full. In this study, we compared the culturable microbe numbers, community structures, and alpha diversities among the different methods, including sonication, oscillation, and centrifugation, and their processing times. The study results showed that sonication significantly increases the culturable colony number compared with oscillation and centrifugation. Furthermore, the sonication strategy was found to be the main factor influencing extraction efficiency, but increased sonication time can aid in recovery from this impact. Finally, the extraction processing times were found to have a significant negative relationship with α-diversity among the extracted microbiota. In conclusion, sonication is the main factor for enriching in situ microbiota, and increased extraction time significantly decreases the α-diversity of the extracted microbiota. The results of this study provide insights into the isolation and utilization of different microorganism sources.
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Affiliation(s)
- Zhuoxin Liu
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Chi Zhang
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Jiejia Ma
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Qianze Peng
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
- National Center of Technology Innovation for Saline-Alkali Tolerant Rice in Sanya City, Sanya 572024, China
| | - Xiaohua Du
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Shu'e Sun
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Ju'e Cheng
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Weiye Peng
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Lijie Chen
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Zepei Gu
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Weixing Zhang
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Pin Su
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- National Center of Technology Innovation for Saline-Alkali Tolerant Rice in Sanya City, Sanya 572024, China
| | - Deyong Zhang
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China
- State Key Laboratory of Hybrid Rice, Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China
- College of Tropical Crops, Hainan University, Haikou 570228, China
- National Center of Technology Innovation for Saline-Alkali Tolerant Rice in Sanya City, Sanya 572024, China
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Prasad M, Brar B, Bala K, Singh N. Emerging Microbial Technologies. Indian J Microbiol 2023; 63:231-234. [PMID: 37781007 PMCID: PMC10533750 DOI: 10.1007/s12088-023-01103-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023] Open
Affiliation(s)
| | - Basanti Brar
- Om Sterling Global University Hisar, Hisar, India
| | - Kiran Bala
- Om Sterling Global University Hisar, Hisar, India
| | - Namita Singh
- Microbial Biotechnology Laboratory, Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, 125001 India
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Zuzolo D, Ranauda MA, Maisto M, Tartaglia M, Prigioniero A, Falzarano A, Marotta G, Sciarrillo R, Guarino C. The rootstock shape microbial diversity and functionality in the rhizosphere of Vitis vinifera L. cultivar Falanghina. FRONTIERS IN PLANT SCIENCE 2023; 14:1205451. [PMID: 37645461 PMCID: PMC10461393 DOI: 10.3389/fpls.2023.1205451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/24/2023] [Indexed: 08/31/2023]
Abstract
The rhizosphere effect occurring at the root-soil interface has increasingly been shown to play a key role in plant fitness and soil functionality, influencing plants resilience. Here, for the first time, we investigated whether the rootstock genotype on which Vitis vinifera L. cultivar Falanghina is grafted can influence the rhizosphere microbiome. Specifically, we evaluated to which extent the 5BB and 1103P rootstocks are able to shape microbial diversity of rhizosphere environment. Moreover, we explored the potential function of microbial community and its shift under plant genotype influence. We investigated seven vineyards subjected to the same pedo-climatic conditions, similar age, training system and management and collected twelve rhizosphere soil samples for metagenomic analyses and composite soil samples for physical-chemical properties. In this study, we used 16S rRNA gene-based metagenomic analysis to investigate the rhizosphere bacterial diversity and composition. Liner discriminant analysis effect size (LEFSe) was conducted for metagenomic biomarker discovery. The functional composition of sampled communities was determined using PICRUSt, which is based on marker gene sequencing profiles. Soil analyses involved the determination of texture, pH, Cation Exchange Capacity (CSC), Organic Carbon (OC), electrical conductivity (EC), calcium (Ca), magnesium (Mg), potassium (K) content, Phosphorous (P), nitrogen (N). The latter revealed that soil features were quite homogenous. The metagenomic data showed that the bacterial alpha-diversity (Observed OTUs) significantly increased in 1103P rhizosphere microbiota. Irrespective of cultivar, Pseudomonadota was the dominant phylum, followed by Actinomycetota > Bacteroidota > Thermoproteota. However, Actinomycetota was the major marker phyla differentiating the rhizosphere microbial communities associated with the different rootstock types. At the genus level, several taxa belonging to Actinomycetota and Alphaproteobacteria classes were enriched in 1103P genotype rhizosphere. Investigating the potential functional profile, we found that most key enzyme-encoding genes involved in N cycling were significantly more abundant in 5BB rootstock rhizosphere soil. However, we found that 1103P rhizosphere was enriched in genes involved in C cycle and Plant Growth Promotion (PGP) functionality. Our results suggest that the different rootstocks not only recruit specific bacterial communities, but also specific functional traits within the same environment.
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Affiliation(s)
- Daniela Zuzolo
- Department of Science and Technologies, University of Sannio, Benevento, Italy
| | | | - Maria Maisto
- Department of Science and Technologies, University of Sannio, Benevento, Italy
| | - Maria Tartaglia
- Department of Science and Technologies, University of Sannio, Benevento, Italy
| | | | | | - Giuseppe Marotta
- Department of Law, Economics, Management and Quantitative Methods (DEMM), University of Sannio, Benevento, Italy
| | - Rosaria Sciarrillo
- Department of Science and Technologies, University of Sannio, Benevento, Italy
| | - Carmine Guarino
- Department of Science and Technologies, University of Sannio, Benevento, Italy
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