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Palanikumar I, Sinha H, Raman K. Panera: An innovative framework for surmounting uncertainty in microbial community modeling using pan-genera metabolic models. iScience 2024; 27:110358. [PMID: 39092173 PMCID: PMC11292516 DOI: 10.1016/j.isci.2024.110358] [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: 11/30/2023] [Revised: 04/10/2024] [Accepted: 06/20/2024] [Indexed: 08/04/2024] Open
Abstract
Utilization of 16S rRNA data in constraint-based modeling to characterize microbial communities confronts a major hurdle of lack of species-level resolution, impeding the construction of community models. We introduce "Panera," an innovative framework designed to model communities under this uncertainty and yet perform metabolic inferences using pan-genus metabolic models (PGMMs). We demonstrated PGMMs' utility for comprehending the metabolic capabilities of a genus and in characterizing community models using amplicon data. The unique, adaptable nature of PGMMs unlocks their potential in building hybrid communities, combining genome-scale metabolic models (GSMMs) and PGMMs. Notably, these models provide predictions comparable to the standard GSMM-based community models, while achieving a nearly 46% reduction in error compared to the genus model-based communities. In essence, "Panera" presents a potent and effective approach to aid in metabolic modeling by enabling robust predictions of community metabolic potential when dealing with amplicon data, and offers insights into genus-level metabolic landscapes.
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Affiliation(s)
- Indumathi Palanikumar
- Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India
- Centre for Integrative Biology and Systems mEdicine (IBSE), IIT Madras, Chennai 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai 600 036, India
| | - Himanshu Sinha
- Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India
- Centre for Integrative Biology and Systems mEdicine (IBSE), IIT Madras, Chennai 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai 600 036, India
| | - Karthik Raman
- Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India
- Centre for Integrative Biology and Systems mEdicine (IBSE), IIT Madras, Chennai 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai 600 036, India
- Department of Data Science and AI, Wadhwani School of Data Science and AI, IIT Madras, Chennai 600 036, India
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Al-Rabaiai A, Menezes-Blackburn D, Al-Ismaily S, Janke R, Al-Alawi A, Al-Kindi M, Bol R. Biochar pH reduction using elemental sulfur and biological activation using compost or vermicompost. BIORESOURCE TECHNOLOGY 2024; 401:130707. [PMID: 38663636 DOI: 10.1016/j.biortech.2024.130707] [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: 01/21/2024] [Revised: 04/04/2024] [Accepted: 04/14/2024] [Indexed: 04/29/2024]
Abstract
This study aimed to improve biochar's quality for arid land applications by using elemental sulfur as a pH reducer agent co-applied with compost or vermicompost as biological activators. Biochar pH was decreased by the addition of elemental sulfur, with the highest reduction from 8.1 to 7.2 occurring when co-amended with vermicompost. Elemental sulfur increased the water-soluble concentrations of calcium, magnesium, and many other elements, and stimulated substrate-induced respiration, especially when co-amended with vermicompost. The bacterial diversity community structure were significantly affected by all treatments. The Shannon index significantly increased in response to compost and sulfur treatments, while the vermicompost treatments showed higher microbial evenness and equitability diversity indices. Multivariate analyses indicated that elemental sulfur oxidation was associated with specific sulfur-oxidizing bacterial clusters. Integrating biochar with sulfur and (vermi)compost was found to be a promising sustainable technology for managing excessive biochar alkalinity, increasing its fertility and potential for application in aridlands.
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Affiliation(s)
- Ahmed Al-Rabaiai
- Department of Soils, Water and Agricultural Engineering, Sultan Qaboos University, P.O. Box 34, Al-Khoud 123, Muscat, Sultanate of Oman
| | - Daniel Menezes-Blackburn
- Department of Soils, Water and Agricultural Engineering, Sultan Qaboos University, P.O. Box 34, Al-Khoud 123, Muscat, Sultanate of Oman.
| | - Said Al-Ismaily
- Department of Soils, Water and Agricultural Engineering, Sultan Qaboos University, P.O. Box 34, Al-Khoud 123, Muscat, Sultanate of Oman
| | - Rhonda Janke
- Department of Plant Sciences, Sultan Qaboos University, P.O. Box 34, Al-Khoud 123, Muscat, Sultanate of Oman
| | - Ahmed Al-Alawi
- Department of Food Sciences and Nutrition, Sultan Qaboos University, P.O. Box 34, Al-Khoud 123, Muscat, Sultanate of Oman
| | - Mohamed Al-Kindi
- Department of Pathology, Sultan Qaboos University, P.O. Box 35, Al-Khoud 123, Muscat, Sultanate of Oman
| | - Roland Bol
- Institute for Bio- and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
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Ren Y, Wang G, Su Y, Li J, Zhang H, Han J. Response of antioxidant activity, active constituent and rhizosphere microorganisms of Salvia miltiorrhiza to combined application of microbial inoculant, microalgae and biochar under Cu stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 925:171812. [PMID: 38508267 DOI: 10.1016/j.scitotenv.2024.171812] [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: 12/20/2023] [Revised: 03/15/2024] [Accepted: 03/16/2024] [Indexed: 03/22/2024]
Abstract
Salvia miltiorrhiza, a widely used medicinal herb renowned for its properties in promoting blood circulation, removing blood stasis and alleviating pain, is currently facing quality degradation due to excessive heavy metal levels, posing a threat to medication safety. In order to investigate the effects of microbial inoculant, microalgae and biochar on the growth of Salvia miltiorrhiza under copper (Cu) stress, as well as its Cu absorption, antioxidant activity, active component contents and rhizosphere microbial community, a pot experiment was conducted. Salvia miltiorrhiza plants were cultivated in the soil containing 400 mg/kg of Cu for six months and treated with microbial inoculant, microalgae and biochar, either individually or in combination. Almost all soil amendment treatments led to an increase in root biomass. Notably, co-application of microbial inoculant and microalgae had the optimal effect with a 63.07 % increase compared to the group treated solely with Cu. Moreover, when microbial inoculant was applied alone or in combination with microalgae, the Cu content in plant roots was reduced by 19.29 % and 25.37 %, respectively, whereas other treatments failed to show a decreasing trend. Intriguingly, Cu stress increased the active component contents in plant roots, and they could also be enhanced beyond non-stress levels when microbial inoculant and microalgae were applied together or in combination with biochar. Analyses of plant antioxidant activity, soil properties and rhizosphere microorganisms indicated that these amendments may alleviate Cu stress by enhancing peroxidase activity, facilitating plant nutrient absorption, and enriching beneficial microorganisms capable of promoting plant growth and mitigating heavy metal-induced damage. This study suggests that the combined application of microbial inoculant and microalgae can reduce Cu levels in Salvia miltiorrhiza while enhancing its quality under Cu stress.
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Affiliation(s)
- Ying Ren
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Gang Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Yuying Su
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Jinfeng Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Hui Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Jianping Han
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
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Idbella M, Baronti S, Vaccari FP, Abd-ElGawad AM, Bonanomi G. Long-Term Application of Biochar Mitigates Negative Plant-Soil Feedback by Shaping Arbuscular Mycorrhizal Fungi and Fungal Pathogens. Microorganisms 2024; 12:810. [PMID: 38674754 PMCID: PMC11052468 DOI: 10.3390/microorganisms12040810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 03/30/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Negative plant-soil feedback (PSF) arises when localized accumulations of pathogens reduce the growth of conspecifics, whereas positive PSF can occur due to the emergence of mutualists. Biochar, a carbon-rich material produced by the pyrolysis of organic matter, has been shown to modulate soil microbial communities by altering their abundance, diversity, and activity. For this reason, to assess the long-term impact of biochar on soil microbiome dynamics and subsequent plant performance, we conducted a PSF greenhouse experiment using field soil conditioned over 10 years with Vitis vinifera (L.), without (e.g., C) or with biochar at two rates (e.g., B and BB). Subsequently, the conditioned soil was employed in a response phase involving either the same plant species or different species, i.e., Medicago sativa (L.), Lolium perenne (L.), and Solanum lycopersicum (L.). We utilized next-generation sequencing to assess the abundance and diversity of fungal pathogens and arbuscular mycorrhizal fungi (AMF) within each conditioned soil. Our findings demonstrate that biochar application exerted a stimulatory effect on the growth of both conspecifics and heterospecifics. In addition, our results show that untreated soils had a higher abundance of grape-specialized fungal pathogens, mainly Ilyonectria liriodendra, with a relative abundance of 20.6% compared to 2.1% and 5.1% in B and BB, respectively. Cryptovalsa ampelina also demonstrated higher prevalence in untreated soils, accounting for 4.3% compared to 0.4% in B and 0.1% in BB. Additionally, Phaeoacremonium iranianum was exclusively present in untreated soils, comprising 12.2% of the pathogens' population. Conversely, the application of biochar reduced generalist fungal pathogens. For instance, Plenodomus biglobosus decreased from 10.5% in C to 7.1% in B and 2.3% in BB, while Ilyonectria mors-panacis declined from 5.8% in C to 0.5% in B and 0.2% in BB. Furthermore, biochar application was found to enrich the AMF community. Notably, certain species like Funneliformis geosporum exhibited increased relative abundance in biochar-treated soils, reaching 46.8% in B and 70.3% in BB, compared to 40.5% in untreated soils. Concurrently, other AMF species, namely Rhizophagus irregularis, Rhizophagus diaphanus, and Claroideoglomus drummondii, were exclusively observed in soils where biochar was applied. We propose that the alleviation of negative PSF can be attributed to the positive influence of AMF in the absence of strong inhibition by pathogens. In conclusion, our study underscores the potential of biochar application as a strategic agricultural practice for promoting sustainable soil management over the long term.
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Affiliation(s)
- Mohamed Idbella
- College for Sustainable Agriculture and Environmental Sciences, Mohammed VI Polytechnic University, Ben Guerir 43150, Morocco
| | - Silvia Baronti
- Institute of BioEconomy (IBE), National Research Council (CNR), Via Giovanni Caproni, 8, 50144 Firenze, Italy; (S.B.); (F.P.V.)
| | - Francesco Primo Vaccari
- Institute of BioEconomy (IBE), National Research Council (CNR), Via Giovanni Caproni, 8, 50144 Firenze, Italy; (S.B.); (F.P.V.)
| | - Ahmed M. Abd-ElGawad
- Plant Production Department, College of Food & Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia;
| | - Giuliano Bonanomi
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy;
- Task Force on Microbiome Studies, University of Naples Federico II, 80138 Naples, Italy
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Deshoux M, Sadet-Bourgeteau S, Gentil S, Prévost-Bouré NC. Effects of biochar on soil microbial communities: A meta-analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 902:166079. [PMID: 37553053 DOI: 10.1016/j.scitotenv.2023.166079] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/10/2023]
Abstract
Changes in soil microbial communities may impact soil fertility and stability because microbial communities are key to soil functioning by supporting soil ecological quality and agricultural production. The effects of soil amendment with biochar on soil microbial communities are widely documented but studies highlighted a high degree of variability in their responses following biochar application. The multiple conditions under which they were conducted (experimental designs, application rates, soil types, biochar properties) make it difficult to identify general trends. This supports the need to better determine the conditions of biochar production and application that promote soil microbial communities. In this context, we performed the first ever meta-analysis of the biochar effects on soil microbial biomass and diversity (prokaryotes and fungi) based on high-throughput sequencing data. The majority of the 181 selected publications were conducted in China and evaluated the short-term impact (<3 months) of biochar. We demonstrated that a large panel of variables corresponding to biochar properties, soil characteristics, farming practices or experimental conditions, can affect the effects of biochar on soil microbial characteristics. Using a variance partitioning approach, we showed that responses of soil microbial biomass and prokaryotic diversity were highly dependent on biochar properties. They were influenced by pyrolysis temperature, biochar pH, application rate and feedstock type, as wood-derived biochars have particular physico-chemical properties (high C:N ratio, low nutrient content, large pores size) compared to non-wood-derived biochars. Fungal community data was more heterogenous and scarcer than prokaryote data (30 publications). Fungal diversity indices were rather dependent on soil properties: they were higher in medium-textured soils, with low pH but high soil organic carbon. Altogether, this meta-analysis illustrates the need for long-term field studies in European agricultural context for documenting responses of soil microbial communities to biochar application under diverse conditions combining biochar types, soil properties and conditions of use.
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Affiliation(s)
- Maëlle Deshoux
- INRAE UMR Agroécologie, Institut Agro, University Bourgogne, University Bourgogne Franche-Comté, F-21000 Dijon, France; Groupe Bordet, Froidvent, F-21290 Leuglay, France.
| | - Sophie Sadet-Bourgeteau
- INRAE UMR Agroécologie, Institut Agro, University Bourgogne, University Bourgogne Franche-Comté, F-21000 Dijon, France
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Chen W, Modi D, Picot A. Soil and Phytomicrobiome for Plant Disease Suppression and Management under Climate Change: A Review. PLANTS (BASEL, SWITZERLAND) 2023; 12:2736. [PMID: 37514350 PMCID: PMC10384710 DOI: 10.3390/plants12142736] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023]
Abstract
The phytomicrobiome plays a crucial role in soil and ecosystem health, encompassing both beneficial members providing critical ecosystem goods and services and pathogens threatening food safety and security. The potential benefits of harnessing the power of the phytomicrobiome for plant disease suppression and management are indisputable and of interest in agriculture but also in forestry and landscaping. Indeed, plant diseases can be mitigated by in situ manipulations of resident microorganisms through agronomic practices (such as minimum tillage, crop rotation, cover cropping, organic mulching, etc.) as well as by applying microbial inoculants. However, numerous challenges, such as the lack of standardized methods for microbiome analysis and the difficulty in translating research findings into practical applications are at stake. Moreover, climate change is affecting the distribution, abundance, and virulence of many plant pathogens, while also altering the phytomicrobiome functioning, further compounding disease management strategies. Here, we will first review literature demonstrating how agricultural practices have been found effective in promoting soil health and enhancing disease suppressiveness and mitigation through a shift of the phytomicrobiome. Challenges and barriers to the identification and use of the phytomicrobiome for plant disease management will then be discussed before focusing on the potential impacts of climate change on the phytomicrobiome functioning and disease outcome.
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Affiliation(s)
- Wen Chen
- Ottawa Research and Development Centre, Science and Technology Branch, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Dixi Modi
- Ottawa Research and Development Centre, Science and Technology Branch, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Adeline Picot
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France
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Timmusk S, Pall T, Raz S, Fetsiukh A, Nevo E. The potential for plant growth-promoting bacteria to impact crop productivity in future agricultural systems is linked to understanding the principles of microbial ecology. Front Microbiol 2023; 14:1141862. [PMID: 37275175 PMCID: PMC10235605 DOI: 10.3389/fmicb.2023.1141862] [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: 01/10/2023] [Accepted: 03/28/2023] [Indexed: 06/07/2023] Open
Abstract
Global climate change poses challenges to land use worldwide, and we need to reconsider agricultural practices. While it is generally accepted that biodiversity can be used as a biomarker for healthy agroecosystems, we must specify what specifically composes a healthy microbiome. Therefore, understanding how holobionts function in native, harsh, and wild habitats and how rhizobacteria mediate plant and ecosystem biodiversity in the systems enables us to identify key factors for plant fitness. A systems approach to engineering microbial communities by connecting host phenotype adaptive traits would help us understand the increased fitness of holobionts supported by genetic diversity. Identification of genetic loci controlling the interaction of beneficial microbiomes will allow the integration of genomic design into crop breeding programs. Bacteria beneficial to plants have traditionally been conceived as "promoting and regulating plant growth". The future perspective for agroecosystems should be that microbiomes, via multiple cascades, define plant phenotypes and provide genetic variability for agroecosystems.
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Affiliation(s)
- Salme Timmusk
- Department of Forest Mycology and Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Taavi Pall
- Estonian Health Care Board Department of Gene Technology, Tallinn, Estonia
| | - Shmuel Raz
- Department of Information Systems, University of Haifa, Haifa, Israel
| | - Anastasiia Fetsiukh
- Department of Forest Mycology and Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Haifa, Israel
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Morales Moreira ZP, Chen MY, Yanez Ortuno DL, Haney CH. Engineering plant microbiomes by integrating eco-evolutionary principles into current strategies. CURRENT OPINION IN PLANT BIOLOGY 2023; 71:102316. [PMID: 36442442 DOI: 10.1016/j.pbi.2022.102316] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/30/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Engineering plant microbiomes has the potential to improve plant health in a rapid and sustainable way. Rapidly changing climates and relatively long timelines for plant breeding make microbiome engineering an appealing approach to improving food security. However, approaches that have shown promise in the lab have not resulted in wide-scale implementation in the field. Here, we suggest the use of an integrated approach, combining mechanistic molecular and genetic knowledge, with ecological and evolutionary theory, to target knowledge gaps in plant microbiome engineering that may facilitate translatability of approaches into the field. We highlight examples where understanding microbial community ecology is essential for a holistic understanding of the efficacy and consequences of microbiome engineering. We also review examples where understanding plant-microbe evolution could facilitate the design of plants able to recruit specific microbial communities. Finally, we discuss possible trade-offs in plant-microbiome interactions that should be considered during microbiome engineering efforts so as not to introduce off-target negative effects. We include classic and emergent approaches, ranging from microbial inoculants to plant breeding to host-driven microbiome engineering, and address areas that would benefit from multidisciplinary approaches.
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Affiliation(s)
- Zayda P Morales Moreira
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Melissa Y Chen
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Daniela L Yanez Ortuno
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Cara H Haney
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada.
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Jutakanoke R, Intaravicha N, Charoensuksai P, Mhuantong W, Boonnorat J, Sichaem J, Phongsopitanun W, Chakritbudsabong W, Rungarunlert S. Alleviation of soil acidification and modification of soil bacterial community by biochar derived from water hyacinth Eichhornia crassipes. Sci Rep 2023; 13:397. [PMID: 36624135 PMCID: PMC9829722 DOI: 10.1038/s41598-023-27557-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
The highly acid sulfate Rangsit soil series of Rangsit, Pathum-Thani district, Thailand poses a major problem for agriculture in the area. Water hyacinth is a naturally occurring weed that can grow aggressively, causing eutrophication and leading to many severe environmental impacts. Here, through the pyrolysis process, we convert water hyacinth to biochar and use it for acid soil amendment. We found the ratio between biochar, soil, and sand suitable for the cultivation of water convolvulus to be 50 g of biochar, 400 g of soil, and 100 g of sand (1:8:2). This soil mixture improved the pH of the soil from 4.73 to 7.57. The plant height of the water convolvulus grown in the soil mixture was the greatest at 20.45 cm and the plant weight with and without roots was greatest at 2.23 g and 2.52 g, respectively. Moreover, we demonstrated the dominance and high abundance of Bacillus among the community in soil with biochar amendment. Here we provide the first assessment of the appropriate amount of water hyacinth-derived biochar for mitigation of soil acidity and promotion of optimal water convolvulus growth. Moreover, biochar can optimally modify soil bacterial communities that benefit plant development.
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Affiliation(s)
- Rumpa Jutakanoke
- grid.412029.c0000 0000 9211 2704Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Mueang, Phitsanulok, 65000 Thailand ,grid.412029.c0000 0000 9211 2704Faculty of Medical Science, Centre of Excellence in Medical Biotechnology (CEMB), Naresuan University, Phitsanulok, 65000 Thailand
| | - Nuttakorn Intaravicha
- Environmental Science and Technology Program, Faculty of EnvironmentalScience and Technology, Pathumwan Institute of Technology, Bangkok, 10330 Thailand
| | - Purin Charoensuksai
- grid.412620.30000 0001 2223 9723Department of Biopharmacy and Bioactives from Natural Resources Research Collaboration for Excellence in Pharmaceutical Sciences, Faculty of Pharmacy, Silpakorn University, Nakhon Pathom, 73000 Thailand
| | - Wuttichai Mhuantong
- grid.425537.20000 0001 2191 4408National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120 Thailand
| | - Jarungwit Boonnorat
- grid.440403.70000 0004 0646 5810Department of Environmental Engineering, Faculty of Engineering, Rajamangala University of Technology Thanyaburi (RMUTT), Klong 6, Pathum Thani, 12110 Thailand
| | - Jirapast Sichaem
- grid.412434.40000 0004 1937 1127Research Unit in Natural Products Chemistry and Bioactivities, Faculty of Science and Technology, Thammasat University Lampang Campus, Lampang, 52190 Thailand
| | - Wongsakorn Phongsopitanun
- grid.7922.e0000 0001 0244 7875Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10240 Thailand
| | - Warunya Chakritbudsabong
- grid.10223.320000 0004 1937 0490Laboratory of Cellular Biomedicine and Veterinary Medicine, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170 Thailand ,grid.10223.320000 0004 1937 0490Department of Preclinic and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170 Thailand
| | - Sasitorn Rungarunlert
- Laboratory of Cellular Biomedicine and Veterinary Medicine, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand. .,Department of Preclinic and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, 73170, Thailand.
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Chen Y, Yang L, Zhang L, Li J, Zheng Y, Yang W, Deng L, Gao Q, Mi Q, Li X, Zeng W, Ding X, Xiang H. Autotoxins in continuous tobacco cropping soils and their management. FRONTIERS IN PLANT SCIENCE 2023; 14:1106033. [PMID: 37139103 PMCID: PMC10149998 DOI: 10.3389/fpls.2023.1106033] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 03/29/2023] [Indexed: 05/05/2023]
Abstract
Tobacco belongs to the family Solanaceae, which easily forms continuous cropping obstacles. Continuous cropping exacerbates the accumulation of autotoxins in tobacco rhizospheric soil, affects the normal metabolism and growth of plants, changes soil microecology, and severely reduces the yield and quality of tobacco. In this study, the types and composition of tobacco autotoxins under continuous cropping systems are summarized, and a model is proposed, suggesting that autotoxins can cause toxicity to tobacco plants at the cell level, plant-growth level, and physiological process level, negatively affecting soil microbial life activities, population number, and community structure and disrupting soil microecology. A combined strategy for managing tobacco autotoxicity is proposed based on the breeding of superior varieties, and this approach can be combined with adjustments to cropping systems, the induction of plant immunity, and the optimization of cultivation and biological control measures. Additionally, future research directions are suggested and challenges associated with autotoxicity are provided. This study aims to serve as a reference and provide inspirations needed to develop green and sustainable strategies and alleviate the continuous cropping obstacles of tobacco. It also acts as a reference for resolving continuous cropping challenges in other crops.
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Affiliation(s)
- Yudong Chen
- Technology Center of China Tobacco Yunnan Industrial Co. Ltd., Kunming, China
- College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Long Yang
- College of Plant Protection, Shandong Agricultural University, Tai’an, China
- *Correspondence: Long Yang, ; Wanli Zeng, ; Xinhua Ding, ; Haiying Xiang,
| | | | - Jianrong Li
- Yuxi Cigarette Factory, Hongta Tobacco Group Co. Ltd., Yuxi, China
| | - Yalin Zheng
- College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Wenwu Yang
- Technology Center of China Tobacco Yunnan Industrial Co. Ltd., Kunming, China
| | - Lele Deng
- Technology Center of China Tobacco Yunnan Industrial Co. Ltd., Kunming, China
| | - Qian Gao
- Technology Center of China Tobacco Yunnan Industrial Co. Ltd., Kunming, China
| | - Qili Mi
- Technology Center of China Tobacco Yunnan Industrial Co. Ltd., Kunming, China
| | - Xuemei Li
- Technology Center of China Tobacco Yunnan Industrial Co. Ltd., Kunming, China
| | - Wanli Zeng
- Technology Center of China Tobacco Yunnan Industrial Co. Ltd., Kunming, China
- *Correspondence: Long Yang, ; Wanli Zeng, ; Xinhua Ding, ; Haiying Xiang,
| | - Xinhua Ding
- College of Plant Protection, Shandong Agricultural University, Tai’an, China
- *Correspondence: Long Yang, ; Wanli Zeng, ; Xinhua Ding, ; Haiying Xiang,
| | - Haiying Xiang
- Technology Center of China Tobacco Yunnan Industrial Co. Ltd., Kunming, China
- *Correspondence: Long Yang, ; Wanli Zeng, ; Xinhua Ding, ; Haiying Xiang,
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Impact of Biochar and Bioorganic Fertilizer on Rhizosphere Bacteria in Saline-Alkali Soil. Microorganisms 2022; 10:microorganisms10122310. [PMID: 36557563 PMCID: PMC9785793 DOI: 10.3390/microorganisms10122310] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/11/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022] Open
Abstract
Biochar and bioorganic fertilizers (BOF) that are used in agriculture can, both directly and indirectly, impact rhizosphere soil microorganisms. However, changes to the halophyte rhizosphere bacterial community after applying biochar and BOF to saline−alkali soil have not been thoroughly described. This study has investigated the bacterial communities of halophytes in saline−alkali soil through the addition of different biochar and BOF formulas using Illumina-based sequencing of the 16S rRNA gene fragment. B_BOF (biochar and BOF combined application) had the best effect, either by promoting the plant growth or by improving the physical and chemical properties of the soil. The concentration of the rhizosphere bacterial communities correlated with the changes in soil organic matter (OM) and organic carbon (OC). Proteobacteria, Actinobacteria, Chloroflexi, and Acidobacteria accounted for >80% of the total bacteria in each treatment. In addition, the abundance of Micromonospora was much higher in response to B_BOF than to the other treatments. BOF, with or without biochar, significantly influenced the bacterial community composition in the saline−alkali soil. The OC, OM, total nitrogen, and the available phosphorus had significant effects on the bacterial structure of this soil. The complex correlation of the bacterial communities between CK and B_BOF was higher compared to that between CK and FB or between CK and BOF. These findings suggested that the plant growth, the soil characteristics, and the diversity or community composition of the rhizosphere bacteria in saline−alkali soil were significantly influenced by B_BOF, followed by BOF, and then biochar; fine biochar had a stronger effect than medium or coarse biochar. This study provides an insight into the complex microbial compositions that emerge in response to biochar and BOF.
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12
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Jia W, Wang S, He X, Zhao X. Different factors drive the assembly of pine and Panax notoginseng-associated microbiomes in Panax notoginseng-pine agroforestry systems. Front Microbiol 2022; 13:1018989. [PMID: 36452920 PMCID: PMC9702986 DOI: 10.3389/fmicb.2022.1018989] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 10/24/2022] [Indexed: 09/06/2024] Open
Abstract
Land-use conversion affects the composition and assembly of plant-associated microbiomes, which in turn affects plant growth, development, and ecosystem functioning. However, agroforestry systems, as sustainable land types, have received little attention regarding the dynamics of different plant-associated microbes. In this study, we used high-throughput sequencing technology to analyze the assembly mechanisms and the driving factors of pine- and Panax notoginseng (P.n.)-associated microbiomes during the conversion of different pine forests (Pinus kesiya var. langbianensis and Pinus armandii) into P.n.-pine agroforestry systems. The results showed that the conversion of pure pine forest into P.n.-pine agroforestry systems significantly altered the diversity of pine-associated fungi rather than the community structure, and the community structure of P.n.-associated fungi rather than the diversity. Additionally, plant-associated fungi were more responsive to land-use change than bacteria. Main effect analysis revealed that compartment rather than genotype was the driving factor of pine- and P.n.-associated microbiomes, but P.n. cultivation also significantly affected the assembly of pine-associated microbiomes. In addition, there was a transfer of P.n. endophytes to pine trees in agroforestry systems and the beneficial microbiomes (Massilia, Marmoricola, Herbaspirillum, etc.) were enlarged in pine roots. Therefore, the diversity of the assembly mechanisms of P.n.- and pine-associated microbiomes played an important role in the P.n.--pine agroforestry systems and were the basis for the sustainable development of the P.n.--pine agroforestry systems.
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Affiliation(s)
- Weijia Jia
- College of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming, China
| | - Shu Wang
- Ministry of Education Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Southwest Forestry University, Kunming, China
| | - Xiahong He
- Ministry of Education Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Southwest Forestry University, Kunming, China
| | - Xiaoyan Zhao
- College of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming, China
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13
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Li T, Hu Y, Wang P, Jin T, Chen Y, Wei G, Chen C. Effect of nanohydroxyapatite/biochar/sodium humate composite on phosphorus availability and microbial community in sandy soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 844:157215. [PMID: 35809728 DOI: 10.1016/j.scitotenv.2022.157215] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/02/2022] [Accepted: 07/03/2022] [Indexed: 06/15/2023]
Abstract
Phosphorus (P) is essential for crop growth as an indispensable nutrient; however, there has been growing concern over the low use efficiency of P used in current fertilizers. We synthesized and characterized a potential P fertilizer nanohydroxyapatite/biochar/sodium humate (nHAP/BC/HANa) composite. To study the impact of the composite on soil chemical properties and microbial community in sandy soils, we set up four treatments as follows: (1) biochar (BC), (2) nanohydroxyapatite (nHAP), (3) nHAP/BC/HANa composite, and (4) sodium humate (HANa) was added separately into soils amended with nHAP/BC (nHAP/BC + HANa) to compare its performance with that of the nHAP/BC/HANa composite. A key finding was that the nHAP/BC/HANa composite not only significantly increased the soil available P content and alkaline phosphatase activity but also the increased organic matter content compared to the control. Additionally, leaching losses of P in soils amended with the nHAP/BC/HANa composite were lower than those in soils amended with the nHAP/BC + HANa, which suggested that the nHAP/BC/HANa composite had great potential to decrease P loss in sandy soils. Moreover, bacterial communities were more sensitive than fungal communities to all treatments. The bacterial communities showed the most significant changes in the nHAP/BC/HANa treatments. Results from Mantel tests further indicated that the strongest correlation between bacterial communities and soil properties occurring in the nHAP/BC/HANa treatments. Random forest analysis was conducted to identify the dominant microbial taxa, such as Proteobacteria, Acidobacteria, and Gemmatimonadetes, for predicting changes in soil properties. There was an asymptotical transition in bacterial community assembly processes from stochastic to deterministic in the nHAP/BC/HANa treatments. In conclusion, we demonstrated that nHAP/BC/HANa composite had the remarkable contribution to soil P availability in sandy soils, and simultaneously promoted the bacterial functions potential for P cycling, which present valuable insights to the development of potential P fertilizer.
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Affiliation(s)
- Tao Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, PR China
| | - Yinwei Hu
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, PR China
| | - Pan Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, PR China
| | - Ting Jin
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, PR China
| | - Yinyuan Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, PR China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, PR China.
| | - Chun Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, PR China.
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14
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Liu C, Xia R, Tang M, Chen X, Zhong B, Liu X, Bian R, Yang L, Zheng J, Cheng K, Zhang X, Drosos M, Li L, Shan S, Joseph S, Pan G. Improved ginseng production under continuous cropping through soil health reinforcement and rhizosphere microbial manipulation with biochar: a field study of Panax ginseng from Northeast China. HORTICULTURE RESEARCH 2022; 9:uhac108. [PMID: 35836471 PMCID: PMC9273955 DOI: 10.1093/hr/uhac108] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/23/2022] [Indexed: 06/15/2023]
Abstract
The production of ginseng, an important Chinese medicine crop, has been increasingly challenged by soil degradation and pathogenic disease under continuous cropping in Northeast China. In a field experiment, an Alfisol garden continuously cropped with Chinese ginseng (Panax ginseng C. A. Meyer) was treated with soil amendment at 20 t ha-1 with maize (MB) and wood (WB) biochar, respectively, compared to conventional manure compost (MC). Two years after the amendment, the rooted topsoil and ginseng plants were sampled. The changes in soil fertility and health, particularly in the soil microbial community and root disease incidence, and in ginseng growth and quality were portrayed using soil physico-chemical assays, biochemical assays of extracellular enzyme activities and gene sequencing assays as well as ginsenoside assays. Topsoil fertility was improved by 23% and 39%, ginseng root biomass increased by 25% and 27%, and root quality improved by 6% and 18% with WB and MB, respectively, compared to MC. In the ginseng rhizosphere, fungal abundance increased by 96% and 384%, with a significant and insignificant increase in bacterial abundance, respectively, under WB and MB. Specifically, the abundance of Fusarium spp. was significantly reduced by 19-35%, while that of Burkholderia spp. increased by folds under biochar amendments over MC. Relevantly, there was a significant decrease in the abundance proportion of pathotrophic fungi but a great increase in that of arbuscular mycorrhizal fungi, along with an enhanced microbial community network complexity, especially fungal community complexity, under biochar amendments. Thus, biochar, particularly from maize residue, could promote ginseng quality production while enhancing soil health and ecological services, including carbon sequestration, in continuously cropped fields.
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Affiliation(s)
- Cheng Liu
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Rong Xia
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Man Tang
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Xue Chen
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Bin Zhong
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Xiaoyu Liu
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Rongjun Bian
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Li Yang
- College of Chinese Medicinal Materials, Jilin Agricultural University, 28888 Xincheng Street, Changchun 130118 China
| | - Jufeng Zheng
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Kun Cheng
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Xuhui Zhang
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Marios Drosos
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Lianqing Li
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Shengdao Shan
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, Zhejiang University of Science and Technology, Hangzhou 310023, China
| | - Stephen Joseph
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
- School of Materials Science and Engineering, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Genxing Pan
- Institute of Resource, Ecosystem and Environment of Agriculture, and Department of Soil Science, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
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15
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Kang S, Kim KT, Choi J, Kim H, Cheong K, Bandara A, Lee YH. Genomics and Informatics, Conjoined Tools Vital for Understanding and Protecting Plant Health. PHYTOPATHOLOGY 2022; 112:981-995. [PMID: 34889667 DOI: 10.1094/phyto-10-21-0418-rvw] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Genomics' impact on crop production continuously expands. The number of sequenced plant and microbial species and strains representing diverse populations of individual species rapidly increases thanks to the advent of next-generation sequencing technologies. Their genomic blueprints revealed candidate genes involved in various functions and processes crucial for crop health and helped in understanding how the sequenced organisms have evolved at the genome level. Functional genomics quickly translates these blueprints into a detailed mechanistic understanding of how such functions and processes work and are regulated; this understanding guides and empowers efforts to protect crops from diverse biotic and abiotic threats. Metagenome analyses help identify candidate microbes crucial for crop health and uncover how microbial communities associated with crop production respond to environmental conditions and cultural practices, presenting opportunities to enhance crop health by judiciously configuring microbial communities. Efficient conversion of disparate types of massive genomics data into actionable knowledge requires a robust informatics infrastructure supporting data preservation, analysis, and sharing. This review starts with an overview of how genomics came about and has quickly transformed life science. We illuminate how genomics and informatics can be applied to investigate various crop health-related problems using selected studies. We end the review by noting why community empowerment via crowdsourcing is crucial to harnessing genomics to protect global food and nutrition security without continuously expanding the environmental footprint of crop production.
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Affiliation(s)
- Seogchan Kang
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Ki-Tae Kim
- Department of Agricultural Life Science, Sunchon National University, Suncheon 57922, Korea
| | - Jaeyoung Choi
- Korea Institute of Science and Technology Gangneung Institute of Natural Products, Gangneung 25451, Korea
| | - Hyun Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Kyeongchae Cheong
- Plant Immunity Research Center, Seoul National University, Seoul 08826, Korea
| | - Ananda Bandara
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- Plant Immunity Research Center, Seoul National University, Seoul 08826, Korea
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16
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Gao Y, Zhang Y, Cheng X, Zheng Z, Wu X, Dong X, Hu Y, Wang X. Agricultural Jiaosu: An Eco-Friendly and Cost-Effective Control Strategy for Suppressing Fusarium Root Rot Disease in Astragalus membranaceus. Front Microbiol 2022; 13:823704. [PMID: 35432283 PMCID: PMC9008360 DOI: 10.3389/fmicb.2022.823704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/07/2022] [Indexed: 11/29/2022] Open
Abstract
Root rot caused by the pathogenic fungi of the Fusarium genus poses a great threat to the yield and quality of medicinal plants. The application of Agricultural Jiaosu (AJ), which contains beneficial microbes and metabolites, represents a promising disease control strategy. However, the action-effect of AJ on Fusarium root rot disease remains unclear. In the present study, we evaluated the characteristics and antifungal activity of AJ fermented using waste leaves and stems of medicinal plants, and elucidated the mechanisms of AJ action by quantitative real-time PCR and redundancy analysis. The effects of AJ and antagonistic microbes isolated from it on disease suppression were further validated through a pot experiment. Our results indicate that the AJ was rich in beneficial microorganisms (Bacillus, Pseudomonas, and Lactobacillus), organic acids (acetic, formic, and butyric acids) and volatile organic compounds (alcohols and esters). It could effectively inhibit Fusarium oxysporum and the half-maximal inhibitory concentration (IC50) was 13.64%. The antifungal contribution rate of the microbial components of AJ reached 46.48%. Notably, the redundancy analysis revealed that the Bacillus and Pseudomonas genera occupied the main niche during the whole inhibition process. Moreover, the abundance of the Bacillus, Pseudomonas, and Lactobacillus genera were positively correlated with the pH-value, lactic, formic and butyric acids. The results showed that the combined effects of beneficial microbes and organic acid metabolites increased the efficacy of the AJ antifungal activity. The isolation and identification of AJ’s antagonistic microbes detected 47 isolates that exhibited antagonistic activities against F. oxysporum in vitro. In particular, Bacillus subtilis and Bacillus velezensis presented the strongest antifungal activity. In the pot experiment, the application of AJ and these two Bacillus species significantly reduced the disease incidence of Fusarium root rot and promoted the growth of Astragalus. The present study provides a cost-effective method to control of Fusarium root rot disease, and establishes a whole-plant recycling pattern to promote the sustainable development of medicinal plant cultivation.
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Affiliation(s)
- Youhui Gao
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yue Zhang
- Biotechnology Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xiaoqian Cheng
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Zehui Zheng
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- Biology Institute, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China
| | - Xuehong Wu
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Xuehui Dong
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yuegao Hu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Xiaofen Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- *Correspondence: Xiaofen Wang,
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17
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Li YB, Zhang ZP, Yuan Y, Huang HC, Mei XY, Du F, Yang M, Liu YX, Zhu SS. Appropriate Soil Heat Treatment Promotes Growth and Disease Suppression of Panax notoginseng by Interfering with the Bacterial Community. J Microbiol Biotechnol 2022; 32:294-301. [PMID: 35283430 PMCID: PMC9628859 DOI: 10.4014/jmb.2112.12005] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/11/2022] [Accepted: 02/15/2022] [Indexed: 12/15/2022]
Abstract
In our greenhouse experiment, soil heat treatment groups (50, 80, and 121°C) significantly promoted growth and disease suppression of Panax notoginseng in consecutively cultivated soil (CCS) samples (p < 0.01), and 80°C worked better than 50°C and 121°C (p < 0.01). Furthermore, we found that heat treatment at 80°C changes the microbial diversity in CCS, and the inhibition ratios of culturable microorganisms, such as fungi and actinomycetes, were nearly 100%. However, the heat-tolerant bacterial community was preserved. The 16S rRNA gene and internal transcribed spacer (ITS) sequencing analyses indicated that the soil heat treatment had a greater effect on the Chao1 index and Shannon's diversity index of bacteria than fungi, and the relative abundances of Firmicutes and Proteobacteria were significantly higher than without heating (80 and 121°C, p < 0.05). Soil probiotic bacteria, such as Bacillus (67%), Sporosarcina (9%), Paenibacillus (6%), Paenisporosarcina (6%), and Cohnella (4%), remained in the soil after the 80°C and 121°C heat treatments. Although steam increased the relative abundances of most of the heat-tolerant microbes before sowing, richness and diversity gradually recovered to the level of CCS, regardless of fungi or bacteria, after replanting. Thus, we added heat-tolerant microbes (such as Bacillus) after steaming, which reduced the relative abundance of pathogens, recruited antagonistic bacteria, and provided a long-term protective effect compared to the steaming and Bacillus alone (p < 0.05). Taken together, the current study provides novel insight into sustainable agriculture in a consecutively cultivated system.
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Affiliation(s)
- Ying-Bin Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, P.R. China,Key Laboratory for Agro-Biodiversity and Pest Control (Ministry of Education), College of Plant Protection, Yunnan Agricultural University, Kunming 650201, P.R. China
| | - Zhi-Ping Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, P.R. China,Key Laboratory for Agro-Biodiversity and Pest Control (Ministry of Education), College of Plant Protection, Yunnan Agricultural University, Kunming 650201, P.R. China
| | - Ye Yuan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, P.R. China,Key Laboratory for Agro-Biodiversity and Pest Control (Ministry of Education), College of Plant Protection, Yunnan Agricultural University, Kunming 650201, P.R. China
| | - Hui-Chuan Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, P.R. China,Key Laboratory for Agro-Biodiversity and Pest Control (Ministry of Education), College of Plant Protection, Yunnan Agricultural University, Kunming 650201, P.R. China
| | - Xin-Yue Mei
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, P.R. China,Key Laboratory for Agro-Biodiversity and Pest Control (Ministry of Education), College of Plant Protection, Yunnan Agricultural University, Kunming 650201, P.R. China
| | - Fen Du
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, P.R. China,Key Laboratory for Agro-Biodiversity and Pest Control (Ministry of Education), College of Plant Protection, Yunnan Agricultural University, Kunming 650201, P.R. China
| | - Min Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, P.R. China,Key Laboratory for Agro-Biodiversity and Pest Control (Ministry of Education), College of Plant Protection, Yunnan Agricultural University, Kunming 650201, P.R. China
| | - Yi-Xiang Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, P.R. China,Key Laboratory for Agro-Biodiversity and Pest Control (Ministry of Education), College of Plant Protection, Yunnan Agricultural University, Kunming 650201, P.R. China,Corresponding authors Y.X. Liu E-mail:
| | - Shu-Sheng Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, P.R. China,Key Laboratory for Agro-Biodiversity and Pest Control (Ministry of Education), College of Plant Protection, Yunnan Agricultural University, Kunming 650201, P.R. China,
S.S. Zhu E-mail:
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18
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Chen Y, Du J, Li Y, Tang H, Yin Z, Yang L, Ding X. Evolutions and Managements of Soil Microbial Community Structure Drove by Continuous Cropping. Front Microbiol 2022; 13:839494. [PMID: 35295291 PMCID: PMC8920486 DOI: 10.3389/fmicb.2022.839494] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/07/2022] [Indexed: 11/17/2022] Open
Abstract
Continuous cropping obstacles have increasingly become an important phenomenon affecting crop yield and quality. Its harm includes the deterioration of soil basic physical and chemical properties, changes of soil microbial community structure, accumulation of autotoxins, weakness of plant growth, and aggravation of diseases and pests. In this review, the evolutionary trend of soil microbial structure driven by continuous cropping was generalized, while drivers of these changes summed up as destruction of soil microbial living environment and competition within the community. We introduced a microorganism proliferation and working model with three basics and a vector, and four corresponding effective measures to reshape the structure were comprehensively expounded. According to the model, we also put forward three optimization strategies of the existing measures. In which, synthetic microbiology provides a new solution for improving soil community structure. Meanwhile, to ensure the survival and reproduction of soil microorganisms, it is necessary to consider their living space and carbon sources in soil fully. This review provided a comprehensive perspective for understanding the evolutionary trend of the soil microbial community under continuous cropping conditions and a summary of reshaping measures and their optimization direction.
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Affiliation(s)
- Yudong Chen
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Jianfeng Du
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Yang Li
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Heng Tang
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Ziyi Yin
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Long Yang
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Xinhua Ding
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an, China
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19
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Sahito ZA, Zehra A, Chen S, Yu S, Tang L, Ali Z, Hamza S, Irfan M, Abbas T, He Z, Yang X. Rhizobium rhizogenes-mediated root proliferation in Cd/Zn hyperaccumulator Sedum alfredii and its effects on plant growth promotion, root exudates and metal uptake efficiency. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127442. [PMID: 34673390 DOI: 10.1016/j.jhazmat.2021.127442] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/29/2021] [Accepted: 10/04/2021] [Indexed: 06/13/2023]
Abstract
In this study, Rhizobium rhizogenes-mediated root proliferation system in Sedum alfredii has been established. Twenty strains of R. rhizogenes were screened for root proliferation. A significant difference (P < 0.01) was observed in plant morphological characters under influence of different bacterial strains. The highest root fresh weight (3.236 g/plant) was observed with strain AS12556. Furthermore, significant difference (P < 0.05) was observed in the chemical composition of organic acids, Tartaric acid (TA), Succinic acid (SA), Malic acid (MA), Citric acid (CA) and Oxalic acid (OA), pH, Total Nitrogen (TN), Total Organic Carbon (TOC) and soluble sugars in root exudates with different R. rhizogenes mediated roots. Furthermore, a series of hydroponics experiments were conducted with varying concentrations of Cd (25, 50 and 75 µM) and Zn (100, 200 and 500 µM) to assess the phytoextraction efficiency of proliferated roots with Rhizobium. Several plants with proliferated roots showed enhanced growth and improved metal extraction efficiency. Five strains (LBA 9402, K599, AS12556, MSU440 and C58C1) were identified as potential strains for root proliferation in Sedum alfredii. R. rhizogenes strain AS12556 improved Cd/Zn phytoextraction by exogenous production of phytochemicals to promote root proliferation, improved shoot biomass, lowered oxidative damage and enhanced phytoextraction efficiency in S. alfredii. Therefore, it has been selected as a potential microbial partner of S. alfredii to develop extensive rooting system for better growth and enhanced phytoremediation potential. Results suggest that R. rhizogenes mediated root proliferation system can be used for optimizing metal extraction from contaminated soils.
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Affiliation(s)
- Zulfiqar Ali Sahito
- Ministry of Education (MOE) Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang University, Hangzhou 310058, People's Republic of China; Department of Earth and Environmental Sciences, Bahria University Karachi Campus, Karachi 75300, Pakistan
| | - Afsheen Zehra
- Ministry of Education (MOE) Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang University, Hangzhou 310058, People's Republic of China; Department of Botany, Federal Urdu University of Arts, Science and Technology, Karachi 75300, Pakistan
| | - Shaoning Chen
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China
| | - Song Yu
- Ministry of Education (MOE) Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Lin Tang
- Ministry of Education (MOE) Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Zarina Ali
- Department of Botany, Federal Urdu University of Arts, Science and Technology, Karachi 75300, Pakistan
| | - Salma Hamza
- Department of Earth and Environmental Sciences, Bahria University Karachi Campus, Karachi 75300, Pakistan
| | - Muhammad Irfan
- Department of Earth and Environmental Sciences, Bahria University Karachi Campus, Karachi 75300, Pakistan
| | - Tanveer Abbas
- Department of Microbiology, University of Karachi, Karachi 75250, Pakistan
| | - Zhenli He
- University of Florida, Institute of Food and Agricultural Sciences, Indian River Research and Education Center, Fort Pierce, FL 34945, United States
| | - Xiaoe Yang
- Ministry of Education (MOE) Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang University, Hangzhou 310058, People's Republic of China.
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20
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Mazarji M, Minkina T, Sushkova S, Mandzhieva S, Fedorenko A, Bauer T, Soldatov A, Barakhov A, Dudnikova T. Biochar-assisted Fenton-like oxidation of benzo[a]pyrene-contaminated soil. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2022; 44:195-206. [PMID: 33411119 DOI: 10.1007/s10653-020-00801-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 12/15/2020] [Indexed: 06/12/2023]
Abstract
In the present study, the biochar derived from sunflower husks was used as a mediator in the heterogeneous Fenton process. The physical and chemical characteristics were studied in terms of specific surface area, elemental contents, surface morphology, surface functional groups, thermal stability, and X-ray crystallography. The main aim was to evaluate the effectiveness of biochar in a heterogeneous Fenton process catalyzed by hematite toward the degradation of benzo[a]pyrene (BaP) in Haplic Chernozem. The Fenton-like reaction was performed at a pH of 7.8 without pH adjustment in chernozem soil. The effects of operating parameters, such as hematite dosage and H2O2 concentrations, were investigated with respect to the removal efficiency of BaP. The overall degradation of 65% was observed at the optimized conditions where 2 mg g-1 hematite and 1.25 M H2O2 corresponded to the H2O2 to Fe ratio of 22:1. Moreover, the biochar amendment showed an increment in the removal efficiency and promotion in the growth of spring barley (Hordeum sativum distichum). The BaP removal was reached 75 and 95% after 2.5 and 5% w/w addition of biochar, respectively. The results suggested that the Fenton-like reaction's effectiveness would be greatly enhanced by the ability of biochar for activation of H2O2 and ejection of the electron to reduce Fe(III) to Fe(II). Finally, the presence of biochar could enhance the soil physicochemical properties, as evidenced by the better growth of Hordeum sativum distichum compared to the soil without biochar. These promising results open up new opportunities toward the application of a modified Fenton reaction with biochar for remediating BaP-polluted soils.
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Affiliation(s)
- Mahmoud Mazarji
- Southern Federal University, Rostov-on-Don, Russian Federation.
| | - Tatiana Minkina
- Southern Federal University, Rostov-on-Don, Russian Federation
| | | | | | - Aleksei Fedorenko
- Southern Federal University, Rostov-on-Don, Russian Federation
- Federal Research Centre the Southern Scientific Centre of the Russian Academy of Sciences, Rostov-on-Don, Russian Federation
| | - Tatiana Bauer
- Southern Federal University, Rostov-on-Don, Russian Federation
- Federal Research Centre the Southern Scientific Centre of the Russian Academy of Sciences, Rostov-on-Don, Russian Federation
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21
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Connolly JA, Harcombe WR, Smanski MJ, Kinkel LL, Takano E, Breitling R. Harnessing intercellular signals to engineer the soil microbiome. Nat Prod Rep 2021; 39:311-324. [PMID: 34850800 DOI: 10.1039/d1np00034a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: Focus on 2015 to 2020Plant and soil microbiomes consist of diverse communities of organisms from across kingdoms and can profoundly affect plant growth and health. Natural product-based intercellular signals govern important interactions between microbiome members that ultimately regulate their beneficial or harmful impacts on the plant. Exploiting these evolved signalling circuits to engineer microbiomes towards beneficial interactions with crops is an attractive goal. There are few reports thus far of engineering the intercellular signalling of microbiomes, but this article argues that it represents a tremendous opportunity for advancing the field of microbiome engineering. This could be achieved through the selection of synergistic consortia in combination with genetic engineering of signal pathways to realise an optimised microbiome.
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Affiliation(s)
- Jack A Connolly
- Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, Faculty of Science and Engineering, School of Natural Sciences, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, UK.
| | - William R Harcombe
- BioTechnology Institute, University of Minnesota, Twin-Cities, Saint Paul, MN55108, USA.,Department of Evolution, and Behaviour, University of Minnesota, Twin-Cities Saint Paul, MN55108, USA
| | - Michael J Smanski
- BioTechnology Institute, University of Minnesota, Twin-Cities, Saint Paul, MN55108, USA.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Twin-Cities, Saint Paul, MN55108, USA
| | - Linda L Kinkel
- BioTechnology Institute, University of Minnesota, Twin-Cities, Saint Paul, MN55108, USA.,Department of Plant Pathology, University of Minnesota, Twin-Cities, Saint Paul, MN 55108, USA
| | - Eriko Takano
- Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, Faculty of Science and Engineering, School of Natural Sciences, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, UK.
| | - Rainer Breitling
- Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, Faculty of Science and Engineering, School of Natural Sciences, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, UK.
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22
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De Tender C, Vandecasteele B, Verstraeten B, Ommeslag S, Kyndt T, Debode J. Biochar-Enhanced Resistance to Botrytis cinerea in Strawberry Fruits (But Not Leaves) Is Associated With Changes in the Rhizosphere Microbiome. FRONTIERS IN PLANT SCIENCE 2021; 12:700479. [PMID: 34497619 PMCID: PMC8419269 DOI: 10.3389/fpls.2021.700479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
Biochar has been reported to play a positive role in disease suppression against airborne pathogens in plants. The mechanisms behind this positive trait are not well-understood. In this study, we hypothesized that the attraction of plant growth-promoting rhizobacteria (PGPR) or fungi (PGPF) underlies the mechanism of biochar in plant protection. The attraction of PGPR and PGPF may either activate the innate immune system of plants or help the plants with nutrient uptake. We studied the effect of biochar in peat substrate (PS) on the susceptibility of strawberry, both on leaves and fruits, against the airborne fungal pathogen Botrytis cinerea. Biochar had a positive impact on the resistance of strawberry fruits but not the plant leaves. On leaves, the infection was more severe compared with plants without biochar in the PS. The different effects on fruits and plant leaves may indicate a trade-off between plant parts. Future studies should focus on monitoring gene expression and metabolites of strawberry fruits to investigate this potential trade-off effect. A change in the microbial community in the rhizosphere was also observed, with increased fungal diversity and higher abundances of amplicon sequence variants classified into Granulicella, Mucilaginibacter, and Byssochlamys surrounding the plant root, where the latter two were reported as biocontrol agents. The change in the microbial community was not correlated with a change in nutrient uptake by the plant in either the leaves or the fruits. A decrease in the defense gene expression in the leaves was observed. In conclusion, the decreased infection of B. cinerea in strawberry fruits mediated by the addition of biochar in the PS is most likely regulated by the changes in the microbial community.
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Affiliation(s)
- Caroline De Tender
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Bart Vandecasteele
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Bruno Verstraeten
- Epigenetics and Defence Research Group, Department Biotechnology, Ghent University, Ghent, Belgium
| | - Sarah Ommeslag
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Tina Kyndt
- Epigenetics and Defence Research Group, Department Biotechnology, Ghent University, Ghent, Belgium
| | - Jane Debode
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
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23
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Irreplaceable Role of Amendment-Based Strategies to Enhance Soil Health and Disease Suppression in Potato Production. Microorganisms 2021; 9:microorganisms9081660. [PMID: 34442738 PMCID: PMC8400219 DOI: 10.3390/microorganisms9081660] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/26/2021] [Accepted: 07/28/2021] [Indexed: 11/22/2022] Open
Abstract
Soilborne diseases are a major constraining factor to soil health and plant health in potato production. In the toolbox of crop management, soil amendments have shown benefits to control these diseases and improve soil quality. Most amendments provide nutrients to plants and suppress multiple soilborne pathogens. Soil amendments are naturally derived materials and products and can be classified into fresh or living plants, organic or inorganic matters, and microbial supplements. Fresh plants have unique functions and continuously exude chemicals to interact with soil microbes. Organic and inorganic matter contain high levels of nutrients, including nitrogen and carbon that plants and soil microorganisms need. Soil microorganisms, whether being artificially added or indigenously existing, are a key factor in plant health. Microbial communities can be considered as a biological reactor in an ecosystem, which suppress soilborne pathogens in various mechanisms and turn soil organic matter into absorbable forms for plants, regardless of amendment types. Therefore, soil amendments serve as an energy input, nutrient source, and a driving force of microbial activities. Advanced technologies, such as microbiome analyses, make it possible to analyze soil microbial communities and soil health. As research advances on mechanisms and functions, amendment-based strategies will play an important role in enhancing soil health and disease suppression for better potato production.
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24
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Hou Q, Kolodkin-Gal I. Harvesting the complex pathways of antibiotic production and resistance of soil bacilli for optimizing plant microbiome. FEMS Microbiol Ecol 2021; 96:5872479. [PMID: 32672816 DOI: 10.1093/femsec/fiaa142] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/13/2020] [Indexed: 01/04/2023] Open
Abstract
A sustainable future increasing depends on our capacity to utilize beneficial plant microbiomes to meet our growing needs. Plant microbiome symbiosis is a hallmark of the beneficial interactions between bacteria and their host. Specifically, colonization of plant roots by biocontrol agents and plant growth-promoting bacteria can play an important role in maintaining the optimal rhizosphere environment, supporting plant growth and promoting its fitness. Rhizosphere communities confer immunity against a wide range of foliar diseases by secreting antibiotics and activating plant defences. At the same time, the rhizosphere is a highly competitive niche, with multiple microbial species competing for space and resources, engaged in an arms race involving the production of a vast array of antibiotics and utilization of a variety of antibiotic resistance mechanisms. Therefore, elucidating the mechanisms that govern antibiotic production and resistance in the rhizosphere is of great significance for designing beneficial communities with enhanced biocontrol properties. In this review, we used Bacillus subtilis and B. amyloliquefaciens as models to investigate the genetics of antibiosis and the potential for its translation of into improved plant microbiome performance.
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Affiliation(s)
- Qihui Hou
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ilana Kolodkin-Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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25
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Regular Biochar and Bacteria-Inoculated Biochar Alter the Composition of the Microbial Community in the Soil of a Chinese Fir Plantation. FORESTS 2020. [DOI: 10.3390/f11090951] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Biochar is a promising material for the improvement of soil quality. However, studies on biochar have mostly been carried out in laboratory conditions or have focused on agricultural aspects. The impacts of the application of biochar on soil characteristics and related ecological processes of the forest ecosystem have not been fully resolved. In this study, we investigated the effects of regular biochar and bacteria-loaded biochar on the microbial communities in the bulk soil and the rhizosphere soil of an annual Chinese fir plantation. In early spring (April), the two types of biochar were added to the soil at the rates of 2.22 t·ha−1, 4.44 t·ha−1, 6.67 t·ha−1, 8.89 t·ha−1, and 11.11 t·ha−1 by ring furrow application around the seedlings, and soil samples were collected at the end of autumn (November). The results showed that biochar addition increased the soil nutrient content and promoted the growth and diversity of soil microbial communities. The diversity of soil fungi was significantly increased, and the diversity of soil bacteria was significantly decreased. Principal component analysis under the different biochar types and application rates demonstrated that microbial communities differed significantly between the treatments and controls and that the effect of biochar on the microbial community of the bulk soil was more significant than that of the rhizosphere soil. Under the same dosage, the effect of bacteria-loaded biochar on soil was more significant than that of regular biochar.
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