1
|
Sadikiel Mmbando G, Ngongolo K. The recent genetic modification techniques for improve soil conservation, nutrient uptake and utilization. GM CROPS & FOOD 2024; 15:233-247. [PMID: 39008437 PMCID: PMC11253881 DOI: 10.1080/21645698.2024.2377408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 07/03/2024] [Indexed: 07/17/2024]
Abstract
Advances in genetic modification (GM) techniques have generated huge interest in improving nutrient utilization, maximizing nutrient uptake, and conserving soil in the pursuit of sustainable agriculture. Unfortunately, little is still known about the recent advancements in the application of GM tactics to enhance each of these areas. This review explores the latest GM strategies intended to support soil conservation, maximize nutrient uptake, and improve nutrient utilization in farming, highlighting the critical roles that soil health and nutrient management play in sustainable farming. GM strategies such as improving the efficiency of nutrient uptake through enhanced root systems and increased nutrient transport mechanisms are well discussed. This study suggests that addressing potential obstacles, such as ethical and regulatory concerns, is a necessity for long-term sustainability applications of GM technologies to raise agricultural yields.
Collapse
Affiliation(s)
- Gideon Sadikiel Mmbando
- Department of Biology, College of Natural and Mathematical Sciences, The University of Dodoma, Dodoma, United Republic of Tanzania
| | - Kelvin Ngongolo
- Department of Biology, College of Natural and Mathematical Sciences, The University of Dodoma, Dodoma, United Republic of Tanzania
| |
Collapse
|
2
|
Zhang J, Song K, Jin F, Jia F, Liang J, Wang F, Zhang J. A novel strategy of artificially regulating plant rhizosphere microbial community to promote plant tolerance to cold stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:175184. [PMID: 39089386 DOI: 10.1016/j.scitotenv.2024.175184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 07/14/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024]
Abstract
Artificial regulation of plant rhizosphere microbial communities through the synthesis of microbial communities is one of the effective ways to improve plant stress resistance. However, the process of synthesizing stress resistant microbial communities with excellent performance is complex, time-consuming, and costly. To address this issue, we proposed a novel strategy for preparing functional microbial communities. We isolated a cultivable cold tolerant bacterial community (PRCBC) from the rhizosphere of peas, and studied its effectiveness in assisting rice to resist stress. The results indicate that PRCBC can not only improve the ability of rice to resist cold stress, but also promote the increase of rice yield after cold stress relieved. This is partly because PRCBC increases the nitrogen content in the rhizosphere soil, and promotes rice's absorption of nitrogen elements, thereby promoting rice growth and enhancing its ability to resist osmotic stress. More importantly, the application of PRCBC drives the succession of rice rhizosphere microbial communities, and promotes the succession of rice rhizosphere microbial communities towards stress resistance. Surprisingly, PRCBC drives the succession of rice rhizosphere microbial communities towards a composition similar to PRCBC. This provides a feasible novel method for artificially and directionally driving microbial succession. In summary, we not only proposed a novel and efficient strategy for preparing stress resistant microbial communities to promote plant stress resistance, but also unexpectedly discovered a possible directionally driving method for soil microbial community succession.
Collapse
Affiliation(s)
- Jianfeng Zhang
- College of Life Science, Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Keji Song
- College of Life Science, Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Fengyuan Jin
- College of Life Science, Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Fang Jia
- College of Life Science, Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Jing Liang
- College of Life Science, Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Fudong Wang
- College of Life Science, Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Jiejing Zhang
- College of Life Science, Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Jilin Agricultural University, Changchun 130118, China.
| |
Collapse
|
3
|
Malla MA, Ansari FA, Bux F, Kumari S. Re-vitalizing wastewater: Nutrient recovery and carbon capture through microbe-algae synergy using omics-biology. ENVIRONMENTAL RESEARCH 2024; 259:119439. [PMID: 38901811 DOI: 10.1016/j.envres.2024.119439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/23/2024] [Accepted: 06/17/2024] [Indexed: 06/22/2024]
Abstract
Increasing amounts of wastewater is the most pervasive and challenging environmental problem globally. Conventional treatment methods are costly and entail huge energy, carbon consumption and greenhouse gas emissions. Owing to their unique ability of carbon capturing and resource recovery, microalgae-microbiome based treatment is a potential approach and is widely used for carbon-neutral wastewater treatment. Microalgae-bacteria synergy (i.e., the functionally beneficial microbial synthetic communities) performs better and enhances carbon-sequestration and nutrient recovery from wastewater treatment plants. This review presents a comprehensive information regarding the potential of microalgae-microbiome as a sustainable agent for wastewater and discusses synergistic approaches for effective nutrient removal. Moreover, this review discusses, the role of omics-biology and Insilco approaches in unravelling and understanding the algae-microbe synergism and their response toward wastewater treatment. Finally, it discusses various microbiome engineering approaches for developing the effective microalgae-bacteria partners for carbon sequestration and nutrient recovery from wastewater, and summarizes future research perspectives on microalgae-microbiome based bioremediation.
Collapse
Affiliation(s)
- Muneer Ahmad Malla
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, South Africa
| | - Faiz Ahmad Ansari
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, South Africa
| | - Faizal Bux
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, South Africa
| | - Sheena Kumari
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, South Africa.
| |
Collapse
|
4
|
Compant S, Cassan F, Kostić T, Johnson L, Brader G, Trognitz F, Sessitsch A. Harnessing the plant microbiome for sustainable crop production. Nat Rev Microbiol 2024:10.1038/s41579-024-01079-1. [PMID: 39147829 DOI: 10.1038/s41579-024-01079-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2024] [Indexed: 08/17/2024]
Abstract
Global research on the plant microbiome has enhanced our understanding of the complex interactions between plants and microorganisms. The structure and functions of plant-associated microorganisms, as well as the genetic, biochemical, physical and metabolic factors that influence the beneficial traits of plant microbiota have also been intensively studied. Harnessing the plant microbiome has led to the development of various microbial applications to improve crop productivity in the face of a range of challenges, for example, climate change, abiotic and biotic stresses, and declining soil properties. Microorganisms, particularly nitrogen-fixing rhizobia as well as mycorrhizae and biocontrol agents, have been applied for decades to improve plant nutrition and health. Still, there are limitations regarding efficacy and consistency under field conditions. Also, the wealth of expanding knowledge on microbiome diversity, functions and interactions represents a huge source of information to exploit for new types of application. In this Review, we explore plant microbiome functions, mechanisms, assembly and types of interaction, and discuss current applications and their pitfalls. Furthermore, we elaborate on how the latest findings in plant microbiome research may lead to the development of new or more advanced applications. Finally, we discuss research gaps to fully leverage microbiome functions for sustainable plant production.
Collapse
Affiliation(s)
| | | | - Tanja Kostić
- AIT Austrian Institute of Technology, Vienna, Austria
| | | | - Günter Brader
- AIT Austrian Institute of Technology, Vienna, Austria
| | | | | |
Collapse
|
5
|
Chompa SS, Zuan ATK, Amin AM, Hun TG, Ghazali AHA, Sadeq BM, Akter A, Rahman ME, Rashid HO. Growth and protein response of rice plant with plant growth-promoting rhizobacteria inoculations under salt stress conditions. Int Microbiol 2024; 27:1151-1168. [PMID: 38172302 DOI: 10.1007/s10123-023-00469-4] [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: 10/30/2023] [Revised: 11/22/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024]
Abstract
Soil salinity has been one of the significant barriers to improving rice production and quality. According to reports, Bacillus spp. can be utilized to boost plant development in saline soil, although the molecular mechanisms behind the interaction of microbes towards salt stress are not fully known. Variations in rice plant protein expression in response to salt stress and plant growth-promoting rhizobacteria (PGPR) inoculations were investigated using a proteomic method and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Findings revealed that 54 salt-responsive proteins were identified by mass spectrometry analysis (LC-MS/MS) with the Bacillus spp. interaction, and the proteins were functionally classified as gene ontology. The initial study showed that all proteins were labeled by mass spectrometry analysis (LC-MS/MS) with Bacillus spp. interaction; the proteins were functionally classified into six groups. Approximately 18 identified proteins (up-regulated, 13; down-regulated, 5) were involved in the photosynthetic process. An increase in the expression of eight up-regulated and two down-regulated proteins in protein synthesis known as chaperones, such as the 60 kDa chaperonin, the 70 kDa heat shock protein BIP, and calreticulin, was involved in rice plant stress tolerance. Several proteins involved in protein metabolism and signaling pathways also experienced significant changes in their expression. The results revealed that phytohormones regulated the manifestation of various chaperones and protein abundance and that protein synthesis played a significant role in regulating salt stress. This study also described how chaperones regulate rice salt stress, their different subcellular localizations, and the activity of chaperones.
Collapse
Affiliation(s)
- Sayma Serine Chompa
- Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Ali Tan Kee Zuan
- Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| | - Adibah Mohd Amin
- Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Tan Geok Hun
- Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | | | - Buraq Musa Sadeq
- Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Amaily Akter
- Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Md Ekhlasur Rahman
- Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Divisional Laboratory, Soil Resource Development Institute, Krishi Khamar Sarak, Farmgate, Dhaka, 1215, Bangladesh
| | - Harun Or Rashid
- Department of Modern Languages & Communications, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| |
Collapse
|
6
|
Marcianò D, Kappel L, Ullah SF, Srivastava V. From glycans to green biotechnology: exploring cell wall dynamics and phytobiota impact in plant glycopathology. Crit Rev Biotechnol 2024:1-19. [PMID: 39004515 DOI: 10.1080/07388551.2024.2370341] [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: 03/06/2024] [Accepted: 06/06/2024] [Indexed: 07/16/2024]
Abstract
Filamentous plant pathogens, including fungi and oomycetes, pose significant threats to cultivated crops, impacting agricultural productivity, quality and sustainability. Traditionally, disease control heavily relied on fungicides, but concerns about their negative impacts motivated stakeholders and government agencies to seek alternative solutions. Biocontrol agents (BCAs) have been developed as promising alternatives to minimize fungicide use. However, BCAs often exhibit inconsistent performances, undermining their efficacy as plant protection alternatives. The eukaryotic cell wall of plants and filamentous pathogens contributes significantly to their interaction with the environment and competitors. This highly adaptable and modular carbohydrate armor serves as the primary interface for communication, and the intricate interplay within this compartment is often mediated by carbohydrate-active enzymes (CAZymes) responsible for cell wall degradation and remodeling. These processes play a crucial role in the pathogenesis of plant diseases and contribute significantly to establishing both beneficial and detrimental microbiota. This review explores the interplay between cell wall dynamics and glycan interactions in the phytobiome scenario, providing holistic insights for efficiently exploiting microbial traits potentially involved in plant disease mitigation. Within this framework, the incorporation of glycobiology-related functional traits into the resident phytobiome can significantly enhance the plant's resilience to biotic stresses. Therefore, in the rational engineering of future beneficial consortia, it is imperative to recognize and leverage the understanding of cell wall interactions and the role of the glycome as an essential tool for the effective management of plant diseases.
Collapse
Affiliation(s)
- Demetrio Marcianò
- Department of Agricultural and Environmental Sciences, University of Milan, Milan, Italy
| | - Lisa Kappel
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden
| | - Sadia Fida Ullah
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden
| | - Vaibhav Srivastava
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden
| |
Collapse
|
7
|
Ngolong Ngea GL, Yang Q, Xu M, Ianiri G, Dhanasekaran S, Zhang X, Bi Y, Zhang H. Revisiting the current and emerging concepts of postharvest fresh fruit and vegetable pathology for next-generation antifungal technologies. Compr Rev Food Sci Food Saf 2024; 23:e13397. [PMID: 38924311 DOI: 10.1111/1541-4337.13397] [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: 02/14/2024] [Revised: 06/01/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024]
Abstract
Fungal infections of fresh fruits and vegetables (FFVs) can lead to safety problems, including consumer poisoning by mycotoxins. Various strategies exist to control fungal infections of FFVs, but their effectiveness and sustainability are limited. Recently, new concepts based on the microbiome and pathobiome have emerged and offer a more holistic perspective for advancing postharvest pathogen control techniques. Understanding the role of the microbiome in FFV infections is essential for developing sustainable control strategies. This review examines current and emerging approaches to postharvest pathology. It reviews what is known about the initiation and development of infections in FFVs. As a promising concept, the pathobiome offers new insights into the basic mechanisms of microbial infections in FFVs. The underlying mechanisms uncovered by the pathobiome are being used to develop more relevant global antifungal strategies. This review will also focus on new technologies developed to target the microbiome and members of the pathobiome to control infections in FFVs and improve safety by limiting mycotoxin contamination. Specifically, this review stresses emerging technologies related to FFVs that are relevant for modifying the interaction between FFVs and the microbiome and include the use of microbial consortia, the use of genomic technology to manipulate host and microbial community genes, and the use of databases, deep learning, and artificial intelligence to identify pathobiome markers. Other approaches include programming the behavior of FFVs using synthetic biology, modifying the microbiome using sRNA technology, phages, quorum sensing, and quorum quenching strategies. Rapid adoption and commercialization of these technologies are recommended to further improve the overall safety of FFVs.
Collapse
Affiliation(s)
- Guillaume Legrand Ngolong Ngea
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
- Département de Transformation et Contrôle de qualité des Produits Halieutiques, Institut des Sciences Halieutiques, Université de Douala à Yabassi, Douala-Bassa, Cameroun
| | - Qiya Yang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Meiqiu Xu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Giuseppe Ianiri
- Department of Agricultural, Environmental and Food Sciences, University of Molise, Campobasso, Italy
| | | | - Xiaoyun Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Yang Bi
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, China
| | - Hongyin Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| |
Collapse
|
8
|
Jin R, Song J, Liu C, Lin R, Liang D, Aweya JJ, Weng W, Zhu L, Shang J, Yang S. Synthetic microbial communities: Novel strategies to enhance the quality of traditional fermented foods. Compr Rev Food Sci Food Saf 2024; 23:e13388. [PMID: 38865218 DOI: 10.1111/1541-4337.13388] [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: 02/21/2024] [Revised: 04/27/2024] [Accepted: 05/19/2024] [Indexed: 06/14/2024]
Abstract
Consumers are attracted to traditional fermented foods due to their unique flavor and nutritional value. However, the traditional fermentation technique can no longer accommodate the requirements of the food industry. Traditional fermented foods produce hazardous compounds, off-odor, and anti-nutritional factors, reducing product stability. The microbial system complexity of traditional fermented foods resulting from the open fermentation process has made it challenging to regulate these problems by modifying microbial behaviors. Synthetic microbial communities (SynComs) have been shown to simplify complex microbial communities and allow for the targeted design of microbial communities, which has been applied in processing traditional fermented foods. Herein, we describe the theoretical information of SynComs, particularly microbial physiological processes and their interactions. This paper discusses current approaches to creating SynComs, including designing, building, testing, and learning, with typical applications and fundamental techniques. Based on various traditional fermented food innovation demands, the potential and application of SynComs in enhancing the quality of traditional fermented foods are highlighted. SynComs showed superior performance in regulating the quality of traditional fermented foods using the interaction of core microorganisms to reduce the hazardous compounds of traditional fermented foods and improve flavor. Additionally, we presented the current status and future perspectives of SynComs for improving the quality of traditional fermented foods.
Collapse
Affiliation(s)
- Ritian Jin
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Jimei University, Xiamen, China
| | - Jing Song
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Jimei University, Xiamen, China
| | - Chang Liu
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Jimei University, Xiamen, China
| | - Rong Lin
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Jimei University, Xiamen, China
| | - Duo Liang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Jimei University, Xiamen, China
| | - Jude Juventus Aweya
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Jimei University, Xiamen, China
| | - Wuyin Weng
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, China
| | - Longji Zhu
- Institute of Urban Environment, Chinese Academy of Science, Xiamen, China
| | - Jiaqi Shang
- Key Laboratory of Bionic Engineering, College of Biological and Agricultural Engineering, Jilin University, Changchun, China
| | - Shen Yang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Jimei University, Xiamen, China
| |
Collapse
|
9
|
Jones EM, Marken JP, Silver PA. Synthetic microbiology in sustainability applications. Nat Rev Microbiol 2024; 22:345-359. [PMID: 38253793 DOI: 10.1038/s41579-023-01007-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2023] [Indexed: 01/24/2024]
Abstract
Microorganisms are a promising means to address many societal sustainability challenges owing to their ability to thrive in diverse environments and interface with the microscale chemical world via diverse metabolic capacities. Synthetic biology can engineer microorganisms by rewiring their regulatory networks or introducing new functionalities, enhancing their utility for target applications. In this Review, we provide a broad, high-level overview of various research efforts addressing sustainability challenges through synthetic biology, emphasizing foundational microbiological research questions that can accelerate the development of these efforts. We introduce an organizational framework that categorizes these efforts along three domains - factory, farm and field - that are defined by the extent to which the engineered microorganisms interface with the natural external environment. Different application areas within the same domain share many fundamental challenges, highlighting productive opportunities for cross-disciplinary collaborations between researchers working in historically disparate fields.
Collapse
Affiliation(s)
- Ethan M Jones
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - John P Marken
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Resnick Sustainability Institute, California Institute of Technology, Pasadena, CA, USA
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
| |
Collapse
|
10
|
Dixon RA, Dickinson AJ. A century of studying plant secondary metabolism-From "what?" to "where, how, and why?". PLANT PHYSIOLOGY 2024; 195:48-66. [PMID: 38163637 PMCID: PMC11060662 DOI: 10.1093/plphys/kiad596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/15/2023] [Indexed: 01/03/2024]
Abstract
Over the past century, early advances in understanding the identity of the chemicals that collectively form a living plant have led scientists to deeper investigations exploring where these molecules localize, how they are made, and why they are synthesized in the first place. Many small molecules are specific to the plant kingdom and have been termed plant secondary metabolites, despite the fact that they can play primary and essential roles in plant structure, development, and response to the environment. The past 100 yr have witnessed elucidation of the structure, function, localization, and biosynthesis of selected plant secondary metabolites. Nevertheless, many mysteries remain about the vast diversity of chemicals produced by plants and their roles in plant biology. From early work characterizing unpurified plant extracts, to modern integration of 'omics technology to discover genes in metabolite biosynthesis and perception, research in plant (bio)chemistry has produced knowledge with substantial benefits for society, including human medicine and agricultural biotechnology. Here, we review the history of this work and offer suggestions for future areas of exploration. We also highlight some of the recently developed technologies that are leading to ongoing research advances.
Collapse
Affiliation(s)
- Richard A Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA
| | - Alexandra Jazz Dickinson
- Department of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA 92093, USA
| |
Collapse
|
11
|
Joshi J, Hanson AD. A pilot oral history of plant synthetic biology. PLANT PHYSIOLOGY 2024; 195:36-47. [PMID: 38163646 PMCID: PMC11060686 DOI: 10.1093/plphys/kiad585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/15/2023] [Indexed: 01/03/2024]
Abstract
The whole field of synthetic biology (SynBio) is only about 20 years old, and plant SynBio is younger still. Nevertheless, within that short time, SynBio in general has drawn more scientific, philosophical, government, and private-sector interest than anything in biology since the recombinant DNA revolution. Plant SynBio, in particular, is now drawing more and more interest in relation to plants' potential to help solve planetary problems such as carbon capture and storage and replacing fossil fuels and feedstocks. As plant SynBio is so young and so fast-developing, we felt it was too soon to try to analyze its history. Instead, we set out to capture the essence of plant SynBio's origins and early development through interviews with 8 of the field's founders, representing 5 countries and 3 continents. We then distilled these founders' personal recollections and reflections into this review, centering the narrative on timelines for pivotal events, articles, funding programs, and quoting from interviews. We have archived the interview recordings and documented timeline entries. This work provides a resource for future historical scholarship.
Collapse
Affiliation(s)
- Jaya Joshi
- Department of Wood Science, University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, 2550 Hull Road, Gainesville, FL 32611, USA
| |
Collapse
|
12
|
Gonzales M, Jacquet P, Gaucher F, Chabrière É, Plener L, Daudé D. AHL-Based Quorum Sensing Regulates the Biosynthesis of a Variety of Bioactive Molecules in Bacteria. JOURNAL OF NATURAL PRODUCTS 2024; 87:1268-1284. [PMID: 38390739 DOI: 10.1021/acs.jnatprod.3c00672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Bacteria are social microorganisms that use communication systems known as quorum sensing (QS) to regulate diverse cellular behaviors including the production of various secreted molecules. Bacterial secondary metabolites are widely studied for their bioactivities including antibiotic, antifungal, antiparasitic, and cytotoxic compounds. Besides playing a crucial role in natural bacterial niches and intermicrobial competition by targeting neighboring organisms and conferring survival advantages to the producer, these bioactive molecules may be of prime interest to develop new antimicrobials or anticancer therapies. This review focuses on bioactive compounds produced under acyl homoserine lactone-based QS regulation by Gram-negative bacteria that are pathogenic to humans and animals, including the Burkholderia, Serratia, Pseudomonas, Chromobacterium, and Pseudoalteromonas genera. The synthesis, regulation, chemical nature, biocidal effects, and potential applications of these identified toxic molecules are presented and discussed in light of their role in microbial interactions.
Collapse
Affiliation(s)
- Mélanie Gonzales
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille 13288, France
- Gene&GreenTK, Marseille 13005, France
| | | | | | - Éric Chabrière
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille 13288, France
| | | | | |
Collapse
|
13
|
Hamrick GS, Maddamsetti R, Son HI, Wilson ML, Davis HM, You L. Programming Dynamic Division of Labor Using Horizontal Gene Transfer. ACS Synth Biol 2024; 13:1142-1151. [PMID: 38568420 DOI: 10.1021/acssynbio.3c00615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
The metabolic engineering of microbes has broad applications, including biomanufacturing, bioprocessing, and environmental remediation. The introduction of a complex, multistep pathway often imposes a substantial metabolic burden on the host cell, restraining the accumulation of productive biomass and limiting pathway efficiency. One strategy to alleviate metabolic burden is the division of labor (DOL) in which different subpopulations carry out different parts of the pathway and work together to convert a substrate into a final product. However, the maintenance of different engineered subpopulations is challenging due to competition and convoluted interstrain population dynamics. Through modeling, we show that dynamic division of labor (DDOL), which we define as the DOL between indiscrete populations capable of dynamic and reversible interchange, can overcome these limitations and enable the robust maintenance of burdensome, multistep pathways. We propose that DDOL can be mediated by horizontal gene transfer (HGT) and use plasmid genomics to uncover evidence that DDOL is a strategy utilized by natural microbial communities. Our work suggests that bioengineers can harness HGT to stabilize synthetic metabolic pathways in microbial communities, enabling the development of robust engineered systems for deployment in a variety of contexts.
Collapse
Affiliation(s)
- Grayson S Hamrick
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
- Center for Quantitative Biodesign, Duke University, Durham, North Carolina 27708, United States
- Center for Biomolecular and Tissue Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Rohan Maddamsetti
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
- Center for Quantitative Biodesign, Duke University, Durham, North Carolina 27708, United States
| | - Hye-In Son
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
- Center for Quantitative Biodesign, Duke University, Durham, North Carolina 27708, United States
| | - Maggie L Wilson
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
- Center for Quantitative Biodesign, Duke University, Durham, North Carolina 27708, United States
| | - Harris M Davis
- Center for Quantitative Biodesign, Duke University, Durham, North Carolina 27708, United States
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
- Center for Quantitative Biodesign, Duke University, Durham, North Carolina 27708, United States
- Center for Biomolecular and Tissue Engineering, Duke University, Durham, North Carolina 27708, United States
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina 27708, United States
| |
Collapse
|
14
|
Amenta ML, Vaccaro F, Varriale S, Sangaré JR, Defez R, Mengoni A, Bianco C. Cereals can trap endophytic bacteria with potential beneficial traits when grown ex-situ in harsh soils. FEMS Microbiol Ecol 2024; 100:fiae041. [PMID: 38544316 PMCID: PMC11009874 DOI: 10.1093/femsec/fiae041] [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: 08/18/2023] [Revised: 03/01/2024] [Accepted: 03/26/2024] [Indexed: 04/13/2024] Open
Abstract
Microbial communities associated with plants growing in harsh conditions, including salinity and water deficiency, have developed adaptive features which permit them to grow and survive under extreme environmental conditions. In the present study, an ex-situ plant trapping method has been applied to collect the culturable microbial diversity associated with the soil from harsh and remote areas. Oryza sativa cv. Baldo and Triticum durum Primadur plants were used as recruiters, while the soil surrounding the roots of Oryza glaberrima plants from remote regions of Mali (West Africa) was used as substrate for their growth. The endophytic communities recruited by the two plant species belonged to Proteobacteria and Firmicutes, and the dominant genera were Bacillus, Kosakonia, and Enterobacter. These endophytes were characterized by analyzing some of the most common plant growth promoting traits. Halotolerant, inorganic phosphate-solubilizing and N-fixing strains were found, and some of them simultaneously showing these three traits. We verified that 'Baldo' recruited mostly halotolerant and P-solubilizers endophytes, while the endophytes selected by 'Primadur' were mainly N-fixers. The applied ex-situ plant trapping method allowed to isolate endophytes with potential beneficial traits that could be applied for the improvement of rice and wheat growth under adverse environmental conditions.
Collapse
Affiliation(s)
- Maria Laura Amenta
- National Research Council, Institute of Biosciences and BioResources, via P. Castellino 111, 80131 Naples, Italy
| | - Francesca Vaccaro
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Stefano Varriale
- National Research Council,
Institute of Biosciences and BioResources, via P. Castellino 111, 80131 Naples, Italy
| | - Jean Rodrigue Sangaré
- Institut d'Economie Rurale (IER), Centre Régional de Recherche Agronomique (CRRA) de Sikasso, B.P: 16, Mali
| | - Roberto Defez
- National Research Council, Institute of Biosciences and BioResources, via P. Castellino 111, 80131 Naples, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Carmen Bianco
- National Research Council, Institute of Biosciences and BioResources, via P. Castellino 111, 80131 Naples, Italy
| |
Collapse
|
15
|
Batool M, Carvalhais LC, Fu B, Schenk PM. Customized plant microbiome engineering for food security. TRENDS IN PLANT SCIENCE 2024; 29:482-494. [PMID: 37977879 DOI: 10.1016/j.tplants.2023.10.012] [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: 05/10/2022] [Revised: 10/15/2023] [Accepted: 10/18/2023] [Indexed: 11/19/2023]
Abstract
Plant microbiomes play a vital role in promoting plant growth and resilience to cope with environmental stresses. Plant microbiome engineering holds significant promise to increase crop yields, but there is uncertainty about how this can best be achieved. We propose a step-by-step approach involving customized direct and indirect methods to condition soils and to match plants and microbiomes. Although three approaches, namely the development of (i) 'plant- and microbe-friendly' soils, (ii) 'microbe-friendly' plants, and (iii) 'plant-friendly' microbiomes, have been successfully tested in isolation, we propose that the combination of all three may lead to a step-change towards higher and more stable crop yields. This review aims to provide knowledge, future directions, and practical guidance to achieve this goal via customized plant microbiome engineering.
Collapse
Affiliation(s)
- Maria Batool
- Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Lilia C Carvalhais
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Brendan Fu
- Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Peer M Schenk
- Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, QLD, 4072, Australia; Sustainable Solutions Hub, Global Sustainable Solutions Pty Ltd, Brisbane, QLD 4105, Australia.
| |
Collapse
|
16
|
Law SR, Mathes F, Paten AM, Alexandre PA, Regmi R, Reid C, Safarchi A, Shaktivesh S, Wang Y, Wilson A, Rice SA, Gupta VVSR. Life at the borderlands: microbiomes of interfaces critical to One Health. FEMS Microbiol Rev 2024; 48:fuae008. [PMID: 38425054 PMCID: PMC10977922 DOI: 10.1093/femsre/fuae008] [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: 07/26/2023] [Revised: 02/12/2024] [Accepted: 02/27/2024] [Indexed: 03/02/2024] Open
Abstract
Microbiomes are foundational components of the environment that provide essential services relating to food security, carbon sequestration, human health, and the overall well-being of ecosystems. Microbiota exert their effects primarily through complex interactions at interfaces with their plant, animal, and human hosts, as well as within the soil environment. This review aims to explore the ecological, evolutionary, and molecular processes governing the establishment and function of microbiome-host relationships, specifically at interfaces critical to One Health-a transdisciplinary framework that recognizes that the health outcomes of people, animals, plants, and the environment are tightly interconnected. Within the context of One Health, the core principles underpinning microbiome assembly will be discussed in detail, including biofilm formation, microbial recruitment strategies, mechanisms of microbial attachment, community succession, and the effect these processes have on host function and health. Finally, this review will catalogue recent advances in microbiology and microbial ecology methods that can be used to profile microbial interfaces, with particular attention to multi-omic, advanced imaging, and modelling approaches. These technologies are essential for delineating the general and specific principles governing microbiome assembly and functions, mapping microbial interconnectivity across varying spatial and temporal scales, and for the establishment of predictive frameworks that will guide the development of targeted microbiome-interventions to deliver One Health outcomes.
Collapse
Affiliation(s)
- Simon R Law
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
| | - Falko Mathes
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Environment, Floreat, WA 6014, Australia
| | - Amy M Paten
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Environment, Canberra, ACT 2601, Australia
| | - Pamela A Alexandre
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, St Lucia, Qld 4072, Australia
| | - Roshan Regmi
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, Urrbrae, SA 5064, Australia
| | - Cameron Reid
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Environment, Urrbrae, SA 5064, Australia
| | - Azadeh Safarchi
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Health and Biosecurity, Westmead, NSW 2145, Australia
| | - Shaktivesh Shaktivesh
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Data 61, Clayton, Vic 3168, Australia
| | - Yanan Wang
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Health and Biosecurity, Adelaide SA 5000, Australia
| | - Annaleise Wilson
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Health and Biosecurity, Geelong, Vic 3220, Australia
| | - Scott A Rice
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture, and Food, Westmead, NSW 2145, Australia
| | - Vadakattu V S R Gupta
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, Urrbrae, SA 5064, Australia
| |
Collapse
|
17
|
Clark G, Tripathy MK, Roux SJ. Growth regulation by apyrases: Insights from altering their expression level in different organisms. PLANT PHYSIOLOGY 2024; 194:1323-1335. [PMID: 37947023 PMCID: PMC10904326 DOI: 10.1093/plphys/kiad590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 11/12/2023]
Abstract
Apyrase (APY) enzymes are nucleoside triphosphate (NTP) diphosphohydrolases that can remove the terminal phosphate from NTPs and nucleoside diphosphates but not from nucleoside monophosphates. They have conserved structures and functions in yeast, plants, and animals. Among the most studied APYs in plants are those in Arabidopsis (Arabidopsis thaliana; AtAPYs) and pea (Pisum sativum; PsAPYs), both of which have been shown to play major roles in regulating plant growth and development. Valuable insights on their functional roles have been gained by transgenically altering their transcript abundance, either by constitutively expressing or suppressing APY genes. This review focuses on recent studies that have provided insights on the mechanisms by which APY activity promotes growth in different organisms. Most of these studies have used transgenic lines that constitutively expressed APY in multiple different plants and in yeast. As APY enzymatic activity can also be changed post-translationally by chemical blockage, this review also briefly covers studies that used inhibitors to suppress APY activity in plants and fungi. It concludes by summarizing some of the main unanswered questions about how APYs regulate plant growth and proposes approaches to answering them.
Collapse
Affiliation(s)
- Greg Clark
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, 100 E 24th Street, TX 78712, USA
| | | | - Stanley J Roux
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, 100 E 24th Street, TX 78712, USA
| |
Collapse
|
18
|
Kimotho RN, Maina S. Unraveling plant-microbe interactions: can integrated omics approaches offer concrete answers? JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1289-1313. [PMID: 37950741 PMCID: PMC10901211 DOI: 10.1093/jxb/erad448] [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: 05/26/2023] [Accepted: 11/08/2023] [Indexed: 11/13/2023]
Abstract
Advances in high throughput omics techniques provide avenues to decipher plant microbiomes. However, there is limited information on how integrated informatics can help provide deeper insights into plant-microbe interactions in a concerted way. Integrating multi-omics datasets can transform our understanding of the plant microbiome from unspecified genetic influences on interacting species to specific gene-by-gene interactions. Here, we highlight recent progress and emerging strategies in crop microbiome omics research and review key aspects of how the integration of host and microbial omics-based datasets can be used to provide a comprehensive outline of complex crop-microbe interactions. We describe how these technological advances have helped unravel crucial plant and microbial genes and pathways that control beneficial, pathogenic, and commensal plant-microbe interactions. We identify crucial knowledge gaps and synthesize current limitations in our understanding of crop microbiome omics approaches. We highlight recent studies in which multi-omics-based approaches have led to improved models of crop microbial community structure and function. Finally, we recommend holistic approaches in integrating host and microbial omics datasets to achieve precision and efficiency in data analysis, which is crucial for biotic and abiotic stress control and in understanding the contribution of the microbiota in shaping plant fitness.
Collapse
Affiliation(s)
- Roy Njoroge Kimotho
- Hebei Key Laboratory of Soil Ecology, Key Laboratory of Agricultural Water Resources, Centre for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Solomon Maina
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, New South Wales 2568, Australia
| |
Collapse
|
19
|
Solanki MK, Joshi NC, Singh PK, Singh SK, Santoyo G, Basilio de Azevedo LC, Kumar A. From concept to reality: Transforming agriculture through innovative rhizosphere engineering for plant health and productivity. Microbiol Res 2024; 279:127553. [PMID: 38007891 DOI: 10.1016/j.micres.2023.127553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/14/2023] [Accepted: 11/19/2023] [Indexed: 11/28/2023]
Abstract
The plant rhizosphere is regarded as a microbial hotspot due to a wide array of root exudates. These root exudates comprise diverse organic compounds such as phenolic, polysaccharides, flavonoids, fatty acids, and amino acids that showed chemotactic responses towards microbial communities and mediate significant roles in root colonization. The rhizospheric microbiome is a crucial driver of plant growth and productivity, contributing directly or indirectly by facilitating nutrient acquisition, phytohormone modulation, and phosphate solubilization under normal and stressful conditions. Moreover, these microbial candidates protect plants from pathogen invasion by secreting antimicrobial and volatile organic compounds. To enhance plant fitness and yield, rhizospheric microbes are frequently employed as microbial inoculants. However, recent developments have shifted towards targeted rhizosphere engineering or microbial recruitments as a practical approach to constructing desired plant rhizospheres for specific outcomes. The rhizosphere, composed of plants, microbes, and soil, can be modified in several ways to improve inoculant efficiency. Rhizosphere engineering is achieved through three essential mechanisms: a) plant-mediated modifications involving genetic engineering, transgenics, and gene editing of plants; b) microbe-mediated modifications involving genetic alterations of microbes through upstream or downstream methodologies; and c) soil amendments. These mechanisms shape the rhizospheric microbiome, making plants more productive and resilient under different stress conditions. This review paper comprehensively summarizes the various aspects of rhizosphere engineering and their potential applications in maintaining plant health and achieving optimum agricultural productivity.
Collapse
Affiliation(s)
- Manoj Kumar Solanki
- Department of Life Sciences and Biological Sciences, IES University, Bhopal, Madhya Pradesh, India; Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-032 Katowice, Poland
| | - Naveen Chandra Joshi
- Amity Institute of Microbial Technology, Amity University, Noida, Uttar Pradesh, 201313, India
| | - Prashant Kumar Singh
- Department of Biotechnology, Pachhunga University College Campus, Mizoram University (A Central University), Aizawl 796001, India
| | - Sandeep Kumar Singh
- Department of Microbiology, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58030, Mexico
| | - Lucas Carvalho Basilio de Azevedo
- Instituto de Ciências Agrárias, Campus Glória-Bloco CCG, Universidade Federal de Uberlândia, RodoviaBR-050, KM 78, S/N, Uberlândia CEP 38410-337, Brazil
| | - Ajay Kumar
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, 201313, India.
| |
Collapse
|
20
|
Wu J, Chen Y, Huang Y, Hao B, Dai S, Zhao L, Zhao Z, Zhao C, Zhang L, Li Y, Xu X, Li N, Huang AC, Zhou J, Tan M, Zhu W, Zhao Q. The cytosolic aminotransferase VAS1 coordinates aromatic amino acid biosynthesis and metabolism. SCIENCE ADVANCES 2024; 10:eadk0738. [PMID: 38198548 PMCID: PMC10780875 DOI: 10.1126/sciadv.adk0738] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024]
Abstract
The aromatic amino acids (AAAs) phenylalanine, tyrosine, and tryptophan are basic protein units and precursors of diverse specialized metabolites that are essential for plant growth. Despite their significance, the mechanisms that regulate AAA homeostasis remain elusive. Here, we identified a cytosolic aromatic aminotransferase, REVERSAL OF SAV3 PHENOTYPE 1 (VAS1), as a suppressor of arogenate dehydrogenase 2 (adh2) in Arabidopsis (Arabidopsis thaliana). Genetic and biochemical analyses determined that VAS1 uses AAAs as amino donors, leading to the formation of 3-carboxyphenylalanine and 3-carboxytyrosine. These pathways represent distinct routes for AAA metabolism that are unique to specific plant species. Furthermore, we show that VAS1 is responsible for cytosolic AAA biosynthesis, and its enzymatic activity can be inhibited by 3-carboxyphenylalanine. These findings provide valuable insights into the crucial role of VAS1 in producing 3-carboxy AAAs, notably via recycling of AAAs in the cytosol, which maintains AAA homeostasis and allows plants to effectively coordinate the complex metabolic and biosynthetic pathways of AAAs.
Collapse
Affiliation(s)
- Jie Wu
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yanhong Chen
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yuxin Huang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bingbing Hao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Shengkun Dai
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Lingling Zhao
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Zhehui Zhao
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Department of Medicinal Chemistry, Institute of Materia Medica, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Cuihuan Zhao
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Limin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yunhai Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuexia Xu
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Nan Li
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Ancheng C. Huang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, SUSTech-PKU Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jiahai Zhou
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Wentao Zhu
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Qiao Zhao
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| |
Collapse
|
21
|
Zhu Z. Early-life airway microbiome and childhood asthma development. Eur Respir J 2024; 63:2302187. [PMID: 38238000 DOI: 10.1183/13993003.02187-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 12/17/2023] [Indexed: 01/23/2024]
Affiliation(s)
- Zhaozhong Zhu
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
22
|
Hayashi I, Fujita H, Toju H. Deterministic and stochastic processes generating alternative states of microbiomes. ISME COMMUNICATIONS 2024; 4:ycae007. [PMID: 38415200 PMCID: PMC10897905 DOI: 10.1093/ismeco/ycae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 01/14/2024] [Accepted: 01/19/2024] [Indexed: 02/29/2024]
Abstract
The structure of microbiomes is often classified into discrete or semi-discrete types potentially differing in community-scale functional profiles. Elucidating the mechanisms that generate such "alternative states" of microbiome compositions has been one of the major challenges in ecology and microbiology. In a time-series analysis of experimental microbiomes, we here show that both deterministic and stochastic ecological processes drive divergence of alternative microbiome states. We introduced species-rich soil-derived microbiomes into eight types of culture media with 48 replicates, monitoring shifts in community compositions at six time points (8 media × 48 replicates × 6 time points = 2304 community samples). We then confirmed that microbial community structure diverged into a few state types in each of the eight medium conditions as predicted in the presence of both deterministic and stochastic community processes. In other words, microbiome structure was differentiated into a small number of reproducible compositions under the same environment. This fact indicates not only the presence of selective forces leading to specific equilibria of community-scale resource use but also the influence of demographic drift (fluctuations) on the microbiome assembly. A reference-genome-based analysis further suggested that the observed alternative states differed in ecosystem-level functions. These findings will help us examine how microbiome structure and functions can be controlled by changing the "stability landscapes" of ecological community compositions.
Collapse
Affiliation(s)
- Ibuki Hayashi
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2133, Japan
| | - Hiroaki Fujita
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2133, Japan
| | - Hirokazu Toju
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2133, Japan
- Center for Living Systems Information Science (CeLiSIS), Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
- Laboratory of Ecosystems and Coevolution, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| |
Collapse
|
23
|
Hawkes CV, Allen X, Balint-Kurti P, Cowger C. Manipulating the plant mycobiome to enhance resilience: Ecological and evolutionary opportunities and challenges. PLoS Pathog 2023; 19:e1011816. [PMID: 38096141 PMCID: PMC10721032 DOI: 10.1371/journal.ppat.1011816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023] Open
Affiliation(s)
- Christine V. Hawkes
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Xavious Allen
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Peter Balint-Kurti
- Plant Science Research Unit, USDA-ARS, Raleigh, North Carolina, United States of America
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Christina Cowger
- Plant Science Research Unit, USDA-ARS, Raleigh, North Carolina, United States of America
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, United States of America
| |
Collapse
|
24
|
Chen J, Cai Y, Wang Z, Xu Z, Li J, Ma X, Zhuang W, Liu D, Wang S, Song A, Xu J, Ying H. Construction of a synthetic microbial community based on multiomics linkage technology and analysis of the mechanism of lignocellulose degradation. BIORESOURCE TECHNOLOGY 2023; 389:129799. [PMID: 37774801 DOI: 10.1016/j.biortech.2023.129799] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/22/2023] [Accepted: 09/22/2023] [Indexed: 10/01/2023]
Abstract
The efficient degradation of lignocellulose is a bottleneck for its integrated utilization. This research performed species analysis and made functional predictions in various ecosystems using multiomics coupling to construct a core synthetic microbial community with efficient lignocellulose degradation function. The synthetic microbial community was employed to degrade corn straw via solid-state fermentation. The degradation mechanisms were resolved using proteomics. The optimum culture conditions included 10% inoculum level (w/v), 4% nitrogen source ratio and a fermentation time of 23 d. Under these conditions, the degradation rates of cellulose, hemicellulose, and lignin were 34.91%, 45.94%, and 23.34%, respectively. Proteomic analysis revealed that lignin 1,4-β-xylanase, β-xylosidase and endo-1,4-β-xylanase were closely related to lignocellulose degradation. The metabolic pathways involved in lignocellulose degradation and the functional roles of eight strains were obtained. The synthesis of a microbial community via multiomics linkage technology can effectively decompose lignocellulose, which is useful for their further utilization.
Collapse
Affiliation(s)
- Jinmeng Chen
- School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, Zhengzhou 450001, China
| | - Yafan Cai
- School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, Zhengzhou 450001, China
| | - Zhi Wang
- School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, Zhengzhou 450001, China
| | - Zhengzhong Xu
- School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, Zhengzhou 450001, China
| | - Jia Li
- School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, Zhengzhou 450001, China
| | - Xiaotian Ma
- School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, Zhengzhou 450001, China
| | - Wei Zhuang
- School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, Zhengzhou 450001, China; National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 210009, China
| | - Dong Liu
- School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, Zhengzhou 450001, China; National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 210009, China
| | - Shilei Wang
- School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, Zhengzhou 450001, China.
| | - Andong Song
- College of Life Science, Henan Agricultural University, 218 Ping An Avenue, Zhengdong New District, Zhengzhou 450002, China
| | - Jingliang Xu
- School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, Zhengzhou 450001, China
| | - Hanjie Ying
- School of Chemical Engineering, Zhengzhou University, 100 Ke xue Dadao, Zhengzhou 450001, China; National Engineering Technique Research Center for Biotechnology, State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 210009, China
| |
Collapse
|
25
|
Singh P, Vaishnav A, Liu H, Xiong C, Singh HB, Singh BK. Seed biopriming for sustainable agriculture and ecosystem restoration. Microb Biotechnol 2023; 16:2212-2222. [PMID: 37490280 PMCID: PMC10686123 DOI: 10.1111/1751-7915.14322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 07/26/2023] Open
Abstract
The utilization of microbial inoculants in the realm of sustainable agricultural and ecosystem restoration has witnessed a surge in recent decades. This rise is largely attributed to advancements in our understanding of plant-microbe interactions, the urgency to reduce the dependence on agrochemicals and the growing societal demand for sustainable strategies in ecosystem management. However, despite the rapid growth of bio-inoculants sector, certain limitations persist concerning their efficacy and performance under the field condition. Here, we propose that seed biopriming, an effective microbial inoculant technique integrating both biological agents (the priming of beneficial microbes on seeds) and physiological aspects (hydration of seeds for improved metabolically activity), has a significant potential to mitigate these limitations. This method increases the protection of seeds against soil-borne pathogens and soil pollutants, such as salts and heavy metals, while promoting germination rate and uniformity, leading to overall improved primary productivity and soil health. Furthermore, we argue that a microbial coating on seeds can facilitate transgenerational associations of beneficial microbes, refine plant and soil microbiomes, and maintain soil legacies of beneficial microflora. This review article aims to improve our understanding of the seed biopriming approach as a potent and valuable tool in achieving sustainable agriculture and successful ecosystem restoration.
Collapse
Affiliation(s)
- Prachi Singh
- Rabindranath Tagore Agriculture College, DeogharBirsa Agriculture UniversityRanchiJharkhandIndia
| | - Anukool Vaishnav
- Department of BiotechnologyGLA UniversityMathuraUttar PradeshIndia
| | - Hongwei Liu
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNew South WalesAustralia
| | - Chao Xiong
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNew South WalesAustralia
| | | | - Brajesh K. Singh
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNew South WalesAustralia
- Global Centre for Land‐Based InnovationWestern Sydney UniversityPenrithNew South WalesAustralia
| |
Collapse
|
26
|
Wu D, Wang W, Yao Y, Li H, Wang Q, Niu B. Microbial interactions within beneficial consortia promote soil health. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 900:165801. [PMID: 37499809 DOI: 10.1016/j.scitotenv.2023.165801] [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: 01/31/2022] [Revised: 04/26/2023] [Accepted: 07/24/2023] [Indexed: 07/29/2023]
Abstract
By ecologically interacting with various biotic and abiotic agents acting in soil ecosystems, highly diverse soil microorganisms establish complex and stable assemblages and survive in a community context in natural settings. Besides facilitating soil microbiome to maintain great levels of population homeostasis, such microbial interactions drive soil microbes to function as the major engine of terrestrial biogeochemical cycling. It is verified that the regulative effect of microbe-microbe interplay plays an instrumental role in microbial-mediated promotion of soil health, including bioremediation of soil pollutants and biocontrol of soil-borne phytopathogens, which is considered an environmentally friendly strategy for ensuring the healthy condition of soils. Specifically, in microbial consortia, it has been proven that microorganism-microorganism interactions are involved in enhancing the soil health-promoting effectiveness (i.e., efficacies of pollution reduction and disease inhibition) of the beneficial microbes, here defined as soil health-promoting agents. These microbial interactions can positively regulate the soil health-enhancing effect by supporting those soil health-promoting agents utilized in combination, as multi-strain soil health-promoting agents, to overcome three main obstacles: inadequate soil colonization, insufficient soil contaminant eradication and inefficient soil-borne pathogen suppression, all of which can restrict their probiotic functionality. Yet the mechanisms underlying such beneficial interaction-related adjustments and how to efficiently assemble soil health-enhancing consortia with the guidance of microbe-microbe communications remain incompletely understood. In this review, we focus on bacterial and fungal soil health-promoting agents to summarize current research progress on the utilization of multi-strain soil health-promoting agents in the control of soil pollution and soil-borne plant diseases. We discuss potential microbial interaction-relevant mechanisms deployed by the probiotic microorganisms to upgrade their functions in managing soil health. We emphasize the interplay-related factors that should be taken into account when building soil health-promoting consortia, and propose a workflow for assembling them by employing a reductionist synthetic community approach.
Collapse
Affiliation(s)
- Di Wu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; The Center for Basic Forestry Research, Northeast Forestry University, Harbin 150040, China; College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Weixiong Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; The Center for Basic Forestry Research, Northeast Forestry University, Harbin 150040, China; College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yanpo Yao
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Hongtao Li
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
| | - Qi Wang
- Department of Plant Pathology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
| | - Ben Niu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; The Center for Basic Forestry Research, Northeast Forestry University, Harbin 150040, China; College of Life Science, Northeast Forestry University, Harbin 150040, China.
| |
Collapse
|
27
|
Kumari P, Deepa N, Trivedi PK, Singh BK, Srivastava V, Singh A. Plants and endophytes interaction: a "secret wedlock" for sustainable biosynthesis of pharmaceutically important secondary metabolites. Microb Cell Fact 2023; 22:226. [PMID: 37925404 PMCID: PMC10625306 DOI: 10.1186/s12934-023-02234-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 10/19/2023] [Indexed: 11/06/2023] Open
Abstract
Many plants possess immense pharmacological properties because of the presence of various therapeutic bioactive secondary metabolites that are of great importance in many pharmaceutical industries. Therefore, to strike a balance between meeting industry demands and conserving natural habitats, medicinal plants are being cultivated on a large scale. However, to enhance the yield and simultaneously manage the various pest infestations, agrochemicals are being routinely used that have a detrimental impact on the whole ecosystem, ranging from biodiversity loss to water pollution, soil degradation, nutrient imbalance and enormous health hazards to both consumers and agricultural workers. To address the challenges, biological eco-friendly alternatives are being looked upon with high hopes where endophytes pitch in as key players due to their tight association with the host plants. The intricate interplay between plants and endophytic microorganisms has emerged as a captivating subject of scientific investigation, with profound implications for the sustainable biosynthesis of pharmaceutically important secondary metabolites. This review delves into the hidden world of the "secret wedlock" between plants and endophytes, elucidating their multifaceted interactions that underpin the synthesis of bioactive compounds with medicinal significance in their plant hosts. Here, we briefly review endophytic diversity association with medicinal plants and highlight the potential role of core endomicrobiome. We also propose that successful implementation of in situ microbiome manipulation through high-end techniques can pave the way towards a more sustainable and pharmaceutically enriched future.
Collapse
Affiliation(s)
- Poonam Kumari
- Division of Crop Production and Protection, Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
| | - Nikky Deepa
- Division of Crop Production and Protection, Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Prabodh Kumar Trivedi
- Division of Plant Biotechnology, Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2753, Australia
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Vaibhav Srivastava
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, 106 91, Stockholm, Sweden.
| | - Akanksha Singh
- Division of Crop Production and Protection, Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
| |
Collapse
|
28
|
Ekta, Biswas D, Mukherjee G, Maiti MK. Rice Big Grain1 enhances biomass and plant growth-promoting traits in rhizospheric yeast Candida tropicalis. Appl Microbiol Biotechnol 2023; 107:6553-6571. [PMID: 37688595 DOI: 10.1007/s00253-023-12740-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 09/11/2023]
Abstract
The Big Grain1 (BG1) gene of rice (Oryza sativa L.) is reported to increase the yield of rice crops; however, its molecular mechanism is largely concealed. To explore its functional prospects, we have taken a structure-function-based approach. In silico analyses suggest OsBG1 is a DNA- and phytohormone-binding protein. Heterologous expression of OsBG1 with galactose-inducible promoter GAL1p in the rhizospheric yeast Candida tropicalis SY005 revealed 7.9- and 1.5-fold higher expression of the gene at 12 and 24 h, respectively, compared to the expression at 36 h post-galactose induction. Functional activity of the induced OsBG1 in engineered yeast increased cell density, specific growth rate, and biomass by 28.5%, 29.8%, and 14.1%, respectively, and decreased the generation time by 21.25%. Flow cytometry-based cell cycle analysis of OsBG1-expressing yeast cells exhibited an increase in the cells of the G2/M population by 15.8% after 12 h of post-galactose induction. The gene expression study of yeast transformants disclosed that OsBG1 regulates cell division by upregulating the expression of the endogenous gene cyclin B1 (CtCYB1) by 1.3- and 1.9-folds at 10 and 12 h, respectively, compared to the control, and is positively influenced by the phytohormone indole acetic acid (IAA). Further, the study revealed that OsBG1 significantly increases biofilm formation, stress tolerance, and IAA production in C. tropicalis SY005, implying its prospective role in enhancing plant growth-promoting traits in microbes. OsBG1-expressing rhizospheric yeast cells significantly improved the germination and growth parameters of the bio-inoculated rice seeds. Altogether, this study suggests OsBG1 can be employed to genetically improve suitable bio-inoculants for their plant growth-promoting traits to augment crop productivity. KEY POINTS: • In silico analyses suggested OsBG1 is a phytohormone-binding transcription factor. • OsBG1 enhanced growth in rhizospheric Candida tropicalis by upregulating CtCYB1. • OsBG1 improved plant growth-promoting traits of the rhizospheric yeast C. tropicalis.
Collapse
Affiliation(s)
- Ekta
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Debarati Biswas
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Gayatri Mukherjee
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Mrinal K Maiti
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India.
| |
Collapse
|
29
|
Solaz-Rodenas L, Penyalver R. r CitrusBBC: a bacterial resource to mine for new agricultural probiotics for citrus. Microbiol Resour Announc 2023; 12:e0040823. [PMID: 37772858 PMCID: PMC10586165 DOI: 10.1128/mra.00408-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/15/2023] [Indexed: 09/30/2023] Open
Abstract
A culture collection of 147 selected bacteria from the rhizospheric citrus microbiome is available at the Valencian Institute of Agricultural Research (València, Spain). The data include information on plant growth-promoting (PGP) traits published to date and the presence of PGP-related genes in the available genomes of the different bacterial species.
Collapse
Affiliation(s)
- Lucía Solaz-Rodenas
- Centre for Plant Protection and Biotechnology of the Valencian Institute of Agricultural Research (IVIA), Moncada, València, Spain
| | - Ramón Penyalver
- Centre for Plant Protection and Biotechnology of the Valencian Institute of Agricultural Research (IVIA), Moncada, València, Spain
| |
Collapse
|
30
|
De Mandal S, Jeon J. Phyllosphere Microbiome in Plant Health and Disease. PLANTS (BASEL, SWITZERLAND) 2023; 12:3481. [PMID: 37836221 PMCID: PMC10575124 DOI: 10.3390/plants12193481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 09/24/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023]
Abstract
The phyllosphere refers to the aboveground surface of plants colonized by diverse microorganisms. Microbes inhabiting this environment play an important role in enhancing the host's genomic and metabolic capabilities, including defense against pathogens. Compared to the large volume of studies on rhizosphere microbiome for plant health and defense, our understanding of phyllosphere microbiome remains in its infancy. In this review, we aim to explore the mechanisms that govern the phyllosphere assembly and their function in host defence, as well as highlight the knowledge gaps. These efforts will help develop strategies to harness the phyllosphere microbiome toward sustainable crop production.
Collapse
Affiliation(s)
| | - Junhyun Jeon
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea;
| |
Collapse
|
31
|
Hamrick GS, Maddamsetti R, Son HI, Wilson ML, Davis HM, You L. Programming dynamic division of labor using horizontal gene transfer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.03.560696. [PMID: 37873187 PMCID: PMC10592921 DOI: 10.1101/2023.10.03.560696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The metabolic engineering of microbes has broad applications, including in biomanufacturing, bioprocessing, and environmental remediation. The introduction of a complex, multi-step pathway often imposes a substantial metabolic burden on the host cell, restraining the accumulation of productive biomass and limiting pathway efficiency. One strategy to alleviate metabolic burden is division of labor (DOL), in which different subpopulations carry out different parts of the pathway and work together to convert a substrate into a final product. However, the maintenance of different engineered subpopulations is challenging due to competition and convoluted inter-strain population dynamics. Through modeling, we show that dynamic division of labor (DDOL) mediated by horizontal gene transfer (HGT) can overcome these limitations and enable the robust maintenance of burdensome, multi-step pathways. We also use plasmid genomics to uncover evidence that DDOL is a strategy utilized by natural microbial communities. Our work suggests that bioengineers can harness HGT to stabilize synthetic metabolic pathways in microbial communities, enabling the development of robust engineered systems for deployment in a variety of contexts.
Collapse
|
32
|
Raio A, Brilli F, Neri L, Baraldi R, Orlando F, Pugliesi C, Chen X, Baccelli I. Stenotrophomonas rhizophila Ep2.2 inhibits growth of Botrytis cinerea through the emission of volatile organic compounds, restricts leaf infection and primes defense genes. FRONTIERS IN PLANT SCIENCE 2023; 14:1235669. [PMID: 37849842 PMCID: PMC10577304 DOI: 10.3389/fpls.2023.1235669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/05/2023] [Indexed: 10/19/2023]
Abstract
The bacterium Stenotrophomonas rhizophila is known to be beneficial for plants and has been frequently isolated from the rhizosphere of crops. In the present work, we isolated from the phyllosphere of an ornamental plant an epiphytic strain of S. rhizophila that we named Ep2.2 and investigated its possible application in crop protection. Compared to S. maltophilia LMG 958, a well-known plant beneficial species which behaves as opportunistic human pathogen, S. rhizophila Ep2.2 showed distinctive features, such as different motility, a generally reduced capacity to use carbon sources, a greater sensitivity to fusidic acid and potassium tellurite, and the inability to grow at the human body temperature. S. rhizophila Ep2.2 was able to inhibit in vitro growth of the plant pathogenic fungi Alternaria alternata and Botrytis cinerea through the emission of volatile compounds. Simultaneous PTR-MS and GC-MS analyses revealed the emission, by S. rhizophila Ep2.2, of volatile organic compounds (VOCs) with well-documented antifungal activity, such as furans, sulphur-containing compounds and terpenes. When sprayed on tomato leaves and plants, S. rhizophila Ep2.2 was able to restrict B. cinerea infection and to prime the expression of Pti5, GluA and PR1 plant defense genes.
Collapse
Affiliation(s)
- Aida Raio
- Institute for Sustainable Plant Protection (IPSP), National Research Council of Italy (CNR), Florence, Italy
| | - Federico Brilli
- Institute for Sustainable Plant Protection (IPSP), National Research Council of Italy (CNR), Florence, Italy
| | - Luisa Neri
- Institute for BioEconomy (IBE), National Research Council of Italy (CNR), Bologna, Italy
| | - Rita Baraldi
- Institute for BioEconomy (IBE), National Research Council of Italy (CNR), Bologna, Italy
| | - Francesca Orlando
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Xiaoyulong Chen
- College of Agriculture, College of Tobacco Science, Guizhou University, Guiyang, China
| | - Ivan Baccelli
- Institute for Sustainable Plant Protection (IPSP), National Research Council of Italy (CNR), Florence, Italy
| |
Collapse
|
33
|
Arora S, Babele PK, Jha PN. Biochemical and metabolic signatures are fundamental to drought adaptation in PGPR Enterobacter bugandensis WRS7. Mol Omics 2023; 19:640-652. [PMID: 37338418 DOI: 10.1039/d3mo00051f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Drought alone causes more annual loss in crop yield than the sum of all other environmental stresses. There is growing interest in harnessing the potential of stress-resilient PGPR in conferring plant resistance and enhancing crop productivity in drought-affected agroecosystems. A detailed understanding of the complex physiological and biochemical responses will open up the avenues to stress adaptation mechanisms of PGPR communities under drought. It will pave the way for rhizosphere engineering through metabolically engineered PGPR. Therefore, to reveal the physiological and metabolic networks in response to drought-mediated osmotic stress, we performed biochemical analyses and applied untargeted metabolomics to investigate the stress adaptation mechanisms of a PGPR Enterobacter bugendensis WRS7 (Eb WRS7). Drought caused oxidative stress and resulted in slower growth rates in Eb WRS7. However, Eb WRS7 could tolerate drought stress and did not show changes in cell morphology under stress conditions. Overproduction of ROS caused lipid peroxidation (increment in MDA) and eventually activated antioxidant systems and cell signalling cascades, which led to the accumulation of ions (Na+, K+, and Ca2+), osmolytes (proline, exopolysaccharides, betaine, and trehalose), and modulated lipid dynamics of the plasma membranes for osmosensing and osmoregulation, suggesting an osmotic stress adaption mechanism in PGPR Eb WRS7. Finally, GC-MS-based metabolite profiling and deregulated metabolic responses highlighted the role of osmolytes, ions, and intracellular metabolites in regulating Eb WRS7 metabolism. Our results suggest that understanding the role of metabolites and metabolic pathways can be exploited for future metabolic engineering of PGPR and developing bio inoculants for plant growth promotion under drought-affected agroecosystems.
Collapse
Affiliation(s)
- Saumya Arora
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani 333031, Rajasthan, India.
| | - Piyoosh K Babele
- College of Agriculture, Rani Lakshmi Bai Central Agricultural University, Jhansi 284003, Uttar Pradesh, India
| | - Prabhat Nath Jha
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani 333031, Rajasthan, India.
| |
Collapse
|
34
|
Ayaz M, Li CH, Ali Q, Zhao W, Chi YK, Shafiq M, Ali F, Yu XY, Yu Q, Zhao JT, Yu JW, Qi RD, Huang WK. Bacterial and Fungal Biocontrol Agents for Plant Disease Protection: Journey from Lab to Field, Current Status, Challenges, and Global Perspectives. Molecules 2023; 28:6735. [PMID: 37764510 PMCID: PMC10537577 DOI: 10.3390/molecules28186735] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/16/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023] Open
Abstract
Plants are constantly exposed to various phytopathogens such as fungi, Oomycetes, nematodes, bacteria, and viruses. These pathogens can significantly reduce the productivity of important crops worldwide, with annual crop yield losses ranging from 20% to 40% caused by various pathogenic diseases. While the use of chemical pesticides has been effective at controlling multiple diseases in major crops, excessive use of synthetic chemicals has detrimental effects on the environment and human health, which discourages pesticide application in the agriculture sector. As a result, researchers worldwide have shifted their focus towards alternative eco-friendly strategies to prevent plant diseases. Biocontrol of phytopathogens is a less toxic and safer method that reduces the severity of various crop diseases. A variety of biological control agents (BCAs) are available for use, but further research is needed to identify potential microbes and their natural products with a broad-spectrum antagonistic activity to control crop diseases. This review aims to highlight the importance of biocontrol strategies for managing crop diseases. Furthermore, the role of beneficial microbes in controlling plant diseases and the current status of their biocontrol mechanisms will be summarized. The review will also cover the challenges and the need for the future development of biocontrol methods to ensure efficient crop disease management for sustainable agriculture.
Collapse
Affiliation(s)
- Muhammad Ayaz
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei 230041, China; (M.A.); (W.Z.); (Y.-K.C.)
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.-Y.Y.); (Q.Y.); (J.-T.Z.); (J.-W.Y.)
| | - Cai-Hong Li
- Cotton Sciences Research Institute of Hunan, Changde 415101, China;
| | - Qurban Ali
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China;
| | - Wei Zhao
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei 230041, China; (M.A.); (W.Z.); (Y.-K.C.)
| | - Yuan-Kai Chi
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei 230041, China; (M.A.); (W.Z.); (Y.-K.C.)
| | - Muhammad Shafiq
- Biology Department and Institute of Marine Sciences, College of Science, Shantou University, Shantou 515063, China;
| | - Farman Ali
- Department of Entomology, Abdul Wali Khan University, Mardan 23200, Pakistan;
| | - Xi-Yue Yu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.-Y.Y.); (Q.Y.); (J.-T.Z.); (J.-W.Y.)
| | - Qing Yu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.-Y.Y.); (Q.Y.); (J.-T.Z.); (J.-W.Y.)
| | - Jing-Tian Zhao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.-Y.Y.); (Q.Y.); (J.-T.Z.); (J.-W.Y.)
| | - Jing-Wen Yu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.-Y.Y.); (Q.Y.); (J.-T.Z.); (J.-W.Y.)
| | - Ren-De Qi
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei 230041, China; (M.A.); (W.Z.); (Y.-K.C.)
| | - Wen-Kun Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.-Y.Y.); (Q.Y.); (J.-T.Z.); (J.-W.Y.)
| |
Collapse
|
35
|
Wu X, Zhao Z, Zhao Z, Zhang Y, Li M, Yu Q. Analysis of the Potassium-Solubilizing Priestia megaterium Strain NK851 and Its Potassium Feldspar-Binding Proteins. Int J Mol Sci 2023; 24:14226. [PMID: 37762528 PMCID: PMC10531590 DOI: 10.3390/ijms241814226] [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: 05/30/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
Potassium-solubilizing bacteria are an important microbial group that play a critical role in releasing mineral potassium from potassium-containing minerals, e.g., potassium feldspar. Their application may reduce eutrophication caused by overused potassium fertilizers and facilitate plants to utilize environmental potassium. In this study, a high-efficiency potassium-solubilizing bacterium, named NK851, was isolated from the Astragalus sinicus rhizosphere soil. This bacterium can grow in the medium with potassium feldspar as the sole potassium source, releasing 157 mg/L and 222 mg/L potassium after 3 days and 5 days of incubation, respectively. 16S rDNA sequencing and cluster analysis showed that this strain belongs to Priestia megaterium. Genome sequencing further revealed that this strain has a genome length of 5,305,142 bp, encoding 5473 genes. Among them, abundant genes are related to potassium decomposition and utilization, e.g., the genes involved in adherence to mineral potassium, potassium release, and intracellular trafficking. Moreover, the strong potassium-releasing capacity of NK851 is not attributed to the acidic pH but is attributed to the extracellular potassium feldspar-binding proteins, such as the elongation factor TU and the enolase that contains potassium feldspar-binding cavities. This study provides new information for exploration of the bacterium-mediated potassium solubilization mechanisms.
Collapse
Affiliation(s)
- Xinyue Wu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China; (X.W.); (Z.Z.); (Z.Z.); (M.L.)
| | - Zijian Zhao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China; (X.W.); (Z.Z.); (Z.Z.); (M.L.)
| | - Zirun Zhao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China; (X.W.); (Z.Z.); (Z.Z.); (M.L.)
| | - Youjun Zhang
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China;
| | - Mingchun Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China; (X.W.); (Z.Z.); (Z.Z.); (M.L.)
| | - Qilin Yu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China; (X.W.); (Z.Z.); (Z.Z.); (M.L.)
| |
Collapse
|
36
|
Khan AL. The phytomicrobiome: solving plant stress tolerance under climate change. FRONTIERS IN PLANT SCIENCE 2023; 14:1219366. [PMID: 37746004 PMCID: PMC10513501 DOI: 10.3389/fpls.2023.1219366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/14/2023] [Indexed: 09/26/2023]
Abstract
With extraordinary global climate changes, increased episodes of extreme conditions result in continuous but complex interaction of environmental variables with plant life. Exploring natural phytomicrobiome species can provide a crucial resource of beneficial microbes that can improve plant growth and productivity through nutrient uptake, secondary metabolite production, and resistance against pathogenicity and abiotic stresses. The phytomicrobiome composition, diversity, and function strongly depend on the plant's genotype and climatic conditions. Currently, most studies have focused on elucidating microbial community abundance and diversity in the phytomicrobiome, covering bacterial communities. However, least is known about understanding the holistic phytomicrobiome composition and how they interact and function in stress conditions. This review identifies several gaps and essential questions that could enhance understanding of the complex interaction of microbiome, plant, and climate change. Utilizing eco-friendly approaches of naturally occurring synthetic microbial communities that enhance plant stress tolerance and leave fewer carbon-foot prints has been emphasized. However, understanding the mechanisms involved in stress signaling and responses by phytomicrobiome species under spatial and temporal climate changes is extremely important. Furthermore, the bacterial and fungal biome have been studied extensively, but the holistic interactome with archaea, viruses, oomycetes, protozoa, algae, and nematodes has seldom been studied. The inter-kingdom diversity, function, and potential role in improving environmental stress responses of plants are considerably important. In addition, much remains to be understood across organismal and ecosystem-level responses under dynamic and complex climate change conditions.
Collapse
Affiliation(s)
- Abdul Latif Khan
- Department of Engineering Technology, University of Houston, Houston, TX, United States
| |
Collapse
|
37
|
Li C, Zheng H, Li H, Liu L, Wang J, Ni J. Synthetic Light-Driven Consortia for Carbon-Negative Biosynthesis. Chembiochem 2023; 24:e202300122. [PMID: 37401840 DOI: 10.1002/cbic.202300122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/07/2023] [Accepted: 07/03/2023] [Indexed: 07/05/2023]
Abstract
Synthetic light-driven consortia composed of phototrophs and heterotrophs have attracted increasing attention owing to their potential to be used in sustainable biotechnology. In recent years, synthetic phototrophic consortia have been used to produce bulk chemicals, biofuels, and other valuable bioproducts. In addition, autotrophic-heterotrophic symbiosis systems have potential applications in wastewater treatment, bioremediation, and as a method for phytoplankton bloom control. Here, we discuss progress made on the biosynthesis of phototrophic microbial consortia. In addition, strategies for optimizing the synthetic light-driven consortia are summarized. Moreover, we highlight current challenges and future research directions for the development of robust and controllable synthetic light-driven consortia.
Collapse
Affiliation(s)
- Chaofeng Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Haotian Zheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hengrun Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Liangxu Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiawei Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jun Ni
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| |
Collapse
|
38
|
Khan HA, Nerva L, Bhatti MF. The good, the bad and the cryptic: The multifaceted roles of mycoviruses and their potential applications for a sustainable agriculture. Virology 2023; 585:259-269. [PMID: 37453341 DOI: 10.1016/j.virol.2023.07.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023]
Abstract
Mycoviruses are natural inhabitants of fungi and have been identified in almost all fungal taxonomic groups. Mycoviruses that infect phytopathogenic fungi are now becoming a hot research area due to their potential for the biocontrol of important plant pathogens. But, before considering a mycovirus for biocontrol, we should be fully aware of the effects it induces in a fungal host and its interactions with other viruses, fungal strains and even the host plants. Mycoviral infections are generally associated with different effects, ranging from hypovirulence to hypervirulence, but they can often be cryptic (latent infections). The cryptic lifestyle has been associated to many mycoviruses, but thanks to growing knowledge we are now aware that it is often associated to axenic conditions while the real effects can be observed only in nature. Other mycoviruses either promote (hypervirulence) or (hypovirulence) fungal pathogenicity by a strong impact on the fungal physiology or by blocking the production of toxins or effectors. Finally, indirect effects of mycoviral infections can also be provided to the plant that hosts the fungal isolate, highlighting not only their potential as direct biocontrol agents but also as priming agents for plant resilience to biotic and abiotic stresses. This review provides a broad overview of mycoviral interactions both with their hosts and with other mycoviruses, highlighting the most interesting examples. In contrast to what has been observed to date, we believe that the collective availability of these data will not only improve our understanding of mycoviruses, but also increase our confidence in considering them as alternative measures against fungal diseases to improve the sustainable production of food and feed commodities.
Collapse
Affiliation(s)
- Haris Ahmed Khan
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan; Department of Biotechnology, University of Mianwali, Punjab, 42200, Pakistan
| | - Luca Nerva
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile, 31015, Conegliano, (TV), Italy.
| | - Muhammad Faraz Bhatti
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| |
Collapse
|
39
|
Pajuelo E, Flores-Duarte NJ, Navarro-Torre S, Rodríguez-Llorente ID, Mateos-Naranjo E, Redondo-Gómez S, Carrasco López JA. Culturomics and Circular Agronomy: Two Sides of the Same Coin for the Design of a Tailored Biofertilizer for the Semi-Halophyte Mesembryanthemum crystallinum. PLANTS (BASEL, SWITZERLAND) 2023; 12:2545. [PMID: 37447105 DOI: 10.3390/plants12132545] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023]
Abstract
According to the EU, the global consumption of biomass, fossil fuels, metals, and minerals is expected to double by 2050, while waste will increase by 70%. In this context, the Circular Economy Action Plan (CEAP) intends to integrate development and sustainability. In this regard, tailored biofertilizers based on plant growth-promoting bacteria (PGPB) can improve plant yield with fewer inputs. In our project, an autochthonous halophyte of the Andalusian marshes, namely Mesembryanthemum crystallinum, was selected for its interest as a source of pharmaceuticals and nutraceuticals. The aim of this work was to use a culturomics approach for the isolation of specific PGPB and endophytes able to promote plant growth and, eventually, modulate the metabolome of the plant. For this purpose, a specific culture medium based on M. crystallinum biomass, called Mesem Agar (MA), was elaborated. Bacteria of three compartments (rhizosphere soil, root endophytes, and shoot endophytes) were isolated on standard tryptone soy agar (TSA) and MA in order to obtain two independent collections. A higher number of bacteria were isolated on TSA than in MA (47 vs. 37). All the bacteria were identified, and although some of them were isolated in both media (Pseudomonas, Bacillus, Priestia, Rosellomorea, etc.), either medium allowed the isolation of specific members of the M. crystallinum microbiome such as Leclercia, Curtobacterium, Pantoea, Lysinibacillus, Mesobacillus, Glutamicibacter, etc. Plant growth-promoting properties and extracellular degrading activities of all the strains were determined, and distinct patterns were found in both media. The three best bacteria of each collection were selected in order to produce two different consortia, whose effects on seed germination, root colonization, plant growth and physiology, and metabolomics were analyzed. Additionally, the results of the plant metabolome revealed a differential accumulation of several primary and secondary metabolites with pharmaceutical properties. Overall, the results demonstrated the feasibility of using "low cost media" based on plant biomass to carry out a culturomics approach in order to isolate the most suitable bacteria for biofertilizers. In this way, a circular model is established in which bacteria help plants to grow, and, in turn, a medium based on plant wastes supports bacterial growth at low prices, which is the reason why this approach can be considered within the model of "circular agronomy".
Collapse
Affiliation(s)
- Eloísa Pajuelo
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, c/Profesor García González, 2, 41012 Sevilla, Spain
| | - Noris J Flores-Duarte
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, c/Profesor García González, 2, 41012 Sevilla, Spain
| | - Salvadora Navarro-Torre
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, c/Profesor García González, 2, 41012 Sevilla, Spain
| | - Ignacio D Rodríguez-Llorente
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, c/Profesor García González, 2, 41012 Sevilla, Spain
| | - Enrique Mateos-Naranjo
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, c/Profesor García González, s/n., 41012 Sevilla, Spain
| | - Susana Redondo-Gómez
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, c/Profesor García González, s/n., 41012 Sevilla, Spain
| | - José A Carrasco López
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, c/Profesor García González, 2, 41012 Sevilla, Spain
| |
Collapse
|
40
|
Shi C, Zhao Z, Zhu N, Yu Q. Magnetic nanoparticle-assisted colonization of synthetic bacteria on plant roots for improved phytoremediation of heavy metals. CHEMOSPHERE 2023; 329:138631. [PMID: 37030349 DOI: 10.1016/j.chemosphere.2023.138631] [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: 02/07/2023] [Revised: 04/01/2023] [Accepted: 04/05/2023] [Indexed: 05/03/2023]
Abstract
Phytoremediation is a facile strategy to remove environmental heavy metals by using metal-accumulating plants from the rhizosphere environment. However, its efficiency is frequently compromised by the weak activity of rhizosphere microbiomes. This study developed a magnetic nanoparticle-assisted root colonization technique of synthetic functional bacteria to regulate rhizosphere microbiome composition for enhanced phytoremediation of heavy metals. The iron oxide magnetic nanoparticles with the size of 15-20 nm were synthesized and grafted by chitosan, a natural bacterium-binding polymer. The synthetic Escherichia coli SynEc2, which highly exposed an artificial heavy metal-capturing protein, was then introduced with the magnetic nanoparticles to bind the Eichhornia crassipes plants. Confocal microscopy, scanning electron microscopy, and microbiome analysis revealed that the grafted magnetic nanoparticles strongly promoted colonization of the synthetic bacteria on the plant roots, leading to remarkable change of rhizosphere microbiome composition, with the increase in the abundance of Enterobacteriaceae, Moraxellaceae, and Sphingomonadaceae. Histological staining and biochemical analysis further showed that the combination of SynEc2 and the magnetic nanoparticles protected the plants from heavy metal-induced tissue damage, and increased plant weights from 29 g to 40 g. Consequently, the plants with the assistance of synthetic bacteria and the magnetic nanoparticles in combination exhibited much higher heavy metal-removing capacity than the plants treated by the synthetic bacteria or the magnetic nanoparticles alone, leading to the decrease in the heavy metal levels from 3 mg/L to 0.128 mg/L for cadmium, and to 0.032 mg/L for lead. This study provided a novel strategy to remodel rhizosphere microbiome of metal-accumulating plants by integrating synthetic microbes and nanomaterials for improving the efficiency of phytoremediation.
Collapse
Affiliation(s)
- Cong Shi
- School of Environmental Science and Engineering, Tiangong University, Tianjin, 300387, PR China
| | - Zirun Zhao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, PR China
| | - Nali Zhu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, PR China
| | - Qilin Yu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, PR China.
| |
Collapse
|
41
|
Sugiyama A. Application of plant specialized metabolites to modulate soil microbiota. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2023; 40:123-133. [PMID: 38250293 PMCID: PMC10797516 DOI: 10.5511/plantbiotechnology.23.0227a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 02/27/2023] [Indexed: 01/23/2024]
Abstract
Plant specialized metabolites (PSMs) are considerably diverse compounds with multifaceted roles in the adaptation of plants to various abiotic and biotic stresses. PSMs are frequently secreted into the rhizosphere, a small region around the roots, where they facilitate interactions between plants and soil microorganisms. PSMs shape the host-specific rhizosphere microbial communities that potentially influence plant growth and tolerance to adverse conditions. Plant mutants defective in PSM biosynthesis contribute to reveal the roles of each PSM in plant-microbiota interactions in the rhizosphere. Recently, various approaches have been used to directly supply PSMs to soil by in vitro methods or through addition in pots with plants. This review focuses on the feasibility of the direct PSM application methods to reveal rhizospheric plant-microbiota interactions and discusses the possibility of applying the knowledge gained to future engineering of rhizospheric traits.
Collapse
Affiliation(s)
- Akifumi Sugiyama
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| |
Collapse
|
42
|
Xie P, Yang S, Liu X, Zhang T, Zhao X, Wen T, Zhang J, Xue C, Shen Q, Yuan J. Learning from Seed Microbes: Trichoderma Coating Intervenes in Rhizosphere Microbiome Assembly. Microbiol Spectr 2023; 11:e0309722. [PMID: 37195176 PMCID: PMC10269462 DOI: 10.1128/spectrum.03097-22] [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: 08/08/2022] [Accepted: 04/28/2023] [Indexed: 05/18/2023] Open
Abstract
Seed-associated microbiomes can impact the later colonization of a plant rhizosphere microbiome. However, there remains little insight into the underlying mechanisms concerning how alterations in the composition of the seed microbiome may intervene in the assembly of a rhizosphere microbiome. In this study, the fungus Trichoderma guizhouense NJAU4742 was introduced to both maize and watermelon seed microbiomes by seed coating. Application was found to significantly promote seed germination and improve plant growth and rhizosphere soil quality. The activities of acid phosphatase, cellulase, peroxidase, sucrase, and α-glucosidase increased significantly in two crops. The introduction of Trichoderma guizhouense NJAU4742 also led to a decrease in the occurrence of disease. Coating with T. guizhouense NJAU4742 did not alter the alpha diversities of the bacterial and fungal communities but formed a key network module that contained both Trichoderma and Mortierella. This key network module comprised of these potentially beneficial microorganisms was positively linked with the belowground biomass and activities of rhizosphere soil enzymes but negatively correlated with disease incidence. Overall, this study provides insights into plant growth promotion and plant health maintenance via seed coating in order to influence the rhizosphere microbiome. IMPORTANCE Seed-associated microbiomes can impact the rhizosphere microbiome assembly and function display. However, there remains little insight into the underlying mechanisms concerning how alterations in the composition of the seed microbiome with the beneficial microbes may intervene in the assembly of a rhizosphere microbiome. Here, we introduced T. guizhouense NJAU4742 to the seed microbiome by seed coating. This introduction led to a decrease in the occurrence of disease and an increase in plant growth; furthermore, it formed a key network module that contained both Trichoderma and Mortierella. Our study provides insights into plant growth promotion and plant health maintenance via seed coating in order to influence the rhizosphere microbiome.
Collapse
Affiliation(s)
- Penghao Xie
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, The Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Shengdie Yang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, The Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Xiaoyu Liu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, The Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Tianyi Zhang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, The Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Xinyuan Zhao
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, The Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Tao Wen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, The Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Jian Zhang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, The Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, China
- The Key Laboratory of Green Intelligent Fertilizer Innovation, Ministry of Agriculture and Rural Affairs, Nanjing, Jiangsu, China
| | - Chao Xue
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, The Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, The Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Jun Yuan
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, The Key Laboratory of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, China
| |
Collapse
|
43
|
Kim M, Jo H, Jung GY, Oh SS. Molecular Complementarity of Proteomimetic Materials for Target-Specific Recognition and Recognition-Mediated Complex Functions. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2208309. [PMID: 36525617 DOI: 10.1002/adma.202208309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/29/2022] [Indexed: 06/02/2023]
Abstract
As biomolecules essential for sustaining life, proteins are generated from long chains of 20 different α-amino acids that are folded into unique 3D structures. In particular, many proteins have molecular recognition functions owing to their binding pockets, which have complementary shapes, charges, and polarities for specific targets, making these biopolymers unique and highly valuable for biomedical and biocatalytic applications. Based on the understanding of protein structures and microenvironments, molecular complementarity can be exhibited by synthesizable and modifiable materials. This has prompted researchers to explore the proteomimetic potentials of a diverse range of materials, including biologically available peptides and oligonucleotides, synthetic supramolecules, inorganic molecules, and related coordination networks. To fully resemble a protein, proteomimetic materials perform the molecular recognition to mediate complex molecular functions, such as allosteric regulation, signal transduction, enzymatic reactions, and stimuli-responsive motions; this can also expand the landscape of their potential bio-applications. This review focuses on the recognitive aspects of proteomimetic designs derived for individual materials and their conformations. Recent progress provides insights to help guide the development of advanced protein mimicry with material heterogeneity, design modularity, and tailored functionality. The perspectives and challenges of current proteomimetic designs and tools are also discussed in relation to future applications.
Collapse
Affiliation(s)
- Minsun Kim
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Hyesung Jo
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
| | - Seung Soo Oh
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
| |
Collapse
|
44
|
Ozfidan-Konakci C, Arikan B, Alp-Turgut FN, Balci M, Uysal A, Yildiztugay E. Halotolerant plant growth-promoting bacteria, Bacillus pumilus, modulates water status, chlorophyll fluorescence kinetics and antioxidant balance in salt and/or arsenic-exposed wheat. ENVIRONMENTAL RESEARCH 2023; 231:116089. [PMID: 37172678 DOI: 10.1016/j.envres.2023.116089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/06/2023] [Accepted: 05/08/2023] [Indexed: 05/15/2023]
Abstract
Seed priming is an effective and novel technique and the use of eco-friendly biological agents improves the physiological functioning in the vegetative stage of plants. This procedure ensures productivity and acquired stress resilience in plants against adverse conditions without contaminating the environment. Though the mechanisms of bio-priming-triggered alterations have been widely explained under induvial stress conditions, the interaction of combined stress conditions on the defense system and the functionality of photosynthetic apparatus in the vegetative stage after the inoculation to seeds has not been fully elucidated. After Bacillus pumilus inoculation to wheat seeds (Triticum aestivum), three-week-old plants were hydroponically exposed to the alone and combination of salt (100 mM NaCl) and 200 μM sodium arsenate (Na2HAsO4·7H2O, As) for 72 h. Salinity and As pollutant resulted in a decline in growth, water content, gas exchange parameters, fluorescence kinetics and performance of photosystem II (PSII). On the other hand, the seed inoculation against stress provided the alleviation of relative growth rate (RGR), relative water content (RWC) and chlorophyll fluorescence. These negative impacts were reversed by B. pumilus inoculation. Since there was no effective antioxidant capacity, As and/or salinity caused induction of H2O2 accumulation and thiobarbituric acid reactive substances content (TBARS) in wheat leaves. The inoculated leaves had high activity of superoxide dismutase (SOD) under stress. B. pumilis decreased the NaCl-induced toxic H2O2 levels by increasing peroxidase (POX) and enzymes/non-enzymes related to ascorbate-glutathione (AsA-GSH) cycle. In the presence of As exposure, the inoculated plants exhibited an induction in CAT activity. On the other hand, for H2O2 scavenging, the improvement in the AsA-GSH cycle was observed in bacterium priming plants plus the combined stress treatment. Since B. pumilus inoculation reduced H2O2 levels against all stress treatments, lipid peroxidation subsequently decreased in wheat leaves. The findings obtained from our study explained that the seed inoculation with B. pumilus provided an activation in the defense system and protection in growth, water status, and gas exchange regulation in wheat leaves against the combination of salt and As.
Collapse
Affiliation(s)
- Ceyda Ozfidan-Konakci
- Department of Molecular Biology and Genetics, Faculty of Science, Necmettin Erbakan University, Meram, 42090, Konya, Turkey.
| | - Busra Arikan
- Department of Biotechnology, Faculty of Science, Selcuk University, Selcuklu, 42130, Konya, Turkey.
| | - Fatma Nur Alp-Turgut
- Department of Biotechnology, Faculty of Science, Selcuk University, Selcuklu, 42130, Konya, Turkey.
| | - Melike Balci
- Department of Biotechnology, Faculty of Science, Selcuk University, Selcuklu, 42130, Konya, Turkey.
| | - Ahmet Uysal
- Department of Medical Services and Techniques, Vocational School of Health Services, Selcuk University, Selcuklu, 42130, Konya, Turkey.
| | - Evren Yildiztugay
- Department of Biotechnology, Faculty of Science, Selcuk University, Selcuklu, 42130, Konya, Turkey.
| |
Collapse
|
45
|
Liu Q, Cheng L, Nian H, Jin J, Lian T. Linking plant functional genes to rhizosphere microbes: a review. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:902-917. [PMID: 36271765 PMCID: PMC10106864 DOI: 10.1111/pbi.13950] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/09/2022] [Accepted: 10/16/2022] [Indexed: 05/04/2023]
Abstract
The importance of rhizomicrobiome in plant development, nutrition acquisition and stress tolerance is unquestionable. Relevant plant genes corresponding to the above functions also regulate rhizomicrobiome construction. Deciphering the molecular regulatory network of plant-microbe interactions could substantially contribute to improving crop yield and quality. Here, the plant gene-related nutrient uptake, biotic and abiotic stress resistance, which may influence the composition and function of microbial communities, are discussed in this review. In turn, the influence of microbes on the expression of functional plant genes, and thereby plant growth and immunity, is also reviewed. Moreover, we have specifically paid attention to techniques and methods used to link plant functional genes and rhizomicrobiome. Finally, we propose to further explore the molecular mechanisms and signalling pathways of microbe-host gene interactions, which could potentially be used for managing plant health in agricultural systems.
Collapse
Affiliation(s)
- Qi Liu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Lang Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Jian Jin
- Northeast Institute of Geography and AgroecologyChinese Academy of SciencesHarbinChina
- Department of Animal, Plant and Soil Sciences, Centre for AgriBioscienceLa Trobe UniversityBundooraVictoriaAustralia
| | - Tengxiang Lian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| |
Collapse
|
46
|
Pallavi, Mishra RK, Sahu PK, Mishra V, Jamal H, Varma A, Tripathi S. Isolation and characterization of halotolerant plant growth promoting rhizobacteria from mangrove region of Sundarbans, India for enhanced crop productivity. FRONTIERS IN PLANT SCIENCE 2023; 14:1122347. [PMID: 37152133 PMCID: PMC10158646 DOI: 10.3389/fpls.2023.1122347] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/24/2023] [Indexed: 12/07/2023]
Abstract
Halotolerant plant growth promoting rhizobacteria (PGPR) are beneficial microorganisms utilized to mitigate the biotic and abiotic stresses in plants. The areas of Sundarban mangroves of West Bengal, India have been reported to be rich in halotolerant microflora, yet major area remains unexplored. The present study, therefore, aims to map down the region-specific native microbial community potent of salt tolerance, plant growth promoting (PGP) activity and antagonistic activity against fungal pathogens. Bacterial samples were isolated from the saline soil of the Sundarban mangroves. A total of 156 bacterial samples were isolated and 20 were screened for their salt tolerance potential. These isolates were characterised using morphological, biochemical, and molecular approaches. Based on 16s rRNA sequencing, they were classified into 4 different genera, including Arthrobacter sp. (01 isolate), Pseudomonas plecoglossicida (01 isolate), Kocuria rosea (01 isolate), and Bacillus (17 isolates). The halotolerant isolates which possessed plant growth promoting traits including phosphate, and zinc solubilization, indole acetic acid production, siderophore, and ammonia generation were selected. Further, the effect of two halotolerant isolates GN-5 and JR-12 which showed most prominent PGP activities was evaluated in pea plant under high salinity conditions. The isolates improved survival by promoting germination (36 to 43%) and root-shoot growth and weight of pea plant in comparison to non-inoculated control plants. In a subsequent dual culture confrontation experiment, both these halo-tolerant isolates showed antagonistic activities against the aggressive root rot disease-causing Macrophomina phaseolina (Tassi) Goid NAIMCC-F-02902. The identified isolates could be used as potential bioagents for saline soils, with potential antagonistic effect on root rot disease. However, further studies at the physiological and molecular level would help to delineate a detail mechanistic understanding of broad-spectrum defence against salinity and potential biotic pathogen.
Collapse
Affiliation(s)
- Pallavi
- Amity Institute of Microbial Technology, Amity University, Noida, India
- Department of Microbiology, Indian Council of Agricultural Research – National Bureau of Agriculturally Important Microorganism, Kushmaur, Mau, Uttar Pradesh, India
| | - Rohit Kumar Mishra
- Centre of Science and Society, University of Allahabad, Prayagraj, Uttar Pradesh, India
| | - Pramod Kumar Sahu
- Department of Microbiology, Indian Council of Agricultural Research – National Bureau of Agriculturally Important Microorganism, Kushmaur, Mau, Uttar Pradesh, India
| | - Vani Mishra
- Nanotechnology Application Centre, University of Allahabad, Prayagraj, Uttar Pradesh, India
| | - Hafiza Jamal
- Amity Institute of Microbial Technology, Amity University, Noida, India
| | - Ajit Varma
- Amity Institute of Microbial Technology, Amity University, Noida, India
| | - Swati Tripathi
- Amity Institute of Microbial Technology, Amity University, Noida, India
| |
Collapse
|
47
|
Li J, Weinberger F, de Nys R, Thomas T, Egan S. A pathway to improve seaweed aquaculture through microbiota manipulation. Trends Biotechnol 2023; 41:545-556. [PMID: 36089422 DOI: 10.1016/j.tibtech.2022.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 08/13/2022] [Accepted: 08/17/2022] [Indexed: 11/19/2022]
Abstract
Eukaryotic hosts are associated with microbial communities that are critical to their function. Microbiota manipulation using beneficial microorganisms, for example, in the form of animal probiotics or plant growth-promoting microorganisms (PGPMs), can enhance host performance and health. Recently, seaweed beneficial microorganisms (SBMs) have been identified that promote the growth and development and/or improve disease resistance of seaweeds. This knowledge coincides with global initiatives seeking to expand and intensify seaweed aquaculture. Here, we provide a pathway with the potential to improve commercial cultivation of seaweeds through microbiota manipulation, highlighting that seaweed restoration practices can also benefit from further understanding SBMs and their modes of action. The challenges and opportunities of different approaches to identify and apply SBMs to seaweed aquaculture are discussed.
Collapse
Affiliation(s)
- Jiasui Li
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, NSW, 2052, Australia
| | - Florian Weinberger
- Marine Ecology Division, GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Rocky de Nys
- Sea Forest Limited, 488 Freestone Point Road, Triabunna, Tasmania 7190, Australia and College of Science and Engineering, James Cook University, Townsville 4810, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, NSW, 2052, Australia
| | - Suhelen Egan
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, NSW, 2052, Australia.
| |
Collapse
|
48
|
Ge J, Li D, Ding J, Xiao X, Liang Y. Microbial coexistence in the rhizosphere and the promotion of plant stress resistance: A review. ENVIRONMENTAL RESEARCH 2023; 222:115298. [PMID: 36642122 DOI: 10.1016/j.envres.2023.115298] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 06/17/2023]
Abstract
Plants can recruit soil microorganisms into the rhizosphere when experiencing various environmental stresses, including biotic (e.g., insect pests) and abiotic (e.g., heavy metal pollution, droughts, floods, and salinity) stresses. However, species coexistence in plant resistance has not received sufficient attention. Current research on microbial coexistence is only at the community scale, and there is a limited understanding of the interaction patterns between species, especially microbe‒microbe interactions. The relevant interaction patterns are limited to a few model strains. The coexisting microbial communities form a stable system involving complex nutritional competition, metabolic exchange, and even interdependent interactions. This pattern of coexistence can ultimately enhance plant stress tolerance. Hence, a systematic understanding of the coexistence pattern of rhizosphere microorganisms under stress is essential for the precise development and utilization of synthetic microbial communities and the achievement of efficient ecological control. Here, we integrated current analytical methods and introduced several new experimental methods to elucidate rhizosphere microbial coexistence patterns. Some advancements (e.g., network analysis, coculture experiments, and synthetic communities) that can be applied to plant stress resistance are also updated. This review aims to summarize the key role and potential application prospects of microbial coexistence in the resistance of plants to environmental stresses. Our suggestions, enhancing plant resistance with coexisting microbes, would allow us to gain further knowledge on plant-microbial and microbial-microbial functions, and facilitate translation to more effective measures.
Collapse
Affiliation(s)
- Jiaqi Ge
- School of Environmental Science and Engineering, Changzhou University, Changzhou, 213164, China; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Dong Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Jixian Ding
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Xian Xiao
- School of Environmental Science and Engineering, Changzhou University, Changzhou, 213164, China.
| | - Yuting Liang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
| |
Collapse
|
49
|
Geller AM, Levy A. "What I cannot create, I do not understand": elucidating microbe-microbe interactions to facilitate plant microbiome engineering. Curr Opin Microbiol 2023; 72:102283. [PMID: 36868050 DOI: 10.1016/j.mib.2023.102283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 01/22/2023] [Accepted: 01/24/2023] [Indexed: 03/05/2023]
Abstract
Plant-microbe interactions are important for both physiological and pathological processes. Despite the significance of plant-microbe interactions, microbe-microbe interactions themselves represent an important, complex, dynamic network that warrants deeper investigation. To understand how microbe-microbe interactions affect plant microbiomes, one approach is to systematically understand all the factors involved in successful engineering of a microbial community. This follows the physicist Richard Feynman's declaration: "what I cannot create, I do not understand". This review highlights recent studies that focus on aspects that we believe are important for building (ergo understanding) microbe-microbe interactions in the plant environment, including pairwise screening, intelligent application of cross-feeding models, spatial distributions of microbes, and understudied interactions between bacteria and fungi, phages, and protists. We offer a framework for systematic collection and centralized integration of data of plant microbiomes that could organize all the factors that can help ecologists understand microbiomes and help synthetic ecologists engineer beneficial microbiomes.
Collapse
Affiliation(s)
- Alexander M Geller
- Department of Plant Pathology and Microbiology, Institute of Environmental Science, Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Asaf Levy
- Department of Plant Pathology and Microbiology, Institute of Environmental Science, Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel.
| |
Collapse
|
50
|
Silverstein MR, Segrè D, Bhatnagar JM. Environmental microbiome engineering for the mitigation of climate change. GLOBAL CHANGE BIOLOGY 2023; 29:2050-2066. [PMID: 36661406 DOI: 10.1111/gcb.16609] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/15/2022] [Indexed: 05/28/2023]
Abstract
Environmental microbiome engineering is emerging as a potential avenue for climate change mitigation. In this process, microbial inocula are introduced to natural microbial communities to tune activities that regulate the long-term stabilization of carbon in ecosystems. In this review, we outline the process of environmental engineering and synthesize key considerations about ecosystem functions to target, means of sourcing microorganisms, strategies for designing microbial inocula, methods to deliver inocula, and the factors that enable inocula to establish within a resident community and modify an ecosystem function target. Recent work, enabled by high-throughput technologies and modeling approaches, indicate that microbial inocula designed from the top-down, particularly through directed evolution, may generally have a higher chance of establishing within existing microbial communities than other historical approaches to microbiome engineering. We address outstanding questions about the determinants of inocula establishment and provide suggestions for further research about the possibilities and challenges of environmental microbiome engineering as a tool to combat climate change.
Collapse
Affiliation(s)
- Michael R Silverstein
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
| | - Daniel Segrè
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Department of Biology, Boston University, Boston, Massachusetts, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Department of Physics, Boston University, Boston, Massachusetts, USA
| | - Jennifer M Bhatnagar
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
- Department of Biology, Boston University, Boston, Massachusetts, USA
| |
Collapse
|