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Gao M, Peng H, Bai L, Ye B, Qiu W, Song Z. Response of wheat (Triticum aestivum L. cv.) to the coexistence of micro-/nanoplastics and phthalate esters alter its growth environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174484. [PMID: 38969134 DOI: 10.1016/j.scitotenv.2024.174484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 07/02/2024] [Accepted: 07/02/2024] [Indexed: 07/07/2024]
Abstract
Micro- and nano-plastics (MPs/NPs) have emerged as a global pollutant, yet their impact on the root environment of plants remains scarcely explored. Given the widespread pollution of phthalate esters (PAEs) in the environment due to the application of plastic products, the co-occurrence of MPs/NPs and PAEs could potentially threaten the growth medium of plants. This study examined the combined effects of polystyrene (PS) MPs/NPs and PAEs, specifically dibutyl phthalate and di-(2-ethylhexyl) phthalate, on the chemical properties and microbial communities in a wheat growth medium. It was observed that the co-pollution with MPs/NPs and PAEs significantly increased the levels of oxalic acid, formic acid, and total organic carbon (TOC), enhanced microbial activity, and promoted the indigenous input and humification of dissolved organic matter, while slightly reducing the pH of the medium solution. Although changes in chemical indices were primarily attributed to the addition of PAEs, no interaction between PS MPs/NPs and PAEs was detected. High-throughput sequencing revealed no significant change in microbial diversity within the media containing both PS MPs/NPs and PAEs compared to the media with PS MPs/NPs alone. However, alterations in energy and carbohydrate metabolism were noted. Proteobacteria dominated the bacterial communities in the medium solution across all treatment groups, followed by Bacteroidetes and Verrucomicrobia. The composition and structure of these microbial communities varied with the particle size of the PS in both single and combined treatments. Moreover, variations in TOC, oxalic acid, and formic acid significantly influenced the bacterial community composition in the medium, suggesting they could modulate the abundance of dominant bacteria to counteract the stress from exogenous pollutants. This research provides new insights into the combined effects of different sizes of PS particles and another abiotic stressor in the wheat root environment, providing a critical foundation for understanding plant adaptation in complex environmental conditions.
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Affiliation(s)
- Mingling Gao
- Department of Materials and Environmental Engineering, Shantou University, Shantou 515063, China
| | - Hongchang Peng
- Department of Materials and Environmental Engineering, Shantou University, Shantou 515063, China
| | - Linsen Bai
- Department of Materials and Environmental Engineering, Shantou University, Shantou 515063, China
| | - Biting Ye
- Department of Materials and Environmental Engineering, Shantou University, Shantou 515063, China
| | - Weiwen Qiu
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 3230, Hamilton 3240, New Zealand
| | - Zhengguo Song
- Department of Materials and Environmental Engineering, Shantou University, Shantou 515063, China.
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2
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Ortiz J, Dias N, Alvarado R, Soto J, Sanhueza T, Rabert C, Jorquera M, Arriagada C. N- acyl homoserine lactones (AHLs) type signal molecules produced by rhizobacteria associated with plants that growing in a metal(oids) contaminated soil: A catalyst for plant growth. Microbiol Res 2024; 281:127606. [PMID: 38277718 DOI: 10.1016/j.micres.2024.127606] [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: 09/22/2023] [Revised: 11/23/2023] [Accepted: 01/08/2024] [Indexed: 01/28/2024]
Abstract
The present study explores the potential of rhizobacteria isolated from Baccharis linearis and Solidago chilensis in metal(loid)-contaminated soil for producing N-acyl-homoserine lactones (AHLs)-type signal molecules and promoting plant growth. A total of 42 strains were isolated, four demonstrating the production of AHL-type signal molecules. Based on 16S rRNA gene sequencing analyses and MALDI-TOF analyses, these four isolates were identified as belonging to the Pseudomonas genus, specifically P. brassicacearum, P. frederickberguensis, P. koreensis, and P. orientalis. The four AHL-producing strains were evaluated for metal(loid)s tolerance, their plant growth promotion traits, AHL quantification, and their impact on in vitro Lactuca sativa plant growth. The study found that four strains exhibited high tolerance to metal(loid)s, particularly As, Cu, and Zn. Additionally, plant growth-promoting traits were detected in AHL-producing bacteria, such as siderophore production, ammonia production, ACC deaminase activity, and P solubilization. Notably, AHL production varied among strains isolated from B. linearis, where C7-HSL and C9-HSL signal molecules were detected, and S. chilensis, where only C7-HSL signal molecules were observed. In the presence of copper, the production of C7-HSL and C9-HSL significantly decreased in B. linearis isolates, while in S. chilensis isolates, C7-HSL production was inhibited. Further, when these strains were inoculated on lettuce seeds and in vitro plants, a significant increase in germination and plant growth was observed. Mainly, the inoculation of P. brassicacearum and P. frederickberguensis led to extensive root hair development, significantly increasing length and root dry weight. Our results demonstrate that rhizospheric strains produce AHL molecules and stimulate plant growth, primarily through root development. However, the presence of copper reduces the production of these molecules, potentially affecting the root development of non-metalloid tolerant plants such as S. chilensis, which would explain its low population in this hostile environment.
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Affiliation(s)
- Javier Ortiz
- Laboratorio de Biorremediación, Facultad de Ciencias Agropecuarias y Mediambiente, Universidad de La Frontera, Temuco, Chile
| | - Nathalia Dias
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile
| | - Roxana Alvarado
- Laboratorio de Biorremediación, Facultad de Ciencias Agropecuarias y Mediambiente, Universidad de La Frontera, Temuco, Chile
| | - Javiera Soto
- Laboratorio de Biorremediación, Facultad de Ciencias Agropecuarias y Mediambiente, Universidad de La Frontera, Temuco, Chile
| | - Tedy Sanhueza
- Laboratorio de Biorremediación, Facultad de Ciencias Agropecuarias y Mediambiente, Universidad de La Frontera, Temuco, Chile
| | - Claudia Rabert
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Temuco, Chile
| | - Milko Jorquera
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile
| | - César Arriagada
- Laboratorio de Biorremediación, Facultad de Ciencias Agropecuarias y Mediambiente, Universidad de La Frontera, Temuco, Chile.
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3
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Boo A, Toth T, Yu Q, Pfotenhauer A, Fields BD, Lenaghan SC, Stewart CN, Voigt CA. Synthetic microbe-to-plant communication channels. Nat Commun 2024; 15:1817. [PMID: 38418817 PMCID: PMC10901793 DOI: 10.1038/s41467-024-45897-6] [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: 02/10/2023] [Accepted: 02/07/2024] [Indexed: 03/02/2024] Open
Abstract
Plants and microbes communicate to collaborate to stop pests, scavenge nutrients, and react to environmental change. Microbiota consisting of thousands of species interact with each other and plants using a large chemical language that is interpreted by complex regulatory networks. In this work, we develop modular interkingdom communication channels, enabling bacteria to convey environmental stimuli to plants. We introduce a "sender device" in Pseudomonas putida and Klebsiella pneumoniae, that produces the small molecule p-coumaroyl-homoserine lactone (pC-HSL) when the output of a sensor or circuit turns on. This molecule triggers a "receiver device" in the plant to activate gene expression. We validate this system in Arabidopsis thaliana and Solanum tuberosum (potato) grown hydroponically and in soil, demonstrating its modularity by swapping bacteria that process different stimuli, including IPTG, aTc and arsenic. Programmable communication channels between bacteria and plants will enable microbial sentinels to transmit information to crops and provide the building blocks for designing artificial consortia.
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Affiliation(s)
- Alice Boo
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Tyler Toth
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Qiguo Yu
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Alexander Pfotenhauer
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Brandon D Fields
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Scott C Lenaghan
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - C Neal Stewart
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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Sharma V, Mohammed SA, Devi N, Vats G, Tuli HS, Saini AK, Dhir YW, Dhir S, Singh B. Unveiling the dynamic relationship of viruses and/or symbiotic bacteria with plant resilience in abiotic stress. STRESS BIOLOGY 2024; 4:10. [PMID: 38311681 PMCID: PMC10838894 DOI: 10.1007/s44154-023-00126-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/22/2023] [Indexed: 02/06/2024]
Abstract
In the ecosphere, plants interact with environmental biotic and abiotic partners, where unbalanced interactions can induce unfavourable stress conditions. Abiotic factors (temperature, water, and salt) are primarily required for plants healthy survival, and any change in their availability is reflected as a stress signal. In certain cases, the presence of infectious pathogens such as viruses, bacteria, fungi, protozoa, nematodes, and insects can also create stress conditions in plants, leading to the emergence of disease or deficiency symptoms. While these symptoms are often typical of abiotic or biotic stress, however, there are instances where they can intensify under specific conditions. Here, we primarily summarize the viral interactions with plants during abiotic stress to understand how these associations are linked together during viral pathogenesis. Secondly, focus is given to the beneficial effects of root-associated symbiotic bacteria in fulfilling the basic needs of plants during normal as well as abiotic stress conditions. The modulations of plant functional proteins, and their occurrence/cross-talk, with pathogen (virus) and symbiont (bacteria) molecules are also discussed. Furthermore, we have highlighted the biochemical and systematic adaptations that develop in plants due to bacterial symbiosis to encounter stress hallmarks. Lastly, directions are provided towards exploring potential rhizospheric bacteria to maintain plant-microbes ecosystem and manage abiotic stress in plants to achieve better trait health in the horticulture crops.
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Affiliation(s)
- Vasudha Sharma
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Shakeel A Mohammed
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Nisha Devi
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Gourav Vats
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Hardeep S Tuli
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Adesh K Saini
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India
| | - Yashika W Dhir
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India.
| | - Sunny Dhir
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India.
| | - Bharat Singh
- Department of Biosciences & Technology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana, 133207, India.
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5
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Jeon SJ, Zhang Y, Castillo C, Nava V, Ristroph K, Therrien B, Meza L, Lowry GV, Giraldo JP. Targeted Delivery of Sucrose-Coated Nanocarriers with Chemical Cargoes to the Plant Vasculature Enhances Long-Distance Translocation. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2304588. [PMID: 37840413 DOI: 10.1002/smll.202304588] [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: 05/31/2023] [Revised: 09/15/2023] [Indexed: 10/17/2023]
Abstract
Current practices for delivering agrochemicals are inefficient, with only a fraction reaching the intended targets in plants. The surfaces of nanocarriers are functionalized with sucrose, enabling rapid and efficient foliar delivery into the plant phloem, a vascular tissue that transports sugars, signaling molecules, and agrochemicals through the whole plant. The chemical affinity of sucrose molecules to sugar membrane transporters on the phloem cells enhances the uptake of sucrose-coated quantum dots (sucQD) and biocompatible carbon dots with β-cyclodextrin molecular baskets (suc-β-CD) that can carry a wide range of agrochemicals. The QD and CD fluorescence emission properties allowed detection and monitoring of rapid translocation (<40 min) in the vasculature of wheat leaves by confocal and epifluorescence microscopy. The suc-β-CDs more than doubled the delivery of chemical cargoes into the leaf vascular tissue. Inductively coupled plasma mass spectrometry (ICP-MS) analysis showed that the fraction of sucQDs loaded into the phloem and transported to roots is over 6.8 times higher than unmodified QDs. The sucrose coating of nanoparticles approach enables unprecedented targeted delivery to roots with ≈70% of phloem-loaded nanoparticles delivered to roots. The use of plant biorecognition molecules mediated delivery provides an efficient approach for guiding nanocarriers containing agrochemicals to the plant vasculature and whole plants.
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Affiliation(s)
- Su-Ji Jeon
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Yilin Zhang
- Department of Civil and Environmental Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Christopher Castillo
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Valeria Nava
- Department of Civil and Environmental Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Kurt Ristroph
- Department of Civil and Environmental Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Benjamin Therrien
- Department of Civil and Environmental Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Leticia Meza
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Gregory V Lowry
- Department of Civil and Environmental Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Juan Pablo Giraldo
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
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6
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Alrajhi K, Bibi S, Abu-Dieyeh M. Diversity, Distribution, and applications of arbuscular mycorrhizal fungi in the Arabian Peninsula. Saudi J Biol Sci 2024; 31:103911. [PMID: 38268781 PMCID: PMC10805673 DOI: 10.1016/j.sjbs.2023.103911] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 12/06/2023] [Accepted: 12/15/2023] [Indexed: 01/26/2024] Open
Abstract
Investigations of arbuscular mycorrhizal fungi (AMF) received extreme interests among scientist including agronomists and environmental scientists. This interest is linked to advantages provided by AMF in enhancing the nutrients of their hosts via improving photosynthetic pigments and antioxidant production. Further, it also positively alters the production of plant hormones. AMF through its associations with plants obtain carbon while in exchange, provide nutrients. AMF have been reported to improve the growth of Tageteserecta, Zea mays, Panicum turgidum, Arachis hypogaea, Triticum aestivum and others. This review further documented the occurrence, diversity, distribution, and agricultural applications of AMF species reported in the Arabian Peninsula. Overall, we documented 20 genera and 61 species of Glomeromycota in the Arabian Peninsula representing 46.51 % of genera and 17.88 % of species of AMF known so far. Funneliformis mosseae has found to be the most widely distributed species followed by Claroideoglomus etuicatum. There are 35 research articles focused on Arabian Peninsula where the stress conditions like drought, salinity and pollutants are prevailed. Only one group studied the influence of AMF on disease resistance, while salinity, drought, and cadmium stresses were investigated in 18, 6, and 4 investigations, respectively. The genus Glomus was the focus of most studies. The conducted research in the Arabian Peninsula is not enough to understand AMF taxonomy and their functional role in plant growth. Expanding the scope of detection of AMF, especially in coastal areas is essential. Future studies on biodiversity of AMF are essential.
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Affiliation(s)
- Khazna Alrajhi
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Shazia Bibi
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Mohammed Abu-Dieyeh
- Biological Science Program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, P.O. Box 2713, Doha, Qatar
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7
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Shobade SO, Zabotina OA, Nilsen-Hamilton M. Plant root associated chitinases: structures and functions. FRONTIERS IN PLANT SCIENCE 2024; 15:1344142. [PMID: 38362446 PMCID: PMC10867124 DOI: 10.3389/fpls.2024.1344142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 01/05/2024] [Indexed: 02/17/2024]
Abstract
Chitinases degrade chitin, a linear homopolymer of β-1,4-linked N-acetyl-D-glucosamine (GlcNAc) residues found in the cell walls of fungi and the exoskeletons of arthropods. They are secreted by the roots into the rhizosphere, a complex and dynamic environment where intense nutrient exchange occurs between plants and microbes. Here we modeled, expressed, purified, and characterized Zea mays and Oryza sativa root chitinases, and the chitinase of a symbiotic bacterium, Chitinophaga oryzae 1303 for their activities with chitin, di-, tri-, and tetra-saccharides and Aspergillus niger, with the goal of determining their role(s) in the rhizosphere and better understanding the molecular mechanisms underlying plant-microbe interactions. We show that Zea mays basic endochitinase (ZmChi19A) and Oryza sativa chitinase (OsChi19A) are from the GH19 chitinase family. The Chitinophaga oryzae 1303 chitinase (CspCh18A) belongs to the GH18 family. The three enzymes have similar apparent K M values of (20-40 µM) for the substrate 4-MU-GlcNAc3. They vary in their pH and temperature optima with OsChi19A activity optimal between pH 5-7 and 30-40°C while ZmChi19A and CspCh18A activities were optimal at pH 7-9 and 50-60°C. Modeling and site-directed mutation of ZmChi19A identified the catalytic cleft and the active residues E147 and E169 strategically positioned at ~8.6Å from each other in the folded protein. Cleavage of 4-MU-GlcNAc3 was unaffected by the absence of the CBD but diminished in the absence of the flexible C-terminal domain. However, unlike for the soluble substrate, the CBD and the newly identified flexible C-terminal domain were vital for inhibiting Aspergillus niger growth. The results are consistent with the involvement of the plant chitinases in defense against pathogens like fungi that have chitin exoskeletons. In summary, we have characterized the functional features and structural domains necessary for the activity of two plant root chitinases that are believed to be involved in plant defense and a bacterial chitinase that, along with the plant chitinases, may participate in nutrient recycling in the rhizosphere.
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Affiliation(s)
- Samuel O. Shobade
- Ames National Laboratory, U. S. Department of Energy, Ames, IA, United States
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Olga A. Zabotina
- Ames National Laboratory, U. S. Department of Energy, Ames, IA, United States
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Marit Nilsen-Hamilton
- Ames National Laboratory, U. S. Department of Energy, Ames, IA, United States
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
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8
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Kumar A, Solanki MK, Wang Z, Solanki AC, Singh VK, Divvela PK. Revealing the seed microbiome: Navigating sequencing tools, microbial assembly, and functions to amplify plant fitness. Microbiol Res 2024; 279:127549. [PMID: 38056172 DOI: 10.1016/j.micres.2023.127549] [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: 09/03/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 12/08/2023]
Abstract
Microbial communities within seeds play a vital role in transmitting themselves to the next generation of plants. These microorganisms significantly impact seed vigor and early seedling growth, for successful crop establishment. Previous studies reported on seed-associated microbial communities and their influence on processes like dormancy release, germination, and disease protection. Modern sequencing and conventional methods reveal microbial community structures and environmental impacts, these information helps in microbial selection and manipulation. These studies form the foundation for using seed microbiomes to enhance crop resilience and productivity. While existing research has primarily focused on characterizing microbiota in dried mature seeds, a significant gap exists in understanding how these microbial communities assemble during seed development. The review also discusses applying seed-associated microorganisms to improve crops in the context of climate change. However, limited knowledge is available about the microbial assembly pattern on seeds, and their impact on plant growth. The review provides insight into microbial composition, functions, and significance for plant health, particularly regarding growth promotion and pest control.
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Affiliation(s)
- Ajay Kumar
- Amity Institute of Biotechnology, Amity University, Sector-125, Noida, Uttar Pradesh 201313, India
| | - 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, Katowice, Poland.
| | - Zhen Wang
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Agricultural College, Yulin Normal University, Yulin 537000, China
| | - Anjali Chandrol Solanki
- Department of Agriculture, Mansarover Global University, Bhopal, Madhya Pradesh 462042, India
| | - Vipin Kumar Singh
- Department of Botany, K.S. Saket P.G. College, Ayodhya 224123, Uttar Pradesh, India
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Yang Y, Qiu K, Xie Y, Li X, Zhang S, Liu W, Huang Y, Cui L, Wang S, Bao P. Geographical, climatic, and soil factors control the altitudinal pattern of rhizosphere microbial diversity and its driving effect on root zone soil multifunctionality in mountain ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166932. [PMID: 37690759 DOI: 10.1016/j.scitotenv.2023.166932] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/05/2023] [Accepted: 09/06/2023] [Indexed: 09/12/2023]
Abstract
Shifts in rhizosphere soil microorganisms of dominant plants' response to climate change profoundly impact mountain soil ecosystem multifunctionality; relatively little is known about the relationship between them and how they depend on long-term environmental drivers. Here, we conducted analyses of rhizosphere microbial altitudinal pattern, community assembly, and co-occurrence network of 6 dominant plants in six typical vegetation zones ranging from 1350 to 2900 m (a.s.l.) in Helan Mountains by absolute quantitative sequencing technology, and finally related the microbiomes to root zone soil multifunctionality ('soil multifunctionality' hereafter), the environmental dependence of the relationship was explored. It was found that the altitudinal pattern of rhizosphere soil bacterial and fungal diversities differed significantly. Higher co-occurrence and more potential interactions of Stipa breviflora and Carex coninux were found at the lowest and highest altitudes. Bacterial α diversity, the identity of some dominant bacterial and fungal taxa, had significant positive or negative effects on soil multifunctionality. The effect sizes of positive effects of microbial diversity on soil multifunctionality were greater than those of negative effects. These results indicated that the balance of positive and negative effects of microbes determines the impact of microbial diversity on soil multifunctionality. As the number of microbes at the phylum level increases, there will be a net gain in soil multifunctionality. Our study reveals that geographical and climatic factors can directly or modulate the effects of soil properties on rhizosphere microbial diversity, thereby affecting the driving effect of microbial diversity on soil multifunctionality, and points to the rhizosphere bacterial diversity rather than the fungi being strongly associated with soil multifunctionality. This work has important ecological implications for predicting how multiple environment-plant-soil-microorganisms interactions in mountain ecosystems will respond to future climate change.
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Affiliation(s)
- Yi Yang
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China; Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Yinchuan, China; Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan, China; Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Ningxia University, Yinchuan, China
| | - Kaiyang Qiu
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China; Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Yinchuan, China; Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan, China; Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Ningxia University, Yinchuan, China.
| | - Yingzhong Xie
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China; Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Yinchuan, China; Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan, China; Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Ningxia University, Yinchuan, China
| | - Xiaocong Li
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China; Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Yinchuan, China; Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan, China; Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Ningxia University, Yinchuan, China
| | - Shuo Zhang
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China; Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Yinchuan, China; Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan, China; Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Ningxia University, Yinchuan, China
| | - Wangsuo Liu
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China; Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Yinchuan, China; Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan, China; Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Ningxia University, Yinchuan, China
| | - Yeyun Huang
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China; Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Yinchuan, China; Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan, China; Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Ningxia University, Yinchuan, China
| | - Luyao Cui
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China; Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Yinchuan, China; Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan, China; Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Ningxia University, Yinchuan, China
| | - Siyao Wang
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China; Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Yinchuan, China; Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan, China; Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Ningxia University, Yinchuan, China
| | - Pingan Bao
- College of Forestry and Prataculture, Ningxia University, Yinchuan, China; Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Yinchuan, China; Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan, China; Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Ningxia University, Yinchuan, China
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10
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Weigh KV, Batista BD, Hoang H, Dennis PG. Characterisation of Soil Bacterial Communities That Exhibit Chemotaxis to Root Exudates from Phosphorus-Limited Plants. Microorganisms 2023; 11:2984. [PMID: 38138128 PMCID: PMC10745596 DOI: 10.3390/microorganisms11122984] [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: 11/24/2023] [Revised: 12/10/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
The ability to sense and direct movement along chemical gradients is known as 'chemotaxis' and is a common trait among rhizosphere microorganisms, which are attracted to organic compounds released from plant roots. In response to stress, the compounds released from roots can change and may recruit symbionts that enhance host stress tolerance. Decoding this language of attraction could support the development of microbiome management strategies that would enhance agricultural production and sustainability. In this study, we employ a culture-independent bait-trap chemotaxis assay to capture microbial communities attracted to root exudates from phosphorus (P)-sufficient and P-deficient Arabidopsis thaliana Col-0 plants. The captured populations were then enumerated and characterised using flow cytometry and phylogenetic marker gene sequencing, respectively. Exudates attracted significantly more cells than the control but did not differ between P treatments. Relative to exudates from P-sufficient plants, those collected from P-deficient plants attracted a significantly less diverse bacterial community that was dominated by members of the Paenibacillus, which is a genus known to include powerful phosphate solubilisers and plant growth promoters. These results suggest that in response to P deficiency, Arabidopsis exudates attract organisms that could help to alleviate nutrient stress.
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Affiliation(s)
| | | | | | - Paul G. Dennis
- School of the Environment, The University of Queensland, Brisbane, QLD 4072, Australia (B.D.B.)
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11
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Shelud'ko A, Volokhina I, Mokeev D, Telesheva E, Yevstigneeva S, Burov A, Tugarova A, Shirokov A, Burigin G, Matora L, Petrova L. Chromosomal gene of hybrid multisensor histidine kinase is involved in motility regulation in the rhizobacterium Azospirillum baldaniorum Sp245 under mechanical and water stress. World J Microbiol Biotechnol 2023; 39:336. [PMID: 37814195 DOI: 10.1007/s11274-023-03785-z] [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: 07/21/2023] [Accepted: 09/29/2023] [Indexed: 10/11/2023]
Abstract
Azospirillum alphaproteobacteria, which live in the rhizosphere of many crops, are used widely as biofertilizers. Two-component signal transduction systems (TCSs) mediate the bacterial perception of signals and the corresponding adjustment of behavior facilitating the adaptation of bacteria to their habitats. In this study, we obtained the A. baldaniorum Sp245 mutant for the AZOBR_150176 gene, which encodes the TCS of the hybrid histidine kinase/response sensory regulator (HSHK-RR). Inactivation of this gene affected bacterial morphology and motility. In mutant Sp245-HSHKΔRR-Km, the cells were still able to synthesize a functioning polar flagellum (Fla), were shorter than those of strain Sp245, and were impaired in aerotaxis, elaboration of inducible lateral flagella (Laf), and motility in semiliquid media. The mutant showed decreased transcription of the genes encoding the proteins of the secretion apparatus, which ensures the assembly of Laf, Laf flagellin, and the repressor protein of translation of the Laf flagellin's mRNA. The study examined the effects of polyethylene glycol 6000 (PEG 6000), an agent used to simulate osmotic stress and drought conditions. Under osmotic stress, the mutant was no longer able to use collective motility in semiliquid media but formed more biofilm biomass than did strain Sp245. Introduction into mutant cells of the AZOBR_150176 gene as part of an expression vector led to recovery of the lost traits, including those mediating bacterial motility under mechanical stress induced by increased medium density. The results suggest that the HSHK-RR under study modulates the response of A. baldaniorum Sp245 to mechanical and osmotic/water stress.
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Affiliation(s)
- Andrei Shelud'ko
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 13 Prospekt Entuziastov, Saratov, 410049, Russia.
| | - Irina Volokhina
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 13 Prospekt Entuziastov, Saratov, 410049, Russia
| | - Dmitry Mokeev
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 13 Prospekt Entuziastov, Saratov, 410049, Russia
| | - Elizaveta Telesheva
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 13 Prospekt Entuziastov, Saratov, 410049, Russia
| | - Stella Yevstigneeva
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 13 Prospekt Entuziastov, Saratov, 410049, Russia
| | - Andrei Burov
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 13 Prospekt Entuziastov, Saratov, 410049, Russia
| | - Anna Tugarova
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 13 Prospekt Entuziastov, Saratov, 410049, Russia
| | - Alexander Shirokov
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 13 Prospekt Entuziastov, Saratov, 410049, Russia
| | - Gennady Burigin
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 13 Prospekt Entuziastov, Saratov, 410049, Russia
| | - Larisa Matora
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 13 Prospekt Entuziastov, Saratov, 410049, Russia
| | - Lilia Petrova
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 13 Prospekt Entuziastov, Saratov, 410049, Russia
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12
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Zuzolo D, Ranauda MA, Maisto M, Tartaglia M, Prigioniero A, Falzarano A, Marotta G, Sciarrillo R, Guarino C. The rootstock shape microbial diversity and functionality in the rhizosphere of Vitis vinifera L. cultivar Falanghina. FRONTIERS IN PLANT SCIENCE 2023; 14:1205451. [PMID: 37645461 PMCID: PMC10461393 DOI: 10.3389/fpls.2023.1205451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/24/2023] [Indexed: 08/31/2023]
Abstract
The rhizosphere effect occurring at the root-soil interface has increasingly been shown to play a key role in plant fitness and soil functionality, influencing plants resilience. Here, for the first time, we investigated whether the rootstock genotype on which Vitis vinifera L. cultivar Falanghina is grafted can influence the rhizosphere microbiome. Specifically, we evaluated to which extent the 5BB and 1103P rootstocks are able to shape microbial diversity of rhizosphere environment. Moreover, we explored the potential function of microbial community and its shift under plant genotype influence. We investigated seven vineyards subjected to the same pedo-climatic conditions, similar age, training system and management and collected twelve rhizosphere soil samples for metagenomic analyses and composite soil samples for physical-chemical properties. In this study, we used 16S rRNA gene-based metagenomic analysis to investigate the rhizosphere bacterial diversity and composition. Liner discriminant analysis effect size (LEFSe) was conducted for metagenomic biomarker discovery. The functional composition of sampled communities was determined using PICRUSt, which is based on marker gene sequencing profiles. Soil analyses involved the determination of texture, pH, Cation Exchange Capacity (CSC), Organic Carbon (OC), electrical conductivity (EC), calcium (Ca), magnesium (Mg), potassium (K) content, Phosphorous (P), nitrogen (N). The latter revealed that soil features were quite homogenous. The metagenomic data showed that the bacterial alpha-diversity (Observed OTUs) significantly increased in 1103P rhizosphere microbiota. Irrespective of cultivar, Pseudomonadota was the dominant phylum, followed by Actinomycetota > Bacteroidota > Thermoproteota. However, Actinomycetota was the major marker phyla differentiating the rhizosphere microbial communities associated with the different rootstock types. At the genus level, several taxa belonging to Actinomycetota and Alphaproteobacteria classes were enriched in 1103P genotype rhizosphere. Investigating the potential functional profile, we found that most key enzyme-encoding genes involved in N cycling were significantly more abundant in 5BB rootstock rhizosphere soil. However, we found that 1103P rhizosphere was enriched in genes involved in C cycle and Plant Growth Promotion (PGP) functionality. Our results suggest that the different rootstocks not only recruit specific bacterial communities, but also specific functional traits within the same environment.
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Affiliation(s)
- Daniela Zuzolo
- Department of Science and Technologies, University of Sannio, Benevento, Italy
| | | | - Maria Maisto
- Department of Science and Technologies, University of Sannio, Benevento, Italy
| | - Maria Tartaglia
- Department of Science and Technologies, University of Sannio, Benevento, Italy
| | | | | | - Giuseppe Marotta
- Department of Law, Economics, Management and Quantitative Methods (DEMM), University of Sannio, Benevento, Italy
| | - Rosaria Sciarrillo
- Department of Science and Technologies, University of Sannio, Benevento, Italy
| | - Carmine Guarino
- Department of Science and Technologies, University of Sannio, Benevento, Italy
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13
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Zhang H, Zheng D, Hu C, Cheng W, Lei P, Xu H, Gao N. Certain Tomato Root Exudates Induced by Pseudomonas stutzeri NRCB010 Enhance Its Rhizosphere Colonization Capability. Metabolites 2023; 13:metabo13050664. [PMID: 37233705 DOI: 10.3390/metabo13050664] [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: 03/29/2023] [Revised: 05/01/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023] Open
Abstract
Plant growth-promoting rhizobacteria (PGPR) can colonize plant root surfaces or form biofilms to promote plant growth and enhance plant resistance to harsh external environments. However, plant-PGPR interactions, especially chemical signaling molecules, are poorly understood. This study aimed to gain an in-depth understanding of the rhizosphere interaction mechanisms between PGPR and tomato plants. This study found that inoculation with a certain concentration of Pseudomonas stutzeri significantly promoted tomato growth and induced significant changes in tomato root exudates. Furthermore, the root exudates significantly induced NRCB010 growth, swarming motility, and biofilm formation. In addition, the composition of the root exudates was analyzed, and four metabolites (methyl hexadecanoate, methyl stearate, 2,4-di-tert-butylphenol, and n-hexadecanoic acid) significantly related to the chemotaxis and biofilm formation of NRCB010 were screened. Further assessment showed that these metabolites positively affected the growth, swarming motility, chemotaxis, or biofilm formation of strain NRCB010. Among these, n-hexadecanoic acid induced the most remarkable growth, chemotactic response, biofilm formation, and rhizosphere colonization. This study will help develop effective PGPR-based bioformulations to improve PGPR colonization and crop yields.
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Affiliation(s)
- Huanhuan Zhang
- School of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Donghui Zheng
- College of 2011, Nanjing Tech University, Nanjing 211816, China
| | - Chun Hu
- School of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Wenwen Cheng
- School of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Peng Lei
- School of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Hong Xu
- School of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Nan Gao
- School of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
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14
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Sharma I, Kashyap S, Agarwala N. Biotic stress-induced changes in root exudation confer plant stress tolerance by altering rhizospheric microbial community. FRONTIERS IN PLANT SCIENCE 2023; 14:1132824. [PMID: 36968415 PMCID: PMC10036841 DOI: 10.3389/fpls.2023.1132824] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Every organism on the earth maintains some kind of interaction with its neighbours. As plants are sessile, they sense the varied above-ground and below-ground environmental stimuli and decipher these dialogues to the below-ground microbes and neighbouring plants via root exudates as chemical signals resulting in the modulation of the rhizospheric microbial community. The composition of root exudates depends upon the host genotype, environmental cues, and interaction of plants with other biotic factors. Crosstalk of plants with biotic agents such as herbivores, microbes, and neighbouring plants can change host plant root exudate composition, which may permit either positive or negative interactions to generate a battlefield in the rhizosphere. Compatible microbes utilize the plant carbon sources as their organic nutrients and show robust co-evolutionary changes in changing circumstances. In this review, we have mainly focused on the different biotic factors responsible for the synthesis of alternative root exudate composition leading to the modulation of rhizosphere microbiota. Understanding the stress-induced root exudate composition and resulting change in microbial community can help us to devise strategies in engineering plant microbiomes to enhance plant adaptive capabilities in a stressful environment.
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15
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Oudova-Rivera B, Crombie AT, Murrell JC, Lehtovirta-Morley LE. Alcohols as inhibitors of ammonia oxidizing archaea and bacteria. FEMS Microbiol Lett 2023; 370:fnad093. [PMID: 37698885 PMCID: PMC11025371 DOI: 10.1093/femsle/fnad093] [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: 05/26/2023] [Revised: 08/23/2023] [Accepted: 09/11/2023] [Indexed: 09/13/2023] Open
Abstract
Ammonia oxidizers are key players in the global nitrogen cycle and are responsible for the oxidation of ammonia to nitrite, which is further oxidized to nitrate by other microorganisms. Their activity can lead to adverse effects on some human-impacted environments, including water pollution through leaching of nitrate and emissions of the greenhouse gas nitrous oxide (N2O). Ammonia monooxygenase (AMO) is the key enzyme in microbial ammonia oxidation and shared by all groups of aerobic ammonia oxidizers. The AMO has not been purified in an active form, and much of what is known about its potential structure and function comes from studies on its interactions with inhibitors. The archaeal AMO is less well studied as ammonia oxidizing archaea were discovered much more recently than their bacterial counterparts. The inhibition of ammonia oxidation by aliphatic alcohols (C1-C8) using the model terrestrial ammonia oxidizing archaeon 'Candidatus Nitrosocosmicus franklandus' C13 and the ammonia oxidizing bacterium Nitrosomonas europaea was examined in order to expand knowledge about the range of inhibitors of ammonia oxidizers. Methanol was the most potent specific inhibitor of the AMO in both ammonia oxidizers, with half-maximal inhibitory concentrations (IC50) of 0.19 and 0.31 mM, respectively. The inhibition was AMO-specific in 'Ca. N. franklandus' C13 in the presence of C1-C2 alcohols, and in N. europaea in the presence of C1-C3 alcohols. Higher chain-length alcohols caused non-specific inhibition and also inhibited hydroxylamine oxidation. Ethanol was tolerated by 'Ca. N. franklandus' C13 at a higher threshold concentration than other chain-length alcohols, with 80 mM ethanol being required for complete inhibition of ammonia oxidation.
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Affiliation(s)
- Barbora Oudova-Rivera
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Andrew T Crombie
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
- School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
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16
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Solanki MK, Solanki AC, Rai S, Srivastava S, Kashyap BK, Divvela PK, Kumar S, Yandigeri MS, Kashyap PL, Shrivastava AK, Ali B, Khan S, Jaremko M, Qureshi KA. Functional interplay between antagonistic bacteria and Rhizoctonia solani in the tomato plant rhizosphere. Front Microbiol 2022; 13:990850. [PMID: 36225362 PMCID: PMC9548980 DOI: 10.3389/fmicb.2022.990850] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 08/18/2022] [Indexed: 12/28/2022] Open
Abstract
Microbial interactions with plant roots play an imperial role in tomato plant growth and defense against the Rhizoctonia solani. This study performed a field experiment with two antagonistic bacteria (Pseudomonas and Bacillus) inoculated in healthy and Rhizoctonia solani treated soil in tomato rhizosphere to understand the metabolic pattern and microbial function during plant disease suppression. In the present study, we assessed soil and microbial enzymes, bacterial and fungal cell forming unit (CFU), and carbon utilization profiling through Bio-Eco plates of rhizoplane samples. Antagonist bacteria and pathogen interaction significantly (p < 0.05) influenced the bacterial count, soil enzymes (chitinase and glucanase), and bacterial function (siderophore and chitinase production). These results indicated that these variables had an imperial role in disease suppression during plant development. Furthermore, the metabolic profiling showed that carbon source utilization enhanced under fruit development and ripening stages. These results suggested that carbon sources were essential in plant/pathogen/antagonist interaction. Substrates like β-methyl-D-glucoside, D-mannitol, D-galacturonic acid, N-acetyl-D-glucosamine, and phenylethylamine strongly connect with the suppuration of root rot disease. These carbon sources may help to propagate a healthy microbial community to reduce the pathogen invasion in the plant root system, and these carbon sources can be stimulators of antagonists against pathogens in the future.
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Affiliation(s)
- Manoj Kumar Solanki
- Faculty of Natural Sciences, Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | | | - Shalini Rai
- Department of Biotechnology, Society of Higher Education and Practical Application (SHEPA), Varanasi, UP, India
| | - Supriya Srivastava
- Department of Health Informatics, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah, Saudi Arabia
| | - Brijendra Kumar Kashyap
- Department of Biotechnology Engineering, Institute of Engineering and Technology, Bundelkhand University, Jhansi, UP, India
| | | | - Sudheer Kumar
- Indian Institute of Wheat and Barley Research (ICAR), Karnal, HR, India
| | - Mahesh S. Yandigeri
- National Bureau of Agricultural Insect Resources (ICAR), Bengaluru, KA, India
- *Correspondence: Mahesh S. Yandigeri,
| | - Prem Lal Kashyap
- Indian Institute of Wheat and Barley Research (ICAR), Karnal, HR, India
| | | | - Baber Ali
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shahid Khan
- Department of Agriculture, University of Swabi, Swabi, Pakistan
- Department of Plant Breeding and Genetics, University of Agriculture Swat, Peshawar, Pakistan
| | - Mariusz Jaremko
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Kamal Ahmad Qureshi
- Department of Pharmaceutics, Unaizah College of Pharmacy, Qassim University, Unaizah, Saudi Arabia
- Kamal Ahmad Qureshi,
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17
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Upadhyay SK, Srivastava AK, Rajput VD, Chauhan PK, Bhojiya AA, Jain D, Chaubey G, Dwivedi P, Sharma B, Minkina T. Root Exudates: Mechanistic Insight of Plant Growth Promoting Rhizobacteria for Sustainable Crop Production. Front Microbiol 2022; 13:916488. [PMID: 35910633 PMCID: PMC9329127 DOI: 10.3389/fmicb.2022.916488] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 06/09/2022] [Indexed: 12/18/2022] Open
Abstract
The breaking silence between the plant roots and microorganisms in the rhizosphere affects plant growth and physiology by impacting biochemical, molecular, nutritional, and edaphic factors. The components of the root exudates are associated with the microbial population, notably, plant growth-promoting rhizobacteria (PGPR). The information accessible to date demonstrates that PGPR is specific to the plant's roots. However, inadequate information is accessible for developing bio-inoculation/bio-fertilizers for the crop in concern, with satisfactory results at the field level. There is a need to explore the perfect candidate PGPR to meet the need for plant growth and yield. The functions of PGPR and their chemotaxis mobility toward the plant root are triggered by the cluster of genes induced by the components of root exudates. Some reports have indicated the benefit of root exudates in plant growth and productivity, yet a methodical examination of rhizosecretion and its consequences in phytoremediation have not been made. In the light of the afore-mentioned facts, in the present review, the mechanistic insight and recent updates on the specific PGPR recruitment to improve crop production at the field level are methodically addressed.
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Affiliation(s)
- Sudhir K. Upadhyay
- Department of Environmental Science, V.B.S. Purvanchal University, Jaunpur, India
| | | | - Vishnu D. Rajput
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Prabhat K. Chauhan
- Department of Environmental Science, V.B.S. Purvanchal University, Jaunpur, India
| | - Ali Asger Bhojiya
- Department of Agriculture and Veterinary Sciences, Mewar University, Chittorgarh, India
| | - Devendra Jain
- Department of Molecular Biology and Biotechnology, Maharana Pratap University of Agriculture and Technology, Udaipur, India
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India
| | - Padmanabh Dwivedi
- Department of Plant Physiology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Bechan Sharma
- Department of Biochemistry, Faculty of Science, University of Allahabad, Allahabad, India
| | - Tatiana Minkina
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
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18
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Ivo Ganchev. Role of Multispecies Biofilms with a Dominance of Bacillus subtilis in the Rhizosphere. BIOL BULL+ 2022. [DOI: 10.1134/s1062359021150061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Interplay between Arabidopsis thaliana Genotype, Plant Growth and Rhizosphere Colonization by Phytobeneficial Phenazine-Producing Pseudomonas chlororaphis. Microorganisms 2022; 10:microorganisms10030660. [PMID: 35336236 PMCID: PMC8950391 DOI: 10.3390/microorganisms10030660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 12/19/2022] Open
Abstract
Rhizosphere colonization by phytobeneficial Pseudomonas spp. is pivotal in triggering their positive effects on plant health. Many Pseudomonas spp. Determinants, involved in rhizosphere colonization, have already been deciphered. However, few studies have explored the role played by specific plant genes in rhizosphere colonization by these bacteria. Using isogenic Arabidopsis thaliana mutants, we studied the effect of 20 distinct plant genes on rhizosphere colonization by two phenazine-producing P. chlororaphis strains of biocontrol interest, differing in their colonization abilities: DTR133, a strong rhizosphere colonizer and ToZa7, which displays lower rhizocompetence. The investigated plant mutations were related to root exudation, immunity, and root system architecture. Mutations in smb and shv3, both involved in root architecture, were shown to positively affect rhizosphere colonization by ToZa7, but not DTR133. While these strains were not promoting plant growth in wild-type plants, increased plant biomass was measured in inoculated plants lacking fez, wrky70, cbp60g, pft1 and rlp30, genes mostly involved in plant immunity. These results point to an interplay between plant genotype, plant growth and rhizosphere colonization by phytobeneficial Pseudomonas spp. Some of the studied genes could become targets for plant breeding programs to improve plant-beneficial Pseudomonas rhizocompetence and biocontrol efficiency in the field.
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20
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Exploring the roles of microbes in facilitating plant adaptation to climate change. Biochem J 2022; 479:327-335. [PMID: 35119455 PMCID: PMC8883484 DOI: 10.1042/bcj20210793] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 12/30/2022]
Abstract
Plants benefit from their close association with soil microbes which assist in their response to abiotic and biotic stressors. Yet much of what we know about plant stress responses is based on studies where the microbial partners were uncontrolled and unknown. Under climate change, the soil microbial community will also be sensitive to and respond to abiotic and biotic stressors. Thus, facilitating plant adaptation to climate change will require a systems-based approach that accounts for the multi-dimensional nature of plant-microbe-environment interactions. In this perspective, we highlight some of the key factors influencing plant-microbe interactions under stress as well as new tools to facilitate the controlled study of their molecular complexity, such as fabricated ecosystems and synthetic communities. When paired with genomic and biochemical methods, these tools provide researchers with more precision, reproducibility, and manipulability for exploring plant-microbe-environment interactions under a changing climate.
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21
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Gu Y, Liu Y, Li J, Cao M, Wang Z, Li J, Meng D, Cao P, Duan S, Zhang M, Tan G, Xiong J, Yin H, Zhou Z. Mechanism of Intermittent Deep Tillage and Different Depths Improving Crop Growth From the Perspective of Rhizosphere Soil Nutrients, Root System Architectures, Bacterial Communities, and Functional Profiles. Front Microbiol 2022; 12:759374. [PMID: 35082764 PMCID: PMC8784561 DOI: 10.3389/fmicb.2021.759374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 11/25/2021] [Indexed: 12/02/2022] Open
Abstract
Long-term conventional shallow tillage reduced soil quality and limited the agriculture development. Intermittent deep tillage could effectively promote agricultural production, through optimizing soil structure, underground ecology system, and soil fertility. However, the microecological mechanism of intermittent deep tillage promoting agriculture production has never been reported, and the effect of tillage depth on crop growth has not been explored in detail. In this study, three levels of intermittent deep tillage (30, 40, and 50 cm) treatments were conducted in an experimental field site with over 10 years of conventional shallow tillage (20 cm). Our results indicated that intermittent deep tillage practices helped to improve plant physiological growth status, chlorophyll a, and resistance to diseases, and the crop yield and value of output were increased with the deeper tillage practices. Crop yield (18.59%) and value of output (37.03%) were highest in IDT-50. There were three mechanisms of intermittent deep tillage practices that improved crop growth: (1) Intermittent deep tillage practices increased soil nutrients and root system architecture traits, which improved the fertility and nutrient uptake of crop through root system. (2) Changing rhizosphere environments, especially for root length, root tips, pH, and available potassium contributed to dissimilarity of bacterial communities and enriched plant growth-promoting species. (3) Functions associated with stress tolerance, including signal transduction and biosynthesis of other secondary metabolites were increased significantly in intermittent deep tillage treatments. Moreover, IDT-30 only increased soil characters and root system architecture traits compared with CK, but deeper tillage could also change rhizosphere bacterial communities and functional profiles. Plant height and stem girth in IDT-40 and IDT-50 were higher compared with IDT-30, and infection rates of black shank and black root rot in IDT-50 were even lower in IDT-40. The study provided a comprehensive explanation into the effects of intermittent deep tillage in plant production and suggested an optimal depth.
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Affiliation(s)
- Yabing Gu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Yongjun Liu
- College of Agronomy, Hunan Agricultural University, Changsha, China
- Tobacco Research Institute of Hunan Province, Changsha, China
| | - Jiaying Li
- Yongzhou Tobacco Company of Hunan Province, Yongzhou, China
| | - Mingfeng Cao
- Changde Tobacco Company of Hunan Province, Changde, China
| | - Zhenhua Wang
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Juan Li
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Peijian Cao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Shuhui Duan
- Tobacco Research Institute of Hunan Province, Changsha, China
| | - Mingfa Zhang
- Xiangxizhou Tobacco Company of Hunan Province, Jishou, China
| | - Ge Tan
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Jing Xiong
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Zhicheng Zhou
- Tobacco Research Institute of Hunan Province, Changsha, China
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22
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Liu Y, Ma W, He H, Wang Z, Cao Y. Effects of Sugarcane and Soybean Intercropping on the Nitrogen-Fixing Bacterial Community in the Rhizosphere. Front Microbiol 2021; 12:713349. [PMID: 34659143 PMCID: PMC8515045 DOI: 10.3389/fmicb.2021.713349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 09/06/2021] [Indexed: 11/24/2022] Open
Abstract
Intercropping between sugarcane and soybean is widely used to increase crop yield and promote the sustainable development of the sugarcane industry. However, our understanding of the soil microenvironment in intercropping systems, especially the effect of crop varieties on rhizosphere soil bacterial communities, remains poor. We selected two excellent sugarcane cultivars, Zhongzhe1 (ZZ1) and Zhongzhe9 (ZZ9), from Guangxi and the local soybean variety GUIZAO2 from Guangxi for field interplanting experiments. These two cultivars of sugarcane have good drought resistance. Rhizosphere soil samples were collected from the two intercropping systems to measure physicochemical properties and soil enzyme activities and to extract total soil DNA for high-throughput sequencing. We found that the diversity of the rhizosphere bacterial community was significantly different between the two intercropping systems. Compared with ZZ1, the ZZ9 intercropping system enriched the nitrogen-fixing bacteria, increasing the available nitrogen content by 18% compared with that with ZZ1. In addition, ZZ9 intercropping with soybean formed a more compact rhizosphere environment than ZZ1, thus providing favorable conditions for sugarcane growth. These results provide guidance for the sugarcane industry, especially for the management of sugarcane and soybean intercropping in Guangxi, China.
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Affiliation(s)
- Yue Liu
- College of Agronomy, Guangxi University, Nanning, China
| | - Wenqing Ma
- Guangxi South Subtropical Agricultural Science Research Institute, Chongzuo, China
| | - Hongliang He
- Guangxi South Subtropical Agricultural Science Research Institute, Chongzuo, China
| | - Ziting Wang
- College of Agronomy, Guangxi University, Nanning, China
| | - Yanhong Cao
- Guangxi Key Laboratory of Livestock Genetic Improvement, The Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, China
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Tal O, Bartuv R, Vetcos M, Medina S, Jiang J, Freilich S. NetCom: A Network-Based Tool for Predicting Metabolic Activities of Microbial Communities Based on Interpretation of Metagenomics Data. Microorganisms 2021; 9:microorganisms9091838. [PMID: 34576734 PMCID: PMC8468097 DOI: 10.3390/microorganisms9091838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 08/08/2021] [Accepted: 08/18/2021] [Indexed: 12/13/2022] Open
Abstract
The study of microbial activity can be viewed as a triangle with three sides: environment (dominant resources in a specific habitat), community (species dictating a repertoire of metabolic conversions) and function (production and/or utilization of resources and compounds). Advances in metagenomics enable a high-resolution description of complex microbial communities in their natural environments and support a systematic study of environment-community-function associations. NetCom is a web-tool for predicting metabolic activities of microbial communities based on network-based interpretation of assembled and annotated metagenomics data. The algorithm takes as an input, lists of differentially abundant enzymatic reactions and generates the following outputs: (i) pathway associations of differently abundant enzymes; (ii) prediction of environmental resources that are unique to each treatment, and their pathway associations; (iii) prediction of compounds that are produced by the microbial community, and pathway association of compounds that are treatment-specific; (iv) network visualization of enzymes, environmental resources and produced compounds, that are treatment specific (2 and 3D). The tool is demonstrated on metagenomic data from rhizosphere and bulk soil samples. By predicting root-specific activities, we illustrate the relevance of our framework for forecasting the impact of soil amendments on the corresponding microbial communities. NetCom is available online.
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Affiliation(s)
- Ofir Tal
- Newe Ya’ar Research Center, Institute of Plant Sciences, The Agricultural Research Organization, Ramat Yishay 30095, Israel; (O.T.); (R.B.); (M.V.); (S.M.)
| | - Rotem Bartuv
- Newe Ya’ar Research Center, Institute of Plant Sciences, The Agricultural Research Organization, Ramat Yishay 30095, Israel; (O.T.); (R.B.); (M.V.); (S.M.)
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot 7628604, Israel
| | - Maria Vetcos
- Newe Ya’ar Research Center, Institute of Plant Sciences, The Agricultural Research Organization, Ramat Yishay 30095, Israel; (O.T.); (R.B.); (M.V.); (S.M.)
| | - Shlomit Medina
- Newe Ya’ar Research Center, Institute of Plant Sciences, The Agricultural Research Organization, Ramat Yishay 30095, Israel; (O.T.); (R.B.); (M.V.); (S.M.)
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China;
| | - Shiri Freilich
- Newe Ya’ar Research Center, Institute of Plant Sciences, The Agricultural Research Organization, Ramat Yishay 30095, Israel; (O.T.); (R.B.); (M.V.); (S.M.)
- Correspondence:
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24
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Shi Y, Yang H, Chu M, Niu X, Huo X, Gao Y, Zeng J, Lin Q, Lou K. Diversity and Spatiotemporal Dynamics of Fungal Communities in the Rhizosphere Soil of Cotton in the Arid Region of Northwest China. MICROBIAL ECOLOGY 2021; 82:87-99. [PMID: 33415384 DOI: 10.1007/s00248-020-01646-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 11/15/2020] [Indexed: 06/12/2023]
Abstract
This study aimed to investigate the fungal diversity and its temporal and spatial dynamics in the rhizosphere soil of healthy cotton by high-throughput sequencing. We studied species richness, composition, and distribution of cotton rhizosphere fungal community with respect to location (Alaer, Kuerle, Tumushuke, Hami, Shihezi, Wusu, and Jinghe) and plant growth period (seedling stage, bud stage, flowering stage, and boll-opening stage) using the methods of PCR-based high-throughput sequencing and real-time quantitative PCR. A total of 1,838,454 fungal nuclear ribosomal internal transcribed spacer region sequences (rRNA ITS) were obtained from all cotton plants sampled at different growth stages in the seven locations in Xinjiang. The most abundant fungal group in the cotton rhizosphere was the Ascomycota (78.72%), followed by the Zygomycota (9.56%) and Basidiomycota (2.77%). These sequences revealed an enormous number of operational taxonomic units (OTUs) in cotton (1802 unique OTUs), with 67-464 OTUs in a single cotton sample, at a 3% threshold and a sequencing depth of 30,000 sequences. We identified 33 classes and 389 genera from the resulting 1,800,714 sequences. Sordariomycetes was the most frequent class in all samples, followed by Leotiomycetes and Eurotiomycetes. There were some differences in OTUs among different growth stages, but the differences were not significant, with 382 OTUs (14.66%) being common to each of the stages. A marked difference in the diversity of fungi in the rhizosphere soil of cotton was evident among the different locations, with the highest number of OTUs being detected in Jinghe (1084 OTUs) and clusters of OTUs representative of northern and eastern Xinjiang being detected. There were significantly more tags of Mortierella in Jinghe and Wusu than in the other sampling sites. The dynamics of the rhizosphere fungal communities were influenced by sampling sites. To the best of our knowledge, the current study is the first application of PCR-based Illumina to characterize and compare the fungal biodiversity in multiple rhizosphere soil samples from cotton.
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Affiliation(s)
- YingWu Shi
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, Xinjiang, China.
- Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, Xinjiang, China.
- Key Laboratory of Agricultural Environment in Northwest Oasis of Ministry of Agriculture and Countryside, Urumqi, 830091, Xinjiang, China.
- Institute of Soil, Fertilizer and Agricultural Water Conservation, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, Xinjiang, China.
| | - HongMei Yang
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, Xinjiang, China
- Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, Xinjiang, China
- Key Laboratory of Agricultural Environment in Northwest Oasis of Ministry of Agriculture and Countryside, Urumqi, 830091, Xinjiang, China
| | - Ming Chu
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, Xinjiang, China
- Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, Xinjiang, China
- Key Laboratory of Agricultural Environment in Northwest Oasis of Ministry of Agriculture and Countryside, Urumqi, 830091, Xinjiang, China
| | - XinXiang Niu
- Key Laboratory of Agricultural Environment in Northwest Oasis of Ministry of Agriculture and Countryside, Urumqi, 830091, Xinjiang, China
- Institute of Soil, Fertilizer and Agricultural Water Conservation, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, Xinjiang, China
| | - XiangDong Huo
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, Xinjiang, China
- Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, Xinjiang, China
| | - Yan Gao
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, Xinjiang, China
- Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, Xinjiang, China
| | - Jun Zeng
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, Xinjiang, China
- Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, Xinjiang, China
| | - Qing Lin
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, Xinjiang, China
- Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, Xinjiang, China
| | - Kai Lou
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, Xinjiang, China
- Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, Xinjiang, China
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25
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Koskey G, Mburu SW, Awino R, Njeru EM, Maingi JM. Potential Use of Beneficial Microorganisms for Soil Amelioration, Phytopathogen Biocontrol, and Sustainable Crop Production in Smallholder Agroecosystems. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.606308] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Smallholder agroecosystems play a key role in the world's food security providing more than 50% of the food produced globally. These unique agroecosystems face a myriad of challenges and remain largely unsupported, yet they are thought to be a critical resource for feeding the projected increasing human population in the coming years. The new challenge to increase food production through agricultural intensification in shrinking per capita arable lands, dwindling world economies, and unpredictable climate change, has led to over-dependence on agrochemical inputs that are often costly and hazardous to both human and animal health and the environment. To ensure healthy crop production approaches, the search for alternative ecofriendly strategies that best fit to the smallholder systems have been proposed. The most common and widely accepted solution that has gained a lot of interest among researchers and smallholder farmers is the use of biological agents; mainly plant growth promoting microorganisms (PGPMs) that provide essential agroecosystem services within a holistic vision of enhancing farm productivity and environmental protection. PGPMs play critical roles in agroecological cycles fundamental for soil nutrient amelioration, crop nutrient improvement, plant tolerance to biotic and abiotic stresses, biocontrol of pests and diseases, and water uptake. This review explores different research strategies involving the use of beneficial microorganisms, within the unique context of smallholder agroecosystems, to promote sustainable maintenance of plant and soil health and enhance agroecosystem resilience against unpredictable climatic perturbations.
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26
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Hu R, Li Q, Huang Y, Zhao Y, Xiao L, Jing Q, Zou Y, Lin L. Intercropping with post-grafting generation of Solanum photeinocarpum decreases cadmium accumulation in soybean ( Glycine max). INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2021; 23:1124-1131. [PMID: 33528274 DOI: 10.1080/15226514.2021.1880366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
A pot experiment was designed to explore the effects of different post-grafting generations of Solanum photeinocarpum Nakamura et Odashima intercropping on growth and cadmium (Cd) accumulation in soybeans (varieties: "Zaodou" and "Liaoxian"). Post generation of S. photeinocarpum (ungrafted, grafted on eggplant, potato, and tomato, respectively) were utilized to intercrop with two varieties of soybean in Cd-contaminated soil. Soybean monoculture was employed as a control. Consequently, intercropping with different post-grafting S. photeinocarpum generation, except for tomato rootstock grafts post-generation, could reduce soybean biomass and photosynthetic pigment content. Additionally, all S. photeinocarpum post-grafting generations had the capacity to reduce Cd content in soybean when intercropping, while tomato rootstock grafts post-generation exhibited an adequate ability to accumulate Cd in S. photeinocarpum compared to the ungrafted treatment. In particular, tomato rootstock grafts post-generation could effectively decrease Cd content in soybean organs by 14.09-62.13%, relative to soybean monoculture, but increased shoot Cd content and shoot Cd extraction of S. photeinocarpum by 10.33-13.49% and 10.38-12.03%, respectively, compared to the ungrafted treatment. Thus, tomato rootstock grafting may enhance the ability of post-grafting generation of S. photeinocarpum to remediate Cd-contaminated soil, and this grafting was able to reduce Cd accumulation in soybean.
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Affiliation(s)
- Rongping Hu
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- MOA Key Laboratory of Integrated Management of Pests on Crops in Southwest China, Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Qinyuan Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Yong Huang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Yan Zhao
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Ling Xiao
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Qianhe Jing
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Yao Zou
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Lijin Lin
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
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27
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Ochieno DMW, Karoney EM, Muge EK, Nyaboga EN, Baraza DL, Shibairo SI, Naluyange V. Rhizobium-Linked Nutritional and Phytochemical Changes Under Multitrophic Functional Contexts in Sustainable Food Systems. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2020.604396] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Rhizobia are bacteria that exhibit both endophytic and free-living lifestyles. Endophytic rhizobial strains are widely known to infect leguminous host plants, while some do infect non-legumes. Infection of leguminous roots often results in the formation of root nodules. Associations between rhizobia and host plants may result in beneficial or non-beneficial effects. Such effects are linked to various biochemical changes that have far-reaching implications on relationships between host plants and the dependent multitrophic biodiversity. This paper explores relationships that exist between rhizobia and various plant species. Emphasis is on nutritional and phytochemical changes that occur in rhizobial host plants, and how such changes affect diverse consumers at different trophic levels. The purpose of this paper is to bring into context various aspects of such interactions that could improve knowledge on the application of rhizobia in different fields. The relevance of rhizobia in sustainable food systems is addressed in context.
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28
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Zhao Z, Chen Y, Li Q, Wu X. Mathematical model for diffusion of the rhizosphere microbial degradation with impulsive feedback control. JOURNAL OF BIOLOGICAL DYNAMICS 2020; 14:566-577. [PMID: 32633218 DOI: 10.1080/17513758.2020.1786860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 06/08/2020] [Indexed: 06/11/2023]
Abstract
Considering the rhizosphere microbes easily affected by the environmental factors, we formulate a three-dimensional diffusion model of the rhizosphere microbes with the impulsive feedback control to describe the complex degradation and movement by introducing beneficial microbes into the plant rhizosphere. The sufficient conditions for existence of the order-1 periodic solution are obtained by using the geometrical theory of the impulsive semi-dynamical system. We show the impulsive control system tends to an order-1 periodic solution if the control measures are achieved. Furthermore, we investigate the stability of the order-1 periodic solution by means of a novel method introduced in the literature [Y. Ye, The Theory of the Limit Cycle, Shanghai Science and Technology Press, 1984.]. Finally, mathematical results are justified by some numerical simulations.
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Affiliation(s)
- Zhong Zhao
- School of Mathematics and Statistics, Huanghuai University, Zhumadian, People's Republic of China
| | - Ying Chen
- School of Mathematics and Statistics, Huanghuai University, Zhumadian, People's Republic of China
| | - Qiuying Li
- School of Mathematics and Statistics, Huanghuai University, Zhumadian, People's Republic of China
| | - Xianbin Wu
- Junior College, Zhejiang Wanli University, Ningbo, People's Republic of China
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29
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Ku YS, Contador CA, Ng MS, Yu J, Chung G, Lam HM. The Effects of Domestication on Secondary Metabolite Composition in Legumes. Front Genet 2020; 11:581357. [PMID: 33193705 PMCID: PMC7530298 DOI: 10.3389/fgene.2020.581357] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 08/31/2020] [Indexed: 12/13/2022] Open
Abstract
Legumes are rich in secondary metabolites, such as polyphenols, alkaloids, and saponins, which are important defense compounds to protect the plant against herbivores and pathogens, and act as signaling molecules between the plant and its biotic environment. Legume-sourced secondary metabolites are well known for their potential benefits to human health as pharmaceuticals and nutraceuticals. During domestication, the color, smell, and taste of crop plants have been the focus of artificial selection by breeders. Since these agronomic traits are regulated by secondary metabolites, the basis behind the genomic evolution was the selection of the secondary metabolite composition. In this review, we will discuss the classification, occurrence, and health benefits of secondary metabolites in legumes. The differences in their profiles between wild legumes and their cultivated counterparts will be investigated to trace the possible effects of domestication on secondary metabolite compositions, and the advantages and drawbacks of such modifications. The changes in secondary metabolite contents will also be discussed at the genetic level to examine the genes responsible for determining the secondary metabolite composition that might have been lost due to domestication. Understanding these genes would enable breeding programs and metabolic engineering to produce legume varieties with favorable secondary metabolite profiles for facilitating adaptations to a changing climate, promoting beneficial interactions with biotic factors, and enhancing health-beneficial secondary metabolite contents for human consumption.
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Affiliation(s)
- Yee-Shan Ku
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, China
| | - Carolina A. Contador
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, China
| | - Ming-Sin Ng
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, China
| | - Jeongjun Yu
- Department of Biotechnology, Chonnam National University, Yeosu, South Korea
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, South Korea
| | - Hon-Ming Lam
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, China
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30
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Solanki MK, Wang Z, Wang FY, Li CN, Gupta CL, Singh RK, Malviya MK, Singh P, Yang LT, Li YR. Assessment of Diazotrophic Proteobacteria in Sugarcane Rhizosphere When Intercropped With Legumes (Peanut and Soybean) in the Field. Front Microbiol 2020; 11:1814. [PMID: 32849421 PMCID: PMC7412970 DOI: 10.3389/fmicb.2020.01814] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 07/10/2020] [Indexed: 12/20/2022] Open
Abstract
Several factors influenced the sugarcane production, and among them, higher use of nitrogen and depletion of soil nutrient constitutes a significant concern in China. Sugarcane-legume intercropping may help to regulate the microbial structure and functions. In the present study, sugarcane rhizosphere soils of three cropping systems: Sugarcane only (S-only), sugarcane with peanut (S + P), and sugarcane + soybean (S + S) were sampled in tillering, elongation, and maturation stages from two different experimental fields. High-throughput sequencing technologies applied to assess the effects of different cropping systems on the structure of nitrogenase (nifH) gene communities. A total of 3818 OTUs (operational taxonomic units) were acquired from all soil samples. Intercropping systems noticeably increased the relative abundance of Proteobacteria in the tillering stage. The increased microbial diversity in the rhizosphere was mainly due to soil organic carbon and total soil N. In contrast, intercropping has no significant negative impact on microbial abundance, but sugarcane growth stages influence it significantly, and two bacteria (Bradyrhizobium and Pseudacidovorax) showed significant shift during plant growth. The results provide insight into the microbial structure of Proteobacteria in the sugarcane legume-intercropping field, and how microbial community behaves in different growth stages. It can boost the microbial activity of the soil, and that could be a new strategy to stimulate soil fertility without causing any negative impact on crop production.
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Affiliation(s)
- Manoj Kumar Solanki
- Guangxi Crop Genetic Improvement and Biotechnology Lab, Guangxi Academy of Agricultural Sciences, Nanning, China.,Department of Food Quality & Safety, The Volcani Center, Institute for Post-harvest and Food Sciences, Agricultural Research Organization, Rishon LeZion, Israel
| | - Zhen Wang
- Guangxi Crop Genetic Improvement and Biotechnology Lab, Guangxi Academy of Agricultural Sciences, Nanning, China.,College of Biology and Pharmacy, Yulin Normal University, Yulin, China
| | - Fei-Yong Wang
- Guangxi Crop Genetic Improvement and Biotechnology Lab, Guangxi Academy of Agricultural Sciences, Nanning, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Agricultural College, Guangxi University, Nanning, China.,Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
| | - Chang-Ning Li
- Guangxi Crop Genetic Improvement and Biotechnology Lab, Guangxi Academy of Agricultural Sciences, Nanning, China.,Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Institute of Guangxi Academy of Agricultural Sciences, Sugarcane Research Center of Chinese Academy of Agricultural Sciences, Nanning, China
| | - Chhedi Lal Gupta
- The Volcani Center, Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Rishon LeZion, Israel
| | - Rajesh Kumar Singh
- Guangxi Crop Genetic Improvement and Biotechnology Lab, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Mukesh Kumar Malviya
- Guangxi Crop Genetic Improvement and Biotechnology Lab, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Pratiksha Singh
- Guangxi Crop Genetic Improvement and Biotechnology Lab, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Li-Tao Yang
- College of Biology and Pharmacy, Yulin Normal University, Yulin, China
| | - Yang-Rui Li
- Guangxi Crop Genetic Improvement and Biotechnology Lab, Guangxi Academy of Agricultural Sciences, Nanning, China.,Department of Food Quality & Safety, The Volcani Center, Institute for Post-harvest and Food Sciences, Agricultural Research Organization, Rishon LeZion, Israel
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31
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Karthika S, Varghese S, Jisha MS. Exploring the efficacy of antagonistic rhizobacteria as native biocontrol agents against tomato plant diseases. 3 Biotech 2020; 10:320. [PMID: 32656053 DOI: 10.1007/s13205-020-02306-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 06/15/2020] [Indexed: 11/24/2022] Open
Abstract
As the environmental and health concerns alert the necessity to move towards a sustainable agriculture system, biological approach using indigenous plant growth-promoting rhizobacteria (PGPR) gains a strong impetus in the field of plant disease control. In this context, the present review article addresses the usage of rhizospheric antagonistic bacteria as a suitable alternative to control tomato fungal diseases namely Fusarium wilt and early blight disease. Biological control has been considered to be an eco-friendly, safe and effective method for disease management. The inherent traits of PGPR to antagonize a pathogen through various mechanisms has been investigated extensively to utilize them as potent biocontrol agents (BCA). Hence, the article provides a detailed account on different biocontrol mechanisms displayed by BCA. It is also suggested that the use of bacterial consortium ensures consistent performance by BCA in field conditions. Likewise, this review also deals with the opportunities and obstacles faced during commercialization of these antagonistic bacteria as biocontrol agents in the market.
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Affiliation(s)
- S Karthika
- School of Biosciences, Mahatma Gandhi University, Kottayam, Kerala 686560 India
| | - Sherin Varghese
- School of Biosciences, Mahatma Gandhi University, Kottayam, Kerala 686560 India
| | - M S Jisha
- School of Biosciences, Mahatma Gandhi University, Kottayam, Kerala 686560 India
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Li J, Chen X, Li S, Zuo Z, Zhan R, He R. Variations of rhizospheric soil microbial communities in response to continuous Andrographis paniculata cropping practices. BOTANICAL STUDIES 2020; 61:18. [PMID: 32542518 PMCID: PMC7295922 DOI: 10.1186/s40529-020-00295-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 06/06/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Changes of soil microbial communities are one of the main factors of continuous cropping problem. Andrographis paniculata has been reported to have replant problem in cultivation. However, little is known about the variations of rhizosphere soil microbial communities of A. paniculata under a continuous cropping system. Here, Illumina MiSeq was used to investigate the shifts of rhizospheric bacterial and fungal communities after continuous cropping of A. paniculata. RESULTS The bacterial diversity increased whereas the fungal diversity decreased in rhizosphere soil after consecutive A. paniculata monoculture; and the soil microbial community structure differed between newly plant soil and continuous cropped soil. Taxonomic analyses further revealed that the bacterial phyla Proteobacteria, Acidobacteria and Bacteroidetes and the fungal phyla Zygomycota, Ascomycota and Cercozoa were the dominant phyla across all soil samples. The relative abundance of phyla Acidobacteria and Zygomycota were significantly increased after continuous cropping. Additionally, the most abundant bacterial genus Pseudolabrys significantly decreased, while the predominant fungal genus Mortierella increased considerably in abundance after continuous cropping. CONCLUSIONS Our results revealed the changes on diversity and composition of bacterial and fungal communities in rhizospheric soil under continuous cropping of A. paniculata. These data contributed to the understanding of soil micro-ecological environments in the rhizosphere of A. paniculata.
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Affiliation(s)
- Junren Li
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, 510006, People's Republic of China
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Guangzhou, 510006, People's Republic of China
| | - Xiuzhen Chen
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, 510006, People's Republic of China
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Guangzhou, 510006, People's Republic of China
| | - Simin Li
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, 510006, People's Republic of China
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Guangzhou, 510006, People's Republic of China
| | - Zimei Zuo
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, 510006, People's Republic of China
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Guangzhou, 510006, People's Republic of China
| | - Ruoting Zhan
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, 510006, People's Republic of China
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Guangzhou, 510006, People's Republic of China
| | - Rui He
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, 510006, People's Republic of China.
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Guangzhou, 510006, People's Republic of China.
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Habiyaremye JDD, Goldmann K, Reitz T, Herrmann S, Buscot F. Tree Root Zone Microbiome: Exploring the Magnitude of Environmental Conditions and Host Tree Impact. Front Microbiol 2020; 11:749. [PMID: 32390986 PMCID: PMC7190799 DOI: 10.3389/fmicb.2020.00749] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/30/2020] [Indexed: 01/14/2023] Open
Abstract
Tree roots attract their associated microbial partners from the local soil community. Accordingly, tree root-associated microbial communities are shaped by both the host tree and local environmental variables. To rationally compare the magnitude of environmental conditions and host tree impact, the "PhytOakmeter" project planted clonal oak saplings (Quercus robur L., clone DF159) as phytometers into different field sites that are within a close geographic space across the Central German lowland region. The PhytOakmeters were produced via micro-propagation to maintain their genetic identity. The current study analyzed the microbial communities in the PhytOakmeter root zone vs. the tree root-free zone of soil two years after out-planting the trees. Soil DNA was extracted, 16S and ITS2 genes were respectively amplified for bacteria and fungi, and sequenced using Illumina MiSeq technology. The obtained microbial communities were analyzed in relation to soil chemistry and weather data as environmental conditions, and the host tree growth. Although microbial diversity in soils of the tree root zone was similar among the field sites, the community structure was site-specific. Likewise, within respective sites, the microbial diversity between PhytOakmeter root and root-free zones was comparable. The number of microbial species exclusive to either zone, however, was higher in the host tree root zone than in the tree root-free zone. PhytOakmeter "core" and "site-specific" microbiomes were identified and attributed to the host tree selection effect and/or to the ambient conditions of the sites, respectively. The identified PhytOakmeter root zone-associated microbiome predominantly included ectomycorrhizal fungi, yeasts and saprotrophs. Soil pH, soil organic matter, and soil temperature were significantly correlated with the microbial diversity and/or community structure. Although the host tree contributed to shape the soil microbial communities, its effect was surpassed by the impact of environmental factors. The current study helps to understand site-specific microbe recruitment processes by young host trees.
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Affiliation(s)
- Jean de Dieu Habiyaremye
- Department of Soil Ecology, Helmholtz Centre for Environmental Research (UFZ), Halle, Germany
- Department of Biology II, Leipzig University, Leipzig, Germany
- Department of Mathematics, Science and Physical Education, University of Rwanda, Kigali, Rwanda
| | - Kezia Goldmann
- Department of Soil Ecology, Helmholtz Centre for Environmental Research (UFZ), Halle, Germany
| | - Thomas Reitz
- Department of Soil Ecology, Helmholtz Centre for Environmental Research (UFZ), Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Sylvie Herrmann
- Department of Soil Ecology, Helmholtz Centre for Environmental Research (UFZ), Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - François Buscot
- Department of Soil Ecology, Helmholtz Centre for Environmental Research (UFZ), Halle, Germany
- Department of Biology II, Leipzig University, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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Lipa P, Janczarek M. Phosphorylation systems in symbiotic nitrogen-fixing bacteria and their role in bacterial adaptation to various environmental stresses. PeerJ 2020; 8:e8466. [PMID: 32095335 PMCID: PMC7020829 DOI: 10.7717/peerj.8466] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/27/2019] [Indexed: 12/23/2022] Open
Abstract
Symbiotic bacteria, commonly called rhizobia, lead a saprophytic lifestyle in the soil and form nitrogen-fixing nodules on legume roots. During their lifecycle, rhizobia have to adapt to different conditions prevailing in the soils and within host plants. To survive under these conditions, rhizobia fine-tune the regulatory machinery to respond rapidly and adequately to environmental changes. Symbiotic bacteria play an essential role in the soil environment from both ecological and economical point of view, since these bacteria provide Fabaceae plants (legumes) with large amounts of accessible nitrogen as a result of symbiotic interactions (i.e., rhizobia present within the nodule reduce atmospheric dinitrogen (N2) to ammonia, which can be utilized by plants). Because of its restricted availability in the soil, nitrogen is one of the most limiting factors for plant growth. In spite of its high content in the atmosphere, plants are not able to assimilate it directly in the N2 form. During symbiosis, rhizobia infect host root and trigger the development of specific plant organ, the nodule. The aim of root nodule formation is to ensure a microaerobic environment, which is essential for proper activity of nitrogenase, i.e., a key enzyme facilitating N2 fixation. To adapt to various lifestyles and environmental stresses, rhizobia have developed several regulatory mechanisms, e.g., reversible phosphorylation. This key mechanism regulates many processes in both prokaryotic and eukaryotic cells. In microorganisms, signal transduction includes two-component systems (TCSs), which involve membrane sensor histidine kinases (HKs) and cognate DNA-binding response regulators (RRs). Furthermore, regulatory mechanisms based on phosphoenolopyruvate-dependent phosphotranspherase systems (PTSs), as well as alternative regulatory pathways controlled by Hanks-type serine/threonine kinases (STKs) and serine/threonine phosphatases (STPs) play an important role in regulation of many cellular processes in both free-living bacteria and during symbiosis with the host plant (e.g., growth and cell division, envelope biogenesis, biofilm formation, response to stress conditions, and regulation of metabolism). In this review, we summarize the current knowledge of phosphorylation systems in symbiotic nitrogen-fixing bacteria, and their role in the physiology of rhizobial cells and adaptation to various environmental conditions.
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Affiliation(s)
- Paulina Lipa
- Department of Genetics and Microbiology, Institute of Biological Sciences, Maria Curie-Sklodowska University Lublin, Lublin, Poland
| | - Monika Janczarek
- Department of Genetics and Microbiology, Institute of Biological Sciences, Maria Curie-Sklodowska University Lublin, Lublin, Poland
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Shi Y, Yang H, Chu M, Niu X, Huo X, Gao Y, Zeng J, Lin Q, Zhang T, Li Y, Outi K, Lou K, Li X, Dang W, Zhang T. Diversity and space-time dynamics of the bacterial communities in cotton ( Gossypium hirsutum) rhizosphere soil. Can J Microbiol 2020; 66:228-242. [PMID: 31944857 DOI: 10.1139/cjm-2019-0196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Rhizosphere bacteria are key determinants of plant health and productivity. In this study, we used PCR-based next-generation sequencing to reveal the diversity and community composition of bacteria in the cotton rhizosphere from samples collected in Xinjiang Province, China. We identified 125 bacterial classes within 49 phyla from these samples. Proteobacteria (33.07% of total sequences), Acidobacteria (19.88%), and Gemmatimonadetes (11.19%) dominated the bacterial community. Marked differences were evident in the α-diversity of rhizosphere bacteria during different cotton plant growth and development stages. The operational taxonomic unit (OTU) numbers were highest in seedling and bud stages and decreased at the flowering and fruit-boll-opening stages. Forty-three OTUs from the Proteobacteria were common to all four periods of cotton development. Proteobacteria were more abundant in the rhizospheres of cotton from southern Xinjiang than from northern Xinjiang, while the opposite trend was observed for Acidobacteria. Gemmatimonadetes frequency was broadly the same in both northern and southern Xinjiang. These results suggest that there is abundant diversity in the microbiota of cotton rhizosphere soil. Proteobacteria and Actinobacteria dominated this microbial niche and bacterial communities in the seedling, bud, flowering, and boll-opening stages appear to be more similar to one another than to communities at the other growth stages.
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Affiliation(s)
- YingWu Shi
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, Xinjiang, P.R. China.,Xinjiang Laboratory of Special Environmental Microbiology, Urumqi 830091, Xinjiang, P.R. China
| | - HongMei Yang
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, Xinjiang, P.R. China.,Xinjiang Laboratory of Special Environmental Microbiology, Urumqi 830091, Xinjiang, P.R. China
| | - Ming Chu
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, Xinjiang, P.R. China.,Xinjiang Laboratory of Special Environmental Microbiology, Urumqi 830091, Xinjiang, P.R. China
| | - XinXiang Niu
- Institute of Soil, Fertilizer and Agricultural Water Conservation, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, Xinjiang, P.R. China
| | - XiangDong Huo
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, Xinjiang, P.R. China.,Xinjiang Laboratory of Special Environmental Microbiology, Urumqi 830091, Xinjiang, P.R. China
| | - Yan Gao
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, Xinjiang, P.R. China.,Xinjiang Laboratory of Special Environmental Microbiology, Urumqi 830091, Xinjiang, P.R. China
| | - Jun Zeng
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, Xinjiang, P.R. China.,Xinjiang Laboratory of Special Environmental Microbiology, Urumqi 830091, Xinjiang, P.R. China
| | - Qing Lin
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, Xinjiang, P.R. China.,Xinjiang Laboratory of Special Environmental Microbiology, Urumqi 830091, Xinjiang, P.R. China
| | - Tao Zhang
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, Xinjiang, P.R. China.,Xinjiang Laboratory of Special Environmental Microbiology, Urumqi 830091, Xinjiang, P.R. China
| | - YuGuo Li
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, Xinjiang, P.R. China.,Xinjiang Laboratory of Special Environmental Microbiology, Urumqi 830091, Xinjiang, P.R. China
| | - KuEr Outi
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, Xinjiang, P.R. China.,Xinjiang Laboratory of Special Environmental Microbiology, Urumqi 830091, Xinjiang, P.R. China
| | - Kai Lou
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, Xinjiang, P.R. China.,Xinjiang Laboratory of Special Environmental Microbiology, Urumqi 830091, Xinjiang, P.R. China
| | - XueYan Li
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, Xinjiang, P.R. China.,Xinjiang Laboratory of Special Environmental Microbiology, Urumqi 830091, Xinjiang, P.R. China
| | - WenFang Dang
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, Xinjiang, P.R. China.,Xinjiang Laboratory of Special Environmental Microbiology, Urumqi 830091, Xinjiang, P.R. China
| | - Tao Zhang
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, Xinjiang, P.R. China.,Xinjiang Laboratory of Special Environmental Microbiology, Urumqi 830091, Xinjiang, P.R. China
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de Castro GLS, Rêgo MCF, Silvestre WVD, Batista TFV, da Silva GB. Açaí palm seedling growth promotion by rhizobacteria inoculation. Braz J Microbiol 2019; 51:205-216. [PMID: 31792759 DOI: 10.1007/s42770-019-00159-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 09/14/2019] [Indexed: 11/27/2022] Open
Abstract
Lower growth rate of the açaí palm seedlings limits the crops' commercial expansion. The goal was evaluating the biometry, biomass accumulation, nutrient contents, chlorophyll-a fluorescence, and gas exchange in açaí seedlings inoculated with rhizobacteria. The treatments were individual inoculations of the seven rhizobacteria isolates and one control (without inoculation) on the roots. Biometry and biomass data were submitted to cluster analysis to separate the isolates into groups according to the similarity degree, and groups' means were compared through the SNK test. Three groups were formed; group 1 was composed of the control; group 2 of the UFRA-35, UFRA-38, UFRA-58, UFRA-61, UFRA-92, and BRM-32111 isolates; and group 3 was composed of the BRM-32113 isolate. Group 2 and 3 isolates promoted an increase in growth, biomass accumulation, higher levels of nutrients and chlorophyll, and improvements in the gas exchange and chlorophyll-a fluorescence in comparison with the control. The results evidenced that the rhizobacteria accelerate the growth, increase the photosynthetic efficiency, and induce the leaf nutrient accumulation in açaí palm seedlings. The rhizobacteria inoculation can contribute to the sustainable management of the açaí palm seedling production in nurseries.
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Affiliation(s)
- Gledson Luiz Salgado de Castro
- Institute of Agricultural Sciences, Plant Protection Laboratory (LPP), Federal Rural University of Amazonia (UFRA), Belém, PA, 66077-830, Brazil
| | - Marcela Cristiane Ferreira Rêgo
- Institute of Agricultural Sciences, Plant Protection Laboratory (LPP), Federal Rural University of Amazonia (UFRA), Belém, PA, 66077-830, Brazil
| | | | - Telma Fátima Vieira Batista
- Institute of Agricultural Sciences, Plant Protection Laboratory (LPP), Federal Rural University of Amazonia (UFRA), Belém, PA, 66077-830, Brazil
| | - Gisele Barata da Silva
- Institute of Agricultural Sciences, Plant Protection Laboratory (LPP), Federal Rural University of Amazonia (UFRA), Belém, PA, 66077-830, Brazil.
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Ankati S, Podile AR. Metabolites in the root exudates of groundnut change during interaction with plant growth promoting rhizobacteria in a strain-specific manner. JOURNAL OF PLANT PHYSIOLOGY 2019; 243:153057. [PMID: 31675630 DOI: 10.1016/j.jplph.2019.153057] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 10/02/2019] [Accepted: 10/04/2019] [Indexed: 05/17/2023]
Abstract
Plant growth promoting rhizobacteria (PGPR) are extensively used as biofertilizers to improve the soil nutrition for a variety of crop plants. The plant-PGPR interaction, with special reference to chemical signalling molecules is not understood clearly, unlike other beneficial plant-microbe interactions. Chemo-attraction of a PGPR from soil microbial pool towards a plant could be dependent on some of the molecules in the plant root exudates (REs), similar to the beneficial association of legume-rhizobia. In this study, a few functional properties of PGPR like growth, chemotaxis, and biofilm formation by two PGPR strains viz., Bacillus sonorensis RS4 and Pseudomonas aeruginosa RP2 were assessed in the presence of groundnut REs. Functional properties of both the strains were significantly influenced by the REs in a strain-dependent manner. Metabolite profiling of the REs from PGPR-bacterized (RS4 or RP2) and non-bacterized seedlings was performed with GC-MS/MS after 12 and 24 days of growth. A total of 75 metabolites were detected in groundnut REs. Threonine and glyoxylic oxime acid were detected in RP2-bacterized REs, while serine, pentanoic acid, glucopyranoside, tartaric acid, and 2-pyrrolidinone were detected in REs of seedlings bacterized with RP2 and RS4. The results suggested that the PGPR induced distinct variations in the REs. Identification of the interaction-specific metabolites will be useful to develop effective PGPR based bio-formulations for better PGPR colonization and improving crop yields.
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Affiliation(s)
- Sravani Ankati
- Department of Plant Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Appa Rao Podile
- Department of Plant Sciences, University of Hyderabad, Hyderabad, Telangana, India.
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38
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Tisarum R, Theerawitaya C, Samphumphuang T, Phisalaphong M, Singh HP, Cha-um S. Promoting water deficit tolerance and anthocyanin fortification in pigmented rice cultivar ( Oryza sativa L. subsp. indica) using arbuscular mycorrhizal fungi inoculation. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2019; 25:821-835. [PMID: 31402812 PMCID: PMC6656829 DOI: 10.1007/s12298-019-00658-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 02/12/2019] [Accepted: 03/18/2019] [Indexed: 05/08/2023]
Abstract
Drought or water deficit is a major abiotic stress that can reduce growth and productivity in the rice crop especially in the rain-fed areas, which face long-term water shortage. The objective of this investigation was to promote the drought tolerant abilities in pigmented rice cv. 'Hom Nil' at booting stage using arbuscular mycorrhizal fungi (AMF)-inoculation, mixed spores of Glomus geosporum, G. etunicatum and G. mosseae in the soil before rice seedling transplantation. At booting stage, the AMF-inoculated (+AMF) and AMF-uninoculated plants (-AMF) were subjected to control (well-watering; 46.6% SWC) and water deficit condition (14 days water withholding; 13.8% SWC). Colonization percentage in the AMF-inoculated root tissues were evidently proved in both with and without water deficit conditions, leading to elevate total phosphorus in root and leaf tissues. Interestingly, sucrose and total soluble sugar concentration in the flag leaf were increased by 5.0 folds and 1.5 folds, respectively in the plants under water deficit (WD). Free proline was accumulated in flag leaf when exposure to water deficit, subsequently regulated by AMF-inoculation. Total soluble sugar and free proline enrichment in 'Hom Nil' was a major mode of osmotic adjustment to control osmotic potential in the cellular level when exposed to water deficit, leading to maintained photosynthetic abilities and growth performances. Concentration of chlorophyll b in AMF-inoculated plants under water deficit stress was retained, causing to improve chlorophyll fluorescence and net photosynthetic rate. Shoot height and number of tillers were significantly declined by 12.5% and 11.6%, respectively, when subjected to WD. At the harvest, grain yield, panicle dry weight and fertility percentage of AMF-inoculated rice from WD were greater than those without AMF by 1.5, 3.9 and 2.4 folds, respectively. Cyanidin-3-glucoside and peonidin-3-glucoside concentrations in pericarp were enriched in the grain derived from AMF-inoculation with water deficit stress. Overall growth characters and physiological adaptations in 'Hom Nil' grown under water deficit condition were retained by AMF inoculation, resulting in enhanced yield attributes and anthocyanin fortification in rice grain.
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Affiliation(s)
- Rujira Tisarum
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120 Thailand
| | - Cattarin Theerawitaya
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120 Thailand
| | - Thapanee Samphumphuang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120 Thailand
| | - Muenduen Phisalaphong
- Department of Chemical Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok, 10330 Thailand
| | - Harminder Pal Singh
- Department of Environment Studies, Faculty of Science, Panjab University, Chandigarh, 160014 India
| | - Suriyan Cha-um
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120 Thailand
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Tian Y, Ma X, Li Y, Cheng C, Ge F, An D. Relationship between microbial diversity and nitrogenase activity of Stipagrostis pennata rhizosheath. J Cell Biochem 2019; 120:13501-13508. [PMID: 30938883 DOI: 10.1002/jcb.28625] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/09/2019] [Accepted: 02/14/2019] [Indexed: 11/09/2022]
Abstract
Nitrogen is the key factor for plant survival and growth, especially in the desert. Stipagrostis pennata, a sand born drought-resistant plant, could colonize pioneerly in Gurbantunggut Desert during revegetation. One strategy for their environment adaptation was the rhizosheath formatted by root-hair, mucilaginous exudates, microbial components, and soil particles, for which not only provides a favorable living microenvironment but also supplies essential nutrients. To understand the relationship between microorganisms living in rhizosheaths and the nitrogen nutrition supply, the microbial diversity and nitrogenase activity was estimated during the growth of S. pennata. Five samples of the rhizosheath, which based on the development periods of the plant, regreen, flowering, filling, seed maturating, and withering period, were collected. The nitrogenase activity was estimated by acetylene reduction and the microbial diversity was analyzed by 16S rRNA high-throughput sequencing. The results showed that the nitrogenase activity was increased slowly during regreen to flowering, while reached a peak rapidly at filling sample and then decreased gradually. A total of 274 operational taxonomic units (OTUs) were identified and significant differences in community structure and composition at each growth period. Among them, the main phyla included Actinobacteria and Proteus, which were the most abundant phyla in all periods. In addition, the microbial diversity in the grain filling period was higher than other periods in view of the analysis of alpha diversity and beta diversity. Furthermore, principal component analysis (PCA) analysis showed that the microbial communities in the filling period was low in similarity with other periods. Most importantly, the OTUs associated with nitrogen fixation is the most during the filling period, involving Phagecidae and Fucoraceae. Overall, the study not only revealed the differences in nitrogenase activity among different developmental periods in S. pennata, but also explored the potential bridges between it and community structure and diversity of bacteria.
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Affiliation(s)
- Yongzhi Tian
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, China
| | - Xiaolin Ma
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, China
| | - Yuanting Li
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, China
| | - Cong Cheng
- Jiangsu Key Laboratory of Microbiology and Functional Genomics, College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Fengwei Ge
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, China
| | - Dengdi An
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi, China
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40
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Sun S, Zhou J. Molecular mechanisms underlying stress response and adaptation. Thorac Cancer 2018; 9:218-227. [PMID: 29278299 PMCID: PMC5792716 DOI: 10.1111/1759-7714.12579] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 11/19/2017] [Indexed: 12/28/2022] Open
Abstract
Environmental stresses are ubiquitous and unavoidable to all living things. Organisms respond and adapt to stresses through defined regulatory mechanisms that drive changes in gene expression, organismal morphology, or physiology. Immune responses illustrate adaptation to bacterial and viral biotic stresses in animals. Dysregulation of the genotoxic stress response system is frequently associated with various types of human cancer. With respect to plants, especially halophytes, complicated systems have been developed to allow for plant growth in high salt environments. In addition, drought, waterlogging, and low temperatures represent other common plant stresses. In this review, we summarize representative examples of organismal response and adaptation to various stresses. We also discuss the molecular mechanisms underlying the above phenomena with a focus on the improvement of organismal tolerance to unfavorable environments.
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Affiliation(s)
- Shuang Sun
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Institute of Biomedical Sciences, College of Life SciencesShandong Normal UniversityJinanChina
| | - Jun Zhou
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Institute of Biomedical Sciences, College of Life SciencesShandong Normal UniversityJinanChina
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Horn P, Schlichting A, Baum C, Hammesfahr U, Thiele-Bruhn S, Leinweber P, Broer I. Reprint of "Fast and sensitive in vivo studies under controlled environmental conditions to substitute long-term field trials with genetically modified plants". J Biotechnol 2017; 257:22-34. [PMID: 28755910 DOI: 10.1016/j.jbiotec.2017.07.012] [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: 10/12/2016] [Revised: 12/14/2016] [Accepted: 12/18/2016] [Indexed: 10/19/2022]
Abstract
We introduce an easy, fast and effective method to analyze the influence of genetically modified (GM) plants on soil and model organisms in the laboratory to substitute laborious and time consuming field trials. For the studies described here we focused on two GM plants of the so-called 3rd generation: GM plants producing pharmaceuticals (PMP) and plant made industrials (PMI). Cyanophycin synthetase (cphA) was chosen as model for PMI and Choleratoxin B (CTB) as model for PMP. The model genes are expressed in transgenic roots of composite Vicia hirsuta plants grown in petri dishes for semi-sterile growth or small containers filled with non-sterile soil. No significant influence of the model gene expression on root induction, growth, biomass, interaction with symbionts such as rhizobia (number, size and functionality of nodules, selection of nodulating strains) or arbuscular mycorrhizal fungi could be detected. In vitro, but not in situ under field conditions, structural diversity of the bulk soil microbial community between transgenic and non-transgenic cultivars was determined by PLFA pattern-derived ratios of bacteria: fungi and of gram+: gram- bacteria. Significant differences in PLFA ratios were associated with dissimilarities in the quantity and molecular composition of rhizodeposits as revealed by Py-FIMS analyses. Contrary to field trials, where small effects based on the transgene expression might be hidden by the immense influence of various environmental factors, our in vitro system can detect even minor effects and correlates them to transgene expression with less space, time and labour.
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Affiliation(s)
- Patricia Horn
- Agrobiotechnology, Faculty of Agricultural and Environmental Sciences, University of Rostock, Germany
| | - André Schlichting
- Soil Science, Faculty of Agricultural and Environmental Sciences, University of Rostock, Germany
| | - Christel Baum
- Soil Science, Faculty of Agricultural and Environmental Sciences, University of Rostock, Germany
| | - Ute Hammesfahr
- Soil Science, Faculty of Regional and Environmental Sciences, University of Trier, Germany
| | - Sören Thiele-Bruhn
- Soil Science, Faculty of Regional and Environmental Sciences, University of Trier, Germany
| | - Peter Leinweber
- Soil Science, Faculty of Agricultural and Environmental Sciences, University of Rostock, Germany
| | - Inge Broer
- Agrobiotechnology, Faculty of Agricultural and Environmental Sciences, University of Rostock, Germany.
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Ofaim S, Ofek-Lalzar M, Sela N, Jinag J, Kashi Y, Minz D, Freilich S. Analysis of Microbial Functions in the Rhizosphere Using a Metabolic-Network Based Framework for Metagenomics Interpretation. Front Microbiol 2017; 8:1606. [PMID: 28878756 PMCID: PMC5572346 DOI: 10.3389/fmicb.2017.01606] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Accepted: 08/07/2017] [Indexed: 12/25/2022] Open
Abstract
Advances in metagenomics enable high resolution description of complex bacterial communities in their natural environments. Consequently, conceptual approaches for community level functional analysis are in high need. Here, we introduce a framework for a metagenomics-based analysis of community functions. Environment-specific gene catalogs, derived from metagenomes, are processed into metabolic-network representation. By applying established ecological conventions, network-edges (metabolic functions) are assigned with taxonomic annotations according to the dominance level of specific groups. Once a function-taxonomy link is established, prediction of the impact of dominant taxa on the overall community performances is assessed by simulating removal or addition of edges (taxa associated functions). This approach is demonstrated on metagenomic data describing the microbial communities from the root environment of two crop plants – wheat and cucumber. Predictions for environment-dependent effects revealed differences between treatments (root vs. soil), corresponding to documented observations. Metabolism of specific plant exudates (e.g., organic acids, flavonoids) was linked with distinct taxonomic groups in simulated root, but not soil, environments. These dependencies point to the impact of these metabolite families as determinants of community structure. Simulations of the activity of pairwise combinations of taxonomic groups (order level) predicted the possible production of complementary metabolites. Complementation profiles allow formulating a possible metabolic role for observed co-occurrence patterns. For example, production of tryptophan-associated metabolites through complementary interactions is unique to the tryptophan-deficient cucumber root environment. Our approach enables formulation of testable predictions for species contribution to community activity and exploration of the functional outcome of structural shifts in complex bacterial communities. Understanding community-level metabolism is an essential step toward the manipulation and optimization of microbial function. Here, we introduce an analysis framework addressing three key challenges of such data: producing quantified links between taxonomy and function; contextualizing discrete functions into communal networks; and simulating environmental impact on community performances. New technologies will soon provide a high-coverage description of biotic and a-biotic aspects of complex microbial communities such as these found in gut and soil. This framework was designed to allow the integration of high-throughput metabolomic and metagenomic data toward tackling the intricate associations between community structure, community function, and metabolic inputs.
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Affiliation(s)
- Shany Ofaim
- Newe Ya'ar Research Center, Agricultural Research OrganizationRamat Yishay, Israel.,Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of TechnologyHaifa, Israel
| | - Maya Ofek-Lalzar
- Institute of Soil, Water and Environmental Sciences, Agricultural Research OrganizationBeit Dagan, Israel
| | - Noa Sela
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, The Volcani CenterBeit Dagan, Israel
| | - Jiandong Jinag
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural UniversityNanjing, China
| | - Yechezkel Kashi
- Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of TechnologyHaifa, Israel
| | - Dror Minz
- Institute of Soil, Water and Environmental Sciences, Agricultural Research OrganizationBeit Dagan, Israel
| | - Shiri Freilich
- Newe Ya'ar Research Center, Agricultural Research OrganizationRamat Yishay, Israel
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43
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Schatschneider S, Schneider J, Blom J, Létisse F, Niehaus K, Goesmann A, Vorhölter FJ. Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris. Microbiology (Reading) 2017; 163:1117-1144. [DOI: 10.1099/mic.0.000473] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Sarah Schatschneider
- Abteilung für Proteom und Metabolomforschung, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Bielefeld, Germany
- Present address: Evonik Nutrition and Care GmbH, Kantstr. 2, 33790 Halle-Künsebeck, Germany
| | - Jessica Schneider
- Bioinformatics Resource Facility, Centrum für Biotechnologie, Universität Bielefeld, Germany
- Present address: Evonik Nutrition and Care GmbH, Kantstr. 2, 33790 Halle-Künsebeck, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Germany
| | - Fabien Létisse
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Karsten Niehaus
- Abteilung für Proteom und Metabolomforschung, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Germany
| | - Frank-Jörg Vorhölter
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany
- Present address: MVZ Dr. Eberhard & Partner Dortmund, Dortmund, Germany
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Horn P, Schlichting A, Baum C, Hammesfahr U, Thiele-Bruhn S, Leinweber P, Broer I. Fast and sensitive in vivo studies under controlled environmental conditions to substitute long-term field trials with genetically modified plants. J Biotechnol 2017; 243:48-60. [PMID: 28011129 DOI: 10.1016/j.jbiotec.2016.12.014] [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: 10/12/2016] [Revised: 12/14/2016] [Accepted: 12/18/2016] [Indexed: 11/30/2022]
Abstract
We introduce an easy, fast and effective method to analyze the influence of genetically modified (GM) plants on soil and model organisms in the laboratory to substitute laborious and time consuming field trials. For the studies described here we focused on two GM plants of the so-called 3rd generation: GM plants producing pharmaceuticals (PMP) and plant made industrials (PMI). Cyanophycin synthetase (cphA) was chosen as model for PMI and Choleratoxin B (CTB) as model for PMP. The model genes are expressed in transgenic roots of composite Vicia hirsuta plants grown in petri dishes for semi-sterile growth or small containers filled with non-sterile soil. No significant influence of the model gene expression on root induction, growth, biomass, interaction with symbionts such as rhizobia (number, size and functionality of nodules, selection of nodulating strains) or arbuscular mycorrhizal fungi could be detected. In vitro, but not in situ under field conditions, structural diversity of the bulk soil microbial community between transgenic and non-transgenic cultivars was determined by PLFA pattern-derived ratios of bacteria: fungi and of gram+: gram- bacteria. Significant differences in PLFA ratios were associated with dissimilarities in the quantity and molecular composition of rhizodeposits as revealed by Py-FIMS analyses. Contrary to field trials, where small effects based on the transgene expression might be hidden by the immense influence of various environmental factors, our in vitro system can detect even minor effects and correlates them to transgene expression with less space, time and labour.
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Affiliation(s)
- Patricia Horn
- Agrobiotechnology, Faculty of Agricultural and Environmental Sciences, University of Rostock, Germany
| | - André Schlichting
- Soil Science, Faculty of Agricultural and Environmental Sciences, University of Rostock, Germany
| | - Christel Baum
- Soil Science, Faculty of Agricultural and Environmental Sciences, University of Rostock, Germany
| | - Ute Hammesfahr
- Soil Science, Faculty of Regional and Environmental Sciences, University of Trier, Germany
| | - Sören Thiele-Bruhn
- Soil Science, Faculty of Regional and Environmental Sciences, University of Trier, Germany
| | - Peter Leinweber
- Soil Science, Faculty of Agricultural and Environmental Sciences, University of Rostock, Germany
| | - Inge Broer
- Agrobiotechnology, Faculty of Agricultural and Environmental Sciences, University of Rostock, Germany.
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45
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Leonard S, Hommais F, Nasser W, Reverchon S. Plant-phytopathogen interactions: bacterial responses to environmental and plant stimuli. Environ Microbiol 2017; 19:1689-1716. [DOI: 10.1111/1462-2920.13611] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 11/09/2016] [Accepted: 11/16/2016] [Indexed: 01/06/2023]
Affiliation(s)
- Simon Leonard
- University of Lyon, Université Claude Bernard Lyon 1; INSA-Lyon, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, 10 rue Raphaël Dubois Villeurbanne F-69622 France
| | - Florence Hommais
- University of Lyon, Université Claude Bernard Lyon 1; INSA-Lyon, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, 10 rue Raphaël Dubois Villeurbanne F-69622 France
| | - William Nasser
- University of Lyon, Université Claude Bernard Lyon 1; INSA-Lyon, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, 10 rue Raphaël Dubois Villeurbanne F-69622 France
| | - Sylvie Reverchon
- University of Lyon, Université Claude Bernard Lyon 1; INSA-Lyon, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, 10 rue Raphaël Dubois Villeurbanne F-69622 France
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46
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Braga RM, Dourado MN, Araújo WL. Microbial interactions: ecology in a molecular perspective. Braz J Microbiol 2016; 47 Suppl 1:86-98. [PMID: 27825606 PMCID: PMC5156507 DOI: 10.1016/j.bjm.2016.10.005] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 10/07/2016] [Indexed: 02/06/2023] Open
Abstract
The microorganism–microorganism or microorganism–host interactions are the key strategy to colonize and establish in a variety of different environments. These interactions involve all ecological aspects, including physiochemical changes, metabolite exchange, metabolite conversion, signaling, chemotaxis and genetic exchange resulting in genotype selection. In addition, the establishment in the environment depends on the species diversity, since high functional redundancy in the microbial community increases the competitive ability of the community, decreasing the possibility of an invader to establish in this environment. Therefore, these associations are the result of a co-evolution process that leads to the adaptation and specialization, allowing the occupation of different niches, by reducing biotic and abiotic stress or exchanging growth factors and signaling. Microbial interactions occur by the transference of molecular and genetic information, and many mechanisms can be involved in this exchange, such as secondary metabolites, siderophores, quorum sensing system, biofilm formation, and cellular transduction signaling, among others. The ultimate unit of interaction is the gene expression of each organism in response to an environmental (biotic or abiotic) stimulus, which is responsible for the production of molecules involved in these interactions. Therefore, in the present review, we focused on some molecular mechanisms involved in the microbial interaction, not only in microbial–host interaction, which has been exploited by other reviews, but also in the molecular strategy used by different microorganisms in the environment that can modulate the establishment and structuration of the microbial community.
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Affiliation(s)
- Raíssa Mesquita Braga
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Manuella Nóbrega Dourado
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Welington Luiz Araújo
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil.
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47
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Ren L, Huo H, Zhang F, Hao W, Xiao L, Dong C, Xu G. The components of rice and watermelon root exudates and their effects on pathogenic fungus and watermelon defense. PLANT SIGNALING & BEHAVIOR 2016; 11:e1187357. [PMID: 27217091 PMCID: PMC4977455 DOI: 10.1080/15592324.2016.1187357] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 04/30/2016] [Accepted: 05/02/2016] [Indexed: 05/26/2023]
Abstract
Watermelon (Citrullus lanatus) is susceptible to wilt disease caused by the fungus Fusarium oxysporum f. sp niveum (FON). Intercropping management of watermelon/aerobic rice (Oryza sativa) alleviates watermelon wilt disease, because some unidentified component(s) in rice root exudates suppress FON sporulation and spore germination. Here, we show that the phenolic acid p-coumaric acid is present in rice root exudates only, and it inhibits FON spore germination and sporulation. We found that exogenously applied p-coumaric acid up-regulated the expression of ClPR3 in roots, as well as increased chitinase activity in leaves. Furthermore, exogenously applied p-coumaric acid increased β-1,3-glucanase activity in watermelon roots. By contrast, we found that ferulic acid was secreted by watermelon roots, but not by rice roots, and that it stimulated spore germination and sporulation of FON. Exogenous application of ferulic acid down-regulated ClPR3 expression and inhibited chitinase activity in watermelon leaves. Salicylic acid was detected in both watermelon and rice root exudates, which stimulated FON spore germination at low concentrations and suppressed spore germination at high concentrations. Exogenously applied salicylic acid did not alter ClPR3 expression, but did increase chitinase and β-1,3-glucanase activities in watermelon leaves. Together, our results show that the root exudates of phenolic acids were different between rice and watermelon, which lead to their special ecological roles on pathogenic fungus and watermelon defense.
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Affiliation(s)
- Lixuan Ren
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Hongwei Huo
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Fang Zhang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Wenya Hao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- Avic Fertilizer Corporation Limited, Beijing, China
| | - Liang Xiao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, China
| | - Caixia Dong
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, China
| | - Guohua Xu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, China
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Green H, Broun P, Cakmak I, Condon L, Fedoroff N, Gonzalez‐Valero J, Graham I, Lewis J, Moloney M, Oniang'o RK, Sanginga N, Shewry P, Roulin A. Planting seeds for the future of food. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2016; 96:1409-14. [PMID: 26619956 PMCID: PMC5064658 DOI: 10.1002/jsfa.7554] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 11/20/2015] [Accepted: 11/25/2015] [Indexed: 05/11/2023]
Abstract
The health and wellbeing of future generations will depend on humankind's ability to deliver sufficient nutritious food to a world population in excess of 9 billion. Feeding this many people by 2050 will require science-based solutions that address sustainable agricultural productivity and enable healthful dietary patterns in a more globally equitable way. This topic was the focus of a multi-disciplinary international conference hosted by Nestlé in June 2015, and provides the inspiration for the present article. The conference brought together a diverse range of expertise and organisations from the developing and industrialised world, all with a common interest in safeguarding the future of food. This article provides a snapshot of three of the recurring topics that were discussed during this conference: soil health, plant science and the future of farming practice. Crop plants and their cultivation are the fundamental building blocks for a food secure world. Whether these are grown for food or feed for livestock, they are the foundation of food and nutrient security. Many of the challenges for the future of food will be faced where the crops are grown: on the farm. Farmers need to plant the right crops and create the right conditions to maximise productivity (yield) and quality (e.g. nutritional content), whilst maintaining the environment, and earning a living. New advances in science and technology can provide the tools and know-how that will, together with a more entrepreneurial approach, help farmers to meet the inexorable demand for the sustainable production of nutritious foods for future generations.
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Affiliation(s)
- Hilary Green
- Department of NutritionHealth and Wellness and SustainabilityNestec SAVeveyCH1800Switzerland
| | - Pierre Broun
- Nestlé Research and Development CentreToursFrance
| | - Ismail Cakmak
- Faculty of Engineering and Natural SciencesSabanci UniversityIstanbul34956Turkey
| | - Liam Condon
- Bayer CropScience AG40789Monheim am RheinGermany
| | - Nina Fedoroff
- Department of BiologyPenn State UniversityPA16802USA
| | | | - Ian Graham
- Department of BiologyCentre for Novel Agricultural ProductsUniversity of YorkYorkYO10 5DDUK
| | - Josette Lewis
- Rothamsted ResearchWest CommonHarpendenHertfordshireAL5 2JQUK
| | | | - Ruth K Oniang'o
- Global Institute for Food SecurityUniversity of SaskatchewanSaskatoonSKCanadaS7N 4J8
| | | | - Peter Shewry
- International Institute of Tropical Agriculture (IITA)P.M.B. 5320, Oyo RoadIbadanNigeria
| | - Anne Roulin
- Department of NutritionHealth and Wellness and SustainabilityNestec SAVeveyCH1800Switzerland
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49
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Senneby E, Göransson L, Weiber S, Rasmussen M. A population-based study of aerococcal bacteraemia in the MALDI-TOF MS-era. Eur J Clin Microbiol Infect Dis 2016; 35:755-62. [PMID: 26838685 DOI: 10.1007/s10096-016-2594-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 01/20/2016] [Indexed: 01/11/2023]
Abstract
The purpose of this study was to determine the incidence of aerococcal bacteraemia in the MALDI-TOF MS-era, to describe the clinical presentation and to determine the MIC values of aerococci for ten antibiotics. Aerococci in blood cultures were identified through searches in the laboratory database for the years 2012-2014. MALDI-TOF MS, sequencing of the 16S rRNA gene and a PYR test were used for species identification. Patients' medical charts were systematically reviewed. Etests were used to determine MIC values. Seventy-seven patients were identified (Aerococcus urinae n = 49, Aerococcus viridans n = 14, Aerococcus sanguinicola n = 13 and Aerococcus christensenii n = 1) corresponding to incidences of 14 cases per 1,000,000 inhabitants per year (A. urinae) and 3.5 cases per 1,000,000 inhabitants per year (A. sanguinicola and A.viridans). A. urinae was in pure culture in 61 %, A. sanguinicola in 46 % and A. viridans in 36 % of the cases. The A. urinae and A. sanguinicola patients were old and many had urinary tract disorders, and a majority had a suspected urinary tract focus of the bacteraemia. Eighty percent of the A. urinae patients were men. Five A. urinae patients were diagnosed with infective endocarditis. Six patients died within 30 days. Most isolates had low MICs to penicillins and carbapenems. MALDI-TOF MS has led to an increased identification of aerococcal bacteremia. A. urinae remains the most common Aerococcus in blood cultures and in aerococcal IE.
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Affiliation(s)
- E Senneby
- Clinical Microbiology, Lund, Region Skåne, Sweden. .,Department of Clinical Sciences, Division of Infection Medicine, Lund University, Tornavägen 10, 221 84, Lund, Sweden.
| | - L Göransson
- Department of Clinical Sciences, Division of Infection Medicine, Lund University, Tornavägen 10, 221 84, Lund, Sweden
| | - S Weiber
- Department of Clinical Sciences, Division of Infection Medicine, Lund University, Tornavägen 10, 221 84, Lund, Sweden
| | - M Rasmussen
- Department of Clinical Sciences, Division of Infection Medicine, Lund University, Tornavägen 10, 221 84, Lund, Sweden
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