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Macharoen P, Mhuantong W, Wannawong T, Leesutthiphonchai W, Tanasupawat S, Suwannarach N, Kuncharoen N. Bacterial diversity, community structure and function in association of potato scabby tubers during storage in northern Thailand. Folia Microbiol (Praha) 2024; 69:941-952. [PMID: 38315309 DOI: 10.1007/s12223-024-01140-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 01/20/2024] [Indexed: 02/07/2024]
Abstract
Potato scab is a common potato tuber disease that affects quality and cost in the marketplace, shortening storage, and increasing the chance for secondary infection. The tubers with disease severity of 1 to 4 are accepted and stored in potato storage for cheap selling in Thailand. However, there are few studies of the bacterial community of the scabby tuber during storage. Thus, we aim to elucidate the diversity, structure, and function of the bacterial community of 30-day storage potato scabby tubers stored in different temperatures using 16S amplicon metagenomic sequencing. Bacterial communities of storage potato scabby tubers (Spunta cultivar) collected from different storage temperatures, 4 °C (MEP1) and 6 °C (MEP2), were characterized using 16S rRNA amplicon metagenomic sequencing. The alpha-diversity abundance in the bacteriome of the scabby tubers stored at 6 °C was higher than in those stored at 4 °C. Actinobacteria (34.7%) was a dominant phylum in MEP1, while Proteobacteria (39.9%) was predominant in MEP2. The top 10 genera of both communities were Rhizobium group, Streptomyces, Pectobacterium, Ruminococcus, Cellulomonas, Promicromonospora, Prevotella, Enterobacter, Pedobacter, and Paenarthrobacter. Moreover, functional profile prediction of both communities reveals essential genes in the pathosystem: nos, bglA, and cebEFG-msiK for potato scab disease and phc and peh operons for rot disease. Our findings are the first study to explore details of the bacteriome of the accepted potato scabby tubers for selling during storage in Thailand and strongly indicate that although potatoes were stored at low temperatures, diseases still occur by secondary pathogens.
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Affiliation(s)
- Pipat Macharoen
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand
| | - Wuttichai Mhuantong
- Food Biotechnology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
- Enzyme Technology Research Team, Biorefinery and Bioproducts Technology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Thippawan Wannawong
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand
| | | | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10300, Thailand
| | - Nakarin Suwannarach
- Center Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, 50200, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Nattakorn Kuncharoen
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand.
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Petrushin IS, Filinova NV, Gutnik DI. Potato Microbiome: Relationship with Environmental Factors and Approaches for Microbiome Modulation. Int J Mol Sci 2024; 25:750. [PMID: 38255824 PMCID: PMC10815375 DOI: 10.3390/ijms25020750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/12/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Every land plant exists in a close relationship with microbial communities of several niches: rhizosphere, endosphere, phyllosphere, etc. The growth and yield of potato-a critical food crop worldwide-highly depend on the diversity and structure of the bacterial and fungal communities with which the potato plant coexists. The potato plant has a specific part, tubers, and the soil near the tubers as a sub-compartment is usually called the "geocaulosphere", which is associated with the storage process and tare soil microbiome. Specific microbes can help the plant to adapt to particular environmental conditions and resist pathogens. There are a number of approaches to modulate the microbiome that provide organisms with desired features during inoculation. The mechanisms of plant-bacterial communication remain understudied, and for further engineering of microbiomes with particular features, the knowledge on the potato microbiome should be summarized. The most recent approaches to microbiome engineering include the construction of a synthetic microbial community or management of the plant microbiome using genome engineering. In this review, the various factors that determine the microbiome of potato and approaches that allow us to mitigate the negative impact of drought and pathogens are surveyed.
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Affiliation(s)
- Ivan S. Petrushin
- Siberian Institute of Plant Physiology and Biochemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk 664033, Russia; (N.V.F.); (D.I.G.)
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Feng C, Xu F, Li L, Zhang J, Wang J, Li Y, Liu L, Han Z, Shi R, Wan X, Song Y. Biological control of Fusarium crown rot of wheat with Chaetomium globosum 12XP1-2-3 and its effects on rhizosphere microorganisms. Front Microbiol 2023; 14:1133025. [PMID: 37077244 PMCID: PMC10106750 DOI: 10.3389/fmicb.2023.1133025] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 02/28/2023] [Indexed: 04/05/2023] Open
Abstract
Chaetomium globosum is a common plant endophytic fungi that exhibits great biocontrol potential in plant disease. Fusarium crown rot (FCR) is an important disease in wheat that seriously threatens wheat production worldwide. The control effect of C. globosum against wheat FCR remains unclear. In this study, we introduced an identified C. globosum 12XP1-2-3 and tested its biological control potential against wheat FCR. The hypha and fermentation broth exhibited an antagonistic effect against Fusarium pseudograminearum. Results from indoor experiments showed that C. globosum 12XP1-2-3 might delay the onset of symptoms of brown stem base and significantly reduced the disease index (37.3%). Field trials showed that wheat seeds coated with a spore suspension of 12XP1-2-3 grew better than the control seeds, had control effects of 25.9–73.1% on FCR disease, and increased wheat yield by 3.2–11.9%. Analysis of rhizosphere microorganisms revealed that seeds coated with C. globosum (‘Cg’ treatment) had a greater effect on fungal rather than on bacterial alpha diversity and may improve the health state of rhizosphere microorganisms, as reflected by the significantly increased fungal Shannon index at Feekes 11 and the increased complexity of the bacterial co-occurrence network but decreased complexity of the fungal network. Moreover, the accumulation of beneficial bacteria such as Bacillus and Rhizobium at Feekes 3, and Sphingomonas at Feekes 7 in the ‘Cg’ treatment may be the important contributions to healthier wheat growth state, significantly reduced relative abundance of Fusarium at Feekes 11, and reduced occurrence of FCR disease. These results provide a basis for further research on the mechanism of action of C. globosum and its application in the biological control of FCR in the field.
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Affiliation(s)
- Chaohong Feng
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- Key Laboratory of Integrated Pest Management on Crops in Southern Part of North China, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Zhengzhou, Henan, China
| | - Fei Xu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- Key Laboratory of Integrated Pest Management on Crops in Southern Part of North China, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Zhengzhou, Henan, China
| | - Lijuan Li
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- Key Laboratory of Integrated Pest Management on Crops in Southern Part of North China, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Zhengzhou, Henan, China
| | - Jiaojiao Zhang
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- Key Laboratory of Integrated Pest Management on Crops in Southern Part of North China, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Zhengzhou, Henan, China
| | - Junmei Wang
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- Key Laboratory of Integrated Pest Management on Crops in Southern Part of North China, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Zhengzhou, Henan, China
| | - Yahong Li
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- Key Laboratory of Integrated Pest Management on Crops in Southern Part of North China, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Zhengzhou, Henan, China
| | - Lulu Liu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- Key Laboratory of Integrated Pest Management on Crops in Southern Part of North China, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Zhengzhou, Henan, China
| | - Zihang Han
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- Key Laboratory of Integrated Pest Management on Crops in Southern Part of North China, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Zhengzhou, Henan, China
| | - Ruijie Shi
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- Key Laboratory of Integrated Pest Management on Crops in Southern Part of North China, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Zhengzhou, Henan, China
| | - Xinru Wan
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- Key Laboratory of Integrated Pest Management on Crops in Southern Part of North China, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Zhengzhou, Henan, China
| | - Yuli Song
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- Key Laboratory of Integrated Pest Management on Crops in Southern Part of North China, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Zhengzhou, Henan, China
- *Correspondence: Yuli Song,
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Pereira LB, Thomazella DPT, Teixeira PJPL. Plant-microbiome crosstalk and disease development. CURRENT OPINION IN PLANT BIOLOGY 2023; 72:102351. [PMID: 36848753 DOI: 10.1016/j.pbi.2023.102351] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/27/2023] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Plants harbor a complex immune system to fight off invaders and prevent diseases. For decades, the interactions between plants and pathogens have been investigated primarily through the lens of binary interactions, largely neglecting the diversity of microbes that naturally inhabit plant tissues. Recent research, however, demonstrates that resident microbes are more than mere spectators. Instead, the plant microbiome extends host immune function and influences the outcome of a pathogen infection. Both plants and the interacting microbes produce a large diversity of metabolites that form an intricate chemical network of nutrients, signals, and antimicrobial molecules. In this review, we discuss the involvement of the plant microbiome in disease development, focusing on the biochemical conversation that occurs between plants and their associated microbiota before, during and after infection. We also highlight outstanding questions and possible directions for future research.
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Affiliation(s)
- Letícia B Pereira
- Department of Biological Sciences, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, Brazil
| | - Daniela P T Thomazella
- Department of Genetics, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, Brazil
| | - Paulo J P L Teixeira
- Department of Biological Sciences, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, Brazil.
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Sun N, Gu Y, Jiang G, Wang Y, Wang P, Song W, Ma P, Duan Y, Jiao Z. Bacterial Communities in the Endophyte and Rhizosphere of White Radish (Raphanus sativus) in Different Compartments and Growth Conditions. Front Microbiol 2022; 13:900779. [PMID: 35847086 PMCID: PMC9277120 DOI: 10.3389/fmicb.2022.900779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/16/2022] [Indexed: 11/22/2022] Open
Abstract
Endophyte resources have important research value in multiresistance breeding, ecological protection, germicide development, and other fields. In this study, high-throughput sequencing (Illumina-MiSeq) technology was employed to analyse the diversity and community composition of white radish (Raphanus sativus) endophytes and rhizosphere bacteria in different compartments and cultivation conditions, including greenhouse and open field cultivation, at both the phylum and genus levels. Alpha diversity index analysis showed that the bacterial richness and diversity values of rhizosphere bacteria were higher than those of endophytes in different compartments. NMDS analysis and microbial co-occurrence network analysis showed that apart from the similarity in the endophytic bacterial composition of the leaf and root endosphere, the endophytic bacterial composition in flesh and epidermis of radish were also more similar. The dominant endophytic bacteria in white radish were Proteobacteria, Bacteroidetes, and Actinomycetes at the phylum level. We analyzed the effects of different ecological compartments and two cultivation environments on radish microorganisms, and found that ecological compartments played an important role, which was related to the mechanism of microbial assembly in plants. The same facility cultivation can also improve the diversity of radish microorganisms in different ecological compartments, and change the biomarkers that play a major role in rhizosphere microorganisms and endophytes of radish. Bacteria plays an important role in the process of plant growth, and the study of endophytes enriches the understanding of microbial diversity in white radish, which helps to provide insight into the ecological function and interaction mechanisms of plants and microorganisms.
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Affiliation(s)
- Nan Sun
- College of Water Resources & Civil Engineering, China Agricultural University, Beijing, China
| | - Yizhu Gu
- College of Water Resources & Civil Engineering, China Agricultural University, Beijing, China
| | - Guoxia Jiang
- Henan Pingdingshan Academy of Agricultural Sciences, Pingdingshan, China
- *Correspondence: Guoxia Jiang
| | - Yuxin Wang
- College of Water Resources & Civil Engineering, China Agricultural University, Beijing, China
- Yuxin Wang
| | - Pingzhi Wang
- College of Water Resources & Civil Engineering, China Agricultural University, Beijing, China
| | - Weitang Song
- College of Water Resources & Civil Engineering, China Agricultural University, Beijing, China
| | - Peifang Ma
- Henan Pingdingshan Academy of Agricultural Sciences, Pingdingshan, China
| | - Yabin Duan
- Henan Pingdingshan Academy of Agricultural Sciences, Pingdingshan, China
| | - Ziyuan Jiao
- Henan Pingdingshan Academy of Agricultural Sciences, Pingdingshan, China
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Jayaraman S, Naorem A, Lal R, Dalal RC, Sinha N, Patra A, Chaudhari S. Disease-Suppressive Soils-Beyond Food Production: a Critical Review. JOURNAL OF SOIL SCIENCE AND PLANT NUTRITION 2021; 21:1437-1465. [PMID: 33746349 PMCID: PMC7953945 DOI: 10.1007/s42729-021-00451-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/21/2021] [Indexed: 05/09/2023]
Abstract
In the pursuit of higher food production and economic growth and increasing population, we have often jeopardized natural resources such as soil, water, vegetation, and biodiversity at an alarming rate. In this process, wider adoption of intensive farming practices, namely changes in land use, imbalanced fertilizer application, minimum addition of organic residue/manure, and non-adoption of site-specific conservation measures, has led to declining in soil health and land degradation in an irreversible manner. In addition, increasing use of pesticides, coupled with soil and water pollution, has led the researchers to search for an environmental-friendly and cost-effective alternatives to controlling soil-borne diseases that are difficult to control, and which significantly limit agricultural productivity. Since the 1960s, disease-suppressive soils (DSS) have been identified and studied around the world. Soil disease suppression is the reduction in the incidence of soil-borne diseases even in the presence of a host plant and inoculum in the soil. The disease-suppressive capacity is mainly attributed to diverse microbial communities present in the soil that could act against soil-borne pathogens in multifaceted ways. The beneficial microorganisms employ some specific functions such as antibiosis, parasitism, competition for resources, and predation. However, there has been increasing evidence on the role of soil abiotic factors that largely influence the disease suppression. The intricate interactions of the soil, plant, and environmental components in a disease triangle make this process complex yet crucial to study to reduce disease incidence. Increasing resistance of the pathogen to presently available chemicals has led to the shift from culturable microbes to unexplored and unculturable microbes. Agricultural management practices such as tillage, fertilization, manures, irrigation, and amendment applications significantly alter the soil physicochemical environment and influence the growth and behaviour of antagonistic microbes. Plant factors such as age, type of crop, and root behaviour of the plant could stimulate or limit the diversity and structure of soil microorganisms in the rhizosphere. Further, identification and in-depth of disease-suppressive soils could lead to the discovery of more beneficial microorganisms with novel anti-microbial and plant promoting traits. To date, several microbial species have been isolated and proposed as key contributors in disease suppression, but the complexities as well as the mechanisms of the microbial and abiotic interactions remain elusive for most of the disease-suppressive soils. Thus, this review critically explores disease-suppressive attributes in soils, mechanisms involved, and biotic and abiotic factors affecting DSS and also briefly reviewing soil microbiome for anti-microbial drugs, in fact, a consequence of DSS phenomenon.
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Affiliation(s)
- Somasundaram Jayaraman
- ICAR–Indian Institute of Soil Science, Nabibagh, Berasia Road, Bhopal, Madhya Pradesh 462038 India
| | - A.K. Naorem
- ICAR– Central Arid Zone Research Institute, Regional Research Station-Kukma, Bhuj, Gujarat 370105 India
| | - Rattan Lal
- Carbon Management Sequestration Center, The Ohio State University, 2021 Coffey Rd, Columbus, OH USA
| | - Ram C. Dalal
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, QLD 4072 Australia
| | - N.K. Sinha
- ICAR–Indian Institute of Soil Science, Nabibagh, Berasia Road, Bhopal, Madhya Pradesh 462038 India
| | - A.K. Patra
- ICAR–Indian Institute of Soil Science, Nabibagh, Berasia Road, Bhopal, Madhya Pradesh 462038 India
| | - S.K. Chaudhari
- Indian Council of Agricultural Research, KAB-II, New Delhi, India
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Soil Microbiome Manipulation Gives New Insights in Plant Disease-Suppressive Soils from the Perspective of a Circular Economy: A Critical Review. SUSTAINABILITY 2020. [DOI: 10.3390/su13010010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This review pays attention to the newest insights on the soil microbiome in plant disease-suppressive soil (DSS) for sustainable plant health management from the perspective of a circular economy that provides beneficial microbiota by recycling agro-wastes into the soil. In order to increase suppression of soil-borne plant pathogens, the main goal of this paper is to critically discuss and compare the potential use of reshaped soil microbiomes by assembling different agricultural practices such as crop selection; land use and conservative agriculture; crop rotation, diversification, intercropping and cover cropping; compost and chitosan application; and soil pre-fumigation combined with organic amendments and bio-organic fertilizers. This review is seen mostly as a comprehensive understanding of the main findings regarding DSS, starting from the oldest concepts to the newest challenges, based on the assumption that sustainability for soil quality and plant health is increasingly viable and supported by microbiome-assisted strategies based on the next-generation sequencing (NGS) methods that characterize in depth the soil bacterial and fungal communities. This approach, together with the virtuous reuse of agro-wastes to produce in situ green composts and organic bio-fertilizers, is the best way to design new sustainable cropping systems in a circular economy system. The current knowledge on soil-borne pathogens and soil microbiota is summarized. How microbiota determine soil suppression and what NGS strategies are available to understand soil microbiomes in DSS are presented. Disturbance of soil microbiota based on combined agricultural practices is deeply considered. Sustainable soil microbiome management by recycling in situ agro-wastes is presented. Afterwards, how the resulting new insights can drive the progress in sustainable microbiome-based disease management is discussed.
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Lebrazi S, Niehaus K, Bednarz H, Fadil M, Chraibi M, Fikri-Benbrahim K. Screening and optimization of indole-3-acetic acid production and phosphate solubilization by rhizobacterial strains isolated from Acacia cyanophylla root nodules and their effects on its plant growth. J Genet Eng Biotechnol 2020; 18:71. [PMID: 33175273 PMCID: PMC7658270 DOI: 10.1186/s43141-020-00090-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 11/02/2020] [Indexed: 11/18/2022]
Abstract
Background Plant growth-promoting rhizobacteria (PGPR) are known to improve plant growth and are used as biofertilizers, thanks to their numerous benefits to agriculture such as phosphorus solubilization and phytohormone production. In this paper, four rhizospheric bacteria (Phyllobacterium sp., Bacillus sp., Agrobacterium sp., and Rhizobium sp.) isolated from surface-sterilized root nodules of Acacia cyanophylla were tested for their ability to solubilize inorganic phosphate and to produce indole-3-acetic acid (IAA) under laboratory conditions. Then, the best IAA producer (Rhizobium sp.) was selected to test optimized conditions for IAA production. Finally, the effect of the four strains on plant growth for A. cyanophylla was evaluated in vivo. Results The results showed that the totality of the tested isolates had solubilized inorganic phosphate (P) in both NBRIP (National Botanical Research Institute Phosphate) and PVK (Pikovskaya) media. Bacillus sp. was a high P-solubilizer and showed maximum solubilization in PVK (519 μg ml-1) and NBRIP (782 μg ml-1). The optimization of maximum phosphate solubilization was done using different sources of carbon (1%) and nitrogen (0.1%). Glucose and ammonium sulfate were selected to be the best carbon and nitrogen source for phosphate solubilization by all tested strains, except for Phyllobacterium sp., which recorded the highest phosphate solubilization with ammonium nitrate. The IAA production by the tested strains indicated that Rhizobium sp. produced the highest amount of IAA (90.21 μg ml-1) in culture media supplemented with L-tryptophan. The best production was observed with L-Trp concentration of 0.2% (116.42 μg ml-1) and at an initial pH of 9 (116.07 μg ml-1). The effect of NaCl on IAA production was tested at concentrations of 0 to 5% and the maximum production of 89.43 μg ml-1 was found at 2% NaCl. The extraction of crude IAA from this strain was done and purity was confirmed with Thin Layer Chromatography (TLC) analysis. A specific spot from the extracted IAA production was found to correspond with a standard spot of IAA with the same Rf value. Finally, the tested PGPR demonstrated growth stimulatory effects on Acacia cyanophylla seedlings in vivo, with a great increase of shoots’ and roots’ dry weights, and shoot length compared to control. The rhizobacterial isolates were identified by 16S rDNA sequence analysis as Agrobacterium sp. NA11001, Phyllobacterium sp. C65, Bacillus sp. CS14, and Rhizobium sp. V3E1. Conclusion This study highlights the importance of the use of phosphate solubilizing and IAA producer microorganisms as biofertilizers to increase crop yields. The studied strains showed a significant phosphate solubilization potential and IAA production. The use of selected strains as inoculants would be interesting, in particular with a view of promoting sustainable agriculture. However, further studies to verify the efficacy of the best isolates in situ is certainly required.
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Affiliation(s)
- Sara Lebrazi
- Laboratory of Microbial Biotechnology, Faculty of Sciences and Technology, Sidi Mohamed Ben Abdellah University, P.O. Box 2202, Fez, Morocco.
| | - Karsten Niehaus
- Proteome and Metabolome Research, Faculty of Biology Center for Biotechnology (CeBiTec), Bielefeld, Germany
| | - Hanna Bednarz
- Proteome and Metabolome Research, Faculty of Biology Center for Biotechnology (CeBiTec), Bielefeld, Germany
| | - Mouhcine Fadil
- Physico-Chemical Laboratory of Inorganic and Organic Materials, Materials Science Center (MSC), Ecole Normale Supérieure, Mohammed V University in Rabat, Rabat, Morocco
| | - Marwa Chraibi
- Laboratory of Microbial Biotechnology, Faculty of Sciences and Technology, Sidi Mohamed Ben Abdellah University, P.O. Box 2202, Fez, Morocco
| | - Kawtar Fikri-Benbrahim
- Laboratory of Microbial Biotechnology, Faculty of Sciences and Technology, Sidi Mohamed Ben Abdellah University, P.O. Box 2202, Fez, Morocco
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Zhu B, Wu J, Ji Q, Wu W, Dong S, Yu J, Zhang Q, Qin L. Diversity of rhizosphere and endophytic fungi in Atractylodes macrocephala during continuous cropping. PeerJ 2020; 8:e8905. [PMID: 32292655 PMCID: PMC7144587 DOI: 10.7717/peerj.8905] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 03/12/2020] [Indexed: 12/03/2022] Open
Abstract
Rhizospheric and endophytic fungi are key factors which influence plant fitness and soil fertility. Atractylodes macrocephala is one of the best-known perennial herbs used in traditional Chinese medicine. Continuous cropping has been shown to have a negative effect on its growth and renders it more susceptible to microbial pathogen attacks. In this study, we investigated the effects of continuous cropping on the endophytic and rhizospheric fungi associated with A. macrocephala using culture-independent Illumina MiSeq. Continuous cropping was found to decrease fungal diversity inside plant roots, stems, leaves and tubers. Additionally, we found that the structure and diversity of rhizospheric and endophytic fungal communities were altered by root-rot disease. Fusarium was overrepresented among root-rot rhizospheric and endophytic fungi, indicating that it has a major negative impact on plant health during A. macrocephala monocropping. Canonical correspondence analysis of the control and diseased samples revealed that pH, hydrolysis N, electrical conductivity and Hg content were well-correlated with fungal community composition during continuous cropping. Taken together, these results highlight the ecological significance of fungal communities in maintaining plant fitness and will guide the development strategies to attenuate the negative impacts of A. macrocephala continuous cropping.
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Affiliation(s)
- Bo Zhu
- School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jianjun Wu
- School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, China
| | - Qingyong Ji
- Lishui Academy of Agricultural and Forestry Sciences, Lishui, China
| | - Wei Wu
- School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, China
| | - Shihui Dong
- School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jiayan Yu
- School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, China
| | - Qiaoyan Zhang
- School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, China
| | - Luping Qin
- School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, China
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Buchholz F, Antonielli L, Kostić T, Sessitsch A, Mitter B. The bacterial community in potato is recruited from soil and partly inherited across generations. PLoS One 2019; 14:e0223691. [PMID: 31703062 PMCID: PMC6839881 DOI: 10.1371/journal.pone.0223691] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 09/25/2019] [Indexed: 01/18/2023] Open
Abstract
Strong efforts have been made to understand the bacterial communities in potato plants and the rhizosphere. Research has focused on the effect of the environment and plant genotype on bacterial community structures and dynamics, while little is known about the origin and assembly of the bacterial community, especially in potato tubers. The tuber microbiota, however, may be of special interest as it could play an important role in crop quality, such as storage stability. Here, we used 16S rRNA gene amplicon sequencing to study the bacterial communities that colonize tubers of different potato cultivars commonly used in Austrian potato production over three generations and grown in different soils. Statistical analysis of sequencing data showed that the bacterial community of potato tubers has changed over generations and has become more similar to the soil bacterial community, while the impact of the potato cultivar on the bacterial assemblage has lost significance over time. The communities in different tuber parts did not differ significantly, while the soil bacterial community showed significant differences to the tuber microbiota composition. Additionally, the presence of OTUs in subsequent tuber generation points to vertical transmission of a subset of the tuber microbiota. Four OTUs were common to all tuber generations and all potato varieties. In summary, we conclude that the microbiota of potato tubers is recruited from the soil largely independent from the plant variety. Furthermore, the bacterial assemblage in potato tubers consists of bacteria transmitted from one tuber generation to the next and bacteria recruited from the soil.
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Affiliation(s)
- Franziska Buchholz
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Livio Antonielli
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Tanja Kostić
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Angela Sessitsch
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Birgit Mitter
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Tulln, Austria
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11
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Kopecky J, Samkova Z, Sarikhani E, Kyselková M, Omelka M, Kristufek V, Divis J, Grundmann GG, Moënne-Loccoz Y, Sagova-Mareckova M. Bacterial, archaeal and micro-eukaryotic communities characterize a disease-suppressive or conducive soil and a cultivar resistant or susceptible to common scab. Sci Rep 2019; 9:14883. [PMID: 31619759 PMCID: PMC6796001 DOI: 10.1038/s41598-019-51570-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 09/28/2019] [Indexed: 12/20/2022] Open
Abstract
Control of common scab disease can be reached by resistant cultivars or suppressive soils. Both mechanisms are likely to translate into particular potato microbiome profiles, but the relative importance of each is not known. Here, microbiomes of bulk and tuberosphere soil and of potato periderm were studied in one resistant and one susceptible cultivar grown in a conducive and a suppressive field. Disease severity was suppressed similarly by both means yet, the copy numbers of txtB gene (coding for a pathogenicity determinant) were similar in both soils but higher in periderms of the susceptible cultivar from conducive soil. Illumina sequencing of 16S rRNA genes for bacteria (completed by 16S rRNA microarray approach) and archaea, and of 18S rRNA genes for micro-eukarytes showed that in bacteria, the more important was the effect of cultivar and diversity decreased from resistant cultivar to bulk soil to susceptible cultivar. The major changes occurred in proportions of Actinobacteria, Chloroflexi, and Proteobacteria. In archaea and micro-eukaryotes, differences were primarily due to the suppressive and conducive soil. The effect of soil suppressiveness × cultivar resistance depended on the microbial community considered, but differed also with respect to soil and plant nutrient contents particularly in N, S and Fe.
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Affiliation(s)
- Jan Kopecky
- Crop Research Institute, Epidemiology and Ecology of Microorganisms, Drnovská 509, 161 06, Prague 6, Czech Republic
| | - Zuzana Samkova
- Crop Research Institute, Epidemiology and Ecology of Microorganisms, Drnovská 509, 161 06, Prague 6, Czech Republic
| | - Ensyeh Sarikhani
- Crop Research Institute, Epidemiology and Ecology of Microorganisms, Drnovská 509, 161 06, Prague 6, Czech Republic
| | - Martina Kyselková
- Biology Centre of the Czech Academy of Sciences, v. v. i., Institute of Soil Biology, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Marek Omelka
- Faculty of Mathematics and Physics, Department of Probability and Mathematical Statistics, Charles University, Sokolovská 83, 186 75, Prague 8, Czech Republic
| | - Vaclav Kristufek
- Biology Centre of the Czech Academy of Sciences, v. v. i., Institute of Soil Biology, Na Sádkách 7, 370 05, České Budějovice, Czech Republic
| | - Jiri Divis
- Faculty of Agriculture, University of South Bohemia, Studentská 13, 370 05, České Budějovice, Czech Republic
| | - Geneviève G Grundmann
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, VetAgro Sup, UMR5557 Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, VetAgro Sup, UMR5557 Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Marketa Sagova-Mareckova
- Crop Research Institute, Epidemiology and Ecology of Microorganisms, Drnovská 509, 161 06, Prague 6, Czech Republic. .,Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamycka 129, Prague 6, Czech Republic.
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12
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Wasai S, Minamisawa K. Plant-Associated Microbes: From Rhizobia To Plant Microbiomes. Microbes Environ 2019; 33:1-3. [PMID: 29593170 PMCID: PMC5877334 DOI: 10.1264/jsme2.me3301rh] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Sawa Wasai
- Graduate School of Life Sciences, Tohoku University
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13
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Shi W, Li M, Wei G, Tian R, Li C, Wang B, Lin R, Shi C, Chi X, Zhou B, Gao Z. The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome. MICROBIOME 2019; 7:14. [PMID: 30709420 PMCID: PMC6359780 DOI: 10.1186/s40168-019-0629-2] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 01/17/2019] [Indexed: 05/17/2023]
Abstract
BACKGROUND Soil microorganisms can mediate the occurrence of plant diseases. Potato common scab (CS) is a refractory disease caused by pathogenic Streptomyces that occurs worldwide, but little is known about the interactions between CS and the soil microbiome. In this study, four soil-root system compartments (geocaulosphere soil (GS), rhizosphere soil (RS), root-zone soil (ZS), and furrow soil (FS)) were analyzed for potato plants with naturally high (H) and low (L) scab severity levels. We aimed to determine the composition and putative function of the soil microbiome associated with potato CS. RESULTS The copy numbers of the scab phytotoxin biosynthetic gene txtAB and the bacterial 16S rRNA gene as well as the diversity and composition of each of the four soil-root system compartments were examined; GS was the only compartment that exhibited significant differences between the H and L groups. Compared to the H group, the L group exhibited a lower txtAB gene copy number, lower bacterial 16S copy number, higher diversity, higher co-occurrence network complexity, and higher community function similarity within the GS microbiome. The community composition and function of the GS samples were further revealed by shotgun metagenomic sequencing. Variovorax, Stenotrophomonas, and Agrobacterium were the most abundant genera that were significantly and positively correlated with the scab severity level, estimated absolute abundance (EAA) of pathogenic Streptomyces, and txtAB gene copy number. In contrast, Geobacillus, Curtobacterium, and unclassified Geodermatophilaceae were significantly negatively correlated with these three parameters. Compared to the function profiles in the L group, several genes involved in "ABC transporters," the "bacterial secretion system," "quorum sensing (QS)," "nitrogen metabolism," and some metabolism by cytochrome P450 were enriched in the H group. In contrast, some antibiotic biosynthesis pathways were enriched in the L group. Based on the differences in community composition and function, a simple model was proposed to explain the putative relationships between the soil microbiome and CS occurrence. CONCLUSIONS The GS microbiome was closely associated with CS severity in the soil-root system, and the occurrence of CS was accompanied by changes in community composition and function. The differential functions provide new clues to elucidate the mechanism underlying the interaction between CS occurrence and the soil microbiome, and varying community compositions provide novel insights into CS occurrence.
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Affiliation(s)
- Wencong Shi
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Mingcong Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Guangshan Wei
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, 361005, China
- South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Sun Yat-Sen University, Guangzhou, 510275, China
| | - Renmao Tian
- Department of Botany and Microbiology, Institute for Environmental Genomics, University of Oklahoma, Norman, USA
| | - Cuiping Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Bing Wang
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, 271018, China
| | - Rongshan Lin
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, 271018, China
| | - Chunyu Shi
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
- College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
| | - Xiuli Chi
- Plant Protection Station, Jiaozhou Agricultural Bureau, Qingdao, 266300, China
| | - Bo Zhou
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.
- National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Tai'an, 271018, China.
| | - Zheng Gao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China.
- College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.
- Department of Botany and Microbiology, Institute for Environmental Genomics, University of Oklahoma, Norman, USA.
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14
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Nahar K, Goyer C, Zebarth BJ, Burton DL, Whitney S. Pathogenic Streptomyces spp. Abundance Affected by Potato Cultivars. PHYTOPATHOLOGY 2018; 108:1046-1055. [PMID: 29658842 DOI: 10.1094/phyto-03-18-0075-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Potato cultivars vary in their tolerance to common scab; however, how they affect common scab-causing Streptomyces spp. populations over time is poorly understood. This study investigated the effects of potato cultivar on pathogenic Streptomyces spp. abundance, measured using quantitative PCR, in three spatial locations in a common scab-infested field: (i) soil close to the plant (SCP); (ii) rhizosphere soil (RS); and (iii) geocaulosphere soil (GS). Two tolerant (Gold Rush, Hindenburg) and two susceptible cultivars (Green Mountain, Agria) were tested. The abundance of pathogenic Streptomyces spp. significantly increased in late August compared with other dates in RS of susceptible cultivars in both years. Abundance of pathogenic Streptomyces spp., when averaged over locations and time, was significantly greater in susceptible cultivars compared with tolerant cultivars in 2014. Principal coordinates analysis showed that SCP and RS soil properties (pH, organic carbon, and nitrogen concentrations) explained 68 and 76% of total variation in Streptomyces spp. abundance among cultivars in 2013, respectively, suggesting that cultivars influenced common scab pathogen growth conditions. The results suggested that the genetic background of potato cultivars influenced the abundance of pathogenic Streptomyces spp., with five to six times more abundant Streptomyces spp. in RS of susceptible cultivars compared with tolerant cultivars, which would result in substantially more inoculum left in the field after harvest.
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Affiliation(s)
- Kamrun Nahar
- First, second, third, and fifth authors: Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, NB, Canada; and fourth author: Department of Environmental Sciences, Dalhousie University, Agricultural Campus, P.O. Box 550, Truro, NS, Canada
| | - Claudia Goyer
- First, second, third, and fifth authors: Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, NB, Canada; and fourth author: Department of Environmental Sciences, Dalhousie University, Agricultural Campus, P.O. Box 550, Truro, NS, Canada
| | - Bernie J Zebarth
- First, second, third, and fifth authors: Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, NB, Canada; and fourth author: Department of Environmental Sciences, Dalhousie University, Agricultural Campus, P.O. Box 550, Truro, NS, Canada
| | - David L Burton
- First, second, third, and fifth authors: Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, NB, Canada; and fourth author: Department of Environmental Sciences, Dalhousie University, Agricultural Campus, P.O. Box 550, Truro, NS, Canada
| | - Sean Whitney
- First, second, third, and fifth authors: Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, NB, Canada; and fourth author: Department of Environmental Sciences, Dalhousie University, Agricultural Campus, P.O. Box 550, Truro, NS, Canada
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15
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Samad A, Trognitz F, Compant S, Antonielli L, Sessitsch A. Shared and host-specific microbiome diversity and functioning of grapevine and accompanying weed plants. Environ Microbiol 2017; 19:1407-1424. [PMID: 27871147 DOI: 10.1111/1462-2920.13618] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 10/11/2016] [Accepted: 11/16/2016] [Indexed: 11/30/2022]
Abstract
Weeds and crop plants select their microbiota from the same pool of soil microorganisms, however, the ecology of weed microbiomes is poorly understood. We analysed the microbiomes associated with roots and rhizospheres of grapevine and four weed species (Lamium amplexicaule L., Veronica arvensis L., Lepidium draba L. and Stellaria media L.) growing in proximity in the same vineyard using 16S rRNA gene sequencing. We also isolated and characterized 500 rhizobacteria and root endophytes from L. draba and grapevine. Microbiome data analysis revealed that all plants hosted significantly different microbiomes in the rhizosphere as well as in root compartment, however, differences were more pronounced in the root compartment. The shared microbiome of grapevine and the four weed species contained 145 OTUs (54.2%) in the rhizosphere, but only nine OTUs (13.2%) in the root compartment. Seven OTUs (12.3%) were shared in all plants and compartments. Approximately 56% of the major OTUs (>1%) showed more than 98% identity to bacteria isolated in this study. Moreover, weed-associated bacteria generally showed a higher species richness in the rhizosphere, whereas the root-associated bacteria were more diverse in the perennial plants grapevine and L. draba. Overall, weed isolates showed more plant growth-promoting characteristics compared with grapevine isolates.
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Affiliation(s)
- Abdul Samad
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Konrad-Lorenz-Straße 24, Tulln, 3430, Austria
| | - Friederike Trognitz
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Konrad-Lorenz-Straße 24, Tulln, 3430, Austria
| | - Stéphane Compant
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Konrad-Lorenz-Straße 24, Tulln, 3430, Austria
| | - Livio Antonielli
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Konrad-Lorenz-Straße 24, Tulln, 3430, Austria
| | - Angela Sessitsch
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Konrad-Lorenz-Straße 24, Tulln, 3430, Austria
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16
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Kalyoncu S, Heaner DP, Kurt Z, Bethel CM, Ukachukwu CU, Chakravarthy S, Spain JC, Lieberman RL. Enzymatic hydrolysis by transition-metal-dependent nucleophilic aromatic substitution. Nat Chem Biol 2016; 12:1031-1036. [PMID: 27694799 PMCID: PMC5110390 DOI: 10.1038/nchembio.2191] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/29/2016] [Indexed: 12/22/2022]
Abstract
Nitroaromatic compounds are typically toxic and resistant to degradation. Bradyrhizobium species strain JS329 metabolizes 5-nitroanthranilic acid (5NAA), which is a molecule secreted by Streptomyces scabies, the plant pathogen responsible for potato scab. The first biodegradation enzyme is 5NAA-aminohydrolase (5NAA-A), a metalloprotease family member that converts 5NAA to 5-nitrosalicylic acid. We characterized 5NAA-A biochemically and obtained snapshots of its mechanism. 5NAA-A, an octamer that can use several divalent transition metals for catalysis in vitro, employs a nucleophilic aromatic substitution mechanism. Unexpectedly, the metal in 5NAA-A is labile but is readily loaded in the presence of substrate. 5NAA-A is specific for 5NAA and cannot hydrolyze other tested derivatives, which are likewise poor inhibitors. The 5NAA-A structure and mechanism expand our understanding of the chemical ecology of an agriculturally important plant and pathogen, and will inform bioremediation and biocatalytic approaches to mitigate the environmental and ecological impact of nitroanilines and other challenging substrates.
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Affiliation(s)
- Sibel Kalyoncu
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA
| | - David P. Heaner
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA
| | - Zohre Kurt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA
| | - Casey M. Bethel
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA
| | | | - Srinivas Chakravarthy
- Biophysics Collaborative Access Team, Advanced Photon Source, Argonne National Labs, Lemont, IL
| | - Jim C. Spain
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA
- Center for Environmental Diagnostics and Bioremediation, University of West Florida, Pensacola, FL
| | - Raquel L. Lieberman
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA
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17
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Thelusmond JR, Strathmann TJ, Cupples AM. The identification of carbamazepine biodegrading phylotypes and phylotypes sensitive to carbamazepine exposure in two soil microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 571:1241-1252. [PMID: 27481454 DOI: 10.1016/j.scitotenv.2016.07.154] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 07/21/2016] [Accepted: 07/22/2016] [Indexed: 06/06/2023]
Abstract
Carbamazepine (CBZ), an antiepileptic drug, has been introduced into agricultural soils via irrigation with treated wastewater and biosolids application. Such contamination is problematic because CBZ is persistent and the risks to ecosystems or human health are unknown. The current study examined CBZ biodegradation in two agricultural soils (soil 1 and 2) and the effects on the soil microbial communities during CBZ exposure. The experimental design involved three CBZ concentrations (50, 500, 5000ng/g), under aerobic as well as anaerobic conditions. CBZ concentrations were determined using solid phase extraction and LC MS/MS. The effect of CBZ on the soil microbial community was investigated using high throughput sequencing and a computational approach to predict functional composition of the metagenomes (phylogenetic investigation of communities by reconstruction of unobserved states, PICRUSt). The most significant CBZ biodegradation occurred in soil 1 under aerobic conditions. In contrast, CBZ biodegradation was limited under anaerobic conditions in soil 1 and under both conditions in soil 2. For soil 1, several phylotypes were enriched following CBZ degradation compared to the controls, including unclassified Sphingomonadaceae, Xanthomonadaceae and Rhodobacteraceae, as well as Sphingomonas, Aquicella and Microvirga. These phylotypes are considered putative CBZ degraders as they appear to be benefiting from CBZ biodegradation. PICRUSt revealed that soil 1 contained a greater abundance of xenobiotic degrading genes compared to soil 2, and thus, this analysis method offers a potential valuable approach for predicting CBZ attenuation in soils. PICRUSt analysis also implicated Sphingomonadaceae and Xanthomonadaceae in drug metabolism. Interestingly, numerous phylotypes decreased in abundance following CBZ exposure and these varied with soil type, concentration, duration of exposure, and the availability of oxygen. For three phylotypes (Flavobacterium, 3 genus incertae sedis and unclassified Bacteroidetes), the relative abundance was reduced in both soils, indicating a notable sensitivity to CBZ for these microorganisms.
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Affiliation(s)
- Jean-Rene Thelusmond
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Timothy J Strathmann
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO 80401, USA
| | - Alison M Cupples
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA.
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Sarikhani E, Sagova-Mareckova M, Omelka M, Kopecky J. The effect of peat and iron supplements on the severity of potato common scab and bacterial community in tuberosphere soil. FEMS Microbiol Ecol 2016; 93:fiw206. [PMID: 27794015 DOI: 10.1093/femsec/fiw206] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2016] [Indexed: 02/03/2023] Open
Abstract
The control of common scab (CS) of potatoes includes resistant cultivars, specific fertilization, increase of soil moisture and chemical treatments. Yet, these management practices do not have common or reproducible results at differing sites. In order to determine the effects of soil organic matter, iron and pH on CS development, peat and DTPA-chelated iron were supplemented to pots filled with soil conducive for CS. All results were compared with the same data obtained for a suppressive soil, which has naturally low severity of CS and occurs nearby. Bacteria, Actinobacteria and the txtB genes from the biosynthetic cluster of thaxtomin, which is responsible for the disease development, were quantified by qPCR in tuberosphere soil and potato periderm. Illumina amplicon sequencing of bacterial 16S rRNA genes was performed for tuberosphere soils. Both peat and iron supplements controlled potato scab, and the combination of the two supplements reduced CS most effectively. The bacterial community was modified by all treatments but the highest number of operational taxonomic units (OTUs) changed towards the suppressive soil after the combined peat and iron treatment. It seemed that iron supplement supported plant defense while both iron and peat additions changed the bacterial community in favor of CS suppression.
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Affiliation(s)
- Ensyeh Sarikhani
- Department of Epidemiology and Ecology of Microorganisms, Crop Research Institute, 16106 Prague, Czech Republic
| | - Marketa Sagova-Mareckova
- Department of Epidemiology and Ecology of Microorganisms, Crop Research Institute, 16106 Prague, Czech Republic
| | - Marek Omelka
- Department of Probability and Mathematical Statistics, Faculty of Mathematics and Physics, Charles University, 186 75 Prague, Czech Republic
| | - Jan Kopecky
- Department of Epidemiology and Ecology of Microorganisms, Crop Research Institute, 16106 Prague, Czech Republic
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