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Li Y, Sun X, Yang R, Guo L, Li C, Wang X, Li B, Liu H, Wang Q, Soleimani M, Ren Y, Sun W. Phototrophic Nitrogen Fixation, a Neglected Biogeochemical Process in Mine Tailings? ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:6192-6203. [PMID: 38551467 DOI: 10.1021/acs.est.3c09460] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Biological nitrogen fixation (BNF) has important ecological significance in mine tailing by contributing to the initial accumulation of nitrogen. In addition to chemolithotrophic and heterotrophic BNF, light may also fuel BNF in oligotrophic mine tailings. However, knowledge regarding the occurrence and ecological significance of this biogeochemical process in mine tailings remains ambiguous. The current study observed phototrophic BNF in enrichment cultures established from three primary successional stages (i.e., original tailings, biological crusts, and pioneer plants) of tailings. Notably, phototrophic BNF in tailings may be more active at vegetation stages (i.e., biological crusts and pioneering plants) than in bare tailings. DNA-stable isotope probing identified Roseomonas species as potential aerobic anoxygenic phototrophs responsible for phototrophic BNF. Furthermore, metagenomic binning as well as genome mining revealed that Roseomonas spp. contained essential genes involved in nitrogen fixation, anoxygenic photosynthesis, and carbon fixation, suggesting their genetic potential to mediate phototrophic BNF. A causal inference framework equipped with the structural causal model suggested that the enrichment of putative phototrophic diazotrophic Roseomonas may contribute to an elevated total nitrogen content during primary succession in these mine tailings. Collectively, our findings suggest that phototrophic diazotrophs may play important roles in nutrient accumulation and hold the potential to facilitate ecological succession in tailings.
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Affiliation(s)
- Yongbin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Rui Yang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Lifang Guo
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Cangbai Li
- Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
| | - Xiaoyu Wang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Baoqin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Huaqing Liu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Qi Wang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Mohsen Soleimani
- Department of Natural Resources, Isfahan University of Technology, Isfahan 84156-83111, Iran
| | - Youhua Ren
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
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de Sousa RDSDR, Lima GVS, Garcias JT, Gomes GDO, Mateus JR, Madeira LDPDS, Seldin L, Rogez HLG, Marques JM. The Microbial Community Structure in the Rhizosphere of Theobroma cacao L. and Euterpe oleracea Mart. Is Influenced by Agriculture System in the Brazilian Amazon. Microorganisms 2024; 12:398. [PMID: 38399802 PMCID: PMC10892126 DOI: 10.3390/microorganisms12020398] [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: 12/15/2023] [Revised: 12/26/2023] [Accepted: 12/27/2023] [Indexed: 02/25/2024] Open
Abstract
This study tested the hypothesis that cocoa monoculture (MS) and cocoa-açai agroforestry systems (AFS) may influence the microbial community structure and populations of plant growth-promoting bacteria (PGPR). Accordingly, the aim was to analyze the microbial community structure and PGPR populations in different agroecosystems in the Brazilian Amazon. To achieve this, the rhizosphere microbial community of cocoa and açai plants in both Amazonian seasons (dry and rainy) was analyzed using culture-dependent (PGPR screening) and -independent methods [PCR-DGGE based on rrs, alp, nifH gene, and intergenic region (ITS) of fungi]. Concerning PGPR screening, out of 48 isolated bacterial strains, 25% were capable of siderophore production, 29% of mineralized organic phosphate, 8% of inorganic phosphate solubilization, and 4% of indole acetic acid production. Moreover, 17% of isolates could inhibit the growth of various phytopathogenic fungi. Statistical analyses of DGGE fingerprints (p < 0.05) showed that bacterial and fungal community structures in the rhizosphere were influenced by the seasons, supporting the results of the physicochemical analysis of the environment. Furthermore, as hypothesized, microbial communities differed statistically when comparing the MS and AFS. These findings provide important insights into the influence of climate and cultivation systems on soil microbial communities to guide the development of sustainable agricultural practices.
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Affiliation(s)
- Rosiane do Socorro dos Reis de Sousa
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Pará, Brazil; (R.d.S.d.R.d.S.); (G.V.S.L.); (J.T.G.); (G.d.O.G.); (L.D.P.d.S.M.); (H.L.G.R.)
| | - Giulia Victória Silva Lima
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Pará, Brazil; (R.d.S.d.R.d.S.); (G.V.S.L.); (J.T.G.); (G.d.O.G.); (L.D.P.d.S.M.); (H.L.G.R.)
| | - Josinete Torres Garcias
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Pará, Brazil; (R.d.S.d.R.d.S.); (G.V.S.L.); (J.T.G.); (G.d.O.G.); (L.D.P.d.S.M.); (H.L.G.R.)
| | - Graziane de Oliveira Gomes
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Pará, Brazil; (R.d.S.d.R.d.S.); (G.V.S.L.); (J.T.G.); (G.d.O.G.); (L.D.P.d.S.M.); (H.L.G.R.)
| | - Jackeline Rossetti Mateus
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Rio de Janeiro, Brazil; (J.R.M.); (L.S.)
| | - Lucimar Di Paula dos Santos Madeira
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Pará, Brazil; (R.d.S.d.R.d.S.); (G.V.S.L.); (J.T.G.); (G.d.O.G.); (L.D.P.d.S.M.); (H.L.G.R.)
| | - Lucy Seldin
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Rio de Janeiro, Brazil; (J.R.M.); (L.S.)
| | - Hervé Louis Ghislain Rogez
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Pará, Brazil; (R.d.S.d.R.d.S.); (G.V.S.L.); (J.T.G.); (G.d.O.G.); (L.D.P.d.S.M.); (H.L.G.R.)
| | - Joana Montezano Marques
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Pará, Brazil; (R.d.S.d.R.d.S.); (G.V.S.L.); (J.T.G.); (G.d.O.G.); (L.D.P.d.S.M.); (H.L.G.R.)
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Rio de Janeiro, Brazil; (J.R.M.); (L.S.)
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Deng L, Luo L, Li Y, Wang L, Zhang J, Zi B, Ye C, Liu Y, Huang H, Mei X, Deng W, He X, Zhu S, Yang M. Autotoxic Ginsenoside Stress Induces Changes in Root Exudates to Recruit the Beneficial Burkholderia Strain B36 as Revealed by Transcriptomic and Metabolomic Approaches. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:4536-4549. [PMID: 36893094 DOI: 10.1021/acs.jafc.3c00311] [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: 06/18/2023]
Abstract
Plants can recruit beneficial microbes to help improve their fitness under abiotic or biotic stress. Our previous studies found that Panax notoginseng could enrich beneficial Burkholderia sp. B36 in the rhizosphere soil under autotoxic ginsenoside stress. Here, we clarified that ginsenoside stress activated the phenylpropanoid biosynthesis and α-linolenic acid metabolism pathways of roots to increase the secretion of cinnamic acid, 2-dodecenoic acid, and 12-oxo-phytodienoic acid. These metabolites could promote the growth of B36. Importantly, cinnamic acid could simultaneously promote the chemotaxis and growth of B36, enhance the colonization of B36 in the rhizosphere, and eventually increase the survival rate of P. notoginseng. Overall, the plants could promote the growth and colonization of beneficial bacteria through key metabolites in root exudates under autotoxin stress. This finding will facilitate the practical application of beneficial bacteria in agricultural production and lead to successful and reproducible biocontrol efficacy by the exogenous addition of key metabolites.
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Affiliation(s)
- Linmei Deng
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, 650201 Kunming, China
- National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, 650201 Kunming, China
| | - Lifen Luo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, 650201 Kunming, China
- National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, 650201 Kunming, China
| | - Yue Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, 650201 Kunming, China
- National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, 650201 Kunming, China
| | - Luotao Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, 650201 Kunming, China
- National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, 650201 Kunming, China
| | - Junxing Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, 650201 Kunming, China
- National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, 650201 Kunming, China
| | - Bianxian Zi
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, 650201 Kunming, China
- National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, 650201 Kunming, China
| | - Chen Ye
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, 650201 Kunming, China
- National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, 650201 Kunming, China
| | - Yixiang Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, 650201 Kunming, China
- National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, 650201 Kunming, China
| | - Huichuan Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, 650201 Kunming, China
- National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, 650201 Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, College of Plant Protection, Yunnan Agricultural University, 650201 Kunming, China
| | - Xinyue Mei
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, 650201 Kunming, China
- National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, 650201 Kunming, China
| | - Weiping Deng
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, 650201 Kunming, China
- National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, 650201 Kunming, China
| | - Xiahong He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, 650201 Kunming, China
- National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, 650201 Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, College of Plant Protection, Yunnan Agricultural University, 650201 Kunming, China
| | - Shusheng Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, 650201 Kunming, China
- National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, 650201 Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, College of Plant Protection, Yunnan Agricultural University, 650201 Kunming, China
| | - Min Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, 650201 Kunming, China
- National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, 650201 Kunming, China
- Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, College of Plant Protection, Yunnan Agricultural University, 650201 Kunming, China
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Li Q, Yang X, Li J, Li M, Li C, Yao T. In-depth characterization of phytase-producing plant growth promotion bacteria isolated in alpine grassland of Qinghai-Tibetan Plateau. Front Microbiol 2023; 13:1019383. [PMID: 36687657 PMCID: PMC9846362 DOI: 10.3389/fmicb.2022.1019383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/30/2022] [Indexed: 01/05/2023] Open
Abstract
The use of plant growth promoting bacteria (PGPB) express phytase (myo-inositol hexakisphosphate phosphohydrolase) capable of hydrolyzing inositol phosphate in soil was a sustainable approach to supply available phosphorus (P) to plants. A total of 73 bacterial isolates with extracellular phytase activity were selected from seven dominant grass species rhizosphere in alpine grassland of Qinghai-Tibetan Plateau. Then, the plant growth promoting (PGP) traits of candidate bacteria were screened by qualitative and quantitative methods, including organic/inorganic Phosphorus solubilization (P. solubilization), plant hormones (PHs) production, nitrogen fixation, 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity and antimicrobial activity. Further experiment were conducted to test their growth promoting effect on Lolium perenne L. under P-limitation. Our results indicated that these bacteria as members of phyla Proteobacteria (90.41%) and Actinobacteria (9.59%) were related to 16 different genera. The isolates of Pseudomonas species showed the highest isolates number (36) and average values of phytase activity (0.267 ± 0.012 U mL-1), and showed a multiple of PGP traits, which was a great candidate for PGPBs. In addition, six strains were positive in phytase gene (β-propeller phytase, bpp) amplification, which significantly increased the shoot length, shoot/root fresh weight, root average diameter and root system phytase activity of Lolium perenne L. under P-limitation, and the expression of phytase gene (bppP) in root system were verified by qPCR. Finally, the PHY101 gene encoding phytase from Pseudomonas mandelii GS10-1 was cloned, sequenced, and recombinantly expressed in Escherichia coli. Biochemical characterization demonstrated that the recombinant phytase PHY101 revealed the highest activity at pH 6 and 40°C temperature. In particular, more than 60% of activity was retained at a low temperature of 15°C. This study demonstrates the opportunity for commercialization of the phytase-producing PGPB to developing localized microbial inoculants and engineering rhizobacteria for sustainable use in alpine grasslands.
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Luo L, Zhang J, Ye C, Li S, Duan S, Wang Z, Huang H, Liu Y, Deng W, Mei X, He X, Yang M, Zhu S. Foliar Pathogen Infection Manipulates Soil Health through Root Exudate-Modified Rhizosphere Microbiome. Microbiol Spectr 2022; 10:e0241822. [PMID: 36445116 PMCID: PMC9769671 DOI: 10.1128/spectrum.02418-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 11/03/2022] [Indexed: 12/03/2022] Open
Abstract
Negative plant-soil feedback (NPSF) due to the buildup of soilborne pathogens in soil is a major obstacle in sustainable agricultural systems. Beneficial rhizosphere microfloras are recruited by plants, and mediating this has become a strategic priority to manipulate plant health. Here, we found that foliar infection of Panax notoginseng by Alternaria panax changed plant-soil feedback from negative to positive. Foliar infection modified the rhizosphere soil microbial community and reversed the direction of the buildup of the soilborne pathogen Ilyonectria destructans and beneficial microbes, including Trichoderma, Bacillus, and Streptomyces, in rhizosphere soil. These beneficial microbes not only showed antagonistic ability against the pathogen I. destructans but also enhanced the resistance of plants to A. panax. Foliar infection enhanced the exudation of short- and long-chain organic acids, sugars, and amino acids from roots. In vitro and in vivo experiments validated that short- and long-chain organic acids and sugars play dual roles in simultaneously suppressing pathogens but enriching beneficial microbes. In summary, foliar infection could change root secretion to drive shifts in the rhizosphere microbial community to enhance soil health, providing a new strategy to alleviate belowground disease in plants through aboveground inducement. IMPORTANCE Belowground soilborne disease is the main factor limiting sustainable agricultural production and is difficult to manage due to the complexity of the soil environment. Here, we found that aboveground parts of plants infected by foliar pathogens could enhance the secretion of organic acids, sugars, and amino acids in root exudates to suppress soilborne pathogens and enrich beneficial microbes, eventually changing the plant and soil feedback from negative to positive and alleviating belowground soilborne disease. This is an exciting strategy by which to achieve belowground soilborne disease management by manipulating the aboveground state through aboveground stimulation.
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Affiliation(s)
- Lifen Luo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Junxing Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Chen Ye
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Su Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Shengshuang Duan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Zhengping Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Huichuan Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, College of Plant Protection, Yunnan Agricultural University, Kunming, China
- National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Yixiang Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, College of Plant Protection, Yunnan Agricultural University, Kunming, China
- National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Weiping Deng
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, College of Plant Protection, Yunnan Agricultural University, Kunming, China
- National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Xinyue Mei
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, College of Plant Protection, Yunnan Agricultural University, Kunming, China
- National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Xiahong He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, College of Plant Protection, Yunnan Agricultural University, Kunming, China
- National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Min Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, College of Plant Protection, Yunnan Agricultural University, Kunming, China
- National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Shusheng Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, College of Plant Protection, Yunnan Agricultural University, Kunming, China
- National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, Kunming, China
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Debnath S, Das A, Maheshwari DK, Pandey P. Treatment with atypical rhizobia, Pararhizobium giardinii and Ochrobactrum sp. modulate the rhizospheric bacterial community, and enhances Lens culinaris growth in fallow-soil. Microbiol Res 2022; 267:127255. [PMID: 36434988 DOI: 10.1016/j.micres.2022.127255] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/26/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022]
Abstract
Diazotrophic nodule isolates are acknowledged promoters of plant growth and rhizospheric community. Consequently, in the lentil agroecosystem, inoculation of atypical rhizobial isolates could be a viable alternative to chemical fertilizers for fallow land usage optimization. The aim of this study is to evaluate and select the rhizobial isolates of lentil nodules with plant-growth-promoting (PGP) attributes and to elucidate their application in rice-fallow soil for determining the growth of lentils and its impact on the rhizospheric bacterial community. Lentil's nodule isolates were identified and screened for their PGP attributes, biofilm, exopolysaccharide (EPS) formation, and early plant growth promotion. The pot experiment with the selected atypical rhizobial isolates Pararhizobium giardinii (P1) and Ochrobactrum sp. (42S) significantly enhanced germination, vigour index, nodule formation (P1 60%, 42S 42% increase), nodule fresh weight, shoot length (65% P1 & 35% 42S), and chlorophyll content as compared to the uninoculated control treatment. The genes for nitrogen fixation nifH and nifK were detected in both isolates. Scanning Electron Microscopy (SEM) revealed successful root and nodule colonization by both isolates, while Transmission Electron Microscopy (TEM) displayed nitrogen-fixing zones within root nodules. Proteobacteria predominated in the lentil rhizosphere of all the treatments. Whereas, application of either P1 or 42S increased Rhizobium, Mesorhizobium, and Bradyrhizobium genra, thus positively modulating rhizospheric community structure. The correlation network analysis revealed an abundance of some interdependent bacterial genera with a possible role in overall plant growth. Functional genes for siderophore biosynthesis and ABC transporter were positively modulated by application of either P1 or 42S. This study showed the significant effect of P. giardinii P1 and Ochrobactrum sp. 42S of L. culinaris on lentil growth, improving fallowsoil health for optimum usage, and modulated rhizospheric community structure which strongly manifest prospects of low-cost, eco-friendly and sustainable biofertilizers.
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Affiliation(s)
- Sourav Debnath
- Department of Microbiology, Assam University, Silchar 788011, India
| | - Ankita Das
- Department of Microbiology, Assam University, Silchar 788011, India
| | - D K Maheshwari
- Department of Botany and Microbiology, Gurukula Kangri University, Haridwar 249404, Uttarakhand, India
| | - Piyush Pandey
- Department of Microbiology, Assam University, Silchar 788011, India.
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7
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Nonthakaew N, Panbangred W, Songnuan W, Intra B. Plant growth-promoting properties of Streptomyces spp. isolates and their impact on mung bean plantlets’ rhizosphere microbiome. Front Microbiol 2022; 13:967415. [PMID: 36090067 PMCID: PMC9453592 DOI: 10.3389/fmicb.2022.967415] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 07/26/2022] [Indexed: 12/02/2022] Open
Abstract
Phytophthora is an important, highly destructive pathogen of many plants, which causes considerable crop loss, especially durians in Thailand. In this study, we selectively isolated Streptomyces from the rhizosphere soil with a potent anti-oomycete activity against Phytophthora palmivora CbP03. Two strains (SNN087 and SNN289) demonstrated exceptional plant growth-promoting properties in pot experiment. Both strains promoted mung bean (Vigna radiate) growth effectively in both sterile and non-sterile soils. Metagenomic analysis revealed that Streptomyces sp. SNN289 may modify the rhizosphere microbial communities, especially promoting microbes beneficial for plant growth. The relative abundance of bacterial genera Bacillus, Sphingomonas, Arthrobacter, and Pseudarthrobacter, and fungal genera Coprinellus and Chaetomium were noticeably increased, whereas a genus Fusarium was slightly reduced. Interestingly, Streptomyces sp. SNN289 exhibited an exploratory growth, which allows it to survive in a highly competitive environment. Based on whole genome sequence analysis combined with an ANI and dDDH values, this strain should be classifiable as a new species. Functional annotation was also used to characterize plant-beneficial genes in SNN087 and SNN289 genomes for production of siderophores, 3-indole acetic acid (IAA), ammonia, and solubilized phosphate. AntiSMASH genome analysis and preliminary annotation revealed biosynthetic gene clusters with possible secondary metabolites. These findings emphasize the potential for application of strain SNN289 as a bioinoculant for sustainable agricultural practice.
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Affiliation(s)
- Napawit Nonthakaew
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Osaka Collaborative Research Center for Bioscience and Biotechnology, Mahidol University-Osaka, Bangkok, Thailand
| | - Watanalai Panbangred
- Research, Innovation, and Partnerships Office (Office of the President), King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Wisuwat Songnuan
- Department of Plant Science, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Bungonsiri Intra
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Osaka Collaborative Research Center for Bioscience and Biotechnology, Mahidol University-Osaka, Bangkok, Thailand
- *Correspondence: Bungonsiri Intra,
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8
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Chen S, Qin R, Yang D, Liu W, Yang S. A Comparison of Rhizospheric and Endophytic Bacteria in Early and Late-Maturing Pumpkin Varieties. Microorganisms 2022; 10:microorganisms10081667. [PMID: 36014084 PMCID: PMC9415385 DOI: 10.3390/microorganisms10081667] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/05/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022] Open
Abstract
To determine whether rhizospheric and endophytic bacteria contribute to the ripening of pumpkins, an analysis was conducted on rhizospheric and endophytic bacteria and soil fertility in the rhizospheres of early and late-maturing pumpkin varieties. The results showed higher nitrogen and abscisic acid content and more gibberellin-producing bacteria in the rhizospheres or endophytes of the early maturing varieties. Greater soil fertility and more abundant rhizospheric and endophytic bacterial genera with a greater metabolic function might be important mechanisms for early ripening. Rhodococcus, Bacillus, and Arthrobacter can be considered the functional bacteria in promoting pumpkin maturation. On the other hand, Ralstonia could be the functional bacterium that delays ripening.
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Affiliation(s)
- Siyu Chen
- Guangxi Key Laboratory of Agro-Environment and Agro-Products Safety, National Demonstration Center for Experimental Plant Science Education, Agricultural College, Guangxi University, Nanning 530004, China
| | - Renliu Qin
- Guangxi Key Laboratory of Agro-Environment and Agro-Products Safety, National Demonstration Center for Experimental Plant Science Education, Agricultural College, Guangxi University, Nanning 530004, China
| | - Da Yang
- Guangxi Key Laboratory of Agro-Environment and Agro-Products Safety, National Demonstration Center for Experimental Plant Science Education, Agricultural College, Guangxi University, Nanning 530004, China
| | - Wenjun Liu
- Vegetable Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Shangdong Yang
- Guangxi Key Laboratory of Agro-Environment and Agro-Products Safety, National Demonstration Center for Experimental Plant Science Education, Agricultural College, Guangxi University, Nanning 530004, China
- Correspondence:
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9
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Qi M, Berry JC, Veley KW, O'Connor L, Finkel OM, Salas-González I, Kuhs M, Jupe J, Holcomb E, Glavina Del Rio T, Creech C, Liu P, Tringe SG, Dangl JL, Schachtman DP, Bart RS. Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multi-system microbiome comparisons. THE ISME JOURNAL 2022; 16:1957-1969. [PMID: 35523959 PMCID: PMC9296637 DOI: 10.1038/s41396-022-01245-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 12/12/2022]
Abstract
Drought is a major abiotic stress limiting agricultural productivity. Previous field-level experiments have demonstrated that drought decreases microbiome diversity in the root and rhizosphere. How these changes ultimately affect plant health remains elusive. Toward this end, we combined reductionist, transitional and ecological approaches, applied to the staple cereal crop sorghum to identify key root-associated microbes that robustly affect drought-stressed plant phenotypes. Fifty-three Arabidopsis-associated bacteria were applied to sorghum seeds and their effect on root growth was monitored. Two Arthrobacter strains caused root growth inhibition (RGI) in Arabidopsis and sorghum. In the context of synthetic communities, Variovorax strains were able to protect plants from Arthrobacter-caused RGI. As a transitional system, high-throughput phenotyping was used to test the synthetic communities. During drought stress, plants colonized by Arthrobacter had reduced growth and leaf water content. Plants colonized by both Arthrobacter and Variovorax performed as well or better than control plants. In parallel, we performed a field trial wherein sorghum was evaluated across drought conditions. By incorporating data on soil properties into the microbiome analysis, we accounted for experimental noise with a novel method and were able to observe the negative correlation between the abundance of Arthrobacter and plant growth. Having validated this approach, we cross-referenced datasets from the high-throughput phenotyping and field experiments and report a list of bacteria with high confidence that positively associated with plant growth under drought stress. In conclusion, a three-tiered experimental system successfully spanned the lab-to-field gap and identified beneficial and deleterious bacterial strains for sorghum under drought.
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Affiliation(s)
- Mingsheng Qi
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | | | - Kira W Veley
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Lily O'Connor
- Donald Danforth Plant Science Center, St. Louis, MO, USA.,Washington University, St. Louis, MO, USA
| | - Omri M Finkel
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Plant and Environmental Sciences, Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Isai Salas-González
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Molly Kuhs
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Julietta Jupe
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Emily Holcomb
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | | | - Cody Creech
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Peng Liu
- Department of Statistics, Iowa State University, Ames, IA, USA
| | - Susannah G Tringe
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Daniel P Schachtman
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA.,Center for Plant Science Innovation, University of Nebraska - Lincoln, Lincoln, NE, USA
| | - Rebecca S Bart
- Donald Danforth Plant Science Center, St. Louis, MO, USA.
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10
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Chauhan J, Gohel S. Exploring plant growth-promoting, biocatalytic, and antimicrobial potential of salt tolerant rhizospheric Georgenia soli strain TSm39 for sustainable agriculture. Braz J Microbiol 2022; 53:1817-1828. [PMID: 35854099 PMCID: PMC9679074 DOI: 10.1007/s42770-022-00794-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 07/06/2022] [Indexed: 01/13/2023] Open
Abstract
To explore the in vivo and in vitro plant growth promoting activities, biocatalytic potential, and antimicrobial activity of salt tolerance rhizoactinobacteria, rhizospheric soil of a halotolerant plant Saueda maritima L. was collected from Rann of Tiker, near Little Rann of Kutch, Gujarat (India). The morphology analysis of the isolated strain TSm39 revealed that the strain belonged to the phylum actinobacteria, as it was stained Gram-positive, displayed filamentous growth, showed spore formation and red pigment production on starch casein agar (SCA). It was identified as Georgenia soli based on 16S rRNA gene sequencing. The Georgenia soli strain TSm39 secreted extracellular amylase, pectinase, and protease. It showed in vitro plant growth-promoting (PGP) activities such as indole acetic acid (IAA) production, siderophore production, ammonia production, and phosphate solubilization. In vivo plant growth-promoting traits of strain TSm39 revealed 30% seed germination on water agar and vigor index 374.4. Additionally, a significant increase (p ≤ 0.05) was found in growth parameters such as root length (16.1 ± 0.22), shoot length (15.2 ± 0.17), the fresh weight (g), and dry weight (g) of the roots (0.43 ± 0.42 and 0.32 ± 0.12), shoots (0.62 ± 0.41 and 0.13 ± 0.03), and leaves (0.42 ± 0.161 and 0.14 ± 0.42) in treated seeds of Vigna radiata L. plant with the strain TSm39 compared to control. The antibiotic susceptibility profile revealed resistance of the strain TSm39 to erythromycin, ampicillin, tetracycline, and oxacillin, while it displayed maximum sensitivity to vancomycin (40 ± 0.72), chloramphenicol (40 ± 0.61), clarithromycin (40 ± 1.30), azithromycin (39 ± 0.42), and least sensitivity to teicoplanin (15 ± 0.15). Moreover, the antimicrobial activity of the strain TSm39 was observed against Gram's positive and Gram's negative microorganisms such as Shigella, Proteus vulgaris, and Bacillus subtilis. These findings indicated that the Georgenia soli strain TSm39 has multiple plant-growth-promoting properties and biocatalytic potential that signifies its agricultural applications in the enhancement of crop yield and quality and would protect the plant against plant pathogens.
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Affiliation(s)
- Jagruti Chauhan
- grid.412428.90000 0000 8662 9555Department of Biosciences, Saurashtra University, Rajkot, 360005 Gujarat India
| | - Sangeeta Gohel
- grid.412428.90000 0000 8662 9555Department of Biosciences, Saurashtra University, Rajkot, 360005 Gujarat India
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11
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Guo Z, Hui W, Li J, Yang C, Zhang H, Wang H. Effects of soft rock on soil properties and bacterial community in Mu Us Sandy Land, China. PeerJ 2022; 10:e13561. [PMID: 35757169 PMCID: PMC9231347 DOI: 10.7717/peerj.13561] [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: 01/12/2022] [Accepted: 05/19/2022] [Indexed: 01/17/2023] Open
Abstract
Soft rock is a new material that could be used for the improvement of Mu Us Sandy Land, China. It can be utilized for wind prevention and sand fixation, both of which are of great importance to ecological restoration aims and cultivated land replenishment in desert areas. Four treatments with different compound ratios of soft rock and sand-0:1 (CK), 1:5 (P1), 1:2 (P2), and 1:1 (P3)-were studied. Fluorescence quantitative PCR (qPCR) and high-throughput sequencing were used to analyze the structure and diversity of the bacterial community in the compound soil and its relationship with physical and chemical parameters in the soil. The results showed that in comparison to CK treatment, soil organic carbon (SOC), total nitrogen (TN), and NH4 +-N increased significantly in the P1 treatment; available phosphorus (AP), available potassium (AK), and NO3 --N increased significantly in the P3 treatment. The bacterial gene copy number with P3 treatment was highest, showing a significant increase of 182.05% compared with the CK treatment. The three bacterial groups with the highest relative abundance at the phylum level were Actinobacteria, Proteobacteria, and Chloroflexi, accounting for more than 70% of the total population. The bacterial α diversity showed the same trend, the diversity and abundance indices of the P1 and P3 treatments were the highest, and the β diversity showed that the community structure of the two groups in these treatments were similar. norank_f__Roseiflexaceae and Gaiella (belonging to Actinobacteria) significantly differed with differing compound ratios in each treatment. NO3 --N, NH4 +-N and SOC were the main factors affecting bacterial community structure, and had a significant positive correlation with Gaiella abundance. These species are known to play an important role in stabilizing the soil structure of sandy land. Overall, 1:5 and 1:1 compound soil mixtures were beneficial towards the microbial community of sandy land, which plays an important role in biological sand fixation. This study provides an important theoretical basis for the supplementation of arable land area and the improvement of sandy land productivity, and has a good promotion prospect.
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Affiliation(s)
- Zhen Guo
- Shaanxi Provincial Land Engineering Construction Group Co., Ltd., Xi’an, Shaanxi, China,Institute of Land Engineering and Technology, Shaanxi Provincial Land Engineering Construction Group Co., Ltd., Xi’an, Shaanxi, China
| | - Wei Hui
- Shaanxi Provincial Land Engineering Construction Group Co., Ltd., Xi’an, Shaanxi, China
| | - Juan Li
- Shaanxi Provincial Land Engineering Construction Group Co., Ltd., Xi’an, Shaanxi, China,Institute of Land Engineering and Technology, Shaanxi Provincial Land Engineering Construction Group Co., Ltd., Xi’an, Shaanxi, China
| | - Chenxi Yang
- Shaanxi Provincial Land Engineering Construction Group Co., Ltd., Xi’an, Shaanxi, China,Institute of Land Engineering and Technology, Shaanxi Provincial Land Engineering Construction Group Co., Ltd., Xi’an, Shaanxi, China
| | - Haiou Zhang
- Shaanxi Provincial Land Engineering Construction Group Co., Ltd., Xi’an, Shaanxi, China,Institute of Land Engineering and Technology, Shaanxi Provincial Land Engineering Construction Group Co., Ltd., Xi’an, Shaanxi, China
| | - Huanyuan Wang
- Shaanxi Provincial Land Engineering Construction Group Co., Ltd., Xi’an, Shaanxi, China,Institute of Land Engineering and Technology, Shaanxi Provincial Land Engineering Construction Group Co., Ltd., Xi’an, Shaanxi, China
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12
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Özdoğan DK, Akçelik N, Akçelik M. Genetic Diversity and Characterization of Plant Growth-Promoting Effects of Bacteria Isolated from Rhizospheric Soils. Curr Microbiol 2022; 79:132. [PMID: 35290524 DOI: 10.1007/s00284-022-02827-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 11/02/2021] [Indexed: 01/18/2023]
Abstract
Plant growth-promoting rhizobacteria (PGPR) have the potential to make a significant contribution to the development of sustainable agricultural systems. Generally, PGPRs function in three different ways, summarized as the synthesis of certain compounds for plants, facilitating the uptake of certain nutrients from the soil and protecting plants from diseases. This study aims to isolate plant growth-promoting bacteria from different plant rhizospheres from Ankara province, to reveal their genetic diversity, and to determine their plant growth-promoting properties. The identification of the 69 isolates was made according to the 16S rDNA sequence results and ARDRA analyses were also performed using AluI, HeaIII, and MspI enzymes. Nitrogen fixation, phosphate dissolving, IAA (indole-3-acetic acid) and siderophore production capacities of the 69 bacterial strains including 12 different genera (30 Pseudomonas, 13 Arthrobacter, 7 Bacillus, 4 Phyllobacter, 4 Variovorax, 3 Olivibacter, 3 Enterobacter, 2 Paenarthrobacter, 1 Stenotrophomonas, 1 Flavobacterium, 1 Caulobacter, 1 Paenibacillus) were evaluated in in vitro conditions. Nitrogen fixation capacities of 55 isolates varied between 2.29 and 46.11 µg mL-1 according to micro-kjeldahl method. Among the strains studied, nifH gene was detected only in Paenibacillus polymyxa H8/2 strain. The highest Phosphorus dissolving and IAA production capacity (in tryptophan-added medium) of isolates were 186.52 µg mL-1, and 50.05 μg mL-1 respectively, and 31 of 69 isolates were able to produce siderophore. Regarding antifungal activities, results showed that 31 bacterial isolates had antagonistic activities against at least one of the tested pathogens. Nitrogen fixation and phosphate solubilizing potential of the promising bacterial strains were determined through two-independent pot experiments with wheat and it has been found that they have positive effects on the yield parameters of wheat.
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Affiliation(s)
- Dilek Kaya Özdoğan
- Soil Fertilizer and Water Resources Center Research Institute, Ankara, Turkey.
| | - Nefise Akçelik
- Biotechnology Institute, Ankara University, Ankara, Turkey
| | - Mustafa Akçelik
- Faculty of Science, Department of Biology, Ankara University, Ankara, Turkey
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13
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Lin Z, Pang S, Zhou Z, Wu X, Li J, Huang Y, Zhang W, Lei Q, Bhatt P, Mishra S, Chen S. Novel pathway of acephate degradation by the microbial consortium ZQ01 and its potential for environmental bioremediation. JOURNAL OF HAZARDOUS MATERIALS 2022; 426:127841. [PMID: 34844804 DOI: 10.1016/j.jhazmat.2021.127841] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 11/10/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
The microbial degradation of acephate in pure cultures has been thoroughly explored, but synergistic metabolism at the community level has rarely been investigated. Here, we report a novel microbial consortium, ZQ01, capable of effectively degrading acephate and its toxic product methamidophos, which can use acephate as a source of carbon, phosphorus and nitrogen. The degradation conditions with consortium ZQ01 were optimized using response surface methodology at a temperature of 34.1 °C, a pH of 8.9, and an inoculum size of 2.4 × 108 CFU·mL-1, with 89.5% of 200 mg L-1 acephate degradation observed within 32 h. According to the main products methamidophos, acetamide and acetic acid, a novel degradation pathway for acephate was proposed to include hydrolysis and oxidation as the main pathways of acephate degradation. Moreover, the bioaugmentation of acephate-contaminated soils with consortium ZQ01 significantly enhanced the removal rate of acephate. The results of the present work demonstrate the potential of microbial consortium ZQ01 to degrade acephate in water and soil environments, with a different and complementary acephate degradation pathway.
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Affiliation(s)
- Ziqiu Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Shimei Pang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Zhe Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Xiaozhen Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Jiayi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yaohua Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Wenping Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Qiqi Lei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Sandhya Mishra
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
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14
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Giannelli G, Bisceglie F, Pelosi G, Bonati B, Cardarelli M, Antenozio ML, Degola F, Visioli G. Phyto-Beneficial Traits of Rhizosphere Bacteria: In Vitro Exploration of Plant Growth Promoting and Phytopathogen Biocontrol Ability of Selected Strains Isolated from Harsh Environments. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11020230. [PMID: 35050118 PMCID: PMC8779669 DOI: 10.3390/plants11020230] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/13/2022] [Accepted: 01/14/2022] [Indexed: 05/04/2023]
Abstract
Beneficial interactions between plants and some bacterial species have been long recognized, as they proved to exert various growth-promoting and health-protective activities on economically relevant crops. In this study, the growth promoting and antifungal activity of six bacterial strains, Paenarthrobacter ureafaciens, Beijerinckia fluminensis, Pseudomonas protegens, Arthrobacter sp., Arthrobacter defluii, and Arthrobacter nicotinovorans, were investigated. The tested strains resulted positive for some plant growth promoting (PGP) traits, such as indole-3-acetic acid (IAA), 1-aminocyclopropane-1-carboxylate-deaminase (ACC-deaminase), siderophore production, and solubilization of phosphates. The effect of the selected bacteria on Arabidopsis thaliana seedlings growth was assessed using different morphological parameters. Bacterial activity against the phytopathogenic fungal species Aspergillus flavus, Fusarium proliferatum, and Fusarium verticillioides was also assessed, since these cause major yield losses in cereal crops and are well-known mycotoxin producers. Strains Pvr_9 (B. fluminensis) and PHA_1 (P. protegens) showed an important growth-promoting effect on A. thaliana coupled with a high antifungal activity on all the three fungal species. The analysis of bacterial broths through ultra performance liquid chromatography-mass spectrometry (UPLC-MS) and liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS/MS) confirmed the presence of potential PGP-compounds, among these are desferrioxamine B, aminochelin, asperchrome B, quinolobactin siderophores, and salicylic acid.
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Affiliation(s)
- Gianluigi Giannelli
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 11/a, 43124 Parma, Italy
| | - Franco Bisceglie
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 11/a, 43124 Parma, Italy
- C.I.R.C.M.S.B.-Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici, Parma Local Unit, 43124 Parma, Italy
| | - Giorgio Pelosi
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 11/a, 43124 Parma, Italy
- C.I.R.C.M.S.B.-Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici, Parma Local Unit, 43124 Parma, Italy
| | - Beatrice Bonati
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 11/a, 43124 Parma, Italy
| | | | - Maria Luisa Antenozio
- IBPM-CNR, P.le A. Moro 5, 00185 Roma, Italy
- Dipartimento di Biologia e Biotecnologie, Università Sapienza di Roma, 00185 Roma, Italy
| | - Francesca Degola
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 11/a, 43124 Parma, Italy
| | - Giovanna Visioli
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 11/a, 43124 Parma, Italy
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15
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Ngosong C, Tatah BN, Olougou MNE, Suh C, Nkongho RN, Ngone MA, Achiri DT, Tchakounté GVT, Ruppel S. Inoculating plant growth-promoting bacteria and arbuscular mycorrhiza fungi modulates rhizosphere acid phosphatase and nodulation activities and enhance the productivity of soybean ( Glycine max). FRONTIERS IN PLANT SCIENCE 2022; 13:934339. [PMID: 36226292 PMCID: PMC9549076 DOI: 10.3389/fpls.2022.934339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/29/2022] [Indexed: 05/06/2023]
Abstract
Soybean [Glycine max (L.) Merrill] cultivation is important for its dual role as rich source of dietary protein and soil fertility enhancer, but production is constrained by soil nutrient deficiencies. This is often resolved using chemical fertilizers that exert deleterious effects on the environment when applied in excess. This field study was conducted at Nkolbisson-Yaoundé in the agro-ecological zone V of Cameroon to assess the performance of soybean when inoculated with plant growth-promoting bacteria (PGPB) and arbuscular mycorrhiza fungi (AMF), with or without NPK fertilizer addition. Ten treatments (Control, PGPB, AMF, PGPB+AMF, PGPB+N, PGPB+PK, PGPB+N+PK, PGPB+AMF+N, PGPB+AMF+PK, and PGPB+AMF+N+PK) were established in a randomized complete block design with three replicates. Mycorrhizal colonization was only observed in AMF-inoculated soybean roots. In comparison to control, sole inoculation of PGPB and AMF increased the number of root nodules by 67.2% and 57%, respectively. Co-application of PGPB and AMF increased the number of root nodules by 68.4%, while the addition of NPK fertilizers significantly increased the number of root nodules by 66.9-68.6% compared to control. Acid phosphatase activity in soybean rhizosphere ranged from 46.1 to 85.1 mg h-1 kg-1 and differed significantly across treatments (p < 0.001). When compared to control, PGPB or AMF or their co-inoculation, and the addition of NPK fertilizers increased the acid phosphatase activity by 45.8%, 27%, 37.6%, and 26.2-37.2%, respectively. Sole inoculation of PGPB or AMF and their integration with NPK fertilizer increased soybean yield and grain contents (e.g., carbohydrate, protein, zinc, and iron) compared to the control (p < 0.001). Soil phosphorus correlated significantly (p < 0.05) with soybean grain protein (r = 0.46) and carbohydrate (r = 0.41) contents. The effective root nodules correlated significantly (p < 0.001) with acid phosphatase (r = 0.67) and soybean yield (r = 0.66). Acid phosphatase correlated significantly (p < 0.001) with soybean grain yield (r = 0.63) and carbohydrate (r = 0.61) content. Effective root nodules correlated significantly with carbohydrate (r = 0.87, p < 0.001), protein (r = 0.46, p < 0.01), zinc (r = 0.59, p < 0.001), and iron (r = 0.77, p < 0.01) contents in soybean grains. Overall, these findings indicate strong relationships between farm management practices, microbial activities in the rhizosphere, and soybean performance.
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Affiliation(s)
- Christopher Ngosong
- Rhizobiology Group, Department of Agronomic and Applied Molecular Sciences, Faculty of Agriculture and Veterinary Medicine, University of Buea, Buea, Cameroon
- *Correspondence: Christopher Ngosong,
| | - Blaise Nangsingnyuy Tatah
- Rhizobiology Group, Department of Agronomic and Applied Molecular Sciences, Faculty of Agriculture and Veterinary Medicine, University of Buea, Buea, Cameroon
| | - Marie Noela Enyoe Olougou
- Rhizobiology Group, Department of Agronomic and Applied Molecular Sciences, Faculty of Agriculture and Veterinary Medicine, University of Buea, Buea, Cameroon
- Research Group on Beneficial Microorganisms and Plant Interactions, Leibniz Institute of Vegetable and Ornamental Crops, Großbeeren, Germany
| | - Christopher Suh
- Institute of Agricultural Research for Development (IRAD), Yaoundé, Cameroon
| | - Raymond Ndip Nkongho
- Rhizobiology Group, Department of Agronomic and Applied Molecular Sciences, Faculty of Agriculture and Veterinary Medicine, University of Buea, Buea, Cameroon
| | - Mercy Abwe Ngone
- Rhizobiology Group, Department of Agronomic and Applied Molecular Sciences, Faculty of Agriculture and Veterinary Medicine, University of Buea, Buea, Cameroon
| | - Denis Tange Achiri
- Rhizobiology Group, Department of Agronomic and Applied Molecular Sciences, Faculty of Agriculture and Veterinary Medicine, University of Buea, Buea, Cameroon
| | | | - Silke Ruppel
- Research Group on Beneficial Microorganisms and Plant Interactions, Leibniz Institute of Vegetable and Ornamental Crops, Großbeeren, Germany
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Enrichment of Burkholderia in the Rhizosphere by Autotoxic Ginsenosides to Alleviate Negative Plant-Soil Feedback. Microbiol Spectr 2021; 9:e0140021. [PMID: 34756064 PMCID: PMC8579924 DOI: 10.1128/spectrum.01400-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The accumulation of autotoxins and soilborne pathogens in soil was shown to be the primary driver of negative plant-soil feedback (NPSF). There is a concerted understanding that plants could enhance their adaptability to biotic or abiotic stress by modifying the rhizosphere microbiome. However, it is not clear whether autotoxins could enrich microbes to degrade themselves or antagonize soilborne pathogens. Here, we found that the microbiome degraded autotoxic ginsenosides, belonging to triterpenoid glycosides, and antagonized pathogens in the rhizosphere soil of Panax notoginseng (sanqi). Deep analysis by 16S rRNA sequencing showed that the bacterial community was obviously changed in the rhizosphere soil and identified the Burkholderia-Caballeronia-Paraburkholderia (BCP) group as the main ginsenoside-enriched bacteria in the rhizosphere soil. Eight strains belonging to the BCP group were isolated, and Burkholderia isolate B36 showed a high ability to simultaneously degrade autotoxic ginsenosides (Rb1, Rg1, and Rd) and antagonize the soilborne pathogen Ilyonectria destructans. Interestingly, ginsenosides could stimulate the growth and biofilm formation of B36, eventually enhancing the antagonistic ability of B36 to I. destructans and the colonization ability in the rhizosphere soil. In summary, autotoxic ginsenosides secreted by P. notoginseng could enrich beneficial microbes in the rhizosphere to simultaneously degrade autotoxins and antagonize pathogen, providing a novel ecological strategy to alleviate NPSF. IMPORTANCE Autotoxic ginsenosides, secreted by sanqi into soil, could enrich Burkholderia sp. to alleviate negative plant-soil feedback (NPSF) by degrading autotoxins and antagonizing the root rot pathogen. In detail, ginsenosides could stimulate the growth and biofilm formation of Burkholderia sp. B36, eventually enhancing the antagonistic ability of Burkholderia sp. B36 to a soilborne pathogen and the colonization of B36 in soil. This ecological strategy could alleviate NPSF by manipulating the rhizosphere microbiome to simultaneously degrade autotoxins and antagonize pathogen.
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Wang Q, Yang R, Peng W, Yang Y, Ma X, Zhang W, Ji A, Liu L, Liu P, Yan L, Hu X. Tea Plants With Gray Blight Have Altered Root Exudates That Recruit a Beneficial Rhizosphere Microbiome to Prime Immunity Against Aboveground Pathogen Infection. Front Microbiol 2021; 12:774438. [PMID: 34925281 PMCID: PMC8672095 DOI: 10.3389/fmicb.2021.774438] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/13/2021] [Indexed: 01/04/2023] Open
Abstract
Tea gray blight disease and its existing control measures have had a negative impact on the sustainable development of tea gardens. However, our knowledge of safe and effective biological control measures is limited. It is critical to explore beneficial microbial communities in the tea rhizosphere for the control of tea gray blight. In this study, we prepared conditioned soil by inoculating Pseudopestalotiopsis camelliae-sinensis on tea seedling leaves. Thereafter, we examined the growth performance and disease resistance of fresh tea seedlings grown in conditioned and control soils. Next, the rhizosphere microbial community and root exudates of tea seedlings infected by the pathogen were analyzed. In addition, we also evaluated the effects of the rhizosphere microbial community and root exudates induced by pathogens on the performance of tea seedlings. The results showed that tea seedlings grown in conditioned soil had lower disease index values and higher growth vigor. Soil microbiome analysis revealed that the fungal and bacterial communities of the rhizosphere were altered upon infection with Ps. camelliae-sinensis. Genus-level analysis showed that the abundance of the fungi Trichoderma, Penicillium, and Gliocladiopsis and the bacteria Pseudomonas, Streptomyces, Bacillus, and Burkholderia were significantly (p < 0.05) increased in the conditioned soil. Through isolation, culture, and inoculation tests, we found that most isolates from the induced microbial genera could inhibit the infection of tea gray blight pathogen and promote tea seedling growth. The results of root exudate analysis showed that infected tea seedlings exhibited significantly higher exudate levels of phenolic acids and flavonoids and lower exudate levels of amino acids and organic acids. Exogenously applied phenolic acids and flavonoids suppressed gray blight disease by regulating the rhizosphere microbial community. In summary, our findings suggest that tea plants with gray blight can recruit beneficial rhizosphere microorganisms by altering their root exudates, thereby improving the disease resistance of tea plants growing in the same soil.
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Affiliation(s)
- Qiaomei Wang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China.,Puer Institute of Pu-Erh Tea, Pu'er City, China.,College of Pu'er Tea, West Yunnan University of Applied Sciences, Pu'er City, China
| | - Ruijuan Yang
- Puer Institute of Pu-Erh Tea, Pu'er City, China.,College of Pu'er Tea, West Yunnan University of Applied Sciences, Pu'er City, China.,College of Food Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Wenshu Peng
- Puer Institute of Pu-Erh Tea, Pu'er City, China.,College of Pu'er Tea, West Yunnan University of Applied Sciences, Pu'er City, China
| | - Yanmei Yang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Xiaoling Ma
- School of Biological and Chemical Science, Pu'er University, Pu'er City, China
| | - Wenjie Zhang
- Puer Institute of Pu-Erh Tea, Pu'er City, China.,College of Pu'er Tea, West Yunnan University of Applied Sciences, Pu'er City, China
| | - Aibing Ji
- Puer Institute of Pu-Erh Tea, Pu'er City, China.,College of Pu'er Tea, West Yunnan University of Applied Sciences, Pu'er City, China
| | - Li Liu
- Puer Institute of Pu-Erh Tea, Pu'er City, China.,College of Pu'er Tea, West Yunnan University of Applied Sciences, Pu'er City, China
| | - Pei Liu
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Liang Yan
- Puer Institute of Pu-Erh Tea, Pu'er City, China.,College of Pu'er Tea, West Yunnan University of Applied Sciences, Pu'er City, China
| | - Xianqi Hu
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
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Cáceres PFF, Vélez LP, Junca H, Moreno-Herrera CX. Theobroma cacao L. agricultural soils with natural low and high cadmium (Cd) in Santander (Colombia), contain a persistent shared bacterial composition shaped by multiple soil variables and bacterial isolates highly resistant to Cd concentrations. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100086. [PMID: 34927107 PMCID: PMC8649583 DOI: 10.1016/j.crmicr.2021.100086] [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: 03/31/2021] [Revised: 11/22/2021] [Accepted: 11/26/2021] [Indexed: 12/21/2022] Open
Abstract
This study report statistically significant differences in beta-diversity correlated with soil properties, including Cd concentrations. Culture-dependent techniques allowed the isolation of bacterial strains tolerating high Cd concentrations up to 120 mgL−1 for potencial Cd biosorption or intracellular sequestration. The combination of different approaches provides a baseline about the bacterial composition and Cd tolerant strains found in these soils influence for lower Cd accumulation in cocoa crops.
Heavy metals can be found in soil as natural components or as product of contaminations events; plants growing in soils are prone to bioaccumulate heavy metals on their biomass. Theobroma cacao L. can bioaccumulate cadmium (Cd) in the seed and could be in derived food products, it considered a human health risk; therefore, removal of Cd is desirable but not vet technically and economically feasible; only to avoid Cd in cocoa is by selecting lands plots exhibiting lower Cd concentrations in soils, imposing a serious limitation to farmers and regulators. The study of bacterial communities and isolation bacteria with tolerance and mechanisms to counteract the translocation of Cd to the parts of cocoa plant exhibits high relevance in Colombia economy and especially to companies producing chocolate and derivatives. Here, we explore bacterial communities associated with soils having relatively high natural Cd concentrations in a large agricultural cocoa plot located in the Santander region. We characterized the bacterial communities’ compositions by amplicon 16S rRNA sequencing from metagenomics soil DNA and by culturing-based enumeration and isolation approaches. Culture-dependent techniques allowed the isolation of bacteria tolerant to Cd concentration, complement the information for Colombia, and expand the number of strains characterized with adaptive capacity against Cd with tolerance in a concentration of 120 mg/L, which represents the first capacity for Exiguobacterium sp., Ralstonia sp., Serratia sp., Dermacoccus sp., Klebsiella sp., Lactococcus sp. and Staphylococcus sp. In addition to confirming that there is a greater diversity of Cd-tolerant bacteria present in soils of farms cultivated with cocoa in Colombia. As for the results of new generation sequencing, they revealed that, the alpha-diversity in bacterial composition, according to the ANOVA, there are statistically significant differences of the bacterial communities present in the samples. Regarding Pearson correlation analysis, it was found the Shannon Simpson indices, have a positive correlation against OM, C, pH, Mn, C.E.C.I., Ca, P and negatively correlated with S; respect to bacterial community structure, a principal component analysis, which revealed that independent of the concentration of Cd present in soil samples, separates them according to pH value. Phyla to high abundance relative in all samples were Proteobacteria, Acidobacteriota, Actinobacteriota, Verrucomicrobiota, Myxococcota, Chloroflexi, Plactomycetota, Bacteroidota, Gemmatimonadota, Nitrospirota, Firmicutes and NB1_J; the bacteria genera with higher relative abundance (>0.5%) Nitrospira, candidatus Udaeobacter, Haliangium, Cupriavidus, MND1, Bacillus, Kitasatospora, Niveibacterium, Acidothermus, Burkholderia, Acidibacter, Terrimonas, Gaiella, candidatus Solibacter, Kitasatospora, Sphingomonas, Streptomyces, this genus with a relationship with the Cd tolerance process. After it, redundancy analysis was performed between the variation of the bacterial communities identified by dependent and independent techniques and edaphic soil variables, where their positive correlation was found against K, OM, C, Ca, pH (p<0.01) and P, C.E.C.I (p<0.05). For soil samples, the bacterial genera that make up the core community were identified, which are present in all samples as Nitrospira sp., Cupriavidus sp., Burkholderia sp., Haliangium sp., candidatus Udaeobacter, MND1, Kitasatospora, Acidothermus, Acidibacter, Streptomyces, Gaiella, candidatus Solibacter and Terramonas; the genera identified has a different and fundamental role in ecosystem functioning. The combination of different approaches offers new clues regarding the assessment of bacterial communities in soils cultivated with cocoa in soils with elevated Cd content in Colombia, and the ecological role and interplay of soil components and bacterial communities that contribute to modulate the effect of bioaccumulation in products.
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Affiliation(s)
- Pedro Felipe Feria Cáceres
- Universidad Nacional de Colombia, Faculty of Science, Microbiodiversity and bioprospecting research group, Cra. 65 #59a-110, Cellular and Molecular Biology laboratory 19-A 310, Medellin, Colombia
- Center for Research, Development and Quality – CIDCA (Spanish acronym), Compañía Nacional de Chocolates, Km.2 Vía Belén-Rionegro-Colombia
- Corresponding authors at: Universidad Nacional de Colombia, Faculty of Science, Microbiodiversity and bioprospecting research group, Cra. 65 # 59a-110, Cellular and Molecular Biology laboratory 19-A 310, Medellin, Colombia.
| | - Lucas Penagos Vélez
- Center for Research, Development and Quality – CIDCA (Spanish acronym), Compañía Nacional de Chocolates, Km.2 Vía Belén-Rionegro-Colombia
| | - Howard Junca
- RG Microbial Ecology: Metabolism, Genomics & Evolution, Div. Ecogenomics and Holobionts, Microbiomas Foundation, LT11A, 250008 Chía, Colombia
| | - Claudia Ximena Moreno-Herrera
- Universidad Nacional de Colombia, Faculty of Science, Microbiodiversity and bioprospecting research group, Cra. 65 #59a-110, Cellular and Molecular Biology laboratory 19-A 310, Medellin, Colombia
- Corresponding authors at: Universidad Nacional de Colombia, Faculty of Science, Microbiodiversity and bioprospecting research group, Cra. 65 # 59a-110, Cellular and Molecular Biology laboratory 19-A 310, Medellin, Colombia.
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Selected Rhizosphere Bacteria Help Tomato Plants Cope with Combined Phosphorus and Salt Stresses. Microorganisms 2020; 8:microorganisms8111844. [PMID: 33238592 PMCID: PMC7700537 DOI: 10.3390/microorganisms8111844] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/16/2020] [Accepted: 11/20/2020] [Indexed: 12/17/2022] Open
Abstract
Plants are often challenged by multiple abiotic stresses simultaneously. The inoculation of beneficial bacteria is known to enhance plant growth under these stresses, such as phosphorus starvation or salt stress. Here, for the first time, we assessed the efficiency of selected beneficial bacterial strains in improving tomato plant growth to better cope with double stresses in salty and P-deficient soil conditions. Six strains of Arthrobacter and Bacillus with different reservoirs of plant growth-promoting traits were tested in vitro for their abilities to tolerate 2-16% (w/v) NaCl concentrations, and shown to retain their motility and phosphate-solubilizing capacity under salt stress conditions. Whether these selected bacteria promote tomato plant growth under combined P and salt stresses was investigated in greenhouse experiments. Bacterial isolates from Cameroonian soils mobilized P from different phosphate sources in shaking culture under both non-saline and saline conditions. They also enhanced plant growth in P-deficient and salt-affected soils by 47-115%, and their PGP effect was even increased in higher salt stress conditions. The results provide valuable information for prospective production of effective bio-fertilizers based on the combined application of local rock phosphate and halotolerant phosphate-solubilizing bacteria. This constitutes a promising strategy to improve plant growth in P-deficient and salt-affected soils.
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20
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Pang Z, Zhao Y, Xu P, Yu D. Microbial Diversity of Upland Rice Roots and Their Influence on Rice Growth and Drought Tolerance. Microorganisms 2020; 8:microorganisms8091329. [PMID: 32878310 PMCID: PMC7564600 DOI: 10.3390/microorganisms8091329] [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: 08/11/2020] [Revised: 08/27/2020] [Accepted: 08/30/2020] [Indexed: 01/25/2023] Open
Abstract
Among abiotic stresses, drought is one of the most important factors limiting plant growth. To increase their drought tolerance and survival, most plants interact directly with a variety of microbes. Upland rice (Oryza sativa L.) is a rice ecotype that differs from irrigated ecotype rice; it is adapted to both drought-stress and aerobic conditions. However, its root microbial resources have not been explored. We isolated bacteria and fungi from roots of upland rice in Xishuangbanna, China. Four hundred sixty-two endophytic and rhizospheric isolates (337 bacteria and 125 fungi) were distributed. They were distributed among 43 genera on the basis of 16S rRNA and internal transcribed spacer (ITS) gene sequence analysis. Notably, these root microbes differed from irrigated rice root microbes in irrigated environments; for example, members of the Firmicutes phylum were enriched (by 28.54%) in the roots of the upland plants. The plant growth-promoting (PGP) potential of 217 isolates was investigated in vitro. The PGP ability of 17 endophytic and 10 rhizospheric isolates from upland rice roots was evaluated under well-irrigated and drought-stress conditions, and 9 fungal strains increased rice seedling shoot length, shoot and root fresh weight (FW), antioxidant capability, and proline (Pro) and soluble sugar contents. Our work suggests that fungi from upland rice roots can increase plant growth under irrigated and drought-stress conditions and can serve as effective microbial resources for sustainable agricultural production in arid regions.
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Affiliation(s)
- Zhiqiang Pang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (Z.P.); (Y.Z.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Zhao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (Z.P.); (Y.Z.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
| | - Peng Xu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (Z.P.); (Y.Z.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
- Correspondence: (P.X.); (D.Y.)
| | - Diqiu Yu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (Z.P.); (Y.Z.)
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
- Correspondence: (P.X.); (D.Y.)
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The Response of Maize to Inoculation with Arthrobacter sp. and Bacillus sp. in Phosphorus-Deficient, Salinity-Affected Soil. Microorganisms 2020; 8:microorganisms8071005. [PMID: 32635586 PMCID: PMC7409341 DOI: 10.3390/microorganisms8071005] [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: 06/09/2020] [Revised: 07/01/2020] [Accepted: 07/03/2020] [Indexed: 01/06/2023] Open
Abstract
Salinity and phosphorus (P) deficiency are among the most serious soil factors constraining crop productivity. A proposed strategy for alleviating these stresses is supporting plants by inoculation with growth-promoting rhizobacteria (PGPR). Here, a comparison of the ability of two maize composite and two F1 hybrid varieties to tolerate a P deficiency in either a saline or a non-saline environment showed that the uptake of nutrients by all four entries was significantly reduced by the imposition of both soil salinity and P deficiency, and that their growth was compromised to a similar extent. Subsequently, the ameliorative effect of inoculation with three strains of either Arthrobacter sp. or Bacillus sp. in an environment, which suffered simultaneously from salinity and P deficiency, was investigated. Inoculation with each of the strains was found to limit the plants’ uptake of sodium cations, to increase their uptake of potassium cations, and to enhance their growth. The extent of the growth stimulation was more pronounced for the composite varieties than for the F1 hybrid ones, although the amount of biomass accumulated by the latter, whether the plants had been inoculated or not, was greater than that of the former varieties. When the bacterial strains were cultured in vitro, each of them was shown as able to produce the phytohormones auxin, abscisic acid, gibberellins, and cytokinins. The implication is that since the presence in the rhizospere of both Arthrobacter sp. and Bacillus sp. strains can support the growth of maize in salinity-affected and P deficient soils in a genotype-dependent fashion, it is important to not only optimize the PGPR strain used for inoculation, but also to select maize varieties which can benefit most strongly from an association with these bacteria.
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Cueva-Yesquén LG, Goulart MC, Attili de Angelis D, Nopper Alves M, Fantinatti-Garboggini F. Multiple Plant Growth-Promotion Traits in Endophytic Bacteria Retrieved in the Vegetative Stage From Passionflower. FRONTIERS IN PLANT SCIENCE 2020; 11:621740. [PMID: 33537051 PMCID: PMC7847900 DOI: 10.3389/fpls.2020.621740] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/23/2020] [Indexed: 05/17/2023]
Abstract
Bacteria exhibiting beneficial traits like increasing the bioavailability of essential nutrients and modulating hormone levels in plants are known as plant growth promoting (PGP) bacteria. The occurrence of this specific group of bacteria in the endophytic environment may reflect the decisive role they play in a particular condition. This study aimed to determine the taxonomical diversity of the culturable bacterial endophytes, isolated in the vegetative stage of passionflower (Passiflora incarnata), and assess its potential to promote plant growth by phenotypic and genotypic approaches. The sequencing and phylogenetic analysis of the 16S rRNA gene allowed us to classify 58 bacterial endophytes into nine genera. Bacillus (70.7%) was the most dominant genus, followed by Pseudomonas (8.6%) and Pantoea (6.9%). A few isolates belonged to Rhodococcus and Paenibacillus, whereas the genera Lysinibacillus, Microvirga, Xanthomonas, and Leclercia were represented by only one isolate. The strains were tested for nitrogen fixation, phosphate solubilization, indole-acetic-acid synthesis, and siderophore production. Moreover, PGP related genes (nifH, ipdC, asb, and AcPho) were detected by PCR-based screening. Most of the isolates (94.8%) displayed a potential for at least one of the PGP traits tested by biochemical assays or PCR-based screening. Nine strains were selected based on results from both approaches and were evaluated for boosting the Cape gooseberry (Physalis peruviana) germination and growth. All tested isolates improved germination in vitro, and the majority (78%) increased growth parameters in vivo. The results suggested that most of culturable bacteria inhabiting P. incarnata in the vegetative stage could be used as probiotics for agricultural systems. Besides, their occurrence may be associated with specific physiological needs typical of this development stage.
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Affiliation(s)
- Luis Gabriel Cueva-Yesquén
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Campinas, Brazil
- Division of Microbial Resources, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas, Paulínia, Brazil
- *Correspondence: Luis Gabriel Cueva-Yesquén,
| | - Marcela Cristina Goulart
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Campinas, Brazil
- Division of Microbial Resources, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas, Paulínia, Brazil
| | - Derlene Attili de Angelis
- Division of Microbial Resources, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas, Paulínia, Brazil
| | - Marcos Nopper Alves
- Division of Agrotechnology, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas, Paulínia, Brazil
| | - Fabiana Fantinatti-Garboggini
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Campinas, Brazil
- Division of Microbial Resources, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas, Paulínia, Brazil
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Rodríguez-Andrade O, Corral-Lugo A, Morales-García YE, Quintero-Hernández V, Rivera-Urbalejo AP, Molina-Romero D, Martínez-Contreras RD, Bernal P, Muñoz-Rojas J. Identification of Klebsiella Variicola T29A Genes Involved In Tolerance To Desiccation. Open Microbiol J 2019. [DOI: 10.2174/1874285801913010256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Introduction:Several plant-beneficial bacteria have the capability to promote the growth of plants through different mechanisms. The survival of such bacteria could be affected by environmental abiotic factors compromising their capabilities of phytostimulation. One of the limiting abiotic factors is low water availability.Materials and Methods:In extreme cases, bacterial cells can suffer desiccation, which triggers harmful effects on cells. Bacteria tolerant to desiccation have developed different strategies to cope with these conditions; however, the genes involved in these processes have not been sufficiently explored.Klebsiella variicolaT29A is a beneficial bacterial strain that promotes the growth of corn plants and is highly tolerant to desiccation. In the present work, we investigated genes involved in desiccation tolerance.Results & Discussion:As a result, a library of 8974 mutants of this bacterial strain was generated by random mutagenesis with mini-Tn5 transposon, and mutants that lost the capability to tolerate desiccation were selected. We found 14 sensitive mutants; those with the lowest bacterial survival rate contained mini-Tn5 transposon inserted into genes encoding a protein domain related to BetR, putative secretion ATPase and dihydroorotase. The mutant in the betR gene had the lowest survival; therefore, the mutagenized gene was validated using specific amplification and sequencing.Conclusion:Trans complementation with the wild-type gene improved the survival of the mutant under desiccation conditions, showing that this gene is a determinant for the survival ofK. variicolaT29A under desiccation conditions.
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Luo L, Guo C, Wang L, Zhang J, Deng L, Luo K, Huang H, Liu Y, Mei X, Zhu S, Yang M. Negative Plant-Soil Feedback Driven by Re-assemblage of the Rhizosphere Microbiome With the Growth of Panax notoginseng. Front Microbiol 2019; 10:1597. [PMID: 31404300 PMCID: PMC6676394 DOI: 10.3389/fmicb.2019.01597] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 06/26/2019] [Indexed: 01/22/2023] Open
Abstract
There is a concerted understanding of the accumulation of soil pathogens as the major driving factor of negative plant-soil feedback (NPSF). However, our knowledge of the connection between plant growth, pathogen build-up and soil microbiome assemblage is limited. In this study, significant negative feedback between the soil and sanqi (Panax notoginseng) was found, which were caused by the build-up of the soil-borne pathogens Fusarium oxysporum, F. solani, and Monographella cucumerina. Soil microbiome analysis revealed that the rhizospheric fungal and bacterial communities were changed with the growth of sanqi. Deep analysis of the phylum and genus levels corroborated that rhizospheric fungal Ascomycota, including the soil-borne pathogens F. oxysporum, F. solani, and especially M. cucumerina, were significantly enriched with the growth of sanqi. However, the bacteria Firmicutes and Acidobacteria, including the genera Pseudomonas, Bacillus, Acinetobacter and Burkholderia, were significantly suppressed with the growth of sanqi. Using microbial isolation and in vitro dual culture tests, we found that most isolates derived from the suppressed bacterial genera showed strong antagonistic ability against the growth of sanqi soil-borne pathogens. Interestingly, inoculation of these suppressed isolates in consecutively cultivated soil could significantly alleviate NPSF. In summary, sanqi growth can suppress antagonistic bacteria through re-assemblage of the rhizosphere microbiome and cause the accumulation of soil-borne pathogens, eventually building negative feedback loops between the soil and plants.
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Affiliation(s)
- Lifen Luo
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Cunwu Guo
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Luotao Wang
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Junxing Zhang
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Linmei Deng
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Kaifeng Luo
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Huichuan Huang
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Yixiang Liu
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Xinyue Mei
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Shusheng Zhu
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Min Yang
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
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Huschek D, Witzel K. Rapid dereplication of microbial isolates using matrix-assisted laser desorption ionization time-of-flight mass spectrometry: A mini-review. J Adv Res 2019; 19:99-104. [PMID: 31341675 PMCID: PMC6629721 DOI: 10.1016/j.jare.2019.03.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 03/20/2019] [Accepted: 03/21/2019] [Indexed: 02/06/2023] Open
Abstract
MALDI-TOF MS is applicable as high-resolution and high-throughput tool. The classification and characterization of cultivable microorganisms is targeted. Advantageous are its simple sample preparation and short measurement time. It accelerates the dereplication of isolates from large-scale screening campaigns. Applications for studying microbial diversity and future trends are discussed.
Matrix-Assisted Laser Desorption Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) has become one of the most popular methods for the rapid, cost-effective and accurate classification and characterization of cultivable microorganisms. Due to its simple sample preparation and short measurement time, MALDI-TOF MS is an excellent choice for the high-throughput study of microbial isolates from rhizospheres or plants grown under diverse environmental conditions. While clinical isolates have a higher identification rate than environmental isolates due to the focus of commercial mass spectral libraries on the former, no identification is necessary in the dereplication step of large environmental studies. The grouping of large sets of isolates according to their intact protein profiles can be performed without knowledge of their taxonomy. Thus, this method is easily applicable to environmental samples containing microorganisms from yet undescribed phylogenetic origins. The main strategies applied to achieve effective dereplication are, first, expanding existing mass spectral libraries and, second, using an additional statistical analysis step to group measured mass spectra and identify unique isolates. In this review, these aspects are addressed. It closes with a prospective view on how MALDI-TOF MS-based microbial characterisation can accelerate the exploitation of plant-associated microbiota.
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Affiliation(s)
- Doreen Huschek
- German Rheumatism Research Centre - A Leibniz Institute, Charitéplatz 1, 10117 Berlin, Germany
| | - Katja Witzel
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
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Tchuisseu Tchakounté GV, Berger B, Patz S, Fankem H, Ruppel S. Data on molecular identification, phylogeny and in vitro characterization of bacteria isolated from maize rhizosphere in Cameroon. Data Brief 2018; 19:1410-1417. [PMID: 30229012 PMCID: PMC6141133 DOI: 10.1016/j.dib.2018.06.003] [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: 05/10/2018] [Revised: 05/16/2018] [Accepted: 06/05/2018] [Indexed: 10/29/2022] Open
Abstract
Bacteria, which establish positive interactions with plant roots, play a key role in agricultural environments and are promising for their potential use in sustainable agriculture. Many of these mutualistic bacteria provide benefits to plant hosts by facilitating soil mineral nutrient uptake, protecting plants from biotic and abiotic stresses and producing substances that promote growth. The dataset presented here, is related to the publication entitled "Community structure and plant growth-promoting potential of cultivable bacteria isolated from Cameroon soil" (Tchuisseu et al., 2018) [1]. The data provide an extended analysis of the occurrence, taxonomical affiliation and functional traits of bacterial groups isolated from the rhizosphere of maize in Cameroon at different taxonomical levels, using a combination of molecular/bioinformatics tools and in vitro studies. Bacteria were isolated from maize rhizosphere soil. Isolated bacteria were identified using the 16s rRNA gene sequencing and phylogenetic analyses. All strains were characterized for their potential of salinity tolerance and growth promotion (phosphate solubilization, nifH gene presence and siderophore production) in order to select efficient bacterial strains for designing biological fertilizer exploitable for agriculture under specific stress conditions of the country. The data will be valuable for further studies on plant associated bacteria in Cameroon, which are still largely unexplored.
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Affiliation(s)
- Gylaine Vanissa Tchuisseu Tchakounté
- Leibniz Institute of Vegetable and Ornamental Crops Grossbeeren/ Erfurt e.V., Theodor- Echtermeyer-Weg 1, 14979 Grossbeeren, Germany.,Faculty of Life sciences Humboldt-University of Berlin, Invalidenstraße 42, 10115 Berlin, Germany
| | - Beatrice Berger
- Leibniz Institute of Vegetable and Ornamental Crops Grossbeeren/ Erfurt e.V., Theodor- Echtermeyer-Weg 1, 14979 Grossbeeren, Germany.,Institute for National and International Plant Health, Julius Kuehn-Institute - Federal Research Centre for Cultivated Plants, Messeweg 11/12, 38104 Braunschweig, Germany
| | - Sascha Patz
- Leibniz Institute of Vegetable and Ornamental Crops Grossbeeren/ Erfurt e.V., Theodor- Echtermeyer-Weg 1, 14979 Grossbeeren, Germany.,Algorithms in Bioinformatics, Center for Bioinformatics, University of Tuebingen, Sand 14, 72076 Tuebingen, Germany
| | - Henri Fankem
- Department of Plant Biology, Faculty of Sciences, University of Douala, P.O.Box: 24157, Douala, Cameroon
| | - Silke Ruppel
- Leibniz Institute of Vegetable and Ornamental Crops Grossbeeren/ Erfurt e.V., Theodor- Echtermeyer-Weg 1, 14979 Grossbeeren, Germany
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