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Zhao H, Li Q, Jin X, Li D, Zhu Z, Li QX. Chiral enantiomers of the plant growth regulator paclobutrazol selectively affect community structure and diversity of soil microorganisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 797:148942. [PMID: 34311352 DOI: 10.1016/j.scitotenv.2021.148942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/29/2021] [Accepted: 07/05/2021] [Indexed: 06/13/2023]
Abstract
Paclobutrazol is a triazole plant growth regulator with a wide range of applications in crop and fruit tree production. Paclobutrazol is used as a racemic mixture in agriculture. However, the effects of paclobutrazol enantiomers on soil microbial community structure and diversity are unclear. In the present study, Illumina high-throughput sequencing was used to study the enantioselective effects of two paclobutrazol enantiomers on soil microbial community. S-paclobutrazol was more persistent than R-paclobutrazol. The half-lives of the S- and R-isomers were 80 d and 50 d, respectively. No interconversion between the two isomers occurred in soils. In addition, the enantiomers had significant enantiomeric effects on soil microbial community and the paclobutrazol degradation was probably attributed to the presence of Pseudomonas and Mycobacterium. Notably, the relative abundance of Fusarium, a genus of filamentous fungi producing gibberellins, could be enantioselectively affected by the chiral enantiomers. Paclobutrazol enantiomers exhibited greater effects on the fungal community structure than bacterial community structure due to the fungicidal activity of paclobutrazol. Finally, R-paclobutrazol had a significant effect on the microbial networks. The findings of the present study suggest that the use of S-paclobutrazol may accomplish both plant growth regulation and the minimization of effects of paclobutrazol on soil microbial communities.
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Affiliation(s)
- Hongwei Zhao
- Center for Eco-Environment Restoration of Hainan Province & Key Laboratory of A&F Environmental Processes and Ecological Regulation of Hainan Province, College of Environment and Ecology, Hainan University, Renmin Ave. 58, Haikou 570228, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
| | - Qiuli Li
- Center for Eco-Environment Restoration of Hainan Province & Key Laboratory of A&F Environmental Processes and Ecological Regulation of Hainan Province, College of Environment and Ecology, Hainan University, Renmin Ave. 58, Haikou 570228, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Xiaotuo Jin
- Center for Eco-Environment Restoration of Hainan Province & Key Laboratory of A&F Environmental Processes and Ecological Regulation of Hainan Province, College of Environment and Ecology, Hainan University, Renmin Ave. 58, Haikou 570228, China
| | - Dong Li
- College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Zhiqiang Zhu
- College of Tropical Crops, Hainan University, Haikou 570228, China.
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
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Hu XL, Lu H, Hassan MM, Zhang J, Yuan G, Abraham PE, Shrestha HK, Villalobos Solis MI, Chen JG, Tschaplinski TJ, Doktycz MJ, Tuskan GA, Cheng ZMM, Yang X. Advances and perspectives in discovery and functional analysis of small secreted proteins in plants. HORTICULTURE RESEARCH 2021; 8:130. [PMID: 34059650 PMCID: PMC8167165 DOI: 10.1038/s41438-021-00570-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 04/26/2021] [Indexed: 05/02/2023]
Abstract
Small secreted proteins (SSPs) are less than 250 amino acids in length and are actively transported out of cells through conventional protein secretion pathways or unconventional protein secretion pathways. In plants, SSPs have been found to play important roles in various processes, including plant growth and development, plant response to abiotic and biotic stresses, and beneficial plant-microbe interactions. Over the past 10 years, substantial progress has been made in the identification and functional characterization of SSPs in several plant species relevant to agriculture, bioenergy, and horticulture. Yet, there are potentially a lot of SSPs that have not been discovered in plant genomes, which is largely due to limitations of existing computational algorithms. Recent advances in genomics, transcriptomics, and proteomics research, as well as the development of new computational algorithms based on machine learning, provide unprecedented capabilities for genome-wide discovery of novel SSPs in plants. In this review, we summarize known SSPs and their functions in various plant species. Then we provide an update on the computational and experimental approaches that can be used to discover new SSPs. Finally, we discuss strategies for elucidating the biological functions of SSPs in plants.
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Affiliation(s)
- Xiao-Li Hu
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Haiwei Lu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Jin Zhang
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Paul E Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Him K Shrestha
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
| | | | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Gerald A Tuskan
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Zong-Ming Max Cheng
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA.
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China.
| | - Xiaohan Yang
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA.
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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Discovery of a Novel Lineage Burkholderia cepacia ST 1870 Endophytically Isolated from Medicinal Polygala paniculata Which Shows Potent In Vitro Antileishmanial and Antimicrobial Effects. Int J Microbiol 2021; 2021:6618559. [PMID: 33679984 PMCID: PMC7904367 DOI: 10.1155/2021/6618559] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 01/29/2021] [Indexed: 02/02/2023] Open
Abstract
In this study, we report the isolation and identification of an endophytic strain of Burkholderia cepacia (COPS strain) associated with Polygala paniculata roots. Polygala plants are rich sources of promising microbiomes, of which the literature reports several pharmacological effects, such as trypanocidal, antinociceptive, anesthetic, anxiolytics, and anticonvulsant activities. B. cepacia COPS belongs to a new sequence type (ST 1870) and harbors a genome estimated in 8.3 Mbp which exhibits the aminoglycosides and beta-lactams resistance genes aph(3′)-IIa and blaTEM-116, respectively. Analysis performed using MLST, average nucleotide identity, and digital DNA-DNA hybridization support its species-level identification and reveals its novel housekeeping genes alleles gyrB, lepA, and phaC. The root endophyte B. cepacia COPS drew our attention from a group of 14 bacterial isolates during the primary screening for being potentially active against Staphylococcus aureus ATCC 29213, Enterococcus faecalis ATCC 29212, Micrococcus luteus ATCC 9341, Escherichia coli ATCC 25922, and Candida albicans ATCC 10231 and exhibited the broad-spectrum activity against phytopathogenic fungi. In addition, COPS strain showed production of protease, lipase, and esterase in solid media, and its natural product extract showed potent inhibition against fungal plant pathogens, such as Moniliophthora perniciosa, whose antagonism index (89.32%) exceeded the positive control (74.17%), whereas Sclerotinia sclerotiorum and Ceratocystis paradoxa showed high percentages of inhibition (85.53% and 82.69%, respectively). COPS crude extract also significantly inhibited S. epidermidis ATCC 35984, E. faecium ATCC 700221 (MIC values of 32 μg/mL for both), E. faecalis ATCC 29212 (64 μg/mL), and S. aureus ATCC 25923 (128 μg/mL). We observed moderate antagonistic activity against A. baumannii ATCC 19606 and E. coli ATCC 25922 (both at 512 μg/mL), as well as potent cytotoxic effects on Leishmania infantum and Leishmania major promastigote forms with 78.25% and 57.30% inhibition. In conclusion, this study presents for the first time the isolation of an endophytic B. cepacia strain associated with P. paniculata and enough evidence that these plants may be considered a rich source of microbes for the fight against neglected diseases.
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Yadav SK, Das J, Kumar R, Jha G. Calcium regulates the mycophagous ability of Burkholderia gladioli strain NGJ1 in a type III secretion system-dependent manner. BMC Microbiol 2020; 20:216. [PMID: 32689944 PMCID: PMC7372643 DOI: 10.1186/s12866-020-01897-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 07/12/2020] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND A rice associated bacterium Burkholderia gladioli strain NGJ1 demonstrates mycophagy, a phenomenon wherein bacteria feed on fungi. Previously, we have reported that NGJ1 utilizes type III secretion system (T3SS) to deliver a prophage tail-like protein (Bg_9562) into fungal cells to establish mycophagy. RESULTS In this study, we report that calcium ion concentration influences the mycophagous ability of NGJ1 on Rhizoctonia solani, an important fungal pathogen. The calcium limiting condition promotes mycophagy while high calcium environment prevents it. The expression of various T3SS apparatus encoding genes of NGJ1 was induced and secretion of several potential T3SS effector proteins (including Bg_9562) into extracellular milieu was triggered under calcium limiting condition. Using LC-MS/MS proteome analysis, we identified several calcium regulated T3SS effector proteins of NGJ1. The expression of genes encoding some of these effector proteins was upregulated during mycophagous interaction of NGJ1 with R. solani. Further, mutation of one of these genes (endo-β-1, 3- glucanase) rendered the mutant NGJ1 bacterium defective in mycophagy while complementation with full length copy of the gene restored its mycophagous activity. CONCLUSION Our study provides evidence that low calcium environment triggers secretion of various T3SS effectors proteins into the extracellular milieu and suggests the importance of cocktail of these proteins in promoting mycophagy.
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Affiliation(s)
- Sunil Kumar Yadav
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Joyati Das
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Rahul Kumar
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Gopaljee Jha
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Bulgari D, Montagna M, Gobbi E, Faoro F. Green Technology: Bacteria-Based Approach Could Lead to Unsuspected Microbe⁻Plant⁻Animal Interactions. Microorganisms 2019; 7:microorganisms7020044. [PMID: 30736387 PMCID: PMC6406919 DOI: 10.3390/microorganisms7020044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/23/2019] [Accepted: 02/02/2019] [Indexed: 12/16/2022] Open
Abstract
The recent and massive revival of green strategies to control plant diseases, mainly as a consequence of the Integrated Pest Management (IPM) rules issued in 2009 by the European Community and the increased consumer awareness of organic products, poses new challenges for human health and food security that need to be addressed in the near future. One of the most important green technologies is biocontrol. This approach is based on living organisms and how these biocontrol agents (BCAs) directly or indirectly interact as a community to control plant pathogens and pest. Although most BCAs have been isolated from plant microbiomes, they share some genomic features, virulence factors, and trans-kingdom infection abilities with human pathogenic microorganisms, thus, their potential impact on human health should be addressed. This evidence, in combination with the outbreaks of human infections associated with consumption of raw fruits and vegetables, opens new questions regarding the role of plants in the human pathogen infection cycle. Moreover, whether BCAs could alter the endophytic bacterial community, thereby leading to the development of new potential human pathogens, is still unclear. In this review, all these issues are debated, highlighting that the research on BCAs and their formulation should include these possible long-lasting consequences of their massive spread in the environment.
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Affiliation(s)
- Daniela Bulgari
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy, University of Milan, Italy, via Celoria 2, 20133 Milan, Italy.
- Piattaforma di Microbiologia Agroalimentare ed Ambientale (Pi.Mi.A.A.), AgroFood Lab, Department ofMolecular and Translational Medicine, University of Brescia; 25121 Brescia, Italy.
| | - Matteo Montagna
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy, University of Milan, Italy, via Celoria 2, 20133 Milan, Italy.
| | - Emanuela Gobbi
- Piattaforma di Microbiologia Agroalimentare ed Ambientale (Pi.Mi.A.A.), AgroFood Lab, Department ofMolecular and Translational Medicine, University of Brescia; 25121 Brescia, Italy.
| | - Franco Faoro
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy, University of Milan, Italy, via Celoria 2, 20133 Milan, Italy.
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Wu H, Chen H, Jin C, Tang C, Zhang Y. The chirality of imazethapyr herbicide selectively affects the bacterial community in soybean field soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:2531-2546. [PMID: 30474807 DOI: 10.1007/s11356-018-3736-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 11/12/2018] [Indexed: 06/09/2023]
Abstract
The chiral herbicide imazethapyr (IM) is frequently used to control weeds in soybean fields in northeast China. However, the impact of IM enantiomers on microbial communities in soil is still unknown. Genetic markers (16S rRNA V3-V4 regions) were used to characterize and evaluate the variation of the bacterial communities potentially effected by IM enantiomers. Globally, the bacterial community structure based on the OTU profiles in (-)-R-IM-treated soils was significantly different from those in (+)-S-IM-treated soils, and the differences were enlarged with the treatment dose increasing. Interestingly, the Rhizobiaceae family and several other beneficial bacteria, including Bradyrhizobium, Methylobacterium, and Paenibacillus, were strongly enriched in (-)-R-IM treatment compared to (+)-S-IM treatment. In contrast, the pathogenic bacteria, including Erwinia, Pseudomonas, Burkholderia, Streptomyces, and Agrobacterium, were suppressed in the presence of (-)-R-IM compared to (+)-S-IM. Furthermore, we also observed that the bacterial community structure in (-)-R-IM-treated soils was more quickly restored to its original state compared with those in (+)-S-IM-treated soils. These findings unveil a new role of chiral herbicide in the development of soil microbial ecology and provide theoretical support for the application of low-persistence, high-efficiency, and eco-friendly optical rotatory (-)-R-IM.
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Affiliation(s)
- Hao Wu
- Ministry of Education Key Laboratory of Environmental Remediation and Ecosystem Health, College of Natural Resources and Environmental Science, Zhejiang University, Hangzhou, 310058, China
| | - Hongshan Chen
- Ministry of Education Key Laboratory of Environmental Remediation and Ecosystem Health, College of Natural Resources and Environmental Science, Zhejiang University, Hangzhou, 310058, China
| | - Chongwei Jin
- Ministry of Education Key Laboratory of Environmental Remediation and Ecosystem Health, College of Natural Resources and Environmental Science, Zhejiang University, Hangzhou, 310058, China
| | - Caixian Tang
- Department of Agricultural Sciences, La Trobe University, Bundoora, Melbourne, VIC, 3086, Australia
| | - Yongsong Zhang
- Ministry of Education Key Laboratory of Environmental Remediation and Ecosystem Health, College of Natural Resources and Environmental Science, Zhejiang University, Hangzhou, 310058, China.
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