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Shchyogolev SY, Burygin GL, Dykman LA, Matora LY. Phylogenetic and pangenomic analyses of members of the family Micrococcaceae related to a plant-growth-promoting rhizobacterium isolated from the rhizosphere of potato (Solanum tuberosum L.). Vavilovskii Zhurnal Genet Selektsii 2024; 28:308-316. [PMID: 38952705 PMCID: PMC11214901 DOI: 10.18699/vjgb-24-35] [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: 09/15/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 07/03/2024] Open
Abstract
We report the results of taxonomic studies on members of the family Micrococcaceae that, according to the 16S rRNA, internal transcribed spacer 1 (ITS1), average nucleotide identity (ANI), and average amino acid identity (AAI) tests, are related to Kocuria rosea strain RCAM04488, a plant-growth-promoting rhizobacterium (PGPR) isolated from the rhizosphere of potato (Solanum tuberosum L.). In these studies, we used whole-genome phylogenetic tests and pangenomic analysis. According to the ANI > 95 % criterion, several known members of K. salina, K. polaris, and K. rosea (including K. rosea type strain ATCC 186T) that are related most closely to isolate RCAM04488 in the ITS1 test should be assigned to the same species with appropriate strain verification. However, these strains were isolated from strongly contrasting ecological and geographical habitats, which could not but affect their genotypes and phenotypes and which should be taken into account in evaluation of their systematic position. This contradiction was resolved by a pangenomic analysis, which showed that the strains differed strongly in the number of accessory and strain-specific genes determining their individuality and possibly their potential for adaptation to different ecological niches. Similar results were obtained in a full-scale AAI test against the UniProt database (about 250 million records), by using the AAI-profiler program and the proteome of K. rosea strain ATCC 186T as a query. According to the AAI > 65 % criterion, members of the genus Arthrobacter and several other genera belonging to the class Actinomycetes, with a very wide geographical and ecological range of sources of isolation, should be placed into the same genus as Kocuria. Within the paradigm with vertically inherited phylogenetic markers, this could be regarded as a signal for their following taxonomic reclassification. An important factor in this case may be the detailing of the gene composition of the strains and the taxonomic ratios resulting from analysis of the pangenomes of the corresponding clades.
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Affiliation(s)
- S Yu Shchyogolev
- Institute of Biochemistry and Physiology of Plants and Microorganisms - Subdivision of the Saratov Federal Scientific Centre of the Russian Academy of Sciences, Saratov, Russia
| | - G L Burygin
- Institute of Biochemistry and Physiology of Plants and Microorganisms - Subdivision of the Saratov Federal Scientific Centre of the Russian Academy of Sciences, Saratov, Russia Saratov State Vavilov Agrarian University, Saratov, Russia
| | - L A Dykman
- Institute of Biochemistry and Physiology of Plants and Microorganisms - Subdivision of the Saratov Federal Scientific Centre of the Russian Academy of Sciences, Saratov, Russia
| | - L Yu Matora
- Institute of Biochemistry and Physiology of Plants and Microorganisms - Subdivision of the Saratov Federal Scientific Centre of the Russian Academy of Sciences, Saratov, Russia
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Ngema SS, Khumalo SH, Ojo MC, Pooe OJ, Malilehe TS, Basson AK, Madoroba E. Evaluation of Antimicrobial Activity by Marine Nocardiopsis dassonvillei against Foodborne Listeria monocytogenes and Shiga Toxin-Producing Escherichia coli. Microorganisms 2023; 11:2539. [PMID: 37894198 PMCID: PMC10609338 DOI: 10.3390/microorganisms11102539] [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: 08/09/2023] [Revised: 09/12/2023] [Accepted: 09/30/2023] [Indexed: 10/29/2023] Open
Abstract
The emergence of multidrug-resistant pathogens creates public health challenges, prompting a continuous search for effective novel antimicrobials. This study aimed to isolate marine actinomycetes from South Africa, evaluate their in vitro antimicrobial activity against Listeria monocytogenes and Shiga toxin-producing Escherichia coli, and characterize their mechanisms of action. Marine actinomycetes were isolated and identified by 16S rRNA sequencing. Gas chromatography-mass spectrometry (GC-MS) was used to identify the chemical constituents of bioactive actinomycetes' secondary metabolites. Antibacterial activity of the secondary metabolites was assessed by the broth microdilution method, and their mode of actions were predicted using computational docking. While five strains showed antibacterial activity during primary screening, only Nocardiopsis dassonvillei strain SOD(B)ST2SA2 exhibited activity during secondary screening for antibacterial activity. GC-MS identified five major bioactive compounds: 1-octadecene, diethyl phthalate, pentadecanoic acid, 6-octadecenoic acid, and trifluoroacetoxy hexadecane. SOD(B)ST2SA2's extract demonstrated minimum inhibitory concentration and minimum bactericidal concentration, ranging from 0.78-25 mg/mL and 3.13 to > 25 mg/mL, respectively. Diethyl phthalate displayed the lowest bacterial protein-binding energies (kcal/mol): -7.2, dihydrofolate reductase; -6.0, DNA gyrase B; and -5.8, D-alanine:D-alanine ligase. Thus, marine N. dassonvillei SOD(B)ST2SA2 is a potentially good source of antibacterial compounds that can be used to control STEC and Listeria monocytogenes.
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Affiliation(s)
- Siyanda S. Ngema
- Department of Biochemistry and Microbiology, University of Zululand, Private Bag X1001, KwaDlangezwa 3886, South Africa; (S.S.N.); (S.H.K.); (M.C.O.); (A.K.B.)
| | - Solomuzi H. Khumalo
- Department of Biochemistry and Microbiology, University of Zululand, Private Bag X1001, KwaDlangezwa 3886, South Africa; (S.S.N.); (S.H.K.); (M.C.O.); (A.K.B.)
| | - Michael C. Ojo
- Department of Biochemistry and Microbiology, University of Zululand, Private Bag X1001, KwaDlangezwa 3886, South Africa; (S.S.N.); (S.H.K.); (M.C.O.); (A.K.B.)
| | - Ofentse J. Pooe
- Discipline of Biochemistry, School of Life Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa;
| | - Tsolanku S. Malilehe
- Department of Water and Sanitation, University of Limpopo, Private Bag X1106, Polokwane 0727, South Africa;
| | - Albertus K. Basson
- Department of Biochemistry and Microbiology, University of Zululand, Private Bag X1001, KwaDlangezwa 3886, South Africa; (S.S.N.); (S.H.K.); (M.C.O.); (A.K.B.)
| | - Evelyn Madoroba
- Department of Biochemistry and Microbiology, University of Zululand, Private Bag X1001, KwaDlangezwa 3886, South Africa; (S.S.N.); (S.H.K.); (M.C.O.); (A.K.B.)
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Delbari Y, Mohassel Y, Kakaei E, Bahrami Y. Identification and anti-bacterial property of endophytic actinobacteria from Thymes kotschyanus, Allium hooshidaryae, and Cerasus microcarpa. Sci Rep 2023; 13:13145. [PMID: 37573468 PMCID: PMC10423286 DOI: 10.1038/s41598-023-40478-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 08/10/2023] [Indexed: 08/14/2023] Open
Abstract
The arbitrary and overuses of antibiotics have resulted in the emergence of multidrug resistance bacteria which encounters human to a serious public health problem. Thus, there is an ever-increasing demand for discovery of novel effective antibiotics with new modes of function against resistant pathogens. Endophytic actinobacteria (EA) have currently been considered as one of the most prospective group of microorganisms for discovery of therapeutic agents. This study aimed to isolate EA from Thymes kotschyanus, Allium hooshidaryae, and Cerasus microcarpa plants and to evaluate their antibacterial properties. The healthy samples were collected, dissected and surface-sterilized before cultured on four different selection media at 28 °C. Nine EA were isolated and identified based on morphological and molecular properties, and scanning electron micrograph analyses. Based on phylogenetic analysis, they were taxonomically grouped into four families Streptomycetaceae, Nocardiaceae, Micromonosporaceae, and Pseudonocardiaceae. Their branched aerial mycelia produced chains of cylindrical or cube or oval shaped spores with smooth or rough surfaces. Four strains; IKBG03, IKBG05, IKBG13, and IKBG17 had less than 98.65% sequence similarity to their closely related strains, which constitute them as novel species/strains. Besides, three strains; IKBG05, IKBG13, and IKBG18 were reported as endophytes for the first time. Preliminary antibacterial activity conducted on the all isolates revealed potent antibacterial effects against Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa. All isolates strongly inhibited the growth of at least one of the tested pathogens. Our results reveals that the test plants are novel sources for isolating a diverse group of rare and common actinobacteria that could produce a wide range of novel biologically active natural products with antibacterial activity which have a great potential in pharmaceutical and biotechnological applications.
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Affiliation(s)
- Yaser Delbari
- Department of Medical Biotechnology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Yaser Mohassel
- Department of Clinical Biochemistry, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Elham Kakaei
- Department of Medical Biotechnology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Yadollah Bahrami
- Department of Medical Biotechnology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran.
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.
- Department of Medical Biotechnology, School of Medicine, College of Medicine and Public Health, Flinders University, Adelaide, SA, 5042, Australia.
- Advanced Marine Biomanufacturing Laboratory, Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Adelaide, SA, 5042, Australia.
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Li H, Liu H, Qiu L, Xie Q, Chen B, Wang H, Long Y, Hu L, Fang C. Mechanism of antibiotic resistance development in an activated sludge system under tetracycline pressure. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:90844-90857. [PMID: 37464207 DOI: 10.1007/s11356-023-28744-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/07/2023] [Indexed: 07/20/2023]
Abstract
The mechanism of antibiotic resistance (AR) development in an activated sludge system under tetracycline (TC) pressure was discussed and analyzed. According to the variation of macro-factors, including TC, COD, TN, TP, NH3-N, pH, heavy metals, and reactor settings, the tet genes respond accordingly. Consequently, the enrichment sites of tet genes form an invisible AR selection zone, where AR microorganisms thrive, gather, reproduce, and spread. The efflux pump genes tetA and tetB prefer anaerobic environment, while ribosome protective protein genes tetM, tetO, tetQ, tetT, and tetW were more concentrated in aerobic situations. As a corresponding micro-effect, different types of tet genes selected the corresponding dominant bacteria such as Thauera and Arthrobacter, suggesting the intrinsic relationship between tet genes and potential hosts. In summary, the macro-response and micro-effect of tet genes constitute an interactive mechanism with tet genes as the core, which is the crucial cause for the continuous development of AR. This study provides an executable strategy to control the development of AR in actual wastewater treatment plants from the perspective of macro-factors and micro-effects.
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Affiliation(s)
- Hong Li
- College of Civil Engineering, Zhejiang University of Technology, Hangzhou, 310023, China
| | - Hongyuan Liu
- College of Civil Engineering, Zhejiang University of Technology, Hangzhou, 310023, China
| | - Libo Qiu
- College of Civil Engineering, Zhejiang University of Technology, Hangzhou, 310023, China
| | - Qiaona Xie
- College of Civil Engineering, Zhejiang University of Technology, Hangzhou, 310023, China
| | - Binhui Chen
- Key Laboratory of Recycling and Eco-Treatment of Waste Biomass of Zhejiang Province, Zhejiang University of Science and Technology, Hangzhou, 310023, China
| | - Hua Wang
- Key Laboratory of Recycling and Eco-Treatment of Waste Biomass of Zhejiang Province, Zhejiang University of Science and Technology, Hangzhou, 310023, China
| | - Yuyang Long
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Zhejiang Gongshang University, Hangzhou, 310012, China
| | - Lifang Hu
- College of Quality and Safety Engineering, Institution of Industrial Carbon Metrology, China Jiliang University, Hangzhou, 310018, China
| | - Chengran Fang
- College of Civil Engineering, Zhejiang University of Technology, Hangzhou, 310023, China.
- Key Laboratory of Recycling and Eco-Treatment of Waste Biomass of Zhejiang Province, Zhejiang University of Science and Technology, Hangzhou, 310023, China.
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Kanchanasin P, Sripreechasak P, Suriyachadkun C, Rueangsawang K, Tanasupawat S, Phongsopitanun W. Streptomyces cylindrosporus sp. nov. and Streptomyces spinosisporus sp. nov.: two new endophytic actinobacteria isolated from the roots of Barleria lupulina Lindl. Int J Syst Evol Microbiol 2023; 73. [PMID: 37256768 DOI: 10.1099/ijsem.0.005926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023] Open
Abstract
Two endophytic actinobacteria, designated as strains 7R015T and 7R016T, were isolated from the roots of Barleria lupulina collected in Thailand. The morphological characteristics and results of chemotaxonomic studies and 16S rRNA gene analysis indicated that both strains represented members of the genus Streptomyces. They contained ll-diaminopimelic acid in the peptidoglycan. Ribose and glucose were detected as the whole-cell sugars. MK-9(H4), MK-9(H6) and MK-9(H8), were found as the membrane menaquinone. The predominant cellular fatty acids detected were iso-C16 : 0 and anteiso-C15 : 0. The genomes of both strains harboured biosynthetic gene clusters for melanin, terpene, lanthipeptide, polyketides, non-ribosomal peptide synthetase, siderophore and ectoine. The 16S rRNA gene sequence of 7R015T showed the highest similarity to that of Streptomyces pseudovenezuelae DSM 40212T (98.6 %), Streptomyces cyaneus NRRL B2296T (98.6 %) and Streptomyces curacoi DSM 40107T (98.6 %). Strain 7R016T showed the highest 16S rRNA gene sequence similarity to Streptomyces gilvifuscus NBRC 110904T (98.2 %), which is lower than the threshold value for 16S rRNA gene sequence similarity for differentiation at the species level (98.65 %). Comparative genome analysis revealed that the genomes of 7R015T, 7R016T and the closely related type strains had an average nucleotide identity (ANI) of less than 95 % and a digital DNA-DNA hybridisation (dDDH) of less than 70 %, the thresholds for species demarcation. On the basis of the results of the polyphasic study, strains 7R015T and 7R016T represent novel species of the genus Streptomyces and are named herein as Streptomyces cylindrosporus sp. nov. (=NBRC 115200T = TBRC 14542T) for strain 7R015T and Streptomyces spinosisporus sp. nov. (=NBRC 115201T = TBRC 14543T) for strain 7R016T.
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Affiliation(s)
- Pawina Kanchanasin
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Paranee Sripreechasak
- Office of Educational Affairs, Faculty of Science, Burapha University, Chonburi 20131, Thailand
| | - Chanwit Suriyachadkun
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Pathum Thani, 12120, Thailand
| | - Kanokorn Rueangsawang
- Department of Biology, Faculty of Science, Ramkhamhaeng University, Bangkok 10240, Thailand
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Wongsakorn Phongsopitanun
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Natural Products and Nanoparticles Research Unit (NP2), Chulalongkorn University, Bangkok 10330, Thailand
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Jalal A, Oliveira CEDS, Rosa PAL, Galindo FS, Teixeira Filho MCM. Beneficial Microorganisms Improve Agricultural Sustainability under Climatic Extremes. Life (Basel) 2023; 13:life13051102. [PMID: 37240747 DOI: 10.3390/life13051102] [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: 02/26/2023] [Revised: 04/08/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
The challenging alterations in climate in the last decades have had direct and indirect influences on biotic and abiotic stresses that have led to devastating implications on agricultural crop production and food security. Extreme environmental conditions, such as abiotic stresses, offer great opportunities to study the influence of different microorganisms in plant development and agricultural productivity. The focus of this review is to highlight the mechanisms of plant growth-promoting microorganisms (especially bacteria and fungi) adapted to environmental induced stresses such as drought, salinity, heavy metals, flooding, extreme temperatures, and intense light. The present state of knowledge focuses on the potential, prospective, and biotechnological approaches of plant growth-promoting bacteria and fungi to improve plant nutrition, physio-biochemical attributes, and the fitness of plants under environmental stresses. The current review focuses on the importance of the microbial community in improving sustainable crop production under changing climatic scenarios.
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Affiliation(s)
- Arshad Jalal
- Department of Plant Health, Rural Engineering and Soils, Faculty of Engineering, São Paulo State University (UNESP), Av. Brasil 56-Centro, Ilha Solteira 15385-000, SP, Brazil
| | - Carlos Eduardo da Silva Oliveira
- Department of Plant Health, Rural Engineering and Soils, Faculty of Engineering, São Paulo State University (UNESP), Av. Brasil 56-Centro, Ilha Solteira 15385-000, SP, Brazil
| | - Poliana Aparecida Leonel Rosa
- Department of Plant Health, Rural Engineering and Soils, Faculty of Engineering, São Paulo State University (UNESP), Av. Brasil 56-Centro, Ilha Solteira 15385-000, SP, Brazil
| | - Fernando Shintate Galindo
- Faculty of Agricultural Sciences and Technology, São Paulo State University (UNESP), Campus of Dracena, Sao Paulo 17900-000, SP, Brazil
| | - Marcelo Carvalho Minhoto Teixeira Filho
- Department of Plant Health, Rural Engineering and Soils, Faculty of Engineering, São Paulo State University (UNESP), Av. Brasil 56-Centro, Ilha Solteira 15385-000, SP, Brazil
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Basavarajappa DS, Kumar RS, Nayaka S. Formulation-based antagonistic endophyte Amycolatopsis sp. SND-1 triggers defense response in Vigna radiata (L.) R. Wilczek. (Mung bean) against Cercospora leaf spot disease. Arch Microbiol 2023; 205:77. [PMID: 36720740 DOI: 10.1007/s00203-023-03419-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 02/02/2023]
Abstract
In the present work, Amycolatopsis sp. SND-1 (SND-1) was isolated from Cleome chellidonii Linn. (C. chellidonii) was performed as biocontrol and resistance elicitor in Vigna radiata (L.) R. Wilczek (mung bean) plants against Cercospora leaf spot causing pathogen Cercospora canescens (C. canescens). The SND-1 isolate showed 74% of inhibition against C. canescens in dual culture and GC-MS analysis revealed the presence of antifungal compounds. Molecular characterization through 16S rRNA showed that the isolated SND-1 belongs to Amycolatopsis sp. The in vitro plant growth trials exhibited production of indole acetic acid, gibberellic acid, cytokinin, ammonia, hydrogen cyanide, and siderophore and phosphate solubilization. In vivo study with talcum formulation of SND-1 revealed a significant increase in plant root length, shoots length, root and shoot fresh weight, and reduced the disease severity in treated mung bean plants. Triggering of resistance by SND-1 formulation was studied by histochemical depositions and biochemical defense enzymes that resulted in the acceleration in defense response in comparison with control plants. The bioactive endophytic Amycolatopsis sp. SND-1 enhanced the defense against C. canescens infection; hence, it can be used as a biological control agent in mung bean cultivars.
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Affiliation(s)
| | - Raju Suresh Kumar
- Department of Chemistry, College of Science, King Saud University, P. O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Sreenivasa Nayaka
- PG Department of Studies in Botany, Karnatak University, Dharwad, Karnataka, 580003, India.
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Mahreen N, Yasmin S, Asif M, Yahya M, Ejaz K, Mehboob-ur-Rahman, Yousaf S, Amin I, Zulfiqar S, Imran A, Khaliq S, Arif M. Mitigation of water scarcity with sustained growth of Rice by plant growth promoting bacteria. FRONTIERS IN PLANT SCIENCE 2023; 14:1081537. [PMID: 36755700 PMCID: PMC9900138 DOI: 10.3389/fpls.2023.1081537] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/02/2023] [Indexed: 11/03/2023]
Abstract
Climate change augments the risk to food security by inducing drought stress and a drastic decline in global rice production. Plant growth-promoting bacteria (PGPB) have been known to improve plant growth under drought stress. Here in the present study, we isolated, identified, and well-characterized eight drought-tolerant bacteria from the rice rhizosphere that are tolerant to 20% PEG-8000. These strains exhibited multiple plant growth-promoting traits, i.e., 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity, exopolysaccharide production, phosphate (P)-solubilizing activity (51-356 µg ml-1), indole-3 acetic acid (IAA) production (14.3-46.2 µg ml-1), and production of organic acids (72-178 µg ml-1). Inoculation of bacterial consortium (Bacillus subtilis NM-2, Brucella haematophilum NM-4, and Bacillus cereus NM-6) significantly improved seedling growth and vigor index (1009.2-1100) as compared to non-inoculated stressed plants (630-957). Through rhizoscanning, efficiency of the consortium was validated by improved root parameters such as root length (17%), diameter, and surface area (18%) of all tested genotypes as compared with respective non-inoculated stressed treatments. Furthermore, the response of consortium inoculation on three rice genotypes was positively correlated with improved plant growth and drought stress ameliorating traits by the accumulation of osmoprotectant, i.e., proline (85.8%-122%), relative water content (51%), membrane stability index (64%), and production of antioxidant enzymes to reduce oxidative damage by reactive oxygen species. A decrease in temperature and improved chlorophyll content of inoculated plants were found using infrared thermal imaging and soil plant analyzer development (SPAD), respectively. The key supporting role of inoculation toward stress responses was validated using robust techniques like infrared thermal imaging and an infrared gas analyzer. Furthermore, principal component analysis depicts the contribution of inoculation on stress responses and yield of tested rice genotypes under water stress. The integration of drought-tolerant rice genotype (NIBGE-DT02) and potential bacterial strains, i.e., NM-2, NM-4, and NM-6, can serve as an effective bioinoculant to cope with water scarcity under current alarming issues related to food security in fluctuating climate.
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Affiliation(s)
- Naima Mahreen
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute for Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Sumera Yasmin
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute for Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Muhammad Asif
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute for Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Mahreen Yahya
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute for Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Khansa Ejaz
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute for Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Mehboob-ur-Rahman
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute for Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Sumaira Yousaf
- Nuclear Institute for Agriculture and Biology (NIAB) College, Pakistan Institute for Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute for Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Sana Zulfiqar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute for Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Asma Imran
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute for Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Shazia Khaliq
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute for Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
| | - Muhammad Arif
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute for Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Punjab, Pakistan
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Numan M, Shah M, Asaf S, Ur Rehman N, Al-Harrasi A. Bioactive Compounds from Endophytic Bacteria Bacillus subtilis Strain EP1 with Their Antibacterial Activities. Metabolites 2022; 12:metabo12121228. [PMID: 36557265 PMCID: PMC9788538 DOI: 10.3390/metabo12121228] [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: 09/28/2022] [Revised: 11/08/2022] [Accepted: 11/11/2022] [Indexed: 12/12/2022] Open
Abstract
Endophytic bacteria boost host plant defense and growth by producing vital compounds. In the current study, a bacterial strain was isolated from the Boswellia sacra plant and identified as Bacillus subtilis strain EP1 (accession number: MT256301) through 16S RNA gene sequencing. From the identified bacteria, four compounds-1 (4-(4-cinnamoyloxy)phenyl)butanoic acid), 2 (cyclo-(L-Pro-D-Tyr)), 3 (cyclo-(L-Val-L-Phe)), and 4 (cyclo-(L-Pro-L-Val))-were isolated and characterized by 1D and 2D NMR and mass spectroscopy. Moreover, antibacterial activity and beta-lactam-producing gene inhibition (δ-(l-α-aminoadipyl)-l-cysteinyl-d-valine synthetase (ACVS) and aminoadipate aminotransferase (AADAT)) assays were performed. Significant antibacterial activity was observed against the human pathogenic bacterial strains (E. coli) by compound 4 with a 13 ± 0.7 mm zone of inhibition (ZOI), followed by compound 1 having an 11 ± 0.7 mm ZOI. In contrast, the least antibacterial activity among the tested samples was offered by compound 2 with a 10 ± 0.9 mm ZOI compared to the standard (26 ± 1.2 mm). Similarly, the molecular analysis of beta-lactam inhibition determined that compounds 3 and 4 inhibited the two genes (2- to 4-fold) in the beta-lactam biosynthesis (ACVS and AADAT) pathway. From these results, it can be concluded that future research on these compounds could lead to the inhibition of antibiotic-resistant pathogenic bacterial strains.
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Affiliation(s)
- Muhammad Numan
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC 27412, USA
| | - Muddaser Shah
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman
- Department of Botany, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan
| | - Sajjad Asaf
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman
| | - Najeeb Ur Rehman
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman
- Correspondence: (N.U.R.); (A.A.-H.)
| | - Ahmed Al-Harrasi
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman
- Correspondence: (N.U.R.); (A.A.-H.)
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10
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Hazarika SN, Saikia K, Thakur D. Characterization and selection of endophytic actinobacteria for growth and disease management of Tea ( Camellia sinensis L.). FRONTIERS IN PLANT SCIENCE 2022; 13:989794. [PMID: 36438109 PMCID: PMC9681920 DOI: 10.3389/fpls.2022.989794] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/24/2022] [Indexed: 06/13/2023]
Abstract
Endophytic microbes are vital for nutrient solubilization and uptake, growth, and survival of plants. Here, 88 endophytic actinobacteria (EnA) associated with five tea clones were isolated, assessed for their diversity, plant growth promoting (PGP), and biocontrol traits, and then used as an inoculant for PGP and disease control in host and non-host plants. Polyphasic methods, including phenotypic and genotypic characteristics led to their identification as Streptomyces, Microbacterium, Curtobacterium, Janibacter, Rhodococcus, Nocardia, Gordonia, Nocardiopsis, and Kribbella. Out of 88 isolates, 35 (39.77%) showed antagonistic activity in vitro against major fungal pathogens, viz. Fusarium oxysporum, Rhizoctonia solani, Exobasidium vexans, Poria hypobrunnea, Phellinus lamaensis, and Nigrospora sphaerica. Regarding PGP activities, the percentage of isolates that produced indole acetic acid, siderophore, and ammonia, as well as P-solubilisation and nitrogen fixation, were 67.05, 75, 80.68, 27.27, 57.95, respectively. A total of 51 and 42 isolates showed chitinase and 1-aminocyclopropane-1-carboxylic acid deaminase activity, respectively. Further, two potent Streptomyces strains KA12 and MA34, selected based on the bonitur scale, were screened for biofilm formation ability and tested in vivo under nursery conditions. Confocal laser scanning microscopy and the crystal violet staining technique revealed that these Streptomyces strains can form biofilms, indicating the potential for plant colonization. In the nursery experiment, they significantly enhanced the shoot and root biomass, shoot and root length, and leaf number in host tea plants. Additionally, treatment of tomato seeds by KA12 suppressed the growth of fungal pathogen Fusarium oxysporum, increased seed germination, and improved root architecture, demonstrating its ability to be used as a seed biopriming agent. Our results confirm the potential of tea endophytic actinobacterial strains with multifarious beneficial traits to enhance plant growth and suppress fungal pathogens, which may be used as bioinoculant for sustainable agriculture.
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Affiliation(s)
- Shabiha Nudrat Hazarika
- Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, India
- Department of Molecular Biology and Biotechnology, Cotton University, Guwahati, India
| | - Kangkon Saikia
- Bioinformatics Infrastructure Facility, Institute of Advanced Study in Science and Technology, Guwahati, India
| | - Debajit Thakur
- Microbial Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, India
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11
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Yang Z, Li L, Zhu W, Xiao S, Chen S, Liu J, Xu Q, Guo F, Lan S. Nitrogen fertilizer amount has minimal effect on rhizosphere bacterial diversity during different growth stages of peanut. PeerJ 2022; 10:e13962. [PMID: 36345480 PMCID: PMC9636873 DOI: 10.7717/peerj.13962] [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: 04/08/2022] [Accepted: 08/08/2022] [Indexed: 01/18/2023] Open
Abstract
The impact of short-term nitrogen fertilizer input on the structure and diversity of peanut rhizosphere microbiota (RM) at different growth stages (GSs) was explored in the southern paddy soil planting environment. Three levels of nitrogen were applied in the field: control (LN, 0 kg/hm2), medium nitrogen (MN, 55.68 kg/hm2), and high nitrogen (HN, 111.36 kg/hm2). The rhizosphere soil was collected during four GSs for high-throughput sequencing and chemical properties analysis. The effect of nitrogen fertilizer application on peanut RM was minimal and was obvious only at the seedling stage. In the four peanut GSs, a significant increase in relative abundance was observed for only one operational taxonomic unit (OTU) of Nitrospira under HN conditions at the seedling stage and mature stage, while there was no consistent change in other OTUs. The difference in RM among different peanut GSs was greater than that caused by the amount of nitrogen fertilizer. This may be due to the substantial differences in soil chemical properties (especially alkali-hydrolyzable nitrogen, pH, and available potassium or total potassium) among peanut GSs, as these significantly affected the RM structure. These results are of great value to facilitate deeper understanding of the effect of nitrogen fertilizer on peanut RM structure.
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Affiliation(s)
- Zheng Yang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
| | - Lin Li
- College of Agronomy, Hunan Agricultural University, Changsha, Hunan, China
| | - Wenjuan Zhu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
| | - Siyuan Xiao
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
| | - Siyu Chen
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
| | - Jing Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
| | - Qian Xu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
| | - Feng Guo
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Shile Lan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
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12
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Genetic Diversity and Anti-Oxidative Potential of Streptomyces spp. Isolated from Unexplored Niches of Meghalaya, India. Curr Microbiol 2022; 79:379. [DOI: 10.1007/s00284-022-03088-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 10/11/2022] [Indexed: 11/06/2022]
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13
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Identification and antibacterial evaluation of endophytic actinobacteria from Luffa cylindrica. Sci Rep 2022; 12:18236. [PMID: 36309579 PMCID: PMC9617871 DOI: 10.1038/s41598-022-23073-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 10/25/2022] [Indexed: 12/31/2022] Open
Abstract
The emergence of antibiotic-resistant bacteria has limited treatment options and led to the untreatable infections, thereby necessitating the discovery of new antibiotics to battel against bacteria. Natural products from endophytic actinobacteria (EA) serve as a reservoir for discovery of new antibiotics. Therefore, the current study focused on the isolation and antibacterial properties of EA isolated from Luffa cylindrica. Six strains were identified using morphological characterization, SEM analyses and 16S rRNA gene sequencing from the roots and leaves of the plant. They were taxonomically classified as Streptomycetaceae family. This is the first report on EA form L. cylindrica. The strains produced a chain of oval, cubed or cylindrical shaped spores with spiny or smooth surfaces. Three strains; KUMS-B3, KUMS-B4 and KUMS-B6 were reported as endophytes for the first time. Fifty percent of isolates were isolated from leaves samples using YECD medium. Our results showed that the sampling time and seasons may affect the bacterial diversity. All six strains had antibacterial activity against at least one of the tested bacteria S. aureus, P. aeruginosa, and E. coli. Among the strains, KUMS-B6 isolate, closely related to S. praecox, exhibited the highest antibacterial activity against both gram-positive and negative bacteria. KUMS-B6, KUMS-B5 and KUMS-B4 isolates strongly inhibited the growth of P. aeruginosa. Interestingly, the strains, isolated from leaves exhibited stronger antagonist activities compared to those isolated from the roots. The study revealed that the isolated strains from Luffa produce a plethora of bioactive substances that are potential source of new drug candidates for the treatment of infections.
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Ali AR, Bahrami Y, Kakaei E, Mohammadzadeh S, Bouk S, Jalilian N. Isolation and identification of endophytic actinobacteria from Citrullus colocynthis (L.) Schrad and their antibacterial properties. Microb Cell Fact 2022; 21:206. [PMID: 36217205 PMCID: PMC9548430 DOI: 10.1186/s12934-022-01936-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 10/02/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Antibiotic resistance poses a major threat to human health globally. Consequently, new antibiotics are desperately required to discover and develop from unexplored habitats to treat life-threatening infections. Microbial natural products (NP) are still remained as primary sources for the discovery of new antibiotics. Endophytic actinobacteria (EA) which are well-known producers of bioactive compounds could provide novel antibiotic against pathogenic bacteria. This research aimed to isolate EA from the Citrullus colocynthis plant and explore the antibacterial properties of their metabolites against pathogenic bacteria. RESULTS The healthy samples were collected, dissected and surface-sterilized before cultured on four different selection media at 28 °C. Six endophytic actinobacteria were isolated from Citrullus colocynthis plant. They were taxonomically classified into two family namely Streptomycetaceae and Nocardiopsaceae, based on colony morphological features, scanning electron microscope analysis and molecular identification of isolates. This is the first report on the identification of EA form Citrullus colocynthis and their antibacterial activity. The strains generated a chain of vibrio-comma, cubed or cylindrical shaped spores with indenting or smooth surfaces. Three of those were reported as endophytes for the first time. The strain KUMS-C1 showed 98.55% sequence similarity to its closely related strains which constitutes as a novel species/ strain for which the name Nocardiopsis colocynthis sp. was proposed for the isolated strain. Five isolated strains had antagonist activity against S. aureus, P. aeruginosa, and E. coli. Among those, stain KUMS-C6 showed the broadest spectrum of antibacterial activity against all test bacteria, whereas the strain KUMS-C4 had no antibacterial activity. CONCLUSIONS NPs have a long history of safe and efficient use for development of pharmaceutical products. Our study highlights that Citrullus colocynthis is an untapped source for the isolation of EA, generating novel and bioactive metabolites by which might lead to discovery of new antibiotic(s). This study reveals the future of new antibiotic developments looks bright against multi-drug resistance diseases by mining under- or unexplored habitats.
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Affiliation(s)
- Aram R Ali
- Department of Medical Biotechnology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Yadollah Bahrami
- Department of Medical Biotechnology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran. .,Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran. .,Department of Medical Biotechnology, School of Medicine, College of Medicine and Public Health, Flinders University, Adelaide, SA, 5042, Australia.
| | - Elham Kakaei
- Department of Medical Biotechnology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sara Mohammadzadeh
- Department of Medical Biotechnology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sasan Bouk
- Department of Medical Biotechnology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Nastaran Jalilian
- Forests and Rangelands Research Department, Kermanshah Agricultural and Natural Resources Research and Education Center, (AREEO), Kermanshah, Iran
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15
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Alam K, Mazumder A, Sikdar S, Zhao YM, Hao J, Song C, Wang Y, Sarkar R, Islam S, Zhang Y, Li A. Streptomyces: The biofactory of secondary metabolites. Front Microbiol 2022; 13:968053. [PMID: 36246257 PMCID: PMC9558229 DOI: 10.3389/fmicb.2022.968053] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Natural products derived from microorganisms serve as a vital resource of valuable pharmaceuticals and therapeutic agents. Streptomyces is the most ubiquitous bacterial genus in the environments with prolific capability to produce diverse and valuable natural products with significant biological activities in medicine, environments, food industries, and agronomy sectors. However, many natural products remain unexplored among Streptomyces. It is exigent to develop novel antibiotics, agrochemicals, anticancer medicines, etc., due to the fast growth in resistance to antibiotics, cancer chemotherapeutics, and pesticides. This review article focused the natural products secreted by Streptomyces and their function and importance in curing diseases and agriculture. Moreover, it discussed genomic-driven drug discovery strategies and also gave a future perspective for drug development from the Streptomyces.
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Affiliation(s)
- Khorshed Alam
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Arpita Mazumder
- Department of Microbiology, University of Chittagong, Chittagong, Bangladesh
| | - Suranjana Sikdar
- Department of Microbiology, University of Chittagong, Chittagong, Bangladesh
| | - Yi-Ming Zhao
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jinfang Hao
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Chaoyi Song
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yanyan Wang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Rajib Sarkar
- Industrial Microbiology Research Division, BCSIR Chattogram Laboratories, Bangladesh Council of Scientific and Industrial Research (BCSIR), Chattogram, Bangladesh
| | - Saiful Islam
- Industrial Microbiology Research Division, BCSIR Chattogram Laboratories, Bangladesh Council of Scientific and Industrial Research (BCSIR), Chattogram, Bangladesh
- Saiful Islam,
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Youming Zhang,
| | - Aiying Li
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- *Correspondence: Aiying Li,
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16
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Kapadia C, Kachhdia R, Singh S, Gandhi K, Poczai P, Alfarraj S, Ansari MJ, Gafur A, Sayyed RZ. Pseudomonas aeruginosa inhibits quorum-sensing mechanisms of soft rot pathogen Lelliottia amnigena RCE to regulate its virulence factors and biofilm formation. Front Microbiol 2022; 13:977669. [PMID: 36090086 PMCID: PMC9450810 DOI: 10.3389/fmicb.2022.977669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 07/25/2022] [Indexed: 01/21/2023] Open
Abstract
The quorum-sensing (QS) cascade is responsible for the colonization and phenotypic behavior of the pathogenic organism and the regulation of diverse signal molecules. The disruption of the quorum-sensing system is an effective strategy to overcome the possibility of antibiotic resistance development in the pathogen. The quorum quenching does not kill the microbes. Instead, it hinders the expression of pathogenic traits. In the present experiment, Pseudomonas aeruginosa RKC1 was used to extract the metabolites responsible for quorum-sensing inhibition in soft rot pathogen Lelliottia amnigena RCE. During the initial screening, P. aeruginosa RKC1 was found to be most promising and inhibits violacein of Chromobacterium violaceum MTCC2656 pyocyanin, swarming-swimming motility of P. aeruginosa MTCC2297. The characterization of metabolites produced by the microbes which are responsible for quorum-sensing inhibition through GC-MS is very scarce in scientific literature. The ethyl acetate extract of P. aeruginosa RKC1 inhibits biofilm formation of L. amnigena RCE while inhibiting growth at higher concentrations. The GC-MS analysis suggested that Cyclic dipeptides (CDPs) such as Cyclo (L-prolyl-L-valine), Cyclo (Pro-Leu), and Cyclo(D-phenylalanyl-L-prolyl) were predominantly found in the ethyl acetate extract of the P. aeruginosa RKC1 (93.72%). This diketopiperazine (DKPs) exhibited quorum-sensing inhibition against the pathogen in liquid media during the active growth phase and regulated diverse metabolites of the pathogen. Moreover, the metabolites data from the clear zone around wells showed a higher concentration of DKSs (9.66%) compared to other metabolites. So far, very few reports indicate the role of DKPs or CDPs in inhibiting the quorum-sensing system in plant pathogenic bacteria. This is one such report that exploits metabolites of P. aeruginosa RKC1. The present investigation provided evidence to use quorum-sensing inhibitor metabolites, to suppress microbes' pathogenesis and thus develop an innovative strategy to overcome antibiotic resistance.
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Affiliation(s)
- Chintan Kapadia
- Department of Plant Molecular Biology and Biotechnology, ASPEE College of Horticulture and Forestry, Navsari Agricultural University, Navsari, India
- *Correspondence: Chintan Kapadia
| | - Rinkal Kachhdia
- Department of Plant Molecular Biology and Biotechnology, ASPEE College of Horticulture and Forestry, Navsari Agricultural University, Navsari, India
| | - Susheel Singh
- Food Quality Testing Laboratory, N. M. College of Agriculture, Navsari Agricultural University, Navsari, India
| | - Kelvin Gandhi
- Food Quality Testing Laboratory, N. M. College of Agriculture, Navsari Agricultural University, Navsari, India
| | - Peter Poczai
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- Peter Poczai
| | - Saleh Alfarraj
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Javed Ansari
- Department of Botany, Hindu College, Moradabad (Mahatma Jyotiba Phule Rohilkhand University Bareilly), Moradabad, India
| | - Abdul Gafur
- Sinarmas Forestry Corporate Research and Development, Perawang, Indonesia
| | - R. Z. Sayyed
- Department of Microbiology, PSGVP Mandals, S I Patil Arts, G B Patel Science and STKV Sangh Commerce College, Shahada, India
- R. Z. Sayyed
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17
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Akter Y, Barua R, Nasir Uddin M, Muhammad Sanaullah AF, Marzan LW. Bioactive potentiality of secondary metabolites from endophytic bacteria against SARS-COV-2: An in-silico approach. PLoS One 2022; 17:e0269962. [PMID: 35925905 PMCID: PMC9352062 DOI: 10.1371/journal.pone.0269962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 05/31/2022] [Indexed: 11/19/2022] Open
Abstract
Five endophytic bacterial isolates were studied to identify morphologically and biochemically, according to established protocols and further confirmed by 16S rDNA Sanger sequencing, as Priestia megaterium, Staphylococcus caprae, Neobacillus drentensis, Micrococcus yunnanensis, and Sphingomonas paucimobiliz, which were then tested for phytohormone, ammonia, and hydrolytic enzyme production. Antioxidant compounds total phenolic content (TPC), and total flavonoid content (TFC) were assessed by using bacterial crude extracts obtained from 24-hour shake-flask culture. Phylogenetic tree analysis of those identified isolates shared sequence similarities with the members of Bacillus, Micrococcus, Staphylococcus, and Pseudomonas species, and after GenBank submission, accession numbers for the nucleotide sequences were found to be MW494406, MW494408, MW494401, MW494402, and MZ021340, respectively. In silico analysis was performed to identify their bioactive genes and compounds in the context of bioactive secondary metabolite production with medicinal value, where nine significant bioactive compounds according to six different types of bioactive secondary metabolites were identified, and their structures, gene associations, and protein-protein networks were analyzed by different computational tools and servers, which were reported earlier with their antimicrobial, anti-infective, antioxidant, and anti-cancer capabilities. These compounds were then docked to the 3-chymotrypsin-like protease (3CLpro) of the novel SARS-COV-2. Docking scores were then compared with 3CLpro reference inhibitor (lopinavir), and docked compounds were further subjected to ADMET and drug-likeness analyses. Ligand-protein interactions showed that two compounds (microansamycin and aureusimine) interacted favorably with coronavirus 3CLpro. Besides, in silico analysis, we also performed NMR for metabolite detection whereas three metabolites (microansamycin, aureusimine, and stenothricin) were confirmed from the 1H NMR profiles. As a consequence, the metabolites found from NMR data aligned with our in-silico analysis that carries a significant outcome of this research. Finally, Endophytic bacteria collected from medicinal plants can provide new leading bioactive compounds against target proteins of SARS-COV-2, which could be an effective approach to accelerate drug innovation and development.
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Affiliation(s)
- Yasmin Akter
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong, Bangladesh
| | - Rocktim Barua
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong, Bangladesh
| | - Md. Nasir Uddin
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong, Bangladesh
| | | | - Lolo Wal Marzan
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong, Bangladesh
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18
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Mathur V, Ulanova D. Microbial Metabolites Beneficial to Plant Hosts Across Ecosystems. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02073-x. [PMID: 35867138 DOI: 10.1007/s00248-022-02073-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
Plants are intimately connected with their associated microorganisms. Chemical interactions via natural products between plants and their microbial symbionts form an important aspect in host health and development, both in aquatic and terrestrial ecosystems. These interactions range from negative to beneficial for microbial symbionts as well as their hosts. Symbiotic microbes synchronize their metabolism with their hosts, thus suggesting a possible coevolution among them. Metabolites, synthesized from plants and microbes due to their association and coaction, supplement the already present metabolites, thus promoting plant growth, maintaining physiological status, and countering various biotic and abiotic stress factors. However, environmental changes, such as pollution and temperature variations, as well as anthropogenic-induced monoculture settings, have a significant influence on plant-associated microbial community and its interaction with the host. In this review, we put the prominent microbial metabolites participating in plant-microbe interactions in the natural terrestrial and aquatic ecosystems in a single perspective and have discussed commonalities and differences in these interactions for adaptation to surrounding environment and how environmental changes can alter the same. We also present the status and further possibilities of employing chemical interactions for environment remediation. Our review thus underlines the importance of ecosystem-driven functional adaptations of plant-microbe interactions in natural and anthropogenically influenced ecosystems and their possible applications.
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Affiliation(s)
- Vartika Mathur
- Animal Plant Interactions Lab, Department of Zoology, Sri Venkateswara College, Benito Juarez Marg, Dhaula Kuan, New Delhi-110021, India.
| | - Dana Ulanova
- Department of Marine Resource Sciences, Faculty of Agriculture and Marine Science, Kochi University, Monobe, Nankoku city, Kochi, 783-8502, Japan.
- Center for Advanced Marine Core Research, Kochi University, Monobe, Nankoku city, Kochi, 783-8502, Japan.
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19
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Retraction: Determination and production of antimicrobial compounds by Aspergillus clavatonanicus strain MJ31, an endophytic fungus from Mirabilis jalapa L. using UPLC-ESI-MS/MS and TD-GC-MS analysis. PLoS One 2022; 17:e0268371. [PMID: 35617424 PMCID: PMC9135329 DOI: 10.1371/journal.pone.0268371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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20
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Xia Y, Liu J, Chen C, Mo X, Tan Q, He Y, Wang Z, Yin J, Zhou G. The Multifunctions and Future Prospects of Endophytes and Their Metabolites in Plant Disease Management. Microorganisms 2022; 10:microorganisms10051072. [PMID: 35630514 PMCID: PMC9146654 DOI: 10.3390/microorganisms10051072] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/19/2022] [Accepted: 05/21/2022] [Indexed: 01/27/2023] Open
Abstract
Endophytes represent a ubiquitous and magical world in plants. Almost all plant species studied by different researchers have been found to harbor one or more endophytes, which protect host plants from pathogen invasion and from adverse environmental conditions. They produce various metabolites that can directly inhibit the growth of pathogens and even promote the growth and development of the host plants. In this review, we focus on the biological control of plant diseases, aiming to elucidate the contribution and key roles of endophytes and their metabolites in this field with the latest research information. Metabolites synthesized by endophytes are part of plant disease management, and the application of endophyte metabolites to induce plant resistance is very promising. Furthermore, multi-omics should be more fully utilized in plant–microbe research, especially in mining novel bioactive metabolites. We believe that the utilization of endophytes and their metabolites for plant disease management is a meaningful and promising research direction that can lead to new breakthroughs in the development of more effective and ecosystem-friendly insecticides and fungicides in modern agriculture.
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Affiliation(s)
- Yandong Xia
- Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Key Laboratory for Non-Wood Forest Cultivation and Conservation of Ministry of Education, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China; (Y.X.); (J.L.); (X.M.); (Q.T.); (Y.H.); (Z.W.)
| | - Junang Liu
- Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Key Laboratory for Non-Wood Forest Cultivation and Conservation of Ministry of Education, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China; (Y.X.); (J.L.); (X.M.); (Q.T.); (Y.H.); (Z.W.)
| | - Cang Chen
- College of Life Science, Hunan Normal University, Changsha 410081, China;
| | - Xiuli Mo
- Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Key Laboratory for Non-Wood Forest Cultivation and Conservation of Ministry of Education, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China; (Y.X.); (J.L.); (X.M.); (Q.T.); (Y.H.); (Z.W.)
| | - Qian Tan
- Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Key Laboratory for Non-Wood Forest Cultivation and Conservation of Ministry of Education, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China; (Y.X.); (J.L.); (X.M.); (Q.T.); (Y.H.); (Z.W.)
| | - Yuan He
- Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Key Laboratory for Non-Wood Forest Cultivation and Conservation of Ministry of Education, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China; (Y.X.); (J.L.); (X.M.); (Q.T.); (Y.H.); (Z.W.)
| | - Zhikai Wang
- Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Key Laboratory for Non-Wood Forest Cultivation and Conservation of Ministry of Education, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China; (Y.X.); (J.L.); (X.M.); (Q.T.); (Y.H.); (Z.W.)
| | - Jia Yin
- College of Life Science, Hunan Normal University, Changsha 410081, China;
- Correspondence: (J.Y.); (G.Z.)
| | - Guoying Zhou
- Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Key Laboratory for Non-Wood Forest Cultivation and Conservation of Ministry of Education, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China; (Y.X.); (J.L.); (X.M.); (Q.T.); (Y.H.); (Z.W.)
- Correspondence: (J.Y.); (G.Z.)
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Boubekri K, Soumare A, Mardad I, Lyamlouli K, Ouhdouch Y, Hafidi M, Kouisni L. Multifunctional role of Actinobacteria in agricultural production sustainability: a review. Microbiol Res 2022; 261:127059. [DOI: 10.1016/j.micres.2022.127059] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/26/2021] [Accepted: 05/01/2022] [Indexed: 12/13/2022]
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22
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Phytostimulating Potential of Endophytic Bacteria from Ethnomedicinal Plants of North-East Indian Himalayan Region. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.2.05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
North-East Indian Himalayan Region has a humid subtropical climate having diverse ecosystems. The majority of the population of the region depends on agriculture for sustainable livelihood. However, it can produce only 1.5% of the country’s food grains, thereby importing from other parts of the country for consumption. To feed the increase in the population of the region, there is an urgent need to augment the agricultural and allied products to sustain the population and uplift the economic conditions. Plant beneficial endophytes isolated from ethnomedicinal plants of North-East India play an important role as a plant growth promoter by the production of phytohormones, solubilization and mobilization of mineral nutrients. It also indirectly promotes growth by protecting the plants from diseases through the production of antibiotics, enzymes and volatile compounds. The bacteria also have the potential to induce systemic resistance against various abiotic stresses. Since the region has various agro-climatic conditions, the plants are continuously affected by abiotic stress particularly, acidity, drought and waterlogging, there is a need to explore the indigenous endophytes that can mitigate the stress and enhance the sustainable development of agricultural products.
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Endophytic bacterial and fungal community compositions in different organs of ginseng (Panax ginseng). Arch Microbiol 2022; 204:208. [PMID: 35275265 DOI: 10.1007/s00203-022-02815-y] [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: 12/01/2021] [Revised: 02/09/2022] [Accepted: 02/23/2022] [Indexed: 01/18/2023]
Abstract
Panax ginseng (Panax ginseng C. A. Mey.) is a perennial herb of the genus ginseng, which is used as medicine with dried roots and rhizomes. With the deepening of research on ginseng, the chemical components and pharmacological effects of ginseng have gradually been discovered. Endophytes are beneficial to host plants. However, the composition of endophytes in different organs from ginseng is poorly elucidated. The report of ginsenoside production by endophytic microbes isolated from Panax sp., motivated us to explore the endophytic microbial diversity related to the roots, stems, and leaves. In this study, the V5-V7 variable region of endophytic bacteria 16S rRNA gene and V1 variable region of endophytic fungi ITS gene in different organs were analyzed by high-throughput sequencing. The diversity and abundance of endophytic microbes in the three organs are different and are affected by the organs. For example, the most abundant endophytic bacterial genus in roots was Mycobacterium, while, the stems and leaves were Ochrobactrum. Similarly, the fungal endophytes, Coniothyrium and Cladosporium, were also found in high abundance in stems, in comparison to roots and leaves. The Shannon index shows that the diversity of endophytic bacteria in roots is the highest, and the richness of endophytic bacterial was root > stem (p < 0.05). Principal coordinate analysis showed that there were obvious microbial differences among the three groups, and the endophytic bacterial composition of the leaves was closer to that of the roots. This study provides an important reference for the study of endophytic microorganisms in ginseng.
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Production, characterization and growth inhibitory potential of metabolites produced by Pseudomonas and Bacillus species. SCIENTIFIC AFRICAN 2022. [DOI: 10.1016/j.sciaf.2021.e01085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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25
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Kapadia C, Patel N, Rana A, Vaidya H, Alfarraj S, Ansari MJ, Gafur A, Poczai P, Sayyed RZ. Evaluation of Plant Growth-Promoting and Salinity Ameliorating Potential of Halophilic Bacteria Isolated From Saline Soil. FRONTIERS IN PLANT SCIENCE 2022; 13:946217. [PMID: 35909789 PMCID: PMC9335293 DOI: 10.3389/fpls.2022.946217] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/17/2022] [Indexed: 05/09/2023]
Abstract
Among the biotic and abiotic stress affecting the physical, chemical, and biological properties of soil, salinity is a major threat that leads to the desertification of cultivable land throughout the world. The existence of diverse and versatile microbial populations inhabiting the nutrient-rich soil and varied soil conditions affects the soil dynamism. A normal soil constitutes 600 million bacteria belonging to about 20,000 species, which is reduced to 1 million with 5,000-8,000 species in stress conditions. Plant growth-promoting rhizobacteria (PGPR) are in symbiotic association with the plant system, which helps in combating the abiotic stress and increases the overall productivity and yield. These microorganisms are actively associated with varied cellular communication processes through quorum sensing and secondary metabolites such as the production of Indole-3-acetic acid (IAA), exopolysaccharide (EPS) siderophore, ammonia, ACC deaminase, and solubilization of phosphate. The present study focused on the isolation, identification, and characterization of the microorganisms isolated from the seacoast of Dandi, Navsari. Twelve isolates exhibited PGP traits at a high salt concentration of 15-20%. AD9 isolate identified as Bacillus halotolerans showed a higher ammonia production (88 ± 1.73 μg/mL) and phosphate solubilization (86 ± 3.06 μg/mL) at 15% salt concentration, while AD32* (Bacillus sp. clone ADCNO) gave 42.67 ±1.20 μg/mL IAA production at 20% salt concentration. AD2 (Streptomyces sp. clone ADCNB) and AD26 (Achromobacter sp. clone ADCNI) showed ACC deaminase activity of 0.61 ± 0.12 and 0.60 ± 0.04 nM α-ketobutyrate/mg protein/h, respectively. AD32 (Bacillus sp. clone ADCNL) gave a high siderophore activity of 65.40 ± 1.65%. These isolates produced salinity ameliorating traits, total antioxidant activities, and antioxidant enzymes viz. superoxide dismutase (SOD), Glutathione oxidase (GSH), and catalase (CAT). Inoculation of the multipotent isolate that produced PGP traits and salinity ameliorating metabolites promoted the plant growth and development in rice under salinity stress conditions. These results in 50% more root length, 25.00% more plant dry weight, and 41% more tillers compared to its control.
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Affiliation(s)
- Chintan Kapadia
- Department of Plant Molecular Biology and Biotechnology, ASPEE College of Horticulture and Forestry, Navsari Agricultural University, Navsari, India
| | - Nafisa Patel
- Naran Lala College of Professional and Applied Sciences, Navsari, India
- *Correspondence: Nafisa Patel
| | - Ankita Rana
- Naran Lala College of Professional and Applied Sciences, Navsari, India
| | - Harihar Vaidya
- Department of Plant Molecular Biology and Biotechnology, ASPEE College of Horticulture and Forestry, Navsari Agricultural University, Navsari, India
| | - Saleh Alfarraj
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Javed Ansari
- Department of Botany, Hindu College (Mahatma Jyotiba Phule Rohilkhand University Bareilly), Moradabad, India
| | - Abdul Gafur
- Sinarmas Forestry Corporate Research and Development, Perawang, Indonesia
| | - Peter Poczai
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- Peter Poczai
| | - R. Z. Sayyed
- Department of Entomology, Asian PGPR Society for Sustainable Agriculture, Auburn University, Auburn, AL, United States
- Department of Microbiology, PSGVP Mandal's‘S I Patil Arts, G B Patel Science, and STKV Sangh Commerce College, Shahada, India
- R. Z. Sayyed
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Insuk C, Pongpamorn P, Forsythe A, Matsumoto A, Ōmura S, Pathom-aree W, Cheeptham N, Xu J. Taxonomic and Metabolite Diversities of Moss-Associated Actinobacteria from Thailand. Metabolites 2021; 12:metabo12010022. [PMID: 35050144 PMCID: PMC8777641 DOI: 10.3390/metabo12010022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/22/2021] [Accepted: 12/25/2021] [Indexed: 01/08/2023] Open
Abstract
Actinobacteria are a group of ecologically important bacteria capable of producing diverse bioactive compounds. However, much remains unknown about the taxonomic and metabolic diversities of actinobacteria from many geographic regions and ecological niches. In this study, we report the isolation of actinobacteria from moss and moss-associated rhizosphere soils in Thailand. Among the 89 isolates analyzed for their bioactivities, 86 strains produced indole-3-acetic acid (IAA, ranging from 0.04 to 59.12 mg/L); 42 strains produced hydroxamate type of siderophore; 35 strains produced catecholate type of siderophore; 21 strains solubilized tricalcium phosphate; and many strains exhibited antagonistic activities against one to several of the seven selected plant, animal, and human pathogens. Overall, actinobacteria from the rhizosphere soil of mosses showed greater abilities to produce IAA and siderophores and to solubilize tricalcium phosphate than those from mosses. Among these 89 isolates, 37 were analyzed for their 16S rRNA gene sequences, which revealed their diverse phylogenetic distributions among seven genera, Streptomyces, Micromonospora, Nocardia, Actinoplanes, Saccharothrix, Streptosporangium, and Cryptosporangium. Furthermore, gas chromatography-mass spectrometry analyses of ethyl acetate crude extracts of three selected isolates with inhibitory effects against a methicillin-resistant Staphylococcus aureus strain revealed diverse metabolites with known antimicrobial activities. Together, our results demonstrate that actinobacteria from mosses in Thailand are taxonomically diverse and capable of producing a range of metabolites with plant-growth-promoting and microbial pathogen-inhibiting potentials.
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Affiliation(s)
- Chadabhorn Insuk
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada; (C.I.); (A.F.)
| | - Pornkanok Pongpamorn
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand;
| | - Adrian Forsythe
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada; (C.I.); (A.F.)
| | - Atsuko Matsumoto
- Kitasato Institute for Life Sciences, Kitasato University, Minato-ku, Tokyo 108-8641, Japan; (A.M.); (S.Ō.)
| | - Satoshi Ōmura
- Kitasato Institute for Life Sciences, Kitasato University, Minato-ku, Tokyo 108-8641, Japan; (A.M.); (S.Ō.)
| | - Wasu Pathom-aree
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Correspondence: (W.P.-a.); (N.C.); (J.X.)
| | - Naowarat Cheeptham
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC V2C 0C8, Canada
- Correspondence: (W.P.-a.); (N.C.); (J.X.)
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada; (C.I.); (A.F.)
- Correspondence: (W.P.-a.); (N.C.); (J.X.)
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Singh RK, Singh P, Guo DJ, Sharma A, Li DP, Li X, Verma KK, Malviya MK, Song XP, Lakshmanan P, Yang LT, Li YR. Root-Derived Endophytic Diazotrophic Bacteria Pantoea cypripedii AF1 and Kosakonia arachidis EF1 Promote Nitrogen Assimilation and Growth in Sugarcane. Front Microbiol 2021; 12:774707. [PMID: 34975800 PMCID: PMC8714890 DOI: 10.3389/fmicb.2021.774707] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/12/2021] [Indexed: 11/15/2022] Open
Abstract
Excessive, long-term application of chemical fertilizers in sugarcane crops disrupts soil microbial flora and causes environmental pollution and yield decline. The role of endophytic bacteria in improving crop production is now well-documented. In this study, we have isolated and identified several endophytic bacterial strains from the root tissues of five sugarcane species. Among them, eleven Gram-negative isolates were selected and screened for plant growth-promoting characteristics, i.e., production of siderophores, indole-3-acetic acid (IAA), ammonia, hydrogen cyanide (HCN), and hydrolytic enzymes, phosphorus solubilization, antifungal activity against plant pathogens, nitrogen-fixation, 1-aminocyclopropane-1-carboxylic acid deaminase activity, and improving tolerance to different abiotic stresses. These isolates had nifH (11 isolates), acdS (8 isolates), and HCN (11 isolates) genes involved in N-fixation, stress tolerance, and pathogen biocontrol, respectively. Two isolates Pantoea cypripedii AF1and Kosakonia arachidis EF1 were the most potent strains and they colonized and grew in sugarcane plants. Both strains readily colonized the leading Chinese sugarcane variety GT42 and significantly increased the activity of nitrogen assimilation enzymes (glutamine synthetase, NADH glutamate dehydrogenase, and nitrate reductase), chitinase, and endo-glucanase and the content of phytohormones gibberellic acid, indole-3-acetic acid, and abscisic acid. The gene expression analysis of GT42 inoculated with isolates of P. cypripedii AF1 or K. arachidis EF1 showed increased activity of nifH and nitrogen assimilation genes. Also, the inoculated diazotrophs significantly increased plant nitrogen content, which was corroborated by the 15N isotope dilution analysis. Collectively, these findings suggest that P. cypripedii and K. arachidis are beneficial endophytes that could be used as a biofertilizer to improve plant nitrogen nutrition and growth of sugarcane. To the best of our knowledge, this is the first report of sugarcane growth enhancement and nitrogen fixation by Gram-negative sugarcane root-associated endophytic bacteria P. cypripedii and K. arachidis. These strains have the potential to be utilized as sugarcane biofertilizers, thus reducing nitrogen fertilizer use and improving disease management.
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Affiliation(s)
- Rajesh Kumar Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Pratiksha Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
- School of Marine Sciences and Biotechnology, Guangxi University for Nationalities, Nanning, China
| | - Dao-Jun Guo
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bio Resources, College of Agriculture, Guangxi University, Nanning, China
| | - Anjney Sharma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Dong-Ping Li
- Microbiology Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xiang Li
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Krishan K. Verma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Mukesh Kumar Malviya
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Xiu-Peng Song
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Prakash Lakshmanan
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
- Interdisciplinary Center for Agriculture Green Development in Yangtze River Basin, College of Resources and Environment, Southwest University, Chongqing, China
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Li-Tao Yang
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bio Resources, College of Agriculture, Guangxi University, Nanning, China
| | - Yang-Rui Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bio Resources, College of Agriculture, Guangxi University, Nanning, China
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Diale MO, Kayitesi E, Serepa-Dlamini MH. Genome In Silico and In Vitro Analysis of the Probiotic Properties of a Bacterial Endophyte, Bacillus Paranthracis Strain MHSD3. Front Genet 2021; 12:672149. [PMID: 34858466 PMCID: PMC8631869 DOI: 10.3389/fgene.2021.672149] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 10/11/2021] [Indexed: 01/25/2023] Open
Abstract
Spore-forming Bacillus species are gaining interest in human health recently, due to their ability to withstand the harsh environment of the gastrointestinal tract. The present study explores probiotic features of Bacillus paranthracis strain MHSD3 through genomic analysis and in vitro probiotic assays. The draft genome of strain MHSD3 contained genes associated with tolerance to gastrointestinal stress and adhesion. Cluster genes responsible for the synthesis of antimicrobial non-ribosomal peptide synthetases, bacteriocins, and linear azole-containing peptides were identified. Additionally, strain MHSD3 was able to survive in an acidic environment, had the tolerance to bile salt, and exhibited the capability to tolerate gastric juices. Moreover, the isolate was found to possess strong cell surface traits such as high auto-aggregation and hydrophobicity indices of 79 and 54%, respectively. Gas chromatography-mass spectrometry analysis showed that the strain produced secondary metabolites such as amino acids, phenolic compounds, and organic acid, known to exert health-promoting properties, including the improvement of gastrointestinal tract health.
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Affiliation(s)
- Mamonokane Olga Diale
- Department of Biotechnology and Food Technology, University of Johannesburg, Johannesburg, South Africa
| | - Eugenie Kayitesi
- Department of Consumer and Food Science, University of Pretoria, Pretoria, South Africa
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Iquebal MA, Passari AK, Jagannadham J, Ahmad F, Leo VV, Singh G, Jaiswal S, Rai A, Kumar D, Singh BP. Microbiome of Pukzing Cave in India shows high antimicrobial activity against plant and animal pathogens. Genomics 2021; 113:4098-4108. [PMID: 34699904 DOI: 10.1016/j.ygeno.2021.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/27/2021] [Accepted: 10/05/2021] [Indexed: 10/20/2022]
Abstract
Pukzing cave, the largest cave of Mizoram, India was explored for bacterial diversity. Culture dependent method revealed 235 bacterial isolates using three different treatments. Identity of the microbial species was confirmed by 16S rDNA sequencing. The highest bacterial population was recovered from heat treatment (n = 97;41.2%) followed by normal (n = 79;33.6%) and cold treatment (n = 59;25.1%) indicating dominance of moderate thermophiles. Antimicrobial potential of isolates showed 20.4% isolates having antimicrobial ability against tested pathogens. Amplicon sequencing of PKSI, PKSII and NRP specific genes revealed presence of AMP genes in the microbial population. Six microbial pathogens were selected for screening as they are well known for different disease cause organism in various fields such as agriculture and human health. Cave environment harbors unique microbial flora and hypervariable region V4 is more informative. Higher activity of AMP assay against these microbes indicates that cave microbial communities could be potential source of future genomic resources.
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Affiliation(s)
- M A Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ajit Kumar Passari
- Department of Biotechnology, Aizawl, Mizoram University, Mizoram, India; Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Mexico 04510, Mexico
| | - Jaisri Jagannadham
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Farzana Ahmad
- Department of Biotechnology, Aizawl, Mizoram University, Mizoram, India
| | | | - Garima Singh
- Department of Botany, Pachhunga University College, Mizoram University, Aizawl 796001, Mizoram, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India.
| | - Bhim Pratap Singh
- Department of Biotechnology, Aizawl, Mizoram University, Mizoram, India; Department of Agriculture and Environmental Sciences, National Institute of Food Technology Entrepreneurship and Management (NIFTEM), Kundli, Sonipat 131028, Haryana, India.
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30
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Adeleke BS, Babalola OO. The plant endosphere-hidden treasures: a review of fungal endophytes. Biotechnol Genet Eng Rev 2021; 37:154-177. [PMID: 34666635 DOI: 10.1080/02648725.2021.1991714] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The endosphere represents intracellular regions within plant tissues colonize by microbial endophytes without causing disease symptoms to host plants. Plants harbor one or two endophytic microbes capable of synthesizing metabolite compounds. Environmental factors determine the plant growth and survival as well as the kind of microorganisms associated with them. Some fungal endophytes that symbiotically colonize the endosphere of medicinal plants with the potential of producing biological products have been employed in traditional and modern medicine. The bioactive resources from endophytic fungi are promising; biotechnologically to produce cheap and affordable commercial bioactive products as alternatives to chemical drugs and other compounds. The exploration of bioactive metabolites from fungal endophytes has been found applicable in agriculture, pharmaceutical, and industries. Thus, fungal endophytes can be engineered to produce a substantive quantity of pharmacological drugs through the biotransformation process. Hence, this review shall provide an overview of fungal endophytes, ecology, their bioactive compounds, and exploration with the biosystematics approach.
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Affiliation(s)
- Bartholomew Saanu Adeleke
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
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31
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Oliveira THBDE, Gusmão NBDE, Silva LAODA, Coelho LCBB. Free Radicals and Actinobacteria as a Misexplored Goldmine of Antioxidant Compounds. AN ACAD BRAS CIENC 2021; 93:e20201925. [PMID: 34586182 DOI: 10.1590/0001-3765202120201925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/23/2021] [Indexed: 11/22/2022] Open
Abstract
Free radicals are highly reactive unstable molecules, which can be synthesized in different ways, considered harmful and threatening to humans; these chemical species have free traffic throughout the human body, interacting with biological molecules and human body organ tissues. The interaction between free radicals and biological molecules is the main factor for disease development or pre-existing disease symptoms aggravation. Antioxidants are chemical compounds able to donate electric charge to stabilize molecules such as free radicals. Recent studies have proved the benefits of antioxidants intake in health improvement. In this way, the search for natural sources of antioxidants has become an ascending trend. In this field, the microbial sources are considered poorly explored compared to the numerous amount of other compounds obtained from them, especially from Actinobacteria. The searched literature about Actinobacteria highlights an important capacity of producing natural antioxidants; however, there is a lack of in vivo studies of these isolated compounds. In this review, we gathered information that supports our point of view that Actinobacteria is a truly renewable and superficially explored source of natural antioxidants. Furthermore, our purpose is also to point this limitation and stimulate more researches in this area.
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Affiliation(s)
- Thales Henrique B DE Oliveira
- Universidade Federal de Pernambuco, Departamento de Bioquímica, Centro de Biociências, Avenida Professor Moraes Rego, s/n, Cidade Universitária, 50670-420 Recife, PE, Brazil
| | - Norma B DE Gusmão
- Universidade Federal de Pernambuco, Departamento de Antibióticos, Centro de Biociências, Avenida dos Economistas, s/n, Cidade Universitária, 52171-011 Recife, PE, Brazil
| | - Leonor A O DA Silva
- Universidade Federal da Paraíba, Departamento de Biologia Molecular, Centro de Ciências Exatas e da Natureza, Conjunto Presidente Castelo Branco III, 58033-455 João Pessoa, PB, Brazil
| | - Luana C B B Coelho
- Universidade Federal de Pernambuco, Departamento de Bioquímica, Centro de Biociências, Avenida Professor Moraes Rego, s/n, Cidade Universitária, 50670-420 Recife, PE, Brazil
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32
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Elicitation of Streptomyces lunalinharesii secondary metabolism through co-cultivation with Rhizoctonia solani. Microbiol Res 2021; 251:126836. [PMID: 34371303 DOI: 10.1016/j.micres.2021.126836] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 07/23/2021] [Accepted: 07/28/2021] [Indexed: 11/20/2022]
Abstract
The concern regarding the emergence of phytopathogens strains which are resistant to conventional agrochemicals has given support to the search for alternatives on the use of chemical pesticides in agriculture. In this context, microorganisms are considered as promising sources of useful natural compounds and actinobacteria are particularly relevant since they are known to produce several bioactive metabolites. The objective of this work was to investigate the production of secondary metabolites with antifungal activity by a strain of the actinobacteria Streptomyces lunalinharesii (A54A) under axenic conditions and in co-cultivation with the phytopathogen Rhizoctonia solani. Tests to evaluate antifungal activity of the extracts indicated the presence of diffusable molecules capable of inhibiting the growth of R. solani produced by S. lunalinharesii, especially when in the presence of the fungus during fermentation. Metabolomic analyzes allowed the putative annotation of the bioactive compounds desferrioxamine E and anisomycin, in addition to the evaluation of the metabolic profile of the isolate when grown in axenic mode and in co-cultivation, while statistical analyzes enabled the comparison of such profiles and the identification of metabolites produced in greater relative quantities in the elicitation condition. Such methodologies provided the selection of unknown features with high bioactive potential for dereplication, and several metabolites of S. lunalinharesii possibly represent novel compounds.
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Singh TA, Passari AK, Jajoo A, Bhasin S, Gupta VK, Hashem A, Alqarawi AA, Abd Allah EF. Tapping Into Actinobacterial Genomes for Natural Product Discovery. Front Microbiol 2021; 12:655620. [PMID: 34239507 PMCID: PMC8258257 DOI: 10.3389/fmicb.2021.655620] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 05/31/2021] [Indexed: 11/27/2022] Open
Abstract
The presence of secondary metabolite biosynthetic gene clusters (BGCs) makes actinobacteria well-known producers of diverse metabolites. These ubiquitous microbes are extensively exploited for their ability to synthesize diverse secondary metabolites. The extent of their ability to synthesize various molecules is yet to be evaluated. Current advancements in genome sequencing, metabolomics, and bioinformatics have provided a plethora of information about the mechanism of synthesis of these bioactive molecules. Accessing the biosynthetic gene cluster responsible for the production of metabolites has always been a challenging assignment. The genomic approach developments have opened a new gateway for examining and manipulating novel antibiotic gene clusters. These advancements have now developed a better understanding of actinobacterial physiology and their genetic regulation for the prolific production of natural products. These new approaches provide a unique opportunity to discover novel bioactive compounds that might replenish antibiotics’ exhausted stock and counter the microbes’ resistance crisis.
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Affiliation(s)
- Tanim Arpit Singh
- Department of Biosciences, Maharaja Ranjit Singh College of Professional Sciences, Indore, India.,School of Life Sciences, Devi Ahilya Vishwavidyalaya, Indore, India
| | - Ajit Kumar Passari
- Departmento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México City, Mexico
| | - Anjana Jajoo
- School of Life Sciences, Devi Ahilya Vishwavidyalaya, Indore, India
| | - Sheetal Bhasin
- Department of Biosciences, Maharaja Ranjit Singh College of Professional Sciences, Indore, India
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Center and Center for Safe and Improved Food, Scotland's Rural College (SRUC), SRUC Barony Campus, Dumfries, United Kingdom
| | - Abeer Hashem
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia.,Department of Mycology and Plant Disease Survey, Plant Pathology Research Institute, Agricultural Research Center (ARC), Giza, Egypt
| | - Abdulaziz A Alqarawi
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Elsayed Fathi Abd Allah
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
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Microbial Isolation and Characterization of New Antibiotic-Producing Strains from Decayed Wood. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2296:43-57. [PMID: 33977441 DOI: 10.1007/978-1-0716-1358-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Microbial drug resistance is increasing over the last years, becoming one of the most important health concerns in the twenty-first century. It encourages the discovery of new antibiotics. Thus, novel antibiotics discovered by exploring different environments that previously have been left out of the scientific focus is a realistic opportunity. One of these habitats can be forest deadwood, which is a specific niche inside of the forest that provides shelter and nutrition to a great variety of organisms, such as fungi, bacteria, or saproxylic insects. Different studies have found the existence of complex antagonisms and symbiotic interactions among them, which points at decayed wood as a competitive environment. Besides, it is an interesting niche to look for new antibiotic producer microorganisms and active chemicals. This chapter describes isolation and screening methods of novel producers of antimicrobial compounds from decayed wood.
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Screening of Antibiotic Gene Clusters in Microorganisms Isolated from Wood. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2296:151-165. [PMID: 33977446 DOI: 10.1007/978-1-0716-1358-0_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The biosphere of Earth is made up of a variety of ecosystems governed by complex biological interactions, some of them mediated by microbial bioactive secondary metabolites. These metabolites such as antibiotics (e.g., polyketides and nonribosomal peptides) have been receiving increasing attention, due to their multiple pharmaceutical uses. Besides, antibiotic resistance is on the rise, and it is currently regarded as one of the greatest threats to global human health. The screening of novel antimicrobial polyketides and nonribosomal peptides in poorly studied ecosystems is an interesting alternative to address the problem of antibiotic resistance. This chapter updates a molecular method to identify antibiotics gene clusters and their subsequent production and activity validation. On the one hand, a PCR method based on degenerated primers for nonribosomal peptide synthases (NRPS) and the polyketide synthases (PKS) genes is used as an initial fast screening. On the other hand, a bioassay-based method is the protocol selected for the production confirmation and antibacterial effect estimation. These methods are applied to screen Actinobacteria and Penicillium species as main antibiotic producers isolated from wood.
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Yadav G, Meena M. Bioprospecting of endophytes in medicinal plants of Thar Desert: An attractive resource for biopharmaceuticals. ACTA ACUST UNITED AC 2021; 30:e00629. [PMID: 34136363 PMCID: PMC8182382 DOI: 10.1016/j.btre.2021.e00629] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 04/28/2021] [Accepted: 05/09/2021] [Indexed: 12/20/2022]
Abstract
Endophytes act as chemical synthesizers of the secondary metabolites of the host plant. Endophytic microflora has been isolated from a wide array of plants. It can serve as a good alternative source for pharmaceutically important compounds. The arid ecosystem of Thar Desert is a rich repository of ethnomedicinal plants. Role of endophytes in the synthesis of bioactive molecules used to enhance production.
Endophytes live asymptomatically within the healthy tissues of plant parts of the host, has grabbed the attention of ecologists, chemists, and researchers to have a broad spectral of biotechnological potential. It has been proven that almost all plants harbor endophytes within themselves. Numerous studies indicated that endophytes act as chemical synthesizers of the secondary metabolites of their host plant. Various medicinal plants of the Thar Desert have been used by the local folks of the Rajasthan to treat several diseases ailments for time immemorial. On the basis of their prior knowledge of ethnopharmacological usage of medicinally important plants of Thar Desert, several researchers directed their studies in search of endophytic microflora of such medicinally important plants for the discovery of novel bioactive molecules of pharmaceutical importance, for instance, taxol producing endophytic fungus Phoma sp. isolated from Calotropis gigantea as well as Aspergillus fumigatus, an endophytic fungus reported from Moringa oleifera demonstrated an effective antibiofilm, antimicrobial and antiproliferative activity. This review sheds light on the endophytic microflora of the ethnomedicinal plants of the Thar Desert and their biopotential as a promising source of pharmaceutically important naturally derived compounds.
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Affiliation(s)
- Garima Yadav
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India
| | - Mukesh Meena
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India
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Bacterial Endophytes of Spring Wheat Grains and the Potential to Acquire Fe, Cu, and Zn under Their Low Soil Bioavailability. BIOLOGY 2021; 10:biology10050409. [PMID: 34063099 PMCID: PMC8148187 DOI: 10.3390/biology10050409] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/27/2021] [Accepted: 05/01/2021] [Indexed: 11/30/2022]
Abstract
Simple Summary Unmasking the overall endophytic bacteria communities from wheat grains may help to identify and describe the microbial colonization of bread and emmer varieties, their link to the bioactive compounds produced, and their possible role in mineral nutrition. The possibility of using microorganisms to improve the microelemental composition of grain is an important food security concern, as approximately one-third of the human population experiences latent starvation caused by Fe (anemia), Zn, or Cu deficiency. Four wheat varieties from T. aestivum L. and T. turgidum subsp. dicoccum were grown in field conditions with low bioavailability of microelements in the soil. Varietal differences in the yield, yield characteristics, and the grain micronutrient concentrations were compared with the endophytic bacteria isolated from the grains. Twelve different bacterial isolates were obtained that represented the genera Staphylococcus, Pantoea, Sphingobium, Bacillus, Kosakonia, and Micrococcus. All studied strains were able to synthesize indole-related compounds (IRCs) with phytohormonal activity. IRCs produced by the bacterial genera Pantoea spp. and Bacillus spp. isolated from high-yielding Oksamyt myronivs’kyi and Holikovs’ka grains may be considered as one of the determinants of the yield of wheat and its nutritional characteristics. Abstract Wheat grains are usually low in essential micronutrients. In resolving the problem of grain micronutritional quality, microbe-based technologies, including bacterial endophytes, seem to be promising. Thus, we aimed to (1) isolate and identify grain endophytic bacteria from selected spring wheat varieties (bread Oksamyt myronivs’kyi, Struna myronivs’ka, Dubravka, and emmer Holikovs’ka), which were all grown in field conditions with low bioavailability of microelements, and (2) evaluate the relationship between endophytes’ abilities to synthesize auxins and the concentration of Fe, Zn, and Cu in grains. The calculated biological accumulation factor (BAF) allowed for comparing the varietal ability to uptake and transport micronutrients to the grains. For the first time, bacterial endophytes were isolated from grains of emmer wheat T. turgidum subsp. dicoccum. Generally, the 12 different isolates identified in the four varieties belonged to the genera Staphylococcus, Pantoea, Sphingobium, Bacillus, Kosakonia, and Micrococcus (NCBI accession numbers: MT302194—MT302204, MT312840). All the studied strains were able to synthesize the indole-related compounds (IRCs; max: 16.57 µg∙mL−1) detected using the Salkowski reagent. The IRCs produced by the bacterial genera Pantoea spp. and Bacillus spp. isolated from high-yielding Oksamyt myronivs’kyi and Holikovs’ka grains may be considered as one of the determinants of the yield of wheat and its nutritional characteristics.
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Root-Associated Endophytic Bacterial Community Composition of Asparagus officinalis of Three Different Varieties. Indian J Microbiol 2021; 61:160-169. [PMID: 33927457 DOI: 10.1007/s12088-021-00926-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 02/11/2021] [Indexed: 10/21/2022] Open
Abstract
Asparagus (Asparagus officinalis L) is an economically important crop, rich in nutrients, and is also conducive to solving ecological and environmental problems. Plants may acquire benefits from root-associated endophytic bacteria. However, the composition of the endophytic bacterial community associated with the roots of asparagus is poorly elucidated. In this study, the nine root samples of asparagus from three different varieties including Asparagus officinalis var. Grande (GLD), A. officinalis var. Jinglvlu3 (JL3) and A. officinalis var. Jingzilu2 (JZL) were investigated by high-throughput sequencing technology of the 16S rDNA V5-V7 hypervariable region of endophytic bacteria. A total of 16 phyla, 29 classes, 90 orders, 171 families, and 312 genera were identified. Endophytic bacteria diversity and bacteria structure was different among the three varieties and was influenced by rhizosphere soil properties and varieties. In the GLD variety, the main phyla were Proteobacteria, Actinobacteria, and Firmicutes. The main phylum in JL3 and JZL varieties was Proteobacteria. The observations showed that GLD had the highest diversity of endophytes as indicated by the Shannon index (GLD > JZL > JL3). The order of the endophytes richness was GLD > JL3 > JZL. The PCA and PCoA analysis revealed the microbial communities were different between three different asparagus varieties, and the microbial composition of GLD and JZL was more similar. This report provides an important reference for the study of endophytic microorganisms of asparagus. Supplementary information The online version contains supplementary material available at (10.1007/s12088-021-00926-6) contains supplementary material, which is available to authorized users.
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Ramírez-Durán N, de la Haba RR, Vera-Gargallo B, Sánchez-Porro C, Alonso-Carmona S, Sandoval-Trujillo H, Ventosa A. Taxogenomic and Comparative Genomic Analysis of the Genus Saccharomonospora Focused on the Identification of Biosynthetic Clusters PKS and NRPS. Front Microbiol 2021; 12:603791. [PMID: 33776952 PMCID: PMC7990883 DOI: 10.3389/fmicb.2021.603791] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 02/17/2021] [Indexed: 11/13/2022] Open
Abstract
Actinobacteria are prokaryotes with a large biotechnological interest due to their ability to produce secondary metabolites, produced by two main biosynthetic gene clusters (BGCs): polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS). Most studies on bioactive products have been carried out on actinobacteria isolated from soil, freshwater or marine habitats, while very few have been focused on halophilic actinobacteria isolated from extreme environments. In this study we have carried out a comparative genomic analysis of the actinobacterial genus Saccharomonospora, which includes species isolated from soils, lake sediments, marine or hypersaline habitats. A total of 19 genome sequences of members of Saccharomonospora were retrieved and analyzed. We compared the 16S rRNA gene-based phylogeny of this genus with evolutionary relationships inferred using a phylogenomic approach obtaining almost identical topologies between both strategies. This method allowed us to unequivocally assign strains into species and to identify some taxonomic relationships that need to be revised. Our study supports a recent speciation event occurring between Saccharomonospora halophila and Saccharomonospora iraqiensis. Concerning the identification of BGCs, a total of 18 different types of BGCs were detected in the analyzed genomes of Saccharomonospora, including PKS, NRPS and hybrid clusters which might be able to synthetize 40 different putative products. In comparison to other genera of the Actinobacteria, members of the genus Saccharomonospora showed a high degree of novelty and diversity of BGCs.
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Affiliation(s)
- Ninfa Ramírez-Durán
- Faculty of Medicine, Autonomous University of the State of Mexico, Toluca, Mexico.,Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Seville, Spain
| | - Rafael R de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Seville, Spain
| | - Blanca Vera-Gargallo
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Seville, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Seville, Spain
| | | | - Horacio Sandoval-Trujillo
- Department of Biological Systems, Metropolitan Autonomous University-Xochimilco, Mexico City, Mexico
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Seville, Spain
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Singh S, Ghadge VA, Kumar P, Mathew DE, Dhimmar A, Sahastrabudhe H, Nalli Y, Rathod MR, Shinde PB. Biodiversity and antimicrobial potential of bacterial endophytes from halophyte Salicornia brachiata. Antonie Van Leeuwenhoek 2021; 114:591-608. [PMID: 33674993 DOI: 10.1007/s10482-021-01544-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/13/2021] [Indexed: 12/01/2022]
Abstract
Extreme natural habitats like halophytes, marsh land, and marine environment are suitable arena for chemical ecology between plants and microbes having environmental impact. Endophytes are an ecofriendly option for the promotion of plant growth and to serve as sustainable resource of novel bioactive natural products. The present study, focusing on biodiversity of bacterial endophytes from Salicornia brachiata, led to isolation of around 336 bacterial endophytes. Phylogenetic analysis of 63 endophytes revealed 13 genera with 27 different species, belonging to 3 major groups: Firmicutes, Proteobacteria, and Actinobacteria. 30% endophytic isolates belonging to various genera demonstrated broad-spectrum antibacterial and antifungal activities against a panel of human, plant, and aquatic infectious agents. An endophytic isolate Bacillus amyloliquefaciens 5NPA-1, exhibited strong in-vitro antibacterial activity against human pathogen Staphylococcus aureus and phytopathogen Xanthomonas campestris. Investigation through LC-MS/MS-based molecular networking and bioactivity-guided purification led to the identification of three bioactive compounds belonging to lipopeptide class based on 1H-, 13C-NMR and MS analysis. To our knowledge, this is the first report studying bacterial endophytic biodiversity of Salicornia brachiata and the isolation of bioactive compounds from its endophyte. Overall, the present study provides insights into the diversity of endophytes associated with the plants from the extreme environment as a rich source of metabolites with remarkable agricultural applications and therapeutic properties.
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Affiliation(s)
- Sanju Singh
- Natural Products and Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar, Gujarat, 364002, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vishal A Ghadge
- Natural Products and Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar, Gujarat, 364002, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Pankaj Kumar
- Natural Products and Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar, Gujarat, 364002, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Doniya Elze Mathew
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.,Applied Phycology and Biotechnology Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar, Gujarat, 364002, India
| | - Asmita Dhimmar
- Natural Products and Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar, Gujarat, 364002, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Harshal Sahastrabudhe
- Natural Products and Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar, Gujarat, 364002, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Yedukondalu Nalli
- Natural Products and Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar, Gujarat, 364002, India
| | - Mina R Rathod
- Natural Products and Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar, Gujarat, 364002, India
| | - Pramod B Shinde
- Natural Products and Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar, Gujarat, 364002, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Webster G, Mullins AJ, Cunningham-Oakes E, Renganathan A, Aswathanarayan JB, Mahenthiralingam E, Vittal RR. Culturable diversity of bacterial endophytes associated with medicinal plants of the Western Ghats, India. FEMS Microbiol Ecol 2021; 96:5876344. [PMID: 32710748 PMCID: PMC7422900 DOI: 10.1093/femsec/fiaa147] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/23/2020] [Indexed: 12/15/2022] Open
Abstract
Bacterial endophytes are found in the internal tissues of plants and have intimate associations with their host. However, little is known about the diversity of medicinal plant endophytes (ME) or their capability to produce specialised metabolites that may contribute to therapeutic properties. We isolated 75 bacterial ME from 24 plant species of the Western Ghats, India. Molecular identification by 16S rRNA gene sequencing grouped MEs into 13 bacterial genera, with members of Gammaproteobacteria and Firmicutes being the most abundant. To improve taxonomic identification, 26 selected MEs were genome sequenced and average nucleotide identity (ANI) used to identify them to the species-level. This identified multiple species in the most common genus as Bacillus. Similarly, identity of the Enterobacterales was also distinguished within Enterobacter and Serratia by ANI and core-gene analysis. AntiSMASH identified non-ribosomal peptide synthase, lantipeptide and bacteriocin biosynthetic gene clusters (BGC) as the most common BGCs found in the ME genomes. A total of five of the ME isolates belonging to Bacillus, Serratia and Enterobacter showed antimicrobial activity against the plant pathogen Pectobacterium carotovorum. Using molecular and genomic approaches we have characterised a unique collection of endophytic bacteria from medicinal plants. Their genomes encode multiple specialised metabolite gene clusters and the collection can now be screened for novel bioactive and medicinal metabolites.
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Affiliation(s)
- Gordon Webster
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, Wales, UK
| | - Alex J Mullins
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, Wales, UK
| | - Edward Cunningham-Oakes
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, Wales, UK
| | - Arun Renganathan
- Department of Studies in Microbiology, University of Mysore, Karnataka, 570006, Mysore, India
| | | | - Eshwar Mahenthiralingam
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, Wales, UK
| | - Ravishankar Rai Vittal
- Department of Studies in Microbiology, University of Mysore, Karnataka, 570006, Mysore, India
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Antimicrobial activity of Actinobacteria isolated from dry land soil in Yazd, Iran. Mol Biol Rep 2021; 48:1717-1723. [PMID: 33599952 DOI: 10.1007/s11033-021-06218-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/06/2021] [Indexed: 10/22/2022]
Abstract
Historically, many important secondary metabolites including antibiotics used in clinic are purified from the cultural broths of Actinobacteria, which were inhabited in soil. Yazd is located in the center of Iran, the south of the Dasht-e Kavir and the west of the Dasht-e Lut; accordingly it has a hot, dry climate with long summers. In the present study, 18 strains of Actinobacteria isolated from 60 soil samples from Yazd-Iran. Pure isolates were screened for antibacterial activity against the ATCC strains by using two methods: single line streak method and spot inoculation method. ATCC strains include four antibiotic resistant ATCC strains (Enterococcus faecalis, Staphylococcus aureus, Klebsiella pneumoniae and, Acinetobacter baumannii) and three antibiotic sensitive strains (Pseudomonas aeruginosa, Staphylococcus aureus, Escherichia coli) and, Bacillus subtilis. Seven isolates exhibited antimicrobial activity against the ATCC strains (38.8%). Identification of type I and type II polyketide synthases (pksI, pksII) and nonribosomal peptide synthetase (NRPS) genes were done for these 7 isolates and all of 7 strains, possessed at least one of these genes. The results of this study confirm that soil Actinobacteria bear a great ability to produce antibacterial compounds against resistant and sensitive test organisms.
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Adegboye MF, Ojuederie OB, Talia PM, Babalola OO. Bioprospecting of microbial strains for biofuel production: metabolic engineering, applications, and challenges. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:5. [PMID: 33407786 PMCID: PMC7788794 DOI: 10.1186/s13068-020-01853-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 12/09/2020] [Indexed: 05/17/2023]
Abstract
The issues of global warming, coupled with fossil fuel depletion, have undoubtedly led to renewed interest in other sources of commercial fuels. The search for renewable fuels has motivated research into the biological degradation of lignocellulosic biomass feedstock to produce biofuels such as bioethanol, biodiesel, and biohydrogen. The model strain for biofuel production needs the capability to utilize a high amount of substrate, transportation of sugar through fast and deregulated pathways, ability to tolerate inhibitory compounds and end products, and increased metabolic fluxes to produce an improved fermentation product. Engineering microbes might be a great approach to produce biofuel from lignocellulosic biomass by exploiting metabolic pathways economically. Metabolic engineering is an advanced technology for the construction of highly effective microbial cell factories and a key component for the next-generation bioeconomy. It has been extensively used to redirect the biosynthetic pathway to produce desired products in several native or engineered hosts. A wide range of novel compounds has been manufactured through engineering metabolic pathways or endogenous metabolism optimizations by metabolic engineers. This review is focused on the potential utilization of engineered strains to produce biofuel and gives prospects for improvement in metabolic engineering for new strain development using advanced technologies.
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Affiliation(s)
- Mobolaji Felicia Adegboye
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, Private Bag X2046, 2735, South Africa
| | - Omena Bernard Ojuederie
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, Private Bag X2046, 2735, South Africa
- Department of Biological Sciences, Faculty of Science, Kings University, Ode-Omu, PMB 555, Osun State, Nigeria
| | - Paola M Talia
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA CICVyA, CNIA, INTA Castelar, Dr. N. Repetto y Los Reseros s/n, (1686) Hurlingham, 1686) Hurlingham, Provincia de Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas Y Tecnológicas (CONICET), Buenos Aires, Provincia de Buenos Aires, Argentina
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, Private Bag X2046, 2735, South Africa.
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Therapeutic applications and biological activities of bacterial bioactive extracts. Arch Microbiol 2021; 203:4755-4776. [PMID: 34370077 PMCID: PMC8349711 DOI: 10.1007/s00203-021-02505-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/24/2021] [Accepted: 07/27/2021] [Indexed: 02/07/2023]
Abstract
Bacteria are rich in a wide variety of secondary metabolites, such as pigments, alkaloids, antibiotics, and others. These bioactive microbial products serve a great application in human and animal health. Their molecular diversity allows these natural products to possess several therapeutic attributes and biological functions. That's why the current natural drug industry focuses on uncovering all the possible ailments and diseases that could be combated by bacterial extracts and their secondary metabolites. In this paper, we review the major utilizations of bacterial natural products for the treatment of cancer, inflammatory diseases, allergies, autoimmune diseases, infections and other diseases that threaten public health. We also elaborate on the identified biological activities of bacterial secondary metabolites including antibacterial, antifungal, antiviral and antioxidant activities all of which are essential nowadays with the emergence of drug-resistant microbial pathogens. Throughout this review, we discuss the possible mechanisms of actions in which bacterial-derived biologically active molecular entities could possess healing properties to inspire the development of new therapeutic agents in academia and industry.
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Messaoudi O, Wink J, Bendahou M. Diversity of Actinobacteria Isolated from Date Palms Rhizosphere and Saline Environments: Isolation, Identification and Biological Activity Evaluation. Microorganisms 2020; 8:E1853. [PMID: 33255541 PMCID: PMC7760371 DOI: 10.3390/microorganisms8121853] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 01/20/2023] Open
Abstract
The diversity of cultural Actinobacteria in two types of Algerian Sahara environments, including saline environments and date palms rhizosphere, was investigated. In this study, a total of 40 strains of actinomycetes was isolated from different soil samples, using a rehydration and centrifugation method. Molecular identification, based on 16S rRNA gene sequence analysis, revealed that these isolates were affiliated to six clusters corresponding to eight genera, including Streptomyces, Nocardiopsis, Saccharopolyspora, Actinomadura, Actinocorallia, Micromonospora, Couchioplanes, and Planomonospora. A taxonomic analysis, based on the morphological, physiological, biochemical, and molecular investigation, of selected strains, which belong to the rare Actinobacteria, was undertaken. Four strains (CG3, A111, A93, and A79) were found to form distinct phyletic lines and represent new actinobacterial taxa. An assessment of antimicrobial proprieties of the 40 obtained actinomycetes strains, showed moderate to strong antimicrobial activities against fungi and bacteria. This study demonstrated the richness of Algerian Sahara with rare Actinobacteria, which can provide novel bioactive metabolites, to solving some of the most challenging problems of the day, such as multi-drug resistance.
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Affiliation(s)
- Omar Messaoudi
- Laboratory of Applied Microbiology in Food, Biomedical and Environment, Abou Bekr Belkaïd University, 13000 Tlemcen, Algeria;
- Department of Biology, Faculty of Science, University of Amar Telidji, 03000 Laghouat, Algeria
- Microbial Strain Collection, Helmholtz Centre for Infection Research GmbH (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany;
| | - Joachim Wink
- Microbial Strain Collection, Helmholtz Centre for Infection Research GmbH (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany;
| | - Mourad Bendahou
- Laboratory of Applied Microbiology in Food, Biomedical and Environment, Abou Bekr Belkaïd University, 13000 Tlemcen, Algeria;
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Ayswaria R, Vasu V, Krishna R. Diverse endophytic Streptomyces species with dynamic metabolites and their meritorious applications: a critical review. Crit Rev Microbiol 2020; 46:750-758. [PMID: 33044894 DOI: 10.1080/1040841x.2020.1828816] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The strains of actinobacteria are unique as they lie between true fungi and bacteria and several of them were reported as endophytic actinobacteria as they were isolated from the inner regions of various plant parts and will enhance uptake of nutrients and improve defense against pathogens. Literature and scientific communications reported the relationship between the endophytes and plants, most of them concluded the association as commensalism. Remarkably, bioactive compounds from endophytic Streptomyces sp. were confirmed with various applications. A retrospective consolidation on the endophytic Streptomyces sp. and their metabolite application in day to day life is presented here. It was deduced that this group of the organism are a source for a wide range of bioactive compounds including anticancer agents, immune suppressor, plant growth promoters, anti-inflammatory agents, anti-tumor agents, enzymes and antimicrobial substances. These antimicrobial metabolites show broad-spectrum activity and are effective against bacteria and fungi. The mechanism of action of secondary metabolites from endophytes and its positive influence on the host plants are noted as involvement in deterrence, antifeedant activity, toxicity against common pests, and as enhancers for physical mechanisms such as water uptake and sunlight absorption, thus supporting the growth of host plants.
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Affiliation(s)
- Reshma Ayswaria
- Microboilte Research Development Private Limited, Manipal-Gok Bioincubator, MAHE Advanced Research Center, Manipal, Karnataka, India
| | - Vineeth Vasu
- Microboilte Research Development Private Limited, Manipal-Gok Bioincubator, MAHE Advanced Research Center, Manipal, Karnataka, India
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In Vivo Studies of Inoculated Plants and In Vitro Studies Utilizing Methanolic Extracts of Endophytic Streptomyces sp. Strain DBT34 Obtained from Mirabilis jalapa L. Exhibit ROS-Scavenging and Other Bioactive Properties. Int J Mol Sci 2020; 21:ijms21197364. [PMID: 33036127 PMCID: PMC7582327 DOI: 10.3390/ijms21197364] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/16/2020] [Accepted: 09/21/2020] [Indexed: 02/06/2023] Open
Abstract
Reactive oxygen species (ROS) and other free radicals cause oxidative damage in cells under biotic and abiotic stress. Endophytic microorganisms reside in the internal tissues of plants and contribute to the mitigation of such stresses by the production of antioxidant enzymes and compounds. We hypothesized that the endophytic actinobacterium Streptomyces sp. strain DBT34, which was previously demonstrated to have plant growth-promoting (PGP) and antimicrobial properties, may also have a role in protecting plants against several stresses through the production of antioxidants. The present study was designed to characterize catalase and superoxide dismutase (SOD), two enzymes involved in the detoxification of ROS, in methanolic extracts derived from six endophytic actinobacterial isolates obtained from the traditional medicinal plant Mirabilis jalapa. The results of a preliminary screen indicated that Streptomyces sp. strain DBT34 was the best overall strain and was therefore used in subsequent detailed analyses. A methanolic extract of DBT34 exhibited significant antioxidant potential in 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2,2'-azino-bis-3-ethylbenzthiazoline-6-sulphonic acid (ABTS) assays. The cytotoxicity of DBT34 against liver hepatocellular cells (HepG2) was also determined. Results indicated that methanolic extract of Streptomyces sp. strain DBT34 exhibited significant catalase and SOD-like activity with 158.21 U resulting in a 55.15% reduction in ROS. The IC50 values of a crude methanolic extract of strain DBT34 on DPPH radical scavenging and ABTS radical cation decolorization were 41.5 µg/mL and 47.8 µg/mL, respectively. Volatile compounds (VOC) were also detected in the methanolic extract of Streptomyces sp. strain DBT34 using GC-MS analysis to correlate their presence with bioactive potential. Treatments of rats with DBT34 extract and sitagliptin resulted in a significant (p ≤ 0.001) reduction in total cholesterol, LDL-cholesterol, and VLDL-cholesterol, relative to the vehicle control and a standard diabetic medicine. The pancreatic histoarchitecture of vehicle control rats exhibited a compact volume of isolated clusters of Langerhans cells surrounded by acinies with proper vaculation. An in-vivo study of Streptomyces sp. strain DBT34 on chickpea seedlings revealed an enhancement in its antioxidant potential as denoted by lower IC50 values for DPPH and ABTS radical scavenging activity under greenhouse conditions in relative comparison to control plants. Results of the study indicate that strain DBT34 provides a defense mechanism to its host through the production of antioxidant therapeutic agents that mitigate ROS in hosts subjected to biotic and abiotic stresses.
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Qiao YJ, Gu CZ, Zhu HT, Wang D, Zhang MY, Zhang YX, Yang CR, Zhang YJ. Allelochemicals of Panax notoginseng and their effects on various plants and rhizosphere microorganisms. PLANT DIVERSITY 2020; 42:323-333. [PMID: 33134615 PMCID: PMC7584786 DOI: 10.1016/j.pld.2020.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 04/17/2020] [Accepted: 04/17/2020] [Indexed: 06/11/2023]
Abstract
Panax notoginseng (Araliaceae) is an important ginseng herb with various health benefits and a history of cultivation in southwestern China over 400 years. In recent years P. notoginseng has faced serious continuous-cropping obstacles due to its large-scale cultivation. In this study, we aim to explore the allelochemicals of P. notoginseng and their interactions with various plants and rhizosphere microorganisms. The chemical constituents of the soil cultivated with 3-year-old P. notoginseng were studied by column chromatography, spectroscopic and GC-MS analyses. We identified 13 volatile components and isolated six triterpenes (1-4, 6-7) and one anthraquinone (5). Compounds 1-7 were tested for their effects on seed germination and root elongation in P. notoginseng, corn, wheat, turnip, water spinach and Arabidopsis thaliana. We also examined the effect of compounds 1-7 on the growth of ten rhizosphere microorganisms of P. notoginseng. At a concentration of 1.0 μg mL-1, compounds 3 and 5-7 caused the death of P. notoginseng root cells and compounds 2, 6 and 7 induced the death of root cells of A. thaliana. Compounds 1-5 and 7 inhibited elongation of A. thaliana root tip cells at a concentration of 10.0 μg mL-1. Moreover, at a concentration of 0.1 mg mL-1, compounds 3, 4, 6 and 7 inhibited the growth of probiotics and promoted the growth of pathogens of P. notoginseng. These results suggest that these isolated ursane-type triterpenoid acids and anthraquinone are potential allelochemicals that contribute to continuous-cropping obstacles of P. notoginseng.
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Affiliation(s)
- Yi-Jun Qiao
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cheng-Zhen Gu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China
- Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hong-Tao Zhu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China
| | - Dong Wang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China
| | - Meng-Yue Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Yi-Xuan Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Chong-Ren Yang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China
| | - Ying-Jun Zhang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China
- Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
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Kusstatscher P, Wicaksono WA, Bergna A, Cernava T, Bergau N, Tissier A, Hause B, Berg G. Trichomes form genotype-specific microbial hotspots in the phyllosphere of tomato. ENVIRONMENTAL MICROBIOME 2020; 15:17. [PMID: 33902724 PMCID: PMC8067393 DOI: 10.1186/s40793-020-00364-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 08/29/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND The plant phyllosphere is a well-studied habitat characterized by low nutrient availability and high community dynamics. In contrast, plant trichomes, known for their production of a large number of metabolites, are a yet unexplored habitat for microbes. We analyzed the phyllosphere as well as trichomes of two tomato genotypes (Solanum lycopersicum LA4024, S. habrochaites LA1777) by targeting bacterial 16S rRNA gene fragments. RESULTS Leaves, leaves without trichomes, and trichomes alone harbored similar abundances of bacteria (108-109 16S rRNA gene copy numbers per gram of sample). In contrast, bacterial diversity was found significantly increased in trichome samples (Shannon index: 4.4 vs. 2.5). Moreover, the community composition was significantly different when assessed with beta diversity analysis and corresponding statistical tests. At the bacterial class level, Alphaproteobacteria (23.6%) were significantly increased, whereas Bacilli (8.6%) were decreased in trichomes. The bacterial family Sphingomonadacea (8.4%) was identified as the most prominent, trichome-specific feature; Burkholderiaceae and Actinobacteriaceae showed similar patterns. Moreover, Sphingomonas was identified as a central element in the core microbiome of trichome samples, while distinct low-abundant bacterial families including Hymenobacteraceae and Alicyclobacillaceae were exclusively found in trichome samples. Niche preferences were statistically significant for both genotypes and genotype-specific enrichments were further observed. CONCLUSION Our results provide first evidence of a highly specific trichome microbiome in tomato and show the importance of micro-niches for the structure of bacterial communities on leaves. These findings provide further clues for breeding, plant pathology and protection as well as so far unexplored natural pathogen defense strategies.
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Affiliation(s)
- Peter Kusstatscher
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Alessandro Bergna
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Graz, Austria
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Nick Bergau
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Alain Tissier
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Bettina Hause
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
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Romano I, Ventorino V, Ambrosino P, Testa A, Chouyia FE, Pepe O. Development and Application of Low-Cost and Eco-Sustainable Bio-Stimulant Containing a New Plant Growth-Promoting Strain Kosakonia pseudosacchari TL13. Front Microbiol 2020; 11:2044. [PMID: 33013749 PMCID: PMC7461993 DOI: 10.3389/fmicb.2020.02044] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 08/03/2020] [Indexed: 01/26/2023] Open
Abstract
The use of beneficial microbes as inoculants able to improve fitness, growth and health of plants also in stress conditions is an attractive low-cost and eco-friendly alternative strategy to harmful chemical inputs. Thirteen potential plant growth-promoting bacteria were isolated from the rhizosphere of wheat plants cultivated under drought stress and nitrogen deficiency. Among these, the two isolates TL8 and TL13 showed multiple plant growth promotion activities as production of indole-3-acetic acid (IAA), siderophores, ammonia, and 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase production, the ability to solubilize phosphate as well as exerted antimicrobial activity against plant pathogens as Botrytis spp. and Phytophthora spp. The two selected strains were identified as Kosakonia pseudosacchari by sequencing of 16S rRNA gene. They resulted also tolerant to abiotic stress and were able to efficiently colonize plant roots as observed in vitro assay under fluorescence microscope. Based on the best PGP properties, the strain K. pseudosacchari TL13 was selected to develop a new microbial based formulate. A sustainable and environmentally friendly process for inoculant production was developed using agro-industrial by-products for microbial growth. Moreover, the application of K. pseudosacchari TL13- based formulates in pot experiment improved growth performance of maize plants.
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Affiliation(s)
- Ida Romano
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
| | - Valeria Ventorino
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
| | - Patrizia Ambrosino
- Agriges S.r.l. - Nutrizione Speciale per L'Agricoltura Biologica e Integrata, San Salvatore Telesino, Italy
| | - Antonino Testa
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
| | - Fatima Ezzahra Chouyia
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy.,Department of Biology, Faculty of Sciences and Techniques, Hassan II University of Casablanca, Casablanca, Morocco
| | - Olimpia Pepe
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
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