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Ghezzi D, Salvi L, Costantini PE, Firrincieli A, Iorio M, Lopo E, Sosio M, Elbanna AH, Khalil ZG, Capon RJ, De Waele J, Vergara F, Sauro F, Cappelletti M. Ancient and remote quartzite caves as a novel source of culturable microbes with biotechnological potential. Microbiol Res 2024; 286:127793. [PMID: 38901277 DOI: 10.1016/j.micres.2024.127793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/23/2024] [Accepted: 05/29/2024] [Indexed: 06/22/2024]
Abstract
Quartzite caves located on table-top mountains (tepuis) in the Guyana Shield, are ancient, remote, and pristine subterranean environments where microbes have evolved peculiar metabolic strategies to thrive in silica-rich, slightly acidic and oligotrophic conditions. In this study, we explored the culturable fraction of the microbiota inhabiting the (ortho)quartzite cave systems in Venezuelan tepui (remote table-top mountains) and we investigated their metabolic and enzymatic activities in relation with silica solubilization and extracellular hydrolytic activities as well as the capacity to produce antimicrobial compounds. Eighty microbial strains were isolated with a range of different enzymatic capabilities. More than half of the isolated strains performed at least three enzymatic activities and four bacterial strains displayed antimicrobial activities. The antimicrobial producers Paraburkholderia bryophila CMB_CA002 and Sphingomonas sp. MEM_CA187, were further analyzed by conducting chemotaxonomy, phylogenomics, and phenomics. While the isolate MEM_CA187 represents a novel species of the genus Sphingomonas, for which the name Sphingomonas imawarii sp. nov. is proposed, P. bryophila CMB_CA002 is affiliated with a few strains of the same species that are antimicrobial producers. Chemical analyses demonstrated that CMB_CA002 produces ditropolonyl sulfide that has a broad range of activity and a possibly novel siderophore. Although the antimicrobial compounds produced by MEM_CA187 could not be identified through HPLC-MS analysis due to the absence of reference compounds, it represents the first soil-associated Sphingomonas strain with the capacity to produce antimicrobials. This work provides first insights into the metabolic potential present in quartzite cave systems pointing out that these environments are a novel and still understudied source of microbial strains with biotechnological potential.
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Affiliation(s)
- Daniele Ghezzi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Luca Salvi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Paolo E Costantini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Andrea Firrincieli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy; Department for Innovation in Biological, Agro-Food and Forest systems, University of Tuscia, Viterbo 01100, Italy
| | | | - Ettore Lopo
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | | | - Ahmed H Elbanna
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; Department of Pharmacognosy, Cairo University, Cairo 11562, Egypt
| | - Zeinab G Khalil
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Robert J Capon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jo De Waele
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna 40126, Italy; La Venta Geographic Explorations Association, Treviso 31100, Italy
| | - Freddy Vergara
- La Venta Geographic Explorations Association, Treviso 31100, Italy; Teraphosa Exploring Team, Puerto Ordaz, Venezuela
| | - Francesco Sauro
- La Venta Geographic Explorations Association, Treviso 31100, Italy
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy; La Venta Geographic Explorations Association, Treviso 31100, Italy.
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Jagadeesan Y, Meenakshisundaram S, Pichaimuthu S, Balaiah A. A scientific version of understanding "Why did the chickens cross the road"? - A guided journey through Bacillus spp. towards sustainable agriculture, circular economy and biofortification. ENVIRONMENTAL RESEARCH 2024; 244:117907. [PMID: 38109965 DOI: 10.1016/j.envres.2023.117907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 12/20/2023]
Abstract
The world, a famished planet with an overgrowing population, requires enormous food crops. This scenario compelled the farmers to use a high quantity of synthetic fertilizers for high food crop productivity. However, prolonged usage of chemical fertilizers results in severe adverse effects on soil and water quality. On the other hand, the growing population significantly consumes large quantities of poultry meats. Eventually, this produces a mammoth amount of poultry waste, chicken feathers. Owing to the protein value of the chicken feathers, these wastes are converted into protein hydrolysate and further extend their application as biostimulants for sustained agriculture. The protein profile of chicken feather protein hydrolysate (CFPH) produced through Bacillus spp. was the maximum compared to physical and chemical protein extraction methods. Several studies proved that the application of CFPH and active Bacillus spp. culture to soil and plants results in enhanced plant growth, phytochemical constituents, crop yield, soil nutrients, fertility, microbiome and resistance against diverse abiotic and biotic stresses. Overall, "CFPH - Jack of all trades" and "Bacillus spp. - an active camouflage to the surroundings where they applied showed profound and significant benefits to the plant growth under the most adverse conditions. In addition, Bacillus spp. coheres the biofortification process in plants through the breakdown of metals into metal ions that eventually increase the nutrient value of the food crops. However, detailed information on them is missing. This can be overcome by further real-world studies on rhizoengineering through a multi-omics approach and their interaction with plants. This review has explored the best possible and efficient strategy for managing chicken feather wastes into protein-rich CFPH through Bacillus spp. bioconversion and utilizing the CFPH and Bacillus spp. as biostimulants, biofertilizers, biopesticides and biofortificants. This paper is an excellent report on organic waste management, circular economy and sustainable agriculture research frontier.
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Affiliation(s)
- Yogeswaran Jagadeesan
- Department of Biotechnology, University College of Engineering, Anna University - BIT Campus, Tiruchirappalli, Tamilnadu, 620 024, India.
| | - Shanmugapriya Meenakshisundaram
- Department of Biotechnology, University College of Engineering, Anna University - BIT Campus, Tiruchirappalli, Tamilnadu, 620 024, India.
| | - Suthakaran Pichaimuthu
- Genprotic Biopharma Private Limited, SPIC Bioprocess Laboratory, Anna University, Taramani Campus, Taramani, Chennai, Tamilnadu, 600113, India.
| | - Anandaraj Balaiah
- Department of Biotechnology, University College of Engineering, Anna University - BIT Campus, Tiruchirappalli, Tamilnadu, 620 024, India.
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Maghrawy HH, El Kareem HA, Gomaa OM. Enhanced exopolysaccharide production in gamma irradiated Bacillus subtilis: A biofilm-mediated strategy for ZnO nanoparticles removal. Int J Biol Macromol 2024; 258:128884. [PMID: 38141708 DOI: 10.1016/j.ijbiomac.2023.128884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 12/05/2023] [Accepted: 12/17/2023] [Indexed: 12/25/2023]
Abstract
Biofilm-mediated strategy was studied for ZnO nanoparticle removal from aqueous media. Bacillus subtilis isolated from the soil rhizosphere was selected based on its high viscosity (133 Pa/s) of the cultivated culture and biofilm formation. The bacterium was exposed to gamma-irradiation to enhance EPS production along with its cultivation in EPS-producing media. The results show an increase in viscosity that reached 160 Pa/s at 2 kGy. EPS production increased from 4.45 to 7.95 mg/mL and the protein/carbohydrate ratio increased from 3 to 4.4 which reflects the stickiness of EPS. Thermal Gravimetric Analysis (TGA) showed 2 phase weight loss for gamma irradiated EPS and defined protein peaks when characterized using Matrix Assisted Laser Desorption Ionization-Time of Flight (MALDI-TOF). Native and gamma-irradiated Bacillus subtilis cells with their enhanced EPS were grown as a biofilm on sterile waste gauze fabric, Scanning Electron Microscopy (SEM) showed an increased biofilm attachment in gamma-irradiated samples. The latter was used for the removal of ZnO NP from aqueous media. Energy dispersive X-ray (EDX) mapping confirms that ZnO NPs were entrapped within the carbon and oxygen elements forming the biofilm with net intensities of 14.04, 1713, and 1190, respectively. The results confirm that biofilm-mediated strategy is effective in nanoparticles removal.
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Affiliation(s)
- Heba Hamed Maghrawy
- Radiation Microbiology Department, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), Cairo, Egypt
| | - Hussein Abd El Kareem
- Radiation Microbiology Department, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), Cairo, Egypt
| | - Ola M Gomaa
- Radiation Microbiology Department, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), Cairo, Egypt.
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Mahlangu SG, Zulu N, Serepa-Dlamini MH, Tai SL. Isolation, identification, and biological characterization of bacterial endophytes isolated from Gunnera perpensa L. FEMS Microbiol Lett 2024; 371:fnae056. [PMID: 39039013 PMCID: PMC11321073 DOI: 10.1093/femsle/fnae056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 05/23/2024] [Accepted: 07/18/2024] [Indexed: 07/24/2024] Open
Abstract
In the present study, eleven endophytic bacterial strains, Herbaspirillum sp. (GP-SGM1, GP-SGM2, GP-SGM3, and GP-SGM11), Pseudomonas sp. (GP-SGM4, GP-SGM5), Novosphingobium sp. GP-SGM6, Chryseobacterium sp. GP-SGM7, Labedella sp. GP-SGM8, Brevibacterium sp. GP-SGM9, and Pseudomonas sp. GP-SGM10, were isolated from the rhizomes of Gunnera perpensa L. The growth kinetics, assessed through maximum growth rates (μmax) and optical density (OD) values, revealed that GP-SGM7 exhibited highest μmax values of 0.33 ± 0.01 hours (h)-1 with an OD of 4.20 ± 0.04. In contrast, GP-SGM11 exhibited the lowest μmax of 0.12 ± 0.05 h-1 and the smallest OD of 1.50 ± 0.00. In addition, the endophyte crude extracts were tested for antibacterial activity against five pathogenic strains using the disk diffusion method, with GP-SGM7 crude extracts exhibiting promising antibacterial activity against Klebsiella pneumoniae and Staphylococcus aureus. Antioxidant activity was determined by DPPH (2, 2-diphenyl-1-picrylhydrazyl) and FRAP (ferric reducing antioxidant power) assays. The crude extracts of GP-SGM1, GP-SGM7, GP-SGM9, and GP-SGM10 were the most effective at scavenging DPPH radicals, with GP-SGM7 also exhibiting a high FRAP value of 0.54 ± 0.01. These findings emphasize the therapeutic potential of endophytic bacteria from G. perpensa L. in addressing skin-related issues, including bacterial infections and free radicals.
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Affiliation(s)
- Siphiwe Godfrey Mahlangu
- Department of Chemical Engineering, Centre for Bioprocess Engineering Research, University of Cape Town, Private Bag X3, Rondebosch, Cape Town 7701, South Africa
| | - Nodumo Zulu
- Department of Chemical Engineering, Centre for Bioprocess Engineering Research, University of Cape Town, Private Bag X3, Rondebosch, Cape Town 7701, South Africa
| | - Mahloro Hope Serepa-Dlamini
- Department of Biotechnology and Food Technology, University of Johannesburg, Doornfontein Campus, PO Box 17011, Johannesburg 2028, South Africa
| | - Siew Leng Tai
- Department of Chemical Engineering, Centre for Bioprocess Engineering Research, University of Cape Town, Private Bag X3, Rondebosch, Cape Town 7701, South Africa
- Department of Chemical Engineering, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
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Anand U, Pal T, Yadav N, Singh VK, Tripathi V, Choudhary KK, Shukla AK, Sunita K, Kumar A, Bontempi E, Ma Y, Kolton M, Singh AK. Current Scenario and Future Prospects of Endophytic Microbes: Promising Candidates for Abiotic and Biotic Stress Management for Agricultural and Environmental Sustainability. MICROBIAL ECOLOGY 2023; 86:1455-1486. [PMID: 36917283 PMCID: PMC10497456 DOI: 10.1007/s00248-023-02190-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Globally, substantial research into endophytic microbes is being conducted to increase agricultural and environmental sustainability. Endophytic microbes such as bacteria, actinomycetes, and fungi inhabit ubiquitously within the tissues of all plant species without causing any harm or disease. Endophytes form symbiotic relationships with diverse plant species and can regulate numerous host functions, including resistance to abiotic and biotic stresses, growth and development, and stimulating immune systems. Moreover, plant endophytes play a dominant role in nutrient cycling, biodegradation, and bioremediation, and are widely used in many industries. Endophytes have a stronger predisposition for enhancing mineral and metal solubility by cells through the secretion of organic acids with low molecular weight and metal-specific ligands (such as siderophores) that alter soil pH and boost binding activity. Finally, endophytes synthesize various bioactive compounds with high competence that are promising candidates for new drugs, antibiotics, and medicines. Bioprospecting of endophytic novel secondary metabolites has given momentum to sustainable agriculture for combating environmental stresses. Biotechnological interventions with the aid of endophytes played a pivotal role in crop improvement to mitigate biotic and abiotic stress conditions like drought, salinity, xenobiotic compounds, and heavy metals. Identification of putative genes from endophytes conferring resistance and tolerance to crop diseases, apart from those involved in the accumulation and degradation of contaminants, could open new avenues in agricultural research and development. Furthermore, a detailed molecular and biochemical understanding of endophyte entry and colonization strategy in the host would better help in manipulating crop productivity under changing climatic conditions. Therefore, the present review highlights current research trends based on the SCOPUS database, potential biotechnological interventions of endophytic microorganisms in combating environmental stresses influencing crop productivity, future opportunities of endophytes in improving plant stress tolerance, and their contribution to sustainable remediation of hazardous environmental contaminants.
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Affiliation(s)
- Uttpal Anand
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Midreshet Ben-Gurion, Israel.
| | - Tarun Pal
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Midreshet Ben-Gurion, Israel
| | - Niraj Yadav
- French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sde Boker Campus, 8499000, Midreshet Ben-Gurion, Israel
| | - Vipin Kumar Singh
- Department of Botany, K.S. Saket P.G. College, Ayodhya affiliated to Dr. Rammanohar Lohia Avadh University, Ayodhya, 224123, Uttar Pradesh, India
| | - Vijay Tripathi
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, 211007, Uttar Pradesh, India
| | - Krishna Kumar Choudhary
- Department of Botany, Mahila Mahavidyalaya, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | - Awadhesh Kumar Shukla
- Department of Botany, K.S. Saket P.G. College, Ayodhya affiliated to Dr. Rammanohar Lohia Avadh University, Ayodhya, 224123, Uttar Pradesh, India
| | - Kumari Sunita
- Department of Botany, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, Uttar Pradesh, 273009, India
| | - Ajay Kumar
- Department of Postharvest Science, Agricultural Research Organization, The Volcani Center, P.O. Box 15159, 7505101, Rishon, Lezion, Israel
| | - Elza Bontempi
- INSTM and Chemistry for Technologies Laboratory, University of Brescia, Via Branze 38, 25123, Brescia, Italy.
| | - Ying Ma
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
| | - Max Kolton
- French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sde Boker Campus, 8499000, Midreshet Ben-Gurion, Israel
| | - Amit Kishore Singh
- Department of Botany, Bhagalpur National College (A constituent unit of Tilka Manjhi Bhagalpur University), Bhagalpur, 812007, Bihar, India.
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Tsipinana S, Husseiny S, Alayande KA, Raslan M, Amoo S, Adeleke R. Contribution of endophytes towards improving plant bioactive metabolites: a rescue option against red-taping of medicinal plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1248319. [PMID: 37771494 PMCID: PMC10522919 DOI: 10.3389/fpls.2023.1248319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 08/11/2023] [Indexed: 09/30/2023]
Abstract
Medicinal plants remain a valuable source for natural drug bioprospecting owing to their multi-target spectrum. However, their use as raw materials for novel drug synthesis has been greatly limited by unsustainable harvesting leading to decimation of their wild populations coupled with inherent low concentrations of constituent secondary metabolites per unit mass. Thus, adding value to the medicinal plants research dynamics calls for adequate attention. In light of this, medicinal plants harbour endophytes which are believed to be contributing towards the host plant survival and bioactive metabolites through series of physiological interference. Stimulating secondary metabolite production in medicinal plants by using endophytes as plant growth regulators has been demonstrated to be one of the most effective methods for increasing metabolite syntheses. Use of endophytes as plant growth promotors could help to ensure continuous supply of medicinal plants, and mitigate issues with fear of extinction. Endophytes minimize heavy metal toxicity in medicinal plants. It has been hypothesized that when medicinal plants are exposed to harsh conditions, associated endophytes are the primary signalling channels that induce defensive reactions. Endophytes go through different biochemical processes which lead to activation of defence mechanisms in the host plants. Thus, through signal transduction pathways, endophytic microorganisms influence genes involved in the generation of secondary metabolites by plant cells. Additionally, elucidating the role of gene clusters in production of secondary metabolites could expose factors associated with low secondary metabolites by medicinal plants. Promising endophyte strains can be manipulated for enhanced production of metabolites, hence, better probability of novel bioactive metabolites through strain improvement, mutagenesis, co-cultivation, and media adjustment.
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Affiliation(s)
- Sinawo Tsipinana
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Samah Husseiny
- Department of Biotechnology and Life Sciences, Faculty of Postgraduate Studies for Advanced Sciences, Beni-Suef University, Beni-Suef, Egypt
| | - Kazeem A. Alayande
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Mai Raslan
- Department of Biotechnology and Life Sciences, Faculty of Postgraduate Studies for Advanced Sciences, Beni-Suef University, Beni-Suef, Egypt
| | - Stephen Amoo
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
- Agricultural Research Council – Vegetables, Industrial and Medicinal Plants, Roodeplaat, Pretoria, South Africa
| | - Rasheed Adeleke
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
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Verma A, Tiwari H, Singh S, Gupta P, Rai N, Kumar Singh S, Singh BP, Rao S, Gautam V. Epigenetic manipulation for secondary metabolite activation in endophytic fungi: current progress and future directions. Mycology 2023; 14:275-291. [PMID: 38187885 PMCID: PMC10769123 DOI: 10.1080/21501203.2023.2241486] [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: 05/11/2023] [Accepted: 07/21/2023] [Indexed: 01/09/2024] Open
Abstract
Fungal endophytes have emerged as a promising source of secondary metabolites with significant potential for various applications in the field of biomedicine. The biosynthetic gene clusters of endophytic fungi are responsible for encoding several enzymes and transcriptional factors that are involved in the biosynthesis of secondary metabolites. The investigation of fungal metabolic potential at genetic level faces certain challenges, including the synthesis of appropriate amounts of chemicals, and loss of the ability of fungal endophytes to produce secondary metabolites in an artificial culture medium. Therefore, there is a need to delve deeper into the field of fungal genomics and transcriptomics to explore the potential of fungal endophytes in generating secondary metabolites governed by biosynthetic gene clusters. The silent biosynthetic gene clusters can be activated by modulating the chromatin structure using chemical compounds. Epigenetic modification plays a significant role by inducing cryptic gene responsible for the production of secondary metabolites using DNA methyl transferase and histone deacetylase. CRISPR-Cas9-based genome editing emerges an effective tool to enhance the production of desired metabolites by modulating gene expression. This review primarily focuses on the significance of epigenetic elicitors and their capacity to boost the production of secondary metabolites from endophytes. This article holds the potential to rejuvenate the drug discovery pipeline by introducing new chemical compounds.
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Affiliation(s)
- Ashish Verma
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Harshita Tiwari
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Swati Singh
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Priyamvada Gupta
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Nilesh Rai
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Santosh Kumar Singh
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Bhim Pratap Singh
- Department of Agriculture & Environmental Sciences (AES), National Institute of Food Technology Entrepreneurship & Management (NIFTEM), Sonepat, India
| | - Sombir Rao
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Vibhav Gautam
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
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Liang X, Zhou K, Li P, Wan D, Liu J, Yi X, Peng Y. Characteristics of endophytic bacteria and active ingredients in the Eucommiae cortex from different origins. Front Microbiol 2023; 14:1164674. [PMID: 37266017 PMCID: PMC10229866 DOI: 10.3389/fmicb.2023.1164674] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/24/2023] [Indexed: 06/03/2023] Open
Abstract
Objective This study aimed to explore the differences between Eucommiae cortex (EC) endophytic bacteria from different origins and their effects on the active ingredients of EC. Methods A total of 10 samples of Eucommia ulmoides Oliv. (E. ulmoides) bark were collected from each of the following four regions, namely, Zunyi in Guizhou (GZ), Baokang in Hubei (HUB), Cili in Hunan (HUN), and Loyang in Shaanxi (SX). Subsequently, the contents of the main active ingredients of EC were determined by ultra-performance liquid chromatography (UPLC), and the endophytic bacteria of EC were detected by 16S rRNA sequencing. The relationship between the dominant endophytic bacteria and the active ingredients was investigated by correlation analysis. Results A total of 4,551 different operational taxonomic units (OTUs) were delineated in the four groups of samples, of which 585, 439, 957, and 684 genera were annotated from GZ, HUB, HUN, and SX, respectively. The richness and diversity of endophytic bacteria from different origins were ranked as HUN > SX > GZ or HUB. The analysis demonstrated that there was no significant correlation between the diversity and richness of endophytic bacteria in EC and its active ingredients. Nevertheless, notable variations in the community structures of endophytic bacteria were observed across different origins, and they had a considerable impact on certain active ingredients in EC. Comamonas and Cedecea were the dominant genera. Characteristic bacteria of different origins could be clearly distinguished. Simultaneous, significant correlations had been identified between some characteristic endophytic bacteria derived from different origins and active ingredients of EC. For example, Delftia, a characteristic bacterium from GZ, showed a significant positive correlation with pinoresinol diglucoside. Paenibacillus and Klebsiella, two characteristic bacteria from HUB, exhibited significant positive correlations with geniposidic acid. Thauera, a characteristic bacterium from HUN, demonstrated a significant positive correlation with geniposide. Brevundimonas, a characteristic bacterium from SX, displayed a significant positive correlation with pinoresinol diglucoside. Conclusion There was a complex correlation between EC endophytic bacteria and active ingredient content, while EC endophytic bacteria from different origins had significant differences at the genus level.
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Affiliation(s)
- Xuejuan Liang
- Innovative Medicine Institute of Traditional Chinese Medicine, Hunan Academy of Chinese Medicine, Changsha, China
| | - Kang Zhou
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, China
| | - Penghui Li
- Innovative Medicine Institute of Traditional Chinese Medicine, Hunan Academy of Chinese Medicine, Changsha, China
| | - Dan Wan
- Innovative Medicine Institute of Traditional Chinese Medicine, Hunan Academy of Chinese Medicine, Changsha, China
| | - Jing Liu
- College of Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
| | - Xin Yi
- College of Pharmacy, Hunan University of Chinese Medicine, Changsha, China
| | - Yanmei Peng
- Innovative Medicine Institute of Traditional Chinese Medicine, Hunan Academy of Chinese Medicine, Changsha, China
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Sayyed SK, Quraishi M, Jobby R, Rameshkumar N, Kayalvizhi N, Krishnan M, Sonawane T. A computational overview of integrase strand transfer inhibitors (INSTIs) against emerging and evolving drug-resistant HIV-1 integrase mutants. Arch Microbiol 2023; 205:142. [PMID: 36966200 PMCID: PMC10039815 DOI: 10.1007/s00203-023-03461-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/26/2023] [Accepted: 03/01/2023] [Indexed: 03/27/2023]
Abstract
AIDS (Acquired immunodeficiency syndrome) is one of the chronic and potentially life-threatening epidemics across the world. Hitherto, the non-existence of definitive drugs that could completely cure the Human immunodeficiency virus (HIV) implies an urgent necessity for the discovery of novel anti-HIV agents. Since integration is the most crucial stage in retroviral replication, hindering it can inhibit overall viral transmission. The 5 FDA-approved integrase inhibitors were computationally investigated, especially owing to the rising multiple mutations against their susceptibility. This comparative study will open new possibilities to guide the rational design of novel lead compounds for antiretroviral therapies (ARTs), more specifically the structure-based design of novel Integrase strand transfer inhibitors (INSTIs) that may possess a better resistance profile than present drugs. Further, we have discussed potent anti-HIV natural compounds and their interactions as an alternative approach, recommending the urgent need to tap into the rich vein of indigenous knowledge for reverse pharmacology. Moreover, herein, we discuss existing evidence that might change in the near future.
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Affiliation(s)
- Sharif Karim Sayyed
- Amity Institute of Biotechnology, Amity University, Mumbai, Maharashtra, 410206, India
| | - Marzuqa Quraishi
- Amity Institute of Biotechnology, Amity University, Mumbai, Maharashtra, 410206, India
| | - Renitta Jobby
- Amity Institute of Biotechnology, Amity University, Mumbai, Maharashtra, 410206, India
| | | | - Nagarajan Kayalvizhi
- Regenerative Medicine Laboratory, Department of Zoology, School of Life Sciences, Periyar University, Salem, Tamil Nadu, 636011, India
| | | | - Tareeka Sonawane
- Amity Institute of Biotechnology, Amity University, Mumbai, Maharashtra, 410206, India.
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Kaur J, Mudgal G, Chand K, Singh GB, Perveen K, Bukhari NA, Debnath S, Mohan TC, Charukesi R, Singh G. An exopolysaccharide-producing novel Agrobacterium pusense strain JAS1 isolated from snake plant enhances plant growth and soil water retention. Sci Rep 2022; 12:21330. [PMID: 36494408 PMCID: PMC9734154 DOI: 10.1038/s41598-022-25225-y] [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: 05/13/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022] Open
Abstract
A peculiar bacterial growth was very often noticed in leaf-initiated tissue cultures of Sansevieria trifasciata, a succulent belonging to the Asparagaceae family. The isolate left trails of some highly viscous material on the walls of the suspension vessels or developed a thick overlay on semisolid media without adversities in plant growth. FTIR identified this substance to be an extracellular polysaccharide. Various morphological, biochemical tests, and molecular analyses using 16S rRNA, atpD, and recA genes characterized this isolate JAS1 as a novel strain of Agrobacterium pusense. Its mucoidal growth over Murashige and Skoog media yielded enormous exopolysaccharide (7252 mg l-1), while in nutrient agar it only developed fast-growing swarms. As a qualifying plant growth-promoting bacteria, it produces significant indole-3-acetic acid (86.95 mg l-1), gibberellic acid (172.98 mg l-1), ammonia (42.66 µmol ml-1). Besides, it produces siderophores, 1-aminocyclopropane-1-carboxylic acid deaminase, fixes nitrogen, forms biofilms, and productively solubilizes soil inorganic phosphates, and zinc. Under various treatments with JAS1, wheat and chickpea resulted in significantly enhanced shoot and root growth parameters. PGP effects of JAS1 positively enhanced plants' physiological growth parameters reflecting significant increments in overall chlorophyll, carotenoids, proline, phenols, flavonoids, and sugar contents. In addition, the isolated strain maintained both plant and soil health under an intermittent soil drying regime, probably by both its PGP and EPS production attributes, respectively.
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Affiliation(s)
- Jaspreet Kaur
- grid.448792.40000 0004 4678 9721University Institute of Biotechnology, Chandigarh University, Gharuan, Mohali, Punjab 140413 India
| | - Gaurav Mudgal
- grid.448792.40000 0004 4678 9721University Institute of Biotechnology, Chandigarh University, Gharuan, Mohali, Punjab 140413 India
| | - Kartar Chand
- grid.448792.40000 0004 4678 9721University Institute of Biotechnology, Chandigarh University, Gharuan, Mohali, Punjab 140413 India
| | - Gajendra B. Singh
- grid.448792.40000 0004 4678 9721University Institute of Biotechnology, Chandigarh University, Gharuan, Mohali, Punjab 140413 India
| | - Kahkashan Perveen
- grid.56302.320000 0004 1773 5396Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11495 Saudi Arabia
| | - Najat A. Bukhari
- grid.56302.320000 0004 1773 5396Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11495 Saudi Arabia
| | - Sandip Debnath
- grid.440987.60000 0001 2259 7889Department of Genetics and Plant Breeding, Palli Siksha Bhavana (Institute of Agriculture), Visva-Bharati University, Sriniketan, Birbhum, West Bengal 731236 India
| | - Thotegowdanapalya C. Mohan
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Bannimantapa Road, Mysore, 570015 India
| | - Rajulu Charukesi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Bannimantapa Road, Mysore, 570015 India
| | - Gaurav Singh
- Stress Signaling to the Nucleus, CNRS-Institute of Molecular Biology of Plants, 12 Rue du General-Zimmer, 67000 Strasbourg, France
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