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Kaale SE, Machangu RS, Lyimo TJ. Molecular characterization and phylogenetic diversity of actinomycetota species isolated from Lake Natron sediments at Arusha, Tanzania. Microbiol Res 2024; 278:127543. [PMID: 37950928 DOI: 10.1016/j.micres.2023.127543] [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: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/13/2023]
Abstract
Soda lakes are naturally occurring ecosystems characterized by extreme environmental conditions especially high pH and salinity levels but harboring valuable microbial communities with medical and biotechnological potentials. Lake Natron is one of the soda lakes situated in eastern branch of the East African Gregory Rift valley, Tanzania. In this study, the taxonomy and phylogenetic diversity of Actinomycetota species were explored in Lake Natron using molecular techniques. The sequencing of their 16S rRNA gene resulted into 13 genera of phylum Actinomycetota namely Streptomyces, Microbacterium, Nocardiopsis, Gordonia, Dietzia, Micromonospora, Microcella, Pseudarthrobacter, Nocardioides, Actinotalea, Cellulomonas, Isoptericola, and Glutamicibacter. We describe for the first time, the isolation of Streptomyces lasalocidi, S. harbinensis, S. anthocyanicus, Microbacterium aureliae, Pseudarthrobacter sp., Nocardioides sp. and Glutamicibacter mishrai from soda lake habitats. It also reports for the first time, the isolation of Gordonia spp., Microcella sp. and Actinotalea sp. from an East African Soda Lake as well as isolation of S. pseudogriseolus, S. calidiresistens and Micromonospora spp. from a Tanzania soda lake. Furthermore, two putative novel species of the phylum Actinomycetota were identified. Given that Actinomycetota are known potential sources of important biotechnological compounds, we recommend the broadening of the scope of bioprospection in future to include the novel species from Lake Natron.
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Affiliation(s)
- Sadikiel E Kaale
- Department of Molecular Biology and Biotechnology, University of Dar es Salaam, Dar es Salaam, Tanzania; Department of Biochemistry and Molecular Biology, Saint Francis University College of Health and Allied Sciences, Ifakara-Morogoro, Tanzania
| | - Robert S Machangu
- Department of Microbiology, Saint Francis University College of Health and Allied Sciences, Ifakara-Morogoro, Tanzania
| | - Thomas J Lyimo
- Department of Molecular Biology and Biotechnology, University of Dar es Salaam, Dar es Salaam, Tanzania.
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Ouertani R, Ouertani A, Mahjoubi M, Bousselmi Y, Najjari A, Cherif H, Chamkhi A, Mosbah A, Khdhira H, Sghaier H, Chouchane H, Cherif A, Neifar M. New Plant Growth-Promoting, Chromium-Detoxifying Microbacterium Species Isolated From a Tannery Wastewater: Performance and Genomic Insights. Front Bioeng Biotechnol 2020; 8:521. [PMID: 32719777 PMCID: PMC7350417 DOI: 10.3389/fbioe.2020.00521] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 05/01/2020] [Indexed: 12/31/2022] Open
Abstract
Hexavalent chromium [Cr(VI)], widely generated by tannery activities, is considered among the most toxic substances and causes a serious damage for the environment and for human health. Interestingly, some microorganisms have a potential of bioremediation of chromium-contaminated wastewaters and soils through the reduction of Cr(VI) (soluble and harmful form) into Cr(III) (stable and non-toxic form). Here, we present the full genome sequence of a novel heavy-metal-resistant, plant growth-promoting bacterium (PGPB), Microbacterium metallidurans TL13, which was isolated from a Tunisian leather industry. The strain TL13 was resistant to many heavy metals, such as chromium, copper, nickel, cobalt, and arsenic. The 50% TL13 growth inhibitory concentration (IC50) values of HgCl2, CoCl2, K2Cr2O7, CuSO4, NiCl2, FeSO4, and Na2HAsO4 are 368, 445, 676, 1,590, 1,680, 4,403, and 7,007 mg/L, respectively, with the following toxicity order: HgCl2 > CoCl2 > K2Cr2O7 > CuSO4 > NiCl2 > FeSO4 > Na2HAsO4. This new strain was also able to promote the growth of the hybrid tomato (Elika F1) under chromium metal stress. Its whole genome sequence length was estimated to be 3,587,460 bp (3,393 coding sequences) with a G + C content of 70.7%. Functional annotation of the genome of TL13 revealed the presence of open reading frames (ORFs) involved in adaptation to metal stress, such as the chromate transport protein, cobalt–zinc–cadmium resistance protein, copper resistance protein, copper responsive transcriptional regulator, multidrug resistance transporters, arsenical resistance operon repressor, arsenate reductase, arsenic resistance protein, mercuric resistance operon regulatory protein, mercuric ion reductase, and organomercurial lyase. Moreover, genes for the production of glutathione peroxidase, catalase, superoxide dismutase, and thioredoxin reductase, which confer a higher tolerance to oxidative/metal stresses, were identified in TL13 genome. In addition, genes for heat shock tolerance, cold shock tolerance, glycine-betaine production, mineral phosphate solubilization, ammonia assimilation, siderophores, exopolysaccharides, polyketides, and lytic enzymes (cellulase, chitinase, and proteases) production that enable bacteria to survive biotic/abiotic stress and to promote plant growth and health were also revealed. Based on genome analysis and experimental approaches, strain TL13 appears to have evolved from various metabolic strategies and could play a role in ensuring sustainable environmental and agricultural systems.
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Affiliation(s)
- Rania Ouertani
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, Sidi Thabet, Tunisia.,Laboratory of Microorganisms and Active Biomolecules, MBA-LR03ES03, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Awatef Ouertani
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, Sidi Thabet, Tunisia
| | - Mouna Mahjoubi
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, Sidi Thabet, Tunisia
| | - Yosra Bousselmi
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, Sidi Thabet, Tunisia
| | - Afef Najjari
- Laboratory of Microorganisms and Active Biomolecules, MBA-LR03ES03, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Hanene Cherif
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, Sidi Thabet, Tunisia
| | - Asma Chamkhi
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, Sidi Thabet, Tunisia
| | - Amor Mosbah
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, Sidi Thabet, Tunisia
| | - Hechmi Khdhira
- Management Environment Responsible in Tanneries Mégisseries du Maghreb, TMM, Grombalia, Tunisia
| | - Haitham Sghaier
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, Sidi Thabet, Tunisia.,Laboratory "Energy and Matter for Development of Nuclear Sciences" (LR16CNSTN02), National Center for Nuclear Sciences and Technology (CNSTN), Sidi Thabet Technopark, Sidi Thabet, Tunisia
| | - Habib Chouchane
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, Sidi Thabet, Tunisia
| | - Ameur Cherif
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, Sidi Thabet, Tunisia
| | - Mohamed Neifar
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, Sidi Thabet, Tunisia
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Learman DR, Ahmad Z, Brookshier A, Henson MW, Hewitt V, Lis A, Morrison C, Robinson A, Todaro E, Wologo E, Wynne S, Alm EW, Kourtev PS. Comparative genomics of 16 Microbacterium spp. that tolerate multiple heavy metals and antibiotics. PeerJ 2019; 6:e6258. [PMID: 30671291 PMCID: PMC6336093 DOI: 10.7717/peerj.6258] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 12/06/2018] [Indexed: 11/20/2022] Open
Abstract
A total of 16 different strains of Microbacterium spp. were isolated from contaminated soil and enriched on the carcinogen, hexavalent chromium [Cr(VI)]. The majority of the isolates (11 of the 16) were able to tolerate concentrations (0.1 mM) of cobalt, cadmium, and nickel, in addition to Cr(VI) (0.5–20 mM). Interestingly, these bacteria were also able to tolerate three different antibiotics (ranges: ampicillin 0–16 μg ml−1, chloramphenicol 0–24 μg ml−1, and vancomycin 0–24 μg ml−1). To gain genetic insight into these tolerance pathways, the genomes of these isolates were assembled and annotated. The genomes of these isolates not only have some shared genes (core genome) but also have a large amount of variability. The genomes also contained an annotated Cr(VI) reductase (chrR) that could be related to Cr(VI) reduction. Further, various heavy metal tolerance (e.g., Co/Zn/Cd efflux system) and antibiotic resistance genes were identified, which provide insight into the isolates’ ability to tolerate metals and antibiotics. Overall, these isolates showed a wide range of tolerances to heavy metals and antibiotics and genetic diversity, which was likely required of this population to thrive in a contaminated environment.
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Affiliation(s)
- Deric R Learman
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Zahra Ahmad
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Allison Brookshier
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Michael W Henson
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Victoria Hewitt
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Amanda Lis
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Cody Morrison
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Autumn Robinson
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Emily Todaro
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Ethan Wologo
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Sydney Wynne
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Elizabeth W Alm
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Peter S Kourtev
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
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