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Kifle BA, Sime AM, Gemeda MT, Woldesemayat AA. Shotgun metagenomic insights into secondary metabolite biosynthetic gene clusters reveal taxonomic and functional profiles of microbiomes in natural farmland soil. Sci Rep 2024; 14:15096. [PMID: 38956049 PMCID: PMC11220033 DOI: 10.1038/s41598-024-63254-x] [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: 10/15/2023] [Accepted: 05/27/2024] [Indexed: 07/04/2024] Open
Abstract
Antibiotic resistance is a worldwide problem that imposes a devastating effect on developing countries and requires immediate interventions. Initially, most of the antibiotic drugs were identified by culturing soil microbes. However, this method is prone to discovering the same antibiotics repeatedly. The present study employed a shotgun metagenomics approach to investigate the taxonomic diversity, functional potential, and biosynthetic capacity of microbiomes from two natural agricultural farmlands located in Bekeka and Welmera Choke Kebelle in Ethiopia for the first time. Analysis of the small subunit rRNA revealed bacterial domain accounting for 83.33% and 87.24% in the two selected natural farmlands. Additionally, the analysis showed the dominance of Proteobacteria representing 27.27% and 28.79% followed by Actinobacteria making up 12.73% and 13.64% of the phyla composition. Furthermore, the analysis revealed the presence of unassigned bacteria in the studied samples. The metagenome functional analysis showed 176,961 and 104, 636 number of protein-coding sequences (pCDS) from the two samples found a match with 172,655 and 102, 275 numbers of InterPro entries, respectively. The Genome ontology annotation suggests the presence of 5517 and 3293 pCDS assigned to the "biosynthesis process". Numerous Kyoto Encyclopedia of Genes and Genomes modules (KEGG modules) involved in the biosynthesis of terpenoids and polyketides were identified. Furthermore, both known and novel Biosynthetic gene clusters, responsible for the production of secondary metabolites, such as polyketide synthases, non-ribosomal peptide synthetase, ribosomally synthesized and post-translationally modified peptides (Ripp), and Terpene, were discovered. Generally, from the results it can be concluded that the microbiomes in the selected sampling sites have a hidden functional potential for the biosynthesis of secondary metabolites. Overall, this study can serve as a strong preliminary step in the long journey of bringing new antibiotics to the market.
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Affiliation(s)
- Bezayit Amare Kifle
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
| | - Amsale Melkamu Sime
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
| | - Mesfin Tafesse Gemeda
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
| | - Adugna Abdi Woldesemayat
- Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia.
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Mao YL, Wang BB, Yin XM, Hou J, Cui HL. Halomontanus rarus gen. nov., sp. nov., a novel halophilic archaeon of the family Natrialbaceae from salt lakes on the Qinghai-Xizang Plateau. Syst Appl Microbiol 2024; 47:126500. [PMID: 38417236 DOI: 10.1016/j.syapm.2024.126500] [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: 12/04/2023] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 03/01/2024]
Abstract
Two halophilic archaeal strains TS33T and KZCA124 were isolated from two distant salt lakes on the Qinghai-Xizang Plateau, respectively. Culture-independent analysis indicated that these two strains were original inhabitants but low abundant taxa in respective salt lakes. Strains TS33T and KZCA124 were able to grow at 20-60 °C (optimum were 42 and 35 °C, respectively), with 0.9-4.8 M NaCl (optimum were 3.0 and 2.6 M, respectively), with 0-0.7 M MgCl2 (optimum, 0.3 M) and at pH 5.0-9.5 (optimum were pH 7.5 and pH 7, respectively). The 16S rRNA and rpoB' gene similarities between these two strains were 99.7% and 99.4%, and these two similarities among strains TS33T, KZCA124, and existing species of the family Natrialbaceae were 90.6-95.5% and 84.4-89.3%, respectively. Phylogenetic and phylogenomic analyses indicated that strains TS33T and KZCA124 formed an independent branch separated from neighboring genera, Saliphagus, Natronosalvus, and Natronobiforma. The averagenucleotideidentity (ANI), digital DNA-DNAhybridization (dDDH), and average amino acid identity (AAI) values between strains TS33T and KZCA124 were 96.4%, 73.1%, and 96.7%, respectively, higher than the thresholds for species demarcation. The overall genome-related indexes between these two strains and existing species of family Natrialbaceae were 73-77%, 21-25%, and 63-70%, respectively, significantly lower than the species boundary thresholds. Strains TS33T and KZCA124 may represent a novel species of a new genus within the family Natrialbaceae judged by the cutoff value of AAI (≤76%) proposed to differentiate genera within the family Natrialbaceae. The major polar lipids of strains TS33T and KZCA124 were phosphatidic acid, phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, sulfated mannosyl glucosyl diether, and sulfated galactosyl mannosyl glucosyl diether. These two strains could be distinguished from the related genera according to differential phenotypic characteristics. These phenotypic, phylogenetic, and genomic analyses revealed that strains TS33T (=KCTC 4310T = MCCC 4K00132T) and KZCA124 (=CGMCC 1.17432 = JCM 34316) represent a novel species of a new genus of the family Natrialbaceae and were named Halomontanus rarus gen. nov., sp. nov.
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Affiliation(s)
- Ya-Ling Mao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, People's Republic of China
| | - Bei-Bei Wang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, People's Republic of China
| | - Xue-Meng Yin
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, People's Republic of China
| | - Jing Hou
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, People's Republic of China
| | - Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, People's Republic of China.
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Giani M, Pire C, Martínez-Espinosa RM. Bacterioruberin: Biosynthesis, Antioxidant Activity, and Therapeutic Applications in Cancer and Immune Pathologies. Mar Drugs 2024; 22:167. [PMID: 38667784 PMCID: PMC11051356 DOI: 10.3390/md22040167] [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: 03/13/2024] [Revised: 04/02/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Halophilic archaea, also termed haloarchaea, are a group of moderate and extreme halophilic microorganisms that constitute the major microbial populations in hypersaline environments. In these ecosystems, mainly aquatic, haloarchaea are constantly exposed to ionic and oxidative stress due to saturated salt concentrations and high incidences of UV radiation (mainly in summer). To survive under these harsh conditions, haloarchaea have developed molecular adaptations including hyperpigmentation. Regarding pigmentation, haloarchaeal species mainly synthesise the rare C50 carotenoid called bacterioruberin (BR) and its derivatives, monoanhydrobacterioruberin and bisanhydrobacterioruberin. Due to their colours and extraordinary antioxidant properties, BR and its derivatives have been the aim of research in several research groups all over the world during the last decade. This review aims to summarise the most relevant characteristics of BR and its derivatives as well as describe their reported antitumoral, immunomodulatory, and antioxidant biological activities. Based on their biological activities, these carotenoids can be considered promising natural biomolecules that could be used as tools to design new strategies and/or pharmaceutical formulas to fight against cancer, promote immunomodulation, or preserve skin health, among other potential uses.
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Affiliation(s)
- Micaela Giani
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (M.G.); (C.P.)
| | - Carmen Pire
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (M.G.); (C.P.)
- Biochemistry and Molecular Biology and Edaphology and Agricultural Chemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Rosa María Martínez-Espinosa
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (M.G.); (C.P.)
- Biochemistry and Molecular Biology and Edaphology and Agricultural Chemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain
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Tan S, Zhu LR, Zhang QK, Dong XY, Hou J, Cui HL. Genome-based classification of the family Haloferacaceae and description of five novel species of Halobaculum. Extremophiles 2024; 28:22. [PMID: 38546878 DOI: 10.1007/s00792-024-01337-3] [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: 01/29/2024] [Accepted: 02/22/2024] [Indexed: 04/02/2024]
Abstract
The taxonomic status of some species of Halobellus, Haloferax, Halogranum, and Haloplanus within the family Haloferacaceae was elucidated by phylogenetic, phylogenomic, and comparative genomic analyses. The relative species of each genus should constitute a single species based on the overall genome-related indexes proposed for species demarcation. The cutoff values of AAI (72.1%), ANI (82.2%), and rpoB' gene similarity (90.7%) were proposed to differentiate genera within the family Haloferacaceae. According to these standards, a novel genus related to the genus Halobaculum was proposed to accommodate Halobaculum halophilum Gai3-2 T and Halobaculum salinum NJ-3-1 T. Five halophilic archaeal strains, DT31T, DT55T, DT92T, SYNS20T, and YSMS11T, isolated from a tidal flat and a marine solar saltern in China, were subjected to polyphasic classification. The phenotypic, phylogenetic, phylogenomic, and comparative genomic analyses revealed that strains DT31T (= CGMCC 1.18923 T = JCM 35417 T), DT55T (= CGMCC 1.19048 T = JCM 36147 T), DT92T (= CGMCC 1.19057 T = JCM 36148 T), SYNS20T (= CGMCC 1.62628 T = JCM 36154 T), and YSMS11T (= CGMCC 1.18927 T = JCM 34912 T) represent five novel species of the genus Halobaculum, for which the names, Halobaculum lipolyticum sp. nov., Halobaculum marinum sp. nov., Halobaculum litoreum sp. nov., Halobaculum halobium sp. nov., and Halobaculum limi sp. nov., are proposed.
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Affiliation(s)
- Shun Tan
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, People's Republic of China
| | - Ling-Rui Zhu
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, People's Republic of China
| | - Qing-Ke Zhang
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, People's Republic of China
| | - Xin-Yue Dong
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, People's Republic of China
| | - Jing Hou
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, People's Republic of China
| | - Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, People's Republic of China.
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Hu Y, Ma X, Tan S, Li XX, Cheng M, Hou J, Cui HL. Genome-based classification of genera Halosegnis and Salella, and description of four novel halophilic archaea isolated from a tidal flat. Antonie Van Leeuwenhoek 2024; 117:51. [PMID: 38472444 DOI: 10.1007/s10482-024-01952-2] [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: 12/30/2023] [Accepted: 02/16/2024] [Indexed: 03/14/2024]
Abstract
The current species of Halosegnis and Salella within the class Halobacteria are closely related based on phylogenetic, phylogenomic, and comparative genomic analyses. The Halosegnis species showed 99.8-100.0% 16S rRNA and 96.6-99.6% rpoB' gene similarities to the Salella species, respectively. Phylogenetic and phylogenomic analyses showed that Salella cibi CBA1133T, the sole species of Salella, formed a single tight cluster with Halosegnis longus F12-1T, then with Halosegnis rubeus F17-44T. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) values between Salella cibi CBA1133T and Halosegnis longus F12-1T were 99.2, 94.2, and 98.6%, respectively, much higher than the thresholds for species demarcation. This genome-based classification revealed that the genus Salella should be merged with Halosegnis, and Salella cibi should be a later heterotypic synonym of Halosegnis longus. Halophilic archaeal strains DT72T, DT80T, DT85T, and DT116T, isolated from the saline soil of a tidal flat in China, were subjected to polyphasic taxonomic characterization. The phenotypic, chemotaxonomic, phylogenetic, and phylogenomic features indicated that strains DT72T (= CGMCC 1.18925T = JCM 35418T), DT80T (= CGMCC 1.18926T = JCM 35419T), DT85T (= CGMCC 1.19049T = JCM 35605T), and DT116T (= CGMCC 1.19045T = JCM 35606T) represent four novel species of the genera Halorussus, Halosegnis and Haloglomus, respectively, for which the names, Halorussus caseinilyticus sp. nov., Halorussus lipolyticus sp. nov., Halosegnis marinus sp. nov., and Haloglomus litoreum sp. nov., are proposed.
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Affiliation(s)
- Yao Hu
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, People's Republic of China
| | - Xue Ma
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, People's Republic of China
| | - Shun Tan
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, People's Republic of China
| | - Xin-Xin Li
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, People's Republic of China
| | - Mu Cheng
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, People's Republic of China
| | - Jing Hou
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, People's Republic of China
| | - Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, People's Republic of China.
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Hu Y, Ma X, Li XX, Tan S, Cheng M, Hou J, Cui HL. Halomicrococcus gelatinilyticus sp. nov. and Halosimplex aquaticum sp. nov., halophilic archaea isolated from saline soil and an inland solar saltern. Int J Syst Evol Microbiol 2024; 74. [PMID: 38197785 DOI: 10.1099/ijsem.0.006231] [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] [Indexed: 01/11/2024] Open
Abstract
Two extremely halophilic archaeal strains, GSLN9T and XZYJT29T, were isolated from the saline soil in different regions of western China. Both strains GSLN9T and XZYJT29T have two 16S rRNA genes with similarities of 95.1 and 94.8 %, respectively. Strain GSLN9T was mostly related to the genus Halomicrococcus based on 16S rRNA (showing 91.0-96.0 % identities) and rpoB' genes (showing 92.0 % identity). Strain XZYJT29T showed 92.1-97.6 % (16S rRNA gene) and 91.4-93.1 % (rpoB' gene) sequence similarities to its relatives in the genus Halosimplex, respectively. The polar lipid profile of strain GSLN9T included phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), phosphatidylglycerol sulphate (PGS), sulphated mannosyl glucosyl diether (S-DGD-1) and sulphated galactosyl mannosyl glucosyl diether (S-TGD-1), mostly similar to that of Halomicrococcus hydrotolerans H22T. PA, PG, PGP-Me, S-DGD-1 (S-DGD-PA), S2-DGD, S-TGD-1 and an unidentified glycolipid were detected in strain XZYJT29T; this polar lipid composition is similar to those of members of the genus Halosimplex. The average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity values between these two strains and their relatives of the genera Halomicrococcus and Halosimplex were no more than 82, 27 and 80 %, respectively, much lower than the thresholds for species demarcation. Other phenotypic characterization results indicated that strains GSLN9T and XZYJT29T can be differentiated from the current species of the genera Halomicrococcus and Halosimplex, respectively. These results revealed that strains GSLN9T (=CGMCC 1.15215T=JCM 30842T) and XZYJT29T (=CGMCC 1.15828T=JCM 31853T) represent novel species of Halomicrococcus and Halosimplex, for which the names Halomicrococcus gelatinilyticus sp. nov. and Halosimplex aquaticum sp. nov. are proposed.
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Affiliation(s)
- Yao Hu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Xue Ma
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Xin-Xin Li
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Shun Tan
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Mu Cheng
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Jing Hou
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
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Kesbiç FI, Metin H, Fazio F, Parrino V, Kesbiç OS. Effects of Bacterioruberin-Rich Haloarchaeal Carotenoid Extract on the Thermal and Oxidative Stabilities of Fish Oil. Molecules 2023; 28:8023. [PMID: 38138512 PMCID: PMC10745883 DOI: 10.3390/molecules28248023] [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: 10/30/2023] [Revised: 11/25/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
This study aimed to assess the efficacy of a bacterioruberin-rich carotenoid extract (HAE) derived from the halophilic archaea Halorubrum ezzemoulense DSM 19316 in protecting crude fish oil against thermal oxidation. The research used fish oil derived from anchovies, which had a peroxide value (PV) of 6.44 ± 0.81 meq O2 kg-1. To assess the impact of HAE on the thermal stability and post-oxidation characteristics of fish oil, several concentrations of HAE were added to the fish oil samples: 0 ppm (no additive) (HAE0), 50 ppm (HAE50), 100 ppm (HAE100), 500 ppm (HAE500), and 1000 ppm (HAE1000). Furthermore, a control group was established with the addition of 100 ppm butylated hydroxytoluene (BHT100) in order to evaluate the effectiveness of HAE with a synthetic antioxidant that is commercially available. Prior to the fast oxidation experiment, thermogravimetric analysis was conducted on samples from all experimental groups. At the conclusion of the examination, it was seen that the HAE500 and HAE1000 groups exhibited a delay in the degradation temperature. The experimental groups underwent oxidation at a temperature of 55.0 ± 0.5 °C for a duration of 96 h. The measurement of PV was conducted every 24 h during this time. PV in all experimental groups exhibited a time-dependent rise (p < 0.05). However, the HAE500 group had the lowest PV measurement at the conclusion of the 96 h period (p < 0.05). Significant disparities were detected in the fatty acid compositions of the experimental groups at the completion of the oxidation experiment. The HAE500 group exhibited the highest levels of EPA, DHA, and ΣPUFA at the end of oxidation, with statistical significance (p < 0.05). Through the examination of volatile component analysis, specifically an oxidation marker, it was shown that the HAE500 group exhibited the lowest level of volatile components (p < 0.05). Consequently, it was concluded that the addition of HAE to fish oil provided superior protection compared to BHT at an equivalent rate. Moreover, the group that used 500 ppm HAE demonstrated the highest level of performance in the investigation.
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Affiliation(s)
| | - Hilal Metin
- Institute of Science, Department of Sustainable Agriculture and Natural Sources, Kastamonu University, 37150 Kastamonu, Turkey;
| | - Francesco Fazio
- Department of Veterinary Sciences, University of Messina, Viale Giovanni Palatucci, 13, 98168 Messina, Italy
| | - Vincenzo Parrino
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98168 Messina, Italy;
| | - Osman Sabri Kesbiç
- Faculty of Veterinary Medicine, Department of Animal Nutrition and Nutritional Diseases, Kastamonu University, 37150 Kastamonu, Turkey;
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Liang H, Song ZM, Zhong Z, Zhang D, Yang W, Zhou L, Older EA, Li J, Wang H, Zeng Z, Li YX. Genomic and metabolic analyses reveal antagonistic lanthipeptides in archaea. MICROBIOME 2023; 11:74. [PMID: 37060102 PMCID: PMC10105419 DOI: 10.1186/s40168-023-01521-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 03/16/2023] [Indexed: 05/12/2023]
Abstract
BACKGROUND Microbes produce diverse secondary metabolites (SMs) such as signaling molecules and antimicrobials that mediate microbe-microbe interaction. Archaea, the third domain of life, are a large and diverse group of microbes that not only exist in extreme environments but are abundantly distributed throughout nature. However, our understanding of archaeal SMs lags far behind our knowledge of those in bacteria and eukarya. RESULTS Guided by genomic and metabolic analysis of archaeal SMs, we discovered two new lanthipeptides with distinct ring topologies from a halophilic archaeon of class Haloarchaea. Of these two lanthipeptides, archalan α exhibited anti-archaeal activities against halophilic archaea, potentially mediating the archaeal antagonistic interactions in the halophilic niche. To our best knowledge, archalan α represents the first lantibiotic and the first anti-archaeal SM from the archaea domain. CONCLUSIONS Our study investigates the biosynthetic potential of lanthipeptides in archaea, linking lanthipeptides to antagonistic interaction via genomic and metabolic analyses and bioassay. The discovery of these archaeal lanthipeptides is expected to stimulate the experimental study of poorly characterized archaeal chemical biology and highlight the potential of archaea as a new source of bioactive SMs. Video Abstract.
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Affiliation(s)
- Haoyu Liang
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Zhi-Man Song
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Chemistry and Chemical Engineering Guangdong Laboratory, Shantou, 515031, China
| | - Zheng Zhong
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Dengwei Zhang
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Wei Yang
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Le Zhou
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Ethan A Older
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Jie Li
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Huan Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Zhirui Zeng
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Yong-Xin Li
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.
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Hu Y, Ma X, Li XX, Tan S, Cheng M, Hou J, Cui HL. Natrinema caseinilyticum sp. nov., Natrinema gelatinilyticum sp. nov., Natrinema marinum sp. nov., Natrinema zhouii sp. nov., extremely halophilic archaea isolated from marine environments and a salt mine. Extremophiles 2023; 27:9. [PMID: 37000350 DOI: 10.1007/s00792-023-01294-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/08/2023] [Indexed: 04/01/2023]
Abstract
Four extremely halophilic archaeal strains (ZJ2T, BND6T, DT87T, and YPL30T) were isolated from marine environments and a salt mine in China. The 16S rRNA and rpoB' gene sequence similarities among strains ZJ2T, BND6T, DT87T, YPL30T and the current species of Natrinema were 93.2-99.3% and 89.2-95.8%, respectively. Both phylogenetic and phylogenomic analyses revealed that strains ZJ2T, BND6T, DT87T, and YPL30T cluster with the Natrinema members. The overall genome-related indexes (ANI, isDDH, and AAI) among these four strains and the current species of genus Natrinema were 70-88%, 22-43% and 75-89%, respectively, clearly below the threshold values for species boundary. Strains ZJ2T, BND6T, DT87T, and YPL30T could be distinguished from the related species according to differential phenotypic characteristics. The major polar lipids of the four strains were phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), sulfated mannosyl glucosyl diether (S-DGD-1), and disulfated mannosyl glucosyl diether (S2-DGD). The phenotypic, chemotaxonomic, phylogenetic and phylogenomic features indicated that strains ZJ2T (= CGMCC 1.18786 T = JCM 34918 T), BND6T (= CGMCC 1.18777 T = JCM 34909 T), DT87T (= CGMCC 1.18921 T = JCM 35420 T), and YPL30T (= CGMCC 1.15337 T = JCM 31113 T) represent four novel species of the genus Natrinema, for which the names, Natrinema caseinilyticum sp. nov., Natrinema gelatinilyticum sp. nov., Natrinema marinum sp. nov., and Natrinema zhouii sp. nov., are proposed.
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Affiliation(s)
- Yao Hu
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, 212013, Zhenjiang, People's Republic of China
| | - Xue Ma
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, 212013, Zhenjiang, People's Republic of China
| | - Xin-Xin Li
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, 212013, Zhenjiang, People's Republic of China
| | - Shun Tan
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, 212013, Zhenjiang, People's Republic of China
| | - Mu Cheng
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, 212013, Zhenjiang, People's Republic of China
| | - Jing Hou
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, 212013, Zhenjiang, People's Republic of China
| | - Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, 212013, Zhenjiang, People's Republic of China.
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10
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Moopantakath J, Imchen M, Anju VT, Busi S, Dyavaiah M, Martínez-Espinosa RM, Kumavath R. Bioactive molecules from haloarchaea: Scope and prospects for industrial and therapeutic applications. Front Microbiol 2023; 14:1113540. [PMID: 37065149 PMCID: PMC10102575 DOI: 10.3389/fmicb.2023.1113540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/14/2023] [Indexed: 04/03/2023] Open
Abstract
Marine environments and salty inland ecosystems encompass various environmental conditions, such as extremes of temperature, salinity, pH, pressure, altitude, dry conditions, and nutrient scarcity. The extremely halophilic archaea (also called haloarchaea) are a group of microorganisms requiring high salt concentrations (2–6 M NaCl) for optimal growth. Haloarchaea have different metabolic adaptations to withstand these extreme conditions. Among the adaptations, several vesicles, granules, primary and secondary metabolites are produced that are highly significant in biotechnology, such as carotenoids, halocins, enzymes, and granules of polyhydroxyalkanoates (PHAs). Among halophilic enzymes, reductases play a significant role in the textile industry and the degradation of hydrocarbon compounds. Enzymes like dehydrogenases, glycosyl hydrolases, lipases, esterases, and proteases can also be used in several industrial procedures. More recently, several studies stated that carotenoids, gas vacuoles, and liposomes produced by haloarchaea have specific applications in medicine and pharmacy. Additionally, the production of biodegradable and biocompatible polymers by haloarchaea to store carbon makes them potent candidates to be used as cell factories in the industrial production of bioplastics. Furthermore, some haloarchaeal species can synthesize nanoparticles during heavy metal detoxification, thus shedding light on a new approach to producing nanoparticles on a large scale. Recent studies also highlight that exopolysaccharides from haloarchaea can bind the SARS-CoV-2 spike protein. This review explores the potential of haloarchaea in the industry and biotechnology as cellular factories to upscale the production of diverse bioactive compounds.
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Affiliation(s)
- Jamseel Moopantakath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kerala, India
| | - Madangchanok Imchen
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - V. T. Anju
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Siddhardha Busi
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Madhu Dyavaiah
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Rosa María Martínez-Espinosa
- Biochemistry, Molecular Biology, Edaphology and Agricultural Chemistry Department, Faculty of Sciences, University of Alicante, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Alicante, Spain
- Rosa María Martínez-Espinosa,
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kerala, India
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, India
- *Correspondence: Ranjith Kumavath, ,
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11
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Wu ZP, Zheng XW, Sun YP, Wang BB, Hou J, Cui HL. Halocatena marina sp. nov., a novel filamentous halophilic archaeon isolated from marine tidal flat and emended description of the genus Halocatena. Extremophiles 2023; 27:7. [PMID: 36906854 DOI: 10.1007/s00792-023-01292-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/26/2023] [Indexed: 03/13/2023]
Abstract
Three novel filamentous halophilic archaea, strains DFN5T, RDMS1, and QDMS1, were isolated from the coastal saline soil samples of the intertidal zones located in different regions of Jiangsu Province, China. The colonies of these strains were pinkish-white due to the presence of white spores. These three strains are extremely halophilic and grew optimally at 35-37 °C and pH 7.0-7.5. Based on 16S rRNA and rpoB' gene analysis, strains DFN5T, RDMS1, and QDMS1 gathered together in phylogenetic trees and then clustered with the current species of the genus Halocatena showing 96.9-97.4% and 82.2-82.5% similarities, respectively. Both the 16S rRNA gene-based and rpoB' gene-based phylogenies were fully supported by the phylogenomic analysis, and the overall genome-related indexes indicated that strains DFN5T, RDMS1, and QDMS1 should be a novel species of the genus Halocatena. Genome mining revealed that there are considerable differences in the genes related to β-carotene synthesis among these three strains and the current species of Halocatena. The major polar lipids of strains DFN5T, RDMS1, and QDMS1 are PA, PG, PGP-Me, S-TGD-1, TGD-1, and TGD-2. The minor polar lipids, S-DGD-1, DGD-1, S2-DGD, and S-TeGD may be detected. According to the phenotypic characteristics, phylogenetic analysis, genomic and chemotaxonomic features, strains DFN5T (= CGMCC 1.19401 T = JCM 35422 T), RDMS1 (= CGMCC 1.19411) and QDMS1 (= CGMCC 1.19410) were classified as a novel species of the genus Halocatena with the proposed name, Halocatena marina sp. nov. This is the first report of the description of a novel filamentous haloarchaeon isolated from marine intertidal zones.
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Affiliation(s)
- Zhang-Ping Wu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Xi-Wen Zheng
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Ya-Ping Sun
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Bei-Bei Wang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Jing Hou
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China.
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12
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Sun YP, Wang BB, Zheng XW, Wu ZP, Hou J, Cui HL. Description of Halosolutus amylolyticus gen. nov., sp. nov., Halosolutus halophilus sp. nov. and Halosolutus gelatinilyticus sp. nov., and genome-based taxonomy of genera Natribaculum and Halovarius. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Three extremely halophilic archaeal strains (LT55T, SQT-29-1T and WLHS5T) were isolated from Gobi saline soil and a salt lake, China. These strains were most related to the genera
Natribaculum
and
Halovarius
(92.6–95.1 % similarities), and showed low similarities with other genera within the family
Natrialbaceae
based on 16S rRNA genes. Phylogenomic analysis confirmed that the three strains formed a distinct clade separated from the related genera
Halostagnicola
and
Natronococcus
, which indicated that they may represent a novel genus of the family
Natrialbaceae
. The average nucleotide identity (ANI), in silico DNA–DNA hybridization (isDDH) and average amino acid identity (AAI) values among the three strains were no more than 87, 34 and 85 %, respectively, much lower than the threshold values for species demarcation. The major phospholipids of the three strains were phosphatidic acid (PA), phosphatidylglycerol (PG) and phosphatidylglycerol phosphate methyl ester (PGP-Me). The glycolipid profiles of the three strains were diverse; sulfated mannosyl glucosyl diether (S-DGD-1) and disulfated mannosyl glucosyl diether (S2-DGD) were found in strains LT55T and WLHS5T, while mannosyl glucosyl diether (DGD-1) and S-DGD-1 in strain SQT-29-1T. The combination of phenotypic, chemotaxonomic, phylogenetic and genomic analyses suggested that strains WLHS5T (=CGMCC 1.13781T = JCM 33558T), SQT-29-1T (=CGMCC 1.16065T = JCM 33554T) and LT55T (=CGMCC 1.15188T = JCM 30838T) represent three novel species of a new genus within the family
Natrialbaceae
, for which the names, Halosolutus amylolyticus gen. nov., sp. nov., Halosolutus gelatinilyticus sp. nov. and Halosolutus halophilus sp. nov., are proposed. Genome-based classification of genera
Natribaculum
and
Halovarius
revealed that
Halovarius luteus
should be transferred to the genus
Natribaculum
as Natribaculum luteum comb. nov. and
Natribaculum longum
as a heterotypic synonym of
Natribaculum breve
Liu et al. 2015.
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Affiliation(s)
- Ya-Ping Sun
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Bei-Bei Wang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Xi-Wen Zheng
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Zhang-Ping Wu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Jing Hou
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
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13
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Vaz BMC, Kholany M, Pinto DCGA, Macário IPE, Veloso T, Caetano T, Pereira JL, Coutinho JAP, Ventura SPM. Recovery of bacterioruberin and proteins using aqueous solutions of surface-active compounds. RSC Adv 2022; 12:30278-30286. [PMID: 36337967 PMCID: PMC9590249 DOI: 10.1039/d2ra02581g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 10/02/2022] [Indexed: 11/30/2022] Open
Abstract
Haloarchaea microorganisms are little explored marine resources that can be a promising source of valuable compounds with unique characteristics, due to their adaptation to extreme environments. In this work, the extraction of bacterioruberin and proteins from Haloferax mediterranei ATCC 33500 was investigated using aqueous solutions of ionic liquids and surfactants, which were further compared with ethanol. Despite the good performance of ethanol in the extraction of bacterioruberin, the use of aqueous solutions of surface-active compounds allowed the simultaneous release of bacterioruberin and proteins in a multi-product process, with the non-ionic surfactants being identified as the most promising. The optimum operational conditions allowed a maximum extraction yield of 0.37 ± 0.01 mgbacterioruberin gwet biomass -1 and 352 ± 9 mgprotein gwet biomass -1 with an aqueous solution of Tween® 20 (at 182.4 mM) as the extraction solvent. In addition, high purities of bacterioruberin were obtained, after performing a simple induced precipitation using ethanol as an antisolvent to recover the proteins present in the initial extract. Finally, a step for polishing the bacterioruberin was performed, to enable solvent recycling, further closing the process to maximize its circularity.
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Affiliation(s)
- Bárbara M. C. Vaz
- CICECO – Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago3810-193 AveiroPortugal
| | - Mariam Kholany
- CICECO – Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago3810-193 AveiroPortugal
| | - Diana C. G. A. Pinto
- LAQV – REQUIMTE, Department of Chemistry, University of Aveiro3810-193 AveiroPortugal
| | - Inês P. E. Macário
- CICECO – Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago3810-193 AveiroPortugal,CESAM – Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro Campus Universitário de Santiago3810-193 AveiroPortugal
| | - Telma Veloso
- CICECO – Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago3810-193 AveiroPortugal,CESAM – Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro Campus Universitário de Santiago3810-193 AveiroPortugal
| | - Tânia Caetano
- CESAM – Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro Campus Universitário de Santiago3810-193 AveiroPortugal
| | - Joana L. Pereira
- CESAM – Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro Campus Universitário de Santiago3810-193 AveiroPortugal
| | - João A. P. Coutinho
- CICECO – Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago3810-193 AveiroPortugal
| | - Sónia P. M. Ventura
- CICECO – Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago3810-193 AveiroPortugal
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