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Yang H, Qian Z, Liu Y, Yu F, Huang T, Zhang B, Peng T, Hu Z. Comparative genomics reveals evidence of polycyclic aromatic hydrocarbon degradation in the moderately halophilic genus Pontibacillus. JOURNAL OF HAZARDOUS MATERIALS 2024; 462:132724. [PMID: 37839372 DOI: 10.1016/j.jhazmat.2023.132724] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/22/2023] [Accepted: 10/04/2023] [Indexed: 10/17/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are a common class of persistent organic pollutants (POPs) that are widely distributed in various environments and pose significant threats to both environmental and human health. The genus Pontibacillus, a type of moderately halophilic bacteria, has demonstrated potential for biodegrading aromatic compounds in high-salinity environments. However, no previous study has comprehensively investigated the PAH degradation mechanisms and environmental adaptability in the genus Pontibacillus. In this study, we sequenced the whole genome of the PAH-degrading strain Pontibacillus chungwhensis HN14 and conducted a comparative genomics analysis of genes associated with PAH degradation, as well as salt and arsenic tolerance using ten other Pontibacillus sp. strains. Here, we elucidated potential degradation pathways for benzo[a]pyrene and phenanthrene, which were initiated by cytochrome P450 monooxygenases, in most Pontibacillus strains. Moreover, four Pontibacillus strains were selected to investigate the biodegradation of benzo[a]pyrene and phenanthrene under high-salt (5% NaCl) stress, and all four strains exhibited exceptional degradation abilities. The results of comparative genomics and phenotypic analyses demonstrate that the genus Pontibacillus have the potential to degrade polycyclic aromatic hydrocarbons in high-salinity environments, thus providing valuable insights for biodegradation in extreme environments.
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Affiliation(s)
- Haichen Yang
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China
| | - Zhihui Qian
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China
| | - Yongjin Liu
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China
| | - Fei Yu
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China
| | - Tongwang Huang
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China
| | - Bing Zhang
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China
| | - Tao Peng
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China.
| | - Zhong Hu
- Department of Biology, Shantou University, Shantou, Guangdong 515063, PR China; Guangdong Research Center of Offshore Environmental Pollution Control Engineering, Shantou University, Shantou 515063, Guangdong, PR China.
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Purohit A, Pawar L, Yadav SK. Structural and functional insights of a cold-adaptive β-glucosidase with very high glucose tolerance from Microbacterium sp. CIAB417. Enzyme Microb Technol 2023; 169:110284. [PMID: 37406591 DOI: 10.1016/j.enzmictec.2023.110284] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/07/2023]
Abstract
A gene glu1 (WP_243232135.1) coding for β-glucosidase from the genome of Microbacterium sp. CIAB417 was characterized for its cold adaptive nature and tolerance to high levels of glucose and ethanol. The phylogenetic analysis suggested the close association of glu1 with a similar gene from a mesophilic bacterium Microbacterium indicum. The purified recombinant GLU1 displayed its optimal activity and stability at pH 5 and temperature 30ᴼC. Additionally, the presence of L3 loop in GLU1 suggested its cold adaptive nature. The glucose tolerant Gate keeper residues (Leu 174 & Trp 169) with a distance of ∼ 6.953 Å between them was also predicted in GLU1. The GLU1 enzyme showed ≥ 95% and ≥ 40% relative activity in the presence of 5 M glucose and 20% ethanol. The Vmax, Km, and Kcat values of GLU1 for cellobiose substrate were observed to be 45.22 U/mg, 3.5 mM, and 41.0157 s-1, respectively. The GLU1 was found to be highly efficient in hydrolysis of celloologosaccharides (C2-C5), lactose and safranal picrocrocin into glucose. Hence, cold adaptive GLU1 with very high glucose and ethanol tolerance could be very useful in bio-refinery, dairy, and flavor industries.
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Affiliation(s)
- Anjali Purohit
- Biotechnology and Synthetic Biology, Center of Innovative and Applied Bioprocessing (CIAB), Knowledge City, Sector-81, Mohali 140306, Punjab, India
| | - Lata Pawar
- Biotechnology and Synthetic Biology, Center of Innovative and Applied Bioprocessing (CIAB), Knowledge City, Sector-81, Mohali 140306, Punjab, India
| | - Sudesh Kumar Yadav
- Biotechnology and Synthetic Biology, Center of Innovative and Applied Bioprocessing (CIAB), Knowledge City, Sector-81, Mohali 140306, Punjab, India; Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, India.
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Qian Z, Peng T, Huang T, Hu Z. Oxidization of benzo[a]pyrene by CYP102 in a novel PAHs-degrader Pontibacillus sp. HN14 with potential application in high salinity environment. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 321:115922. [PMID: 36027730 DOI: 10.1016/j.jenvman.2022.115922] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/25/2022] [Accepted: 07/30/2022] [Indexed: 06/15/2023]
Abstract
Benzo [a]pyrene (BaP) is a type of high-molecular-weight polycyclic aromatic hydrocarbons (PAHs) with potent carcinogenicity; however, there are limited studies on its degradation mechanism. Here, a strain of Pontibacillus sp. HN14 with BaP degradation ability was isolated from mangrove sediments in Dongzhai Port, Hainan Province. Our study showed that biodegradation efficiencies reached 42.15% after Pontibacillus sp. HN14 was cultured with 20 mg L-1 BaP as the sole carbon source for 25 days and still had degradability of BaP at a 25% high salinity level. Moreover, 9,10-dihydrobenzo [a]pyrene-7(8H)-one, an intermediate metabolite, was detected during BaP degradation in the HN14 strain. Genome analysis identified a gene encoding the CYP102(HN14) enzyme. The results showed that the E. coli strain with CYP102(HN14) overexpression could transfer BaP to 9,10-dihydrobenzo [a]pyrene-7(8H)-one with a conversion rate of 43.5%, indicating that CYP102(HN14) played an essential role in BaP degradation in Pontibacillus sp. HN14. Thus, our results provide a novel BaP biodegradation molecule, which could be used in BaP bioremediation in high salinity conditions. This study is the first to show that CYP102(HN14) had the BaP oxidization ability in bacteria. CYP102(HN14) could be essential in removing PAHs in saline-alkali soil and other high salt environments through enzyme immobilization.
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Affiliation(s)
- Zhihui Qian
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, PR China
| | - Tao Peng
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, PR China
| | - Tongwang Huang
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, PR China
| | - Zhong Hu
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, Guangdong, PR China.
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Pontibacillus sp. ALD_SL1 and Psychroflexus sp. ALD_RP9, two novel moderately halophilic bacteria isolated from sediment and water from the Aldabra Atoll, Seychelles. PLoS One 2021; 16:e0256639. [PMID: 34437618 PMCID: PMC8389477 DOI: 10.1371/journal.pone.0256639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/11/2021] [Indexed: 12/04/2022] Open
Abstract
Pontibacillus sp. ALD_SL1 and Psychroflexus sp. ALD_RP9 are two novel bacterial isolates from mangrove sediment and a moderately hypersaline pool on the Aldabra Atoll, Seychelles. The isolates represent two novel species were characterised physiologically and genomically. Pontibacillus sp. ALD_SL1 is a facultatively anaerobic yellow, motile, rod-shaped Gram-positive, which grows optimally at a NaCl concentration of 11%, pH 7 and 28°C. It is the third facultatively anaerobic member of the genus Pontibacillus. The organism gains energy through the fermentation of pyruvate to acetate and ethanol under anaerobic conditions. The genome is the first among Pontibacillus that harbours a megaplasmid. Psychroflexus sp. ALD_RP9 is an aerobic heterotroph, which can generate energy by employing bacteriorhodopsins. It forms Gram-negative, orange, non-motile rods. The strain grows optimally at NaCl concentrations of 10%, pH 6.5–8 and 20°C. The Psychroflexus isolate tolerated pH conditions up to 10.5, which is the highest pH tolerance currently recorded for the genus. Psychroflexus sp. ALD_RP9 taxonomically belongs to the clade with the smallest genomes. Both isolates show extensive adaptations to their saline environments yet utilise different mechanisms to ensure survival.
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Martin‐Cuadrado A, Senel E, Martínez‐García M, Cifuentes A, Santos F, Almansa C, Moreno‐Paz M, Blanco Y, García‐Villadangos M, Cura MÁG, Sanz‐Montero ME, Rodríguez‐Aranda JP, Rosselló‐Móra R, Antón J, Parro V. Prokaryotic and viral community of the sulfate‐rich crust from Peñahueca ephemeral lake, an astrobiology analogue. Environ Microbiol 2019; 21:3577-3600. [DOI: 10.1111/1462-2920.14680] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 05/09/2019] [Accepted: 05/11/2019] [Indexed: 11/29/2022]
Affiliation(s)
| | - Ece Senel
- Department of Physiology, Genetics and MicrobiologyUniversity of Alicante Alicante Spain
- Department of BiologyGraduate School of Sciences, Eskisehir Technical University Yunusemre Campus, Eskisehir 26470 Turkey
| | - Manuel Martínez‐García
- Department of Physiology, Genetics and MicrobiologyUniversity of Alicante Alicante Spain
| | - Ana Cifuentes
- Department of Ecology and Marine Resources, Marine Microbiology GroupMediterranean Institute for Advanced Studies (IMEDEA, CSIC‐UIB) Esporles Spain
| | - Fernando Santos
- Department of Physiology, Genetics and MicrobiologyUniversity of Alicante Alicante Spain
| | - Cristina Almansa
- Research Technical Services (SSTTI), Microscopy UnitUniversity of Alicante Alicante Spain
| | - Mercedes Moreno‐Paz
- Department of Molecular EvolutionCentro de Astrobiología (INTA‐CSIC) Madrid Spain
| | - Yolanda Blanco
- Department of Molecular EvolutionCentro de Astrobiología (INTA‐CSIC) Madrid Spain
| | | | | | | | | | - Ramon Rosselló‐Móra
- Department of BiologyGraduate School of Sciences, Eskisehir Technical University Yunusemre Campus, Eskisehir 26470 Turkey
| | - Josefa Antón
- Department of Physiology, Genetics and MicrobiologyUniversity of Alicante Alicante Spain
| | - Víctor Parro
- Department of Molecular EvolutionCentro de Astrobiología (INTA‐CSIC) Madrid Spain
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Sultanpuram VR, Mothe T, Mohammed F, Chintalapati S, Chintalapati VR. Pontibacillus salipaludis sp. nov., a slightly halophilic bacterium isolated from a salt pan. Int J Syst Evol Microbiol 2016; 66:3884-3889. [PMID: 27381178 DOI: 10.1099/ijsem.0.001281] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel Gram-stain-positive, facultatively anerobic, rod-shaped, motile, endospore-forming bacterial strains, 9DMT and 6DM, were isolated from Tuticorn, India. The high 16S rRNA gene sequence similarity (99.9 %) and DNA-DNA relatedness (88±2 %) indicated that strains 9DMT and 6DM were members of a single species. Based on 16S rRNA gene sequence analysis these strains were identified as belonging to the genus Pontibacillus and were related most closely to the type strains of Pontibacillus chungwhensis (99.7 % sequence similarity) and Pontibacillus marinus (97.9 %). The DNA G+C content of strains 9DMT and 6DM was 41.6 and 41.4 mol%, respectively. However, the level of DNA-DNA relatedness of these strains with P. chungwhensis KCTC 3890T and P. marinus KCTC 3917T was only 40.9 + 0.8 and 39.8 + 0.9 %, respectively. Strains 9DMT and 6DM were facultative anaerobes with optimal growth at 37 °C, at pH 7.0-8.0 and with 2-3 % (w/v) NaCl. The cell-wall peptidoglycan of strain 9DMT contained meso-diaminopimelic acid. Polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, a phospholipid and three unknown lipids. The isoprenoid quinone was MK-7. Major fatty acids of strain 9DMT were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The results of phylogenetic, chemotaxonomic and biochemical tests allowed the clear differentiation of strains 9DMT and 6DM, which are considered to represent a novel member of the genus Pontibacillus, for which the name Pontibacillus salipaludis sp. nov. is proposed. The type strain is 9DMT (= KCTC 33742T=LMG 29102T= CGMCC 1.15353T).
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Affiliation(s)
- Vishnuvardhan Reddy Sultanpuram
- Microbial Ecology Lab, Department of Biochemistry, Mahatma Gandhi University, Anneparthy, Yellareddygudem (PO), Nalgonda-508254, Telangana, India
| | - Thirumala Mothe
- Microbial Ecology Lab, Department of Biochemistry, Mahatma Gandhi University, Anneparthy, Yellareddygudem (PO), Nalgonda-508254, Telangana, India
| | - Farooq Mohammed
- Microbial Ecology Lab, Department of Biochemistry, Mahatma Gandhi University, Anneparthy, Yellareddygudem (PO), Nalgonda-508254, Telangana, India
| | - Sasikala Chintalapati
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University, Kukatpally, Hyderabad-500085, Telangana, India
| | - Venkata Ramana Chintalapati
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad-500046, Telangana, India
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Huang J, Qiao ZX, Tang JW, Wang G. High quality draft genome sequence of the moderately halophilic bacterium Pontibacillus yanchengensis Y32(T) and comparison among Pontibacillus genomes. Stand Genomic Sci 2015; 10:93. [PMID: 26561516 PMCID: PMC4641356 DOI: 10.1186/s40793-015-0085-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 10/19/2015] [Indexed: 11/10/2022] Open
Abstract
Pontibacillus yanchengensis Y32(T) is an aerobic, motile, Gram-positive, endospore-forming, and moderately halophilic bacterium isolated from a salt field. In this study, we describe the features of P. yanchengensis strain Y32(T) together with a comparison with other four Pontibacillus genomes. The 4,281,464 bp high-quality-draft genome of strain Y32(T) is arranged into 153 contigs containing 3,965 protein-coding genes and 77 RNA encoding genes. The genome of strain Y32(T) possesses many genes related to its halophilic character, flagellar assembly and chemotaxis to support its survival in a salt-rich environment.
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Affiliation(s)
- Jing Huang
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070 P. R. China
| | - Zi xu Qiao
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070 P. R. China
| | - Jing wei Tang
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070 P. R. China
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070 P. R. China
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Pontibacillus salicampi sp. nov., a moderately halophilic bacterium isolated from saltern soil. Int J Syst Evol Microbiol 2015; 65:375-380. [DOI: 10.1099/ijs.0.066423-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
A Gram-stain-positive, moderately halophilic bacterium, designated BH043T, was isolated from saltern soil of Gomso in Korea. Cells were motile rods, producing ellipsoidal endospores at a terminal position in swollen sporangia. Strain BH043T was strictly aerobic, grew at pH 6.0–10.0 (optimal growth at pH 7.5), at 10–55 °C (optimal growth at 30 °C) and at salinities of 1–20 % (w/v) NaCl, growing optimally with 7 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain BH043T belongs to the family
Bacillaceae
and was most closely related to the type strains of the five recognized species of the genus
Pontibacillus
, showing sequence similarity to
Pontibacillus yanchengensis
Y32T (97.5 % similarity),
Pontibacillus marinus
BH030004T (97.4 %),
Pontibacillus chungwhensis
BH030062T (97.0 %),
Pontibacillus litoralis
JSM 072002T (96.4 %) and
Pontibacillus halophilus
JSM 076056T (96.2 %). The major cellular fatty acids of strain BH043T were iso-C15 : 0 and anteiso-C15 : 0. The genomic DNA G+C content was 42.5 mol%. The major isoprenoid quinone was MK-7 and meso-diaminopimelic acid was present in the cell-wall peptidoglycan as the diagnostic diamino acid. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. DNA–DNA relatedness between strain BH043T and the type strains of other species of the genus
Pontibacillus
,
P. yanchengensis
CGMCC 1.10680T and
P. marinus
KCTC 3917T and
P. chungwhensis
KCTC 3890T, was 35, 24 and 18 %, respectively. On the basis of polyphasic analysis from this study, strain BH043T represents a novel species of the genus
Pontibacillus
for which the name Pontibacillus
salicampi sp. nov. is proposed. The type strain is BH043T ( = KACC 17607T = NBRC 109831T = NCAIM B.02529T).
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Abstract
ABSTRACT
The family
Bacillaceae
constitutes a phenotypically diverse and globally ubiquitous assemblage of bacteria. Investigation into how evolution has shaped, and continues to shape, this family has relied on several widely ranging approaches from classical taxonomy, ecological field studies, and evolution in soil microcosms to genomic-scale phylogenetics, laboratory, and directed evolution experiments. One unifying characteristic of the
Bacillaceae
, the endospore, poses unique challenges to answering questions regarding both the calculation of evolutionary rates and claims of extreme longevity in ancient environmental samples.
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