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Feng Z, Wang Y, Ma L, Huang S, Wang L, He J, Guo C. Genomic Characteristics and Functional Analysis of Brucella sp. Strain WY7 Isolated from Antarctic Krill. Microorganisms 2023; 11:2281. [PMID: 37764125 PMCID: PMC10536100 DOI: 10.3390/microorganisms11092281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Antarctic krill (Euphausia superba) is a key species of the Antarctic ecosystem whose unique ecological status and great development potential have attracted extensive attention. However, the genomic characteristics and potential biological functions of the symbiotic microorganisms of Antarctic krill remain unknown. In this study, we cultured and identified a strain of Brucella sp. WY7 from Antarctic krill using whole-genome sequencing and assembly, functional annotation, and comparative genomics analysis. First, based on 16S rDNA sequence alignment and phylogenetic tree analysis, we identified strain WY7 as Brucella. The assembled genome of strain WY7 revealed that it has two chromosomes and a plasmid, with a total genome length of 4,698,850 bp and an average G + C content of 57.18%. The DNA-DNA hybridization value and average nucleotide identity value of strain WY7 and Brucella anthropi ATCC® 49188TM, a type strain isolated from human clinical specimens, were 94.8% and 99.07%, respectively, indicating that strain WY7 is closely related to Brucella anthropi. Genomic island prediction showed that the strain has 60 genomic islands, which may produce HigB and VapC toxins. AntiSMASH analysis results showed that strain WY7 might produce many secondary metabolites, such as terpenes, siderophores and ectoine. Moreover, the genome contains genes involved in the degradation of aromatic compounds, suggesting that strain WY7 can use aromatic compounds in its metabolism. Our work will help to understand the genomic characteristics and metabolic potential of bacterial strains isolated from Antarctic krill, thereby revealing their roles in Antarctic krill and marine ecosystems.
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Affiliation(s)
- Zhengqi Feng
- State Key Laboratory for Biocontrol and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, China; (Z.F.); (Y.W.); (S.H.); (J.H.)
| | - Yuanyuan Wang
- State Key Laboratory for Biocontrol and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, China; (Z.F.); (Y.W.); (S.H.); (J.H.)
| | - Lingbo Ma
- Key Laboratory of the East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Shanghai 116023, China; (L.M.); (L.W.)
| | - Shanzi Huang
- State Key Laboratory for Biocontrol and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, China; (Z.F.); (Y.W.); (S.H.); (J.H.)
| | - Lumin Wang
- Key Laboratory of the East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Shanghai 116023, China; (L.M.); (L.W.)
| | - Jianguo He
- State Key Laboratory for Biocontrol and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, China; (Z.F.); (Y.W.); (S.H.); (J.H.)
- Guangdong Province Key Laboratory for Aquatic Economic Animals, and Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, China
| | - Changjun Guo
- State Key Laboratory for Biocontrol and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, China; (Z.F.); (Y.W.); (S.H.); (J.H.)
- Guangdong Province Key Laboratory for Aquatic Economic Animals, and Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Sun Yat-sen University, 135 Xingang Road West, Guangzhou 510275, China
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Groups of Geomicrobiological Indicators Are Spread across Gas-Hydrate and Non-Gas-Hydrate Areas in the Northern Part of the Sea of Japan. BIOLOGY 2022; 11:biology11121802. [PMID: 36552312 PMCID: PMC9774978 DOI: 10.3390/biology11121802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/03/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022]
Abstract
The bioindication of oil and gas fields is a field of geomicrobiology that is mainly devoted to the detection of hydrocarbon-oxidizing microbial indicator species or functional genes in total DNA. However, it appears promising to use the physiological properties of microorganisms detection deposit type of hydrocarbons, in particular their ability to oxidize hydrocarbons under aerobic and anaerobic conditions. In this study, the most promising approach in this area was the method used for assessing the anaerobic degradation of hydrocarbons. When comparing molecular genetics and cultured methods of bioindication, it can be concluded that molecular biomarkers of functional genes for the anaerobic destruction of hydrocarbons (masD) make it possible to separate areas with traditional and gas-hydrate types of deposits. Using cultured methods, we found that representatives of the Nocardiaceae family of the phylum Actinomycetota were tied to the areas where gas hydrates were found. The ability of aerobic and facultative anaerobic hydrocarbon-oxidizing microorganisms to anaerobically utilize hydrocarbons was determined with cultured methods. For the first time, this ability was revealed for the genera Stenotrophomonas, Psychrobacter, Micrococcus and Peribacillus. The wide distribution of this ability that we found in strains isolated from both study regions suggests its prominent role in the destruction of hydrocarbons in marine sediments.
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Trindade M, Sithole N, Kubicki S, Thies S, Burger A. Screening Strategies for Biosurfactant Discovery. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2021; 181:17-52. [PMID: 34518910 DOI: 10.1007/10_2021_174] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The isolation and screening of bacteria and fungi for the production of surface-active compounds has been the basis for the majority of the biosurfactants discovered to date. Hence, a wide variety of well-established and relatively simple methods are available for screening, mostly focused on the detection of surface or interfacial activity of the culture supernatant. However, the success of any biodiscovery effort, specifically aiming to access novelty, relies directly on the characteristics being screened for and the uniqueness of the microorganisms being screened. Therefore, given that rather few novel biosurfactant structures have been discovered during the last decade, advanced strategies are now needed to widen access to novel chemistries and properties. In addition, more modern Omics technologies should be considered to the traditional culture-based approaches for biosurfactant discovery. This chapter summarizes the screening methods and strategies typically used for the discovery of biosurfactants and highlights some of the Omics-based approaches that have resulted in the discovery of unique biosurfactants. These studies illustrate the potentially enormous diversity that has yet to be unlocked and how we can begin to tap into these biological resources.
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Affiliation(s)
- Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Cape Town, South Africa.
| | - Nombuso Sithole
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Cape Town, South Africa
| | - Sonja Kubicki
- Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Stephan Thies
- Institute of Molecular Enzyme Technology, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Anita Burger
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Cape Town, South Africa
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França ÍWL, Oliveira DWF, Giro MEA, Melo VMM, Gonçalves LRB. Production of surfactin by
Bacillus subtilis
LAMI005
and evaluation of its potential as tensoactive and emulsifier. CAN J CHEM ENG 2021. [DOI: 10.1002/cjce.24240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | | | | | - Vânia Maria Maciel Melo
- Departamento de Biologia ‐ LemBiotech ‐ Laboratório de Ecologia Microbiana e Biotecnologia Universidade Federal do Ceará Fortaleza Brazil
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Optimization of an Autochthonous Bacterial Consortium Obtained from Beach Sediments for Bioremediation of Petroleum Hydrocarbons. WATER 2020. [DOI: 10.3390/w13010066] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Oil spill pollution remains a serious concern in marine environments and the development of effective oil bioremediation techniques are vital. This work is aimed at developing an autochthonous hydrocarbon-degrading consortium with bacterial strains with high potential for hydrocarbons degradation, optimizing first the growth conditions for the consortium, and then testing its hydrocarbon-degrading performance in microcosm bioremediation experiments. Bacterial strains, previously isolated from a sediment and cryopreserved in a georeferenced microbial bank, belonged to the genera Pseudomonas, Rhodococcus and Acinetobacter. Microcosms were assembled with natural seawater and petroleum, for testing: natural attenuation (NA); biostimulation (BS) (nutrients addition); bioaugmentation with inoculum pre-grown in petroleum (BA/P) and bioaugmentation with inoculum pre-grown in acetate (BA/A). After 15 days, a clear blending of petroleum with seawater was observed in BS, BA/P and BA/A but not in NA. Acetate was the best substrate for consortium growth. BA/A showed the highest hydrocarbons degradation (66%). All bacterial strains added as inoculum were recovered at the end of the experiment. This study provides an insight into the capacity of autochthonous communities to degrade hydrocarbons and on the use of alternative carbon sources for bacterial biomass growth for the development of bioremediation products to respond to oil spills.
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