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Cooper ZS, Rapp JZ, Shoemaker AMD, Anderson RE, Zhong ZP, Deming JW. Evolutionary Divergence of Marinobacter Strains in Cryopeg Brines as Revealed by Pangenomics. Front Microbiol 2022; 13:879116. [PMID: 35733954 PMCID: PMC9207381 DOI: 10.3389/fmicb.2022.879116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/05/2022] [Indexed: 11/30/2022] Open
Abstract
Marinobacter spp. are cosmopolitan in saline environments, displaying a diverse set of metabolisms that allow them to competitively occupy these environments, some of which can be extreme in both salinity and temperature. Here, we introduce a distinct cluster of Marinobacter genomes, composed of novel isolates and in silico assembled genomes obtained from subzero, hypersaline cryopeg brines, relic seawater-derived liquid habitats within permafrost sampled near Utqiaġvik, Alaska. Using these new genomes and 45 representative publicly available genomes of Marinobacter spp. from other settings, we assembled a pangenome to examine how the new extremophile members fit evolutionarily and ecologically, based on genetic potential and environmental source. This first genus-wide genomic analysis revealed that Marinobacter spp. in general encode metabolic pathways that are thermodynamically favored at low temperature, cover a broad range of organic compounds, and optimize protein usage, e.g., the Entner–Doudoroff pathway, the glyoxylate shunt, and amino acid metabolism. The new isolates contributed to a distinct clade of subzero brine-dwelling Marinobacter spp. that diverged genotypically and phylogenetically from all other Marinobacter members. The subzero brine clade displays genomic characteristics that may explain competitive adaptations to the extreme environments they inhabit, including more abundant membrane transport systems (e.g., for organic substrates, compatible solutes, and ions) and stress-induced transcriptional regulatory mechanisms (e.g., for cold and salt stress) than in the other Marinobacter clades. We also identified more abundant signatures of potential horizontal transfer of genes involved in transcription, the mobilome, and a variety of metabolite exchange systems, which led to considering the importance of this evolutionary mechanism in an extreme environment where adaptation via vertical evolution is physiologically rate limited. Assessing these new extremophile genomes in a pangenomic context has provided a unique view into the ecological and evolutionary history of the genus Marinobacter, particularly with regard to its remarkable diversity and its opportunism in extremely cold and saline environments.
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Affiliation(s)
- Zachary S. Cooper
- School of Oceanography, University of Washington, Seattle, WA, United States
- Astrobiology Program, University of Washington, Seattle, WA, United States
- *Correspondence: Zachary S. Cooper, , orcid.org/0000-0001-6515-7971
| | - Josephine Z. Rapp
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Center for Northern Studies (CEN), Université Laval, Québec, QC, Canada
- Institute of Integrative Biology and Systems (IBIS), Université Laval, Québec, QC, Canada
| | - Anna M. D. Shoemaker
- Department of Earth Sciences, Montana State University, Bozeman, MT, United States
| | - Rika E. Anderson
- Department of Biology, Carleton College, Northfield, MN, United States
| | - Zhi-Ping Zhong
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, United States
- Department of Microbiology, Ohio State University, Columbus, OH, United States
- Center of Microbiome Science, Ohio State University, Columbus, OH, United States
| | - Jody W. Deming
- School of Oceanography, University of Washington, Seattle, WA, United States
- Astrobiology Program, University of Washington, Seattle, WA, United States
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Chen M, Qin Y, Deng F, Zhou H, Wang R, Li P, Liu Y, Jiang L. Illumina MiSeq sequencing reveals microbial community succession in salted peppers with different salinity during preservation. Food Res Int 2021; 143:110234. [PMID: 33992347 DOI: 10.1016/j.foodres.2021.110234] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 02/08/2021] [Accepted: 02/14/2021] [Indexed: 12/26/2022]
Abstract
Chopped pepper is one of the traditional fermented pepper products in China. At present, the industrial production method is mainly to preserve the peppers with high salt about 1 year, and then make the product after desalination and seasoning when it is processed. However, the composition and succession of the bacterial community involved in the long-term preservation of salted pepper was complex. In this study, Illumina Miseq sequencing technology was used to reveal the succession in the bacterial community structure of different salted pepper within 10 months of preservation. The results showed that Firmicutes and Proteobacteria were dominant bacteria in all samples at the Phylum level. At the Genus level, among fresh unsalted capsicum, Fructobacillus (44.66%), Enterobacteriaceae unclassified (26.78%), Leuconostoc (12.04%) and Lactococcus (8.45%) had relatively high abundance. Enterobacteriaceae unclassified, Lactobacillus, Marinospirillum and Halomonas were identified as the main dominant bacteria in the samples with 6%-12% (w/w) salinity, and Enterobacteriaceae unclassified mainly appeared in the early stage of preservation. In 15% and 18%(w/w) salinity samples, with the increase of preservation time, the dominant genus was changed from Enterobacteriaceae unclassified to Chromohalobacterter, Tetragenococcus, Halomonas, Halovibrio, etc., while the relative abundance of Lactobacillus remained at an extremely low level. The bacterial structure of 6% (w/w) salinity samples changed significantly during preservation, while the distribution in PCoA analysis of salinity samples of 9% was similar to that of 12%. In the high-salinity samples (15%-18%), the composition of the community was highly similar in 0-6 months, but the composition changed significantly with the increase of the preservation time and the growth of halophilic bacteria (p < 0.01). Pearson correlation analysis was used to investigate that Lactobacillus exhibited a negative correlation with salinity (p < 0.01). And the salinity had a positive correlation with both the species richness and evenness in the samples, which might be the key factor for the change of the microbial community.
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Affiliation(s)
- Mengjuan Chen
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, People's Republic of China
| | - Yeyou Qin
- Hunan tantanxiang Biotechnology Co., Ltd, Changsha 410128, People's Republic of China
| | - Fangming Deng
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, People's Republic of China; Hunan Provincial Key Laboratory of Food Science and Biotechnology, Changsha 410128, People's Republic of China
| | - Hui Zhou
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, People's Republic of China; Hunan Provincial Key Laboratory of Food Science and Biotechnology, Changsha 410128, People's Republic of China
| | - Rongrong Wang
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, People's Republic of China; Hunan Provincial Key Laboratory of Food Science and Biotechnology, Changsha 410128, People's Republic of China
| | - Pao Li
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, People's Republic of China; Hunan Provincial Key Laboratory of Food Science and Biotechnology, Changsha 410128, People's Republic of China
| | - Yang Liu
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, People's Republic of China; Hunan Provincial Key Laboratory of Food Science and Biotechnology, Changsha 410128, People's Republic of China
| | - Liwen Jiang
- College of Food Science and Technology, Hunan Agricultural University, Changsha 410128, People's Republic of China; Hunan Provincial Key Laboratory of Food Science and Biotechnology, Changsha 410128, People's Republic of China.
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Li G, Wang S, Gai Y, Liu X, Lai Q, Shao Z. Marinobacter changyiensis, sp. nov., isolated from offshore sediment. Int J Syst Evol Microbiol 2020; 70:3004-3011. [PMID: 32320379 DOI: 10.1099/ijsem.0.004118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, Gram-stain-negative bacterium, designated CLL7-20T, was isolated from a marine sediment sample from offshore of Changyi, Shandong Province, China. Cells of strain CLL7-20T were rod-shaped, motile with one or more polar flagella, and grew optimally at pH 7.0, at 28 °C and with 3 % (w/v) NaCl. The principal fatty acids of strain CLL7-20T were C16 : 0 and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c). The main polar lipids of strain CLL7-20T were phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG) and an unidentified aminolipid (AL). Strain CLL7-20T contained Q-9 as the major respiratory quinone. The G+C content of its genomic DNA was 56.2 mol%. Phylogenetically, strain CLL7-20T branched within the genus Marinobacter, with M. daqiaonensis YCSA40T being its closest phylogenetic relative (96.7 % 16S rRNA gene sequence similarity), followed by M. sediminum R65T (96.6 %). Average nucleotide identity and in silico DNA-DNA hybridization values between strain CLL7-20T and the closest related reference strains were 73.2% and 19.8 %, respectively. On the basis of its phenotypic, phylogenetic and chemotaxonomic characteristics, we suggest that strain CLL7-20T (=MCCC 1A14855T=KCTC 72664T) is the type strain of a novel species in the genus Marinobacter, for which the name Marinobacter changyiensis sp. nov. is proposed. Based on the genomic analysis, siderophore genes were found from strain CLL7-20T, which indicate its potential as a promising alternative to chemical fertilizers in iron-limitated environments such as saline soils.
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Affiliation(s)
- Guangyu Li
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, PR China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, PR China
| | - Shanshan Wang
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, PR China
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, PR China
| | - Yingbao Gai
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, PR China
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, PR China
| | - Xiupian Liu
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, PR China
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, PR China
| | - Qiliang Lai
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, PR China
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, PR China
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, PR China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, PR China
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Wang L, Li Y, Niu L, Zhang W, Li J, Yang N. Experimental studies and kinetic modeling of the growth of phenol-degrading bacteria in turbulent fluids. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:22711-22720. [PMID: 27557974 DOI: 10.1007/s11356-016-7460-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/10/2016] [Indexed: 06/06/2023]
Abstract
Understanding the interaction between microorganisms and fluid dynamics is important for aquatic ecosystems, though only sporadic attention has been focused on this topic in the past. In this study, particular attention was paid to the phenol-degrading bacterial strains Microbacterium oxydans LY1 and Alcaligenes faecalis LY2 subjected to controlled fluid flow under laboratory conditions. These two strains were found to be able to degrade phenols over a concentration range from 50 to 500 mg/L under different turbulence conditions ranging from 0 to 250 rpm. The time it took to reach total phenol degradation decreased when the turbulence was increased in both strains, with increasing energy dissipation rates ranging from 0.110 to 6.241 W/kg, corresponding to changes in the bacterial diffusive sublayer thickness (δ) and enhanced oxygen uptake. Moreover, the maximum specific growth rates of the two strains also increased with the enhancement of turbulence. A model integrating growth inhibition and fluid motion was proposed based on the self-inhibition Haldane model by introducing a turbulence parameter, α. The resulting modified Haldane model was designed to include fluid motion as a variable in the quantification of the physiological responses of microorganisms. This modified Haldane model could be considered a useful laboratory reference when modeling procedures for water environment bioremediation. Graphical abstract Cell nutrition uptake cartoon schematic diagram for M. oxydans LY1 under different turbulent condition (50 and 200 rpm).
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Affiliation(s)
- Linqiong Wang
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, People's Republic of China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, People's Republic of China.
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, People's Republic of China
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, People's Republic of China
| | - Jie Li
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, People's Republic of China
| | - Nan Yang
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, People's Republic of China
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Halophiles: biology, adaptation, and their role in decontamination of hypersaline environments. World J Microbiol Biotechnol 2016; 32:135. [PMID: 27344438 DOI: 10.1007/s11274-016-2081-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/07/2016] [Indexed: 10/21/2022]
Abstract
The unique cellular enzymatic machinery of halophilic microbes allows them to thrive in extreme saline environments. That these microorganisms can prosper in hypersaline environments has been correlated with the elevated acidic amino acid content in their proteins, which increase the negative protein surface potential. Because these microorganisms effectively use hydrocarbons as their sole carbon and energy sources, they may prove to be valuable bioremediation agents for the treatment of saline effluents and hypersaline waters contaminated with toxic compounds that are resistant to degradation. This review highlights the various strategies adopted by halophiles to compensate for their saline surroundings and includes descriptions of recent studies that have used these microorganisms for bioremediation of environments contaminated by petroleum hydrocarbons. The known halotolerant dehalogenase-producing microbes, their dehalogenation mechanisms, and how their proteins are stabilized is also reviewed. In view of their robustness in saline environments, efforts to document their full potential regarding remediation of contaminated hypersaline ecosystems merits further exploration.
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