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Villacís JE, Castelán-Sánchez HG, Rojas-Vargas J, Rodríguez-Cruz UE, Albán V, Reyes JA, Meza-Rodríguez PM, Dávila-Ramos S, Villavicencio F, Galarza M, Gestal MC. Emergence of Raoultella ornithinolytica in human infections from different hospitals in Ecuador with OXA-48-producing resistance. Front Microbiol 2023; 14:1216008. [PMID: 37692398 PMCID: PMC10484340 DOI: 10.3389/fmicb.2023.1216008] [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: 05/03/2023] [Accepted: 08/01/2023] [Indexed: 09/12/2023] Open
Abstract
Purpose The purpose of this study was to highlight the clinical and molecular features of 13 Raoultella ornithinolytica strains isolated from clinical environments in Ecuador, and to perform comparative genomics with previously published genomes of Raoultella spp. As Raoultella is primarily found in environmental, clinical settings, we focused our work on identifying mechanisms of resistance that can provide this bacterium an advantage to establish and persist in hospital environments. Methods We analyzed 13 strains of Raoultella ornithinolytica isolated from patients with healthcare associated infections (HAI) in three hospitals in Quito and one in Santo Domingo de Los Tsáchilas, Ecuador, between November 2017 and April 2018. These isolates were subjected to phenotypic antimicrobial susceptibility testing, end-point polymerase chain reaction (PCR) to detect the presence of carbapenemases and whole-genome sequencing. Results Polymerase chain reaction revealed that seven isolates were positive isolates for blaOXA-48 and one for blaKPC-2 gene. Of the seven strains that presented the blaOXA-48 gene, six harbored it on an IncFII plasmid, one was inserted into the bacterial chromosome. The blaKPC gene was detected in an IncM2/IncR plasmid. From the bioinformatics analysis, nine genomes had the gene blaOXA-48, originating from Ecuador. Moreover, all R. ornithinolytica strains contained the ORN-1 gene, which confers resistance for β-lactams, such as penicillins and cephalosporins. Comparative genome analysis of the strains showed that the pangenome of R. ornithinolytica is considered an open pangenome, with 27.77% of core genes, which could be explained by the fact that the antibiotic resistance genes in the ancestral reconstruction are relatively new, suggesting that this genome is constantly incorporating new genes. Conclusion These results reveal the genome plasticity of R. ornithinolytica, particularly in acquiring antibiotic-resistance genes. The genomic surveillance and infectious control of these uncommon species are important since they may contribute to the burden of antimicrobial resistance and human health.
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Affiliation(s)
- José E. Villacís
- Centro de Investigación para la Salud en América Latina (CISeAL), Pontificia Universidad Católica del Ecuador, Quito, Ecuador
- Centro de Referencia Nacional de Resistencia a los Antimicrobianos, Instituto Nacional de Investigación en Salud Pública, “Leopoldo Izquieta Pérez,” Quito, Ecuador
| | - Hugo G. Castelán-Sánchez
- Programa Investigadoras e Investigadores por México, Grupo de Genómica y Dinámica Evolutiva de Microorganismos Emergentes, Consejo Nacional de Ciencia y Tecnología, México City, Mexico
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Jorge Rojas-Vargas
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Ulises E. Rodríguez-Cruz
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, México City, Mexico
| | - Viviana Albán
- Centro de Referencia Nacional de Resistencia a los Antimicrobianos, Instituto Nacional de Investigación en Salud Pública, “Leopoldo Izquieta Pérez,” Quito, Ecuador
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, United States
| | - Jorge A. Reyes
- Facultad de Ciencias Químicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Pablo M. Meza-Rodríguez
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Sonia Dávila-Ramos
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Fernando Villavicencio
- Centro de Referencia Nacional de Resistencia a los Antimicrobianos, Instituto Nacional de Investigación en Salud Pública, “Leopoldo Izquieta Pérez,” Quito, Ecuador
| | | | - Monica C. Gestal
- Department of Microbiology and Immunology, Louisiana State University (LSU), Health Science Center at Shreveport, Shreveport, LA, United States
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Zhang X, Xiao L, Liu J, Tian Q, Xie J. Trade-off in genome turnover events leading to adaptive evolution of Microcystis aeruginosa species complex. BMC Genomics 2023; 24:462. [PMID: 37592233 PMCID: PMC10433662 DOI: 10.1186/s12864-023-09555-3] [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: 03/21/2023] [Accepted: 08/04/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND Numerous studies in the past have expanded our understanding of the genetic differences of global distributed cyanobacteria that originated around billions of years ago, however, unraveling how gene gain and loss drive the genetic evolution of cyanobacterial species, and the trade-off of these evolutionary forces are still the central but poorly understood issues. RESULTS To delineate the contribution of gene flow in mediating the hereditary differentiation and shaping the microbial evolution, a global genome-wide study of bloom-forming cyanobacterium, Microcystis aeruginosa species complex, provided robust evidence for genetic diversity, reflected by enormous variation in gene repertoire among various strains. Mathematical extrapolation showed an 'open' microbial pan-genome of M. aeruginosa species, since novel genes were predicted to be introduced after new genomes were sequenced. Identification of numerous horizontal gene transfer's signatures in genome regions of interest suggested that genome expansion via transformation and phage-mediated transduction across bacterial lineage as an evolutionary route may contribute to the differentiation of Microcystis functions (e.g., carbohydrate metabolism, amino acid metabolism, and energy metabolism). Meanwhile, the selective loss of some dispensable genes at the cost of metabolic versatility is as a mean of adaptive evolution that has the potential to increase the biological fitness. CONCLUSIONS Now that the recruitment of novel genes was accompanied by a parallel loss of some other ones, a trade-off in gene content may drive the divergent differentiation of M. aeruginosa genomes. Our study provides a genetic framework for the evolution of M. aeruginosa species and illustrates their possible evolutionary patterns.
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Affiliation(s)
- Xian Zhang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China.
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Central South University, Changsha, China.
| | - Lijun Xiao
- Guangdong Corps Hospital of Chinese People's Armed Police Forces, Guangzhou, China
| | - Jiahui Liu
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
| | - Qibai Tian
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
| | - Jiaqi Xie
- Hunan Food and Drug Vocational College, Changsha, China
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3
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Huang S, Li H, Ma L, Liu R, Li Y, Wang H, Lu X, Huang X, Wu X, Liu X. Insertion sequence contributes to the evolution and environmental adaptation of Acidithiobacillus. BMC Genomics 2023; 24:282. [PMID: 37231368 DOI: 10.1186/s12864-023-09372-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/10/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND The genus Acidithiobacillus has been widely concerned due to its superior survival and oxidation ability in acid mine drainage (AMD). However, the contribution of insertion sequence (IS) to their biological evolution and environmental adaptation is very limited. ISs are the simplest kinds of mobile genetic elements (MGEs), capable of interrupting genes, operons, or regulating the expression of genes through transposition activity. ISs could be classified into different families with their own members, possessing different copies. RESULTS In this study, the distribution and evolution of ISs, as well as the functions of the genes around ISs in 36 Acidithiobacillus genomes, were analyzed. The results showed that 248 members belonging to 23 IS families with a total of 10,652 copies were identified within the target genomes. The IS families and copy numbers among each species were significantly different, indicating that the IS distribution of Acidithiobacillus were not even. A. ferrooxidans had 166 IS members, which may develop more gene transposition strategies compared with other Acidithiobacillus spp. What's more, A. thiooxidans harbored the most IS copies, suggesting that their ISs were the most active and more likely to transpose. The ISs clustered in the phylogenetic tree approximately according to the family, which were mostly different from the evolutionary trends of their host genomes. Thus, it was suggested that the recent activity of ISs of Acidithiobacillus was not only determined by their genetic characteristics, but related with the environmental pressure. In addition, many ISs especially Tn3 and IS110 families were inserted around the regions whose functions were As/Hg/Cu/Co/Zn/Cd translocation and sulfur oxidation, implying that ISs could improve the adaptive capacities of Acidithiobacillus to the extremely acidic environment by enhancing their resistance to heavy metals and utilization of sulfur. CONCLUSIONS This study provided the genomic evidence for the contribution of IS to evolution and adaptation of Acidithiobacillus, opening novel sights into the genome plasticity of those acidophiles.
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Affiliation(s)
- Shanshan Huang
- School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, China
| | - Huiying Li
- School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, China
| | - Liyuan Ma
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, 430074, Wuhan, China.
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China.
| | - Rui Liu
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, 430074, Wuhan, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Yiran Li
- School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, China
| | - Hongmei Wang
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, 430074, Wuhan, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Xiaolu Lu
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, 430074, Wuhan, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Xinping Huang
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, 430074, Wuhan, China
| | - Xinhong Wu
- School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, China
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Zhao Y, Wei HM, Yuan JL, Xu L, Sun JQ. A comprehensive genomic analysis provides insights on the high environmental adaptability of Acinetobacter strains. Front Microbiol 2023; 14:1177951. [PMID: 37138596 PMCID: PMC10149724 DOI: 10.3389/fmicb.2023.1177951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 03/28/2023] [Indexed: 05/05/2023] Open
Abstract
Acinetobacter is ubiquitous, and it has a high species diversity and a complex evolutionary pattern. To elucidate the mechanism of its high ability to adapt to various environment, 312 genomes of Acinetobacter strains were analyzed using the phylogenomic and comparative genomics methods. It was revealed that the Acinetobacter genus has an open pan-genome and strong genome plasticity. The pan-genome consists of 47,500 genes, with 818 shared by all the genomes of Acinetobacter, while 22,291 are unique genes. Although Acinetobacter strains do not have a complete glycolytic pathway to directly utilize glucose as carbon source, most of them harbored the n-alkane-degrading genes alkB/alkM (97.1% of tested strains) and almA (96.7% of tested strains), which were responsible for medium-and long-chain n-alkane terminal oxidation reaction, respectively. Most Acinetobacter strains also have catA (93.3% of tested strains) and benAB (92.0% of tested strains) genes that can degrade the aromatic compounds catechol and benzoic acid, respectively. These abilities enable the Acinetobacter strains to easily obtain carbon and energy sources from their environment for survival. The Acinetobacter strains can manage osmotic pressure by accumulating potassium and compatible solutes, including betaine, mannitol, trehalose, glutamic acid, and proline. They respond to oxidative stress by synthesizing superoxide dismutase, catalase, disulfide isomerase, and methionine sulfoxide reductase that repair the damage caused by reactive oxygen species. In addition, most Acinetobacter strains contain many efflux pump genes and resistance genes to manage antibiotic stress and can synthesize a variety of secondary metabolites, including arylpolyene, β-lactone and siderophores among others, to adapt to their environment. These genes enable Acinetobacter strains to survive extreme stresses. The genome of each Acinetobacter strain contained different numbers of prophages (0-12) and genomic islands (GIs) (6-70), and genes related to antibiotic resistance were found in the GIs. The phylogenetic analysis revealed that the alkM and almA genes have a similar evolutionary position with the core genome, indicating that they may have been acquired by vertical gene transfer from their ancestor, while catA, benA, benB and the antibiotic resistance genes could have been acquired by horizontal gene transfer from the other organisms.
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Affiliation(s)
- Yang Zhao
- Lab for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Hua-Mei Wei
- Lab for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Jia-Li Yuan
- Lab for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Lian Xu
- Jiangsu Key Lab for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Ji-Quan Sun
- Lab for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
- *Correspondence: Ji-Quan Sun,
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Gushgari-Doyle S, Lui LM, Nielsen TN, Wu X, Malana RG, Hendrickson AJ, Carion H, Poole FL, Adams MWW, Arkin AP, Chakraborty R. Genotype to ecotype in niche environments: adaptation of Arthrobacter to carbon availability and environmental conditions. ISME COMMUNICATIONS 2022; 2:32. [PMID: 37938300 PMCID: PMC9723602 DOI: 10.1038/s43705-022-00113-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 02/23/2022] [Accepted: 03/07/2022] [Indexed: 07/04/2023]
Abstract
Niche environmental conditions influence both the structure and function of microbial communities and the cellular function of individual strains. The terrestrial subsurface is a dynamic and diverse environment that exhibits specific biogeochemical conditions associated with depth, resulting in distinct environmental niches. Here, we present the characterization of seven distinct strains belonging to the genus Arthrobacter isolated from varying depths of a single sediment core and associated groundwater from an adjacent well. We characterized genotype and phenotype of each isolate to connect specific cellular functions and metabolisms to ecotype. Arthrobacter isolates from each ecotype demonstrated functional and genomic capacities specific to their biogeochemical conditions of origin, including laboratory-demonstrated characterization of salinity tolerance and optimal pH, and genes for utilization of carbohydrates and other carbon substrates. Analysis of the Arthrobacter pangenome revealed that it is notably open with a volatile accessory genome compared to previous pangenome studies on other genera, suggesting a high potential for adaptability to environmental niches.
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Affiliation(s)
| | - Lauren M Lui
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Xiaoqin Wu
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ria G Malana
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Heloise Carion
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Farris L Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Adam P Arkin
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- University of California, Berkeley, CA, USA
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6
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Fu X, Gong L, Liu Y, Lai Q, Li G, Shao Z. Bacillus pumilus Group Comparative Genomics: Toward Pangenome Features, Diversity, and Marine Environmental Adaptation. Front Microbiol 2021; 12:571212. [PMID: 34025591 PMCID: PMC8139322 DOI: 10.3389/fmicb.2021.571212] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 04/12/2021] [Indexed: 11/13/2022] Open
Abstract
Background Members of the Bacillus pumilus group (abbreviated as the Bp group) are quite diverse and ubiquitous in marine environments, but little is known about correlation with their terrestrial counterparts. In this study, 16 marine strains that we had isolated before were sequenced and comparative genome analyses were performed with a total of 52 Bp group strains. The analyses included 20 marine isolates (which included the 16 new strains) and 32 terrestrial isolates, and their evolutionary relationships, differentiation, and environmental adaptation. Results Phylogenomic analysis revealed that the marine Bp group strains were grouped into three species: B. pumilus, B. altitudinis and B. safensis. All the three share a common ancestor. However, members of B. altitudinis were observed to cluster independently, separating from the other two, thus diverging from the others. Consistent with the universal nature of genes involved in the functioning of the translational machinery, the genes related to translation were enriched in the core genome. Functional genomic analyses revealed that the marine-derived and the terrestrial strains showed differences in certain hypothetical proteins, transcriptional regulators, K+ transporter (TrK) and ABC transporters. However, species differences showed the precedence of environmental adaptation discrepancies. In each species, land specific genes were found with possible functions that likely facilitate survival in diverse terrestrial niches, while marine bacteria were enriched with genes of unknown functions and those related to transcription, phage defense, DNA recombination and repair. Conclusion Our results indicated that the Bp isolates show distinct genomic features even as they share a common core. The marine and land isolates did not evolve independently; the transition between marine and non-marine habitats might have occurred multiple times. The lineage exhibited a priority effect over the niche in driving their dispersal. Certain intra-species niche specific genes could be related to a strains adaptation to its respective marine or terrestrial environment(s). In summary, this report describes the systematic evolution of 52 Bp group strains and will facilitate future studies toward understanding their ecological role and adaptation to marine and/or terrestrial environments.
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Affiliation(s)
- Xiaoteng Fu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Linfeng Gong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Yang Liu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Guangyu Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
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Ruiz-Perez CA, Bertagnolli AD, Tsementzi D, Woyke T, Stewart FJ, Konstantinidis KT. Description of Candidatus Mesopelagibacter carboxydoxydans and Candidatus Anoxipelagibacter denitrificans: Nitrate-reducing SAR11 genera that dominate mesopelagic and anoxic marine zones. Syst Appl Microbiol 2021; 44:126185. [PMID: 33676264 DOI: 10.1016/j.syapm.2021.126185] [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: 08/10/2020] [Revised: 11/25/2020] [Accepted: 12/09/2020] [Indexed: 11/29/2022]
Abstract
The diverse and ubiquitous members of the SAR11 lineage (Alphaproteobacteria) represent up to 30-40% of the surface and mesopelagic oceanic microbial communities. However, the molecular and ecological mechanisms that differentiate closely related, yet distinct, SAR11 members that often co-occur under similar environmental conditions remain speculative. Recently, two mesopelagic and oxygen minimum zone (OMZ)-associated subclades of SAR11 (Ic and IIa.A) were described using single-cell amplified genomes (SAGs) linked to nitrate reduction in OMZs. In this current study, the collection of genomes belonging to these two subclades was expanded with thirteen new metagenome-assembled genomes (MAGs), thus providing a more detailed phylogenetic and functional characterization of these subclades. Gene content-based predictions of metabolic functions revealed similarities in central carbon metabolism between subclades Ic and IIa.A and surface SAR11 clades, with small variations in central pathways. These variations included more versatile sulfur assimilation pathways, as well as a previously predicted capacity for nitrate reduction that conferred unique versatility on mesopelagic-adapted clades compared to their surface counterparts. Finally, consistent with previously reported abundances of carbon monoxide (CO) in surface and mesopelagic waters, subclades Ia (surface) and Ic (mesopelagic) have the genetic potential to oxidize carbon monoxide (CO), presumably taking advantage of this abundant compound as an electron donor. Based on genomic analyses, environmental distribution and metabolic reconstruction, we propose two new SAR11 genera, Ca. Mesopelagibacter carboxydoxydans (subclade Ic) and Ca. Anoxipelagibacter denitrificans (subclade IIa.A), which represent members of the mesopelagic and OMZ-adapted SAR11 clades.
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Affiliation(s)
- Carlos A Ruiz-Perez
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Anthony D Bertagnolli
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Despina Tsementzi
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, One Cyclotron Road, Mail Stop 91R0183, Berkeley, CA 94720, USA
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA; Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332, USA; Department of Microbiology & Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Konstantinos T Konstantinidis
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA; School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA; Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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Genome-Wide Analysis Reveals Genetic Potential for Aromatic Compounds Biodegradation of Sphingopyxis. BIOMED RESEARCH INTERNATIONAL 2020; 2020:5849123. [PMID: 32596333 PMCID: PMC7273453 DOI: 10.1155/2020/5849123] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 04/20/2020] [Indexed: 11/22/2022]
Abstract
Members of genus Sphingopyxis are frequently found in diverse eco-environments worldwide and have been traditionally considered to play vital roles in the degradation of aromatic compounds. Over recent decades, many aromatic-degrading Sphingopyxis strains have been isolated and recorded, but little is known about their genetic nature related to aromatic compounds biodegradation. In this study, bacterial genomes of 19 Sphingopyxis strains were used for comparative analyses. Phylogeny showed an ambiguous relatedness between bacterial strains and their habitat specificity, while clustering based on Cluster of Orthologous Groups suggested the potential link of functional profile with substrate-specific traits. Pan-genome analysis revealed that 19 individuals were predicted to share 1,066 orthologous genes, indicating a high genetic homogeneity among Sphingopyxis strains. Notably, KEGG Automatic Annotation Server results suggested that most genes pertaining aromatic compounds biodegradation were predicted to be involved in benzoate, phenylalanine, and aminobenzoate metabolism. Among them, β-ketoadipate biodegradation might be the main pathway in Sphingopyxis strains. Further inspection showed that a number of mobile genetic elements varied in Sphingopyxis genomes, and plasmid-mediated gene transfer coupled with prophage- and transposon-mediated rearrangements might play prominent roles in the evolution of bacterial genomes. Collectively, our findings presented that Sphingopyxis isolates might be the promising candidates for biodegradation of aromatic compounds in pollution sites.
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Zhang X, Yang F, Chen L, Feng H, Yin S, Chen M. Insights into ecological roles and potential evolution of Mlr-dependent microcystin-degrading bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 710:136401. [PMID: 31926423 DOI: 10.1016/j.scitotenv.2019.136401] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 12/12/2019] [Accepted: 12/27/2019] [Indexed: 06/10/2023]
Abstract
Over decades many studies have focused on the biodegradation of microcystins (MCs), and some Mlr-dependent MC-degrading bacteria were recorded, but the ecological functions, metabolic traits, and potential evolution of these organisms remain poorly understood. In this study, 16S rRNA-based phylogeny unraveled a wide range of genetic diversity across bacterial lineage, accompanied by re-evaluation of taxonomic placement of some MC-degrading species. Genome-wide comparison showed that considerable genes unique in individual organisms were identified, suggesting genetic differentiation among these Mlr-dependent MC-degrading bacteria. Notably, analyses of metabolic profiles first revealed the presence of functional genes involved in phenylacetate biodegradation in the specialized genomic regions, and mlr gene cluster was located around the neighborhood. The identification of transposable elements further indicated that these genomic regions might undergo horizontal gene transfer events to recruit novel functionalities, suggesting an adaptive force driving genome evolution of these organisms. In short, phylogenetic and genetic content analyses of Mlr-dependent MC-degraders shed light on their metabolic potential, ecological roles, and bacterial evolution, and expand the understanding of ecological status of MCs biodegradation.
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Affiliation(s)
- Xian Zhang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China.
| | - Fei Yang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China; Key Laboratory of Hunan Province for Water Environment and Agriculture Product Safety, Central South University, Changsha, China
| | - Lv Chen
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
| | - Hai Feng
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
| | - Shiqian Yin
- School of Environmental Science and Engineering, Qilu University of Technology, Jinan, China
| | - Mengshi Chen
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, China
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10
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Fariq A, Blazier JC, Yasmin A, Gentry TJ, Deng Y. Whole genome sequence analysis reveals high genetic variation of newly isolated Acidithiobacillus ferrooxidans IO-2C. Sci Rep 2019; 9:13049. [PMID: 31506467 PMCID: PMC6736930 DOI: 10.1038/s41598-019-49213-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 08/20/2019] [Indexed: 12/30/2022] Open
Abstract
Acidithiobacillus ferrooxidans, a chemolithoautotrophic bacterium, is well known for its mineral oxidizing properties. The current study combines experimental and whole genome sequencing approaches to investigate an iron oxidizing, extreme acidophilic bacterium, A. ferrooxidans isolate (IO-2C) from an acid seep area near Carlos, TX, USA. Strain IO-2C was capable of oxidizing iron i.e. iron sulphate and iron ammonium sulphate yielding shwertmannite and jarosite minerals. Further, the bacterium's genome was sequenced, assembled and annotated to study its general features, structure and functions. To determine genetic heterogeneity, it was compared with the genomes of other published A. ferrooxidans strains. Pan-genome analysis displayed low gene conservation and significant genetic diversity in A. ferrooxidans species comprising of 6926 protein coding sequences with 23.04% (1596) core genes, 46.13% (3195) unique and 30.82% (2135) accessory genes. Variant analysis showed >75,000 variants, 287 of them with a predicted high impact, in A. ferrooxidans IO-2C genome compared to the reference strain, resulting in abandonment of some important functional key genes. The genome contains numerous functional genes for iron and sulphur metabolism, nitrogen fixation, secondary metabolites, degradation of aromatic compounds, and multidrug and heavy metal resistance. This study demonstrated the bio-oxidation of iron by newly isolated A. ferrooxidans IO-2C under acidic conditions, which was further supported by genomic analysis. Genomic analysis of this strain provided valuable information about the complement of genes responsible for the utilization of iron and tolerance of other metals.
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Affiliation(s)
- Anila Fariq
- Microbiology & Biotechnology Research Lab, Department of Biotechnology, Fatima Jinnah Women University, Rawalpindi, 46000, Pakistan.,Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - John C Blazier
- Texas A&M Institute of Genome Sciences and Society, Texas A&M University, College Station, TX, 77843, USA
| | - Azra Yasmin
- Microbiology & Biotechnology Research Lab, Department of Biotechnology, Fatima Jinnah Women University, Rawalpindi, 46000, Pakistan.
| | - Terry J Gentry
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Youjun Deng
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843, USA
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Zhang X, Liu X, Li L, Wei G, Zhang D, Liang Y, Miao B. Phylogeny, Divergent Evolution, and Speciation of Sulfur-Oxidizing Acidithiobacillus Populations. BMC Genomics 2019; 20:438. [PMID: 31146680 PMCID: PMC6543593 DOI: 10.1186/s12864-019-5827-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 05/23/2019] [Indexed: 01/18/2023] Open
Abstract
Background Habitats colonized by acidophiles as an ideal physical barrier may induce genetic exchange of microbial members within the common communities, but little is known about how species in extremely acidic environments diverge and evolve. Results Using the acidophilic sulfur-oxidizer Acidithiobacillus as a case study, taxonomic reclassifications of many isolates provides novel insights into their phylogenetic lineage. Whole-genome-based comparisons were attempted to investigate the intra- and inter-species divergence. Recent studies clarified that functional and structural specificities of bacterial strains might provide opportunities for adaptive evolution responding to local environmental conditions. Acidophilic microorganisms play a key role in the acidification of natural waters and thus the formation of extremely acidic environments, and the feedbacks of the latter might confer the distinct evolutionary patterns of Acidithiobacillus spp. Varied horizontal gene transfer events occurred in different bacterial strains, probably resulting in the expansion of Acidithiobacillus genomes. Gene loss as another evolutionary force might cause the adaptive phenotypic diversity. A conceptual model for potential community-dependent evolutionary adaptation was thus proposed to illustrate the observed genome differentiation. Conclusions Collectively, the findings shed light on the phylogeny and divergent evolution of Acidithiobacillus strains, and provided a useful reference for evolutionary studies of other extremophiles. Electronic supplementary material The online version of this article (10.1186/s12864-019-5827-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xian Zhang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China.
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Guanyun Wei
- School of Life Sciences, Nantong University, Nantong, China
| | - Danli Zhang
- Department of Biology, Taiyuan Normal University, Taiyuan, China
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Bo Miao
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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12
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Zhang X, Liu Z, Wei G, Yang F, Liu X. In Silico Genome-Wide Analysis Reveals the Potential Links Between Core Genome of Acidithiobacillus thiooxidans and Its Autotrophic Lifestyle. Front Microbiol 2018; 9:1255. [PMID: 29937764 PMCID: PMC6002666 DOI: 10.3389/fmicb.2018.01255] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 05/24/2018] [Indexed: 12/27/2022] Open
Abstract
The coinage “pan-genome” was first introduced dating back to 2005, and was used to elaborate the entire gene repertoire of any given species. Core genome consists of genes shared by all bacterial strains studied and is considered to encode essential functions associated with species’ basic biology and phenotypes, yet its relatedness with bacterial lifestyle of the species remains elusive. We performed the pan-genome analysis of sulfur-oxidizing acidophile Acidithiobacillus thiooxidans as a case study to highlight species’ core genome and its relevance with autotrophic lifestyle of bacterial species. The mathematical modeling based on bacterial genomes of A. thiooxidans species, including a novel strain ZBY isolated from Zambian copper mine plus eight other recognized strains, was attempted to extrapolate the expansion of its pan-genome, suggesting that A. thiooxidans pan-genome is closed. Further investigation revealed a common set of genes, many of which were assigned to metabolic profiles, notably with respect to energy metabolism, amino acid metabolism, and carbohydrate metabolism. The predicted metabolic profiles of A. thiooxidans were characterized by the fixation of inorganic carbon, assimilation of nitrogen compounds, and aerobic oxidation of various sulfur species. Notably, several hydrogenase (H2ase)-like genes dispersed in core genome might represent the novel classes due to the potential functional disparities, despite being closely related homologous genes that code for H2ase. Overall, the findings shed light on the distinguishing features of A. thiooxidans genomes on a global scale, and extend the understanding of its conserved core genome pertaining to autotrophic lifestyle.
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Affiliation(s)
- Xian Zhang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
| | - Zhenghua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Guanyun Wei
- College of Life Science, Nanjing Normal University, Nanjing, China
| | - Fei Yang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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