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Zhao H, Yang S, Qin X, Huang J, Huang H, Li W, Jiang G, Tang J, Dong K, Li N. Disentangling the Ecological Processes and Driving Forces Shaping the Seasonal Pattern of Halobacteriovorax Communities in a Subtropical Estuary. MICROBIAL ECOLOGY 2023; 86:1881-1892. [PMID: 36799977 DOI: 10.1007/s00248-023-02195-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/11/2023] [Indexed: 06/18/2023]
Abstract
Halobacteriovorax are predatory bacteria that have a significant ecological role in marine environments. However, understanding of dynamics of populations, driving forces, and community composition of Halobacteriovorax groups in natural marine environments is still limited. Here, we used high-throughput sequencing to study the underlying mechanisms governing the diversity and assembly of the Halobacteriovorax community at spatiotemporal scales in a subtropical estuary. Phylogenetic analysis showed that 10 of 15 known Halobacteriovorax clusters were found in the studied estuary. Halobacteriovorax α-diversity and β-diversity exhibited significant seasonal variation. Variation partitioning analysis showed that the effect of nutrients was greater than that of other measured water properties on Halobacteriovorax community distribution. The results of Spearman's and Mantel's tests indicated that the trophic pollutants dissolved inorganic phosphorus (DIP) and NH4+-N in the estuary were the key factors that significantly affected Halobacteriovorax species and community diversity. In addition, this work indicated that the biological stoichiometry (especially N/P) of nutrients exerted a significant influence on the Halobacteriovorax community. Furthermore, we found that both deterministic and stochastic processes contributed to the turnover of Halobacteriovorax communities, and environmental filtering dominated the assembly of estuarine Halobacteriovorax communities. Overall, we provide new insights into the mechanisms in the generation and maintenance of the Halobacteriovorax community in marine environments.
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Affiliation(s)
- Huaxian Zhao
- Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning, 530001, China
| | - Shu Yang
- Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning, 530001, China
| | - Xinyi Qin
- Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning, 530001, China
| | - Jiongqing Huang
- Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning, 530001, China
| | - Haifeng Huang
- Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning, 530001, China
| | - Wenjing Li
- Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning, 530001, China
| | - Gonglingxia Jiang
- Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning, 530001, China
| | - Jinli Tang
- Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning, 530001, China
| | - Ke Dong
- Department of Biological Sciences, Kyonggi University, 154-42, Gwanggyosan-ro, Yeongtong-gu Gyeonggi-do, Suwon-si, 16227, South Korea
| | - Nan Li
- Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning, 530001, China.
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Kamada S, Wakabayashi R, Naganuma T. Phylogenetic Revisit to a Review on Predatory Bacteria. Microorganisms 2023; 11:1673. [PMID: 37512846 PMCID: PMC10385382 DOI: 10.3390/microorganisms11071673] [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: 05/29/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Predatory bacteria, along with the biology of their predatory behavior, have attracted interest in terms of their ecological significance and industrial applications, a trend that has been even more pronounced since the comprehensive review in 2016. This mini-review does not cover research trends, such as the role of outer membrane vesicles in myxobacterial predation, but provides an overview of the classification and newly described taxa of predatory bacteria since 2016, particularly with regard to phylogenetic aspects. Among them, it is noteworthy that in 2020 there was a major phylogenetic reorganization that the taxa hosting Bdellovibrio and Myxococcus, formerly classified as Deltaproteobacteria, were proposed as the new phyla Bdellovibrionota and Myxococcota, respectively. Predatory bacteria have been reported from other phyla, especially from the candidate divisions. Predatory bacteria that prey on cyanobacteria and predatory cyanobacteria that prey on Chlorella have also been found. These are also covered in this mini-review, and trans-phylum phylogenetic trees are presented.
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Affiliation(s)
- Saki Kamada
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashihiroshima 739-8528, Japan
| | - Ryoka Wakabayashi
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashihiroshima 739-8528, Japan
| | - Takeshi Naganuma
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashihiroshima 739-8528, Japan
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Wang X, Zhao N, Cai L, Liu N, Zhu J, Yang B. High-quality chromosome-level scaffolds of the plant bug Pachypeltis micranthus provide insights into the availability of Mikania micrantha control. BMC Genomics 2023; 24:339. [PMID: 37340339 DOI: 10.1186/s12864-023-09445-8] [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: 04/03/2023] [Accepted: 06/13/2023] [Indexed: 06/22/2023] Open
Abstract
BACKGROUND The plant bug, Pachypeltis micranthus Mu et Liu (Hemiptera: Miridae), is an effective potential biological control agent for Mikania micrantha H.B.K. (Asteraceae; one of the most notorious invasive weeds worldwide). However, limited knowledge about this species hindered its practical application and research. Accordingly, sequencing the genome of this mirid bug holds great significance in controlling M. micrantha. RESULTS Here, 712.72 Mb high-quality chromosome-level scaffolds of P. micranthus were generated, of which 707.51 Mb (99.27%) of assembled sequences were anchored onto 15 chromosome-level scaffolds with contig N50 of 16.84 Mb. The P. micranthus genome had the highest GC content (42.43%) and the second highest proportion of repetitive sequences (375.82 Mb, 52.73%) than the three other mirid bugs (i.e., Apolygus lucorum, Cyrtorhinus lividipennis, and Nesidiocoris tenuis). Phylogenetic analysis showed that P. micranthus clustered with other mirid bugs and diverged from the common ancestor approximately 200 million years ago. Gene family expansion and/or contraction were analyzed, and significantly expanded gene families associated with P. micranthus feeding and adaptation to M. micrantha were manually identified. Compared with the whole body, transcriptome analysis of the salivary gland revealed that most of the upregulated genes were significantly associated with metabolism pathways and peptidase activity, particularly among cysteine peptidase, serine peptidase, and polygalacturonase; this could be one of the reasons for precisely and highly efficient feeding by the oligophagous bug P. micranthus on M. micrantha. CONCLUSION Collectively, this work provides a crucial chromosome-level scaffolds resource to study the evolutionary adaptation between mirid bug and their host. It is also helpful in searching for novel environment-friendly biological strategies to control M. micrantha.
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Affiliation(s)
- Xiafei Wang
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Ning Zhao
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Liqiong Cai
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Naiyong Liu
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Jiaying Zhu
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Bin Yang
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China.
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Deb S. Pan-genome evolution and its association with divergence of metabolic functions in Bifidobacterium genus. World J Microbiol Biotechnol 2022; 38:231. [PMID: 36205822 DOI: 10.1007/s11274-022-03430-1] [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: 06/02/2022] [Accepted: 09/30/2022] [Indexed: 10/10/2022]
Abstract
Previous studies were mainly focused on genomic evolution and diversity of type species of Bifidobacterium genus due to their health-promoting effect on host. However, those studies were mainly based on species-level taxonomic resolution, adaptation, and characterization of carbohydrate metabolic features of the bifidobacterial species. Here, a comprehensive analysis of the type strain genome unveils the association of pan-genome evolution with the divergence of metabolic function of the Bifidobacterium genus. This study has also demonstrated that horizontal gene transfer, as well as genome expansion and reduction events, leads to the divergence of metabolic functions in Bifidobacterium genus. Furthermore, the genome-based search of probiotic traits among all the available bifidobacterial type strains gives hints on type species, that could confer health benefits to nutrient-deficient individuals. Altogether, the present study provides insight into the developments of genomic evolution, functional divergence, and potential probiotic type species of the Bifidobacterium genus.
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Affiliation(s)
- Sushanta Deb
- Department of Molecular Biology and Bioinformatics, Tripura University, Suryamaninagar, 799022, Tripura, India. .,All India Institute of Medical Sciences (AIIMS), New Delhi, 110029, India.
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Strain-specific predation of Bdellovibrio bacteriovorus on Pseudomonas aeruginosa with a higher range for cystic fibrosis than for bacteremia isolates. Sci Rep 2022; 12:10523. [PMID: 35732651 PMCID: PMC9217795 DOI: 10.1038/s41598-022-14378-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 06/06/2022] [Indexed: 12/23/2022] Open
Abstract
This work aimed to evaluate the predatory activity of Bdellovibrio bacteriovorus 109J on clinical isolates of Pseudomonas aeruginosa selected from well-characterized collections of cystic fibrosis (CF) lung colonization (n = 30) and bloodstream infections (BSI) (n = 48) including strains selected by genetic lineage (frequent and rare sequence types), antibiotic resistance phenotype (susceptible and multidrug-resistant isolates), and colony phenotype (mucoid and non-mucoid isolates). The intraspecies predation range (I-PR) was defined as the proportion of susceptible strains within the entire collection. In contrast, the predation efficiency (PE) is the ratio of viable prey cells remaining after predation compared to the initial inoculum. I-PR was significantly higher for CF (67%) than for BSI P. aeruginosa isolates (35%) probably related to an environmental origin of CF strains whereas invasive strains are more adapted to humans. I-PR correlation with bacterial features such as mucoid morphotype, genetic background, or antibiotic susceptibility profile was not detected. To test the possibility of increasing I-PR of BSI isolates, a polyhydroxyalkanoate depolymerase deficient B. bacteriovorus bd2637 mutant was used. Global median I-PR and PE values remained constant for both predators, but 31.2% of 109J-resistant isolates were susceptible to the mutant, and 22.9% of 109J-susceptible isolates showed resistance to predation by the mutant, pointing to a predator–prey specificity process. The potential use of predators in the clinical setting should be based on the determination of the I-PR for each species, and the PE of each particular target strain.
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Abstract
Akkermansia muciniphila is a commensal bacterium using mucin as its sole carbon and nitrogen source. A. muciniphila is a promising candidate for next-generation probiotics to prevent inflammatory and metabolic disorders, including diabetes and obesity, and to increase the response to cancer immunotherapy. In this study, a comparative pan-genome analysis was conducted to investigate the genomic diversity and evolutionary relationships between complete genomes of 27 A. muciniphila strains, including KGMB strains isolated from healthy Koreans. The analysis showed that A. muciniphila strains formed two clades of group A and B in a phylogenetic tree constructed using 1,219 orthologous single-copy core genes. Interestingly, group A comprised of strains from human feces in Korea, whereas most of group B comprised strains from human feces in Europe and China, and from mouse feces. As group A and B branched, mucin hydrolysis played an important role in the stability of the core genome and drove evolution in the direction of defense against invading pathogens, survival in, and colonization in the mucus layer. In addition, WapA and anSME, which function in competition and post-translational modification of sulfatase, respectively, have been a particularly important selective pressure in the evolution of group A. KGMB strains in group A with anSME gene showed sulfatase activity, but KCTC 15667T in group B without anSME did not. Our findings revealed that KGMB strains evolved to gain an edge in the competition with other gut bacteria by increasing the utilization of sulfated mucin, which will allow it to become highly colonized in the gut environment.
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Affiliation(s)
- Ji-Sun Kim
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Se Won Kang
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Ju Huck Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Seung-Hwan Park
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea
| | - Jung-Sook Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Republic of Korea,Department of Environmental Biotechnology, University of Science and Technology, Yuseong-gu, Republic of Korea,CONTACT Jung-Sook Lee Korean Collection for Type Cultures,Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si56212Republic of Korea
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Wambui J, Stevens MJA, Cernela N, Stephan R. Unraveling the Genotypic and Phenotypic Diversity of the Psychrophilic Clostridium estertheticum Complex, a Meat Spoilage Agent. Front Microbiol 2022; 13:856810. [PMID: 35418954 PMCID: PMC8996182 DOI: 10.3389/fmicb.2022.856810] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 03/04/2022] [Indexed: 11/13/2022] Open
Abstract
The spoilage of vacuum-packed meat by Clostridium estertheticum complex (CEC), which is accompanied by or without production of copious amounts of gas, has been linked to the acetone–butyrate–ethanol fermentation, but the mechanism behind the variable gas production has not been fully elucidated. The reconstruction and comparison of intra- and interspecies metabolic pathways linked to meat spoilage at the genomic level can unravel the genetic basis for the variable phenotype. However, this is hindered by unavailability of CEC genomes, which in addition, has hampered the determination of genetic diversity and its drivers within CEC. Therefore, the current study aimed at determining the diversity of CEC through comprehensive comparative genomics. Fifty CEC genomes from 11 CEC species were compared. Recombination and gene gain/loss events were identified as important sources of natural variation within CEC, with the latter being pronounced in genomospecies2 that has lost genes related to flagellar assembly and signaling. Pan-genome analysis revealed variations in carbohydrate metabolic and hydrogenases genes within the complex. Variable inter- and intraspecies gas production in meat by C. estertheticum and Clostridium tagluense were associated with the distribution of the [NiFe]-hydrogenase hyp gene cluster whose absence or presence was associated with occurrence or lack of pack distention, respectively. Through comparative genomics, we have shown CEC species exhibit high genetic diversity that can be partly attributed to recombination and gene gain/loss events. We have also shown genetic basis for variable gas production in meat can be attributed to the presence/absence of the hyp gene cluster.
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Affiliation(s)
- Joseph Wambui
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Marc J A Stevens
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Nicole Cernela
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
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Cao H, Xu D, Zhang T, Ren Q, Xiang L, Ning C, Zhang Y, Gao R. Comprehensive and functional analyses reveal the genomic diversity and potential toxicity of Microcystis. HARMFUL ALGAE 2022; 113:102186. [PMID: 35287927 DOI: 10.1016/j.hal.2022.102186] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Microcystis is a cyanobacteria that is widely distributed across the world. It has attracted great attention because it produces the hepatotoxin microcystin (MC) that can inhibit eukaryotic protein phosphatases and pose a great risk to animal and human health. Due to the high diversity of morphospecies and genomes, it is still difficult to classify Microcystis species. In this study, we investigated the pangenome of 23 Microcystis strains to detect the genetic diversity and evolutionary dynamics. Microcystis revealed an open pangenome containing 22,009 gene families and exhibited different functional constraints. The core-genome phylogenetic analysis accurately differentiated the toxic and nontoxic strains and could be used as a taxonomic standard at the genetic level. We also investigated the functions of HGT events, of which were mostly conferred from cyanobacteria and closely related species. In order to detect the potential toxicity of Microcystis, we searched and characterized MC biosynthetic gene clusters and other secondary metabolite gene clusters. Our work provides insights into the genetic diversity, evolutionary dynamics, and potential toxicity of Microcystis, which could benefit the species classification and development of new methods for drinking water quality control and management of bloom formation in the future.
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Affiliation(s)
- Hengchun Cao
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, Shandong, China
| | - Da Xu
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, Shandong, China
| | - Tiantian Zhang
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, Shandong, China
| | - Qiufang Ren
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, Shandong, China
| | - Li Xiang
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, Shandong, China
| | - Chunhui Ning
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, Shandong, China
| | - Yusen Zhang
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, Shandong, China.
| | - Rui Gao
- School of Control Science and Engineering, Shandong University, Jinan 250061, Shandong, China.
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Huang J, Zhao Z, Zhang Q, Zhang S, Zhang S, Chen M, Qiu H, Cao Y, Li B. Phylogenetic Analysis Reveals Distinct Evolutionary Trajectories of the Fluoroquinolones-Resistant Escherichia coli ST1193 From Fuzhou, China. Front Microbiol 2021; 12:746995. [PMID: 34803966 PMCID: PMC8602892 DOI: 10.3389/fmicb.2021.746995] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 10/13/2021] [Indexed: 01/27/2023] Open
Abstract
Escherichia coli (E. coli) ST1193 is an emerging fluoroquinolones-resistant and virulent lineage. Large gaps remain in our understanding of the evolutionary processes and differences of this lineage. Therefore, we used 76 E. coli ST1193 genomes to detect strain-level genetic diversity and phylogeny of this lineage globally. All E. coli ST1193 possessed fimH64, filCH5, and fumC14. There was 94.7% of isolates classified as O-type O75. There was 9.33% of E. coli ST1193 that possessed K5 capsular, while 90.67% of isolates possessed K1 capsular. The core genome analysis revealed that all isolates were divided into two phylogenetic clades (clade A and B). Clade A included 25 non-Chinese E. coli ST1193, and clade B contained all isolates collected from Fuzhou, China, respectively. The results of comparative genomics indicated Indels were identified in 150 clade-specific genes, which were enriched into the biological process and molecular function. Accessory genome phylogenetic tree showed a high degree of correlation between accessory genome clusters and core genome clades. There was significant difference in antibiotic resistance genes (ARGs) [bla CTX-M-55 , bla TEM-1 , sul2, tet(B), tet(R), APH(6)-Id, and AAC(3)-IId], virulence factors (cia, neuC, gad, and traT), and plasmid replicon types (IncQ1, Col156, and IncB/O/K/Z) between clade A (non-Chinese isolates) and clade B (Chinese isolates) (p < 0.05). Further analysis of the genetic environments of bla CTX-M-55 demonstrated that the flanking contexts of bla CTX-M-55 were diverse. In conclusion, our results reveal the distinct evolutionary trajectories of the spread of E. coli ST1193 in Fuzhou, China and non-China regions. This supports both global transmission and localized lineage expansion of this lineage following specific introductions into a geographic locality.
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Affiliation(s)
- Jiangqing Huang
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
| | - Zhichang Zhao
- Department of Pharmacy, Fujian Medical University Union Hospital, Fuzhou, China
| | - Qianwen Zhang
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
| | - Shengcen Zhang
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
| | - Shuyu Zhang
- Department of Laboratory Medicine, Fujian Medical University, Fuzhou, China
| | - Min Chen
- Department of Laboratory Medicine, Fujian Medical University, Fuzhou, China
| | - Hongqiang Qiu
- Department of Pharmacy, Fujian Medical University Union Hospital, Fuzhou, China
| | - Yingping Cao
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
| | - Bin Li
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
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Rosselli R, La Porta N, Muresu R, Stevanato P, Concheri G, Squartini A. Pangenomics of the Symbiotic Rhizobiales. Core and Accessory Functions Across a Group Endowed with High Levels of Genomic Plasticity. Microorganisms 2021; 9:microorganisms9020407. [PMID: 33669391 PMCID: PMC7920277 DOI: 10.3390/microorganisms9020407] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 11/16/2022] Open
Abstract
Pangenome analyses reveal major clues on evolutionary instances and critical genome core conservation. The order Rhizobiales encompasses several families with rather disparate ecological attitudes. Among them, Rhizobiaceae, Bradyrhizobiaceae, Phyllobacteriacreae and Xanthobacteriaceae, include members proficient in mutualistic symbioses with plants based on the bacterial conversion of N2 into ammonia (nitrogen-fixation). The pangenome of 12 nitrogen-fixing plant symbionts of the Rhizobiales was analyzed yielding total 37,364 loci, with a core genome constituting 700 genes. The percentage of core genes averaged 10.2% over single genomes, and between 5% to 7% were found to be plasmid-associated. The comparison between a representative reference genome and the core genome subset, showed the core genome highly enriched in genes for macromolecule metabolism, ribosomal constituents and overall translation machinery, while membrane/periplasm-associated genes, and transport domains resulted under-represented. The analysis of protein functions revealed that between 1.7% and 4.9% of core proteins could putatively have different functions.
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Affiliation(s)
- Riccardo Rosselli
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute of Sea Research, NL-1790 AB Den Burg, The Netherlands;
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, 03690 Alicante, Spain
| | - Nicola La Porta
- Department of Sustainable Agrobiosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, 38098 San Michele all’Adige, Italy;
- MOUNTFOR Project Centre, European Forest Institute, 38098 San Michele all’Adige, Italy
| | - Rosella Muresu
- Institute of Animal Production Systems in Mediterranean Environments-National Research Council, 07040 Sassari, Italy;
| | - Piergiorgio Stevanato
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, Italy; (P.S.); (G.C.)
| | - Giuseppe Concheri
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, Italy; (P.S.); (G.C.)
| | - Andrea Squartini
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, Italy; (P.S.); (G.C.)
- Correspondence: ; Tel.: +39-049-8272-923
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Horizontal Gene Transfer Clarifies Taxonomic Confusion and Promotes the Genetic Diversity and Pathogenicity of Plesiomonas shigelloides. mSystems 2020; 5:5/5/e00448-20. [PMID: 32934114 PMCID: PMC7498682 DOI: 10.1128/msystems.00448-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The taxonomic position of P. shigelloides has been the subject of debate for a long time, and until now, the evolutionary dynamics and pathogenesis of P. shigelloides were unclear. In this study, pan-genome analysis indicated extensive genetic diversity and the presence of large and variable gene repertoires. Our results revealed that horizontal gene transfer was the focal driving force for the genetic diversity of the P. shigelloides pan-genome and might have contributed to the emergence of novel properties. Vibrionaceae and Aeromonadaceae were found to be the predominant donor taxa for horizontal genes, which might have caused the taxonomic confusion historically. Comparative genomic analysis revealed the potential of P. shigelloides to cause intestinal and invasive diseases. Our results could advance the understanding of the evolution and pathogenesis of P. shigelloides, particularly in elucidating the role of horizontal gene transfer and investigating virulence-related elements. Plesiomonas shigelloides is an emerging pathogen that has been shown to be involved in gastrointestinal diseases and extraintestinal infections in humans. However, the taxonomic position, evolutionary dynamics, and pathogenesis of P. shigelloides remain unclear. We reported the draft genome sequences of 12 P. shigelloides strains representing different serogroups. We were able to determine a clear distinction between P. shigelloides and other members of Enterobacterales via core genome phylogeny, Neighbor-Net network, and average genome identity analysis. The pan-genome analysis of P. shigelloides revealed extensive genetic diversity and presented large flexible gene repertoires, while the core genome phylogeny exhibited a low level of clonality. The discordance between the core genome phylogeny and the pan-genome phylogeny indicated that flexible accessory genomes account for an important proportion of the evolution of P. shigelloides, which was subsequently characterized by determinations of hundreds of horizontally transferred genes (horizontal genes), massive gene expansions and contractions, and diverse mobile genetic elements (MGEs). The apparently high levels of horizontal gene transfer (HGT) in P. shigelloides were conferred from bacteria with novel properties from other taxa (mainly Vibrionaceae and Aeromonadaceae), which caused the historical taxonomic confusion and shaped the virulence gene pools. Furthermore, P. shigelloides genomes contain many macromolecular secretion system genes, virulence factor genes, and resistance genes, indicating its potential to cause intestinal and invasive infections. Collectively, our work provides insights into the phylogenetic position, evolutionary dynamic, and pathogenesis of P. shigelloides at the genomic level, which could facilitate the observation and research of this important pathogen. IMPORTANCE The taxonomic position of P. shigelloides has been the subject of debate for a long time, and until now, the evolutionary dynamics and pathogenesis of P. shigelloides were unclear. In this study, pan-genome analysis indicated extensive genetic diversity and the presence of large and variable gene repertoires. Our results revealed that horizontal gene transfer was the focal driving force for the genetic diversity of the P. shigelloides pan-genome and might have contributed to the emergence of novel properties. Vibrionaceae and Aeromonadaceae were found to be the predominant donor taxa for horizontal genes, which might have caused the taxonomic confusion historically. Comparative genomic analysis revealed the potential of P. shigelloides to cause intestinal and invasive diseases. Our results could advance the understanding of the evolution and pathogenesis of P. shigelloides, particularly in elucidating the role of horizontal gene transfer and investigating virulence-related elements.
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Pattanayak S, Priyadarsini S, Paul A, Kumar PR, Sahoo PK. Diversity of virulence-associated genes in pathogenic Aeromonas hydrophila isolates and their in vivo modulation at varied water temperatures. Microb Pathog 2020; 147:104424. [PMID: 32771658 DOI: 10.1016/j.micpath.2020.104424] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 07/13/2020] [Accepted: 07/27/2020] [Indexed: 12/11/2022]
Abstract
Most environmental parameters have no consistent effect on the expression of bacterial genes responsible for their virulence. However, as fish are poikilothermic, the possibility of temperature variation having a pronounced effect on the expression of virulence-associated gene(s) of bacteria infecting the host needs to be investigated. In this study, the diversity of virulence genes in seven Aeromonas hydrophila isolates collected from diseased fish from different parts of India was characterized, and the effect of temperature variation on the extent of expression of their virulence was investigated. All bacterial isolates were screened for a total of nine bacterial virulent genes {aerolysin, hemolysin, cytoen, outer membrane protein TS (Omp TS), elastase, flagellin, lipase, β hemolysin and type 3 secretion system}, and the diversity in their presence or absence were marked at a particular in vitro condition. Three bacterial isolates (nos. 1, 7 and 2) were selected for further study, based on their ability to cause varied mortalities (20-100%) in Labeo rohita juveniles in intraperitoneal challenge study. Further, three isolates were injected intraperitoneally into L. rohita fingerlings at three different temperatures (i.e., 20, 28 and 37 °C) and at 6 h post-challenge, the kidney samples were collected to measure the levels of all nine bacterial virulence genes using semi-quantitative PCR. The maximum level of amplicons of virulence genes in all three A. hydrophila isolates was noticed at 28 °C as compared to 37 °C and 20 °C. It was also observed that haemolysin played a more prominent role in the expression of virulence, when compared to cytoen gene. Hence, it was concluded that water temperature does play a crucial role in governing virulence gene expression, and a temperature of 28 °C would be considered as suitable for looking into the pathogenicity of A. hydrophila for conducting any challenge study with this organism in tropical environment.
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Affiliation(s)
- Sabyasachi Pattanayak
- National Referral Laboratory for Freshwater Fish Diseases, Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India
| | - Swatismita Priyadarsini
- National Referral Laboratory for Freshwater Fish Diseases, Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India
| | - Anirban Paul
- National Referral Laboratory for Freshwater Fish Diseases, Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India
| | - P Rajesh Kumar
- National Referral Laboratory for Freshwater Fish Diseases, Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India
| | - P K Sahoo
- National Referral Laboratory for Freshwater Fish Diseases, Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India.
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Castillo AI, Chacón-Díaz C, Rodríguez-Murillo N, Coletta-Filho HD, Almeida RPP. Impacts of local population history and ecology on the evolution of a globally dispersed pathogen. BMC Genomics 2020; 21:369. [PMID: 32434538 PMCID: PMC7238557 DOI: 10.1186/s12864-020-06778-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 05/12/2020] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Pathogens with a global distribution face diverse biotic and abiotic conditions across populations. Moreover, the ecological and evolutionary history of each population is unique. Xylella fastidiosa is a xylem-dwelling bacterium infecting multiple plant hosts, often with detrimental effects. As a group, X. fastidiosa is divided into distinct subspecies with allopatric historical distributions and patterns of multiple introductions from numerous source populations. The capacity of X. fastidiosa to successfully colonize and cause disease in naïve plant hosts varies among subspecies, and potentially, among populations. Within Central America (i.e. Costa Rica) two X. fastidiosa subspecies coexist: the native subsp. fastidiosa and the introduced subsp. pauca. Using whole genome sequences, the patterns of gene gain/loss, genomic introgression, and genetic diversity were characterized within Costa Rica and contrasted to other X. fastidiosa populations. RESULTS Within Costa Rica, accessory and core genome analyses showed a highly malleable genome with numerous intra- and inter-subspecific gain/loss events. Likewise, variable levels of inter-subspecific introgression were found within and between both coexisting subspecies; nonetheless, the direction of donor/recipient subspecies to the recombinant segments varied. Some strains appeared to recombine more frequently than others; however, no group of genes or gene functions were overrepresented within recombinant segments. Finally, the patterns of genetic diversity of subsp. fastidiosa in Costa Rica were consistent with those of other native populations (i.e. subsp. pauca in Brazil). CONCLUSIONS Overall, this study shows the importance of characterizing local evolutionary and ecological history in the context of world-wide pathogen distribution.
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Affiliation(s)
- Andreina I Castillo
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Carlos Chacón-Díaz
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Neysa Rodríguez-Murillo
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | | | - Rodrigo P P Almeida
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA.
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Wang XS, Zhang S, Xu Z, Zheng SQ, Long J, Wang DS. Genome-wide identification, evolution of ATF/CREB family and their expression in Nile tilapia. Comp Biochem Physiol B Biochem Mol Biol 2019; 237:110324. [DOI: 10.1016/j.cbpb.2019.110324] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 08/09/2019] [Accepted: 08/22/2019] [Indexed: 01/06/2023]
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Comprehensive Analysis Reveals the Evolution and Pathogenicity of Aeromonas, Viewed from Both Single Isolated Species and Microbial Communities. mSystems 2019; 4:4/5/e00252-19. [PMID: 31641046 PMCID: PMC6811364 DOI: 10.1128/msystems.00252-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The genus Aeromonas is a common gastrointestinal pathogen associated with human and animal infections. Due to the high level of cross-species similarity, their evolutionary dynamics and genetic diversity are still fragmented. Hereby, we investigated the pan-genomes of 29 Aeromonas species, as well as Aeromonas species in microbial communities, to clarify their evolutionary dynamics and genetic diversity, with special focus on virulence factors and horizontal gene transfer events. Our study revealed an open pan-genome of Aeromonas containing 10,144 gene families. These Aeromonas species exhibited different functional constraints, with the single-copy core genes and most accessory genes experiencing purifying selection. The significant congruence between core genome and pan-genome trees revealed that core genes mainly affected evolutionary divergences of Aeromonas species. Gene gains and losses revealed a high level of genome plasticity, exhibited by hundreds of gene expansions and contractions, horizontally transferred genes, and mobile genetic elements. The selective constraints shaped virulence gene pools of these Aeromonas strains, where genes encoding hemolysin were ubiquitous. Of these strains, Aeromonas aquatica MX16A seemed to be more resistant, as it harbored most resistance genes. Finally, the virulence factors of Aeromonas in microbial communities were quite dynamic in response to environment changes. For example, the virulence diversity of Aeromonas in microbial communities could reach levels that match some of the most virulent Aeromonas species (such as A. hydrophila) in penetrated-air and modified-air packaging. Our work shed some light onto genetic diversity, evolutionary history, and functional features of Aeromonas, which could facilitate the detection and prevention of infections.IMPORTANCE Aeromonas has long been known as a gastrointestinal pathogen, yet it has many species whose evolutionary dynamics and genetic diversity had been unclear until now. We have conducted pan-genome analysis for 29 Aeromonas species and revealed a high level of genome plasticity exhibited by hundreds of gene expansions and contractions, horizontally transferred genes, and mobile genetic elements. These species also contained many virulence factors both identified from single isolated species and microbial community. This pan-genome study could elevate the level for detection and prevention of Aeromonas infections.
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Kalesinskas L, Cudone E, Fofanov Y, Putonti C. S-plot2: Rapid Visual and Statistical Analysis of Genomic Sequences. Evol Bioinform Online 2018; 14:1176934318797354. [PMID: 30245567 PMCID: PMC6144591 DOI: 10.1177/1176934318797354] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 08/08/2018] [Indexed: 12/12/2022] Open
Abstract
With the daily release of data from whole genome sequencing projects, tools to facilitate comparative studies are hard-pressed to keep pace. Graphical software solutions can readily recognize synteny by measuring similarities between sequences. Nevertheless, regions of dissimilarity can prove to be equally informative; these regions may harbor genes acquired via lateral gene transfer (LGT), signify gene loss or gain, or include coding regions under strong selection. Previously, we developed the software S-plot. This tool employed an alignment-free approach for comparing bacterial genomes and generated a heatmap representing the genomes’ similarities and dissimilarities in nucleotide usage. In prior studies, this tool proved valuable in identifying genome rearrangements as well as exogenous sequences acquired via LGT in several bacterial species. Herein, we present the next generation of this tool, S-plot2. Similar to its predecessor, S-plot2 creates an interactive, 2-dimensional heatmap capturing the similarities and dissimilarities in nucleotide usage between genomic sequences (partial or complete). This new version, however, includes additional metrics for analysis, new reporting options, and integrated BLAST query functionality for the user to interrogate regions of interest. Furthermore, S-plot2 can evaluate larger sequences, including whole eukaryotic chromosomes. To illustrate some of the applications of the tool, 2 case studies are presented. The first examines strain-specific variation across the Pseudomonas aeruginosa genome and strain-specific LGT events. In the second case study, corresponding human, chimpanzee, and rhesus macaque autosomes were studied and lineage specific contributions to divergence were estimated. S-plot2 provides a means to both visually and quantitatively compare nucleotide sequences, from microbial genomes to eukaryotic chromosomes. The case studies presented illustrate just 2 potential applications of the tool, highlighting its capability to identify and investigate the variation in molecular divergence rates across sequences. S-plot2 is freely available through https://bitbucket.org/lkalesinskas/splot and is supported on the Linux and MS Windows operating systems.
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Affiliation(s)
- Laurynas Kalesinskas
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA.,Department of Biology, Loyola University Chicago, Chicago, IL, USA
| | - Evan Cudone
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA.,Department of Mathematics and Statistics, Loyola University Chicago, Chicago, IL, USA
| | - Yuriy Fofanov
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA.,Department of Biology, Loyola University Chicago, Chicago, IL, USA.,Department of Computer Science, Loyola University Chicago, Chicago, IL, USA
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