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Fang GY, Liu XQ, Jiang YJ, Mu XJ, Huang BW. Horizontal gene transfer in activated sludge enhances microbial antimicrobial resistance and virulence. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168908. [PMID: 38013098 DOI: 10.1016/j.scitotenv.2023.168908] [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: 09/04/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 11/29/2023]
Abstract
Activated sludge (AS) plays a vital role in removing organic pollutants and nutrients from wastewater. However, the risks posed by horizontal gene transfer (HGT) between bacteria in AS are still unclear. Here, a total of 478 high-quality non-redundant metagenome-assembled genomes (MAGs) were obtained. >50 % and 5 % of MAGs were involved in at least one HGT and recent HGT, respectively. Most of the transfers (82.4 %) of antimicrobial resistance genes (ARGs) occurred among the classes of Alphaproteobacteria and Gammaproteobacteria. The bacteria involved in the transfers of virulence factor genes (VFGs) mainly include Alphaproteobacteria (42.3 %), Bacteroidia (19.2 %), and Gammaproteobacteria (11.5 %). Moreover, the number of ARGs and VFGs in the classes of Alphaproteobacteria and Gammaproteobacteria was higher than that in other bacteria (P < 0.001). Mobile genetic elements were important contributors to ARGs and VFGs in AS bacteria. These results have implications for the management of antimicrobial resistance and virulence in activated sludge microorganisms.
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Affiliation(s)
- Guan-Yu Fang
- College of Food and Health, Zhejiang A&F University, Hangzhou 311300, PR China; National Grain Industry (High-Quality Rice Storage in Temperate and Humid Region) Technology Innovation Center, Zhejiang A&F University, Hangzhou 311300, PR China.
| | - Xing-Quan Liu
- College of Food and Health, Zhejiang A&F University, Hangzhou 311300, PR China; National Grain Industry (High-Quality Rice Storage in Temperate and Humid Region) Technology Innovation Center, Zhejiang A&F University, Hangzhou 311300, PR China
| | - Yu-Jian Jiang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, PR China
| | - Xiao-Jing Mu
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, PR China
| | - Bing-Wen Huang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, PR China
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2
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Zhu S, Hong J, Wang T. Horizontal gene transfer is predicted to overcome the diversity limit of competing microbial species. Nat Commun 2024; 15:800. [PMID: 38280843 PMCID: PMC10821886 DOI: 10.1038/s41467-024-45154-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 01/17/2024] [Indexed: 01/29/2024] Open
Abstract
Natural microbial ecosystems harbor substantial diversity of competing species. Explaining such diversity is challenging, because in classic theories it is extremely infeasible for a large community of competing species to stably coexist in homogeneous environments. One important aspect mostly overlooked in these theories, however, is that microbes commonly share genetic materials with their neighbors through horizontal gene transfer (HGT), which enables the dynamic change of species growth rates due to the fitness effects of the mobile genetic elements (MGEs). Here, we establish a framework of species competition by accounting for the dynamic gene flow among competing microbes. Combining theoretical derivation and numerical simulations, we show that in many conditions HGT can surprisingly overcome the biodiversity limit predicted by the classic model and allow the coexistence of many competitors, by enabling dynamic neutrality of competing species. In contrast with the static neutrality proposed by previous theories, the diversity maintained by HGT is highly stable against random perturbations of microbial fitness. Our work highlights the importance of considering gene flow when addressing fundamental ecological questions in the world of microbes and has broad implications for the design and engineering of complex microbial consortia.
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Affiliation(s)
- Shiben Zhu
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Juken Hong
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Teng Wang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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3
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Zhao L, Lv Z, Lin L, Li X, Xu J, Huang S, Chen Y, Fu Y, Peng C, Cao T, Ke Y, Xia X. Impact of COVID-19 pandemic on profiles of antibiotic-resistant genes and bacteria in hospital wastewater. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 334:122133. [PMID: 37399936 DOI: 10.1016/j.envpol.2023.122133] [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: 12/02/2022] [Revised: 06/21/2023] [Accepted: 07/01/2023] [Indexed: 07/05/2023]
Abstract
The COVID-19 pandemic has severely affected healthcare worldwide and has led to the excessive use of disinfectants and antimicrobial agents. However, the impact of excessive disinfection measures and specific medication prescriptions on the development and dissemination of bacterial drug resistance during the pandemic remains unclear. This study investigated the influence of the pandemic on the composition of antibiotics, antibiotic resistance genes (ARGs), and pathogenic communities in hospital wastewater using ultra-performance liquid chromatography-tandem mass spectrometry and metagenome sequencing. The overall level of antibiotics decreased after the COVID-19 outbreak, whereas the abundance of various ARGs increased in hospital wastewater. After COVID-19 outbreak, blaOXA, sul2, tetX, and qnrS had higher concentrations in winter than in summer. Seasonal factors and the COVID-19 pandemic have affected the microbial structure in wastewater, especially of Klebsiella, Escherichia, Aeromonas, and Acinetobacter. Further analysis revealed the co-existence of qnrS, blaNDM, and blaKPC during the pandemic. Various ARGs significantly correlated with mobile genetic elements, implying their potential mobility. A network analysis revealed that many pathogenic bacteria (Klebsiella, Escherichia, and Vibrio) were correlated with ARGs, indicating the existence of multi-drug resistant pathogens. Although the calculated resistome risk score did not change significantly, our results suggest that the COVID-19 pandemic shifted the composition of residual antibiotics and ARGs in hospital wastewater and contributed to the dissemination of bacterial drug resistance.
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Affiliation(s)
- Liang Zhao
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Ziquan Lv
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Liangqiang Lin
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Xiaowei Li
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Jian Xu
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Suli Huang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Yuhua Chen
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Yulin Fu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Changfeng Peng
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Tingting Cao
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Yuebin Ke
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Xi Xia
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.
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4
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Moradigaravand D, Li L, Dechesne A, Nesme J, de la Cruz R, Ahmad H, Banzhaf M, Sørensen SJ, Smets BF, Kreft JU. Plasmid permissiveness of wastewater microbiomes can be predicted from 16S rRNA sequences by machine learning. Bioinformatics 2023; 39:btad400. [PMID: 37348862 PMCID: PMC10318386 DOI: 10.1093/bioinformatics/btad400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 06/13/2023] [Accepted: 06/21/2023] [Indexed: 06/24/2023] Open
Abstract
MOTIVATION Wastewater treatment plants (WWTPs) harbor a dense and diverse microbial community. They constantly receive antimicrobial residues and resistant strains, and therefore provide conditions for horizontal gene transfer (HGT) of antimicrobial resistance (AMR) determinants. This facilitates the transmission of clinically important genes between, e.g. enteric and environmental bacteria, and vice versa. Despite the clinical importance, tools for predicting HGT remain underdeveloped. RESULTS In this study, we examined to which extent water cycle microbial community composition, as inferred by partial 16S rRNA gene sequences, can predict plasmid permissiveness, i.e. the ability of cells to receive a plasmid through conjugation, based on data from standardized filter mating assays using fluorescent bio-reporter plasmids. We leveraged a range of machine learning models for predicting the permissiveness for each taxon in the community, representing the range of hosts a plasmid is able to transfer to, for three broad host-range resistance IncP plasmids (pKJK5, pB10, and RP4). Our results indicate that the predicted permissiveness from the best performing model (random forest) showed a moderate-to-strong average correlation of 0.49 for pB10 [95% confidence interval (CI): 0.44-0.55], 0.43 for pKJK5 (0.95% CI: 0.41-0.49), and 0.53 for RP4 (0.95% CI: 0.48-0.57) with the experimental permissiveness in the unseen test dataset. Predictive phylogenetic signals occurred despite the broad host-range nature of these plasmids. Our results provide a framework that contributes to the assessment of the risk of AMR pollution in wastewater systems. AVAILABILITY AND IMPLEMENTATION The predictive tool is available as an application at https://github.com/DaneshMoradigaravand/PlasmidPerm.
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Affiliation(s)
- Danesh Moradigaravand
- Laboratory of Infectious Disease Epidemiology, KAUST Smart-Health Initiative and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- KAUST Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Liguan Li
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
- Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Arnaud Dechesne
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | - Joseph Nesme
- Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Roberto de la Cruz
- Center for Computational Biology, University of Birmingham, Birmingham, B15 2TT, United Kingdom
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, United Kingdom
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Huda Ahmad
- Laboratory of Infectious Disease Epidemiology, KAUST Smart-Health Initiative and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- KAUST Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Center for Computational Biology, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Manuel Banzhaf
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, United Kingdom
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Søren J Sørensen
- Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Barth F Smets
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | - Jan-Ulrich Kreft
- Center for Computational Biology, University of Birmingham, Birmingham, B15 2TT, United Kingdom
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, United Kingdom
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
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5
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Hwang Y, Roux S, Coclet C, Krause SJE, Girguis PR. Viruses interact with hosts that span distantly related microbial domains in dense hydrothermal mats. Nat Microbiol 2023; 8:946-957. [PMID: 37024618 PMCID: PMC10159854 DOI: 10.1038/s41564-023-01347-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 02/25/2023] [Indexed: 04/08/2023]
Abstract
Many microbes in nature reside in dense, metabolically interdependent communities. We investigated the nature and extent of microbe-virus interactions in relation to microbial density and syntrophy by examining microbe-virus interactions in a biomass dense, deep-sea hydrothermal mat. Using metagenomic sequencing, we find numerous instances where phylogenetically distant (up to domain level) microbes encode CRISPR-based immunity against the same viruses in the mat. Evidence of viral interactions with hosts cross-cutting microbial domains is particularly striking between known syntrophic partners, for example those engaged in anaerobic methanotrophy. These patterns are corroborated by proximity-ligation-based (Hi-C) inference. Surveys of public datasets reveal additional viruses interacting with hosts across domains in diverse ecosystems known to harbour syntrophic biofilms. We propose that the entry of viral particles and/or DNA to non-primary host cells may be a common phenomenon in densely populated ecosystems, with eco-evolutionary implications for syntrophic microbes and CRISPR-mediated inter-population augmentation of resilience against viruses.
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Affiliation(s)
- Yunha Hwang
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Simon Roux
- DOE (Department of Energy) Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Clément Coclet
- DOE (Department of Energy) Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sebastian J E Krause
- Department of Earth, Planetary, and Space Sciences, University of California, Los Angeles, CA, USA
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
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6
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Comparative genomics reveals the evolution of antimicrobial resistance in Bacteroides nordii. Microb Pathog 2022; 173:105811. [PMID: 36183960 DOI: 10.1016/j.micpath.2022.105811] [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: 06/15/2022] [Revised: 09/24/2022] [Accepted: 09/26/2022] [Indexed: 11/22/2022]
Abstract
Bacteroides nordii, is an understudied member of the pathogenic B. fragilis group which comprises several multidrug-resistant (MDR) strains. Thus, it is of great interest to study the genome biology of Bacteroides nordii. However, no detailed study is available that characterized B. nordii at the genetic level and explored its role as a potential pathogen. We isolated an MDR strain viz., B. nordii PGMM4098 from the pus sample and subjected it to whole genome sequencing using Illumina technology. The draft genome was de-novo assembled and annotated, followed by comprehensive comparative genomics analyses using the publicly available genome dataset of B. nordii. The pan-genome analysis revealed the open nature of B. nordii, indicating the continuous accumulation of novel genes in non-core components leading to the emergence of new strains of this species. The thirteen antimicrobial resistance (AMR) genes identified in the genomes of all B. nordii strains were part of the non-core component of the pan-genome. Of these, four AMR genes, nimE, aadS, mef(En2), and ermB/F/G were found to be acquired via the process of horizontal gene transfer (HGT) from anaerobic Bacteroidetes. Importantly, the nimE gene conferring metronidazole resistance was found to be present only in B. nordii PGMM4098, which harbors five other AMR genes encoded in its genome. Of these, nimE (metronidazole resistance), ermB/F/G (macrolide-lincosamide-streptogramin B resistance), and cfxA2/A3 (class A β-lactam resistance) genes were further validated using targeted polymerase chain reaction assay. Notably, these three genes were also found to be under the operation of positive selective pressure suggesting the diversification of these genes, which might lead to the emergence of new MDR strains of B. nordii in the near future. Our study reported and characterized the genome of the first MDR strain of B. nordii and revealed the AMR evolution in this species using a comprehensive comparative genomics approach.
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7
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Sharma V, Vashishtha A, Jos ALM, Khosla A, Basu N, Yadav R, Bhatt A, Gulani A, Singh P, Lakhera S, Verma M. Phylogenomics of the Phylum Proteobacteria: Resolving the Complex Relationships. Curr Microbiol 2022; 79:224. [PMID: 35704242 DOI: 10.1007/s00284-022-02910-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 05/20/2022] [Indexed: 11/28/2022]
Abstract
Proteobacteria is one of the largest and phenotypically most diverse divisions within the domain bacteria. Due to the economic importance, this phylum demands an urgent need for a clear and scientifically sound classification system to streamline their characterization. The goal of our study was to carefully reevaluate the current system of classification and suggest changes wherein necessary. Phylogenetic trees of 84 Proteobacteria were constructed using single gene-based phylogeny involving 16S rRNA genes and protein sequences of 85 conserved genes, whole genome-based phylogenetic tree using CVtree3.0, amino acid Identity matrix tree, and concatenated tree with aforementioned conserved genes. The results of our study confirm the polyphyletic relationship between Desulfurella acetivorans, a Deltaproteobacteria with Epsilonproteobacteria. The group Syntrophobacterales was found to be polyphyletic with respect to Desulfarculus baarsii and the group Thiotrichales was found to be splitting in different phylogenetic trees. Placement of phylogenetic groups belonging to Rhodocyclales, Oceonospirilalles, and Chromatiales is controversial and requires further study and revisions. Based on our analysis, we strongly support reclassification of Magnetococcales as a separate class Etaproteobacteria. From our results, we conclude that concatenated trees of conserved proteins are a more accurate method for phylogenetic analysis, as compared to other methods used.
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Affiliation(s)
- Vaibhav Sharma
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Amit Vashishtha
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Arsha Liz M Jos
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Akshita Khosla
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Nirmegh Basu
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Rishabh Yadav
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Amit Bhatt
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Akshanshi Gulani
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Pushpa Singh
- Swami Shraddhanand College, University of Delhi, Alipur, New Delhi, Delhi, 110036, India
| | - Sanidhya Lakhera
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India
| | - Mansi Verma
- Sri Venkateswara College, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, Delhi, 110021, India. .,Department of Zoology, Sri Venkateswara College, South Campus, University of Delhi, New Delhi, Delhi, 110021, India.
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8
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Comparative Genomics Unveils the Habitat Adaptation and Metabolic Profiles of
Clostridium
in an Artificial Ecosystem for Liquor Production. mSystems 2022; 7:e0029722. [PMID: 35491831 PMCID: PMC9238394 DOI: 10.1128/msystems.00297-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pit mud is a typical artificial ecosystem for Chinese liquor production.
Clostridium
inhabiting pit mud plays essential roles in the flavor formation of strong-flavor baijiu. The relative abundance of
Clostridium
increased with pit mud quality, further influencing the quality of baijiu.
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9
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Abstract
Sialic acids are present in humans and other metazoans, playing essential roles in physiological and pathological processes. Commensal and pathogenic bacteria have evolved the capacity to utilize sialic acids as nutrient and energy sources. However, in some actinobacteria, sialic acid catabolism (SAC) is associated with free-living populations. To unravel the distribution and evolutionary history of SAC in the phylum Actinobacteria, we analyzed the presence and diversity of the putative SAC gene cluster (nan) in 7,180 high-quality, nonredundant actinobacterial genomes that covered 1,969 species. The results showed that ∼13% of actinobacterial species had the potential to utilize sialic acids, with 45 species capable of anhydro-SAC, all except two of them through the canonical pathway. These species belonged to 20 orders and 81 genera, with ∼36% of them from four genera, Actinomyces, Bifidobacterium, Corynebacterium, and Streptomyces. Moreover, ∼40% of the nan-positive species are free living. Phylogenetic analysis of the key nan genes, nanA, nanK, and nanE, revealed a strong signal of horizontal gene transfer (HGT), accompanied with vertical inheritance and gene loss. This evolutionary pattern led to high diversity and differential distribution of nan among actinobacterial taxa and might cause the cluster to spread to some free-living species while losing in some host-associated species. The evolution of SAC in actinobacteria probably represents the evolution of certain kinds of noncore bacterial functions for environmental adaptation and lifestyle switch, in which HGT plays a dominant role. IMPORTANCE Sialic acids play essential roles in the physiology of humans and other metazoan animals, and microbial sialic acid catabolism (SAC) is one of the processes critical for pathogenesis. To date, microbial SAC is studied mainly in commensals and pathogens, while its distribution in free-living microbes and evolutionary pathway remain largely unexplored. Here, by examining all actinobacterial genomes available, we demonstrate that putative SAC is present in a small proportion of actinobacterial species, of which, however, ∼40% are free-living species. We also reveal remarkable difference in the distribution of SAC among actinobacterial taxa and high diversity of the putative SAC gene clusters. HGT plays a significant role in the evolution of SAC, accompanied with vertical inheritance and gene loss. Our results provide a comprehensive and systematic picture of the distribution and evolutionary history of SAC in actinobacteria, expanding the current knowledge on bacterial adaptation and diversification.
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10
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Nobs SJ, MacLeod FI, Wong HL, Burns BP. Eukarya the chimera: eukaryotes, a secondary innovation of the two domains of life? Trends Microbiol 2021; 30:421-431. [PMID: 34863611 DOI: 10.1016/j.tim.2021.11.003] [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: 06/03/2021] [Revised: 10/31/2021] [Accepted: 11/03/2021] [Indexed: 10/19/2022]
Abstract
One of the most significant events in the evolution of life is the origin of the eukaryotic cell, an increase in cellular complexity that occurred approximately 2 billion years ago. Ground-breaking research has centered around unraveling the characteristics of the Last Eukaryotic Common Ancestor (LECA) and the nuanced archaeal and bacterial contributions in eukaryogenesis, resulting in fundamental changes in our understanding of the Tree of Life. The archaeal and bacterial roles are covered by theories of endosymbiogenesis wherein an ancestral host archaeon and a bacterial endosymbiont merged to create a new complex cell type - Eukarya - and its mitochondrion. Eukarya is often regarded as a unique and distinct domain due to complex innovations not found in archaea or bacteria, despite housing a chimeric genome containing genes of both archaeal and bacterial origin. However, the discovery of complex cell machineries in recently described Asgard archaeal lineages, and the growing support for diverse bacterial gene transfers prior to and during the time of LECA, is redefining our understanding of eukaryogenesis. Indeed, the uniqueness of Eukarya, as a domain, is challenged. It is likely that many microbial syntrophies, encompassing a 'microbial village', were required to 'raise' a eukaryote during the process of eukaryogenesis.
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Affiliation(s)
- Stephanie-Jane Nobs
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia; Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia
| | - Fraser I MacLeod
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia; Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia
| | - Hon Lun Wong
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia; Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia; Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Brendan P Burns
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia; Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia.
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11
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Ma T, McAllister TA, Guan LL. A review of the resistome within the digestive tract of livestock. J Anim Sci Biotechnol 2021; 12:121. [PMID: 34763729 PMCID: PMC8588621 DOI: 10.1186/s40104-021-00643-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/07/2021] [Indexed: 12/25/2022] Open
Abstract
Antimicrobials have been widely used to prevent and treat infectious diseases and promote growth in food-production animals. However, the occurrence of antimicrobial resistance poses a huge threat to public and animal health, especially in less developed countries where food-producing animals often intermingle with humans. To limit the spread of antimicrobial resistance from food-production animals to humans and the environment, it is essential to have a comprehensive knowledge of the role of the resistome in antimicrobial resistance (AMR), The resistome refers to the collection of all antimicrobial resistance genes associated with microbiota in a given environment. The dense microbiota in the digestive tract is known to harbour one of the most diverse resistomes in nature. Studies of the resistome in the digestive tract of humans and animals are increasing exponentially as a result of advancements in next-generation sequencing and the expansion of bioinformatic resources/tools to identify and describe the resistome. In this review, we outline the various tools/bioinformatic pipelines currently available to characterize and understand the nature of the intestinal resistome of swine, poultry, and ruminants. We then propose future research directions including analysis of resistome using long-read sequencing, investigation in the role of mobile genetic elements in the expression, function and transmission of AMR. This review outlines the current knowledge and approaches to studying the resistome in food-producing animals and sheds light on future strategies to reduce antimicrobial usage and control the spread of AMR both within and from livestock production systems.
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Affiliation(s)
- Tao Ma
- Key laboratory of Feed Biotechnology of the Ministry of Agriculture, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.,Department of Agricultural, Food and Nutritional Science, University of Alberta, T6G2P5, Edmonton, AB, Canada
| | - Tim A McAllister
- Lethbridge Research and Development Centre, Lethbridge, AB, T1J 4P4, Canada
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, T6G2P5, Edmonton, AB, Canada.
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12
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Zhou H, Beltrán JF, Brito IL. Functions predict horizontal gene transfer and the emergence of antibiotic resistance. SCIENCE ADVANCES 2021; 7:eabj5056. [PMID: 34678056 PMCID: PMC8535800 DOI: 10.1126/sciadv.abj5056] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Phylogenetic distance, shared ecology, and genomic constraints are often cited as key drivers governing horizontal gene transfer (HGT), although their relative contributions are unclear. Here, we apply machine learning algorithms to a curated set of diverse bacterial genomes to tease apart the importance of specific functional traits on recent HGT events. We find that functional content accurately predicts the HGT network [area under the receiver operating characteristic curve (AUROC) = 0.983], and performance improves further (AUROC = 0.990) for transfers involving antibiotic resistance genes (ARGs), highlighting the importance of HGT machinery, niche-specific, and metabolic functions. We find that high-probability not-yet detected ARG transfer events are almost exclusive to human-associated bacteria. Our approach is robust at predicting the HGT networks of pathogens, including Acinetobacter baumannii and Escherichia coli, as well as within localized environments, such as an individual’s gut microbiome.
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Affiliation(s)
- Hao Zhou
- Department of Microbiology, Cornell University, Ithaca, NY, USA
| | - Juan Felipe Beltrán
- Quantum-Si, Guildford, CT, USA
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Ilana Lauren Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
- Corresponding author.
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13
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Colombi E, Perry BJ, Sullivan JT, Bekuma AA, Terpolilli JJ, Ronson CW, Ramsay JP. Comparative analysis of integrative and conjugative mobile genetic elements in the genus Mesorhizobium. Microb Genom 2021; 7. [PMID: 34605762 PMCID: PMC8627217 DOI: 10.1099/mgen.0.000657] [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] [Indexed: 11/18/2022] Open
Abstract
Members of the Mesorhizobium genus are soil bacteria that often form nitrogen-fixing symbioses with legumes. Most characterised Mesorhizobium spp. genomes are ~8 Mb in size and harbour extensive pangenomes including large integrative and conjugative elements (ICEs) carrying genes required for symbiosis (ICESyms). Here, we document and compare the conjugative mobilome of 41 complete Mesorhizobium genomes. We delineated 56 ICEs and 24 integrative and mobilizable elements (IMEs) collectively occupying 16 distinct integration sites, along with 24 plasmids. We also demonstrated horizontal transfer of the largest (853,775 bp) documented ICE, the tripartite ICEMspSymAA22. The conjugation systems of all identified ICEs and several plasmids were related to those of the paradigm ICESym ICEMlSymR7A, with each carrying conserved genes for conjugative pilus formation (trb), excision (rdfS), DNA transfer (rlxS) and regulation (fseA). ICESyms have likely evolved from a common ancestor, despite occupying a variety of distinct integration sites and specifying symbiosis with diverse legumes. We found extensive evidence for recombination between ICEs and particularly ICESyms, which all uniquely lack the conjugation entry-exclusion factor gene trbK. Frequent duplication, replacement and pseudogenization of genes for quorum-sensing-mediated activation and antiactivation of ICE transfer suggests ICE transfer regulation is constantly evolving. Pangenome-wide association analysis of the ICE identified genes potentially involved in symbiosis, rhizosphere colonisation and/or adaptation to distinct legume hosts. In summary, the Mesorhizobium genus has accumulated a large and dynamic pangenome that evolves through ongoing horizontal gene transfer of large conjugative elements related to ICEMlSymR7A.
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Affiliation(s)
- Elena Colombi
- Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia.,Curtin Medical School, Curtin University, Perth, WA, Australia
| | - Benjamin J Perry
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - John T Sullivan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Amanuel A Bekuma
- Centre for Rhizobium Studies, Food Futures Institute, Murdoch University, Perth, WA, Australia, Murdoch University, Perth, WA, Australia.,Present address: Western Australian Department of Primary Industries and Regional Development, Research and Industry Innovation, South Perth, WA, Australia
| | - Jason J Terpolilli
- Centre for Rhizobium Studies, Food Futures Institute, Murdoch University, Perth, WA, Australia, Murdoch University, Perth, WA, Australia
| | - Clive W Ronson
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Joshua P Ramsay
- Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia.,Curtin Medical School, Curtin University, Perth, WA, Australia
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14
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Chen Z, Liu WS, Zhong X, Zheng M, Fei YH, He H, Ding K, Chao Y, Tang YT, Wang S, Qiu R. Genome- and community-level interaction insights into the ecological role of archaea in rare earth element mine drainage in South China. WATER RESEARCH 2021; 201:117331. [PMID: 34153824 DOI: 10.1016/j.watres.2021.117331] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 06/13/2023]
Abstract
Microbial communities play crucial roles in mine drainage generation and remediation. Despite the wide distribution of archaea in the mine ecosystem, their diversity and ecological roles remain less understood than bacteria. Here, we retrieved 56 archaeal metagenome-assembled genomes from a river impacted by rare earth element (REE) mining activities in South China. Genomic analysis showed that archaea represented four distinct lineages, including phyla of Thaumarchaeota, Micrarchaeota, Nanoarchaeota and Thermoplasmata. These archaea represented a considerable fraction (up to 40%) of the total prokaryote community, which might contribute to nitrogen and sulfur cycling in the REE mine drainage. Reconstructed metabolic potential among diverse archaea taxa revealed that archaea were involved in the network of ammonia oxidation, denitrification, sulfate redox reaction, and required substrates supplied by other community members. As the dominant driver of ammonia oxidation, Thaumarchaeota might provide substrates to support the survival of two nano-sized archaea belonging to Micrarchaeota and Nanoarchaeota. Despite the absence of biosynthesis pathways for amino acids and nucleotides, the potential capacity for nitrite reduction (nirD) was observed in Micrarchaeota, indicating that these nano-sized archaea encompassed diverse metabolisms. Moreover, Thermoplasmata, as keystone taxa in community, might be the main genetic donor for the other three archaeal phyla, transferring many environmental resistance related genes (e.g., V/A-type ATPase and Vitamin B12-transporting ATPase). The genetic interactions within archaeal community through horizontal gene transfer might be the key to the formation of archaeal resistance and functional partitioning. This study provides putative metabolic and genetic insights into the diverse archaea taxa from community-level perspectives, and highlights the ecological roles of archaea in REE contaminated aquatic environment.
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Affiliation(s)
- Ziwu Chen
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Wen-Shen Liu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China
| | - Xi Zhong
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Mengyuan Zheng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Ying-Heng Fei
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Huan He
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Kengbo Ding
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuanqing Chao
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China.
| | - Ye-Tao Tang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China
| | - Shizhong Wang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China
| | - Rongliang Qiu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China.
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15
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Sheinman M, Arkhipova K, Arndt PF, Dutilh BE, Hermsen R, Massip F. Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain. eLife 2021; 10:62719. [PMID: 34121661 PMCID: PMC8270642 DOI: 10.7554/elife.62719] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 06/13/2021] [Indexed: 12/19/2022] Open
Abstract
Horizontal gene transfer (HGT) is an essential force in microbial evolution. Despite detailed studies on a variety of systems, a global picture of HGT in the microbial world is still missing. Here, we exploit that HGT creates long identical DNA sequences in the genomes of distant species, which can be found efficiently using alignment-free methods. Our pairwise analysis of 93,481 bacterial genomes identified 138,273 HGT events. We developed a model to explain their statistical properties as well as estimate the transfer rate between pairs of taxa. This reveals that long-distance HGT is frequent: our results indicate that HGT between species from different phyla has occurred in at least 8% of the species. Finally, our results confirm that the function of sequences strongly impacts their transfer rate, which varies by more than three orders of magnitude between different functional categories. Overall, we provide a comprehensive view of HGT, illuminating a fundamental process driving bacterial evolution.
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Affiliation(s)
- Michael Sheinman
- Theoretical Biology and Bioinformatics, Biology Department, Utrecht University, Utrecht, Netherlands.,Division of Molecular Carcinogenesis, the Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Ksenia Arkhipova
- Theoretical Biology and Bioinformatics, Biology Department, Utrecht University, Utrecht, Netherlands
| | - Peter F Arndt
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Biology Department, Utrecht University, Utrecht, Netherlands
| | - Rutger Hermsen
- Theoretical Biology and Bioinformatics, Biology Department, Utrecht University, Utrecht, Netherlands
| | - Florian Massip
- Berlin Institute for Medical Systems Biology, Max Delbrück Center, Berlin, Germany.,Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villleurbanne, France
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16
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Evidence for Horizontal and Vertical Transmission of Mtr-Mediated Extracellular Electron Transfer among the Bacteria. mBio 2021; 13:e0290421. [PMID: 35100867 PMCID: PMC8805035 DOI: 10.1128/mbio.02904-21] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Some bacteria and archaea have evolved the means to use extracellular electron donors and acceptors for energy metabolism, a phenomenon broadly known as extracellular electron transfer (EET). One such EET mechanism is the transmembrane electron conduit MtrCAB, which has been shown to transfer electrons derived from metabolic substrates to electron acceptors, like Fe(III) and Mn(IV) oxides, outside the cell. Although most studies of MtrCAB-mediated EET have been conducted in Shewanella oneidensis MR-1, recent investigations in Vibrio and Aeromonas species have revealed that the electron-donating proteins that support MtrCAB in Shewanella are not as representative as previously thought. This begs the question of how widespread the capacity for MtrCAB-mediated EET is, the changes it has accrued in different lineages, and where these lineages persist today. Here, we employed a phylogenetic and comparative genomics approach to identify the MtrCAB system across all domains of life. We found mtrCAB in the genomes of numerous diverse Bacteria from a wide range of environments, and the patterns therein strongly suggest that mtrCAB was distributed through both horizontal and subsequent vertical transmission, and with some cases indicating downstream modular diversification of both its core and accessory components. Our data point to an emerging evolutionary story about metal-oxidizing and -reducing metabolism, demonstrates that this capacity for EET has broad relevance to a diversity of taxa and the biogeochemical cycles they drive, and lays the foundation for further studies to shed light on how this mechanism may have coevolved with Earth's redox landscape. IMPORTANCE While many metabolisms make use of soluble, cell-permeable substrates like oxygen or hydrogen, there are other substrates, like iron or manganese, that cannot be brought into the cell. Some bacteria and archaea have evolved the means to directly "plug in" to such environmental electron reservoirs in a process known as extracellular electron transfer (EET), making them powerful agents of biogeochemical change and promising vehicles for bioremediation and alternative energy. Yet the diversity, distribution, and evolution of EET mechanisms are poorly constrained. Here, we present findings showing that the genes encoding one such EET system (mtrCAB) are present in a broad diversity of bacteria found in a wide range of environments, emphasizing the ubiquity and potential impact of EET in our biosphere. Our results suggest that these genes have been disseminated largely through horizontal transfer, and the changes they have accrued in these lineages potentially reflect adaptations to changing environments.
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17
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Comparative Genomic Analysis of Mycobacteriaceae Reveals Horizontal Gene Transfer-Mediated Evolution of the CRISPR-Cas System in the Mycobacterium tuberculosis Complex. mSystems 2021; 6:6/1/e00934-20. [PMID: 33468705 PMCID: PMC7820667 DOI: 10.1128/msystems.00934-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) genes are conserved genetic elements in many prokaryotes, including Mycobacterium tuberculosis, the causative agent of tuberculosis. Although knowledge of CRISPR locus variability has been utilized in M. tuberculosis strain genotyping, its evolutionary path in Mycobacteriaceae is not well understood. In this study, we have performed a comparative analysis of 141 mycobacterial genomes and identified the exclusive presence of the CRISPR-Cas type III-A system in M. tuberculosis complex (MTBC). Our global phylogenetic analysis of CRISPR repeats and Cas10 proteins offers evidence of horizontal gene transfer (HGT) of the CRISPR-Cas module in the last common ancestor of MTBC and Mycobacterium canettii from a Streptococcus-like environmental bacterium. Additionally, our results show that the variation of CRISPR-Cas organization in M. tuberculosis lineages, especially in the Beijing sublineage of lineage 2, is due to the transposition of insertion sequence IS6110 The direct repeat (DR) region of the CRISPR-Cas locus acts as a hot spot for IS6110 insertion. We show in M. tuberculosis H37Rv that the repeat at the 5' end of CRISPR1 of the forward strand is an atypical repeat made up partly of IS-terminal inverted repeat and partly CRISPR DR. By tracing an undetectable spacer sequence in the DR region, the two CRISPR loci could theoretically be joined to reconstruct the ancestral single CRISPR-Cas locus organization, as seen in M. canettii This study retracing the evolutionary events of HGT and IS6110-driven genomic deletions helps us to better understand the strain-specific variations in M. tuberculosis lineages.IMPORTANCE Comparative genomic analysis of prokaryotes has led to a better understanding of the biology of several pathogenic microorganisms. One such clinically important pathogen is M. tuberculosis, the leading cause of bacterial infection worldwide. Recent evidence on the functionality of the CRISPR-Cas system in M. tuberculosis has brought back focus on these conserved genetic elements, present in many prokaryotes. Our study advances understanding of mycobacterial CRISPR-Cas origin and its diversity among the different species. We provide phylogenetic evidence of acquisition of CRISPR-Cas type III-A in the last common ancestor shared between MTBC and M. canettii, by HGT-mediated events. The most likely source of HGT was an environmental Firmicutes bacterium. Genomic mapping of the CRISPR loci showed the IS6110 transposition-driven variations in M. tuberculosis strains. Thus, this study offers insights into events related to the evolution of CRISPR-Cas in M. tuberculosis lineages.
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18
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Vannier T, Hingamp P, Turrel F, Tanet L, Lescot M, Timsit Y. Diversity and evolution of bacterial bioluminescence genes in the global ocean. NAR Genom Bioinform 2020; 2:lqaa018. [PMID: 33575578 PMCID: PMC7671414 DOI: 10.1093/nargab/lqaa018] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 02/14/2020] [Accepted: 03/06/2020] [Indexed: 12/19/2022] Open
Abstract
Although bioluminescent bacteria are the most abundant and widely distributed of all light-emitting organisms, the biological role and evolutionary history of bacterial luminescence are still shrouded in mystery. Bioluminescence has so far been observed in the genomes of three families of Gammaproteobacteria in the form of canonical lux operons that adopt the CDAB(F)E(G) gene order. LuxA and luxB encode the two subunits of bacterial luciferase responsible for light-emission. Our deep exploration of public marine environmental databases considerably expands this view by providing a catalog of new lux homolog sequences, including 401 previously unknown luciferase-related genes. It also reveals a broader diversity of the lux operon organization, which we observed in previously undescribed configurations such as CEDA, CAED and AxxCE. This expanded operon diversity provides clues for deciphering lux operon evolution and propagation within the bacterial domain. Leveraging quantitative tracking of marine bacterial genes afforded by planetary scale metagenomic sampling, our study also reveals that the novel lux genes and operons described herein are more abundant in the global ocean than the canonical CDAB(F)E(G) operon.
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Affiliation(s)
- Thomas Vannier
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM110, 13288 Marseille, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Pascal Hingamp
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM110, 13288 Marseille, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Floriane Turrel
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM110, 13288 Marseille, France
| | - Lisa Tanet
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM110, 13288 Marseille, France
| | - Magali Lescot
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM110, 13288 Marseille, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Youri Timsit
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM110, 13288 Marseille, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 3 rue Michel-Ange, 75016 Paris, France
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19
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Lal Gupta C, Kumar Tiwari R, Cytryn E. Platforms for elucidating antibiotic resistance in single genomes and complex metagenomes. ENVIRONMENT INTERNATIONAL 2020; 138:105667. [PMID: 32234679 DOI: 10.1016/j.envint.2020.105667] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/15/2020] [Accepted: 03/16/2020] [Indexed: 05/21/2023]
Abstract
Antibiotic or antimicrobial resistance (AR) facilitated by the vertical and/or horizontal transfer of antibiotic resistance genes (ARGs), is a serious global health challenge. While traditionally associated with pathogens in clinical environments, it is becoming increasingly clear that non-clinical environments may also be reservoirs of ARGs. The recent improvements in rapid and affordable next generation sequencing technologies along with sophisticated bioinformatics platforms has the potential to revolutionize diagnostic microbiology and microbial surveillance. Through the study and characterization of ARGs in bacterial genomes and complex metagenomes, we are now able to reveal the genetic scope of AR in single bacteria and complex communities, and obtain important insights into AR dynamics at species, population and community levels, providing novel epidemiological and ecological perspectives. A suite of bioinformatics pipelines and ARG databases are currently available for genomic and metagenomic data analyses. However, different platforms may significantly vary and therefore, it is crucial to choose the tools that are most suitable for the specific analysis being conducted. This review provides a detailed account of available bioinformatics platforms for identification and characterization of ARGs and associated genetic elements within single bacterial isolates and complex environmental samples. It focuses primarily on currently available ARG databases, employing a comprehensive benchmarking pipeline to identify ARGs in four bacterial genomes (Aeromonas salmonicida, Bacillus cereus, Burkholderia sp. and Escherichia coli) and three shotgun metagenomes (human gut, poultry litter and soil) providing insight into which databases should be used for different analytical scenarios.
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Affiliation(s)
- Chhedi Lal Gupta
- Institute of Soil, Water and Environmental Sciences, Volcani Research Center, Agriculture Research Organization, Rishon Lezion 7528809, Israel
| | - Rohit Kumar Tiwari
- Department of Biosciences, Integral University, Lucknow 226026, UP, India
| | - Eddie Cytryn
- Institute of Soil, Water and Environmental Sciences, Volcani Research Center, Agriculture Research Organization, Rishon Lezion 7528809, Israel.
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20
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The complex phylogenetic relationships of a 4mC/6mA DNA methyltransferase in prokaryotes. Mol Phylogenet Evol 2020; 149:106837. [PMID: 32304827 DOI: 10.1016/j.ympev.2020.106837] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 01/30/2020] [Accepted: 04/09/2020] [Indexed: 01/04/2023]
Abstract
DNA methyltransferases are proteins that modify DNA via attachment of methyl groups to nucleobases and are ubiquitous across the bacterial, archaeal, and eukaryotic domains of life. Here, we investigated the complex evolutionary history of the large and consequential 4mC/6mA DNA methyltransferase protein family using phylogenetic reconstruction of amino acid sequences. We present a well-supported phylogeny of this family based on systematic sampling of taxa across superphyla of bacteria and archaea. We compared the phylogeny to a current representation of the species tree of life and found that the 4mC/6mA methyltransferase family has a strikingly complex evolutionary history that likely began sometime after the last universal common ancestor of life diverged into the bacterial and archaeal lineages and probably involved many horizontal gene transfers within and between domains. Despite the complexity of its evolutionary history, we inferred that only one significant shift in molecular evolutionary rate characterizes the diversification of this protein family.
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21
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Lee K, Kim DW, Lee DH, Kim YS, Bu JH, Cha JH, Thawng CN, Hwang EM, Seong HJ, Sul WJ, Wellington EMH, Quince C, Cha CJ. Mobile resistome of human gut and pathogen drives anthropogenic bloom of antibiotic resistance. MICROBIOME 2020; 8:2. [PMID: 31910889 PMCID: PMC6947943 DOI: 10.1186/s40168-019-0774-7] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 12/09/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND The impact of human activities on the environmental resistome has been documented in many studies, but there remains the controversial question of whether the increased antibiotic resistance observed in anthropogenically impacted environments is just a result of contamination by resistant fecal microbes or is mediated by indigenous environmental organisms. Here, to determine exactly how anthropogenic influences shape the environmental resistome, we resolved the microbiome, resistome, and mobilome of the planktonic microbial communities along a single river, the Han, which spans a gradient of human activities. RESULTS The bloom of antibiotic resistance genes (ARGs) was evident in the downstream regions and distinct successional dynamics of the river resistome occurred across the spatial continuum. We identified a number of widespread ARG sequences shared between the river, human gut, and pathogenic bacteria. These human-related ARGs were largely associated with mobile genetic elements rather than particular gut taxa and mainly responsible for anthropogenically driven bloom of the downstream river resistome. Furthermore, both sequence- and phenotype-based analyses revealed environmental relatives of clinically important proteobacteria as major carriers of these ARGs. CONCLUSIONS Our results demonstrate a more nuanced view of the impact of anthropogenic activities on the river resistome: fecal contamination is present and allows the transmission of ARGs to the environmental resistome, but these mobile genes rather than resistant fecal bacteria proliferate in environmental relatives of their original hosts. Video abstract.
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Affiliation(s)
- Kihyun Lee
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Dae-Wi Kim
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Do-Hoon Lee
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Yong-Seok Kim
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Ji-Hye Bu
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Ju-Hee Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Cung Nawl Thawng
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Eun-Mi Hwang
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Hoon Je Seong
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Woo Jun Sul
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | | | | | - Chang-Jun Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea.
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22
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Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes. Cell 2019; 178:1245-1259.e14. [PMID: 31402174 DOI: 10.1016/j.cell.2019.07.016] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/06/2019] [Accepted: 07/11/2019] [Indexed: 12/12/2022]
Abstract
Small proteins are traditionally overlooked due to computational and experimental difficulties in detecting them. To systematically identify small proteins, we carried out a comparative genomics study on 1,773 human-associated metagenomes from four different body sites. We describe >4,000 conserved protein families, the majority of which are novel; ∼30% of these protein families are predicted to be secreted or transmembrane. Over 90% of the small protein families have no known domain and almost half are not represented in reference genomes. We identify putative housekeeping, mammalian-specific, defense-related, and protein families that are likely to be horizontally transferred. We provide evidence of transcription and translation for a subset of these families. Our study suggests that small proteins are highly abundant and those of the human microbiome, in particular, may perform diverse functions that have not been previously reported.
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23
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Horizontal Gene Transfer as an Indispensable Driver for Evolution of Neocallimastigomycota into a Distinct Gut-Dwelling Fungal Lineage. Appl Environ Microbiol 2019; 85:AEM.00988-19. [PMID: 31126947 DOI: 10.1128/aem.00988-19] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 05/19/2019] [Indexed: 01/01/2023] Open
Abstract
Survival and growth of the anaerobic gut fungi (AGF; Neocallimastigomycota) in the herbivorous gut necessitate the possession of multiple abilities absent in other fungal lineages. We hypothesized that horizontal gene transfer (HGT) was instrumental in forging the evolution of AGF into a phylogenetically distinct gut-dwelling fungal lineage. The patterns of HGT were evaluated in the transcriptomes of 27 AGF strains, 22 of which were isolated and sequenced in this study, and 4 AGF genomes broadly covering the breadth of AGF diversity. We identified 277 distinct incidents of HGT in AGF transcriptomes, with subsequent gene duplication resulting in an HGT frequency of 2 to 3.5% in AGF genomes. The majority of HGT events were AGF specific (91.7%) and wide (70.8%), indicating their occurrence at early stages of AGF evolution. The acquired genes allowed AGF to expand their substrate utilization range, provided new venues for electron disposal, augmented their biosynthetic capabilities, and facilitated their adaptation to anaerobiosis. The majority of donors were anaerobic fermentative bacteria prevalent in the herbivorous gut. This study strongly indicates that HGT indispensably forged the evolution of AGF as a distinct fungal phylum and provides a unique example of the role of HGT in shaping the evolution of a high-rank taxonomic eukaryotic lineage.IMPORTANCE The anaerobic gut fungi (AGF) represent a distinct basal phylum lineage (Neocallimastigomycota) commonly encountered in the rumen and alimentary tracts of herbivores. Survival and growth of anaerobic gut fungi in these anaerobic, eutrophic, and prokaryote-dominated habitats necessitates the acquisition of several traits absent in other fungal lineages. We assess here the role of horizontal gene transfer as a relatively fast mechanism for trait acquisition by the Neocallimastigomycota postsequestration in the herbivorous gut. Analysis of 27 transcriptomes that represent the broad diversity of Neocallimastigomycota identified 277 distinct HGT events, with subsequent gene duplication resulting in an HGT frequency of 2 to 3.5% in AGF genomes. These HGT events have allowed AGF to survive in the herbivorous gut by expanding their substrate utilization range, augmenting their biosynthetic pathway, providing new routes for electron disposal by expanding fermentative capacities, and facilitating their adaptation to anaerobiosis. HGT in the AGF is also shown to be mainly a cross-kingdom affair, with the majority of donors belonging to the bacteria. This study represents a unique example of the role of HGT in shaping the evolution of a high-rank taxonomic eukaryotic lineage.
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Song W, Wemheuer B, Zhang S, Steensen K, Thomas T. MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches. MICROBIOME 2019; 7:36. [PMID: 30832740 PMCID: PMC6399960 DOI: 10.1186/s40168-019-0649-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 02/19/2019] [Indexed: 05/28/2023]
Abstract
BACKGROUND Metagenomic datasets provide an opportunity to study horizontal gene transfer (HGT) on the level of a microbial community. However, current HGT detection methods cannot be applied to community-level datasets or require reference genomes. Here, we present MetaCHIP, a pipeline for reference-independent HGT identification at the community level. RESULTS Assessment of MetaCHIP's performance on simulated datasets revealed that it can predict HGTs with various degrees of genetic divergence from metagenomic datasets. The results also indicated that the detection of very recent gene transfers (i.e. those with low levels of genetic divergence) from metagenomics datasets is largely affected by the read assembly step. Comparison of MetaCHIP with a previous analysis on soil bacteria showed a high level of consistency for the prediction of recent HGTs and revealed a large number of additional non-recent gene transfers, which can provide new biological and ecological insight. Assessment of MetaCHIP's performance on real metagenomic datasets confirmed the role of HGT in the spread of genes related to antibiotic resistance in the human gut microbiome. Further testing also showed that functions related to energy production and conversion as well as carbohydrate transport and metabolism are frequently transferred among free-living microorganisms. CONCLUSION MetaCHIP provides an opportunity to study HGTs among members of a microbial community and therefore has several applications in the field of microbial ecology and evolution. MetaCHIP is implemented in Python and freely available at https://github.com/songweizhi/MetaCHIP .
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Affiliation(s)
- Weizhi Song
- Centre for Marine Bio-Innovation, University of New South Wales, Sydney, NSW 2052 Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052 Australia
| | - Bernd Wemheuer
- Centre for Marine Bio-Innovation, University of New South Wales, Sydney, NSW 2052 Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052 Australia
| | - Shan Zhang
- Centre for Marine Bio-Innovation, University of New South Wales, Sydney, NSW 2052 Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052 Australia
| | - Kerrin Steensen
- Centre for Marine Bio-Innovation, University of New South Wales, Sydney, NSW 2052 Australia
- Department of Genomic and Applied Microbiology, Georg-August-University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Torsten Thomas
- Centre for Marine Bio-Innovation, University of New South Wales, Sydney, NSW 2052 Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052 Australia
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Abstract
Multiple drug resistance (MDR) to widening range of antibiotics emerging in increasing variety of pathogenic bacteria is a serious threat to the health of mankind nowadays. This is partially due to an uncontrolled usage of antibiotics not only in clinical practice, but also in various branches of agriculture. MDR is affected by two mechanisms: (1) accumulation of resistance genes as a result of intensive selection caused by antibiotics, and (2) active horizontal transfer of resistance genes. To unveil the reasons of bacterial multiresistance to antibiotics, it is necessary to understand the mechanisms of antibiotics action as well as the ways how either resistance to certain antibiotics emerge or resistance genes accumulate and transfer among bacterial strains. Current review is devoted to all these problems.
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26
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Difford GF, Plichta DR, Løvendahl P, Lassen J, Noel SJ, Højberg O, Wright ADG, Zhu Z, Kristensen L, Nielsen HB, Guldbrandtsen B, Sahana G. Host genetics and the rumen microbiome jointly associate with methane emissions in dairy cows. PLoS Genet 2018; 14:e1007580. [PMID: 30312316 PMCID: PMC6200390 DOI: 10.1371/journal.pgen.1007580] [Citation(s) in RCA: 165] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 10/24/2018] [Accepted: 07/20/2018] [Indexed: 01/23/2023] Open
Abstract
Cattle and other ruminants produce large quantities of methane (~110 million metric tonnes per annum), which is a potent greenhouse gas affecting global climate change. Methane (CH4) is a natural by-product of gastro-enteric microbial fermentation of feedstuffs in the rumen and contributes to 6% of total CH4 emissions from anthropogenic-related sources. The extent to which the host genome and rumen microbiome influence CH4 emission is not yet well known. This study confirms individual variation in CH4 production was influenced by individual host (cow) genotype, as well as the host's rumen microbiome composition. Abundance of a small proportion of bacteria and archaea taxa were influenced to a limited extent by the host's genotype and certain taxa were associated with CH4 emissions. However, the cumulative effect of all bacteria and archaea on CH4 production was 13%, the host genetics (heritability) was 21% and the two are largely independent. This study demonstrates variation in CH4 emission is likely not modulated through cow genetic effects on the rumen microbiome. Therefore, the rumen microbiome and cow genome could be targeted independently, by breeding low methane-emitting cows and in parallel, by investigating possible strategies that target changes in the rumen microbiome to reduce CH4 emissions in the cattle industry.
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Affiliation(s)
- Gareth Frank Difford
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
- Wageningen University & Research, Animal Breeding & Genomics, AH Wageningen, Netherlands
| | - Damian Rafal Plichta
- Center for Biological Sequence Analysis, Dept. of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
- Clinical-Microbiomics A/S, Copenhagen, Denmark
| | - Peter Løvendahl
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Jan Lassen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
- Viking Genetics, Randers SØ, Denmark
| | | | - Ole Højberg
- Department of Animal Science, Aarhus University, Tjele, Denmark
| | - André-Denis G. Wright
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, United States of America
| | - Zhigang Zhu
- Department of Animal Science, Aarhus University, Tjele, Denmark
| | - Lise Kristensen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Henrik Bjørn Nielsen
- Center for Biological Sequence Analysis, Dept. of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
- Clinical-Microbiomics A/S, Copenhagen, Denmark
| | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
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27
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Hua ZS, Qu YN, Zhu Q, Zhou EM, Qi YL, Yin YR, Rao YZ, Tian Y, Li YX, Liu L, Castelle CJ, Hedlund BP, Shu WS, Knight R, Li WJ. Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota. Nat Commun 2018; 9:2832. [PMID: 30026532 PMCID: PMC6053391 DOI: 10.1038/s41467-018-05284-4] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 06/13/2018] [Indexed: 12/30/2022] Open
Abstract
Microbes of the phylum Aigarchaeota are widely distributed in geothermal environments, but their physiological and ecological roles are poorly understood. Here we analyze six Aigarchaeota metagenomic bins from two circumneutral hot springs in Tengchong, China, to reveal that they are either strict or facultative anaerobes, and most are chemolithotrophs that can perform sulfide oxidation. Applying comparative genomics to the Thaumarchaeota and Aigarchaeota, we find that they both originated from thermal habitats, sharing 1154 genes with their common ancestor. Horizontal gene transfer played a crucial role in shaping genetic diversity of Aigarchaeota and led to functional partitioning and ecological divergence among sympatric microbes, as several key functional innovations were endowed by Bacteria, including dissimilatory sulfite reduction and possibly carbon monoxide oxidation. Our study expands our knowledge of the possible ecological roles of the Aigarchaeota and clarifies their evolutionary relationship to their sister lineage Thaumarchaeota.
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Affiliation(s)
- Zheng-Shuang Hua
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yan-Ni Qu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
| | - En-Min Zhou
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yan-Ling Qi
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yi-Rui Yin
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yang-Zhi Rao
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Ye Tian
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yu-Xian Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Cindy J Castelle
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.,Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, 510631, Guangzhou, China
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, 92093, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, 92093, USA
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China. .,College of Fisheries, Henan Normal University, 453007, Xinxiang, China.
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28
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Kim H, Kwak W, Yoon SH, Kang DK, Kim H. Horizontal gene transfer of Chlamydia: Novel insights from tree reconciliation. PLoS One 2018; 13:e0195139. [PMID: 29621277 PMCID: PMC5886423 DOI: 10.1371/journal.pone.0195139] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 03/16/2018] [Indexed: 01/07/2023] Open
Abstract
Recent comparative genomics studies have suggested that horizontal gene transfer (HGT) is one of the major processes in bacterial evolution. In this study, HGT events of 64 Chlamydia strains were investigated based on the pipeline employed in HGTree database constructed in our recent study. Tree reconciliation method was applied in order to calculate feasible HGT events. Following initial detection and an evaluation procedure, evidence of the HGT was identified in 548 gene families including 42 gene families transferred from outside of Chlamydiae phylum with high reliability. The donor species of inter-phylum HGT consists of 12 different bacterial and archaeal phyla, suggesting that Chlamydia might have even more various host range than in previous reports. In addition, each species of Chlamydia showed varying preference towards HGT, and genes engaged in HGT within Chlamydia and between other species showed different functional distribution. Also, examination of individual gene flows of niche-specific genes suggested that many of such genes are transferred mainly within Chlamydia genus. Our results uncovered novel features of HGT acting on Chlamydia genome evolution, and it would be also strong evidence that HGT is an ongoing process for intracellular pathogens. We expect that the results provide more insight into lineage- and niche-specific adaptations regarding their infectivity and pathogenicity.
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Affiliation(s)
- Hyaekang Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Woori Kwak
- C&K genomics, Seoul National University Research Park, Seoul, Republic of Korea
| | - Sook Hee Yoon
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Dae-Kyung Kang
- Department of Animal Resources Science, Dankook University, Cheonan, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- C&K genomics, Seoul National University Research Park, Seoul, Republic of Korea
- * E-mail:
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29
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Abstract
Antibiotic natural products are ancient and so is resistance. Consequently, environmental bacteria harbor numerous and varied antibiotic resistance elements. Nevertheless, despite long histories of antibiotic production and exposure, environmental bacteria are not resistant to all known antibiotics. This means that there are barriers to the acquisition of a complete resistance armamentarium. The sources, distribution, and movement of resistance mechanisms in different microbes and bacterial populations are mosaic features that act as barriers to slow this movement, thus moderating the emergence of bacterial pan-resistance. This is highly relevant to understanding the emergence of resistance in pathogenic bacteria that can inform better antibiotic management practices and influence new drug discovery.
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Affiliation(s)
- Nicholas Waglechner
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8N 4K1, Canada
| | - Gerard D Wright
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8N 4K1, Canada.
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30
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Alamos P, Tello M, Bustamante P, Gutiérrez F, Shmaryahu A, Maldonado J, Levicán G, Orellana O. Functionality of tRNAs encoded in a mobile genetic element from an acidophilic bacterium. RNA Biol 2017; 15:518-527. [PMID: 28708455 DOI: 10.1080/15476286.2017.1349049] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
The genome of the acidophilic, bioleaching bacterium Acidithiobacillus ferrooxidans, strain ATCC 23270, contains 95 predicted tRNA genes. Thirty-six of these genes (all 20 species) are clustered within an actively excising integrative-conjugative element (ICEAfe1). We speculated that these tRNA genes might have a role in adapting the bacterial tRNA pool to the codon usage of ICEAfe1 genes. To answer this question, we performed theoretical calculations of the global tRNA adaptation index to the entire A. ferrooxidans genome with and without the ICEAfe1 encoded tRNA genes. Based on these calculations, we observed that tRNAs encoded in ICEAfe1 negatively contribute to adapt the tRNA pool to the codon use in A. ferrooxidans. Although some of the tRNAs encoded in ICEAfe1 are functional in aminoacylation or protein synthesis, we found that they are expressed at low levels. These findings, along with the identification of a tRNA-like RNA encoded in the same cluster, led us to speculate that tRNA genes encoded in the mobile genetic element ICEAfe1 might have acquired mutations that would result in either inactivation or the acquisition of new functions.
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Affiliation(s)
- Pamela Alamos
- a Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Independencia 1027 , Santiago , Chile
| | - Mario Tello
- b Centro de Biotecnología Acuícola, Departamento de Biología , Facultad de Química y Biología, Universidad de Santiago de Chile
| | - Paula Bustamante
- a Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Independencia 1027 , Santiago , Chile
| | - Fernanda Gutiérrez
- a Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Independencia 1027 , Santiago , Chile
| | - Amir Shmaryahu
- c Fundación Ciencia y Vida , Zañartu 1482, Santiago , Chile
| | - Juan Maldonado
- a Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Independencia 1027 , Santiago , Chile
| | - Gloria Levicán
- d Departamento de Biología , Facultad de Química y Biología, Universidad de Santiago de Chile , Santiago , Chile
| | - Omar Orellana
- a Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Independencia 1027 , Santiago , Chile
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31
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Recurrent horizontal transfer of arsenite methyltransferase genes facilitated adaptation of life to arsenic. Sci Rep 2017; 7:7741. [PMID: 28798375 PMCID: PMC5552862 DOI: 10.1038/s41598-017-08313-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 07/07/2017] [Indexed: 12/12/2022] Open
Abstract
The toxic metalloid arsenic has been environmentally ubiquitous since life first arose nearly four billion years ago and presents a challenge for the survival of all living organisms. Its bioavailability has varied dramatically over the history of life on Earth. As life spread, biogeochemical and climate changes cyclically increased and decreased bioavailable arsenic. To elucidate the history of arsenic adaptation across the tree of life, we reconstructed the phylogeny of the arsM gene that encodes the As(III) S-adenosylmethionine (SAM) methyltransferase. Our results suggest that life successfully moved into arsenic-rich environments in the late Archean Eon and Proterozoic Eon, respectively, by the spread of arsM genes. The arsM genes of bacterial origin have been transferred to other kingdoms of life on at least six occasions, and the resulting domesticated arsM genes promoted adaptation to environmental arsenic. These results allow us to peer into the history of arsenic adaptation of life on our planet and imply that dissemination of genes encoding diverse adaptive functions to toxic chemicals permit adaptation to changes in concentrations of environmental toxins over evolutionary history.
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32
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Delavat F, Miyazaki R, Carraro N, Pradervand N, van der Meer JR. The hidden life of integrative and conjugative elements. FEMS Microbiol Rev 2017; 41:512-537. [PMID: 28369623 PMCID: PMC5812530 DOI: 10.1093/femsre/fux008] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 02/20/2017] [Indexed: 01/01/2023] Open
Abstract
Integrative and conjugative elements (ICEs) are widespread mobile DNA that transmit both vertically, in a host-integrated state, and horizontally, through excision and transfer to new recipients. Different families of ICEs have been discovered with more or less restricted host ranges, which operate by similar mechanisms but differ in regulatory networks, evolutionary origin and the types of variable genes they contribute to the host. Based on reviewing recent experimental data, we propose a general model of ICE life style that explains the transition between vertical and horizontal transmission as a result of a bistable decision in the ICE-host partnership. In the large majority of cells, the ICE remains silent and integrated, but hidden at low to very low frequencies in the population specialized host cells appear in which the ICE starts its process of horizontal transmission. This bistable process leads to host cell differentiation, ICE excision and transfer, when suitable recipients are present. The ratio of ICE bistability (i.e. ratio of horizontal to vertical transmission) is the outcome of a balance between fitness costs imposed by the ICE horizontal transmission process on the host cell, and selection for ICE distribution (i.e. ICE 'fitness'). From this emerges a picture of ICEs as elements that have adapted to a mostly confined life style within their host, but with a very effective and dynamic transfer from a subpopulation of dedicated cells.
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Affiliation(s)
- François Delavat
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne Switzerland
| | - Ryo Miyazaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Ibaraki 305-8566, Japan
| | - Nicolas Carraro
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne Switzerland
| | - Nicolas Pradervand
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne Switzerland
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Pinos S, Pontarotti P, Raoult D, Merhej V. Identification of constraints influencing the bacterial genomes evolution in the PVC super-phylum. BMC Evol Biol 2017; 17:75. [PMID: 28274202 PMCID: PMC5343374 DOI: 10.1186/s12862-017-0921-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 02/21/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Horizontal transfer plays an important role in the evolution of bacterial genomes, yet it obeys several constraints, including the ecological opportunity to meet other organisms, the presence of transfer systems, and the fitness of the transferred genes. Bacteria from the Planctomyctetes, Verrumicrobia, Chlamydiae (PVC) super-phylum have a compartmentalized cell plan delimited by an intracytoplasmic membrane that might constitute an additional constraint with particular impact on bacterial evolution. In this investigation, we studied the evolution of 33 genomes from PVC species and focused on the rate and the nature of horizontally transferred sequences in relation to their habitat and their cell plan. RESULTS Using a comparative phylogenomic approach, we showed that habitat influences the evolution of the bacterial genome's content and the flux of horizontal transfer of DNA (HT). Thus bacteria from soil, from insects and ubiquitous bacteria presented the highest average of horizontal transfer compared to bacteria living in water, extracellular bacteria in vertebrates, bacteria from amoeba and intracellular bacteria in vertebrates (with a mean of 379 versus 110 events per species, respectively and 7.6% of each genomes due to HT against 4.8%). The partners of these transfers were mainly bacterial organisms (94.9%); they allowed us to differentiate environmental bacteria, which exchanged more with Proteobacteria, and bacteria from vertebrates, which exchanged more with Firmicutes. The functional analysis of the horizontal transfers revealed a convergent evolution, with an over-representation of genes encoding for membrane biogenesis and lipid metabolism, among compartmentalized bacteria in the different habitats. CONCLUSIONS The presence of an intracytoplasmic membrane in PVC species seems to affect the genome's evolution through the selection of transferred DNA, according to their encoded functions.
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Affiliation(s)
- Sandrine Pinos
- Aix Marseille Université, CNRS, Centrale Marseille, I2M UMR 7373, Evolution Biologique et Modélisation, 3 place Victor Hugo, Marseille, 13331 France
- Aix Marseille Univ, CNRS, IRD, INSERM, AP-HM URMITE, IHU -Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille, 13005 France
| | - Pierre Pontarotti
- Aix Marseille Université, CNRS, Centrale Marseille, I2M UMR 7373, Evolution Biologique et Modélisation, 3 place Victor Hugo, Marseille, 13331 France
| | - Didier Raoult
- Aix Marseille Univ, CNRS, IRD, INSERM, AP-HM URMITE, IHU -Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille, 13005 France
| | - Vicky Merhej
- Aix Marseille Univ, CNRS, IRD, INSERM, AP-HM URMITE, IHU -Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille, 13005 France
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34
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Ji B, Zhang SD, Zhang WJ, Rouy Z, Alberto F, Santini CL, Mangenot S, Gagnot S, Philippe N, Pradel N, Zhang L, Tempel S, Li Y, Médigue C, Henrissat B, Coutinho PM, Barbe V, Talla E, Wu LF. The chimeric nature of the genomes of marine magnetotactic coccoid-ovoid bacteria defines a novel group of P
roteobacteria. Environ Microbiol 2017; 19:1103-1119. [DOI: 10.1111/1462-2920.13637] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 11/23/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Boyang Ji
- Aix Marseille Univ, CNRS, LCB; Marseille France
| | - Sheng-Da Zhang
- Aix Marseille Univ, CNRS, LCB; Marseille France
- Centre National de la Recherche Scientifique; Laboratoire International Associé de la Bio-Minéralisation et Nano-Structures (LIA-BioMNSL); Marseille cedex 20 F-13402 France
| | - Wei-Jia Zhang
- Aix Marseille Univ, CNRS, LCB; Marseille France
- Centre National de la Recherche Scientifique; Laboratoire International Associé de la Bio-Minéralisation et Nano-Structures (LIA-BioMNSL); Marseille cedex 20 F-13402 France
- State Key Laboratories for Agro-biotechnology and College of Biological Sciences; China Agricultural University; Beijing 100193 China
| | - Zoe Rouy
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique-Génoscope; Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme; 2 rue Gaston Crémieux Evry F-91057 France
- Centre National de la Recherche Scientifique; Unité Mixte de Recherche 8030; 2 rue Gaston Crémieux Evry F-91057 France
- UEVE; Université d'Evry, Boulevard François Mitterrand; Evry F-91025 France
| | - François Alberto
- Aix Marseille Univ, CNRS, LCB; Marseille France
- Centre National de la Recherche Scientifique; Laboratoire International Associé de la Bio-Minéralisation et Nano-Structures (LIA-BioMNSL); Marseille cedex 20 F-13402 France
| | - Claire-Lise Santini
- Aix Marseille Univ, CNRS, LCB; Marseille France
- Centre National de la Recherche Scientifique; Laboratoire International Associé de la Bio-Minéralisation et Nano-Structures (LIA-BioMNSL); Marseille cedex 20 F-13402 France
| | - Sophie Mangenot
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique-Génoscope; Laboratoire de Biologie Moléculaire pour l'Etude des Génomes; 2 rue Gaston Crémieux Evry cedex CP 5706 - 91057 France
| | | | | | - Nathalie Pradel
- Centre National de la Recherche Scientifique; Laboratoire International Associé de la Bio-Minéralisation et Nano-Structures (LIA-BioMNSL); Marseille cedex 20 F-13402 France
- Aix Marseille Univ, Univ Toulon, CNRS, IRD; Marseille France
| | | | | | - Ying Li
- Centre National de la Recherche Scientifique; Laboratoire International Associé de la Bio-Minéralisation et Nano-Structures (LIA-BioMNSL); Marseille cedex 20 F-13402 France
- State Key Laboratories for Agro-biotechnology and College of Biological Sciences; China Agricultural University; Beijing 100193 China
| | - Claudine Médigue
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique-Génoscope; Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme; 2 rue Gaston Crémieux Evry F-91057 France
- Centre National de la Recherche Scientifique; Unité Mixte de Recherche 8030; 2 rue Gaston Crémieux Evry F-91057 France
- UEVE; Université d'Evry, Boulevard François Mitterrand; Evry F-91025 France
| | | | | | - Valérie Barbe
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Génomique-Génoscope; Laboratoire de Biologie Moléculaire pour l'Etude des Génomes; 2 rue Gaston Crémieux Evry cedex CP 5706 - 91057 France
| | | | - Long-Fei Wu
- Aix Marseille Univ, CNRS, LCB; Marseille France
- Centre National de la Recherche Scientifique; Laboratoire International Associé de la Bio-Minéralisation et Nano-Structures (LIA-BioMNSL); Marseille cedex 20 F-13402 France
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Lifestyle and Horizontal Gene Transfer-Mediated Evolution of Mucispirillum schaedleri, a Core Member of the Murine Gut Microbiota. mSystems 2017; 2:mSystems00171-16. [PMID: 28168224 PMCID: PMC5285517 DOI: 10.1128/msystems.00171-16] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Accepted: 01/04/2017] [Indexed: 01/01/2023] Open
Abstract
Shifts in gut microbiota composition have been associated with intestinal inflammation, but it remains unclear whether inflammation-associated bacteria are commensal or detrimental to their host. Here, we studied the lifestyle of the gut bacterium Mucispirillum schaedleri, which is associated with inflammation in widely used mouse models. We found that M. schaedleri has specialized systems to handle oxidative stress during inflammation. Additionally, it expresses secretion systems and effector proteins and can modify the mucosal gene expression of its host. This suggests that M. schaedleri undergoes intimate interactions with its host and may play a role in inflammation. The insights presented here aid our understanding of how commensal gut bacteria may be involved in altering susceptibility to disease. Mucispirillum schaedleri is an abundant inhabitant of the intestinal mucus layer of rodents and other animals and has been suggested to be a pathobiont, a commensal that plays a role in disease. In order to gain insights into its lifestyle, we analyzed the genome and transcriptome of M. schaedleri ASF 457 and performed physiological experiments to test traits predicted by its genome. Although described as a mucus inhabitant, M. schaedleri has limited capacity for degrading host-derived mucosal glycans and other complex polysaccharides. Additionally, M. schaedleri reduces nitrate and expresses systems for scavenging oxygen and reactive oxygen species in vivo, which may account for its localization close to the mucosal tissue and expansion during inflammation. Also of note, M. schaedleri harbors a type VI secretion system and putative effector proteins and can modify gene expression in mucosal tissue, suggesting intimate interactions with its host and a possible role in inflammation. The M. schaedleri genome has been shaped by extensive horizontal gene transfer, primarily from intestinal Epsilon- and Deltaproteobacteria, indicating that horizontal gene transfer has played a key role in defining its niche in the gut ecosystem. IMPORTANCE Shifts in gut microbiota composition have been associated with intestinal inflammation, but it remains unclear whether inflammation-associated bacteria are commensal or detrimental to their host. Here, we studied the lifestyle of the gut bacterium Mucispirillum schaedleri, which is associated with inflammation in widely used mouse models. We found that M. schaedleri has specialized systems to handle oxidative stress during inflammation. Additionally, it expresses secretion systems and effector proteins and can modify the mucosal gene expression of its host. This suggests that M. schaedleri undergoes intimate interactions with its host and may play a role in inflammation. The insights presented here aid our understanding of how commensal gut bacteria may be involved in altering susceptibility to disease.
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Dynamic models of the complex microbial metapopulation of lake mendota. NPJ Syst Biol Appl 2016; 2:16007. [PMID: 28725469 PMCID: PMC5516861 DOI: 10.1038/npjsba.2016.7] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 12/09/2015] [Accepted: 12/17/2015] [Indexed: 12/31/2022] Open
Abstract
Like many other environments, Lake Mendota, WI, USA, is populated by many thousand microbial species. Only about 1,000 of these constitute between 80 and 99% of the total microbial community, depending on the season, whereas the remaining species are rare. The functioning and resilience of the lake ecosystem depend on these microorganisms, and it is therefore important to understand their dynamics throughout the year. We propose a two-layered set of dynamic mathematical models that capture and interpret the yearly abundance patterns of the species within the metapopulation. The first layer analyzes the interactions between 14 subcommunities (SCs) that peak at different times of the year and together contain all species whereas the second layer focuses on interactions between individual species and SCs. Each SC contains species from numerous families, genera, and phyla in strikingly different abundances. The dynamic models quantify the importance of environmental factors in shaping the dynamics of the lake’s metapopulation and reveal positive or negative interactions between species and SCs. Three environmental factors, namely temperature, ammonia/phosphorus, and nitrate+nitrite, positively affect almost all SCs, whereas by far the most interactions between SCs are inhibitory. As far as the interactions can be independently validated, they are supported by literature information. The models are quite robust and permit predictions of species abundances over many years both, under the assumption that conditions do not change drastically, or in response to environmental perturbations.
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