1
|
Morel-Letelier I, Yuen B, Kück AC, Camacho-García YE, Petersen JM, Lara M, Leray M, Eisen JA, Osvatic JT, Gros O, Wilkins LGE. Adaptations to nitrogen availability drive ecological divergence of chemosynthetic symbionts. PLoS Genet 2024; 20:e1011295. [PMID: 38820540 PMCID: PMC11168628 DOI: 10.1371/journal.pgen.1011295] [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: 11/17/2023] [Revised: 06/12/2024] [Accepted: 05/08/2024] [Indexed: 06/02/2024] Open
Abstract
Bacterial symbionts, with their shorter generation times and capacity for horizontal gene transfer (HGT), play a critical role in allowing marine organisms to cope with environmental change. The closure of the Isthmus of Panama created distinct environmental conditions in the Tropical Eastern Pacific (TEP) and Caribbean, offering a "natural experiment" for studying how closely related animals evolve and adapt under environmental change. However, the role of bacterial symbionts in this process is often overlooked. We sequenced the genomes of endosymbiotic bacteria in two sets of sister species of chemosymbiotic bivalves from the genera Codakia and Ctena (family Lucinidae) collected on either side of the Isthmus, to investigate how differing environmental conditions have influenced the selection of symbionts and their metabolic capabilities. The lucinid sister species hosted different Candidatus Thiodiazotropha symbionts and only those from the Caribbean had the genetic potential for nitrogen fixation, while those from the TEP did not. Interestingly, this nitrogen-fixing ability did not correspond to symbiont phylogeny, suggesting convergent evolution of nitrogen fixation potential under nutrient-poor conditions. Reconstructing the evolutionary history of the nifHDKT operon by including other lucinid symbiont genomes from around the world further revealed that the last common ancestor (LCA) of Ca. Thiodiazotropha lacked nif genes, and populations in oligotrophic habitats later re-acquired the nif operon through HGT from the Sedimenticola symbiont lineage. Our study suggests that HGT of the nif operon has facilitated niche diversification of the globally distributed Ca. Thiodiazotropha endolucinida species clade. It highlights the importance of nitrogen availability in driving the ecological diversification of chemosynthetic symbiont species and the role that bacterial symbionts may play in the adaptation of marine organisms to changing environmental conditions.
Collapse
Affiliation(s)
- Isidora Morel-Letelier
- Eco-Evolutionary Interactions Group, Max Planck Institute for Marine Microbiology (MPIMM), Bremen, Germany
| | - Benedict Yuen
- Eco-Evolutionary Interactions Group, Max Planck Institute for Marine Microbiology (MPIMM), Bremen, Germany
| | - A. Carlotta Kück
- Eco-Evolutionary Interactions Group, Max Planck Institute for Marine Microbiology (MPIMM), Bremen, Germany
| | - Yolanda E. Camacho-García
- Centro de Investigación en Ciencias del Mar y Limnología (CIMAR), Universidad de Costa Rica, San Pedro, San José, Costa Rica
- Centro de Investigación en Biodiversidad y Ecología Tropical (CIBET), Universidad de Costa Rica, San Pedro, San José, Costa Rica
- Escuela de Biología, Universidad de Costa Rica, San Pedro, San José, Costa Rica
| | - Jillian M. Petersen
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Minor Lara
- Diving Center Cuajiniquil, Provincia de Guanacaste, Cuajiniquil, Costa Rica
| | - Matthieu Leray
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panamá
| | - Jonathan A. Eisen
- Department of Evolution and Ecology, University of California, Davis, Davis, California, United States of America
- Department of Medical Microbiology and Immunology, University of California, Davis, Davis, California, United States of America
| | - Jay T. Osvatic
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Olivier Gros
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, Université des Antilles, Pointe-à-Pitre, France
| | - Laetitia G. E. Wilkins
- Eco-Evolutionary Interactions Group, Max Planck Institute for Marine Microbiology (MPIMM), Bremen, Germany
| |
Collapse
|
2
|
He Q, Wang S, Feng K, Michaletz ST, Hou W, Zhang W, Li F, Zhang Y, Wang D, Peng X, Yang X, Deng Y. High speciation rate of niche specialists in hot springs. THE ISME JOURNAL 2023:10.1038/s41396-023-01447-4. [PMID: 37286739 DOI: 10.1038/s41396-023-01447-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 06/09/2023]
Abstract
Ecological and evolutionary processes simultaneously regulate microbial diversity, but the evolutionary processes and their driving forces remain largely unexplored. Here we investigated the ecological and evolutionary characteristics of microbiota in hot springs spanning a broad temperature range (54.8-80 °C) by sequencing the 16S rRNA genes. Our results demonstrated that niche specialists and niche generalists are embedded in a complex interaction of ecological and evolutionary dynamics. On the thermal tolerance niche axis, thermal (T) sensitive (at a specific temperature) versus T-resistant (at least in five temperatures) species were characterized by different niche breadth, community abundance and dispersal potential, consequently differing in potential evolutionary trajectory. The niche-specialized T-sensitive species experienced strong temperature barriers, leading to completely species shift and high fitness but low abundant communities at each temperature ("home niche"), and such trade-offs thus reinforced peak performance, as evidenced by high speciation across temperatures and increasing diversification potential with temperature. In contrast, T-resistant species are advantageous of niche expansion but with poor local performance, as shown by wide niche breadth with high extinction, indicating these niche generalists are "jack-of-all-trades, master-of-none". Despite of such differences, the T-sensitive and T-resistant species are evolutionarily interacted. Specifically, the continuous transition from T-sensitive to T-resistant species insured the exclusion probability of T-resistant species at a relatively constant level across temperatures. The co-evolution and co-adaptation of T-sensitive and T-resistant species were in line with the red queen theory. Collectively, our findings demonstrate that high speciation of niche specialists could alleviate the environmental-filtering-induced negative effect on diversity.
Collapse
Affiliation(s)
- Qing He
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Shang Wang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China.
| | - Kai Feng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
| | - Sean T Michaletz
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Weiguo Hou
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Wenhui Zhang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Fangru Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Yidi Zhang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Danrui Wang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Xi Peng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Xingsheng Yang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100190, China.
| |
Collapse
|
3
|
Osvatic JT, Wilkins LGE, Leibrecht L, Leray M, Zauner S, Polzin J, Camacho Y, Gros O, van Gils JA, Eisen JA, Petersen JM, Yuen B. Global biogeography of chemosynthetic symbionts reveals both localized and globally distributed symbiont groups. Proc Natl Acad Sci U S A 2021; 118:e2104378118. [PMID: 34272286 PMCID: PMC8307296 DOI: 10.1073/pnas.2104378118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the ocean, most hosts acquire their symbionts from the environment. Due to the immense spatial scales involved, our understanding of the biogeography of hosts and symbionts in marine systems is patchy, although this knowledge is essential for understanding fundamental aspects of symbiosis such as host-symbiont specificity and evolution. Lucinidae is the most species-rich and widely distributed family of marine bivalves hosting autotrophic bacterial endosymbionts. Previous molecular surveys identified location-specific symbiont types that "promiscuously" form associations with multiple divergent cooccurring host species. This flexibility of host-microbe pairings is thought to underpin their global success, as it allows hosts to form associations with locally adapted symbionts. We used metagenomics to investigate the biodiversity, functional variability, and genetic exchange among the endosymbionts of 12 lucinid host species from across the globe. We report a cosmopolitan symbiont species, Candidatus Thiodiazotropha taylori, associated with multiple lucinid host species. Ca. T. taylori has achieved more success at dispersal and establishing symbioses with lucinids than any other symbiont described thus far. This discovery challenges our understanding of symbiont dispersal and location-specific colonization and suggests both symbiont and host flexibility underpin the ecological and evolutionary success of the lucinid symbiosis.
Collapse
Affiliation(s)
- Jay T Osvatic
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1090 Vienna, Austria
| | - Laetitia G E Wilkins
- Genome and Biomedical Sciences Facility, Genome Center, University of California, Davis, CA 95616
- Department of Symbiosis, Max Planck Institute for Marine Microbiology, 28209 Bremen, Germany
| | - Lukas Leibrecht
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1090 Vienna, Austria
| | - Matthieu Leray
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Republic of Panama
| | - Sarah Zauner
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1090 Vienna, Austria
| | - Julia Polzin
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1090 Vienna, Austria
| | - Yolanda Camacho
- Centro de Investigación en Ciencias del Mar y Limnología, Escuela de Biología, Universidad de Costa Rica, San Pedro 11501-2060, Costa Rica
| | - Olivier Gros
- UMR 7205, Institut de Systématique, Évolution, Biodiversité, Equipe Biologie de la Mangrove, Département de Biologie, Université des Antilles, 97159 Pointe-à-Pitre Cedex, Guadeloupe
| | - Jan A van Gils
- Royal Netherlands Institute for Sea Research,1790 AB Den Burg, The Netherlands
| | - Jonathan A Eisen
- Genome and Biomedical Sciences Facility, Genome Center, University of California, Davis, CA 95616
- Department of Evolution and Ecology, University of California, Davis, CA 95616
- Department of Medical Microbiology and Immunology, University of California, Davis, CA 95616
| | - Jillian M Petersen
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1090 Vienna, Austria;
| | - Benedict Yuen
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1090 Vienna, Austria;
| |
Collapse
|
4
|
Mitousis L, Thoma Y, Musiol-Kroll EM. An Update on Molecular Tools for Genetic Engineering of Actinomycetes-The Source of Important Antibiotics and Other Valuable Compounds. Antibiotics (Basel) 2020; 9:E494. [PMID: 32784409 PMCID: PMC7460540 DOI: 10.3390/antibiotics9080494] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 02/06/2023] Open
Abstract
The first antibiotic-producing actinomycete (Streptomyces antibioticus) was described by Waksman and Woodruff in 1940. This discovery initiated the "actinomycetes era", in which several species were identified and demonstrated to be a great source of bioactive compounds. However, the remarkable group of microorganisms and their potential for the production of bioactive agents were only partially exploited. This is caused by the fact that the growth of many actinomycetes cannot be reproduced on artificial media at laboratory conditions. In addition, sequencing, genome mining and bioactivity screening disclosed that numerous biosynthetic gene clusters (BGCs), encoded in actinomycetes genomes are not expressed and thus, the respective potential products remain uncharacterized. Therefore, a lot of effort was put into the development of technologies that facilitate the access to actinomycetes genomes and activation of their biosynthetic pathways. In this review, we mainly focus on molecular tools and methods for genetic engineering of actinomycetes that have emerged in the field in the past five years (2015-2020). In addition, we highlight examples of successful application of the recently developed technologies in genetic engineering of actinomycetes for activation and/or improvement of the biosynthesis of secondary metabolites.
Collapse
Affiliation(s)
| | | | - Ewa M. Musiol-Kroll
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (L.M.); (Y.T.)
| |
Collapse
|
5
|
Iranzo J, Wolf YI, Koonin EV, Sela I. Gene gain and loss push prokaryotes beyond the homologous recombination barrier and accelerate genome sequence divergence. Nat Commun 2019; 10:5376. [PMID: 31772262 PMCID: PMC6879757 DOI: 10.1038/s41467-019-13429-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 11/07/2019] [Indexed: 02/05/2023] Open
Abstract
Bacterial and archaeal evolution involve extensive gene gain and loss. Thus, phylogenetic trees of prokaryotes can be constructed both by traditional sequence-based methods (gene trees) and by comparison of gene compositions (genome trees). Comparing the branch lengths in gene and genome trees with identical topologies for 34 clusters of closely related bacterial and archaeal genomes, we show here that terminal branches of gene trees are systematically compressed compared to those of genome trees. Thus, sequence evolution is delayed compared to genome evolution by gene gain and loss. The extent of this delay differs widely among bacteria and archaea. Mathematical modeling shows that the divergence delay can result from sequence homogenization by homologous recombination. The model explains how homologous recombination maintains the cohesiveness of the core genome of a species while allowing extensive gene gain and loss within the accessory genome. Once evolving genomes become isolated by barriers impeding homologous recombination, gene and genome evolution processes settle into parallel trajectories, and genomes diverge, resulting in speciation. A significant proportion of the molecular evolution of bacteria and archaea occurs through gene gain and loss. Here Iranzo et al. develop a mathematical model that explains observed differential patterns of sequence evolution vs. gene content evolution as a consequence of homologous recombination.
Collapse
Affiliation(s)
- Jaime Iranzo
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.,Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo-UPM, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
| | - Itamar Sela
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
| |
Collapse
|
6
|
Gaiarsa S, Batisti Biffignandi G, Esposito EP, Castelli M, Jolley KA, Brisse S, Sassera D, Zarrilli R. Comparative Analysis of the Two Acinetobacter baumannii Multilocus Sequence Typing (MLST) Schemes. Front Microbiol 2019; 10:930. [PMID: 31130931 PMCID: PMC6510311 DOI: 10.3389/fmicb.2019.00930] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 04/12/2019] [Indexed: 01/22/2023] Open
Abstract
Acinetobacter species assigned to the Acinetobacter calcoaceticus-baumannii (Acb) complex, are Gram-negative bacteria responsible for a large number of human infections. The population structure of Acb has been studied using two 7-gene MLST schemes, introduced by Bartual and coworkers (Oxford scheme) and by Diancourt and coworkers (Pasteur scheme). The schemes have three genes in common but underlie two coexisting nomenclatures of sequence types and clonal complexes, which complicates communication on A. baumannii genotypes. The aim of this study was to compare the characteristics of the two schemes to make a recommendation about their usage. Using genome sequences of 730 strains of the Acb complex, we evaluated the phylogenetic congruence of MLST schemes, the correspondence between sequence types, their discriminative power and genotyping reliability from genomic sequences. In silico ST re-assignments highlighted the presence of a second copy of the Oxford gdhB locus, present in 553/730 genomes that has led to the creation of artefactual profiles and STs. The reliability of the two MLST schemes was tested statistically comparing MLST-based phylogenies to two reference phylogenies (core-genome genes and genome-wide SNPs) using topology-based and likelihood-based tests. Additionally, each MLST gene fragment was evaluated by correlating the pairwise nucleotide distances between each pair of genomes calculated on the core-genome and on each single gene fragment. The Pasteur scheme appears to be less discriminant among closely related isolates, but less affected by homologous recombination and more appropriate for precise strain classification in clonal groups, which within this scheme are more often correctly monophyletic. Statistical tests evaluate the tree deriving from the Oxford scheme as more similar to the reference genome trees. Our results, together with previous work, indicate that the Oxford scheme has important issues: gdhB paralogy, recombination, primers sequences, position of the genes on the genome. While there is no complete agreement in all analyses, when considered as a whole the above results indicate that the Pasteur scheme is more appropriate for population biology and epidemiological studies of A. baumannii and related species and we propose that it should be the scheme of choice during the transition toward, and in parallel with, core genome MLST.
Collapse
Affiliation(s)
- Stefano Gaiarsa
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.,Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | | | - Eliana Pia Esposito
- Department of Public Health, University of Naples "Federico II", Naples, Italy
| | - Michele Castelli
- Romeo and Enrica Invernizzi Pediatric Research Center, Department of Biosciences, University of Milan, Milan, Italy
| | - Keith A Jolley
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Sylvain Brisse
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France
| | - Davide Sassera
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Raffaele Zarrilli
- Department of Public Health, University of Naples "Federico II", Naples, Italy
| |
Collapse
|
7
|
Järvenpää M, Gutmann MU, Vehtari A, Marttinen P. Gaussian process modelling in approximate Bayesian computation to estimate horizontal gene transfer in bacteria. Ann Appl Stat 2018. [DOI: 10.1214/18-aoas1150] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
8
|
Wright ES, Baum DA. Exclusivity offers a sound yet practical species criterion for bacteria despite abundant gene flow. BMC Genomics 2018; 19:724. [PMID: 30285620 PMCID: PMC6171291 DOI: 10.1186/s12864-018-5099-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 09/21/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The question of whether bacterial species objectively exist has long divided microbiologists. A major source of contention stems from the fact that bacteria regularly engage in horizontal gene transfer (HGT), making it difficult to ascertain relatedness and draw boundaries between taxa. A natural way to define taxa is based on exclusivity of relatedness, which applies when members of a taxon are more closely related to each other than they are to any outsider. It is largely unknown whether exclusive bacterial taxa exist when averaging over the genome or are rare due to rampant hybridization. RESULTS Here, we analyze a collection of 701 genomes representing a wide variety of environmental isolates from the family Streptomycetaceae, whose members are competent at HGT. We find that the presence/absence of auxiliary genes in the pan-genome displays a hierarchical (tree-like) structure that correlates significantly with the genealogy of the core-genome. Moreover, we identified the existence of many exclusive taxa, although individual genes often contradict these taxa. These conclusions were supported by repeating the analysis on 1,586 genomes belonging to the genus Bacillus. However, despite confirming the existence of exclusive groups (taxa), we were unable to identify an objective threshold at which to assign the rank of species. CONCLUSIONS The existence of bacterial taxa is justified by considering average relatedness across the entire genome, as captured by exclusivity, but is rejected if one requires unanimous agreement of all parts of the genome. We propose using exclusivity to delimit taxa and conventional genome similarity thresholds to assign bacterial taxa to the species rank. This approach recognizes species that are phylogenetically meaningful, while also establishing some degree of comparability across species-ranked taxa in different bacterial clades.
Collapse
Affiliation(s)
- Erik S Wright
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, USA.
- Pittsburgh Center for Evolutionary Biology and Medicine, Pittsburgh, USA.
| | - David A Baum
- Department of Botany, University of Wisconsin-Madison, Madison, USA
| |
Collapse
|
9
|
Jibrin MO, Potnis N, Timilsina S, Minsavage GV, Vallad GE, Roberts PD, Jones JB, Goss EM. Genomic Inference of Recombination-Mediated Evolution in Xanthomonas euvesicatoria and X. perforans. Appl Environ Microbiol 2018; 84:e00136-18. [PMID: 29678917 PMCID: PMC6007113 DOI: 10.1128/aem.00136-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 04/06/2018] [Indexed: 01/23/2023] Open
Abstract
Recombination is a major driver of evolution in bacterial populations, because it can spread and combine independently evolved beneficial mutations. Recombinant lineages of bacterial pathogens of plants are typically associated with the colonization of novel hosts and the emergence of new diseases. Here we show that recombination between evolutionarily and phenotypically distinct plant-pathogenic lineages generated recombinant lineages with unique combinations of pathogenicity and virulence factors. Xanthomonas euvesicatoria and Xanthomonas perforans are two closely related lineages causing bacterial spot disease on tomato and pepper worldwide. We sequenced the genomes of atypical strains collected from tomato in Nigeria and observed recombination in the type III secretion system and effector genes, which showed alleles from both X. euvesicatoria and X. perforans Wider horizontal gene transfer was indicated by the fact that the lipopolysaccharide cluster of one strain was most similar to that of a distantly related Xanthomonas pathogen of barley. This strain and others have experienced extensive genomewide homologous recombination, and both species exhibited dynamic open pangenomes. Variation in effector gene repertoires within and between species must be taken into consideration when one is breeding tomatoes for disease resistance. Resistance breeding strategies that target specific effectors must consider possibly dramatic variation in bacterial spot populations across global production regions, as illustrated by the recombinant strains observed here.IMPORTANCE The pathogens that cause bacterial spot of tomato and pepper are extensively studied models of plant-microbe interactions and cause problematic disease worldwide. Atypical bacterial spot strains collected from tomato in Nigeria, and other strains from Italy, India, and Florida, showed evidence of genomewide recombination that generated genetically distinct pathogenic lineages. The strains from Nigeria and Italy were found to have a mix of type III secretion system genes from X. perforans and X. euvesicatoria, as well as effectors from Xanthomonas gardneri These genes and effectors are important in the establishment of disease, and effectors are common targets of resistance breeding. Our findings point to global diversity in the genomes of bacterial spot pathogens, which is likely to affect the host-pathogen interaction and influence management decisions.
Collapse
Affiliation(s)
- Mustafa O Jibrin
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- Southwest Research and Education Center, University of Florida, Immokalee, Florida, USA
- Department of Crop Protection, Ahmadu Bello University, Zaria, Nigeria
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, USA
| | - Sujan Timilsina
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Gerald V Minsavage
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Gary E Vallad
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- Gulf Coast Research and Education Center, University of Florida, Wimauma, Florida, USA
| | - Pamela D Roberts
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- Southwest Research and Education Center, University of Florida, Immokalee, Florida, USA
| | - Jeffrey B Jones
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Erica M Goss
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| |
Collapse
|
10
|
Hoetzinger M, Hahn MW. Genomic divergence and cohesion in a species of pelagic freshwater bacteria. BMC Genomics 2017; 18:794. [PMID: 29037158 PMCID: PMC5644125 DOI: 10.1186/s12864-017-4199-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 10/08/2017] [Indexed: 11/15/2022] Open
Abstract
Background In many prokaryotic genera a clustered phylogeny is observed, akin to the occurrence of species in sexually reproducing organisms. For some taxa, homologous recombination has been invoked as the underlying mechanism providing genomic cohesion among conspecific individuals. Whether this mechanism is applicable to prokaryotes in freshwaters with low habitat connectivity – i.e. elevated geographic barriers to gene flow – is unclear. To investigate further we studied genomic trends within the globally abundant PnecC cluster (genus Polynucleobacter, Betaproteobacteria) and analyzed homologous recombination within the affiliated species P. asymbioticus. Results Comparisons among 20 PnecC genomes revealed a clearly discontinuous distribution of nucleotide sequence similarities. Among the nine conspecific individuals (P. asymbioticus) all average nucleotide identity (ANI) values were greater than 97%, whereas all other comparisons exhibited ANI values lower than 85%. The reconstruction of recombination and mutation events for the P. asymbioticus core genomes yielded an r/m ratio of 7.4, which is clearly above estimated thresholds for recombination to act as a cohesive force. Hotspots of recombination were found to be located in the flanking regions of genomic islands. Even between geographically separated habitats a high flux of recombination was evident. While a biogeographic population structure was suggested from MLST data targeting rather conserved loci, such a structure was barely visible when whole genome data was considered. However, both MLST and whole genome data showed evidence of differentiation between two lineages of P. asymbioticus. The ratios of non-synonymous to synonymous substitution rates as well as growth rates in transplantation experiments suggested that this divergence was not selectively neutral. Conclusions The high extent of homologous recombination among P. asymbioticus bacteria can act as a cohesive force that effectively counteracts genetic divergence. At least on a regional scale, homologous recombination can act across geographically separated ecosystems and therefore plays an important role in the evolution and consistency of bacterial freshwater species. A species model akin to the biological species concept may be applicable for P. asymbioticus. Nonetheless, two genetically distinct lineages have emerged and further research may clarify if their divergence has been initiated by reinforced geographical barriers or has been evolving in sympatry. Electronic supplementary material The online version of this article (10.1186/s12864-017-4199-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Matthias Hoetzinger
- Research Institute for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310, Mondsee, Austria.
| | - Martin W Hahn
- Research Institute for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310, Mondsee, Austria
| |
Collapse
|
11
|
Recombination-Driven Genome Evolution and Stability of Bacterial Species. Genetics 2017; 207:281-295. [PMID: 28751420 DOI: 10.1534/genetics.117.300061] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 07/18/2017] [Indexed: 01/21/2023] Open
Abstract
While bacteria divide clonally, horizontal gene transfer followed by homologous recombination is now recognized as an important contributor to their evolution. However, the details of how the competition between clonality and recombination shapes genome diversity remains poorly understood. Using a computational model, we find two principal regimes in bacterial evolution and identify two composite parameters that dictate the evolutionary fate of bacterial species. In the divergent regime, characterized by either a low recombination frequency or strict barriers to recombination, cohesion due to recombination is not sufficient to overcome the mutational drift. As a consequence, the divergence between pairs of genomes in the population steadily increases in the course of their evolution. The species lacks genetic coherence with sexually isolated clonal subpopulations continuously formed and dissolved. In contrast, in the metastable regime, characterized by a high recombination frequency combined with low barriers to recombination, genomes continuously recombine with the rest of the population. The population remains genetically cohesive and temporally stable. Notably, the transition between these two regimes can be affected by relatively small changes in evolutionary parameters. Using the Multi Locus Sequence Typing (MLST) data, we classify a number of bacterial species to be either the divergent or the metastable type. Generalizations of our framework to include selection, ecologically structured populations, and horizontal gene transfer of nonhomologous regions are discussed as well.
Collapse
|
12
|
Marttinen P, Hanage WP. Speciation trajectories in recombining bacterial species. PLoS Comput Biol 2017; 13:e1005640. [PMID: 28671999 PMCID: PMC5542674 DOI: 10.1371/journal.pcbi.1005640] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 08/03/2017] [Accepted: 06/15/2017] [Indexed: 01/26/2023] Open
Abstract
It is generally agreed that bacterial diversity can be classified into genetically and ecologically cohesive units, but what produces such variation is a topic of intensive research. Recombination may maintain coherent species of frequently recombining bacteria, but the emergence of distinct clusters within a recombining species, and the impact of habitat structure in this process are not well described, limiting our understanding of how new species are created. Here we present a model of bacterial evolution in overlapping habitat space. We show that the amount of habitat overlap determines the outcome for a pair of clusters, which may range from fast clonal divergence with little interaction between the clusters to a stationary population structure, where different clusters maintain an equilibrium distance between each other for an indefinite time. We fit our model to two data sets. In Streptococcus pneumoniae, we find a genomically and ecologically distinct subset, held at a relatively constant genetic distance from the majority of the population through frequent recombination with it, while in Campylobacter jejuni, we find a minority population we predict will continue to diverge at a higher rate. This approach may predict and define speciation trajectories in multiple bacterial species.
Collapse
Affiliation(s)
- Pekka Marttinen
- Helsinki Institute for Information Technology HIIT, Department of Computer Science, Aalto University, Espoo, Finland
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - William P. Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA
| |
Collapse
|
13
|
Choudoir MJ, Panke-Buisse K, Andam CP, Buckley DH. Genome Surfing As Driver of Microbial Genomic Diversity. Trends Microbiol 2017; 25:624-636. [PMID: 28283403 DOI: 10.1016/j.tim.2017.02.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 02/03/2017] [Accepted: 02/10/2017] [Indexed: 01/20/2023]
Abstract
Historical changes in population size, such as those caused by demographic range expansions, can produce nonadaptive changes in genomic diversity through mechanisms such as gene surfing. We propose that demographic range expansion of a microbial population capable of horizontal gene exchange can result in genome surfing, a mechanism that can cause widespread increase in the pan-genome frequency of genes acquired by horizontal gene exchange. We explain that patterns of genetic diversity within Streptomyces are consistent with genome surfing, and we describe several predictions for testing this hypothesis both in Streptomyces and in other microorganisms.
Collapse
Affiliation(s)
- Mallory J Choudoir
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14850 USA
| | - Kevin Panke-Buisse
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14850 USA
| | - Cheryl P Andam
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham NH 03824, USA
| | - Daniel H Buckley
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14850 USA.
| |
Collapse
|
14
|
Pirogov S, Rybko A, Kalinina A, Gelfand M. Recombination Processes and Nonlinear Markov Chains. J Comput Biol 2016; 23:711-7. [PMID: 27386932 DOI: 10.1089/cmb.2016.0051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Bacteria are known to exchange genetic information by horizontal gene transfer. Since the frequency of homologous recombination depends on the similarity between the recombining segments, several studies examined whether this could lead to the emergence of subspecies. Most of them simulated fixed-size Wright-Fisher populations, in which the genetic drift should be taken into account. Here, we use nonlinear Markov processes to describe a bacterial population evolving under mutation and recombination. We consider a population structure as a probability measure on the space of genomes. This approach implies the infinite population size limit, and thus, the genetic drift is not assumed. We prove that under these conditions, the emergence of subspecies is impossible.
Collapse
Affiliation(s)
- Sergey Pirogov
- 1 A.A. Kharkevich Institute for Information Transmission Problems , RAS, Moscow, Russia
| | - Alexander Rybko
- 1 A.A. Kharkevich Institute for Information Transmission Problems , RAS, Moscow, Russia
| | - Anastasia Kalinina
- 1 A.A. Kharkevich Institute for Information Transmission Problems , RAS, Moscow, Russia
| | - Mikhail Gelfand
- 1 A.A. Kharkevich Institute for Information Transmission Problems , RAS, Moscow, Russia .,2 Department of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University , Moscow, Russia
| |
Collapse
|
15
|
Andam CP, Choudoir MJ, Vinh Nguyen A, Sol Park H, Buckley DH. Contributions of ancestral inter-species recombination to the genetic diversity of extant Streptomyces lineages. ISME JOURNAL 2016; 10:1731-41. [PMID: 26849310 DOI: 10.1038/ismej.2015.230] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 10/27/2015] [Accepted: 11/06/2015] [Indexed: 11/10/2022]
Abstract
Streptomyces species produce many important antibiotics and have a crucial role in soil nutrient cycling. However, their evolutionary history remains poorly characterized. We have evaluated the impact of homologous recombination on the evolution of Streptomyces using multi-locus sequence analysis of 234 strains that represent at least 11 species clusters. Evidence of inter-species recombination is widespread but not uniform within the genus and levels of mosaicism vary between species clusters. Most phylogenetically incongruent loci are monophyletic at the scale of species clusters and their subclades, suggesting that these recombination events occurred in shared ancestral lineages. Further investigation of two mosaic species clusters suggests that genes acquired by inter-species recombination may have become fixed in these lineages during periods of demographic expansion; implicating a role for phylogeography in determining contemporary patterns of genetic diversity. Only by examining the phylogeny at the scale of the genus is apparent that widespread phylogenetically incongruent loci in Streptomyces are derived from a far smaller number of ancestral inter-species recombination events.
Collapse
Affiliation(s)
- Cheryl P Andam
- Soil and Crop Sciences, School of Integrative Plant Sciences, Cornell University, Ithaca, NY USA
| | - Mallory J Choudoir
- Soil and Crop Sciences, School of Integrative Plant Sciences, Cornell University, Ithaca, NY USA
| | - Anh Vinh Nguyen
- Soil and Crop Sciences, School of Integrative Plant Sciences, Cornell University, Ithaca, NY USA
| | - Han Sol Park
- Soil and Crop Sciences, School of Integrative Plant Sciences, Cornell University, Ithaca, NY USA
| | - Daniel H Buckley
- Soil and Crop Sciences, School of Integrative Plant Sciences, Cornell University, Ithaca, NY USA
| |
Collapse
|
16
|
Lassalle F, Muller D, Nesme X. Ecological speciation in bacteria: reverse ecology approaches reveal the adaptive part of bacterial cladogenesis. Res Microbiol 2015; 166:729-41. [DOI: 10.1016/j.resmic.2015.06.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 06/28/2015] [Accepted: 06/30/2015] [Indexed: 11/30/2022]
|
17
|
Marttinen P, Croucher NJ, Gutmann MU, Corander J, Hanage WP. Recombination produces coherent bacterial species clusters in both core and accessory genomes. Microb Genom 2015; 1:e000038. [PMID: 28348822 PMCID: PMC5320679 DOI: 10.1099/mgen.0.000038] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 10/06/2015] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Population samples show bacterial genomes can be divided into a core of ubiquitous genes and accessory genes that are present in a fraction of isolates. The ecological significance of this variation in gene content remains unclear. However, microbiologists agree that a bacterial species should be 'genomically coherent', even though there is no consensus on how this should be determined. RESULTS We use a parsimonious model combining diversification in both the core and accessory genome, including mutation, homologous recombination (HR) and horizontal gene transfer (HGT) introducing new loci, to produce a population of interacting clusters of strains with varying genome content. New loci introduced by HGT may then be transferred on by HR. The model fits well to a systematic population sample of 616 pneumococcal genomes, capturing the major features of the population structure with parameter values that agree well with empirical estimates. CONCLUSIONS The model does not include explicit selection on individual genes, suggesting that crude comparisons of gene content may be a poor predictor of ecological function. We identify a clearly divergent subpopulation of pneumococci that are inconsistent with the model and may be considered genomically incoherent with the rest of the population. These strains have a distinct disease tropism and may be rationally defined as a separate species. We also find deviations from the model that may be explained by recent population bottlenecks or spatial structure.
Collapse
Affiliation(s)
- Pekka Marttinen
- Aalto University, Espoo, Finland
- Center for Communicable Disease Dynamics, Harvard School of Public Health, Boston, MA, USA
| | | | | | | | - William P. Hanage
- Center for Communicable Disease Dynamics, Harvard School of Public Health, Boston, MA, USA
| |
Collapse
|
18
|
Krause DJ, Whitaker RJ. Inferring Speciation Processes from Patterns of Natural Variation in Microbial Genomes. Syst Biol 2015; 64:926-35. [PMID: 26316424 PMCID: PMC4604833 DOI: 10.1093/sysbio/syv050] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 06/09/2015] [Indexed: 01/22/2023] Open
Abstract
Microbial species concepts have long been the focus of contentious debate, fueled by technological limitations to the genetic resolution of species, by the daunting task of investigating phenotypic variation among individual microscopic organisms, and by a lack of understanding of gene flow in reproductively asexual organisms that are prone to promiscuous horizontal gene transfer. Population genomics, the emerging approach of analyzing the complete genomes of a multitude of closely related organisms, is poised to overcome these limitations by providing a window into patterns of genome variation revealing the evolutionary processes through which species diverge. This new approach is more than just an extension of previous multilocus sequencing technologies, in that it provides a comprehensive view of interacting evolutionary processes. Here we argue that the application of population genomic tools in a rigorous population genetic framework will help to identify the processes of microbial speciation and ultimately lead to a general species concept based on the unique biology and ecology of microorganisms.
Collapse
Affiliation(s)
- David J Krause
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Rachel J Whitaker
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| |
Collapse
|
19
|
Doroghazi JR, Buckley DH. Intraspecies comparison of Streptomyces pratensis genomes reveals high levels of recombination and gene conservation between strains of disparate geographic origin. BMC Genomics 2014; 15:970. [PMID: 25399205 PMCID: PMC4239341 DOI: 10.1186/1471-2164-15-970] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 10/29/2014] [Indexed: 01/23/2023] Open
Abstract
Background Streptomyces are widespread bacteria that contribute to the terrestrial carbon cycle and produce the majority of clinically useful antibiotics. While interspecific genomic diversity has been investigated among Streptomyces, information is lacking on intraspecific genomic diversity. Streptomyces pratensis has high rates of homologous recombination but the impact of such gene exchange on genome evolution and the evolution of natural product gene clusters remains uncharacterized. Results We report draft genome sequences of four S. pratensis strains and compare to the complete genome of Streptomyces flavogriseus IAF-45-CD (=ATCC 33331), a strain recently reclassified to S. pratensis. Despite disparate geographic origins, the genomes are highly similar with 85.9% of genes present in the core genome and conservation of all natural product gene clusters. Natural products include a novel combination of carbapenem and beta-lactamase inhibitor gene clusters. While high intraspecies recombination rates abolish the phylogenetic signal across the genome, intraspecies recombination is suppressed in two genomic regions. The first region is centered on an insertion/deletion polymorphism and the second on a hybrid NRPS-PKS gene. Finally, two gene families accounted for over 25% of the divergent genes in the core genome. The first includes homologs of bldB (required for spore development and antibiotic production) while the second includes homologs of an uncharacterized protein with a helix-turn-helix motif (hpb). Genes from these families co-occur with fifteen pairs spread across the genome. These genes have evidence for co-evolution of co-localized pairs, supporting previous assertions that these genes may function akin to a toxin-antitoxin system. Conclusions S. pratensis genomes are highly similar with exceptional levels of recombination which erase phylogenetic signal among strains of the species. This species has a large core genome and variable terminal regions that are smaller than those found in interspecies comparisons. There is no geographic differentiation between these strains, but there is evidence for local linkage disequilibrium affecting two genomic regions. We have also shown further observational evidence that the DUF397-HTH (bldB and hpb) are a novel toxin-antitoxin pair.
Collapse
Affiliation(s)
| | - Daniel H Buckley
- Department of Crop and Soil Sciences, Cornell University, Ithaca, USA.
| |
Collapse
|
20
|
Aberer AJ, Stamatakis A. Rapid forward-in-time simulation at the chromosome and genome level. BMC Bioinformatics 2013; 14:216. [PMID: 23834340 PMCID: PMC3718712 DOI: 10.1186/1471-2105-14-216] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Accepted: 07/03/2013] [Indexed: 11/10/2022] Open
Abstract
Background In population genetics, simulation is a fundamental tool for analyzing how basic evolutionary forces such as natural selection, recombination, and mutation shape the genetic landscape of a population. Forward simulation represents the most powerful, but, at the same time, most compute-intensive approach for simulating the genetic material of a population. Results We introduce AnA-FiTS, a highly optimized forward simulation software, that is up to two orders of magnitude faster than current state-of-the-art software. In addition, we present a novel algorithm that further improves runtimes by up to an additional order of magnitude, for simulations where a fraction of the mutations is neutral (e.g., only 10% of mutations have an effect on fitness). Apart from simulated sequences, our tool also generates a graph structure that depicts the complete observable history of neutral mutations. Conclusions The substantial performance improvements allow for conducting forward simulations at the chromosome and genome level. The graph structure generated by our algorithm can give rise to novel approaches for visualizing and analyzing the output of forward simulations.
Collapse
Affiliation(s)
- Andre J Aberer
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, Heidelberg D-69118, Germany.
| | | |
Collapse
|