1
|
Foresto E, Revale S, Nievas F, Carezzano ME, Puente M, Alzari P, Martinez M, Ben-Assaya M, Mornico D, Santoro M, Martinez-Abarca F, Giordano W, Bogino P. Genome sequence of Mesorhizobium mediterraneum strain R31, a nitrogen-fixing rhizobium used as an inoculant for chickpea in Argentina. Microbiol Resour Announc 2023; 12:e0058123. [PMID: 37772816 PMCID: PMC10586107 DOI: 10.1128/mra.00581-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 08/24/2023] [Indexed: 09/30/2023] Open
Abstract
Here, we report the complete genome sequence of Mesorhizobium mediterraneum R31, a rhizobial strain recommended and used as a commercial inoculant for chickpea in Argentina. The genome consists of 7.25 Mb, distributed into four circular replicons: a chromosome of 6.72 Mbp and three plasmids of 0.29, 0.17, and 0.07 Mbp.
Collapse
Affiliation(s)
- Emiliano Foresto
- Departamento de Biología Molecular, Instituto de Biotecnología Ambiental y Salud (INBIAS-CONICET), Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - Santiago Revale
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Fiorela Nievas
- Departamento de Biología Molecular, Instituto de Biotecnología Ambiental y Salud (INBIAS-CONICET), Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - María Evangelina Carezzano
- Departamento de Biología Molecular, Instituto de Biotecnología Ambiental y Salud (INBIAS-CONICET), Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - Mariana Puente
- Instituto de Microbiología y Zoología Agrícola, Instituto Nacional de Tecnología Agropecuaria (IMYZA-INTA), Castelar, Argentina
| | - Pedro Alzari
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, Université de Paris, Paris, France
| | - Mariano Martinez
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, Université de Paris, Paris, France
| | - Mathilde Ben-Assaya
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, Université de Paris, Paris, France
| | - Damien Mornico
- Département Biologie Computationnelle, Hub de Bioinformatique et Biostatistique, CNRS USR 3756, Institut Pasteur, Paris, France
| | - Maricel Santoro
- Department of Biochemistry, Max Planck for Chemical Ecology, Jena, Germany
| | | | - Walter Giordano
- Departamento de Biología Molecular, Instituto de Biotecnología Ambiental y Salud (INBIAS-CONICET), Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - Pablo Bogino
- Departamento de Biología Molecular, Instituto de Biotecnología Ambiental y Salud (INBIAS-CONICET), Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| |
Collapse
|
2
|
Carscadden KA, Batstone RT, Hauser FE. Origins and evolution of biological novelty. Biol Rev Camb Philos Soc 2023; 98:1472-1491. [PMID: 37056155 DOI: 10.1111/brv.12963] [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: 01/28/2022] [Revised: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 04/15/2023]
Abstract
Understanding the origins and impacts of novel traits has been a perennial interest in many realms of ecology and evolutionary biology. Here, we build on previous evolutionary and philosophical treatments of this subject to encompass novelties across biological scales and eco-evolutionary perspectives. By defining novelties as new features at one biological scale that have emergent effects at other biological scales, we incorporate many forms of novelty that have previously been treated in isolation (such as novelty from genetic mutations, new developmental pathways, new morphological features, and new species). Our perspective is based on the fundamental idea that the emergence of a novelty, at any biological scale, depends on its environmental and genetic context. Through this lens, we outline a broad array of generative mechanisms underlying novelty and highlight how genomic tools are transforming our understanding of the origins of novelty. Lastly, we present several case studies to illustrate how novelties across biological scales and systems can be understood based on common mechanisms of change and their environmental and genetic contexts. Specifically, we highlight how gene duplication contributes to the evolution of new complex structures in visual systems; how genetic exchange in symbiosis alters functions of both host and symbiont, resulting in a novel organism; and how hybridisation between species can generate new species with new niches.
Collapse
Affiliation(s)
- Kelly A Carscadden
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 1900 Pleasant St, Boulder, CO, 80309, USA
| | - Rebecca T Batstone
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Frances E Hauser
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, M1C 1A4, Canada
| |
Collapse
|
3
|
Weisberg AJ, Chang JH. Mobile Genetic Element Flexibility as an Underlying Principle to Bacterial Evolution. Annu Rev Microbiol 2023; 77:603-624. [PMID: 37437216 DOI: 10.1146/annurev-micro-032521-022006] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Mobile genetic elements are key to the evolution of bacteria and traits that affect host and ecosystem health. Here, we use a framework of a hierarchical and modular system that scales from genes to populations to synthesize recent findings on mobile genetic elements (MGEs) of bacteria. Doing so highlights the role that emergent properties of flexibility, robustness, and genetic capacitance of MGEs have on the evolution of bacteria. Some of their traits can be stored, shared, and diversified across different MGEs, taxa of bacteria, and time. Collectively, these properties contribute to maintaining functionality against perturbations while allowing changes to accumulate in order to diversify and give rise to new traits. These properties of MGEs have long challenged our abilities to study them. Implementation of new technologies and strategies allows for MGEs to be analyzed in new and powerful ways.
Collapse
Affiliation(s)
- Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA;
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA;
| |
Collapse
|
4
|
Audrey B, Cellier N, White F, Jacques PÉ, Burrus V. A systematic approach to classify and characterize genomic islands driven by conjugative mobility using protein signatures. Nucleic Acids Res 2023; 51:8402-8412. [PMID: 37526274 PMCID: PMC10484663 DOI: 10.1093/nar/gkad644] [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: 11/14/2022] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 08/02/2023] Open
Abstract
Genomic islands (GIs) play a crucial role in the spread of antibiotic resistance, virulence factors and antiviral defense systems in a broad range of bacterial species. However, the characterization and classification of GIs are challenging due to their relatively small size and considerable genetic diversity. Predicting their intercellular mobility is of utmost importance in the context of the emerging crisis of multidrug resistance. Here, we propose a large-scale classification method to categorize GIs according to their mobility profile and, subsequently, analyze their gene cargo. We based our classification decision scheme on a collection of mobility protein motif definitions available in publicly accessible databases. Our results show that the size distribution of GI classes correlates with their respective structure and complexity. Self-transmissible GIs are usually the largest, except in Bacillota and Actinomycetota, accumulate antibiotic and phage resistance genes, and favour the use of a tyrosine recombinase to insert into a host's replicon. Non-mobilizable GIs tend to use a DDE transposase instead. Finally, although tRNA genes are more frequently targeted as insertion sites by GIs encoding a tyrosine recombinase, most GIs insert in a protein-encoding gene. This study is a stepping stone toward a better characterization of mobile GIs in bacterial genomes and their mechanism of mobility.
Collapse
Affiliation(s)
- Bioteau Audrey
- Département de biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | | | - Frédérique White
- Département de biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | | | - Vincent Burrus
- Département de biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| |
Collapse
|
5
|
McKeithen-Mead SA, Grossman AD. Timing of integration into the chromosome is critical for the fitness of an integrative and conjugative element and its bacterial host. PLoS Genet 2023; 19:e1010524. [PMID: 36780569 PMCID: PMC9956884 DOI: 10.1371/journal.pgen.1010524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 02/24/2023] [Accepted: 01/31/2023] [Indexed: 02/15/2023] Open
Abstract
Integrative and conjugative elements (ICEs) are major contributors to genome plasticity in bacteria. ICEs reside integrated in the chromosome of a host bacterium and are passively propagated during chromosome replication and cell division. When activated, ICEs excise from the chromosome and may be transferred through the ICE-encoded conjugation machinery into a recipient cell. Integration into the chromosome of the new host generates a stable transconjugant. Although integration into the chromosome of a new host is critical for the stable acquisition of ICEs, few studies have directly investigated the molecular events that occur in recipient cells during generation of a stable transconjugant. We found that integration of ICEBs1, an ICE of Bacillus subtilis, occurred several generations after initial transfer to a new host. Premature integration in new hosts led to cell death and hence decreased fitness of the ICE and transconjugants. Host lethality due to premature integration was caused by rolling circle replication that initiated in the integrated ICEBs1 and extended into the host chromosome, resulting in catastrophic genome instability. Our results demonstrate that the timing of integration of an ICE is linked to cessation of autonomous replication of the ICE, and that perturbing this linkage leads to a decrease in ICE and host fitness due to a loss of viability of transconjugants. Linking integration to cessation of autonomous replication appears to be a conserved regulatory scheme for mobile genetic elements that both replicate and integrate into the chromosome of their host.
Collapse
Affiliation(s)
- Saria A. McKeithen-Mead
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Alan D. Grossman
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| |
Collapse
|
6
|
Colombi E, Hill Y, Lines R, Sullivan JT, Kohlmeier MG, Christophersen CT, Ronson CW, Terpolilli JJ, Ramsay JP. Population genomics of Australian indigenous Mesorhizobium reveals diverse nonsymbiotic genospecies capable of nitrogen-fixing symbioses following horizontal gene transfer. Microb Genom 2023; 9:mgen000918. [PMID: 36748564 PMCID: PMC9973854 DOI: 10.1099/mgen.0.000918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Mesorhizobia are soil bacteria that establish nitrogen-fixing symbioses with various legumes. Novel symbiotic mesorhizobia frequently evolve following horizontal transfer of symbiosis-gene-carrying integrative and conjugative elements (ICESyms) to indigenous mesorhizobia in soils. Evolved symbionts exhibit a wide range in symbiotic effectiveness, with some fixing nitrogen poorly or not at all. Little is known about the genetic diversity and symbiotic potential of indigenous soil mesorhizobia prior to ICESym acquisition. Here we sequenced genomes of 144 Mesorhizobium spp. strains cultured directly from cultivated and uncultivated Australian soils. Of these, 126 lacked symbiosis genes. The only isolated symbiotic strains were either exotic strains used previously as legume inoculants, or indigenous mesorhizobia that had acquired exotic ICESyms. No native symbiotic strains were identified. Indigenous nonsymbiotic strains formed 22 genospecies with phylogenomic diversity overlapping the diversity of internationally isolated symbiotic Mesorhizobium spp. The genomes of indigenous mesorhizobia exhibited no evidence of prior involvement in nitrogen-fixing symbiosis, yet their core genomes were similar to symbiotic strains and they generally lacked genes for synthesis of biotin, nicotinate and thiamine. Genomes of nonsymbiotic mesorhizobia harboured similar mobile elements to those of symbiotic mesorhizobia, including ICESym-like elements carrying aforementioned vitamin-synthesis genes but lacking symbiosis genes. Diverse indigenous isolates receiving ICESyms through horizontal gene transfer formed effective symbioses with Lotus and Biserrula legumes, indicating most nonsymbiotic mesorhizobia have an innate capacity for nitrogen-fixing symbiosis following ICESym acquisition. Non-fixing ICESym-harbouring strains were isolated sporadically within species alongside effective symbionts, indicating chromosomal lineage does not predict symbiotic potential. Our observations suggest previously observed genomic diversity amongst symbiotic Mesorhizobium spp. represents a fraction of the extant diversity of nonsymbiotic strains. The overlapping phylogeny of symbiotic and nonsymbiotic clades suggests major clades of Mesorhizobium diverged prior to introduction of symbiosis genes and therefore chromosomal genes involved in symbiosis have evolved largely independent of nitrogen-fixing symbiosis.
Collapse
Affiliation(s)
- Elena Colombi
- Curtin Medical School, Curtin University, Bentley, Western Australia 6102, Australia.,Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia 6102, Australia.,Present address: School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia
| | - Yvette Hill
- Legume Rhizobium Sciences, Food Futures Institute, Murdoch University, 90 South St, Murdoch, Western Australia 6150, Australia
| | - Rose Lines
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Kent Street, Bentley, Western Australia 6102, Australia
| | - John T Sullivan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - MacLean G Kohlmeier
- Legume Rhizobium Sciences, Food Futures Institute, Murdoch University, 90 South St, Murdoch, Western Australia 6150, Australia
| | - Claus T Christophersen
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Kent Street, Bentley, Western Australia 6102, Australia.,School of Medical & Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia.,Centre for Integrative Metabolomics and Computational Biology, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Clive W Ronson
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Jason J Terpolilli
- Legume Rhizobium Sciences, Food Futures Institute, Murdoch University, 90 South St, Murdoch, Western Australia 6150, Australia
| | - Joshua P Ramsay
- Curtin Medical School, Curtin University, Bentley, Western Australia 6102, Australia.,Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia 6102, Australia
| |
Collapse
|
7
|
Nodulation and Growth Promotion of Chickpea by Mesorhizobium Isolates from Diverse Sources. Microorganisms 2022; 10:microorganisms10122467. [PMID: 36557720 PMCID: PMC9783758 DOI: 10.3390/microorganisms10122467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/08/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022] Open
Abstract
The cultivation of chickpea (Cicer arietinum L.) in South Africa is dependent on the application of suitable Mesorhizobium inoculants. Therefore, we evaluated the symbiotic effectiveness of several Mesorhizobium strains with different chickpea genotypes under controlled conditions. The tested parameters included shoot dry weight (SDW), nodule fresh weight (NFW), plant height, relative symbiotic effectiveness (RSE) on the plant as well as indole acetic acid (IAA) production and phosphate solubilization on the rhizobia. Twenty-one Mesorhizobium strains and six desi chickpea genotypes were laid out in a completely randomized design (CRD) with three replicates in a glasshouse pot experiment. The factors, chickpea genotype and Mesorhizobium strain, had significant effects on the measured parameters (p < 0.001) but lacked significant interactions based on the analysis of variance (ANOVA). The light variety desi genotype outperformed the other chickpea genotypes on all tested parameters. In general, inoculation with strains LMG15046, CC1192, XAP4, XAP10, and LMG14989 performed best for all the tested parameters. All the strains were able to produce IAA and solubilize phosphate except the South African field isolates, which could not solubilize phosphate. Taken together, inoculation with compatible Mesorhizobium promoted chickpea growth. This is the first study to report on chickpea-compatible Mesorhizobium strains isolated from uninoculated South African soils with no history of chickpea production; although, their plant growth promotion ability was poorer compared to some of the globally sourced strains. Since this study was conducted under controlled conditions, we recommend field studies to assess the performance of the five highlighted strains under environmental conditions in South Africa.
Collapse
|
8
|
Gonçalves OS, de Assis JCS, Santana MF. Breaking the ICE: an easy workflow for identifying and analyzing integrative and conjugative elements in bacterial genomes. Funct Integr Genomics 2022; 22:1139-1145. [PMID: 36149586 DOI: 10.1007/s10142-022-00903-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/13/2022] [Accepted: 09/19/2022] [Indexed: 01/18/2023]
Affiliation(s)
- Osiel Silva Gonçalves
- Grupo de Genômica Evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Jessica Catarine Silva de Assis
- Grupo de Genômica Evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Mateus Ferreira Santana
- Grupo de Genômica Evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
| |
Collapse
|
9
|
Foresto E, Revale S, Primo E, Nievas F, Carezzano E, Puente M, Alzari P, Martínez M, Ben-Assaya M, Mornico D, Santoro M, Martínez-Abarca F, Giordano W, Bogino P. Complete Genome Sequence of Mesorhizobium ciceri Strain R30, a Rhizobium Used as a Commercial Inoculant for Chickpea in Argentina. Microbiol Resour Announc 2022; 11:e0077922. [PMID: 36287006 PMCID: PMC9671018 DOI: 10.1128/mra.00779-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022] Open
Abstract
We report the complete genome sequence of Mesorhizobium ciceri strain R30, a rhizobium strain recommended and used as a commercial inoculant for chickpea in Argentina. The genome consists of almost 7 Mb, distributed into two circular replicons: a chromosome of 6.49 Mb and a plasmid of 0.46 Mb.
Collapse
Affiliation(s)
- Emiliano Foresto
- Instituto de Biotecnología Ambiental y Salud (INBIAS-CONICET), Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - Santiago Revale
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Emiliano Primo
- Instituto de Biotecnología Ambiental y Salud (INBIAS-CONICET), Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - Fiorela Nievas
- Instituto de Biotecnología Ambiental y Salud (INBIAS-CONICET), Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - Evangelina Carezzano
- Instituto de Biotecnología Ambiental y Salud (INBIAS-CONICET), Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - Mariana Puente
- Instituto de Microbiología y Zoología Agrícola (IMYZA-INTA), Castelar, Buenos Aires, Argentina
| | - Pedro Alzari
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, Université de Paris, Paris, France
| | - Mariano Martínez
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, Université de Paris, Paris, France
| | - Mathilde Ben-Assaya
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, Université de Paris, Paris, France
| | - Damien Mornico
- Hub de Bioinformatique et Biostatistique, Département Biologie Computationnelle, CNRS USR 3756, Institut Pasteur, Paris, France
| | - Maricel Santoro
- Department of Biochemistry, Max Planck for Chemical Ecology, Jena, Germany
| | | | - Walter Giordano
- Instituto de Biotecnología Ambiental y Salud (INBIAS-CONICET), Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - Pablo Bogino
- Instituto de Biotecnología Ambiental y Salud (INBIAS-CONICET), Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| |
Collapse
|
10
|
Verdonk CJ, Marshall AC, Ramsay JP, Bond CS. Crystallographic and X-ray scattering study of RdfS, a recombination directionality factor from an integrative and conjugative element. Acta Crystallogr D Struct Biol 2022; 78:1210-1220. [PMID: 36189741 PMCID: PMC9527761 DOI: 10.1107/s2059798322008579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/25/2022] [Indexed: 11/24/2022] Open
Abstract
The recombination directionality factors from Mesorhizobium spp. (RdfS) are involved in regulating the excision and transfer of integrative and conjugative elements. Here, solution small-angle X-ray scattering, and crystallization and preliminary structure solution of RdfS from Mesorhizobium japonicum R7A are presented. RdfS crystallizes in space group P212121, with evidence of eightfold rotational crystallographic/noncrystallographic symmetry. Initial structure determination by molecular replacement using ab initio models yielded a partial model (three molecules), which was completed after manual inspection revealed unmodelled electron density. The finalized crystal structure of RdfS reveals a head-to-tail polymer forming left-handed superhelices with large solvent channels. Additionally, RdfS has significant disorder in the C-terminal region of the protein, which is supported by the solution scattering data and the crystal structure. The steps taken to finalize structure determination, as well as the scattering and crystallographic characteristics of RdfS, are discussed.
Collapse
Affiliation(s)
- Callum J. Verdonk
- School of Molecular Sciences, University of Western Australia, Perth, Western Australia 6009, Australia
- Curtin Health Innovation Research Institute and Curtin Medical School, Curtin University, Perth, Western Australia 6102, Australia
| | - Andrew C. Marshall
- School of Molecular Sciences, University of Western Australia, Perth, Western Australia 6009, Australia
| | - Joshua P. Ramsay
- Curtin Health Innovation Research Institute and Curtin Medical School, Curtin University, Perth, Western Australia 6102, Australia
| | - Charles S. Bond
- School of Molecular Sciences, University of Western Australia, Perth, Western Australia 6009, Australia
- Marshall Centre for Infectious Disease, Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, Western Australia 6009, Australia
| |
Collapse
|
11
|
Lau JA, Hammond MD, Schmidt JE, Weese DJ, Yang WH, Heath KD. Contemporary evolution rivals the effects of rhizobium presence on community and ecosystem properties in experimental mesocosms. Oecologia 2022; 200:133-143. [PMID: 36125524 DOI: 10.1007/s00442-022-05253-1] [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: 07/29/2022] [Accepted: 09/01/2022] [Indexed: 11/25/2022]
Abstract
Because genotypes within a species commonly differ in traits that influence other species, whole communities, or even ecosystem functions, evolutionary change within one key species may affect the community and ecosystem processes. Here we use experimental mesocosms to test how the evolution of reduced cooperation in rhizobium mutualists in response to 20 years of nitrogen fertilization compares to the effects of rhizobium presence on soil nitrogen availability and plant community composition and diversity. The evolution of reduced rhizobium cooperation caused reductions in soil nitrogen, biological nitrogen fixation, and leaf nitrogen concentrations that were as strong as, or even stronger than, experimental rhizobium inoculation (presence/absence) treatments. Effects of both rhizobium evolution and rhizobium inoculation on legume dominance, plant community composition, and plant species diversity were often smaller in magnitude, but suggest that rhizobium evolution can alter the relative abundance of plant functional groups. Our findings indicate that the consequences of rapid microbial evolution for ecosystems and communities can rival the effects resulting from the presence or abundance of keystone mutualists.
Collapse
Affiliation(s)
- Jennifer A Lau
- Kellogg Biological Station & Department of Plant Biology, Michigan State University, 3700 E. Gull Lake Dr., Hickory Corners, MI, 49060, USA.
- Department of Biology & the Environmental Resilience Institute, Indiana University, 1001 E 3rd St., Bloomington, IN, 47401, USA.
| | - Mark D Hammond
- Kellogg Biological Station & Department of Plant Biology, Michigan State University, 3700 E. Gull Lake Dr., Hickory Corners, MI, 49060, USA
| | - Jennifer E Schmidt
- Kellogg Biological Station & Department of Plant Biology, Michigan State University, 3700 E. Gull Lake Dr., Hickory Corners, MI, 49060, USA
- Department of Plant Sciences, University of California, Davis, Davis, CA, 95616, USA
| | - Dylan J Weese
- Kellogg Biological Station & Department of Plant Biology, Michigan State University, 3700 E. Gull Lake Dr., Hickory Corners, MI, 49060, USA
| | - Wendy H Yang
- Department of Plant Biology, University of Illinois, 505 South Goodwin Ave, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois, 1206 W. Gregory Dr., Urbana, IL, 61801, USA
- Department of Geology, University of Illinois, 1301 West Green St, Urbana, IL, 61801, USA
| | - Katy D Heath
- Department of Plant Biology, University of Illinois, 505 South Goodwin Ave, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois, 1206 W. Gregory Dr., Urbana, IL, 61801, USA
| |
Collapse
|
12
|
Heath KD, Batstone RT, Cerón Romero M, McMullen JG. MGEs as the MVPs of Partner Quality Variation in Legume-Rhizobium Symbiosis. mBio 2022; 13:e0088822. [PMID: 35758609 PMCID: PMC9426554 DOI: 10.1128/mbio.00888-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Despite decades of research, we are only just beginning to understand the forces maintaining variation in the nitrogen-fixing symbiosis between rhizobial bacteria and leguminous plants. In their recent work, Alexandra Weisberg and colleagues use genomics to document the breadth of mobile element diversity that carries the symbiosis genes of Bradyrhizobium in natural populations. Studying rhizobia from the perspective of their mobile genetic elements, which have their own transmission modes and fitness interests, reveals novel mechanisms for the generation and maintenance of diversity in natural populations of these ecologically and economically important mutualisms.
Collapse
Affiliation(s)
- Katy D. Heath
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana-Champaign, Illinois
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana-Champaign, Illinois
| | - Rebecca T. Batstone
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana-Champaign, Illinois
| | - Mario Cerón Romero
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana-Champaign, Illinois
| | | |
Collapse
|
13
|
Weisberg AJ, Sachs JL, Chang JH. Dynamic interactions between mega symbiosis ICEs and bacterial chromosomes maintain genome architecture. Genome Biol Evol 2022; 14:6593308. [PMID: 35639596 PMCID: PMC9174649 DOI: 10.1093/gbe/evac078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2022] [Indexed: 11/19/2022] Open
Abstract
Acquisition of mobile genetic elements can confer novel traits to bacteria. Some integrative and conjugative elements confer upon members of Bradyrhizobium the capacity to fix nitrogen in symbiosis with legumes. These so-called symbiosis integrative conjugative elements (symICEs) can be extremely large and vary as monopartite and polypartite configurations within chromosomes of related strains. These features are predicted to impose fitness costs and have defied explanation. Here, we show that chromosome architecture is largely conserved despite diversity in genome composition, variations in locations of attachment sites recognized by integrases of symICEs, and differences in large-scale chromosomal changes that occur upon integration. Conversely, many simulated nonnative chromosome–symICE combinations are predicted to result in lethal deletions or disruptions to architecture. Findings suggest that there is compatibility between chromosomes and symICEs. We hypothesize that the size and structural flexibility of symICEs are important for generating combinations that maintain chromosome architecture across a genus of nitrogen-fixing bacteria with diverse and dynamic genomes.
Collapse
Affiliation(s)
- Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97333, USA
| | - Joel L Sachs
- Department of Evolution Ecology and Organismal Biology, University of California Riverside, Riverside, CA 92521, USA.,Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA 92521, USA.,Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97333, USA
| |
Collapse
|
14
|
Abstract
Root nodulating rhizobia are nearly ubiquitous in soils and provide the critical service of nitrogen fixation to thousands of legume species, including staple crops. However, the magnitude of fixed nitrogen provided to hosts varies markedly among rhizobia strains, despite host legumes having mechanisms to selectively reward beneficial strains and to punish ones that do not fix sufficient nitrogen. Variation in the services of microbial mutualists is considered paradoxical given host mechanisms to select beneficial genotypes. Moreover, the recurrent evolution of non-fixing symbiont genotypes is predicted to destabilize symbiosis, but breakdown has rarely been observed. Here, we deconstructed hundreds of genome sequences from genotypically and phenotypically diverse Bradyrhizobium strains and revealed mechanisms that generate variation in symbiotic nitrogen fixation. We show that this trait is conferred by a modular system consisting of many extremely large integrative conjugative elements and few conjugative plasmids. Their transmissibility and propensity to reshuffle genes generate new combinations that lead to uncooperative genotypes and make individual partnerships unstable. We also demonstrate that these same properties extend beneficial associations to diverse host species and transfer symbiotic capacity among diverse strains. Hence, symbiotic nitrogen fixation is underpinned by modularity, which engenders flexibility, a feature that reconciles evolutionary robustness and instability. These results provide new insights into mechanisms driving the evolution of mobile genetic elements. Moreover, they yield a new predictive model on the evolution of rhizobial symbioses, one that informs on the health of organisms and ecosystems that are hosts to symbionts and that helps resolve the long-standing paradox.
Collapse
|
15
|
Zhao Y, Wang W, Yao J, Wang X, Liu D, Wang P. The HipAB Toxin-Antitoxin System Stabilizes a Composite Genomic Island in Shewanella putrefaciens CN-32. Front Microbiol 2022; 13:858857. [PMID: 35387082 PMCID: PMC8978831 DOI: 10.3389/fmicb.2022.858857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 02/24/2022] [Indexed: 11/25/2022] Open
Abstract
Composite genomic islands (GIs) are useful models for studying GI evolution if they can revert into the previous components. In this study, CGI48—a 48,135-bp native composite GI that carries GI21, whose homologies specifically integrated in the conserved yicC gene—were identified in Shewanella putrefaciens CN-32. CGI48 was integrated into the tRNATrp gene, which is a conserved gene locus for the integration of genomic islands in Shewanella. Upon expressing integrase and excisionase, CGI48 and GI21 are excised from chromosomes via site-specific recombination. The shorter attachment sites of GI21 facilitated the capture of GI21 into CGI48. Moreover, GI21 encodes a functional HipAB toxin–antitoxin system, thus contributing to the maintenance of CGI48 in the host bacteria. This study provides new insights into GI evolution by performing the excision process of the inserting GI and improves our understanding of the maintenance mechanisms of composite GI.
Collapse
Affiliation(s)
- Yi Zhao
- College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Weiquan Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jianyun Yao
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Dong Liu
- College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Pengxia Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
16
|
Bioinformatic and experimental characterization of SEN1998: a conserved gene carried by the Enterobacteriaceae-associated ROD21-like family of genomic islands. Sci Rep 2022; 12:2435. [PMID: 35165310 PMCID: PMC8844411 DOI: 10.1038/s41598-022-06183-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 01/12/2022] [Indexed: 12/20/2022] Open
Abstract
Genomic islands (GIs) are horizontally transferred elements that shape bacterial genomes and contributes to the adaptation to different environments. Some GIs encode an integrase and a recombination directionality factor (RDF), which are the molecular GI-encoded machinery that promotes the island excision from the chromosome, the first step for the spread of GIs by horizontal transfer. Although less studied, this process can also play a role in the virulence of bacterial pathogens. While the excision of GIs is thought to be similar to that observed in bacteriophages, this mechanism has been only studied in a few families of islands. Here, we aimed to gain a better understanding of the factors involved in the excision of ROD21 a pathogenicity island of the food-borne pathogen Salmonella enterica serovar Enteritidis and the most studied member of the recently described Enterobacteriaceae-associated ROD21-like family of GIs. Using bioinformatic and experimental approaches, we characterized the conserved gene SEN1998, showing that it encodes a protein with the features of an RDF that binds to the regulatory regions involved in the excision of ROD21. While deletion or overexpression of SEN1998 did not alter the expression of the integrase-encoding gene SEN1970, a slight but significant trend was observed in the excision of the island. Surprisingly, we found that the expression of both genes, SEN1998 and SEN1970, were negatively correlated to the excision of ROD21 which showed a growth phase-dependent pattern. Our findings contribute to the growing body of knowledge regarding the excision of GIs, providing insights about ROD21 and the recently described EARL family of genomic islands.
Collapse
|
17
|
Wardell GE, Hynes MF, Young PJ, Harrison E. Why are rhizobial symbiosis genes mobile? Philos Trans R Soc Lond B Biol Sci 2022; 377:20200471. [PMID: 34839705 PMCID: PMC8628070 DOI: 10.1098/rstb.2020.0471] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/28/2021] [Indexed: 11/12/2022] Open
Abstract
Rhizobia are one of the most important and best studied groups of bacterial symbionts. They are defined by their ability to establish nitrogen-fixing intracellular infections within plant hosts. One surprising feature of this symbiosis is that the bacterial genes required for this complex trait are not fixed within the chromosome, but are encoded on mobile genetic elements (MGEs), namely plasmids or integrative and conjugative elements. Evidence suggests that many of these elements are actively mobilizing within rhizobial populations, suggesting that regular symbiosis gene transfer is part of the ecology of rhizobial symbionts. At first glance, this is counterintuitive. The symbiosis trait is highly complex, multipartite and tightly coevolved with the legume hosts, while transfer of genes can be costly and disrupt coadaptation between the chromosome and the symbiosis genes. However, horizontal gene transfer is a process driven not only by the interests of the host bacterium, but also, and perhaps predominantly, by the interests of the MGEs that facilitate it. Thus understanding the role of horizontal gene transfer in the rhizobium-legume symbiosis requires a 'mobile genetic element's-eye view' on the ecology and evolution of this important symbiosis. This article is part of the theme issue 'The secret lives of microbial mobile genetic elements'.
Collapse
Affiliation(s)
- Grace E. Wardell
- Department of Animal Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 1EA, UK
| | - Michael F. Hynes
- Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4
| | - Peter J. Young
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Ellie Harrison
- Department of Animal Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 1EA, UK
| |
Collapse
|
18
|
Arashida H, Odake H, Sugawara M, Noda R, Kakizaki K, Ohkubo S, Mitsui H, Sato S, Minamisawa K. Evolution of rhizobial symbiosis islands through insertion sequence-mediated deletion and duplication. THE ISME JOURNAL 2022; 16:112-121. [PMID: 34272493 PMCID: PMC8692435 DOI: 10.1038/s41396-021-01035-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/27/2021] [Accepted: 06/03/2021] [Indexed: 11/08/2022]
Abstract
Symbiosis between organisms influences their evolution via adaptive changes in genome architectures. Immunity of soybean carrying the Rj2 allele is triggered by NopP (type III secretion system [T3SS]-dependent effector), encoded by symbiosis island A (SymA) in B. diazoefficiens USDA122. This immunity was overcome by many mutants with large SymA deletions that encompassed T3SS (rhc) and N2 fixation (nif) genes and were bounded by insertion sequence (IS) copies in direct orientation, indicating homologous recombination between ISs. Similar deletion events were observed in B. diazoefficiens USDA110 and B. japonicum J5. When we cultured a USDA122 strain with a marker gene sacB inserted into the rhc gene cluster, most sucrose-resistant mutants had deletions in nif/rhc gene clusters, similar to the mutants above. Some deletion mutants were unique to the sacB system and showed lower competitive nodulation capability, indicating that IS-mediated deletions occurred during free-living growth and the host plants selected the mutants. Among 63 natural bradyrhizobial isolates, 2 possessed long duplications (261-357 kb) harboring nif/rhc gene clusters between IS copies in direct orientation via homologous recombination. Therefore, the structures of symbiosis islands are in a state of flux via IS-mediated duplications and deletions during rhizobial saprophytic growth, and host plants select mutualistic variants from the resultant pools of rhizobial populations. Our results demonstrate that homologous recombination between direct IS copies provides a natural mechanism generating deletions and duplications on symbiosis islands.
Collapse
Affiliation(s)
- Haruka Arashida
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-Ku, Sendai, 980-8577, Japan
| | - Haruka Odake
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-Ku, Sendai, 980-8577, Japan
| | - Masayuki Sugawara
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-Ku, Sendai, 980-8577, Japan
| | - Ryota Noda
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-Ku, Sendai, 980-8577, Japan
| | - Kaori Kakizaki
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-Ku, Sendai, 980-8577, Japan
| | - Satoshi Ohkubo
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-Ku, Sendai, 980-8577, Japan
| | - Hisayuki Mitsui
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-Ku, Sendai, 980-8577, Japan
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-Ku, Sendai, 980-8577, Japan
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-Ku, Sendai, 980-8577, Japan.
| |
Collapse
|
19
|
Ramsay JP, Bastholm TR, Verdonk CJ, Tambalo DD, Sullivan JT, Harold LK, Panganiban BA, Colombi E, Perry BJ, Jowsey W, Morris C, Hynes MF, Bond CS, Cameron ADS, Yost CK, Ronson CW. An epigenetic switch activates bacterial quorum sensing and horizontal transfer of an integrative and conjugative element. Nucleic Acids Res 2021; 50:975-988. [PMID: 34904658 PMCID: PMC8789080 DOI: 10.1093/nar/gkab1217] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 11/13/2022] Open
Abstract
Horizontal transfer of the integrative and conjugative element ICEMlSymR7A converts non-symbiotic Mesorhizobium spp. into nitrogen-fixing legume symbionts. Here, we discover subpopulations of Mesorhizobium japonicum R7A become epigenetically primed for quorum-sensing (QS) and QS-activated horizontal transfer. Isolated populations in this state termed R7A* maintained these phenotypes in laboratory culture but did not transfer the R7A* state to recipients of ICEMlSymR7A following conjugation. We previously demonstrated ICEMlSymR7A transfer and QS are repressed by the antiactivator QseM in R7A populations and that the adjacently-coded DNA-binding protein QseC represses qseM transcription. Here RNA-sequencing revealed qseM expression was repressed in R7A* cells and that RNA antisense to qseC was abundant in R7A but not R7A*. Deletion of the antisense-qseC promoter converted cells into an R7A*-like state. An adjacently coded QseC2 protein bound two operator sites and repressed antisense-qseC transcription. Plasmid overexpression of QseC2 stimulated the R7A* state, which persisted following curing of this plasmid. The epigenetic maintenance of the R7A* state required ICEMlSymR7A-encoded copies of both qseC and qseC2. Therefore, QseC and QseC2, together with their DNA-binding sites and overlapping promoters, form a stable epigenetic switch that establishes binary control over qseM transcription and primes a subpopulation of R7A cells for QS and horizontal transfer.
Collapse
Affiliation(s)
- Joshua P Ramsay
- Curtin Medical School and Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
| | - Tahlia R Bastholm
- Curtin Medical School and Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
| | - Callum J Verdonk
- School of Molecular Sciences, University of Western Australia, Perth, WA 6009, Australia.,Curtin Medical School and Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
| | - Dinah D Tambalo
- Biology Department, University of Regina, Regina, SK S4S 0A2, Canada
| | - John T Sullivan
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Liam K Harold
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Beatrice A Panganiban
- Curtin Medical School and Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
| | - Elena Colombi
- Curtin Medical School and Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
| | - Benjamin J Perry
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - William Jowsey
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Calum Morris
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Michael F Hynes
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 4V8, Canada
| | - Charles S Bond
- School of Molecular Sciences, University of Western Australia, Perth, WA 6009, Australia
| | | | | | - Clive W Ronson
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| |
Collapse
|
20
|
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.
Collapse
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
| |
Collapse
|
21
|
Haskett TL, Knights HE, Jorrin B, Mendes MD, Poole PS. A Simple in situ Assay to Assess Plant-Associative Bacterial Nitrogenase Activity. Front Microbiol 2021; 12:690439. [PMID: 34248916 PMCID: PMC8261070 DOI: 10.3389/fmicb.2021.690439] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 05/25/2021] [Indexed: 11/23/2022] Open
Abstract
Assessment of plant-associative bacterial nitrogen (N) fixation is crucial for selection and development of elite diazotrophic inoculants that could be used to supply cereal crops with nitrogen in a sustainable manner. Although diazotrophic bacteria possess diverse oxygen tolerance mechanisms, most require a sub 21% oxygen environment to achieve optimal stability and function of the N-fixing catalyst nitrogenase. Consequently, assessment of N fixation is routinely carried out on “free-living” bacteria grown in the absence of a host plant and such experiments may not accurately divulge activity in the rhizosphere where the availability and forms of nutrients such as carbon and N, which are key regulators of N fixation, may vary widely. Here, we present a modified in situ acetylene reduction assay (ARA), utilizing the model cereal barley as a host to comparatively assess nitrogenase activity in diazotrophic bacteria. The assay is rapid, highly reproducible, applicable to a broad range of diazotrophs, and can be performed with simple equipment commonly found in most laboratories that investigate plant-microbe interactions. Thus, the assay could serve as a first point of order for high-throughput identification of elite plant-associative diazotrophs.
Collapse
Affiliation(s)
- Timothy L Haskett
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Hayley E Knights
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Beatriz Jorrin
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Marta D Mendes
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
22
|
Evolution of diverse effective N 2-fixing microsymbionts of Cicer arietinum following horizontal transfer of the Mesorhizobium ciceri CC1192 symbiosis integrative and conjugative element. Appl Environ Microbiol 2021; 87:AEM.02558-20. [PMID: 33355157 PMCID: PMC8090884 DOI: 10.1128/aem.02558-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Rhizobia are soil bacteria capable of forming N2-fixing symbioses with legumes, with highly effective strains often selected in agriculture as inoculants to maximize symbiotic N2 fixation. When rhizobia in the genus Mesorhizobium have been introduced with exotic legumes into farming systems, horizontal transfer of symbiosis Integrative and Conjugative Elements (ICEs) from the inoculant strain to soil bacteria has resulted in the evolution of ineffective N2-fixing rhizobia that are competitive for nodulation with the target legume. In Australia, Cicer arietinum (chickpea) has been inoculated since the 1970's with Mesorhizobium ciceri sv. ciceri CC1192, a highly effective strain from Israel. Although the full genome sequence of this organism is available, little is known about the mobility of its symbiosis genes and the diversity of cultivated C. arietinum-nodulating organisms. Here, we show the CC1192 genome harbors a 419-kb symbiosis ICE (ICEMcSym1192) and a 648-kb repABC-type plasmid pMC1192 carrying putative fix genes. We sequenced the genomes of 11 C. arietinum nodule isolates from a field site exclusively inoculated with CC1192 and showed they were diverse unrelated Mesorhizobium carrying ICEMcSym1192, indicating they had acquired the ICE by environmental transfer. No exconjugants harboured pMc1192 and the plasmid was not essential for N2 fixation in CC1192. Laboratory conjugation experiments confirmed ICEMcSym1192 is mobile, integrating site-specifically within the 3' end of one of the four ser-tRNA genes in the R7ANS recipient genome. Strikingly, all ICEMcSym1192 exconjugants were as efficient at fixing N2 with C. arietinum as CC1192, demonstrating ICE transfer does not necessarily yield ineffective microsymbionts as previously observed.Importance Symbiotic N2 fixation is a key component of sustainable agriculture and in many parts of the world legumes are inoculated with highly efficient strains of rhizobia to maximise fixed N2 inputs into farming systems. Symbiosis genes for Mesorhizobium spp. are often encoded chromosomally within mobile gene clusters called Integrative and Conjugative Elements or ICEs. In Australia, where all agricultural legumes and their rhizobia are exotic, horizontal transfer of ICEs from inoculant Mesorhizobium strains to native rhizobia has led to the evolution of inefficient strains that outcompete the original inoculant, with the potential to render it ineffective. However, the commercial inoculant strain for Cicer arietinum (chickpea), M. ciceri CC1192, has a mobile symbiosis ICE (ICEMcSym1192) which can support high rates of N2 fixation following either environmental or laboratory transfer into diverse Mesorhizobium backgrounds, demonstrating ICE transfer does not necessarily yield ineffective microsymbionts as previously observed.
Collapse
|
23
|
Gonçalves OS, Santana MF. The coexistence of monopartite integrative and conjugative elements in the genomes of Acidobacteria. Gene 2021; 777:145476. [PMID: 33549716 DOI: 10.1016/j.gene.2021.145476] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 01/15/2021] [Accepted: 01/28/2021] [Indexed: 10/22/2022]
Abstract
Soil bacteria can rapidly adapt to environmental perturbations through horizontal gene transfer. Acidobacteria is one of the most persistent dominant phyla in the soil. However, the role of these organisms in terrestrial ecosystems remains elusive. Here we identified and describe the integrative and conjugative elements (ICEs) in the published complete genomes of Acidobacteria. In total, ten novel ICEs were identified, in which nine were found integrated as three separated monopartite ICEs in the single chromosome sequences of three Acidobacteria. These ICEs carry a repertoire of genes with potential environmental roles, including heavy metal resistance, iron uptake, secondary metabolism, and antibiotic resistance. To our knowledge, these are the first evidence of three monopartite ICEs identified in the single chromosome, and this might be due to the absence of recognizable entry exclusion systems. We hypothesis that the coexistence of multiples ICEs in the chromosome of Acidobacteria might reflect a major advantage for the survival, resistance, and persistence of phylum in the environment.
Collapse
Affiliation(s)
- Osiel Silva Gonçalves
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil
| | - Mateus Ferreira Santana
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG 36570-000, Brazil.
| |
Collapse
|
24
|
Epstein B, Tiffin P. Comparative genomics reveals high rates of horizontal transfer and strong purifying selection on rhizobial symbiosis genes. Proc Biol Sci 2021; 288:20201804. [PMID: 33402066 DOI: 10.1098/rspb.2020.1804] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Horizontal transfer (HT) alters the repertoire of symbiosis genes in rhizobial genomes and may play an important role in the on-going evolution of the rhizobia-legume symbiosis. To gain insight into the extent of HT of symbiosis genes with different functional roles (nodulation, N-fixation, host benefit and rhizobial fitness), we conducted comparative genomic and selection analyses of the full-genome sequences from 27 rhizobial genomes. We find that symbiosis genes experience high rates of HT among rhizobial lineages but also bear signatures of purifying selection (low Ka : Ks). HT and purifying selection appear to be particularly strong in genes involved in initiating the symbiosis (e.g. nodulation) and in genome-wide association candidates for mediating benefits provided to the host. These patterns are consistent with rhizobia adapting to the host environment through the loss and gain of symbiosis genes, but not with host-imposed positive selection driving divergence of symbiosis genes through recurring bouts of positive selection.
Collapse
Affiliation(s)
- Brendan Epstein
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, USA
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, USA
| |
Collapse
|
25
|
Fagorzi C, Ilie A, Decorosi F, Cangioli L, Viti C, Mengoni A, diCenzo GC. Symbiotic and Nonsymbiotic Members of the Genus Ensifer (syn. Sinorhizobium) Are Separated into Two Clades Based on Comparative Genomics and High-Throughput Phenotyping. Genome Biol Evol 2020; 12:2521-2534. [PMID: 33283865 PMCID: PMC7719227 DOI: 10.1093/gbe/evaa221] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2020] [Indexed: 01/03/2023] Open
Abstract
Rhizobium–legume symbioses serve as paradigmatic examples for the study of mutualism evolution. The genus Ensifer (syn. Sinorhizobium) contains diverse plant-associated bacteria, a subset of which can fix nitrogen in symbiosis with legumes. To gain insights into the evolution of symbiotic nitrogen fixation (SNF), and interkingdom mutualisms more generally, we performed extensive phenotypic, genomic, and phylogenetic analyses of the genus Ensifer. The data suggest that SNF likely emerged several times within the genus Ensifer through independent horizontal gene transfer events. Yet, the majority (105 of 106) of the Ensifer strains with the nodABC and nifHDK nodulation and nitrogen fixation genes were found within a single, monophyletic clade. Comparative genomics highlighted several differences between the “symbiotic” and “nonsymbiotic” clades, including divergences in their pangenome content. Additionally, strains of the symbiotic clade carried 325 fewer genes, on average, and appeared to have fewer rRNA operons than strains of the nonsymbiotic clade. Initial characterization of a subset of ten Ensifer strains identified several putative phenotypic differences between the clades. Tested strains of the nonsymbiotic clade could catabolize 25% more carbon sources, on average, than strains of the symbiotic clade, and they were better able to grow in LB medium and tolerate alkaline conditions. On the other hand, the tested strains of the symbiotic clade were better able to tolerate heat stress and acidic conditions. We suggest that these data support the division of the genus Ensifer into two main subgroups, as well as the hypothesis that pre-existing genetic features are required to facilitate the evolution of SNF in bacteria.
Collapse
Affiliation(s)
- Camilla Fagorzi
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Alexandru Ilie
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Francesca Decorosi
- Genexpress Laboratory, Department of Agriculture, Food, Environment and Forestry, University of Florence, Sesto Fiorentino, Italy
| | - Lisa Cangioli
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Carlo Viti
- Genexpress Laboratory, Department of Agriculture, Food, Environment and Forestry, University of Florence, Sesto Fiorentino, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - George C diCenzo
- Department of Biology, University of Florence, Sesto Fiorentino, Italy.,Department of Biology, Queen's University, Kingston, Ontario, Canada
| |
Collapse
|
26
|
Saak CC, Dinh CB, Dutton RJ. Experimental approaches to tracking mobile genetic elements in microbial communities. FEMS Microbiol Rev 2020; 44:606-630. [PMID: 32672812 PMCID: PMC7476777 DOI: 10.1093/femsre/fuaa025] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/29/2020] [Indexed: 12/19/2022] Open
Abstract
Horizontal gene transfer is an important mechanism of microbial evolution and is often driven by the movement of mobile genetic elements between cells. Due to the fact that microbes live within communities, various mechanisms of horizontal gene transfer and types of mobile elements can co-occur. However, the ways in which horizontal gene transfer impacts and is impacted by communities containing diverse mobile elements has been challenging to address. Thus, the field would benefit from incorporating community-level information and novel approaches alongside existing methods. Emerging technologies for tracking mobile elements and assigning them to host organisms provide promise for understanding the web of potential DNA transfers in diverse microbial communities more comprehensively. Compared to existing experimental approaches, chromosome conformation capture and methylome analyses have the potential to simultaneously study various types of mobile elements and their associated hosts. We also briefly discuss how fermented food microbiomes, given their experimental tractability and moderate species complexity, make ideal models to which to apply the techniques discussed herein and how they can be used to address outstanding questions in the field of horizontal gene transfer in microbial communities.
Collapse
Affiliation(s)
- Christina C Saak
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Cong B Dinh
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Rachel J Dutton
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| |
Collapse
|
27
|
Perry BJ, Sullivan JT, Colombi E, Murphy RJT, Ramsay JP, Ronson CW. Symbiosis islands of Loteae-nodulating Mesorhizobium comprise three radiating lineages with concordant nod gene complements and nodulation host-range groupings. Microb Genom 2020; 6. [PMID: 32845829 PMCID: PMC7643969 DOI: 10.1099/mgen.0.000426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Mesorhizobium is a genus of soil bacteria, some isolates of which form an endosymbiotic relationship with diverse legumes of the Loteae tribe. The symbiotic genes of these mesorhizobia are generally carried on integrative and conjugative elements termed symbiosis islands (ICESyms). Mesorhizobium strains that nodulate Lotus spp. have been divided into host-range groupings. Group I (GI) strains nodulate L. corniculatus and L. japonicus ecotype Gifu, while group II (GII) strains have a broader host range, which includes L. pedunculatus. To identify the basis of this extended host range, and better understand Mesorhizobium and ICESym genomics, the genomes of eight Mesorhizobium strains were completed using hybrid long- and short-read assembly. Bioinformatic comparison with previously sequenced mesorhizobia genomes indicated host range was not predicted by Mesorhizobium genospecies but rather by the evolutionary relationship between ICESym symbiotic regions. Three radiating lineages of Loteae ICESyms were identified on this basis, which correlate with Lotus spp. host-range grouping and have lineage-specific nod gene complements. Pangenomic analysis of the completed GI and GII ICESyms identified 155 core genes (on average 30.1 % of a given ICESym). Individual GI or GII ICESyms carried diverse accessory genes with an average of 34.6 % of genes unique to a given ICESym. Identification and comparative analysis of NodD symbiotic regulatory motifs – nod boxes – identified 21 branches across the NodD regulons. Four of these branches were associated with seven genes unique to the five GII ICESyms. The nod boxes preceding the host-range gene nodZ in GI and GII ICESyms were disparate, suggesting regulation of nodZ may differ between GI and GII ICESyms. The broad host-range determinant(s) of GII ICESyms that confer nodulation of L. pedunculatus are likely present amongst the 53 GII-unique genes identified.
Collapse
Affiliation(s)
- 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
| | - Elena Colombi
- School of Pharmacy and Biomedical Science, Curtin University, Perth, Australia
| | - Riley J T Murphy
- School of Pharmacy and Biomedical Science, Curtin University, Perth, Australia
| | - Joshua P Ramsay
- School of Pharmacy and Biomedical Science, Curtin University, Perth, Australia
| | - Clive W Ronson
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| |
Collapse
|
28
|
Younginger BS, Friesen ML. Connecting signals and benefits through partner choice in plant-microbe interactions. FEMS Microbiol Lett 2020; 366:5626345. [PMID: 31730203 DOI: 10.1093/femsle/fnz217] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 10/17/2019] [Indexed: 12/20/2022] Open
Abstract
Stabilizing mechanisms in plant-microbe symbioses are critical to maintaining beneficial functions, with two main classes: host sanctions and partner choice. Sanctions are currently presumed to be more effective and widespread, based on the idea that microbes rapidly evolve cheating while retaining signals matching cooperative strains. However, hosts that effectively discriminate among a pool of compatible symbionts would gain a significant fitness advantage. Using the well-characterized legume-rhizobium symbiosis as a model, we evaluate the evidence for partner choice in the context of the growing field of genomics. Empirical studies that rely upon bacteria varying only in nitrogen-fixation ability ignore host-symbiont signaling and frequently conclude that partner choice is not a robust stabilizing mechanism. Here, we argue that partner choice is an overlooked mechanism of mutualism stability and emphasize that plants need not use the microbial services provided a priori to discriminate among suitable partners. Additionally, we present a model that shows that partner choice signaling increases symbiont and host fitness in the absence of sanctions. Finally, we call for a renewed focus on elucidating the signaling mechanisms that are critical to partner choice while further aiming to understand their evolutionary dynamics in nature.
Collapse
Affiliation(s)
- Brett S Younginger
- Department of Plant Pathology, Washington State University, PO Box 646430, 345 Johnson Hall, Pullman, WA 99164, USA
| | - Maren L Friesen
- Department of Plant Pathology, Washington State University, PO Box 646430, 345 Johnson Hall, Pullman, WA 99164, USA.,Department of Crop and Soil Sciences, Washington State University, PO Box 646420, 115 Johnson Hall, Pullman, WA 99164, USA
| |
Collapse
|
29
|
Botelho J, Schulenburg H. The Role of Integrative and Conjugative Elements in Antibiotic Resistance Evolution. Trends Microbiol 2020; 29:8-18. [PMID: 32536522 DOI: 10.1016/j.tim.2020.05.011] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/07/2020] [Accepted: 05/14/2020] [Indexed: 02/07/2023]
Abstract
Mobile genetic elements (MGEs), such as plasmids and integrative and conjugative elements (ICEs), are main drivers for the spread of antibiotic resistance (AR). Coevolution between bacteria and plasmids shapes the transfer and stability of plasmids across bacteria. Although ICEs outnumber conjugative plasmids, the dynamics of ICE-bacterium coevolution, ICE transfer rates, and fitness costs are as yet largely unexplored. Conjugative plasmids and ICEs are both transferred by type IV secretion systems, but ICEs are typically immune to segregational loss, suggesting that the evolution of ICE-bacterium associations varies from that of plasmid-bacterium associations. Considering the high abundance of ICEs among bacteria, ICE-bacterium dynamics represent a promising challenge for future research that will enhance our understanding of AR spread in human pathogens.
Collapse
Affiliation(s)
- João Botelho
- Antibiotic Resistance Evolution Group, Max-Planck-Institute for Evolutionary Biology, Plön, Germany; Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University, Kiel, Germany.
| | - Hinrich Schulenburg
- Antibiotic Resistance Evolution Group, Max-Planck-Institute for Evolutionary Biology, Plön, Germany; Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University, Kiel, Germany
| |
Collapse
|
30
|
Liu M, Li X, Xie Y, Bi D, Sun J, Li J, Tai C, Deng Z, Ou HY. ICEberg 2.0: an updated database of bacterial integrative and conjugative elements. Nucleic Acids Res 2020; 47:D660-D665. [PMID: 30407568 PMCID: PMC6323972 DOI: 10.1093/nar/gky1123] [Citation(s) in RCA: 276] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 10/23/2018] [Indexed: 12/30/2022] Open
Abstract
ICEberg 2.0 (http://db-mml.sjtu.edu.cn/ICEberg/) is an updated database that provides comprehensive information about bacterial integrative and conjugative elements (ICEs). Compared with the previous version, three major improvements were made. First, with the aid of text mining and manual curation, it now recorded the details of 1032 ICEs, including 270 with experimental supports and 762 from bioinformatics prediction. Second, as increasing evidence has shown that ICEs frequently mobilize the so-called ‘hitchhikers’, such as integrative and mobilizable elements (IMEs) and cis-mobilizable elements (CIMEs), 83 known transfer interactions between 49 IMEs and 7 CIMEs with 19 ICEs taken from the literature were included and illustrated with visually intuitive directed graphs. An expanded collection of 260 chromosome-borne IMEs and 235 CIMEs was also added. At last, ICEberg 2.0 provides an online tool ICEfinder to predict ICEs or IMEs in bacterial genome sequences. It combines a similarity search for the integrase, relaxase and/or type IV secretion system and the co-localization of these corresponding homologous genes. With the recent updates, ICEberg 2.0 might provide better support for understanding the biological traits of ICEs, especially as their interaction with cognate mobilizable elements may further promote horizontal gene flow.
Collapse
Affiliation(s)
- Meng Liu
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China.,Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaobin Li
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yingzhou Xie
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Dexi Bi
- Department of Pathology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Jingyong Sun
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jun Li
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Cui Tai
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Hong-Yu Ou
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China.,Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
31
|
Horizontally Acquired Homologs of Xenogeneic Silencers: Modulators of Gene Expression Encoded by Plasmids, Phages and Genomic Islands. Genes (Basel) 2020; 11:genes11020142. [PMID: 32013150 PMCID: PMC7074111 DOI: 10.3390/genes11020142] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 01/19/2020] [Accepted: 01/20/2020] [Indexed: 02/08/2023] Open
Abstract
Acquisition of mobile elements by horizontal gene transfer can play a major role in bacterial adaptation and genome evolution by providing traits that contribute to bacterial fitness. However, gaining foreign DNA can also impose significant fitness costs to the host bacteria and can even produce detrimental effects. The efficiency of horizontal acquisition of DNA is thought to be improved by the activity of xenogeneic silencers. These molecules are a functionally related group of proteins that possess affinity for the acquired DNA. Binding of xenogeneic silencers suppresses the otherwise uncontrolled expression of genes from the newly acquired nucleic acid, facilitating their integration to the bacterial regulatory networks. Even when the genes encoding for xenogeneic silencers are part of the core genome, homologs encoded by horizontally acquired elements have also been identified and studied. In this article, we discuss the current knowledge about horizontally acquired xenogeneic silencer homologs, focusing on those encoded by genomic islands, highlighting their distribution and the major traits that allow these proteins to become part of the host regulatory networks.
Collapse
|
32
|
Pastor-Bueis R, Sánchez-Cañizares C, James EK, González-Andrés F. Formulation of a Highly Effective Inoculant for Common Bean Based on an Autochthonous Elite Strain of Rhizobium leguminosarum bv. phaseoli, and Genomic-Based Insights Into Its Agronomic Performance. Front Microbiol 2019; 10:2724. [PMID: 31920999 PMCID: PMC6927923 DOI: 10.3389/fmicb.2019.02724] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 11/08/2019] [Indexed: 01/08/2023] Open
Abstract
Common bean is a poor symbiotic N-fixer, with a low response to inoculation owing to its promiscuous nodulation with competitive but inefficient resident rhizobia. Consequently, farmers prefer to fertilize them rather than rely on their capacity for Biological Nitrogen Fixation (BNF). However, when rhizobial inoculants are based on autochthonous strains, they often have superior BNF performance in the field due to their genetic adaptations to the local environment. Nevertheless, there is scant information at the genomic level explaining their superiority or on how their genomes may influence the inoculant performance. This information is especially important in technologically advanced agri-systems like Europe, where environmental concerns and increasingly stringent fertilizer regulations are encouraging a return to the use of rhizobial inoculants, but based upon strains that have been thoroughly characterized in terms of their symbiotic performance and their genetics. The aim of this study was to design an inoculant formulation based on a superior autochthonous strain, Rhizobium leguminosarum bv. phaseoli LCS0306, to assess its performance in the field, and to determine the genomic features contributing to the high effectiveness of its symbiosis with common bean. Plants inoculated with the autochthonous strain LCS0306 fixed significantly more nitrogen than those with the allochthonous strains R. phaseoli ATCC 14482T and R. etli CFN42T, and had grain yield similar to the nitrogen-fertilized controls. Inoculation with LCS0306 was particularly efficacious when formulated with a carrier based upon a mixture of perlite and biochar. Whole genome comparisons revealed no differences in the classical symbiotic genes of strain LCS0306 within the symbiovar phaseoli. However, its symbiotic superior performance might be due to its genomic versatility, as it harbors a large assortment of genes contributing to fitness and competitiveness. It is concluded that inoculation with elite rhizobia formulated with perlite-biochar carriers might constitute a step-change in the sustainable cultivation of common bean in Spanish soils.
Collapse
Affiliation(s)
- Raquel Pastor-Bueis
- Institute of Environment, Natural Resources and Biodiversity, Universidad de León, León, Spain
| | | | - Euan K James
- The James Hutton Institute, Dundee, United Kingdom
| | | |
Collapse
|
33
|
Greenlon A, Chang PL, Damtew ZM, Muleta A, Carrasquilla-Garcia N, Kim D, Nguyen HP, Suryawanshi V, Krieg CP, Yadav SK, Patel JS, Mukherjee A, Udupa S, Benjelloun I, Thami-Alami I, Yasin M, Patil B, Singh S, Sarma BK, von Wettberg EJB, Kahraman A, Bukun B, Assefa F, Tesfaye K, Fikre A, Cook DR. Global-level population genomics reveals differential effects of geography and phylogeny on horizontal gene transfer in soil bacteria. Proc Natl Acad Sci U S A 2019; 116:15200-15209. [PMID: 31285337 PMCID: PMC6660780 DOI: 10.1073/pnas.1900056116] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Although microorganisms are known to dominate Earth's biospheres and drive biogeochemical cycling, little is known about the geographic distributions of microbial populations or the environmental factors that pattern those distributions. We used a global-level hierarchical sampling scheme to comprehensively characterize the evolutionary relationships and distributional limitations of the nitrogen-fixing bacterial symbionts of the crop chickpea, generating 1,027 draft whole-genome sequences at the level of bacterial populations, including 14 high-quality PacBio genomes from a phylogenetically representative subset. We find that diverse Mesorhizobium taxa perform symbiosis with chickpea and have largely overlapping global distributions. However, sampled locations cluster based on the phylogenetic diversity of Mesorhizobium populations, and diversity clusters correspond to edaphic and environmental factors, primarily soil type and latitude. Despite long-standing evolutionary divergence and geographic isolation, the diverse taxa observed to nodulate chickpea share a set of integrative conjugative elements (ICEs) that encode the major functions of the symbiosis. This symbiosis ICE takes 2 forms in the bacterial chromosome-tripartite and monopartite-with tripartite ICEs confined to a broadly distributed superspecies clade. The pairwise evolutionary relatedness of these elements is controlled as much by geographic distance as by the evolutionary relatedness of the background genome. In contrast, diversity in the broader gene content of Mesorhizobium genomes follows a tight linear relationship with core genome phylogenetic distance, with little detectable effect of geography. These results illustrate how geography and demography can operate differentially on the evolution of bacterial genomes and offer useful insights for the development of improved technologies for sustainable agriculture.
Collapse
Affiliation(s)
- Alex Greenlon
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - Peter L Chang
- Department of Plant Pathology, University of California, Davis, CA 95616
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089
| | - Zehara Mohammed Damtew
- College of Natural Sciences, Addis Ababa University, Addis Ababa, 32853 Ethiopia
- Debre Zeit Agricultural Research Center, Ethiopian Institute for Agricultural Research, Bishoftu, Ethiopia
| | - Atsede Muleta
- College of Natural Sciences, Addis Ababa University, Addis Ababa, 32853 Ethiopia
| | | | - Donghyun Kim
- International Crop Research Institute for the Semi-Arid Tropics, Hyderabad 502324, India
| | - Hien P Nguyen
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, 183-8509 Tokyo, Japan
| | - Vasantika Suryawanshi
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089
| | - Christopher P Krieg
- Department of Biological Sciences, Florida International University, Miami, FL 33199
| | - Sudheer Kumar Yadav
- Department of Mycology and Plant Pathology, Banaras Hindu University, Varanasi 221005, India
| | - Jai Singh Patel
- Department of Mycology and Plant Pathology, Banaras Hindu University, Varanasi 221005, India
| | - Arpan Mukherjee
- Department of Mycology and Plant Pathology, Banaras Hindu University, Varanasi 221005, India
| | - Sripada Udupa
- Biodiversity and Integrated Gene Management Program, International Center for Agricultural Research in the Dry Areas, 10112 Rabat, Morocco
| | - Imane Benjelloun
- Institute National de la Recherche Agronomique, 10100 Rabat, Morocco
| | - Imane Thami-Alami
- Institute National de la Recherche Agronomique, 10100 Rabat, Morocco
| | | | - Bhuvaneshwara Patil
- Department of Genetics and Plant Breeding, University of Agricultural Sciences, Dharwad 580001, India
| | - Sarvjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana 141027, India
| | - Birinchi Kumar Sarma
- Department of Mycology and Plant Pathology, Banaras Hindu University, Varanasi 221005, India
| | - Eric J B von Wettberg
- Department of Biological Sciences, Florida International University, Miami, FL 33199
- Department of Plant and Soil Science, University of Vermont, Burlington, VT 05405
| | - Abdullah Kahraman
- Department of Field Crops, Faculty of Agriculture, Harran University, 63100 Sanliurfa, Turkey
| | - Bekir Bukun
- Department of Plant Protection, Dicle University, 21280 Diyarbakir, Turkey
| | - Fassil Assefa
- College of Natural Sciences, Addis Ababa University, Addis Ababa, 32853 Ethiopia
| | - Kassahun Tesfaye
- College of Natural Sciences, Addis Ababa University, Addis Ababa, 32853 Ethiopia
| | - Asnake Fikre
- Debre Zeit Agricultural Research Center, Ethiopian Institute for Agricultural Research, Bishoftu, Ethiopia
| | - Douglas R Cook
- Department of Plant Pathology, University of California, Davis, CA 95616;
| |
Collapse
|
34
|
Antibiotic resistance in Pseudomonas aeruginosa - Mechanisms, epidemiology and evolution. Drug Resist Updat 2019; 44:100640. [PMID: 31492517 DOI: 10.1016/j.drup.2019.07.002] [Citation(s) in RCA: 252] [Impact Index Per Article: 50.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 12/13/2022]
Abstract
Antibiotics are powerful drugs used in the treatment of bacterial infections. The inappropriate use of these medicines has driven the dissemination of antibiotic resistance (AR) in most bacteria. Pseudomonas aeruginosa is an opportunistic pathogen commonly involved in environmental- and difficult-to-treat hospital-acquired infections. This species is frequently resistant to several antibiotics, being in the "critical" category of the WHO's priority pathogens list for research and development of new antibiotics. In addition to a remarkable intrinsic resistance to several antibiotics, P. aeruginosa can acquire resistance through chromosomal mutations and acquisition of AR genes. P. aeruginosa has one of the largest bacterial genomes and possesses a significant assortment of genes acquired by horizontal gene transfer (HGT), which are frequently localized within integrons and mobile genetic elements (MGEs), such as transposons, insertion sequences, genomic islands, phages, plasmids and integrative and conjugative elements (ICEs). This genomic diversity results in a non-clonal population structure, punctuated by specific clones that are associated with significant morbidity and mortality worldwide, the so-called high-risk clones. Acquisition of MGEs produces a fitness cost in the host, that can be eased over time by compensatory mutations during MGE-host coevolution. Even though plasmids and ICEs are important drivers of AR, the underlying evolutionary traits that promote this dissemination are poorly understood. In this review, we provide a comprehensive description of the main strategies involved in AR in P. aeruginosa and the leading drivers of HGT in this species. The most recently developed genomic tools that allowed a better understanding of the features contributing for the success of P. aeruginosa are discussed.
Collapse
|
35
|
Botelho J, Grosso F, Peixe L. WITHDRAWN: Antibiotic resistance in Pseudomonas aeruginosa – mechanisms, epidemiology and evolution. Drug Resist Updat 2019. [DOI: 10.1016/j.drup.2019.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
36
|
Verdonk CJ, Sullivan JT, Williman KM, Nicholson L, Bastholm TR, Hynes MF, Ronson CW, Bond CS, Ramsay JP. Delineation of the integrase-attachment and origin-of-transfer regions of the symbiosis island ICEMlSymR7A. Plasmid 2019; 104:102416. [DOI: 10.1016/j.plasmid.2019.102416] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 04/12/2019] [Accepted: 05/07/2019] [Indexed: 12/12/2022]
|
37
|
León-Sampedro R, Fernández-de-Bobadilla MD, San Millán Á, Baquero F, Coque TM. Transfer dynamics of Tn6648, a composite integrative conjugative element generated by tandem accretion of Tn5801 and Tn6647 in Enterococcus faecalis. J Antimicrob Chemother 2019; 74:2517-2523. [DOI: 10.1093/jac/dkz239] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 04/30/2019] [Accepted: 05/08/2019] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Tn5801 [tet(M)], a Tn916-like element with site-specific affinity for the 3′ end of the housekeeping gene guaA, may integrate at different chromosomal sites.
Objectives
To characterize the genetic context of Tn5801 to define its transfer dynamics and impact on the evolution of Enterococcus faecalis (Efs).
Methods
WGS (Illumina HiSeq 2500) was performed on the Efs clinical strain Ef1 and primary and secondary transconjugants of Efs strains JH2-2 [which naturally contains Tn5801.B23, an unusual variant that lacks tet(M)], OG1RF and OG1SS carrying different copies of Tn5801-like elements. The transposon structures were analysed using a range of bioinformatics tools allowing us to identify the context of Tn5801-like elements. Growth rates at different tetracycline concentrations (0.5–20 mg/L) were estimated using a Synergy HTX plate reader.
Results
Tn5801.B15 [tet(M), 20.3 kb] exists and can be transferred either singly or within Tn6648 (53.2 kb), a composite element that comprises Tn5801.B15 and Tn6647, a newly identified 32.8 kb transposon that contains the prgABCT operon of pheromone-responsive plasmids. These transposons are able to integrate at specific 11 nt sequences at the 3′ end of guaA and at other chromosomal sites in Efs genomes, thus being able to generate tandem accretions. These events may increase the number of tet(M) copies, enhancing tetracycline resistance in the recipient strain.
Conclusions
This study describes Tn6647 and Tn6648 (comprising Tn6647 and Tn5801.B15) and highlights the diversity of mechanisms for conjugative mobilization and chromosomal insertion of these elements, which can result in tandem accretion. This strategy would facilitate the adaptation of Efs clones to environmental challenges.
Collapse
Affiliation(s)
- Ricardo León-Sampedro
- Servicio de Microbiologia, Hospital Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBER-ESP), Madrid, Spain
| | - Miguel D Fernández-de-Bobadilla
- Servicio de Microbiologia, Hospital Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Álvaro San Millán
- Servicio de Microbiologia, Hospital Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBER-ESP), Madrid, Spain
| | - Fernando Baquero
- Servicio de Microbiologia, Hospital Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBER-ESP), Madrid, Spain
- Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Teresa M Coque
- Servicio de Microbiologia, Hospital Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBER-ESP), Madrid, Spain
- Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| |
Collapse
|
38
|
Press MO, Hall AN, Morton EA, Queitsch C. Substitutions Are Boring: Some Arguments about Parallel Mutations and High Mutation Rates. Trends Genet 2019; 35:253-264. [PMID: 30797597 PMCID: PMC6435258 DOI: 10.1016/j.tig.2019.01.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 12/20/2018] [Accepted: 01/14/2019] [Indexed: 12/31/2022]
Abstract
Extant genomes are largely shaped by global transposition, copy-number fluctuation, and rearrangement of DNA sequences rather than by substitutions of single nucleotides. Although many of these large-scale mutations have low probabilities and are unlikely to repeat, others are recurrent or predictable in their effects, leading to stereotyped genome architectures and genetic variation in both eukaryotes and prokaryotes. Such recurrent, parallel mutation modes can profoundly shape the paths taken by evolution and undermine common models of evolutionary genetics. Similar patterns are also evident at the smaller scales of individual genes or short sequences. The scale and extent of this 'non-substitution' variation has recently come into focus through the advent of new genomic technologies; however, it is still not widely considered in genotype-phenotype association studies. In this review we identify common features of these disparate mutational phenomena and comment on the importance and interpretation of these mutational patterns.
Collapse
Affiliation(s)
| | - Ashley N Hall
- Department of Genome Sciences, University of Washington, Seattle, WA 91895, USA; Department of Molecular and Cellular Biology, University of Washington, Seattle, WA 91895, USA
| | - Elizabeth A Morton
- Department of Genome Sciences, University of Washington, Seattle, WA 91895, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA 91895, USA.
| |
Collapse
|
39
|
Abstract
Transposable elements (TEs) are ubiquitous in both prokaryotes and eukaryotes, and the dynamic character of their interaction with host genomes brings about numerous evolutionary innovations and shapes genome structure and function in a multitude of ways. In traditional classification systems, TEs are often being depicted in simplistic ways, based primarily on the key enzymes required for transposition, such as transposases/recombinases and reverse transcriptases. Recent progress in whole-genome sequencing and long-read assembly, combined with expansion of the familiar range of model organisms, resulted in identification of unprecedentedly long transposable units spanning dozens or even hundreds of kilobases, initially in prokaryotic and more recently in eukaryotic systems. Here, we focus on such oversized eukaryotic TEs, including retrotransposons and DNA transposons, outline their complex and often combinatorial nature and closely intertwined relationship with viruses, and discuss their potential for participating in transfer of long stretches of DNA in eukaryotes.
Collapse
Affiliation(s)
- Irina R Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts
- Corresponding author: E-mail:
| | - Irina A Yushenova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts
| |
Collapse
|
40
|
Wasai S, Minamisawa K. Plant-Associated Microbes: From Rhizobia To Plant Microbiomes. Microbes Environ 2019; 33:1-3. [PMID: 29593170 PMCID: PMC5877334 DOI: 10.1264/jsme2.me3301rh] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Sawa Wasai
- Graduate School of Life Sciences, Tohoku University
| | | |
Collapse
|
41
|
diCenzo GC, Zamani M, Checcucci A, Fondi M, Griffitts JS, Finan TM, Mengoni A. Multidisciplinary approaches for studying rhizobium–legume symbioses. Can J Microbiol 2019; 65:1-33. [DOI: 10.1139/cjm-2018-0377] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The rhizobium–legume symbiosis is a major source of fixed nitrogen (ammonia) in the biosphere. The potential for this process to increase agricultural yield while reducing the reliance on nitrogen-based fertilizers has generated interest in understanding and manipulating this process. For decades, rhizobium research has benefited from the use of leading techniques from a very broad set of fields, including population genetics, molecular genetics, genomics, and systems biology. In this review, we summarize many of the research strategies that have been employed in the study of rhizobia and the unique knowledge gained from these diverse tools, with a focus on genome- and systems-level approaches. We then describe ongoing synthetic biology approaches aimed at improving existing symbioses or engineering completely new symbiotic interactions. The review concludes with our perspective of the future directions and challenges of the field, with an emphasis on how the application of a multidisciplinary approach and the development of new methods will be necessary to ensure successful biotechnological manipulation of the symbiosis.
Collapse
Affiliation(s)
- George C. diCenzo
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Maryam Zamani
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Alice Checcucci
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Marco Fondi
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Joel S. Griffitts
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Turlough M. Finan
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Alessio Mengoni
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| |
Collapse
|
42
|
Frare R, Ayub N, Alleva K, Soto G. The Ammonium Channel NOD26 is the Evolutionary Innovation that Drives the Emergence, Consolidation, and Dissemination of Nitrogen-Fixing Symbiosis in Angiosperms. J Mol Evol 2018; 86:554-565. [DOI: 10.1007/s00239-018-9867-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 09/12/2018] [Indexed: 12/01/2022]
|
43
|
Porter SS, Faber-Hammond J, Montoya AP, Friesen ML, Sackos C. Dynamic genomic architecture of mutualistic cooperation in a wild population of Mesorhizobium. ISME JOURNAL 2018; 13:301-315. [PMID: 30218020 PMCID: PMC6331556 DOI: 10.1038/s41396-018-0266-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/01/2018] [Accepted: 08/04/2018] [Indexed: 12/14/2022]
Abstract
Research on mutualism seeks to explain how cooperation can be maintained when uncooperative mutants co-occur with cooperative kin. Gains and losses of the gene modules required for cooperation punctuate symbiont phylogenies and drive lifestyle transitions between cooperative symbionts and uncooperative free-living lineages over evolutionary time. Yet whether uncooperative symbionts commonly evolve from within cooperative symbiont populations or from within distantly related lineages with antagonistic or free-living lifestyles (i.e., third-party mutualism exploiters or parasites), remains controversial. We use genomic data to show that genotypes that differ in the presence or absence of large islands of symbiosis genes are common within a single wild recombining population of Mesorhizobium symbionts isolated from host tissues and are an important source of standing heritable variation in cooperation in this population. In a focal population of Mesorhizobium, uncooperative variants that lack a symbiosis island segregate at 16% frequency in nodules, and genome size and symbiosis gene number are positively correlated with cooperation. This finding contrasts with the genomic architecture of variation in cooperation in other symbiont populations isolated from host tissues in which the islands of genes underlying cooperation are ubiquitous and variation in cooperation is primarily driven by allelic substitution and individual gene gain and loss events. Our study demonstrates that uncooperative mutants within mutualist populations can comprise a significant component of genetic variation in nature, providing biological rationale for models and experiments that seek to explain the maintenance of mutualism in the face of non-cooperators.
Collapse
Affiliation(s)
- Stephanie S Porter
- School of Biological Sciences, Washington State University, Vancouver, WA, 98686, USA.
| | - Joshua Faber-Hammond
- School of Biological Sciences, Washington State University, Vancouver, WA, 98686, USA
| | - Angeliqua P Montoya
- School of Biological Sciences, Washington State University, Vancouver, WA, 98686, USA
| | - Maren L Friesen
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.,Department of Plant Pathology, Washington State University, Pullman, WA, 99164, USA.,Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Cynthia Sackos
- School of Biological Sciences, Washington State University, Vancouver, WA, 98686, USA
| |
Collapse
|
44
|
Piña-Iturbe A, Ulloa-Allendes D, Pardo-Roa C, Coronado-Arrázola I, Salazar-Echegarai FJ, Sclavi B, González PA, Bueno SM. Comparative and phylogenetic analysis of a novel family of Enterobacteriaceae-associated genomic islands that share a conserved excision/integration module. Sci Rep 2018; 8:10292. [PMID: 29980701 PMCID: PMC6035254 DOI: 10.1038/s41598-018-28537-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 06/25/2018] [Indexed: 02/06/2023] Open
Abstract
Genomic Islands (GIs) are DNA regions acquired through horizontal gene transfer that encode advantageous traits for bacteria. Many GIs harbor genes that encode the molecular machinery required for their excision from the bacterial chromosome. Notably, the excision/integration dynamics of GIs may modulate the virulence of some pathogens. Here, we report a novel family of GIs found in plant and animal Enterobacteriaceae pathogens that share genes with those found in ROD21, a pathogenicity island whose excision is involved in the virulence of Salmonella enterica serovar Enteritidis. In these GIs we identified a conserved set of genes that includes an excision/integration module, suggesting that they are excisable. Indeed, we found that GIs within carbapenem-resistant Klebsiella pneumoniae ST258 KP35 and enteropathogenic Escherichia coli O127:H6 E2348/69 are excised from the bacterial genome. In addition to putative virulence factors, these GIs encode conjugative transfer-related proteins and short and full-length homologues of the global transcriptional regulator H-NS. Phylogenetic analyses suggest that the identified GIs likely originated in phytopathogenic bacteria. Taken together, our findings indicate that these GIs are excisable and may play a role in bacterial interactions with their hosts.
Collapse
Affiliation(s)
- Alejandro Piña-Iturbe
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Diego Ulloa-Allendes
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Catalina Pardo-Roa
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Irenice Coronado-Arrázola
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Francisco J Salazar-Echegarai
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Bianca Sclavi
- Laboratoire de Biologie et Pharmacologie Appliquée, Centre National de la Recherche Scientifique UMR 8113, École Normale Supérieure Paris-Saclay, Cachan, France
| | - Pablo A González
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Susan M Bueno
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.
| |
Collapse
|
45
|
Andrews M, De Meyer S, James EK, Stępkowski T, Hodge S, Simon MF, Young JPW. Horizontal Transfer of Symbiosis Genes within and Between Rhizobial Genera: Occurrence and Importance. Genes (Basel) 2018; 9:E321. [PMID: 29954096 PMCID: PMC6071183 DOI: 10.3390/genes9070321] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 06/21/2018] [Accepted: 06/21/2018] [Indexed: 01/17/2023] Open
Abstract
Rhizobial symbiosis genes are often carried on symbiotic islands or plasmids that can be transferred (horizontal transfer) between different bacterial species. Symbiosis genes involved in horizontal transfer have different phylogenies with respect to the core genome of their ‘host’. Here, the literature on legume⁻rhizobium symbioses in field soils was reviewed, and cases of phylogenetic incongruence between rhizobium core and symbiosis genes were collated. The occurrence and importance of horizontal transfer of rhizobial symbiosis genes within and between bacterial genera were assessed. Horizontal transfer of symbiosis genes between rhizobial strains is of common occurrence, is widespread geographically, is not restricted to specific rhizobial genera, and occurs within and between rhizobial genera. The transfer of symbiosis genes to bacteria adapted to local soil conditions can allow these bacteria to become rhizobial symbionts of previously incompatible legumes growing in these soils. This, in turn, will have consequences for the growth, life history, and biogeography of the legume species involved, which provides a critical ecological link connecting the horizontal transfer of symbiosis genes between rhizobial bacteria in the soil to the above-ground floral biodiversity and vegetation community structure.
Collapse
Affiliation(s)
- Mitchell Andrews
- Faculty of Agriculture and Life Sciences, Lincoln University, P.O. Box 84, Lincoln 7647, New Zealand.
| | - Sofie De Meyer
- Centre for Rhizobium Studies, Murdoch University, Murdoch 6150, Australia.
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium.
| | - Euan K James
- James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.
| | - Tomasz Stępkowski
- Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences (SGGW), 02-776 Warsaw, Poland.
| | - Simon Hodge
- Faculty of Agriculture and Life Sciences, Lincoln University, P.O. Box 84, Lincoln 7647, New Zealand.
| | - Marcelo F Simon
- Embrapa Genetic Resources and Biotechnology, Brasilia DF 70770-917, Brazil.
| | - J Peter W Young
- Department of Biology, University of York, York YO10 5DD, UK.
| |
Collapse
|
46
|
Horizontal operon transfer, plasmids, and the evolution of photosynthesis in Rhodobacteraceae. ISME JOURNAL 2018; 12:1994-2010. [PMID: 29795276 PMCID: PMC6052148 DOI: 10.1038/s41396-018-0150-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/23/2018] [Accepted: 04/26/2018] [Indexed: 01/24/2023]
Abstract
The capacity for anoxygenic photosynthesis is scattered throughout the phylogeny of the Proteobacteria. Their photosynthesis genes are typically located in a so-called photosynthesis gene cluster (PGC). It is unclear (i) whether phototrophy is an ancestral trait that was frequently lost or (ii) whether it was acquired later by horizontal gene transfer. We investigated the evolution of phototrophy in 105 genome-sequenced Rhodobacteraceae and provide the first unequivocal evidence for the horizontal transfer of the PGC. The 33 concatenated core genes of the PGC formed a robust phylogenetic tree and the comparison with single-gene trees demonstrated the dominance of joint evolution. The PGC tree is, however, largely incongruent with the species tree and at least seven transfers of the PGC are required to reconcile both phylogenies. The origin of a derived branch containing the PGC of the model organism Rhodobacter capsulatus correlates with a diagnostic gene replacement of pufC by pufX. The PGC is located on plasmids in six of the analyzed genomes and its DnaA-like replication module was discovered at a conserved central position of the PGC. A scenario of plasmid-borne horizontal transfer of the PGC and its reintegration into the chromosome could explain the current distribution of phototrophy in Rhodobacteraceae.
Collapse
|
47
|
Haskett TL, Terpolilli JJ, Ramachandran VK, Verdonk CJ, Poole PS, O’Hara GW, Ramsay JP. Sequential induction of three recombination directionality factors directs assembly of tripartite integrative and conjugative elements. PLoS Genet 2018; 14:e1007292. [PMID: 29565971 PMCID: PMC5882170 DOI: 10.1371/journal.pgen.1007292] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 04/03/2018] [Accepted: 03/06/2018] [Indexed: 12/14/2022] Open
Abstract
Tripartite integrative and conjugative elements (ICE3) are a novel form of ICE that exist as three separate DNA regions integrated within the genomes of Mesorhizobium spp. Prior to conjugative transfer the three ICE3 regions of M. ciceri WSM1271 ICEMcSym1271 combine and excise to form a single circular element. This assembly requires three coordinated recombination events involving three site-specific recombinases IntS, IntG and IntM. Here, we demonstrate that three excisionases–or recombination directionality factors—RdfS, RdfG and RdfM are required for ICE3 excision. Transcriptome sequencing revealed that expression of ICE3 transfer and conjugation genes was induced by quorum sensing. Quorum sensing activated expression of rdfS, and in turn RdfS stimulated transcription of both rdfG and rdfM. Therefore, RdfS acts as a “master controller” of ICE3 assembly and excision. The dependence of all three excisive reactions on RdfS ensures that ICE3 excision occurs via a stepwise sequence of recombination events that avoids splitting the chromosome into a non-viable configuration. These discoveries expose a surprisingly simple control system guiding molecular assembly of these novel and complex mobile genetic elements and highlight the diverse and critical functions of excisionase proteins in control of horizontal gene transfer. Bacteria evolve and adapt quickly through the horizontal transfer of DNA. A major mechanism facilitating this transfer is conjugation. Conjugative DNA elements that integrate into the chromosome are termed ‘Integrative and Conjugative Elements’ (ICE). We recently discovered a unique form of ICE that undergoes a complex series of recombination events with the host chromosome to split itself into three separate parts. This tripartite ICE must also precisely order its recombination when leaving the current host to avoid splitting the host chromosome and the ICE into non-viable parts. In this work, we show that the tripartite ICEs use chemical cell-cell communication to stimulate recombination and that recombination events are specifically ordered through cascaded transcriptional activation of small DNA-binding proteins called recombination directionality factors. Despite the inherent complexity of tripartite ICEs this work exposes a surprisingly simple system to stimulate their precise and ordered molecular assembly prior to horizontal transfer.
Collapse
Affiliation(s)
- Timothy L. Haskett
- Centre for Rhizobium Studies, School of Veterinary and Life Sciences, Murdoch University, Perth, WA, Australia
- * E-mail:
| | - Jason J. Terpolilli
- Centre for Rhizobium Studies, School of Veterinary and Life Sciences, Murdoch University, Perth, WA, Australia
| | | | - Callum J. Verdonk
- School of Pharmacy and Biomedical Sciences and the Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Phillip S. Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Graham W. O’Hara
- Centre for Rhizobium Studies, School of Veterinary and Life Sciences, Murdoch University, Perth, WA, Australia
| | - Joshua P. Ramsay
- School of Pharmacy and Biomedical Sciences and the Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| |
Collapse
|
48
|
Abstract
Rhizobia are some of the best-studied plant microbiota. These oligotrophic Alphaproteobacteria or Betaproteobacteria form symbioses with their legume hosts. Rhizobia must exist in soil and compete with other members of the microbiota before infecting legumes and forming N2-fixing bacteroids. These dramatic lifestyle and developmental changes are underpinned by large genomes and even more complex pan-genomes, which encompass the whole population and are subject to rapid genetic exchange. The ability to respond to plant signals and chemoattractants and to colonize nutrient-rich roots are crucial for the competitive success of these bacteria. The availability of a large body of genomic, physiological, biochemical and ecological studies makes rhizobia unique models for investigating community interactions and plant colonization.
Collapse
|
49
|
Porter SS, Faber-Hammond JJ, Friesen ML. Co-invading symbiotic mutualists of Medicago polymorpha retain high ancestral diversity and contain diverse accessory genomes. FEMS Microbiol Ecol 2017; 94:4705886. [DOI: 10.1093/femsec/fix168] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 11/29/2017] [Indexed: 02/06/2023] Open
Affiliation(s)
- Stephanie S Porter
- School of Biological Sciences, Washington State University, 14204 NE Salmon Creek Ave, Vancouver, WA 98686, USA
| | - Joshua J Faber-Hammond
- School of Biological Sciences, Washington State University, 14204 NE Salmon Creek Ave, Vancouver, WA 98686, USA
| | - Maren L Friesen
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824, USA
- Department of Plant Pathology, Washington State University, P.O. Box 646430 Pullman, WA 99164, USA
- Department of Crop and Soil Sciences, Washington State University, P.O. Box 646420 Pullman, WA 99164, USA
| |
Collapse
|
50
|
Wang P, Zeng Z, Wang W, Wen Z, Li J, Wang X. Dissemination and loss of a biofilm-related genomic island in marine Pseudoalteromonas mediated by integrative and conjugative elements. Environ Microbiol 2017; 19:4620-4637. [PMID: 28892292 DOI: 10.1111/1462-2920.13925] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 08/31/2017] [Accepted: 08/31/2017] [Indexed: 01/24/2023]
Abstract
Acquisition of genomic islands (GIs) plays a central role in the diversification and adaptation of bacteria. Some GIs can be mobilized in trans by integrative and conjugative elements (ICEs) or conjugative plasmids if the GIs carry specific transfer-related sequences. However, the transfer mechanism of GIs lacking such elements remains largely unexplored. Here, we investigated the transmissibility of a GI found in a coral-associated marine bacterium. This GI does not carry genes with transfer functions, but it carries four genes required for robust biofilm formation. Notably, this GI is inserted in the integration site for SXT/R391 ICEs. We demonstrated that acquisition of an SXT/R391 ICE results in either a tandem GI/ICE arrangement or the complete displacement of the GI. The GI displacement by the ICE greatly reduces biofilm formation. In contrast, the tandem integration of the ICE with the GI in cis allows the GI to hijack the transfer machinery of the ICE to excise, transfer and re-integrate into a new host. Collectively, our findings reveal that the integration of an ICE into a GI integration site enables rapid genome dynamics and a new mechanism by which SXT/R391 ICEs can augment genome plasticity.
Collapse
Affiliation(s)
- Pengxia Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Zhenshun Zeng
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Weiquan Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhongling Wen
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, the South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|