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Vaschalde PJ, Flores FS, Facelli Fernández MC, Barolin J, Tauro LB, Monje LD. Anaplasmataceae presence in Amblyomma calcaratum associated with anteaters (Tamandua tetradactyla) in the rainforest ecoregion, Argentina. Ticks Tick Borne Dis 2023; 14:102222. [PMID: 37418999 DOI: 10.1016/j.ttbdis.2023.102222] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 04/12/2023] [Accepted: 06/12/2023] [Indexed: 07/09/2023]
Abstract
Bacteria of the sister genera Ehrlichia and Anaplasma (Anaplasmataceae) are obligate intracellular Alphaproteobacteria that are transmitted mostly through arthropod vectors. These agents can infect different vertebrate cells, depending on the species involved, and can cause diseases in animals and humans. In this study, we evaluated the presence of Anaplasmataceae bacteria in Amblyomma calcaratum ticks collected from a road-killed Tamandua tetradactyla in the Rainforest ecoregion in Argentina. All samples were screened for Anaplasmataceae DNA using a real-time PCR assay targeting the 16S rRNA gene. Evidence of Anaplasmataceae DNA was detected in three out of thirty-nine Am. calcaratum ticks. Phylogenetic analysis of a portion of 16S rRNA gene positioned one sample (Ehrlichia sp. strain Ac124) with Ehrlichia sequences and the other two samples with Anaplasma sequences; Anaplasma sp. strain Ac145 close to Anaplasma odocoilei and Anaplasma sp. strain Ac152 in an ancestral position to most Anaplasma species. The groEL sequence obtained showed that Ehrlichia sp. strain Ac124 was phylogenetically related to Ehrlichia sp. strain Iberá reported infecting Amblyomma tigrinum from Iberá wetlands in Argentina. Phylogenetic analysis using the rpoB sequence positioned Anaplasma sp. strain Ac145 close to the canine pathogen Anaplasma platys, while Anaplasma sp. strain Ac152 was positioned close to the bovine pathogen Anaplasma marginale. In this study, three Anaplasmataceae agents were detected in adults of Am. calcaratum associated with a T. tetradactyla. These results suggest that the number of Anaplasmataceae species, as well as their distribution, is largely unknown.
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Affiliation(s)
- Paula J Vaschalde
- Laboratorio de Ecología de Enfermedades, Instituto de Ciencias Veterinarias del Litoral (ICIVET-Litoral), Universidad Nacional del Litoral (UNL) / Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Esperanza, Santa Fe, Argentina
| | - Fernando S Flores
- Centro de Investigaciones Entomológicas de Córdoba (CIEC), Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina; Instituto de Investigaciones Biológicas y Tecnológicas (IIByT - CONICET), Córdoba, Argentina
| | - M Celeste Facelli Fernández
- Laboratorio de Ecología de Enfermedades, Instituto de Ciencias Veterinarias del Litoral (ICIVET-Litoral), Universidad Nacional del Litoral (UNL) / Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Esperanza, Santa Fe, Argentina
| | - Johann Barolin
- Laboratorio de Ecología de Enfermedades, Instituto de Ciencias Veterinarias del Litoral (ICIVET-Litoral), Universidad Nacional del Litoral (UNL) / Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Esperanza, Santa Fe, Argentina
| | - Laura B Tauro
- Instituto de Biología Subtropical, Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional de Misiones, Puerto Iguazú, Argentina
| | - Lucas D Monje
- Laboratorio de Ecología de Enfermedades, Instituto de Ciencias Veterinarias del Litoral (ICIVET-Litoral), Universidad Nacional del Litoral (UNL) / Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Esperanza, Santa Fe, Argentina; Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL), Santa Fe, Santa Fe, Argentina.
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Ma T, Xue H, Piao C, Jiang N, Li Y. Genome-based analyses of family Oxalobacteraceae reveal the taxonomic classification. Res Microbiol 2023; 174:104076. [PMID: 37137377 DOI: 10.1016/j.resmic.2023.104076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 04/20/2023] [Accepted: 04/26/2023] [Indexed: 05/05/2023]
Abstract
Family Oxalobacteraceae is known for the indicator of bacterial diversity in the environment and many of which are important beneficial bacteria. Previous studies on the taxonomic structure of family Oxalobacteraceae mostly relied on 16S rRNA gene analysis, or core-genome phylogeny of a limited number of species and resulted in taxonomic confusion within several genera. Developments in sequencing technologies have allowed more genome sequences to be obtained, enabling the revision of family Oxalobacteraceae. Here, we report a comprehensive analysis of phylogenomic trees, concatenated protein and up-to-date bacterial core gene phylogenetic trees, and genomic metrics for genus demarcation on 135 genomes of Oxalobacteraceae species to elucidate their interrelationships. Following this framework for classification of species in family Oxalobacteraceae, all the proposed genera formed monophyletic lineages in the phylogenomic trees and could also be clearly separated from others in the genomic similarity indexes of average amino acid identity, percentage of conserved proteins and core-proteome average amino acid identity.
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Affiliation(s)
- Tengfei Ma
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China.
| | - Han Xue
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China.
| | - Chungen Piao
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China.
| | - Ning Jiang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China.
| | - Yong Li
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China.
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Lee D, Oh T, Kang B, Ahn JS, Cho Y. Throughput screening of Bacillus subtilis strains that abundantly secrete surfactin in vitro identifies effective probiotic candidates. PLoS One 2022; 17:e0277412. [PMID: 36417387 PMCID: PMC9683610 DOI: 10.1371/journal.pone.0277412] [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: 07/28/2022] [Accepted: 10/26/2022] [Indexed: 11/24/2022] Open
Abstract
Since the prohibition of antibiotics as animal growth promoters, demand for effective probiotic strains has steadily increased. The goal is to maintain productivity and mitigate environmental concerns in the livestock industry. There are many probiotic animal-diet supplements available, over 2,000 products in the Republic of Korea alone, with little explanation about the desirable properties of each probiotic strain. The purpose of this study was to describe the underlying logic and methods used to select two novel strains of probiotic candidates. To economically screen these candidates, the abundance of surfactin secreted was used as an in vitro marker. We used a modified oil-misting method to screen ~2,000 spore-forming bacteria for novel strains of Bacillus subtilis. Of these, 18 strains were initially selected based on the semiquantitative criterion that they secreted more surfactin than B. subtilis ATCC21322 on Luria-Berani (LB) agar plates. The whole genome sequence was determined for two of the 18 strains to verify their identity. A phylogeny of 1,162 orthologous genes, genome contents, and genome organization confirmed them as novel strains. The surfactin profiles produced by these two strains consisted of at least four isoforms similar to standard surfactin and enhanced cellulase activities up to 50%. Four fractionated individual isoforms of surfactin suppressed inflammation induced by lipopolysaccharides. The half-maximal inhibitory concentration (IC50) was about 20 μM for each isoform. Both selected strains were susceptible to seven important antibiotics. Our results implied that an abundant secretion of surfactin was a useful biomarker in vitro and could be utilized for mining probiotic candidates through high-throughput screening of environmental samples.
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Affiliation(s)
- Dongho Lee
- Molpaxbio, Yuseong-gu, Daejeon, Republic of Korea
| | - Taehoon Oh
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang-eup, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do, Republic of Korea
| | | | - Jong Seok Ahn
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang-eup, Cheongwon-gu, Cheongju-si, Chungcheongbuk-do, Republic of Korea
- * E-mail: (YC); (JSA)
| | - Yangrae Cho
- ProxEnrem, Osong-eup, Chungju-si, Republic of Korea
- * E-mail: (YC); (JSA)
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Rajkumari J, Katiyar P, Dheeman S, Pandey P, Maheshwari DK. The changing paradigm of rhizobial taxonomy and its systematic growth upto postgenomic technologies. World J Microbiol Biotechnol 2022; 38:206. [PMID: 36008736 DOI: 10.1007/s11274-022-03370-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 07/28/2022] [Indexed: 11/29/2022]
Abstract
Rhizobia are a diazotrophic group of bacteria that are usually isolated form the nodules in roots, stem of leguminous plants and are able to form nodules in the host plant owing to the presence of symbiotic genes. The rhizobial community is highly diverse, and therefore, the taxonomy and genera-wise classification of rhizobia has been constantly changing since the last three decades. This is mainly due to technical advancements, and shifts in definitions, resulting in a changing paradigm of rhizobia taxonomy. Initially, the taxonomic definitions at the species and sub species level were based on phylogenetic analysis of 16S rRNA sequence, followed by polyphasic approach to have phenotypic, biochemical, and genetic analysis including multilocus sequence analysis. Rhizobia mainly belonging to α- and β-proteobacteria, and recently new additions from γ-proteobacteria had been classified. Nowadays rhizobial taxonomy has been replaced by genome-based taxonomy that allows gaining more insights of genomic characteristics. These omics-technologies provide genome specific information that considers nodulation and symbiotic genes, along with molecular markers as taxonomic traits. Taxonomy based on complete genome sequence (genotaxonomy), average nucleotide identity, is now being considered as primary approach, resulting in an ongoing paradigm shift in rhizobial taxonomy. Also, pairwise whole-genome comparisons, phylogenomic analyses offer correlations between DNA and DNA re-association values that have delineated biologically important species. This review elaborates the present classification and taxonomy of rhizobia, vis-a-vis development of technical advancements, parameters and controversies associated with it, and describe the updated information on evolutionary lineages of rhizobia.
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Affiliation(s)
- Jina Rajkumari
- Department of Microbiology, Assam University, Silchar, Assam, 788011, India
| | - Prashant Katiyar
- Department of Botany and Microbiology, Gurukula Kangri Vishwavidyalaya, Haridwar, 249-404, India
| | - Shrivardhan Dheeman
- Department of Microbiology, Sardar Bhagwan Singh University, Dehra Dun, Uttarakhand, 248161, India
| | - Piyush Pandey
- Department of Microbiology, Assam University, Silchar, Assam, 788011, India.
| | - Dinesh Kumar Maheshwari
- Department of Botany and Microbiology, Gurukula Kangri Vishwavidyalaya, Haridwar, 249-404, India.
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Hassler HB, Probert B, Moore C, Lawson E, Jackson RW, Russell BT, Richards VP. Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies. MICROBIOME 2022; 10:104. [PMID: 35799218 PMCID: PMC9264627 DOI: 10.1186/s40168-022-01295-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 05/23/2022] [Indexed: 05/02/2023]
Abstract
BACKGROUND The 16S rRNA gene is used extensively in bacterial phylogenetics, in species delineation, and now widely in microbiome studies. However, the gene suffers from intragenomic heterogeneity, and reports of recombination and an unreliable phylogenetic signal are accumulating. Here, we compare core gene phylogenies to phylogenies constructed using core gene concatenations to estimate the strength of signal for the 16S rRNA gene, its hypervariable regions, and all core genes at the intra- and inter-genus levels. Specifically, we perform four intra-genus analyses (Clostridium, n = 65; Legionella, n = 47; Staphylococcus, n = 36; and Campylobacter, n = 17) and one inter-genus analysis [41 core genera of the human gut microbiome (31 families, 17 orders, and 12 classes), n = 82]. RESULTS At both taxonomic levels, the 16S rRNA gene was recombinant and subject to horizontal gene transfer. At the intra-genus level, the gene showed one of the lowest levels of concordance with the core genome phylogeny (50.7% average). Concordance for hypervariable regions was lower still, with entropy masking providing little to no benefit. A major factor influencing concordance was SNP count, which showed a positive logarithmic association. Using this relationship, we determined that 690 ± 110 SNPs were required for 80% concordance (average 16S rRNA gene SNP count was 254). We also found a wide range in 16S-23S-5S rRNA operon copy number among genomes (1-27). At the inter-genus level, concordance for the whole 16S rRNA gene was markedly higher (73.8% - 10th out of 49 loci); however, the most concordant hypervariable regions (V4, V3-V4, and V1-V2) ranked in the third quartile (62.5 to 60.0%). CONCLUSIONS Ramifications of a poor phylogenetic performance for the 16S rRNA gene are far reaching. For example, in addition to incorrect species/strain delineation and phylogenetic inference, it has the potential to confound community diversity metrics if phylogenetic information is incorporated - for example, with popular approaches such as Faith's phylogenetic diversity and UniFrac. Our results highlight the problematic nature of these approaches and their use (along with entropy masking) is discouraged. Lastly, the wide range in 16S rRNA gene copy number among genomes also has a strong potential to confound diversity metrics. Video Abstract.
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Affiliation(s)
- Hayley B. Hassler
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC 29634 USA
| | - Brett Probert
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC 29634 USA
| | - Carson Moore
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC 29634 USA
| | - Elizabeth Lawson
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC 29634 USA
| | | | - Brook T. Russell
- School of Mathematical and Statistical Sciences, Clemson University, Clemson, SC 29634 USA
| | - Vincent P. Richards
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC 29634 USA
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Hsouna J, Gritli T, Ilahi H, Ellouze W, Mansouri M, Chihaoui SA, Bouhnik O, Missbah El Idrissi M, Abdelmoumen H, Wipf D, Courty PE, Bekki A, Tambong JT, Mnasri B. Genotypic and symbiotic diversity studies of rhizobia nodulating Acacia saligna in Tunisia reveal two novel symbiovars within the Rhizobium leguminosarum complex and Bradyrhizobium. Syst Appl Microbiol 2022; 45:126343. [PMID: 35759954 DOI: 10.1016/j.syapm.2022.126343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/08/2022] [Accepted: 06/12/2022] [Indexed: 11/15/2022]
Abstract
Acacia saligna is an invasive alien species that has the ability to establish symbiotic relationships with rhizobia. In the present study, genotypic and symbiotic diversity of native rhizobia associated with A. saligna in Tunisia were studied. A total of 100 bacterial strains were selected and three different ribotypes were identified based on rrs PCR-RFLP analysis. Sequence analyses of rrs and four housekeeping genes (recA, atpD, gyrB and glnII) assigned 30 isolates to four putative new lineages and a single strain to Sinorhizobium meliloti. Thirteen slow-growing isolates representing the most dominant IGS (intergenic spacer) profile clustered distinctly from known rhizobia species within Bradyrhizobium with the closest related species being Bradyrhizobium shewense and Bradyrhizobium niftali, which had 95.17% and 95.1% sequence identity, respectively. Two slow-growing isolates, 1AS28L and 5AS6L, had B. frederekii as their closest species with a sequence identity of 95.2%, an indication that these strains could constitute a new lineage. Strains 1AS14I, 1AS12I and 6AS6 clustered distinctly from known rhizobia species but within the Rhizobium leguminosarum complex (Rlc) with the most closely related species being Rhizobium indicum with 96.3% sequence identity. Similarly, the remaining 11 strains showed 96.9 % and 97.2% similarity values with R. changzhiense and R. indicum, respectively. Based on nodC and nodA phylogenies and cross inoculation tests, these 14 strains of Rlc species clearly diverged from strains of Sinorhizobium and Rlc symbiovars, and formed a new symbiovar for which the name sv. "salignae" is proposed. Bacterial strains isolated in this study that were taxonomically assigned to Bradyrhizobium harbored different symbiotic genes and the data suggested a new symbiovar, for which sv. "cyanophyllae" is proposed. Isolates formed effective nodules on A. saligna.
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Affiliation(s)
- Jihed Hsouna
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cédria, BP 901 Hammam-lif 2050, Tunisia
| | - Takwa Gritli
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cédria, BP 901 Hammam-lif 2050, Tunisia
| | - Houda Ilahi
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cédria, BP 901 Hammam-lif 2050, Tunisia
| | - Walid Ellouze
- Agriculture and Agri-Food Canada, 4902 Victoria Avenue North, Vineland Station, Ontario L0R 2E0, Canada.
| | - Maroua Mansouri
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cédria, BP 901 Hammam-lif 2050, Tunisia
| | - Saif-Allah Chihaoui
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cédria, BP 901 Hammam-lif 2050, Tunisia
| | - Omar Bouhnik
- Faculty of Sciences, Centre de Biotechnologies Végétale et Microbienne, Biodiversité et Environnement, Mohammed V University, Rabat, Morocco
| | - Mustapha Missbah El Idrissi
- Faculty of Sciences, Centre de Biotechnologies Végétale et Microbienne, Biodiversité et Environnement, Mohammed V University, Rabat, Morocco
| | - Hanaa Abdelmoumen
- Faculty of Sciences, Centre de Biotechnologies Végétale et Microbienne, Biodiversité et Environnement, Mohammed V University, Rabat, Morocco
| | - Daniel Wipf
- Agroécologie, Institut Agro Dijon, CNRS, Univ. Bourgogne, INRAE, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Pierre Emmanuel Courty
- Agroécologie, Institut Agro Dijon, CNRS, Univ. Bourgogne, INRAE, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Abdelkader Bekki
- Laboratory of Rhizobia Biotechnology and Plant Breeding, University Oran1, Es Senia 31000, Algeria
| | - James T Tambong
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - Bacem Mnasri
- Laboratory of Legumes and Sustainable Agroecosystems, Centre of Biotechnology of Borj-Cédria, BP 901 Hammam-lif 2050, Tunisia.
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Avni E, Snir S. A New Phylogenomic Approach For Quantifying Horizontal Gene Transfer Trends in Prokaryotes. Sci Rep 2020; 10:12425. [PMID: 32709941 PMCID: PMC7381616 DOI: 10.1038/s41598-020-62446-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 01/27/2020] [Indexed: 11/09/2022] Open
Abstract
It is well established nowadays that among prokaryotes, various families of orthologous genes exhibit conflicting evolutionary history. A prime factor for this conflict is horizontal gene transfer (HGT) - the transfer of genetic material not via vertical descent. Thus, the prevalence of HGT is challenging the meaningfulness of the classical Tree of Life concept. Here we present a comprehensive study of HGT representing the entire prokaryotic world. We mainly rely on a novel analytic approach for analyzing an aggregate of gene histories, by means of the quartet plurality distribution (QPD) that we develop. Through the analysis of real and simulated data, QPD is used to reveal evidence of a barrier against HGT, separating the archaea from the bacteria and making HGT between the two domains, in general, quite rare. In contrast, bacteria's confined HGT is substantially more frequent than archaea's. Our approach also reveals that despite intensive HGT, a strong tree-like signal can be extracted, corroborating several previous works. Thus, QPD, which enables one to analytically combine information from an aggregate of gene trees, can be used for understanding patterns and rates of HGT in prokaryotes, as well as for validating or refuting models of horizontal genetic transfers and evolution in general.
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Affiliation(s)
- Eliran Avni
- Department of Evolutionary Biology, University of Haifa, Haifa, 31905, Israel.
| | - Sagi Snir
- Department of Evolutionary Biology, University of Haifa, Haifa, 31905, Israel.
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Gritli T, Ellouze W, Chihaoui SA, Barhoumi F, Mhamdi R, Mnasri B. Genotypic and symbiotic diversity of native rhizobia nodulating red pea (Lathyrus cicera L.) in Tunisia. Syst Appl Microbiol 2019; 43:126049. [PMID: 31870686 DOI: 10.1016/j.syapm.2019.126049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 11/24/2019] [Accepted: 12/02/2019] [Indexed: 11/15/2022]
Abstract
Nodulation and genetic diversity of native rhizobia nodulating Lathyrus cicera plants grown in 24 cultivated and marginal soils collected from northern and central Tunisia were studied. L. cicera plants were nodulated and showed the presence of native rhizobia in 21 soils. A total of 196 bacterial strains were selected and three different ribotypes were revealed after PCR-RFLP analysis. The sequence analysis of the rrs and two housekeeping genes (recA and thrC) from 36 representative isolates identified Rhizobium laguerreae as the dominant (53%) rhizobia nodulating L. cicera. To the best of our knowledge, this is the first time that this species has been reported among wild populations of the rhizobia-nodulating Lathyrus genus. Twenty-five percent of the isolates were identified as R. leguminosarum and isolates LS11.5, LS11.7 and LS8.8 clustered with Ensifer meliloti. Interestingly, five isolates (LS20.3, LS18.3, LS19.10, LS1.2 and LS21.20) were segregated from R. laguerreae and clustered as a separate clade. These isolates possibly belong to new species. According to nodC and nodA phylogeny, strains of R. laguerreae and R. leguminosarum harbored the symbiotic genes of symbiovar viciae and clustered in three different clades showing heterogeneity within the symbiovar. Strains of E. meliloti harbored symbiotic genes of Clade V and induced inefficient nodules.
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Affiliation(s)
- Takwa Gritli
- Laboratory of Legumes, Centre of Biotechnology of Borj-Cédria, BP 901, Hammam-lif 2050, Tunisia
| | - Walid Ellouze
- Agriculture and Agri-Food Canada, Vineland Station, Ontario L0R 2E0, Canada
| | - Saif-Allah Chihaoui
- Laboratory of Legumes, Centre of Biotechnology of Borj-Cédria, BP 901, Hammam-lif 2050, Tunisia
| | - Fathi Barhoumi
- Laboratory of Legumes, Centre of Biotechnology of Borj-Cédria, BP 901, Hammam-lif 2050, Tunisia
| | - Ridha Mhamdi
- Laboratory of Legumes, Centre of Biotechnology of Borj-Cédria, BP 901, Hammam-lif 2050, Tunisia
| | - Bacem Mnasri
- Laboratory of Legumes, Centre of Biotechnology of Borj-Cédria, BP 901, Hammam-lif 2050, Tunisia.
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Ormeño-Orrillo E, Martínez-Romero E. A Genomotaxonomy View of the Bradyrhizobium Genus. Front Microbiol 2019; 10:1334. [PMID: 31263459 PMCID: PMC6585233 DOI: 10.3389/fmicb.2019.01334] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/28/2019] [Indexed: 11/13/2022] Open
Abstract
Whole genome analysis of the Bradyrhizobium genus using average nucleotide identity (ANI) and phylogenomics showed the genus to be essentially monophyletic with seven robust groups within this taxon that includes nitrogen-fixing nodule forming bacteria as well as free living strains. Despite the wide genetic diversity of these bacteria no indication was found to suggest that the Bradyrhizobium genus have to split in different taxa. Bradyrhizobia have larger genomes than other genera of the Bradyrhizobiaceae family, probably reflecting their metabolic diversity and different lifestyles. Few plasmids in the sequenced strains were revealed from rep gene analysis and a relatively low proportion of the genome is devoted to mobile genetic elements. Sequence diversity of recA and glnII gene metadata was used to theoretically estimate the number of existing species and to predict how many would exist. There may be many more species than those presently described with predictions of around 800 species in nature. Different arguments are presented suggesting that nodulation might have arose in the ancestral genus Bradyrhizobium.
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Affiliation(s)
- Ernesto Ormeño-Orrillo
- Laboratorio de Ecología Microbiana y Biotecnología, Departamento de Biología, Facultad de Ciencias, Universidad Nacional Agraria La Molina, Lima, Peru
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de Lajudie PM, Andrews M, Ardley J, Eardly B, Jumas-Bilak E, Kuzmanović N, Lassalle F, Lindström K, Mhamdi R, Martínez-Romero E, Moulin L, Mousavi SA, Nesme X, Peix A, Puławska J, Steenkamp E, Stępkowski T, Tian CF, Vinuesa P, Wei G, Willems A, Zilli J, Young P. Minimal standards for the description of new genera and species of rhizobia and agrobacteria. Int J Syst Evol Microbiol 2019; 69:1852-1863. [PMID: 31140963 DOI: 10.1099/ijsem.0.003426] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Herein the members of the Subcommittee on Taxonomy of Rhizobia and Agrobacteria of the International Committee on Systematics of Prokaryotes review recent developments in rhizobial and agrobacterial taxonomy and propose updated minimal standards for the description of new species (and genera) in these groups. The essential requirements (minimal standards) for description of a new species are (1) a genome sequence of at least the proposed type strain and (2) evidence for differentiation from other species based on genome sequence comparisons. It is also recommended that (3) genetic variation within the species is documented with sequence data from several clearly different strains and (4) phenotypic features are described, and their variation documented with data from a relevant set of representative strains. Furthermore, it is encouraged that information is provided on (5) nodulation or pathogenicity phenotypes, as appropriate, with relevant gene sequences. These guidelines supplement the current rules of general bacterial taxonomy, which require (6) a name that conforms to the International Code of Nomenclature of Prokaryotes, (7) validation of the name by publication either directly in the International Journal of Systematic and Evolutionary Microbiology or in a validation list when published elsewhere, and (8) deposition of the type strain in two international culture collections in separate countries.
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Affiliation(s)
| | - Mitchell Andrews
- 2Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Julie Ardley
- 3School of Veterinary and Life Sciences, Murdoch University, Murdoch, Australia
| | | | - Estelle Jumas-Bilak
- 5UMR 5569, Department of Microbiology, Faculty of Pharmacy, University of Montpellier, France
| | - Nemanja Kuzmanović
- 6Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104 Braunschweig, Germany
| | - Florent Lassalle
- 7Department of Infectious Disease Epidemiology - MRC Centre for Outbreak Analysis and Modelling, St Mary's Hospital, Praed Street, London W2 1NY, UK
| | - Kristina Lindström
- 8Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki FI-00014, Finland
| | - Ridha Mhamdi
- 9Centre of Biotechnology of Borj-Cedria, BP 901 Hammam-lif 2050, Tunisia
| | - Esperanza Martínez-Romero
- 10Centro de Ciencias Genómicas, Universidad Nacional Autónoma de Mexico, Cuernavaca, Morelos, Mexico
| | - Lionel Moulin
- 11IRD, CIRAD, University of Montpellier, IPME, Montpellier, France
| | - Seyed Abdollah Mousavi
- 8Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki FI-00014, Finland
| | - Xavier Nesme
- 12LEM, UCBL, CNRS, INRA, Univ Lyon, Villeurbanne, France
| | - Alvaro Peix
- 13Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, c/Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Joanna Puławska
- 14Department of Phytopathology, Research Institute of Horticulture, ul. Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland
| | - Emma Steenkamp
- 15Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria 0002, South Africa
| | - Tomasz Stępkowski
- 16Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Chang-Fu Tian
- 17State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, Rhizobium Research Center, College of Biological Sciences, China Agricultural University, 100193, Beijing, PR China
| | - Pablo Vinuesa
- 10Centro de Ciencias Genómicas, Universidad Nacional Autónoma de Mexico, Cuernavaca, Morelos, Mexico
| | - Gehong Wei
- 18Northwest A&F University, Yangling, Shaanxi, PR China
| | - Anne Willems
- 19Department Biochemistry and Microbiology, Lab. Microbiology, Ghent University, Belgium
| | - Jerri Zilli
- 20Embrapa Agrobiologia, BR 465 km 07, Seropédica, Rio de Janeiro, Brazil, 23891-000, Brazil
| | - Peter Young
- 21Department of Biology, University of York, York YO10 5DD, UK
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11
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Caputo A, Fournier PE, Raoult D. Genome and pan-genome analysis to classify emerging bacteria. Biol Direct 2019; 14:5. [PMID: 30808378 PMCID: PMC6390601 DOI: 10.1186/s13062-019-0234-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 02/14/2019] [Indexed: 12/21/2022] Open
Abstract
Background In the recent years, genomic and pan-genomic studies have become increasingly important. Culturomics allows to study human microbiota through the use of different culture conditions, coupled with a method of rapid identification by MALDI-TOF, or 16S rRNA. Bacterial taxonomy is undergoing many changes as a consequence. With the help of pan-genomic analyses, species can be redefined, and new species definitions generated. Results Genomics, coupled with culturomics, has led to the discovery of many novel bacterial species or genera, including Akkermansia muciniphila and Microvirga massiliensis. Using the genome to define species has been applied within the genus Klebsiella. A discontinuity or an abrupt break in the core/pan-genome ratio can uncover novel species. Conclusions Applying genomic and pan-genomic analyses to the reclassification of other bacterial species or genera will be important in the future of medical microbiology. The pan-genome is one of many new innovative tools in bacterial taxonomy. Reviewers This article was reviewed by William Martin, Eric Bapteste and James Mcinerney. Open peer review Reviewed by William Martin, Eric Bapteste and James Mcinerney.
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Affiliation(s)
- Aurélia Caputo
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | | | - Didier Raoult
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France.
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12
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Avni E, Snir S. A New Quartet-Based Statistical Method for Comparing Sets of Gene Trees Is Developed Using a Generalized Hoeffding Inequality. J Comput Biol 2018; 26:27-37. [PMID: 30422680 DOI: 10.1089/cmb.2018.0129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Extracting the strength of the tree signal that is encompassed by a collection of gene trees is an exceptionally challenging problem in phylogenomics. Often, this problem not only involves the construction of individual phylogenies based on different genes, which may be a difficult endeavor on its own, but is also exacerbated by many factors that create conflicts between the evolutionary histories of different gene families, such as duplications or losses of genes; hybridization events; incomplete lineage sorting; and horizontal gene transfer, the latter two play central roles in the evolution of eukaryotes and prokaryotes, respectively. In this work, we tackle the aforementioned problem by focusing on quartet trees, which are the most basic unit of information in the context of unrooted phylogenies. In the first part, we show how a theorem of Janson that generalizes the classical Hoeffding inequality can be used to develop a statistical test involving quartets. In the second part, we study real and simulated data using this theoretical advancement, thus demonstrating how the significance of the differences between sets of quartets can be assessed. Our results are particularly intriguing since they nonstandardly require the analysis of dependent random variables.
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Affiliation(s)
- Eliran Avni
- Department of Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Sagi Snir
- Department of Evolutionary Biology, University of Haifa, Haifa, Israel
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13
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Avni E, Montoya D, Lopez D, Modlin R, Pellegrini M, Snir S. A phylogenomic study quantifies competing mechanisms for pseudogenization in prokaryotes-The Mycobacterium leprae case. PLoS One 2018; 13:e0204322. [PMID: 30383852 PMCID: PMC6211624 DOI: 10.1371/journal.pone.0204322] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 09/06/2018] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Pseudogenes are non-functional sequences in the genome with homologous sequences that are functional (i.e. genes). They are abundant in eukaryotes where they have been extensively investigated, while in prokaryotes they are significantly scarcer and less well studied. Here we conduct a comprehensive analysis of the evolution of orthologs of Mycobacterium leprae pseudogenes in prokaryotes. The leprosy pathogen M. leprae is of particular interest since it contains an unusually large number of pseudogenes, comprising approximately 40% of its entire genome. The analysis is conducted in both broad and narrow phylogenetic ranges. RESULTS We have developed an informatics-based approach to characterize the evolution of pseudogenes. This approach combines tools from phylogenomics, genomics, and transcriptomics. The results we obtain are used to assess the contributions of two mechanisms for pseudogene formation: failed horizontal gene transfer events and disruption of native genes. CONCLUSIONS We conclude that, although it was reported that in most bacteria the former is most likely responsible for the majority of pseudogenization events, in mycobacteria, and in particular in M. leprae with its exceptionally high pseudogene numbers, the latter predominates. We believe that our study sheds new light on the evolution of pseudogenes in bacteria, by utilizing new methodologies that are applied to the unusually abundant M. leprae pseudogenes and their orthologs.
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Affiliation(s)
- Eliran Avni
- Dept. of Evolutionary Biology and the Institute of Evolution, University of Haifa, Haifa, Israel
| | - Dennis Montoya
- Dept. of Molecular, Cell and Developmental Biology; University of California Los Angeles, Los Angeles, CA 90095, United States of America
| | - David Lopez
- Dept. of Molecular, Cell and Developmental Biology; University of California Los Angeles, Los Angeles, CA 90095, United States of America
| | - Robert Modlin
- Dept. of Microbiology, Immunology and Molecular Genetics, and Division of Dermatology, David Geffen School of Medicine University of California Los Angeles, Los Angeles, CA 90095, United States of America
| | - Matteo Pellegrini
- Dept. of Molecular, Cell and Developmental Biology; University of California Los Angeles, Los Angeles, CA 90095, United States of America
| | - Sagi Snir
- Dept. of Evolutionary Biology and the Institute of Evolution, University of Haifa, Haifa, Israel
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14
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Abstract
BACKGROUND Deciphering the history of life on Earth has long been regarded as one of the most central tasks in biology. In past years, widespread discordance between the evolutionary histories of different groups of orthologous genes of prokaryotes have been revealed, primarily due to horizontal gene transfers (HGTs). Nonetheless, evidence that support a strong tree-like signal of evolution have been uncovered, despite the presence of HGT events. Therefore, a challenging task is to distill this tree-like signal from the noise induced by all sources of non-tree-like events. RESULTS In this work we tackle this question, using real and simulated data. We first tighten a recent related theoretical result in this field. In a simulation study, we infer individual quartet topologies, and then use the inferred quartets to reconstruct simulated species trees. We demonstrate that accurate tree reconstruction is feasible despite surprisingly high rates of HGT. In a real data study, we construct phylogenies of two sets of prokaryotes, and show that our tree reconstruction scheme is comparable with (and complementary better than) other commonly used methods. CONCLUSIONS Using a blend of theoretical and empirical investigations, our study proves the feasibility of accurate quartet-based phylogenetic reconstruction, the vast impact of HGT events notwithstanding.
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Affiliation(s)
- Eliran Avni
- Department of Evolutionary Biology, University of Haifa, 199 Aba Khoushy Ave. Mount Carmel, Haifa, 3498838, Israel
| | - Sagi Snir
- Department of Evolutionary Biology, University of Haifa, 199 Aba Khoushy Ave. Mount Carmel, Haifa, 3498838, Israel.
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15
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Distribution and Phylogeny of Microsymbionts Associated with Cowpea (Vigna unguiculata) Nodulation in Three Agroecological Regions of Mozambique. Appl Environ Microbiol 2018; 84:AEM.01712-17. [PMID: 29101189 PMCID: PMC5752868 DOI: 10.1128/aem.01712-17] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/19/2017] [Indexed: 11/22/2022] Open
Abstract
Cowpea derives most of its N nutrition from biological nitrogen fixation (BNF) via symbiotic bacteroids in root nodules. In Sub-Saharan Africa, the diversity and biogeographic distribution of bacterial microsymbionts nodulating cowpea and other indigenous legumes are not well understood, though needed for increased legume production. The aim of this study was to describe the distribution and phylogenies of rhizobia at different agroecological regions of Mozambique using PCR of the BOX element (BOX-PCR), restriction fragment length polymorphism of the internal transcribed spacer (ITS-RFLP), and sequence analysis of ribosomal, symbiotic, and housekeeping genes. A total of 122 microsymbionts isolated from two cowpea varieties (IT-1263 and IT-18) grouped into 17 clades within the BOX-PCR dendrogram. The PCR-ITS analysis yielded 17 ITS types for the bacterial isolates, while ITS-RFLP analysis placed all test isolates in six distinct clusters (I to VI). BLASTn sequence analysis of 16S rRNA and four housekeeping genes (glnII, gyrB, recA, and rpoB) showed their alignment with Rhizobium and Bradyrhizobium species. The results revealed a group of highly diverse and adapted cowpea-nodulating microsymbionts which included Bradyrhizobium pachyrhizi, Bradyrhizobium arachidis, Bradyrhizobium yuanmingense, and a novel Bradyrhizobium sp., as well as Rhizobium tropici, Rhizobium pusense, and Neorhizobium galegae in Mozambican soils. Discordances observed in single-gene phylogenies could be attributed to horizontal gene transfer and/or subsequent recombinations of the genes. Natural deletion of 60 bp of the gyrB region was observed in isolate TUTVU7; however, this deletion effect on DNA gyrase function still needs to be confirmed. The inconsistency of nifH with core gene phylogenies suggested differences in the evolutionary history of both chromosomal and symbiotic genes. IMPORTANCE A diverse group of both Bradyrhizobium and Rhizobium species responsible for cowpea nodulation in Mozambique was found in this study. Future studies could prove useful in evaluating these bacterial isolates for symbiotic efficiency and strain competitiveness in Mozambican soils.
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Degefu T, Wolde-Meskel E, Rasche F. Genetic diversity and symbiotic effectiveness of Bradyrhizobium strains nodulating selected annual grain legumes growing in Ethiopia. Int J Syst Evol Microbiol 2017; 68:449-460. [PMID: 29143730 DOI: 10.1099/ijsem.0.002486] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Vigna unguiculata, Vigna radiata and Arachis hypogaea growing in Ethiopia are nodulated by a genetically diverse group of Bradyrhizobium strains. To determine the genetic identity and symbiotic effectiveness of these bacteria, a collection of 36 test strains originating from the root nodules of the three hosts was investigated using multilocus sequence analyses (MLSA) of core genes including 16S rRNA, recA, glnII, gyrB, atpD and dnaK. Sequence analysis of nodA and nifH genes along with tests for symbiotic effectiveness using δ15N analysis were also carried out. The phylogenetic trees derived from the MLSA grouped most test strains into four well-supported distinct positions designated as genospecies I-IV. The maximum likelihood (ML) tree that was constructed based on the nodA gene sequences separated the entire test strains into two lineages, where the majority of the test strains were clustered on one of a well-supported large branch that comprise Bradyrhizobium species from the tropics. This clearly suggested the monophyletic origin of the nodA genes within the bradyrhizobia of tropical origin. The δ15N-based symbiotic effectiveness test of seven selected strains revealed that strains GN100 (δ15N=0.73) and GN102 (δ15N=0.79) were highly effective nitrogen fixers when inoculated to cowpea, thus can be considered as inoculants in cowpea production. It was concluded that Ethiopian soils are a hotspot for rhizobial diversity. This calls for further research to unravel as yet unknown bradyrhizobia nodulating legume host species growing in the country. In this respect, prospective research should also address the mechanisms of symbiotic specificity that could lead to high nitrogen fixation in target legumes.
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Affiliation(s)
- Tulu Degefu
- School of Applied Natural Sciences, Applied Biology Program, Adama Science and Technology University, P.O. Box 1888, Adama, Ethiopia
| | | | - Frank Rasche
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute), University of Hohenheim, 70593 Stuttgart, Germany
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17
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Osman WAM, van Berkum P, León-Barrios M, Velázquez E, Elia P, Tian R, Ardley J, Gollagher M, Seshadri R, Reddy TBK, Ivanova N, Woyke T, Pati A, Markowitz V, Baeshen MN, Baeshen NN, Kyrpides N, Reeve W. High-quality draft genome sequence of Ensifer meliloti Mlalz-1, a microsymbiont of Medicago laciniata (L.) miller collected in Lanzarote, Canary Islands, Spain. Stand Genomic Sci 2017; 12:58. [PMID: 28975015 PMCID: PMC5613336 DOI: 10.1186/s40793-017-0270-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 09/14/2017] [Indexed: 11/26/2022] Open
Abstract
10.1601/nm.1335 Mlalz-1 (INSDC = ATZD00000000) is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing nodule of Medicago laciniata (L.) Miller from a soil sample collected near the town of Guatiza on the island of Lanzarote, the Canary Islands, Spain. This strain nodulates and forms an effective symbiosis with the highly specific host M. laciniata. This rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) sequencing project. Here the features of 10.1601/nm.1335 Mlalz-1 are described, together with high-quality permanent draft genome sequence information and annotation. The 6,664,116 bp high-quality draft genome is arranged in 99 scaffolds of 100 contigs, containing 6314 protein-coding genes and 74 RNA-only encoding genes. Strain Mlalz-1 is closely related to 10.1601/nm.1335 10.1601/strainfinder?urlappend=%3Fid%3DIAM+12611 T, 10.1601/nm.1334 A 321T and 10.1601/nm.17831 10.1601/strainfinder?urlappend=%3Fid%3DORS+1407 T, based on 16S rRNA gene sequences. gANI values of ≥98.1% support the classification of strain Mlalz-1 as 10.1601/nm.1335. Nodulation of M. laciniata requires a specific nodC allele, and the nodC gene of strain Mlalz-1 shares ≥98% sequence identity with nodC of M. laciniata-nodulating 10.1601/nm.1328 strains, but ≤93% with nodC of 10.1601/nm.1328 strains that nodulate other Medicago species. Strain Mlalz-1 is unique among sequenced 10.1601/nm.1335 strains in possessing genes encoding components of a T2SS and in having two versions of the adaptive acid tolerance response lpiA-acvB operon. In 10.1601/nm.1334 strain 10.1601/strainfinder?urlappend=%3Fid%3DWSM+419, lpiA is essential for enhancing survival in lethal acid conditions. The second copy of the lpiA-acvB operon of strain Mlalz-1 has highest sequence identity (> 96%) with that of 10.1601/nm.1334 strains, which suggests genetic recombination between strain Mlalz-1 and 10.1601/nm.1334 and the horizontal gene transfer of lpiA-acvB.
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Affiliation(s)
| | - Peter van Berkum
- U.S. Department of Agriculture, Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, 10300 Baltimore Avenue, Bldg. 006, Beltsville, MD 20705 USA
| | - Milagros León-Barrios
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna, Tenerife, Spain
| | - Encarna Velázquez
- Departamento de Microbiología y Genetica and Instituto Hispanoluso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Salamanca, Spain
| | - Patrick Elia
- U.S. Department of Agriculture, Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, 10300 Baltimore Avenue, Bldg. 006, Beltsville, MD 20705 USA
| | - Rui Tian
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA Australia
| | - Julie Ardley
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA Australia
| | - Margaret Gollagher
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA Australia
| | | | | | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Amrita Pati
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Mohamed N. Baeshen
- Department of Biology, Faculty of Science, University of Jeddah, Jeddah, Saudi Arabia
| | | | | | - Wayne Reeve
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA Australia
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18
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Molecular diversity and phylogeny of indigenous Rhizobium leguminosarum strains associated with Trifolium repens plants in Romania. Antonie van Leeuwenhoek 2017; 111:135-153. [DOI: 10.1007/s10482-017-0934-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 08/20/2017] [Indexed: 11/30/2022]
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19
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Muñoz-Azcarate O, González AM, Santalla M. Natural rhizobial diversity helps to reveal genes and QTLs associated with biological nitrogen fixation in common bean. AIMS Microbiol 2017; 3:435-466. [PMID: 31294170 PMCID: PMC6604995 DOI: 10.3934/microbiol.2017.3.435] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 05/25/2017] [Indexed: 11/18/2022] Open
Abstract
Common bean is one of the most important crops for human feed, and the most important legume for direct consumption by millions of people, especially in developing countries. It is a promiscuous host legume in terms of nodulation, able to associate with a broad and diverse range of rhizobia, although the competitiveness for nodulation and the nitrogen fixation capacity of most of these strains is generally low. As a result, common bean is very inefficient for symbiotic nitrogen fixation, and nitrogen has to be supplied with chemical fertilizers. In the last years, symbiotic nitrogen fixation has received increasing attention as a sustainable alternative to nitrogen fertilizers, and also as a more economic and available one in poor countries. Therefore, optimization of nitrogen fixation of bean-rhizobia symbioses and selection of efficient rhizobial strains should be a priority, which begins with the study of the natural diversity of the symbioses and the rhizobial populations associated. Natural rhizobia biodiversity that nodulates common bean may be a source of adaptive alleles acting through phenotypic plasticity. Crosses between accessions differing for nitrogen fixation may combine alleles that never meet in nature. Another way to discover adaptive genes is to use association genetics to identify loci that common bean plants use for enhanced biological nitrogen fixation and, in consequence, for marker assisted selection for genetic improvement of symbiotic nitrogen fixation. In this review, rhizobial biodiversity resources will be discussed, together with what is known about the loci that underlie such genetic variation, and the potential candidate genes that may influence the symbiosis' fitness benefits, thus achieving an optimal nitrogen fixation capacity in order to help reduce reliance on nitrogen fertilizers in common bean.
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Affiliation(s)
- Olaya Muñoz-Azcarate
- Departamento de Recursos Fitogenéticos, Grupo de Biología de Agrosistemas, Misión Biológica de Galicia-CSIC. P.O. Box 28. 36080 Pontevedra, Spain
| | - Ana M González
- Departamento de Recursos Fitogenéticos, Grupo de Biología de Agrosistemas, Misión Biológica de Galicia-CSIC. P.O. Box 28. 36080 Pontevedra, Spain
| | - Marta Santalla
- Departamento de Recursos Fitogenéticos, Grupo de Biología de Agrosistemas, Misión Biológica de Galicia-CSIC. P.O. Box 28. 36080 Pontevedra, Spain
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20
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Degefu T, Wolde-meskel E, Woliy K, Frostegård Å. Phylogenetically diverse groups of Bradyrhizobium isolated from nodules of tree and annual legume species growing in Ethiopia. Syst Appl Microbiol 2017; 40:205-214. [DOI: 10.1016/j.syapm.2017.04.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/29/2017] [Accepted: 04/01/2017] [Indexed: 11/27/2022]
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21
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Permanent Draft Genome Sequence of Rhizobium sp. Strain LCM 4573, a Salt-Tolerant, Nitrogen-Fixing Bacterium Isolated from Senegalese Soils. GENOME ANNOUNCEMENTS 2017; 5:5/18/e00285-17. [PMID: 28473386 PMCID: PMC5477193 DOI: 10.1128/genomea.00285-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The genus Rhizobium contains many species that are able to form nitrogen-fixing nodules on plants of the legume family. Here, we report the 5.5-Mb draft genome sequence of the salt-tolerant Rhizobium sp. strain LCM 4573, which has a G+C content of 61.2% and 5,356 candidate protein-encoding genes.
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22
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de Oliveira-Francesquini JP, Hungria M, Savi DC, Glienke C, Aluizio R, Kava V, Galli-Terasawa LV. Differential colonization by bioprospected rhizobial bacteria associated with common bean in different cropping systems. Can J Microbiol 2017; 63:682-689. [PMID: 28376308 DOI: 10.1139/cjm-2016-0784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study, we evaluated the diversity of rhizobia isolated from root nodules on common bean (Phaseolus vulgaris) derived from Andean and Mesoamerican centers and grown under field and greenhouse conditions. Genetic characterization of isolates was performed by sequencing analyses of the 16S rRNA gene and 2 housekeeping genes, recA and glnII, and by the amplification of nifH. Symbiotic efficiency was evaluated by examining nodulation, plant biomass production, and plant nitrogen (N) accumulation. The influence of the environment was observed in nodulation capacity, where Rhizobium miluonense was dominant under greenhouse conditions and the Rhizobium acidisoli group prevailed under field conditions. However, strain LGMB41 fit into a separate group from the type strain of R. acidisoli in terms of multilocus phylogeny, implying that it could belong to a new species. Rhizobium miluonense LGMB73 showed the best symbiotic efficiency performance, i.e., with the highest shoot-N content (77.7 mg/plant), superior to the commercial standard strain (56.9 mg/plant). Biodiversity- and bioprospecting-associated studies are important to better understand ecosystems and to develop more effective strategies to improve plant growth using a N-fixation process.
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Affiliation(s)
| | | | - Daiani Cristina Savi
- a Universidade Federal do Paraná, Department of Genetics, C.P. 19071, 81531-980, Curitiba, PR, Brazil
| | - Chirlei Glienke
- a Universidade Federal do Paraná, Department of Genetics, C.P. 19071, 81531-980, Curitiba, PR, Brazil
| | - Rodrigo Aluizio
- a Universidade Federal do Paraná, Department of Genetics, C.P. 19071, 81531-980, Curitiba, PR, Brazil
| | - Vanessa Kava
- a Universidade Federal do Paraná, Department of Genetics, C.P. 19071, 81531-980, Curitiba, PR, Brazil
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23
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Reeve W, van Berkum P, Ardley J, Tian R, Gollagher M, Marinova D, Elia P, Reddy TBK, Pillay M, Varghese N, Seshadri R, Ivanova N, Woyke T, Baeshen MN, Baeshen NA, Kyrpides N. High-quality permanent draft genome sequence of the Bradyrhizobium elkanii type strain USDA 76 T, isolated from Glycine max (L.) Merr. Stand Genomic Sci 2017; 12:26. [PMID: 28270909 PMCID: PMC5336687 DOI: 10.1186/s40793-017-0238-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 02/21/2017] [Indexed: 11/10/2022] Open
Abstract
Bradyrhizobium elkanii USDA 76T (INSCD = ARAG00000000), the type strain for Bradyrhizobium elkanii, is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing root nodule of Glycine max (L. Merr) grown in the USA. Because of its significance as a microsymbiont of this economically important legume, B. elkanii USDA 76T was selected as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria sequencing project. Here the symbiotic abilities of B. elkanii USDA 76T are described, together with its genome sequence information and annotation. The 9,484,767 bp high-quality draft genome is arranged in 2 scaffolds of 25 contigs, containing 9060 protein-coding genes and 91 RNA-only encoding genes. The B. elkanii USDA 76T genome contains a low GC content region with symbiotic nod and fix genes, indicating the presence of a symbiotic island integration. A comparison of five B. elkanii genomes that formed a clique revealed that 356 of the 9060 protein coding genes of USDA 76T were unique, including 22 genes of an intact resident prophage. A conserved set of 7556 genes were also identified for this species, including genes encoding a general secretion pathway as well as type II, III, IV and VI secretion system proteins. The type III secretion system has previously been characterized as a host determinant for Rj and/or rj soybean cultivars. Here we show that the USDA 76T genome contains genes encoding all the type III secretion system components, including a translocon complex protein NopX required for the introduction of effector proteins into host cells. While many bradyrhizobial strains are unable to nodulate the soybean cultivar Clark (rj1), USDA 76T was able to elicit nodules on Clark (rj1), although in reduced numbers, when plants were grown in Leonard jars containing sand or vermiculite. In these conditions, we postulate that the presence of NopX allows USDA 76T to introduce various effector molecules into this host to enable nodulation.
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Affiliation(s)
- Wayne Reeve
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Australia
| | - Peter van Berkum
- U.S. Department of Agriculture, Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, 10300 Baltimore Avenue, Bldg. 006, Beltsville, MD 20705 USA
| | - Julie Ardley
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Australia
| | - Rui Tian
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Australia
| | - Margaret Gollagher
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA Australia
| | - Dora Marinova
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA Australia
| | - Patrick Elia
- U.S. Department of Agriculture, Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, 10300 Baltimore Avenue, Bldg. 006, Beltsville, MD 20705 USA
| | - T B K Reddy
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Manoj Pillay
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | | | | | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Mohamed N Baeshen
- Department of Biology, Faculty of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Nabih A Baeshen
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, CA USA.,Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
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Snir S. Ordered orthology as a tool in prokaryotic evolutionary inference. Mob Genet Elements 2017; 6:e1120576. [PMID: 28090377 DOI: 10.1080/2159256x.2015.1120576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 10/27/2015] [Accepted: 11/10/2015] [Indexed: 10/22/2022] Open
Abstract
Molecular data is accumulated at exponentially increasing pace. This deluge of information should have brought us closer to resolving one of the most fundamental issues in biology - deciphering the history of life on Earth. So far, however, this abundance of data only seems to blur our understanding of the problem. This is largely due to horizontal gene transfer (HGT), the transfer of genetic material between evolutionarily unrelated organisms that transforms the prokaryotic tree into a network of relationships. Recently, we developed a method to infer evolutionary relationships among closely related species where the conventional evolutionary markers do not provide a strong enough signal. The method relies on the loss of synteny, gene order conservation among species that provides a stronger signal, sufficient to classify even strains of a given species. Here we elaborate on this method and suggest further uses of it in the context of detecting HGT events and genome architecture.
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Affiliation(s)
- Sagi Snir
- Department of Evolutionary Biology, University of Haifa , Haifa, Israel
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25
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Beligala DH, Michaels HJ, Devries M, Phuntumart V. Multilocus Sequence Analysis of Root Nodule Bacteria Associated with <i>Lupinus</i> spp. and <i>Glycine max</i>. ACTA ACUST UNITED AC 2017. [DOI: 10.4236/aim.2017.711063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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26
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Fossou RK, Ziegler D, Zézé A, Barja F, Perret X. Two Major Clades of Bradyrhizobia Dominate Symbiotic Interactions with Pigeonpea in Fields of Côte d'Ivoire. Front Microbiol 2016; 7:1793. [PMID: 27891120 PMCID: PMC5104742 DOI: 10.3389/fmicb.2016.01793] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 10/25/2016] [Indexed: 12/03/2022] Open
Abstract
In smallholder farms of Côte d'Ivoire, particularly in the northeast of the country, Cajanus cajan (pigeonpea) has become an important crop because of its multiple beneficial facets. Pigeonpea seeds provide food to make ends meet, are sold on local markets, and aerial parts serve as forage for animals. Since it fixes atmospheric nitrogen in symbiosis with soil bacteria collectively known as rhizobia, C. cajan also improves soil fertility and reduces fallow time. Yet, seed yields remain low mostly because farmers cannot afford chemical fertilizers. To identify local rhizobial strains susceptible to be used as bio-inoculants to foster pigeonpea growth, root nodules were collected in six fields of three geographically distant regions of Côte d'Ivoire. Nodule bacteria were isolated and characterized using various molecular techniques including matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry (MS) and DNA sequencing. These molecular analyses showed that 63 out of 85 nodule isolates belonged to two major clades of bradyrhizobia, one of which is known as the Bradyrhizobium elkanii super clade. Phylogenies of housekeeping (16S-ITS-23S, rpoB) and symbiotic (nifH) genes were not always congruent suggesting that lateral transfer of nitrogen fixation genes also contributed to define the genome of these bradyrhizobial isolates. Interestingly, no field-, plant-, or cultivar-specific effect was found to shape the profiles of symbiotic strains. In addition, nodule isolates CI-1B, CI-36E, and CI-41A that belong to distinct species, showed similar symbiotic efficiencies suggesting that any of these strains might serve as a proficient inoculant for C. cajan.
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Affiliation(s)
- Romain K Fossou
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva Geneva, Switzerland
| | - Dominik Ziegler
- Microbiology Unit, Department of Botany and Plant Biology, University of GenevaGeneva, Switzerland; Mabritec AGRiehen, Switzerland
| | - Adolphe Zézé
- Laboratoire de Biotechnologies Végétale et Microbienne, Unité Mixte de Recherche et d'Innovation en Sciences Agronomiques et Génie Rural, Institut National Polytechnique Félix Houphouët-Boigny (INPHB) Yamoussoukro, Côte d'Ivoire
| | - François Barja
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva Geneva, Switzerland
| | - Xavier Perret
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva Geneva, Switzerland
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27
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Frenkel Z, Kiat Y, Izhaki I, Snir S. Convex recoloring as an evolutionary marker. Mol Phylogenet Evol 2016; 107:209-220. [PMID: 27818264 DOI: 10.1016/j.ympev.2016.10.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 10/16/2016] [Accepted: 10/25/2016] [Indexed: 11/27/2022]
Abstract
With the availability of enormous quantities of genetic data it has become common to construct very accurate trees describing the evolutionary history of the species under study, as well as every single gene of these species. These trees allow us to examine the evolutionary compliance of given markers (characters). A marker compliant with the history of the species investigated, has undergone mutations along the species tree branches, such that every subtree of that tree exhibits a different state. Convex recoloring (CR) uses combinatorial representation to measure the adequacy of a taxonomic classifier to a given tree. Despite its biological origins, research on CR has been almost exclusively dedicated to mathematical properties of the problem, or variants of it with little, if any, relationship to taxonomy. In this work we return to the origins of CR. We put CR in a statistical framework and introduce and learn the notion of the statistical significance of a character. We apply this measure to two data sets - Passerine birds and prokaryotes, and four examples. These examples demonstrate various applications of CR, from evolutionary relatedness, through lateral evolution, to supertree construction. The above study was done with a new software that we provide, containing algorithmic improvement with a graphical output of a (optimally) recolored tree. AVAILABILITY A code implementing the features and a README is available at http://research.haifa.ac.il/ssagi/software/convexrecoloring.zip.
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Affiliation(s)
- Zeev Frenkel
- Department of Ecology and Evolutionary Biology, University of Haifa, Israel
| | - Yosef Kiat
- Israeli Bird Ringing Center, Society for the Protection of Nature in Israel, Israel
| | - Ido Izhaki
- Department of Ecology and Evolutionary Biology, University of Haifa, Israel
| | - Sagi Snir
- Department of Ecology and Evolutionary Biology, University of Haifa, Israel
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28
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Zhao L, Wang X, Huo H, Yuan G, Sun Y, Zhang D, Cao Y, Xu L, Wei G. Phylogenetic Diversity of Ammopiptanthus Rhizobia and Distribution of Rhizobia Associated with Ammopiptanthus mongolicus in Diverse Regions of Northwest China. MICROBIAL ECOLOGY 2016; 72:231-239. [PMID: 27079453 DOI: 10.1007/s00248-016-0759-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 03/22/2016] [Indexed: 06/05/2023]
Abstract
Aiming to investigate the diversity and distribution of rhizobia associated with Ammopiptanthus, an endangered evergreen legume widely distributed in deserts, we characterized a total of 219 nodule isolates from nine sampling sites in Northwest China with different soil characteristics based upon restriction fragment length polymorphism (RFLP) analysis of 16S ribosomal RNA (rRNA) and symbiotic genes (nodC and nifH). Ten isolates representing different 16S rRNA-RFLP types were selected for further sequence analyses of 16S rRNA and four housekeeping genes. As results, nine genospecies belonging to the genera Ensifer, Neorhizobium, Agrobacterium, Pararhizobium, and Rhizobium could be defined among the isolates. The nodC and nifH phylogenies of 14 isolates representing different symbiotic-RFLP types revealed five lineages linked to Ensifer fredii, Ensifer meliloti, Rhizobium leguminosarum, Mesorhizobium amorphae, and Rhizobium gallicum, which demonstrated the various origins and lateral transfers of symbiotic genes between different genera and species. The rhizobial diversities of Ammopiptanthus mongolicus varied among regions, and the community compositions of rhizobia associated with A. mongolicus were significantly different in wild and cultured fields. Constrained correspondence analysis showed that the distribution of A. mongolicus rhizobia could be explained by available potassium content and that the assembly of symbiotic types was mainly affected by available phosphorus content and carbon-nitrogen ratio.
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Affiliation(s)
- Liang Zhao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xinye Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Haibo Huo
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Guiji Yuan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yali Sun
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Dehui Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ying Cao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lin Xu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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29
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Genetic diversity and distribution of bradyrhizobia nodulating peanut in acid-neutral soils in Guangdong Province. Syst Appl Microbiol 2016; 39:418-27. [PMID: 27499533 DOI: 10.1016/j.syapm.2016.06.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 06/02/2016] [Accepted: 06/06/2016] [Indexed: 11/20/2022]
Abstract
To reveal the genetic diversity and geographic distribution of peanut (Arachis hypogaea L.) rhizobia in Guangdong Province, one of the main peanut producing regions in China, 216 bradyrhizobial isolates were trapped by peanut plants inoculated with soil samples (pH 4.7-7.4) collected from ten sites in Guangdong. Based on BOX-PCR fingerprinting analysis, 71 representative isolates were selected for sequence analyses of ribosomal IGS, recA, atpD and symbiotic gene nodA. As a result, 22 genospecies were detected in the peanut rhizobia, including eight minor groups or single strains corresponding to Bradyrhizobium diazoefficiens, B. japonicum, B. yuanmingense, B. arachidis, B. guangdongense, B. guangxiense, B. iriomotense and B. liaoningense, as well as 14 novel Bradyrhizobium genospecies covering the majority of isolates. Five symbiotic clusters were obtained based on the phylogenetic relationships of nodA genes, related to the soybean-nodulating or peanut-nodulating reference strains. Biogeographic patterns, which were mainly correlated with potassium content and pH, were detected in the peanut bradyrhizobial community in Guangdong Province. These findings enriched the diversity of peanut rhizobia, and added the K content as a special determinant for peanut rhizobial distribution in acid soils.
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The Plasmid Mobilome of the Model Plant-Symbiont Sinorhizobium meliloti: Coming up with New Questions and Answers. Microbiol Spectr 2016; 2. [PMID: 26104371 DOI: 10.1128/microbiolspec.plas-0005-2013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rhizobia are Gram-negative Alpha- and Betaproteobacteria living in the underground which have the ability to associate with legumes for the establishment of nitrogen-fixing symbioses. Sinorhizobium meliloti in particular-the symbiont of Medicago, Melilotus, and Trigonella spp.-has for the past decades served as a model organism for investigating, at the molecular level, the biology, biochemistry, and genetics of a free-living and symbiotic soil bacterium of agricultural relevance. To date, the genomes of seven different S. meliloti strains have been fully sequenced and annotated, and several other draft genomic sequences are also available. The vast amount of plasmid DNA that S. meliloti frequently bears (up to 45% of its total genome), the conjugative ability of some of those plasmids, and the extent of the plasmid diversity has provided researchers with an extraordinary system to investigate functional and structural plasmid molecular biology within the evolutionary context surrounding a plant-associated model bacterium. Current evidence indicates that the plasmid mobilome in S. meliloti is composed of replicons varying greatly in size and having diverse conjugative systems and properties along with different evolutionary stabilities and biological roles. While plasmids carrying symbiotic functions (pSyms) are known to have high structural stability (approaching that of chromosomes), the remaining plasmid mobilome (referred to as the non-pSym, functionally cryptic, or accessory compartment) has been shown to possess remarkable diversity and to be highly active in conjugation. In light of the modern genomic and current biochemical data on the plasmids of S. meliloti, the current article revises their main structural components, their transfer and regulatory mechanisms, and their potential as vehicles in shaping the evolution of the rhizobial genome.
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31
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Lemaire B, Van Cauwenberghe J, Chimphango S, Stirton C, Honnay O, Smets E, Muasya AM. Recombination and horizontal transfer of nodulation and ACC deaminase (acdS) genes within Alpha- and Betaproteobacteria nodulating legumes of the Cape Fynbos biome. FEMS Microbiol Ecol 2015; 91:fiv118. [PMID: 26433010 DOI: 10.1093/femsec/fiv118] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2015] [Indexed: 11/14/2022] Open
Abstract
The goal of this work is to study the evolution and the degree of horizontal gene transfer (HGT) within rhizobial genera of both Alphaproteobacteria (Mesorhizobium, Rhizobium) and Betaproteobacteria (Burkholderia), originating from South African Fynbos legumes. By using a phylogenetic approach and comparing multiple chromosomal and symbiosis genes, we revealed conclusive evidence of high degrees of horizontal transfer of nodulation genes among closely related species of both groups of rhizobia, but also among species with distant genetic backgrounds (Rhizobium and Mesorhizobium), underscoring the importance of lateral transfer of symbiosis traits as an important evolutionary force among rhizobia of the Cape Fynbos biome. The extensive exchange of symbiosis genes in the Fynbos is in contrast with a lack of significant events of HGT among Burkholderia symbionts from the South American Cerrado and Caatinga biome. Furthermore, homologous recombination among selected housekeeping genes had a substantial impact on sequence evolution within Burkholderia and Mesorhizobium. Finally, phylogenetic analyses of the non-symbiosis acdS gene in Mesorhizobium, a gene often located on symbiosis islands, revealed distinct relationships compared to the chromosomal and symbiosis genes, suggesting a different evolutionary history and independent events of gene transfer. The observed events of HGT and incongruence between different genes necessitate caution in interpreting topologies from individual data types.
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Affiliation(s)
- Benny Lemaire
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 7701, Cape Town, South Africa Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, PO Box 02435, 3001 Heverlee, Belgium
| | - Jannick Van Cauwenberghe
- Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, PO Box 02435, 3001 Heverlee, Belgium Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Samson Chimphango
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 7701, Cape Town, South Africa
| | - Charles Stirton
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 7701, Cape Town, South Africa
| | - Olivier Honnay
- Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, PO Box 02435, 3001 Heverlee, Belgium
| | - Erik Smets
- Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, PO Box 02435, 3001 Heverlee, Belgium Naturalis Biodiversity Center, Leiden University, 2300 RA Leiden, the Netherlands
| | - A Muthama Muasya
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch 7701, Cape Town, South Africa
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32
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Hammerl JA, Ulrich RG, Imholt C, Scholz HC, Jacob J, Kratzmann N, Nöckler K, Al Dahouk S. Molecular Survey on Brucellosis in Rodents and Shrews - Natural Reservoirs of Novel Brucella Species in Germany? Transbound Emerg Dis 2015; 64:663-671. [PMID: 26398680 DOI: 10.1111/tbed.12425] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Indexed: 11/26/2022]
Abstract
Brucellosis is a widespread zoonotic disease introduced from animal reservoirs to humans. In Germany, bovine and ovine/caprine brucellosis were eradicated more than a decade ago and mandatory measures in livestock have been implemented to keep the officially brucellosis-free status. In contrast, surveillance of wildlife is still challenging, and reliable data on the prevalence of brucellae in small mammal populations do not exist. To assess the epidemiology of Brucella spp. in rodents and shrews, a molecular survey was carried out. A total of 537 rodents and shrews were trapped in four federal states located throughout Germany and investigated for the presence of Brucella. Using a two-step molecular assay based on the detection of the Brucella-specific bcsp31 and IS711 sequences in tissue samples, 14.2% (n = 76) of the tested animals were positive. These originated mainly from western and south-western Germany, where preliminary analyses indicate population density-dependent Brucella prevalence in voles (Myodes glareolus) and mice (Apodemus spp.). recA typing revealed a close relationship to a potentially novel Brucella species recently isolated from red foxes (Vulpes vulpes) in Austria. The molecular detection of brucellae in various rodent taxa and for the first time in shrew species shows that these animals may be naturally infected or at least have a history of exposure to Brucella spp.
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Affiliation(s)
- J A Hammerl
- Department of Biological Safety, Federal Institute for Risk Assessment, Berlin, Germany
| | - R G Ulrich
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, OIE Collaborating Centre for Zoonoses in Europe, Institute for Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
| | - C Imholt
- Julius Kühn-Institut, Federal Research Institute for Cultivated Plants, Institute for Plant Protection in Horticulture and Forests, Vertebrate Research Group, Münster, Germany
| | - H C Scholz
- Bundeswehr Institute of Microbiology, Munich, Germany.,German Center for Infection Research (DZIF), Munich, Germany
| | - J Jacob
- Julius Kühn-Institut, Federal Research Institute for Cultivated Plants, Institute for Plant Protection in Horticulture and Forests, Vertebrate Research Group, Münster, Germany
| | - N Kratzmann
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, OIE Collaborating Centre for Zoonoses in Europe, Institute for Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
| | - K Nöckler
- Department of Biological Safety, Federal Institute for Risk Assessment, Berlin, Germany
| | - S Al Dahouk
- Department of Biological Safety, Federal Institute for Risk Assessment, Berlin, Germany.,Department of Internal Medicine III, RWTH Aachen University, Aachen, Germany
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33
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Tian RM, Cai L, Zhang WP, Cao HL, Qian PY. Rare Events of Intragenus and Intraspecies Horizontal Transfer of the 16S rRNA Gene. Genome Biol Evol 2015. [PMID: 26220935 PMCID: PMC4558861 DOI: 10.1093/gbe/evv143] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Horizontal gene transfer (HGT) of operational genes has been widely reported in prokaryotic organisms. However, informational genes such as those involved in transcription and translation processes are very difficult to be horizontally transferred, as described by Woese’s complexity hypothesis. Here, we analyzed all of the completed prokaryotic genome sequences (2,143 genomes) in the NCBI (National Center for Biotechnology Information) database, scanned for genomes with high intragenomic heterogeneity of 16S rRNA gene copies, and explored potential HGT events of ribosomal RNA genes based on the phylogeny, genomic organization, and secondary structures of the ribosomal RNA genes. Our results revealed 28 genomes with relatively high intragenomic heterogeneity of multiple 16S rRNA gene copies (lowest pairwise identity <98.0%), and further analysis revealed HGT events and potential donors of the heterogeneous copies (such as HGT from Chlamydia suis to Chlamydia trachomatis) and mutation events of some heterogeneous copies (such as Streptococcus suis JS14). Interestingly, HGT of the 16S rRNA gene only occurred at intragenus or intraspecies levels, which is quite different from the HGT of operational genes. Our results improve our understanding regarding the exchange of informational genes.
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Affiliation(s)
- Ren-Mao Tian
- Division of Life Science, Hong Kong University of Science and Technology, China
| | - Lin Cai
- Division of Life Science, Hong Kong University of Science and Technology, China
| | - Wei-Peng Zhang
- Division of Life Science, Hong Kong University of Science and Technology, China
| | - Hui-Luo Cao
- Division of Life Science, Hong Kong University of Science and Technology, China
| | - Pei-Yuan Qian
- Division of Life Science, Hong Kong University of Science and Technology, China
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Phylogenetic diversity on housekeeping and symbiotic genes of rhizobial from Sphaerophysa in China. World J Microbiol Biotechnol 2015; 31:1451-9. [PMID: 26149957 DOI: 10.1007/s11274-015-1898-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 07/03/2015] [Indexed: 10/23/2022]
Abstract
This study explored the diversity and phylogeny of rhizobia collected from nodules of Sphaerophysa salsula in different geographical regions of Northwest China. The 16S rRNA gene sequences divided the strains into the following distinct groups: Mesorhizobium, Rhizobium and Shinella. The phylogenies of recA and atpD genes showed low correlation with nifH and nodA gene in most species, which indicated that, the gene recombination between species and genera might have been exist. To our knowledge, this is the first study using the multilocus sequencing analysis Sphaerophysa rhizobia in order to understand the relation between genetic diversity and ecology.
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35
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Mousavi SA, Willems A, Nesme X, de Lajudie P, Lindström K. Revised phylogeny of Rhizobiaceae: Proposal of the delineation of Pararhizobium gen. nov., and 13 new species combinations. Syst Appl Microbiol 2015; 38:84-90. [DOI: 10.1016/j.syapm.2014.12.003] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 12/07/2014] [Accepted: 12/12/2014] [Indexed: 01/26/2023]
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36
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Phylogenetic multilocus sequence analysis of native rhizobia nodulating faba bean (Vicia faba L.) in Egypt. Syst Appl Microbiol 2014; 37:560-9. [DOI: 10.1016/j.syapm.2014.10.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 10/01/2014] [Accepted: 10/03/2014] [Indexed: 11/22/2022]
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Zilli JE, Baraúna AC, da Silva K, De Meyer SE, Farias ENC, Kaminski PE, da Costa IB, Ardley JK, Willems A, Camacho NN, Dourado FDS, O'Hara G. Bradyrhizobium neotropicale sp. nov., isolated from effective nodules of Centrolobium paraense. Int J Syst Evol Microbiol 2014; 64:3950-3957. [PMID: 25205796 DOI: 10.1099/ijs.0.065458-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Root nodule bacteria were isolated from Centrolobium paraense Tul. grown in soils from the Amazon region, State of Roraima (Brazil). 16S rRNA gene sequence analysis of seven strains (BR 10247(T), BR 10296, BR 10297, BR 10298, BR 10299, BR 10300 and BR 10301) placed them in the genus Bradyrhizobium with the closest neighbours being the type strains of Bradyrhizobium paxllaeri (98.8 % similarity), Bradyrhizobium icense (98.8 %), Bradyrhizobium lablabi (98.7 %), Bradyrhizobium jicamae (98.6 %), Bradyrhizobium elkanii (98.6 %), Bradyrhizobium pachyrhizi (98.6 %) and Bradyrhizobium retamae (98.3 %). This high similarity, however, was not confirmed by the intergenic transcribed spacer (ITS) 16S-23S rRNA region sequence analysis nor by multi-locus sequence analysis. Phylogenetic analyses of five housekeeping genes (dnaK, glnII, gyrB, recA and rpoB) revealed Bradyrhizobium iriomotense EK05(T) ( = LMG 24129(T)) to be the most closely related type strain (95.7 % sequence similarity or less). Chemotaxonomic data, including fatty acid profiles [major components being C16 : 0 and summed feature 8 (18 : 1ω6c/18 : 1ω7c)], DNA G+C content, slow growth rate and carbon compound utilization patterns, supported the placement of the novel strains in the genus Bradyrhizobium. Results of DNA-DNA relatedness studies and physiological data (especially carbon source utilization) differentiated the strains from the closest recognized species of the genus Bradyrhizobium. Symbiosis-related genes for nodulation (nodC) and nitrogen fixation (nifH) placed the novel species in a new branch within the genus Bradyrhizobium. Based on the current data, these seven strains represent a novel species for which the name Bradyrhizobium neotropicale sp. nov. is proposed. The type strain is BR 10247(T) ( = HAMBI 3599(T)).
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Affiliation(s)
- Jerri E Zilli
- Embrapa Agrobiologia, Rodovia BR 465 km 07, Seropédica, Rio de Janeiro 23891-000, Brazil
| | - Alexandre C Baraúna
- Universidade Federal Rural do Rio de Janeiro, Rodovia BR 465 km 07, Seropédica, Rio de Janeiro 23890-000, Brazil
| | - Krisle da Silva
- Embrapa Roraima, Rodovia BR 174 km 08, Boa Vista, Roraima 69301-970, Brazil
| | - Sofie E De Meyer
- Laboratory of Microbiology, Department of Biochemistry and Microbiology (WE10), Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
- Centre for Rhizobium Studies, Murdoch University, 90 South Street, Murdoch 6150, Western Australia, Australia
| | - Eliane N C Farias
- Embrapa Roraima, Rodovia BR 174 km 08, Boa Vista, Roraima 69301-970, Brazil
| | - Paulo E Kaminski
- Embrapa Roraima, Rodovia BR 174 km 08, Boa Vista, Roraima 69301-970, Brazil
| | - Ismaele B da Costa
- Embrapa Roraima, Rodovia BR 174 km 08, Boa Vista, Roraima 69301-970, Brazil
| | - Julie K Ardley
- Centre for Rhizobium Studies, Murdoch University, 90 South Street, Murdoch 6150, Western Australia, Australia
| | - Anne Willems
- Laboratory of Microbiology, Department of Biochemistry and Microbiology (WE10), Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Natália N Camacho
- Embrapa Agrobiologia, Rodovia BR 465 km 07, Seropédica, Rio de Janeiro 23891-000, Brazil
| | - Fernanda Dos S Dourado
- Embrapa Agrobiologia, Rodovia BR 465 km 07, Seropédica, Rio de Janeiro 23891-000, Brazil
| | - Graham O'Hara
- Centre for Rhizobium Studies, Murdoch University, 90 South Street, Murdoch 6150, Western Australia, Australia
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Zhao L, Fan M, Zhang D, Yang R, Zhang F, Xu L, Wei X, Shen Y, Wei G. Distribution and diversity of rhizobia associated with wild soybean (Glycine soja Sieb. & Zucc.) in Northwest China. Syst Appl Microbiol 2014; 37:449-56. [PMID: 25052953 DOI: 10.1016/j.syapm.2014.05.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 05/18/2014] [Accepted: 05/19/2014] [Indexed: 10/25/2022]
Abstract
A total of 155 nodule isolates that originated from seven sites in Northwest China were characterized by PCR-RFLP of the 16S rRNA gene and sequence analysis of multiple core genes (16S rRNA, recA, atpD, and glnII) in order to investigate the diversity and biogeography of Glycine soja-nodulating rhizobia. Among the isolates, 80 were Ensifer fredii, 19 were Ensifer morelense, 49 were Rhizobium radiobacter, and 7 were putative novel Rhizobium species. The phylogenies of E. fredii and E. morelense isolates in a concatenate tree (assembly of all housekeeping genes) were generally consistent with those in individual gene trees. However, incongruence was found in the phylogenies of the different genes of Rhizobium isolates, indicating that lateral transfer or recombination possibly occurred in these gene loci. Despite their species identity, all the isolates in this study formed a single lineage related to E. fredii in nodAand nifH gene phylogenies, which also indicated that the symbiotic genes were laterally transferred between different species. Biogeographic patterns were found at the species and strain genomic type levels, as revealed by BOXA1R fingerprinting, demonstrating that the evolution of rhizobial populations in different geographic locations was related to soil types, altitude and spatial effects. This study is the first to report that E. morelense, R. radiobacter, and Rhizobium sp. are microsymbionts of G. soja, as well as showing that the diversity of G. soja rhizobia is enhanced and new rhizobia have evolved in Northwest China.
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Affiliation(s)
- Liang Zhao
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Miaochun Fan
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dehui Zhang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ruiping Yang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Feilong Zhang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lin Xu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiuli Wei
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yaoyao Shen
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Gehong Wei
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.
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Intracellular diversity of the V4 and V9 regions of the 18S rRNA in marine protists (radiolarians) assessed by high-throughput sequencing. PLoS One 2014; 9:e104297. [PMID: 25090095 PMCID: PMC4121268 DOI: 10.1371/journal.pone.0104297] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 07/12/2014] [Indexed: 11/25/2022] Open
Abstract
Metabarcoding is a powerful tool for exploring microbial diversity in the environment, but its accurate interpretation is impeded by diverse technical (e.g. PCR and sequencing errors) and biological biases (e.g. intra-individual polymorphism) that remain poorly understood. To help interpret environmental metabarcoding datasets, we investigated the intracellular diversity of the V4 and V9 regions of the 18S rRNA gene from Acantharia and Nassellaria (radiolarians) using 454 pyrosequencing. Individual cells of radiolarians were isolated, and PCRs were performed with generalist primers to amplify the V4 and V9 regions. Different denoising procedures were employed to filter the pyrosequenced raw amplicons (Acacia, AmpliconNoise, Linkage method). For each of the six isolated cells, an average of 541 V4 and 562 V9 amplicons assigned to radiolarians were obtained, from which one numerically dominant sequence and several minor variants were found. At the 97% identity, a diversity metrics commonly used in environmental surveys, up to 5 distinct OTUs were detected in a single cell. However, most amplicons grouped within a single OTU whereas other OTUs contained very few amplicons. Different analytical methods provided evidence that most minor variants forming different OTUs correspond to PCR and sequencing artifacts. Duplicate PCR and sequencing from the same DNA extract of a single cell had only 9 to 16% of unique amplicons in common, and alignment visualization of V4 and V9 amplicons showed that most minor variants contained substitutions in highly-conserved regions. We conclude that intracellular variability of the 18S rRNA in radiolarians is very limited despite its multi-copy nature and the existence of multiple nuclei in these protists. Our study recommends some technical guidelines to conservatively discard artificial amplicons from metabarcoding datasets, and thus properly assess the diversity and richness of protists in the environment.
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Lateral transfer of eukaryotic ribosomal RNA genes: an emerging concern for molecular ecology of microbial eukaryotes. ISME JOURNAL 2014; 8:1544-7. [PMID: 24451210 PMCID: PMC4069394 DOI: 10.1038/ismej.2013.252] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Revised: 12/19/2013] [Accepted: 12/20/2013] [Indexed: 11/20/2022]
Abstract
Ribosomal RNA (rRNA) genes are widely utilized in depicting organismal diversity and distribution in a wide range of environments. Although a few cases of lateral transfer of rRNA genes between closely related prokaryotes have been reported, it remains to be reported from eukaryotes. Here, we report the first case of lateral transfer of eukaryotic rRNA genes. Two distinct sequences of the 18S rRNA gene were detected from a clonal culture of the stramenopile, Ciliophrys infusionum. One was clearly derived from Ciliophrys, but the other gene originated from a perkinsid alveolate. Genome-walking analyses revealed that this alveolate-type rRNA gene is immediately adjacent to two protein-coding genes (ubc12 and usp39), and the origin of both genes was shown to be a stramenopile (that is, Ciliophrys) in our phylogenetic analyses. These findings indicate that the alveolate-type rRNA gene is encoded on the Ciliophrys genome and that eukaryotic rRNA genes can be transferred laterally.
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Radl V, Simões-Araújo JL, Leite J, Passos SR, Martins LMV, Xavier GR, Rumjanek NG, Baldani JI, Zilli JE. Microvirga vignae sp. nov., a root nodule symbiotic bacterium isolated from cowpea grown in semi-arid Brazil. Int J Syst Evol Microbiol 2013; 64:725-730. [PMID: 24179178 DOI: 10.1099/ijs.0.053082-0] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
16S rRNA gene sequence analysis of eight strains (BR 3299(T), BR 3296, BR 10192, BR 10193, BR 10194, BR 10195, BR 10196 and BR 10197) isolated from nodules of cowpea collected from a semi-arid region of Brazil showed 97 % similarity to sequences of recently described rhizobial species of the genus Microvirga. Phylogenetic analyses of four housekeeping genes (gyrB, recA, dnaK and rpoB), DNA-DNA relatedness and AFLP further indicated that these strains belong to a novel species within the genus Microvirga. Our data support the hypothesis that genes related to nitrogen fixation were obtained via horizontal gene transfer, as sequences of nifH genes were very similar to those found in members of the genera Rhizobium and Mesorhizobium, which are not immediate relatives of the genus Microvirga, as shown by 16S rRNA gene sequence analysis. Phenotypic traits, such as host range and carbon utilization, differentiate the novel strains from the most closely related species, Microvirga lotononidis, Microvirga zambiensis and Microvirga lupini. Therefore, these symbiotic nitrogen-fixing bacteria are proposed to be representatives of a novel species, for which the name Microvirga vignae sp. nov. is suggested. The type strain is BR3299(T) ( = HAMBI 3457(T)).
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Affiliation(s)
- Viviane Radl
- Embrapa Agrobiologia, Rodovia BR 465 km 07, Seropédica 23891-000, Brazil
| | | | - Jakson Leite
- Departamento de Solos - Universidade Federal Rural do Rio de Janeiro, Rodovia BR 465 km 07, Seropédica 23891-000, Brazil
| | - Samuel Ribeiro Passos
- Departamento de Solos - Universidade Federal Rural do Rio de Janeiro, Rodovia BR 465 km 07, Seropédica 23891-000, Brazil
| | - Lindete Míria Vieira Martins
- Universidade do Estado da Bahia (UNEB), Departmento de Tecnologia e Ciências Sociais. Avenida Edgard Chastinet, s/n, Juazeiro 48900-000, Brazil
| | | | | | - José Ivo Baldani
- Embrapa Agrobiologia, Rodovia BR 465 km 07, Seropédica 23891-000, Brazil
| | - Jerri Edson Zilli
- Embrapa Agrobiologia, Rodovia BR 465 km 07, Seropédica 23891-000, Brazil
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Roch S, Snir S. Recovering the treelike trend of evolution despite extensive lateral genetic transfer: a probabilistic analysis. J Comput Biol 2013; 20:93-112. [PMID: 23383996 DOI: 10.1089/cmb.2012.0234] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Lateral gene transfer (LGT) is a common mechanism of nonvertical evolution, during which genetic material is transferred between two more or less distantly related organisms. It is particularly common in bacteria where it contributes to adaptive evolution with important medical implications. In evolutionary studies, LGT has been shown to create widespread discordance between gene trees as genomes become mosaics of gene histories. In particular, the Tree of Life has been questioned as an appropriate representation of bacterial evolutionary history. Nevertheless a common hypothesis is that prokaryotic evolution is primarily treelike, but that the underlying trend is obscured by LGT. Extensive empirical work has sought to extract a common treelike signal from conflicting gene trees. Here we give a probabilistic perspective on the problem of recovering the treelike trend despite LGT. Under a model of randomly distributed LGT, we show that the species phylogeny can be reconstructed even in the presence of surprisingly many (almost linear number of) LGT events per gene tree. Our results, which are optimal up to logarithmic factors, are based on the analysis of a robust, computationally efficient reconstruction method and provides insight into the design of such methods. Finally, we show that our results have implications for the discovery of highways of gene sharing.
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Affiliation(s)
- Sebastien Roch
- Department of Mathematics and Bioinformatics Program, University of California at Los Angeles, Los Angeles, CA, USA.
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Polyphasic characterization of rhizobia isolated from Leucaena leucocephala from Panxi, China. World J Microbiol Biotechnol 2013; 29:2303-15. [PMID: 23749221 DOI: 10.1007/s11274-013-1396-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 05/31/2013] [Indexed: 10/26/2022]
Abstract
Leucaena leucocephala was introduced into Panxi, Sichuan, China, in the 1980s and 1990s for afforestation and preventing water loss and soil erosion in this area. The co-introduction of rhizobial symbionts of introduced plants has drawn attention since they may influence local soil communities. We studied the phylogenetic position of the L. leucocephala isolates and assessed if the rhizobia were introduced together with the host to Panxi, Sichuan, China. The glnII and atpD genes of fifteen representative isolates were sequenced and analyzed, and applied multilocus sequence analyses in which the housekeeping genes recA, glnII and atpD were included. Furthermore, we estimated the within species diversity directly with 23S rDNA and IGS RFLP and indirectly through phenotypic analysis of forty L. leucocephala isolates. The isolates represented seven species and 38 diversified strains in the genera Ensifer, Mesorhizobium, Bradyrhizobium and Rhizobium. The within species diversity of the Ensifer isolates was large, proposing a potential to occupy novel niches. There was not conclusive evidence to show that any of the strains would have been co-introduced with L. leucocephala. On the contrary, we came to a conclusion that the possible introduction should not be inferred from sequence data alone.
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Gupta V, Ratha SK, Sood A, Chaudhary V, Prasanna R. New insights into the biodiversity and applications of cyanobacteria (blue-green algae)—Prospects and challenges. ALGAL RES 2013. [DOI: 10.1016/j.algal.2013.01.006] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Aserse AA, Räsänen LA, Aseffa F, Hailemariam A, Lindström K. Phylogenetically diverse groups of Bradyrhizobium isolated from nodules of Crotalaria spp., Indigofera spp., Erythrina brucei and Glycine max growing in Ethiopia. Mol Phylogenet Evol 2012; 65:595-609. [PMID: 22842091 DOI: 10.1016/j.ympev.2012.07.008] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 07/09/2012] [Accepted: 07/14/2012] [Indexed: 12/16/2022]
Abstract
Ethiopian Bradyrhizobium strains isolated from root nodules of Crotalaria spp., Indigofera spp., Erythina brucei and soybean (Glycine max) represented genetically diverse phylogenetic groups of the genus Bradyrhizobium. Strains were characterized using the amplified fragment length polymorphism fingerprinting technique (AFLP) and multilocus sequence analysis (MLSA) of core and symbiotic genes. Based on phylogenetic analyses of concatenated recA-glnII-rpoB-16S rRNA genes sequences, Bradyrhizobium strains were distributed into fifteen phylogenetic groups under B. japonicum and B. elkanii super clades. Some of the isolates belonged to the species B. yuanmingense, B. elkanii and B. japonicum type I. However, the majority of the isolates represented unnamed Bradyrhizobium genospecies and of these, two unique lineages that most likely represent novel Bradyrhizobium species were identified among Ethiopian strains. The nodulation nodA gene sequence analysis revealed that all Ethiopian Bradyrhizobium isolates belonged to nodA sub-clade III.3. Strains were further classified into 14 groups together with strains from Africa, as well as some originating from the other tropical and subtropics regions. Strains were also clustered into 14 groups in nodY/K phylogeny similarly to the nodA tree. The nifH phylogenies of the Ethiopian Bradyrhizobium were generally also congruent with the nodA gene phylogeny, supporting the monophyletic origin of the symbiotic genes in Bradyrhizobium. The phylogenies of nodA and nifH genes were also partially congruent with that inferred from the concatenated core genes sequences, reflecting that the strains obtained their symbiotic genes vertically from their ancestor as well as horizontally from more distantly related Bradyrhizobium species.
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Affiliation(s)
- Aregu Amsalu Aserse
- University of Helsinki, Department of Food and Environmental Sciences, POB 56, FIN-00014 Helsinki, Finland.
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Roger F, Lamy B, Jumas-Bilak E, Kodjo A, Marchandin H. Ribosomal multi-operon diversity: an original perspective on the genus Aeromonas. PLoS One 2012; 7:e46268. [PMID: 23032081 PMCID: PMC3459834 DOI: 10.1371/journal.pone.0046268] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 08/28/2012] [Indexed: 12/31/2022] Open
Abstract
16S rRNA gene (rrs) is considered of low taxonomic interest in the genus Aeromonas. Here, 195 Aeromonas strains belonging to populations structured by multilocus phylogeny were studied using an original approach that considered Ribosomal Multi-Operon Diversity. This approach associated pulsed-field gel electrophoresis (PFGE) to assess rrn operon number and distribution across the chromosome and PCR-temporal temperature gel electrophoresis (TTGE) to assess rrs V3 region heterogeneity. Aeromonads harbored 8 to 11 rrn operons, 10 operons being observed in more than 92% of the strains. Intraspecific variability was low or nul except for A. salmonicida and A. aquariorum suggesting that large chromosomic rearrangements might occur in these two species while being extremely rarely encountered in the evolution of other taxa. rrn operon number at 8 as well as PFGE patterns were shown valuable for taxonomic purpose allowing resolution of species complexes. PCR-TTGE revealed a high rate of strains (41.5%) displaying intragenomic rrs heterogeneity. Strains isolated from human samples more frequently displayed intragenomic heterogeneity than strains recovered from non-human and environmental specimens. Intraspecific variability ranged from 0 to 76.5% of the strains. The observation of species-specific TTGE bands, the recovery of identical V3 regions in different species and the variability of intragenomic heterogeneity (1-13 divergent nucleotides) supported the occurrence of mutations and horizontal transfer in aeromonad rrs evolution. Altogether, the presence of a high number of rrn operon, the high proportion of strains harboring divergent rrs V3 region and the previously demonstrated high level of genetic diversity argued in favor of highly adaptative capabilities of aeromonads. Outstanding features observed for A. caviae supported the ongoing process of adaptation to a specialized niche represented by the gut, previously hypothesized. 16S rRNA gene is an informative marker in the genus Aeromonas for both evolutionary and polyphasic taxonomic studies provided that multi-operon fingerprinting approaches are used.
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Affiliation(s)
- Frédéric Roger
- UMR 5119 ECOSYM, Equipe Pathogènes et Environnements, U.F.R. des Sciences Pharmaceutiques et Biologiques, Université Montpellier 1, Montpellier, France
| | - Brigitte Lamy
- UMR 5119 ECOSYM, Equipe Pathogènes et Environnements, U.F.R. des Sciences Pharmaceutiques et Biologiques, Université Montpellier 1, Montpellier, France
- Laboratoire de Bactériologie, Hôpital Arnaud de Villeneuve, Centre Hospitalier Régional Universitaire de Montpellier, Montpellier, France
- Groupe d’Etude Français des Aeromonas (GFA), Lyon, France
| | - Estelle Jumas-Bilak
- UMR 5119 ECOSYM, Equipe Pathogènes et Environnements, U.F.R. des Sciences Pharmaceutiques et Biologiques, Université Montpellier 1, Montpellier, France
- Laboratoire d’Hygiène hospitalière, Centre Hospitalier Régional Universitaire de Montpellier, Montpellier, France
| | - Angeli Kodjo
- Groupe d’Etude Français des Aeromonas (GFA), Lyon, France
- CNRS UMR 5557 Ecologie microbienne, VetAgro Sup Campus vétérinaire de Lyon, Université Claude Bernard Lyon 1, Marcy-l’Étoile, France
| | | | - Hélène Marchandin
- UMR 5119 ECOSYM, Equipe Pathogènes et Environnements, U.F.R. des Sciences Pharmaceutiques et Biologiques, Université Montpellier 1, Montpellier, France
- Laboratoire de Bactériologie, Hôpital Arnaud de Villeneuve, Centre Hospitalier Régional Universitaire de Montpellier, Montpellier, France
- * E-mail:
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Porter SS, Rice KJ. TRADE-OFFS, SPATIAL HETEROGENEITY, AND THE MAINTENANCE OF MICROBIAL DIVERSITY. Evolution 2012; 67:599-608. [DOI: 10.1111/j.1558-5646.2012.01788.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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48
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Laranjo M, Young JPW, Oliveira S. Multilocus sequence analysis reveals multiple symbiovars within Mesorhizobium species. Syst Appl Microbiol 2012; 35:359-67. [DOI: 10.1016/j.syapm.2012.06.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 06/07/2012] [Accepted: 06/09/2012] [Indexed: 10/28/2022]
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49
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Symbiotic efficiency and phylogeny of the rhizobia isolated from Leucaena leucocephala in arid–hot river valley area in Panxi, Sichuan, China. Appl Microbiol Biotechnol 2012; 97:783-93. [DOI: 10.1007/s00253-012-4246-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 06/12/2012] [Accepted: 06/14/2012] [Indexed: 11/30/2022]
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50
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Ramírez-Bahena MH, Hernández M, Peix Á, Velázquez E, León-Barrios M. Mesorhizobial strains nodulating Anagyris latifolia and Lotus berthelotii in Tamadaya ravine (Tenerife, Canary Islands) are two symbiovars of the same species, Mesorhizobium tamadayense sp. nov. Syst Appl Microbiol 2012; 35:334-41. [DOI: 10.1016/j.syapm.2012.05.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 04/25/2012] [Accepted: 05/06/2012] [Indexed: 10/28/2022]
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