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Royo-Llonch M, Ferrera I, Cornejo-Castillo FM, Sánchez P, Salazar G, Stepanauskas R, González JM, Sieracki ME, Speich S, Stemmann L, Pedrós-Alió C, Acinas SG. Exploring Microdiversity in Novel Kordia sp. (Bacteroidetes) with Proteorhodopsin from the Tropical Indian Ocean via Single Amplified Genomes. Front Microbiol 2017; 8:1317. [PMID: 28790980 PMCID: PMC5525439 DOI: 10.3389/fmicb.2017.01317] [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: 02/10/2017] [Accepted: 06/29/2017] [Indexed: 12/03/2022] Open
Abstract
Marine Bacteroidetes constitute a very abundant bacterioplankton group in the oceans that plays a key role in recycling particulate organic matter and includes several photoheterotrophic members containing proteorhodopsin. Relatively few marine Bacteroidetes species have been described and, moreover, they correspond to cultured isolates, which in most cases do not represent the actual abundant or ecologically relevant microorganisms in the natural environment. In this study, we explored the microdiversity of 98 Single Amplified Genomes (SAGs) retrieved from the surface waters of the underexplored North Indian Ocean, whose most closely related isolate is Kordia algicida OT-1. Using Multi Locus Sequencing Analysis (MLSA) we found no microdiversity in the tested conserved phylogenetic markers (16S rRNA and 23S rRNA genes), the fast-evolving Internal Transcribed Spacer and the functional markers proteorhodopsin and the beta-subunit of RNA polymerase. Furthermore, we carried out a Fragment Recruitment Analysis (FRA) with marine metagenomes to learn about the distribution and dynamics of this microorganism in different locations, depths and size fractions. This analysis indicated that this taxon belongs to the rare biosphere, showing its highest abundance after upwelling-induced phytoplankton blooms and sinking to the deep ocean with large organic matter particles. This uncultured Kordia lineage likely represents a novel Kordia species (Kordia sp. CFSAG39SUR) that contains the proteorhodopsin gene and has a widespread spatial and vertical distribution. The combination of SAGs and MLSA makes a valuable approach to infer putative ecological roles of uncultured abundant microorganisms.
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Affiliation(s)
- Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones CientíficasBarcelona, Spain
| | - Isabel Ferrera
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones CientíficasBarcelona, Spain
| | - Francisco M Cornejo-Castillo
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones CientíficasBarcelona, Spain
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones CientíficasBarcelona, Spain
| | - Guillem Salazar
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones CientíficasBarcelona, Spain
| | | | - José M González
- Department of Microbiology, University of La LagunaLa Laguna, Spain
| | | | - Sabrina Speich
- École Normale Supérieure, Département de Géosciences, Laboratoire de Météorologie Dynamique, UMR 8539 ENS-CNRS- École PolytechniqueParis, France
| | - Lars Stemmann
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire d'Océanographie de Villefranche (LOV) UMR7093, Observatoire OcéanologiqueVillefranche-sur-Mer, France
| | - Carlos Pedrós-Alió
- Systems Biology Program, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones CientíficasBarcelona, Spain.,Departament de Genética i de Microbiologia, Facultat de Biociències, Universitat Autònoma de BarcelonaBellaterra, Spain
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202
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The rhizosphere microbiome of burned holm-oak: potential role of the genus Arthrobacter in the recovery of burned soils. Sci Rep 2017; 7:6008. [PMID: 28729641 PMCID: PMC5519729 DOI: 10.1038/s41598-017-06112-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 06/08/2017] [Indexed: 12/17/2022] Open
Abstract
After a forest wildfire, the microbial communities have a transient alteration in their composition. The role of the soil microbial community in the recovery of an ecosystem following such an event remains poorly understood. Thus, it is necessary to understand the plant-microbe interactions that occur in burned soils. By high-throughput sequencing, we identified the main bacterial taxa of burnt holm-oak rhizosphere, then we obtained an isolate collection of the most abundant genus and its growth promoting activities were characterised. 16S rRNA amplicon sequencing showed that the genus Arthrobacter comprised more than 21% of the total community. 55 Arthrobacter strains were isolated and characterized using RAPDs and sequencing of the almost complete 16S rRNA gene. Our results indicate that isolated Arthrobacter strains present a very high genetic diversity, and they could play an important ecological role in interaction with the host plant by enhancing aerial growth. Most of the selected strains exhibited a great ability to degrade organic polymers in vitro as well as possibly presenting a direct mechanism for plant growth promotion. All the above data suggests that Arthrobacter can be considered as an excellent PGP rhizobacterium that may play an important role in the recovery of burned holm-oak forests.
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203
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Liu Y, Lai Q, Shao Z. A Multilocus Sequence Analysis Scheme for Phylogeny of Thioclava Bacteria and Proposal of Two Novel Species. Front Microbiol 2017; 8:1321. [PMID: 28751885 PMCID: PMC5508018 DOI: 10.3389/fmicb.2017.01321] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 06/29/2017] [Indexed: 11/13/2022] Open
Abstract
A multilocus sequence analysis (MLSA) was established and performed on the genus Thioclava, including 23 strains isolated from diverse marine environments, with the aim of better differentiation of strains and species within this genus. The study was based on sequences of 16S rRNA gene and five protein-coding housekeeping genes, gyrB, rpoD, dnaK, trpB, and recA. In contrast to 16S rRNA gene-based tree that was unable to separate some species within this genus, each tree based on a single housekeeping gene and MLSA had consistently defined seven clades, corresponding to the five established ones and two novel ones. The digital DNA-DNA hybridization and average nucleotide identity analyses based on genome sequences of the representative strains reconfirmed the validity of the MLSA analysis, and recommended a 97.3% MLSA similarity as the soft species threshold and nine species representing the five known and four putative novel species. Two of the four new species were identified as Thioclava sediminum sp. nov. (type strain TAW-CT134T = MCCC 1A10143T = LMG 29615T) and Thioclava marinus sp. nov. (type strain 11.10-0-13T = MCCC 1A03502T = LMG 29618T) by using a polyphasic taxonomic approach. Taken together, the newly established MLSA in this study first described the variability and phylogeny of the genus Thioclava which contributes to better understanding its ecology and evolution.
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Affiliation(s)
- Yang Liu
- School of Municipal and Environmental Engineering, Harbin Institute of TechnologyHarbin, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian ProvinceXiamen, China
| | - Qiliang Lai
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian ProvinceXiamen, China
| | - Zongze Shao
- School of Municipal and Environmental Engineering, Harbin Institute of TechnologyHarbin, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian ProvinceXiamen, China
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204
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Kook JK, Park SN, Lim YK, Cho E, Jo E, Roh H, Shin Y, Paek J, Kim HS, Kim H, Shin JH, Chang YH. Genome-Based Reclassification of Fusobacterium nucleatum Subspecies at the Species Level. Curr Microbiol 2017; 74:1137-1147. [PMID: 28687946 DOI: 10.1007/s00284-017-1296-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 06/29/2017] [Indexed: 10/19/2022]
Abstract
Fusobacterium nucleatum is classified as four subspecies, subsp. nucleatum, polymorphum, vincentii, and animalis, based on DNA-DNA hybridization (DDH) patterns, phenotypic characteristics, and/or multilocus sequence analysis (MLSA). The gold standards for classification of bacterial species are DDH and 16S ribosomal RNA gene (16S rDNA) sequence homology. The thresholds of DDH and 16S rDNA similarity for delineation of bacterial species have been suggested to be >70 and 98.65%, respectively. Average nucleotide identity (ANI) and genome-to-genome distance (GGD) analysis based on genome sequences were recently introduced as a replacement for DDH to delineate bacterial species with ANI (95-96%) and GGD (70%) threshold values. In a previous study, F. hwasookii was classified as a new species based on MLSA and DDH results. 16S rDNA similarity between F. hwasookii type strain and F. nucleatum subspecies type strains was higher than that between F. nucleatum subspecies type strains. Therefore, it is possible that the four F. nucleatum subspecies can be classified as Fusobacterium species. In this study, we performed ANI and GGD analyses using the genome sequences of 36 F. nucleatum, five F. hwasookii, and one Fusobacterium periodonticum strain to determine whether the four F. nucleatum subspecies could be classified as species using OrthoANI and ANI web-based softwares provided by ChunLab and Kostas lab, respectively, and GGD calculator offered by German Collection of Microorganisms and Cell Cultures. ANI values calculated from OrthoANI and ANI calculators between the type strains of F. nucleatum subspecies ranged from 89.80 to 92.97 and from 90.40 to 91.90%, respectively. GGD values between the type strains of F. nucleatum subspecies ranged from 42.3 to 46.0%. ANI and GGD values among strains belonging to the same F. nucleatum subspecies, subsp. nucleatum, subsp. polymorphum, subsp. vincentii, and subsp. animalis were >96 and >68.2%, respectively. These results strongly suggest that F. nucleatum subsp. nucleatum, subsp. polymorphum, subsp. vincentii, and subsp. animalis should be classified as F. nucleatum, F. polymorphum, F. vincentii, and F. animalis, respectively.
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Affiliation(s)
- Joong-Ki Kook
- Korean Collection for Oral Microbiology, Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea. .,Oral Biology Research Institute, Chosun University, Gwangju, Republic of Korea.
| | - Soon-Nang Park
- Korean Collection for Oral Microbiology, Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Yun Kyong Lim
- Korean Collection for Oral Microbiology, Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Eugene Cho
- Korean Collection for Oral Microbiology, Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Eojin Jo
- Korean Collection for Oral Microbiology, Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | | | - Yeseul Shin
- ABS Research Support Center, KRIBB, Daejeon, Republic of Korea
| | - Jayoung Paek
- ABS Research Support Center, KRIBB, Daejeon, Republic of Korea
| | - Hwa-Sook Kim
- Department of Dental Hygiene, Chunnam Techno University, Gokseong-gun, Chunnam, Republic of Korea
| | - Hongik Kim
- Vitabio, Inc., Daejeon, Republic of Korea
| | - Jeong Hwan Shin
- Department of Laboratory Medicine, Inje University College of Medicine, Busan, Republic of Korea
| | - Young-Hyo Chang
- ABS Research Support Center, KRIBB, Daejeon, Republic of Korea.
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205
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Evolution of the Staphylococcus argenteus ST2250 Clone in Northeastern Thailand Is Linked with the Acquisition of Livestock-Associated Staphylococcal Genes. mBio 2017; 8:mBio.00802-17. [PMID: 28679748 PMCID: PMC5573676 DOI: 10.1128/mbio.00802-17] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Staphylococcus argenteus is a newly named species previously described as a divergent lineage of Staphylococcus aureus that has recently been shown to have a global distribution. Despite growing evidence of the clinical importance of this species, knowledge about its population epidemiology and genomic architecture is limited. We used whole-genome sequencing to evaluate and compare S. aureus (n = 251) and S. argenteus (n = 68) isolates from adults with staphylococcal sepsis at several hospitals in northeastern Thailand between 2006 and 2013. The majority (82%) of the S. argenteus isolates were of multilocus sequence type 2250 (ST2250). S. aureus was more diverse, although 43% of the isolates belonged to ST121. Bayesian analysis suggested an S. argenteus ST2250 substitution rate of 4.66 (95% confidence interval [CI], 3.12 to 6.38) mutations per genome per year, which was comparable to the S. aureus ST121 substitution rate of 4.07 (95% CI, 2.61 to 5.55). S. argenteus ST2250 emerged in Thailand an estimated 15 years ago, which contrasts with the S. aureus ST1, ST88, and ST121 clades that emerged around 100 to 150 years ago. Comparison of S. argenteus ST2250 genomes from Thailand and a global collection indicated a single introduction into Thailand, followed by transmission to local and more distant countries in Southeast Asia and further afield. S. argenteus and S. aureus shared around half of their core gene repertoire, indicating a high level of divergence and providing strong support for their classification as separate species. Several gene clusters were present in ST2250 isolates but absent from the other S. argenteus and S. aureus study isolates. These included multiple exotoxins and antibiotic resistance genes that have been linked previously with livestock-associated S. aureus, consistent with a livestock reservoir for S. argenteus. These genes appeared to be associated with plasmids and mobile genetic elements and may have contributed to the biological success of ST2250. In this study, we used whole-genome sequencing to understand the genome evolution and population structure of a systematic collection of ST2250 S. argenteus isolates. A newly identified ancestral species of S. aureus, S. argenteus has become increasingly known as a clinically important species that has been reported recently across various countries. Our results indicate that S. argenteus has spread at a relatively rapid pace over the past 2 decades across northeastern Thailand and acquired multiple exotoxin and antibiotic resistance genes that have been linked previously with livestock-associated S. aureus. Our findings highlight the clinical importance and potential pathogenicity of S. argenteus as a recently emerging pathogen.
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206
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Beukes CW, Palmer M, Manyaka P, Chan WY, Avontuur JR, van Zyl E, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Daum C, Shapiro N, Markowitz V, Ivanova N, Kyrpides N, Woyke T, Blom J, Whitman WB, Venter SN, Steenkamp ET. Genome Data Provides High Support for Generic Boundaries in Burkholderia Sensu Lato. Front Microbiol 2017; 8:1154. [PMID: 28694797 PMCID: PMC5483467 DOI: 10.3389/fmicb.2017.01154] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 06/07/2017] [Indexed: 12/21/2022] Open
Abstract
Although the taxonomy of Burkholderia has been extensively scrutinized, significant uncertainty remains regarding the generic boundaries and composition of this large and heterogeneous taxon. Here we used the amino acid and nucleotide sequences of 106 conserved proteins from 92 species to infer robust maximum likelihood phylogenies with which to investigate the generic structure of Burkholderia sensu lato. These data unambiguously supported five distinct lineages, of which four correspond to Burkholderia sensu stricto and the newly introduced genera Paraburkholderia, Caballeronia, and Robbsia. The fifth lineage was represented by P. rhizoxinica. Based on these findings, we propose 13 new combinations for those species previously described as members of Burkholderia but that form part of Caballeronia. These findings also suggest revision of the taxonomic status of P. rhizoxinica as it is does not form part of any of the genera currently recognized in Burkholderia sensu lato. From a phylogenetic point of view, Burkholderia sensu stricto has a sister relationship with the Caballeronia+Paraburkholderia clade. Also, the lineages represented by P. rhizoxinica and R. andropogonis, respectively, emerged prior to the radiation of the Burkholderia sensu stricto+Caballeronia+Paraburkholderia clade. Our findings therefore constitute a solid framework, not only for supporting current and future taxonomic decisions, but also for studying the evolution of this assemblage of medically, industrially and agriculturally important species.
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Affiliation(s)
- Chrizelle W Beukes
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Marike Palmer
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Puseletso Manyaka
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Wai Y Chan
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Juanita R Avontuur
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Elritha van Zyl
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | | | - Alicia Clum
- DOE Joint Genome Institute, Walnut CreekCA, United States
| | - Manoj Pillay
- DOE Joint Genome Institute, Walnut CreekCA, United States
| | | | - Neha Varghese
- DOE Joint Genome Institute, Walnut CreekCA, United States
| | | | | | - T B K Reddy
- DOE Joint Genome Institute, Walnut CreekCA, United States
| | - Chris Daum
- DOE Joint Genome Institute, Walnut CreekCA, United States
| | - Nicole Shapiro
- DOE Joint Genome Institute, Walnut CreekCA, United States
| | | | | | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut CreekCA, United States
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut CreekCA, United States
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University GiessenGiessen, Germany
| | - William B Whitman
- Department of Microbiology, University of Georgia, AthensGA, United States
| | - Stephanus N Venter
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Emma T Steenkamp
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
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207
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Jimenez-Infante F, Ngugi DK, Vinu M, Blom J, Alam I, Bajic VB, Stingl U. Genomic characterization of two novel SAR11 isolates from the Red Sea, including the first strain of the SAR11 Ib clade. FEMS Microbiol Ecol 2017. [DOI: 10.1093/femsec/fix083] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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208
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Louca S, Jacques SMS, Pires APF, Leal JS, González AL, Doebeli M, Farjalla VF. Functional structure of the bromeliad tank microbiome is strongly shaped by local geochemical conditions. Environ Microbiol 2017; 19:3132-3151. [PMID: 28488752 DOI: 10.1111/1462-2920.13788] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 04/24/2017] [Indexed: 11/27/2022]
Abstract
Phytotelmata in tank-forming Bromeliaceae plants are regarded as potential miniature models for aquatic ecology, but detailed investigations of their microbial communities are rare. Hence, the biogeochemistry in bromeliad tanks remains poorly understood. Here we investigate the structure of bacterial and archaeal communities inhabiting the detritus within the tanks of two bromeliad species, Aechmea nudicaulis and Neoregelia cruenta, from a Brazilian sand dune forest. We used metagenomic sequencing for functional community profiling and 16S sequencing for taxonomic profiling. We estimated the correlation between functional groups and various environmental variables, and compared communities between bromeliad species. In all bromeliads, microbial communities spanned a metabolic network adapted to oxygen-limited conditions, including all denitrification steps, ammonification, sulfate respiration, methanogenesis, reductive acetogenesis and anoxygenic phototrophy. Overall, CO2 reducers dominated in abundance over sulfate reducers, and anoxygenic phototrophs largely outnumbered oxygenic photoautotrophs. Functional community structure correlated strongly with environmental variables, between and within a single bromeliad species. Methanogens and reductive acetogens correlated with detrital volume and canopy coverage, and exhibited higher relative abundances in N. cruenta. A comparison of bromeliads to freshwater lake sediments and soil from around the world, revealed stark differences in terms of taxonomic as well as functional microbial community structure.
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Affiliation(s)
- Stilianos Louca
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.,Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Saulo M S Jacques
- Department of Ecology, Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Programa de Pós-Graduação em Ecologia e Evolução, Universidade Estadual do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Aliny P F Pires
- Department of Ecology, Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Juliana S Leal
- Department of Ecology, Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Programa de Pós-Graduação em Ecologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Angélica L González
- Biology Department & Center for Computational & Integrative Biology, Rutgers University, Camden, NJ, USA
| | - Michael Doebeli
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.,Department of Zoology, University of British Columbia, Vancouver, BC, Canada.,Department of Mathematics, University of British Columbia, Vancouver, BC, Canada
| | - Vinicius F Farjalla
- Department of Ecology, Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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209
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González-Rocha G, Muñoz-Cartes G, Canales-Aguirre CB, Lima CA, Domínguez-Yévenes M, Bello-Toledo H, Hernández CE. Diversity structure of culturable bacteria isolated from the Fildes Peninsula (King George Island, Antarctica): A phylogenetic analysis perspective. PLoS One 2017. [PMID: 28632790 PMCID: PMC5478107 DOI: 10.1371/journal.pone.0179390] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It has been proposed that Antarctic environments select microorganisms with unique biochemical adaptations, based on the tenet 'Everything is everywhere, but, the environment selects' by Baas-Becking. However, this is a hypothesis that has not been extensively evaluated. This study evaluated the fundamental prediction contained in this hypothesis-in the sense that species are structured in the landscape according to their local habitats-, using as study model the phylogenetic diversity of the culturable bacteria of Fildes Peninsula (King George Island, Antarctica). Eighty bacterial strains isolated from 10 different locations in the area, were recovered. Based on phylogenetic analysis of 16S rRNA gene sequences, the isolates were grouped into twenty-six phylotypes distributed in three main clades, of which only six are exclusive to Antarctica. Results showed that phylotypes do not group significantly by habitat type; however, local habitat types had phylogenetic signal, which support the phylogenetic niche conservatism hypothesis and not a selective role of the environment like the Baas-Becking hypothesis suggests. We propose that, more than habitat selection resulting in new local adaptations and diversity, local historical colonization and species sorting (i.e. differences in speciation and extinction rates that arise by interaction of species level traits with the environment) play a fundamental role on the culturable bacterial diversity in Antarctica.
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Affiliation(s)
- Gerardo González-Rocha
- Laboratorio de Investigación en Agentes Antibacterianos. Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Gabriel Muñoz-Cartes
- Laboratorio de Investigación en Agentes Antibacterianos. Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Cristian B. Canales-Aguirre
- Laboratorio de Ecología Evolutiva y Filoinformática. Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
- Centro i~mar, Universidad de Los Lagos, Camino a Chinquihue 6 km, Puerto Montt, Chile
| | - Celia A. Lima
- Laboratorio de Investigación en Agentes Antibacterianos. Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Mariana Domínguez-Yévenes
- Laboratorio de Investigación en Agentes Antibacterianos. Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Helia Bello-Toledo
- Laboratorio de Investigación en Agentes Antibacterianos. Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Cristián E. Hernández
- Laboratorio de Ecología Evolutiva y Filoinformática. Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
- * E-mail:
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210
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Brady C, Arnold D, McDonald J, Denman S. Taxonomy and identification of bacteria associated with acute oak decline. World J Microbiol Biotechnol 2017. [PMID: 28623563 PMCID: PMC5486618 DOI: 10.1007/s11274-017-2296-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Acute oak decline (AOD) is a relatively newly described disorder affecting native oak species in Britain. Symptomatic trees are characterised by stem bleeds from vertical fissures, necrotic lesions in the live tissue beneath and larval galleries of the two spotted oak buprestid (Agrilus biguttatus). Several abiotic and biotic factors can be responsible for tree death, however the tissue necrosis and stem weeping is thought to be caused by a combination of bacterial species. Following investigations of the current episode of AOD which began in 2008, numerous strains belonging to several different bacteria in the family Enterobacteriaceae have been consistently isolated from symptomatic tissue. The majority of these enterobacteria were found to be novel species, subspecies and even genera, which have now been formally classified. The most frequently isolated species from symptomatic oak are Gibbsiella quercinecans, Brenneria goodwinii and Rahnella victoriana. Identification of these bacteria is difficult due to similarities in colony morphology, phenotypic profile and 16S rRNA gene sequences. Current identification relies heavily on gyrB gene amplification and sequencing, which is time consuming and laborious. However, newer techniques based on detection of single nucleotide polymorphisms show greater promise for rapid and reliable identification of the bacteria associated with AOD.
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Affiliation(s)
- Carrie Brady
- Faculty of Health and Life Sciences, Centre for Research in Bioscience, University of the West of England, Frenchay Campus, Coldharbour Lane, Bristol, BS16 1QY, UK.
| | - Dawn Arnold
- Faculty of Health and Life Sciences, Centre for Research in Bioscience, University of the West of England, Frenchay Campus, Coldharbour Lane, Bristol, BS16 1QY, UK
| | - James McDonald
- School of Biological Sciences, Bangor University, Bangor, Gwynedd, UK
| | - Sandra Denman
- Centre for Ecosystems, Society and Biosecurity, Forest Research, Alice Holt Lodge, Surrey, UK
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211
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Millán-Aguiñaga N, Chavarria KL, Ugalde JA, Letzel AC, Rouse GW, Jensen PR. Phylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations. Sci Rep 2017; 7:3564. [PMID: 28620214 PMCID: PMC5472633 DOI: 10.1038/s41598-017-02845-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 04/18/2017] [Indexed: 11/12/2022] Open
Abstract
Bacteria represent the most genetically diverse kingdom of life. While great progress has been made in describing this diversity, it remains difficult to identify the phylogenetic and ecological characteristics that delineate groups of bacteria that possess species-like properties. One major challenge associated with species delineations is that not all shared genes have the same evolutionary history, and thus the choice of loci can have a major impact on phylogenetic reconstruction. Sequencing the genomes of large numbers of closely related strains provides new opportunities to distinguish ancestral from acquired alleles and assess the effects of recombination on phylogenetic inference. Here we analyzed the genomes of 119 strains of the marine actinomycete genus Salinispora, which is currently comprised of three named species that share 99% 16S rRNA gene sequence identity. While 63% of the core genome showed evidence of recombination, this had no effect on species-level phylogenomic resolution. Recombination did however blur intra-species relationships and biogeographic resolution. The genome-wide average nucleotide identity provided a new perspective on Salinispora diversity, revealing as many as seven new species. Patterns of orthologous group distributions reveal a genetic basis to delineation the candidate taxa and insight into the levels of genetic cohesion associated with bacterial species.
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Affiliation(s)
- Natalie Millán-Aguiñaga
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States.,Universidad Autónoma de Baja California. Facultad de Ciencias Marinas, Ensenada, Baja California, Mexico
| | - Krystle L Chavarria
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States
| | - Juan A Ugalde
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States.,Centro de Bioinformática y Biología Integrativa, Facultad de Ciencias Biológicas, Universidad Andrés Bella, Santiago, Chile
| | - Anne-Catrin Letzel
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States
| | - Greg W Rouse
- Marine Biology Research Division Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States. .,Marine Biology Research Division Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States.
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212
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Hoza AS, Mfinanga SG, Moser I, König B. Isolation, biochemical and molecular identification of Nocardia species among TB suspects in northeastern, Tanzania; a forgotten or neglected threat? BMC Infect Dis 2017; 17:407. [PMID: 28595598 PMCID: PMC5463502 DOI: 10.1186/s12879-017-2520-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 06/01/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Pulmonary nocardiosis mimic pulmonary tuberculosis in most clinical and radiological manifestations. In Tanzania, where tuberculosis is one of the major public health threat clinical impact of nocardiosis as the cause of the human disease remains unknown. The objective of the present study was to isolate and identify Nocardia isolates recovered from TB suspects in Northeastern, Tanzania by using biochemical and molecular methods. METHODS The study involved 744 sputum samples collected from 372 TB suspects from four periphery diagnostic centers in Northeastern, Tanzania. Twenty patients were diagnosed as having presumptively Nocardia infections based on microscopic, cultural characteristics and biomèrieux ID 32C Yeast Identification system and confirmed using 16S rRNA and hsp65 gene specific primers for Nocardia species and sequencing. RESULTS Biochemically, the majority of the isolates were N. asteroides (n = 8/20, 40%), N. brasiliensis (n = 4/20, 20%), N. farcinica (n = 3/20, 15%), N. nova (n = 1/20, 5%). Other aerobic actinomycetales included Streptomyces cyanescens (n = 2/20, 10%), Streptomyces griseus, Actinomadura madurae each (n = 1/20, 5%). Results of 16S rRNA and hsp65 sequencing were concordant in 15/17 (88. 2%) isolates and discordant in 2/17 (11.8%) isolates. Majority of the isolates belonged to N. cyriacigeorgica and N. farcinica, four (23.5%) each. CONCLUSIONS Our findings suggest that Nocardia species may be an important cause of pulmonary nocardiosis that is underdiagnosed or ignored. This underscores needs to consider pulmonary nocardiosis as a differential diagnosis when there is a failure of anti-TB therapy and as a possible cause of human infections.
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Affiliation(s)
- Abubakar S. Hoza
- Department of Medical Microbiology and Epidemiology of Infectious Diseases, Faculty of Medicine, University of Leipzig, Liebig Str. 21, 04103 Leipzig, Germany
- Department of Microbiology, Parasitology and Immunology, College of Veterinary and Medical Sciences, Sokoine University of Agriculture, P. O. Box, 3019 Morogoro, Tanzania
| | - Sayoki G.S. Mfinanga
- National Institute for Medical Research, Muhimbili Medical Research Centre, P. O. Box, 3436 Dar es Salaam, Tanzania
| | - Irmgard Moser
- Friedrich Loeffler Institut, Institute of Molecular Pathogenesis, Naumburger Str. 96a, 07743 Jena, Germany
| | - Brigitte König
- Department of Medical Microbiology and Epidemiology of Infectious Diseases, Faculty of Medicine, University of Leipzig, Liebig Str. 21, 04103 Leipzig, Germany
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213
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Kaczmarek M, Mullett MS, McDonald JE, Denman S. Multilocus sequence typing provides insights into the population structure and evolutionary potential of Brenneria goodwinii, associated with acute oak decline. PLoS One 2017; 12:e0178390. [PMID: 28570630 PMCID: PMC5453491 DOI: 10.1371/journal.pone.0178390] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 05/14/2017] [Indexed: 11/18/2022] Open
Abstract
Brenneria goodwinii is one of the most frequently isolated Gram-negative bacteria from native oak species, Quercus robur and Q. petraea, affected by acute oak decline (AOD) in the UK. We investigated the population biology of this bacterial species using a multilocus sequence analysis to determine the population structure and evolutionary potential. Seven partial housekeeping genes were used in the analyses. Amongst 44 bacterial strains from seven different locations, we identified 22 unique sequence types [STs]; only one ST was found at two separate locations. Phylogenetic and cluster-based analyses suggested that B. goodwinii STs form two main distinct groups; however, no geographical pattern of their distribution could be observed. Clonality and recombination tests demonstrated that the studied population is primarily clonal, however both mutation and recombination processes play a role in shaping the genetic structure and evolution of the population. Our study suggests that the B. goodwinii population on oak in the UK has an endemic form, with background recombination appearing to generate new alleles more frequently than mutation, despite the introduction of nucleotide substitutions being approximately twice less likely than mutation. The newly emerged STs subsequently undergo clonal expansion to become dominant genotypes within their specific geographical locations and even within the individual host oak trees.
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Affiliation(s)
- Maciej Kaczmarek
- Bangor University, School of Biological Sciences, Bangor, Gwynedd, United Kingdom
- Forest Research, Centre for Ecosystems, Society and Biosecurity, Alice Holt Lodge, Farnham, Surrey, United Kingdom
- * E-mail: (SD); (MK)
| | - Martin S. Mullett
- Forest Research, Centre for Ecosystems, Society and Biosecurity, Alice Holt Lodge, Farnham, Surrey, United Kingdom
| | - James E. McDonald
- Bangor University, School of Biological Sciences, Bangor, Gwynedd, United Kingdom
| | - Sandra Denman
- Forest Research, Centre for Ecosystems, Society and Biosecurity, Alice Holt Lodge, Farnham, Surrey, United Kingdom
- * E-mail: (SD); (MK)
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214
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Chen Y, Kuang J, Jia P, Cadotte MW, Huang L, Li J, Liao B, Wang P, Shu W. Effect of Environmental Variation on Estimating the Bacterial Species Richness. Front Microbiol 2017; 8:690. [PMID: 28469618 PMCID: PMC5395623 DOI: 10.3389/fmicb.2017.00690] [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: 02/06/2017] [Accepted: 04/04/2017] [Indexed: 11/13/2022] Open
Abstract
Estimating the species richness of microorganisms is of great importance in predicting, maintaining and managing microbial communities. Although the roles of environmental heterogeneity and geographical distance in structuring soil microbial communities have been studied intensively, the effects of environmental and spatial variation on the species richness estimation have not been examined. To this end, we have explored their effects on estimating the belowground soil bacterial species richness within a 50 ha forest dynamic plot (FDP) using a published massive sequencing dataset with intensive sampling scheme. Our resampling analyses showed that, for a given sequencing depth, increasing the sample size could significantly enhance the detection of rare species by capturing more of the environmental and spatial variation, thus obtaining higher observed and estimated species richness. Additionally, the estimates of bacterial species richness were significantly and positively correlated with environmental variation among samples, indicating that environmental filtering was the main mechanism driving the processes of community assembly for belowground soil bacterial communities in the plot. Moreover, this effect of environmental variation could be markedly alleviated when the sample size was higher than 450, and thus we predicted that there were at least 42,866 soil bacterial species based on 8,296,878 sequences from 550 samples in the whole 50 ha FDP. Furthermore, we built a power law environmental heterogeneity equation (EHE) as a decision-tool to determine an approximate sample size for comprehensively capturing the environmental gradient within a given habitat. Collectively, this work further links the inherent environmental and spatial variation to the estimation of soil bacterial species richness within a given region, and provides a useful tool of sampling design for a better understanding of microbial biogeographic patterns and estimation of microbial biodiversity.
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Affiliation(s)
- Yongjian Chen
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen UniversityGuangzhou, China
| | - Jialiang Kuang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen UniversityGuangzhou, China
| | - Pu Jia
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen UniversityGuangzhou, China.,Department of Biological Sciences, University of Toronto Scarborough, TorontoON, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, TorontoON, Canada
| | - Marc W Cadotte
- Department of Biological Sciences, University of Toronto Scarborough, TorontoON, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, TorontoON, Canada
| | - Linan Huang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen UniversityGuangzhou, China
| | - Jintian Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen UniversityGuangzhou, China
| | - Bin Liao
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen UniversityGuangzhou, China
| | - Pandeng Wang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen UniversityGuangzhou, China
| | - Wensheng Shu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen UniversityGuangzhou, China
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215
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Venter SN, Palmer M, Beukes CW, Chan WY, Shin G, van Zyl E, Seale T, Coutinho TA, Steenkamp ET. Practically delineating bacterial species with genealogical concordance. Antonie van Leeuwenhoek 2017; 110:1311-1325. [DOI: 10.1007/s10482-017-0869-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 03/30/2017] [Indexed: 10/19/2022]
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216
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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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217
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Mohamad R, Willems A, Le Quéré A, Maynaud G, Pervent M, Bonabaud M, Dubois E, Cleyet-Marel JC, Brunel B. Mesorhizobium delmotii and Mesorhizobium prunaredense are two new species containing rhizobial strains within the symbiovar anthyllidis. Syst Appl Microbiol 2017; 40:135-143. [DOI: 10.1016/j.syapm.2017.01.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 01/18/2017] [Accepted: 01/27/2017] [Indexed: 11/28/2022]
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218
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Wang L, Wang J, Jing C. Comparative Genomic Analysis Reveals Organization, Function and Evolution of ars Genes in Pantoea spp. Front Microbiol 2017; 8:471. [PMID: 28377759 PMCID: PMC5360009 DOI: 10.3389/fmicb.2017.00471] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 03/07/2017] [Indexed: 11/21/2022] Open
Abstract
Numerous genes are involved in various strategies to resist toxic arsenic (As). However, the As resistance strategy in genus Pantoea is poorly understood. In this study, a comparative genome analysis of 23 Pantoea genomes was conducted. Two vertical genetic arsC-like genes without any contribution to As resistance were found to exist in the 23 Pantoea strains. Besides the two arsC-like genes, As resistance gene clusters arsRBC or arsRBCH were found in 15 Pantoea genomes. These ars clusters were found to be acquired by horizontal gene transfer (HGT) from sources related to Franconibacter helveticus, Serratia marcescens, and Citrobacter freundii. During the history of evolution, the ars clusters were acquired more than once in some species, and were lost in some strains, producing strains without As resistance capability. This study revealed the organization, distribution and the complex evolutionary history of As resistance genes in Pantoea spp.. The insights gained in this study improved our understanding on the As resistance strategy of Pantoea spp. and its roles in the biogeochemical cycling of As.
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Affiliation(s)
- Liying Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of SciencesBeijing, China; College of Resources and Environment, University of Chinese Academy of SciencesBeijing, China
| | - Jin Wang
- Department of Municipal and Environmental Engineering, School of Civil Engineering, Beijing Jiaotong University Beijing, China
| | - Chuanyong Jing
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of SciencesBeijing, China; College of Resources and Environment, University of Chinese Academy of SciencesBeijing, China
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219
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Ahn AC, Meier-Kolthoff JP, Overmars L, Richter M, Woyke T, Sorokin DY, Muyzer G. Genomic diversity within the haloalkaliphilic genus Thioalkalivibrio. PLoS One 2017; 12:e0173517. [PMID: 28282461 PMCID: PMC5345834 DOI: 10.1371/journal.pone.0173517] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 02/21/2017] [Indexed: 12/24/2022] Open
Abstract
Thioalkalivibrio is a genus of obligate chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacteria. Their habitat are soda lakes which are dual extreme environments with a pH range from 9.5 to 11 and salt concentrations up to saturation. More than 100 strains of this genus have been isolated from various soda lakes all over the world, but only ten species have been effectively described yet. Therefore, the assignment of the remaining strains to either existing or novel species is important and will further elucidate their genomic diversity as well as give a better general understanding of this genus. Recently, the genomes of 76 Thioalkalivibrio strains were sequenced. On these, we applied different methods including (i) 16S rRNA gene sequence analysis, (ii) Multilocus Sequence Analysis (MLSA) based on eight housekeeping genes, (iii) Average Nucleotide Identity based on BLAST (ANIb) and MUMmer (ANIm), (iv) Tetranucleotide frequency correlation coefficients (TETRA), (v) digital DNA:DNA hybridization (dDDH) as well as (vi) nucleotide- and amino acid-based Genome BLAST Distance Phylogeny (GBDP) analyses. We detected a high genomic diversity by revealing 15 new "genomic" species and 16 new "genomic" subspecies in addition to the ten already described species. Phylogenetic and phylogenomic analyses showed that the genus is not monophyletic, because four strains were clearly separated from the other Thioalkalivibrio by type strains from other genera. Therefore, it is recommended to classify the latter group as a novel genus. The biogeographic distribution of Thioalkalivibrio suggested that the different "genomic" species can be classified as candidate disjunct or candidate endemic species. This study is a detailed genome-based classification and identification of members within the genus Thioalkalivibrio. However, future phenotypical and chemotaxonomical studies will be needed for a full species description of this genus.
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Affiliation(s)
- Anne-Catherine Ahn
- Microbial Systems Ecology, Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Jan P. Meier-Kolthoff
- Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Lex Overmars
- Microbial Systems Ecology, Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, United States of America
| | - Dimitry Y. Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
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220
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A proposal for a portal to make earth's microbial diversity easily accessible and searchable. Antonie van Leeuwenhoek 2017; 110:1271-1279. [PMID: 28281028 DOI: 10.1007/s10482-017-0849-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 02/22/2017] [Indexed: 11/27/2022]
Abstract
Estimates of the number of bacterial species range from 107 to 1012. At the pace at which descriptions of new species are currently being published, the description of all bacterial species on earth will only be completed in thousands of years. However, even if one day all species were named and described, these names and descriptions would still be of little practical value unless they could be easily searched and accessed, so that novel strains could be easily identified as members of any of these species. To complicate the situation further, many of the currently known species contain significant genotypic and phenotypic diversity that would still be missed if description of microbial diversity were limited to species. The solution to this problem could be a database in which every bacterial species and every intra-specific group is anchored to a genome-similarity framework. This ideal database should be searchable using complete or partial genome sequences as well as phenotypes. Moreover, the database should include functions to easily add newly sequenced novel strains, automatically place them into the genome-similarity framework, identify them as members of an already named species, or tag them as members of yet to be described species or new intra-specific groups. Here, we propose the means to develop such a database by taking advantage of the concept of genome sequence similarity-based codes, called Life Identification Numbers or LINs.
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221
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Berry MA, White JD, Davis TW, Jain S, Johengen TH, Dick GJ, Sarnelle O, Denef VJ. Are Oligotypes Meaningful Ecological and Phylogenetic Units? A Case Study of Microcystis in Freshwater Lakes. Front Microbiol 2017; 8:365. [PMID: 28337183 PMCID: PMC5341627 DOI: 10.3389/fmicb.2017.00365] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 02/21/2017] [Indexed: 11/13/2022] Open
Abstract
Oligotyping is a computational method used to increase the resolution of marker gene microbiome studies. Although oligotyping can distinguish highly similar sequence variants, the resulting units are not necessarily phylogenetically and ecologically informative due to limitations of the selected marker gene. In this perspective, we examine how oligotyping data is interpreted in recent literature, and we illustrate some of the method’s constraints with a case study of the harmful bloom-forming cyanobacterium Microcystis. We identified three Microcystis oligotypes from a western Lake Erie bacterial community 16S rRNA gene (V4 region) survey that had previously clustered into one OTU. We found the same three oligotypes and two additional sequence variants in 46 Microcystis cultures isolated from Michigan inland lakes spanning a trophic gradient. In Lake Erie, shifts in Microcystis oligotypes corresponded to spatial nutrient gradients and temporal transitions in bloom toxicity. In the cultures, Microcystis oligotypes showed preferential distributions for different trophic states, but genomic data revealed that the oligotypes identified in Lake Erie did not correspond to toxin gene presence. Thus, oligotypes could not be used for inferring toxic ecotypes. Most strikingly, Microcystis oligotypes were not monophyletic. Our study supports the utility of oligotyping for distinguishing sequence types along certain ecological features, while it stresses that 16S rRNA gene sequence types may not reflect ecologically or phylogenetically cohesive populations. Therefore, we recommend that studies employing oligotyping or related tools consider these caveats during data interpretation.
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Affiliation(s)
- Michelle A Berry
- Department of Ecology and Evolutionary Biology, University of Michigan Ann Arbor, MI, USA
| | - Jeffrey D White
- Department of Biology, Framingham State University Framingham, MA, USA
| | - Timothy W Davis
- NOAA Great Lakes Environmental Research Laboratory Ann Arbor, MI, USA
| | - Sunit Jain
- Department of Earth and Environmental Sciences, University of Michigan Ann Arbor, MI, USA
| | - Thomas H Johengen
- Cooperative Institute for Limnology and Ecosystems Research, University of Michigan Ann Arbor, MI, USA
| | - Gregory J Dick
- Department of Earth and Environmental Sciences, University of Michigan Ann Arbor, MI, USA
| | - Orlando Sarnelle
- Department of Fisheries and Wildlife, Michigan State University East Lansing, MI, USA
| | - Vincent J Denef
- Department of Ecology and Evolutionary Biology, University of Michigan Ann Arbor, MI, USA
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222
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Baltrus DA, McCann HC, Guttman DS. Evolution, genomics and epidemiology of Pseudomonas syringae: Challenges in Bacterial Molecular Plant Pathology. MOLECULAR PLANT PATHOLOGY 2017; 18:152-168. [PMID: 27798954 PMCID: PMC6638251 DOI: 10.1111/mpp.12506] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 10/25/2016] [Accepted: 10/26/2016] [Indexed: 05/12/2023]
Abstract
A remarkable shift in our understanding of plant-pathogenic bacteria is underway. Until recently, nearly all research on phytopathogenic bacteria was focused on a small number of model strains, which provided a deep, but narrow, perspective on plant-microbe interactions. Advances in genome sequencing technologies have changed this by enabling the incorporation of much greater diversity into comparative and functional research. We are now moving beyond a typological understanding of a select collection of strains to a more generalized appreciation of the breadth and scope of plant-microbe interactions. The study of natural populations and evolution has particularly benefited from the expansion of genomic data. We are beginning to have a much deeper understanding of the natural genetic diversity, niche breadth, ecological constraints and defining characteristics of phytopathogenic species. Given this expanding genomic and ecological knowledge, we believe the time is ripe to evaluate what we know about the evolutionary dynamics of plant pathogens.
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Affiliation(s)
| | - Honour C. McCann
- New Zealand Institute for Advanced StudyMassey UniversityAuckland 0632New Zealand
| | - David S. Guttman
- Department of Cell and Systems BiologyUniversity of TorontoTorontoON M5S 3B2Canada
- Centre for the Analysis of Genome Evolution and FunctionUniversity of TorontoTorontoON M5S 3B2Canada
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223
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Scholz CFP, Jensen A. Development of a Single Locus Sequence Typing (SLST) Scheme for Typing Bacterial Species Directly from Complex Communities. Methods Mol Biol 2017; 1535:97-107. [PMID: 27914075 DOI: 10.1007/978-1-4939-6673-8_7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The protocol describes a computational method to develop a Single Locus Sequence Typing (SLST) scheme for typing bacterial species. The resulting scheme can be used to type bacterial isolates as well as bacterial species directly from complex communities using next-generation sequencing technologies.
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Affiliation(s)
- Christian F P Scholz
- Department of Biomedicine, Aarhus University, Wilhelms Meyers Allé 4, 8000, Aarhus, Denmark.
| | - Anders Jensen
- Department of Biomedicine, Aarhus University, Wilhelms Meyers Allé 4, 8000, Aarhus, Denmark
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224
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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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225
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Louca S, Jacques SMS, Pires APF, Leal JS, Srivastava DS, Parfrey LW, Farjalla VF, Doebeli M. High taxonomic variability despite stable functional structure across microbial communities. Nat Ecol Evol 2016; 1:15. [PMID: 28812567 DOI: 10.1038/s41559-016-0015] [Citation(s) in RCA: 235] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 05/03/2016] [Indexed: 01/08/2023]
Abstract
Understanding the processes that are driving variation of natural microbial communities across space or time is a major challenge for ecologists. Environmental conditions strongly shape the metabolic function of microbial communities; however, other processes such as biotic interactions, random demographic drift or dispersal limitation may also influence community dynamics. The relative importance of these processes and their effects on community function remain largely unknown. To address this uncertainty, here we examined bacterial and archaeal communities in replicate 'miniature' aquatic ecosystems contained within the foliage of wild bromeliads. We used marker gene sequencing to infer the taxonomic composition within nine metabolic functional groups, and shotgun environmental DNA sequencing to estimate the relative abundances of these groups. We found that all of the bromeliads exhibited remarkably similar functional community structures, but that the taxonomic composition within individual functional groups was highly variable. Furthermore, using statistical analyses, we found that non-neutral processes, including environmental filtering and potentially biotic interactions, at least partly shaped the composition within functional groups and were more important than spatial dispersal limitation and demographic drift. Hence both the functional structure and taxonomic composition within functional groups of natural microbial communities may be shaped by non-neutral and roughly separate processes.
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Affiliation(s)
- Stilianos Louca
- Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada.,Institute of Applied Mathematics, University of British Columbia, Vancouver, V6T 1Z2, Canada
| | - Saulo M S Jacques
- Department of Ecology, Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-590, Brazil.,Programa de Pós-Graduação em Ecologia e Evolugão, Universidade Estadual do Rio de Janeiro, Rio de Janeiro, 20550-013, Brazil
| | - Aliny P F Pires
- Department of Ecology, Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-590, Brazil
| | - Juliana S Leal
- Department of Ecology, Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-590, Brazil.,Programa de Pós-Graduação em Ecologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-971, Brazil
| | - Diane S Srivastava
- Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada.,Department of Zoology, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Laura Wegener Parfrey
- Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada.,Department of Zoology, University of British Columbia, Vancouver, V6T 1Z4, Canada.,Department of Botany, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Vinicius F Farjalla
- Department of Ecology, Biology Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-590, Brazil
| | - Michael Doebeli
- Biodiversity Research Centre, University of British Columbia, Vancouver, V6T 1Z4, Canada.,Department of Zoology, University of British Columbia, Vancouver, V6T 1Z4, Canada.,Department of Mathematics, University of British Columbia, Vancouver, V6T 1Z2, Canada
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226
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Genome-based phylogeny and taxonomy of the ‘Enterobacteriales’: proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov. Int J Syst Evol Microbiol 2016; 66:5575-5599. [DOI: 10.1099/ijsem.0.001485] [Citation(s) in RCA: 556] [Impact Index Per Article: 69.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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227
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Palau M, Kulmann M, Ramírez-Lázaro MJ, Lario S, Quilez ME, Campo R, Piqué N, Calvet X, Miñana-Galbis D. Usefulness of Housekeeping Genes for the Diagnosis of Helicobacter pylori Infection, Strain Discrimination and Detection of Multiple Infection. Helicobacter 2016; 21:481-487. [PMID: 26991758 DOI: 10.1111/hel.12304] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND Helicobacter pylori infects human stomachs of over half the world's population, evades the immune response and establishes a chronic infection. Although most people remains asymptomatic, duodenal and gastric ulcers, MALT lymphoma and progression to gastric cancer could be developed. Several virulence factors such as flagella, lipopolysaccharide, adhesins and especially the vacuolating cytotoxin VacA and the oncoprotein CagA have been described for H. pylori. Despite the extensive published data on H. pylori, more research is needed to determine new virulence markers, the exact mode of transmission or the role of multiple infection. MATERIALS AND METHODS Amplification and sequencing of six housekeeping genes (amiA, cgt, cpn60, cpn70, dnaJ, and luxS) related to H. pylori pathogenesis have been performed in order to evaluate their usefulness for the specific detection of H. pylori, the genetic discrimination at strain level and the detection of multiple infection. A total of 52 H. pylori clones, isolated from 14 gastric biopsies from 11 patients, were analyzed for this purpose. RESULTS All genes were specifically amplified for H. pylori and all clones isolated from different patients were discriminated, with gene distances ranged from 0.9 to 7.8%. Although most clones isolated from the same patient showed identical gene sequences, an event of multiple infection was detected in all the genes and microevolution events were showed for amiA and cpn60 genes. CONCLUSIONS These results suggested that housekeeping genes could be useful for H. pylori detection and to elucidate the mode of transmission and the relevance of the multiple infection.
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Affiliation(s)
- Montserrat Palau
- Departament de Microbiologia i Parasitologia Sanitàries, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Marcos Kulmann
- Departament de Microbiologia i Parasitologia Sanitàries, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - María José Ramírez-Lázaro
- Digestive Diseases Service, Hospital de Sabadell, Institut Universitari Parc Taulí, Departament de Medicina, Universitat Autònoma de Barcelona, Sabadell, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain
| | - Sergio Lario
- Digestive Diseases Service, Hospital de Sabadell, Institut Universitari Parc Taulí, Departament de Medicina, Universitat Autònoma de Barcelona, Sabadell, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain
| | - María Elisa Quilez
- Digestive Diseases Service, Hospital de Sabadell, Institut Universitari Parc Taulí, Departament de Medicina, Universitat Autònoma de Barcelona, Sabadell, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain
| | - Rafael Campo
- Digestive Diseases Service, Hospital de Sabadell, Institut Universitari Parc Taulí, Departament de Medicina, Universitat Autònoma de Barcelona, Sabadell, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain
| | - Núria Piqué
- Departament de Microbiologia i Parasitologia Sanitàries, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Xavier Calvet
- Digestive Diseases Service, Hospital de Sabadell, Institut Universitari Parc Taulí, Departament de Medicina, Universitat Autònoma de Barcelona, Sabadell, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III, Madrid, Spain
| | - David Miñana-Galbis
- Departament de Microbiologia i Parasitologia Sanitàries, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Catalonia, Spain
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228
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Tena W, Wolde-Meskel E, Degefu T, Walley F. Lentil (Lens culinaris Medik.) nodulates with genotypically and phenotypically diverse rhizobia in Ethiopian soils. Syst Appl Microbiol 2016; 40:22-33. [PMID: 27931748 DOI: 10.1016/j.syapm.2016.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 10/29/2016] [Accepted: 11/04/2016] [Indexed: 11/30/2022]
Abstract
Forty-eight lentil-nodulating rhizobia were isolated from soil samples collected from diverse agro-ecological locations in Ethiopia, and characterized based on 76 phenotypic traits. Furthermore, 26 representative strains were selected and characterized using multilocus sequence analyses (MLSA) of core (16S rRNA, recA, atpD, glnII and gyrB) and symbiotic (nodA and nifH) genes. Numerical analysis of phenotypic characteristics showed that the 48 test strains fell into three major distinct clusters. The phylogenetic trees based on 16S rRNA genes showed that they belong to the Rhizobium genus. Our phylogenetic reconstruction based on combined gene trees (recA, atpD and glnII) supported three distinct sub-lineages (Clades I-III). While genospecies I and II could be classified with Rhizobium etli and Rhizobium leguminosarum, respectively, genospecies III, might be an unnamed genospecies within the genus Rhizobium. Phylogenetic reconstruction based on the symbiosis-related genes supported a single cluster, indicating differences in the evolutionary histories between chromosomal and symbiotic genes. Overall, these results confirmed the presence of a great diversity of lentil-nodulating Rhizobium species in Ethiopia, inviting further exploration. Moreover, the differences in symbiotic effectiveness of the test strains indicated the potential for selecting and using them as inoculants to improve the productivity of lentil in the country.
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Affiliation(s)
- Wondwosen Tena
- Debreberhan University, Department of Plant Science, P.O. Box 445, Debreberhan, Ethiopia.
| | | | - Tulu Degefu
- Hawassa University, Department of Biology, P.O. Box 05, Ethiopia
| | - Fran Walley
- Department of Soil Science, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, S7N 5A8, Canada
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229
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Bao YJ, Shapiro BJ, Lee SW, Ploplis VA, Castellino FJ. Phenotypic differentiation of Streptococcus pyogenes populations is induced by recombination-driven gene-specific sweeps. Sci Rep 2016; 6:36644. [PMID: 27821851 PMCID: PMC5099688 DOI: 10.1038/srep36644] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 10/13/2016] [Indexed: 01/05/2023] Open
Abstract
Genomic recombination plays an important role in driving adaptive evolution and population differentiation in bacteria. However, controversy exists as to the effects of recombination on population diversity and differentiation, i.e., recombination is frequent enough to sweep through the population at selected gene loci (gene-specific sweeps), or the recombination rate is low without interfering genome-wide selective sweeps. Observations supporting either view are sparse. Pathogenic bacteria causing infectious diseases are promising candidates to provide observations of recombination. However, phenotype-associated differentiations are usually vague among them due to diverse disease manifestations. Here we report a population genomic study of the group A Streptococcus pyogenes (GAS), a human pathogen with highly recombining genomes. By employing a genome-wide association study on single nucleotide polymorphisms (SNPs), we demonstrate a phenotypic differentiation of GAS, represented by separate clustering of two sublineages associated with niche-specific infections, i.e., skin infection and pharyngitis-induced acute rheumatic fever. By quantifying SNPs associated with the differentiation in a statistical and phylogenetic context, we propose that the phenotype-associated differentiation arose through recombination-driven gene-specific sweeps, rather than genome-wide sweeps. Our work provides a novel paradigm of phenotype-associated differentiation induced by gene-specific sweeps in a human pathogen and has implications for understanding of driving forces of bacterial evolution.
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Affiliation(s)
- Yun-Juan Bao
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, USA
| | - B Jesse Shapiro
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Shaun W Lee
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, USA.,Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Victoria A Ploplis
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, USA.,Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Francis J Castellino
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, USA.,Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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230
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Effects of Proton Pump Inhibitors on the Gastric Mucosa-Associated Microbiota in Dyspeptic Patients. Appl Environ Microbiol 2016; 82:6633-6644. [PMID: 27590821 DOI: 10.1128/aem.01437-16] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 08/27/2016] [Indexed: 02/07/2023] Open
Abstract
Besides being part of anti-Helicobacter pylori treatment regimens, proton pump inhibitors (PPIs) are increasingly being used to treat dyspepsia. However, little is known about the effects of PPIs on the human gastric microbiota, especially those related to H. pylori infection. The goal of this study was to characterize the stomach microbial communities in patients with dyspepsia and to investigate their relationships with PPI use and H. pylori status. Using 16S rRNA gene pyrosequencing, we analyzed the mucosa-associated microbial populations of 24 patients, of whom 12 were treated with the PPI omeprazole and 9 (5 treated and 4 untreated) were positive for H. pylori infection. The Proteobacteria, Firmicutes, Bacteroidetes, Fusobacteria, and Actinobacteria phyla accounted for 98% of all of the sequences, with Helicobacter, Streptococcus, and Prevotella ranking among the 10 most abundant genera. H. pylori infection or PPI treatment did not significantly influence gastric microbial species composition in dyspeptic patients. Principal-coordinate analysis of weighted UniFrac distances in these communities revealed clear but significant separation according to H. pylori status only. However, in PPI-treated patients, Firmicutes, particularly Streptococcaceae, were significantly increased in relative abundance compared to those in untreated patients. Consistently, Streptococcus was also found to significantly increase in relation to PPI treatment, and this increase seemed to occur independently of H. pylori infection. Our results suggest that Streptococcus may be a key indicator of PPI-induced gastric microbial composition changes in dyspeptic patients. Whether the gastric microbiota alteration contributes to dyspepsia needs further investigation. IMPORTANCE Although PPIs have become a popular treatment choice, a growing number of dyspeptic patients may be treated unnecessarily. We found that patients treated with omeprazole showed gastric microbial communities that were different from those of untreated patients. These differences regarded the abundances of specific taxa. By understanding the relationships between PPIs and members of the gastric microbiota, it will be possible to envisage new strategies for better managing patients with dyspepsia.
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231
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Methodological and Clinical Aspects of the Molecular Epidemiology of Mycobacterium tuberculosis and Other Mycobacteria. Clin Microbiol Rev 2016; 29:239-90. [PMID: 26912567 DOI: 10.1128/cmr.00055-15] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Molecular typing has revolutionized epidemiological studies of infectious diseases, including those of a mycobacterial etiology. With the advent of fingerprinting techniques, many traditional concepts regarding transmission, infectivity, or pathogenicity of mycobacterial bacilli have been revisited, and their conventional interpretations have been challenged. Since the mid-1990s, when the first typing methods were introduced, a plethora of other modalities have been proposed. So-called molecular epidemiology has become an essential subdiscipline of modern mycobacteriology. It serves as a resource for understanding the key issues in the epidemiology of tuberculosis and other mycobacterial diseases. Among these issues are disclosing sources of infection, quantifying recent transmission, identifying transmission links, discerning reinfection from relapse, tracking the geographic distribution and clonal expansion of specific strains, and exploring the genetic mechanisms underlying specific phenotypic traits, including virulence, organ tropism, transmissibility, or drug resistance. Since genotyping continues to unravel the biology of mycobacteria, it offers enormous promise in the fight against and prevention of the diseases caused by these pathogens. In this review, molecular typing methods for Mycobacterium tuberculosis and nontuberculous mycobacteria elaborated over the last 2 decades are summarized. The relevance of these methods to the epidemiological investigation, diagnosis, evolution, and control of mycobacterial diseases is discussed.
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232
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Planet PJ, Narechania A, Chen L, Mathema B, Boundy S, Archer G, Kreiswirth B. Architecture of a Species: Phylogenomics of Staphylococcus aureus. Trends Microbiol 2016; 25:153-166. [PMID: 27751626 DOI: 10.1016/j.tim.2016.09.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 09/07/2016] [Accepted: 09/22/2016] [Indexed: 12/11/2022]
Abstract
A deluge of whole-genome sequencing has begun to give insights into the patterns and processes of microbial evolution, but genome sequences have accrued in a haphazard manner, with biased sampling of natural variation that is driven largely by medical and epidemiological priorities. For instance, there is a strong bias for sequencing epidemic lineages of methicillin-resistant Staphylococcus aureus (MRSA) over sensitive isolates (methicillin-sensitive S. aureus: MSSA). As more diverse genomes are sequenced the emerging picture is of a highly subdivided species with a handful of relatively clonal groups (complexes) that, at any given moment, dominate in particular geographical regions. The establishment of hegemony of particular clones appears to be a dynamic process of successive waves of replacement of the previously dominant clone. Here we review the phylogenomic structure of a diverse range of S. aureus, including both MRSA and MSSA. We consider the utility of the concept of the 'core' genome and the impact of recombination and horizontal transfer. We argue that whole-genome surveillance of S. aureus populations could lead to better forecasting of antibiotic resistance and virulence of emerging clones, and a better understanding of the elusive biological factors that determine repeated strain replacement.
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Affiliation(s)
- Paul J Planet
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA; Department of Pediatrics, Division of Pediatric Infectious Diseases, Children's Hospital of Philadelphia & University of Pennsylvania, Philadelphia, PA, USA.
| | - Apurva Narechania
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
| | - Liang Chen
- Public Health Research Institute Center, New Jersey Medical School, Rutgers, Newark, NJ, USA
| | - Barun Mathema
- Public Health Research Institute Center, New Jersey Medical School, Rutgers, Newark, NJ, USA; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Sam Boundy
- Department of Internal Medicine, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Gordon Archer
- Department of Internal Medicine, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Barry Kreiswirth
- Public Health Research Institute Center, New Jersey Medical School, Rutgers, Newark, NJ, USA
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233
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Huang CH, Huang L, Chang MT, Chen KL. Establishment and application of an analytical in-house database (IHDB) for rapid discrimination of Bacillus subtilis group (BSG) using whole-cell MALDI-TOF MS technology. Mol Cell Probes 2016; 30:312-319. [DOI: 10.1016/j.mcp.2016.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 07/19/2016] [Accepted: 08/05/2016] [Indexed: 10/21/2022]
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234
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Espariz M, Zuljan FA, Esteban L, Magni C. Taxonomic Identity Resolution of Highly Phylogenetically Related Strains and Selection of Phylogenetic Markers by Using Genome-Scale Methods: The Bacillus pumilus Group Case. PLoS One 2016; 11:e0163098. [PMID: 27658251 PMCID: PMC5033322 DOI: 10.1371/journal.pone.0163098] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 09/02/2016] [Indexed: 01/31/2023] Open
Abstract
Bacillus pumilus group strains have been studied due their agronomic, biotechnological or pharmaceutical potential. Classifying strains of this taxonomic group at species level is a challenging procedure since it is composed of seven species that share among them over 99.5% of 16S rRNA gene identity. In this study, first, a whole-genome in silico approach was used to accurately demarcate B. pumilus group strains, as a case of highly phylogenetically related taxa, at the species level. In order to achieve that and consequently to validate or correct taxonomic identities of genomes in public databases, an average nucleotide identity correlation, a core-based phylogenomic and a gene function repertory analyses were performed. Eventually, more than 50% such genomes were found to be misclassified. Hierarchical clustering of gene functional repertoires was also used to infer ecotypes among B. pumilus group species. Furthermore, for the first time the machine-learning algorithm Random Forest was used to rank genes in order of their importance for species classification. We found that ybbP, a gene involved in the synthesis of cyclic di-AMP, was the most important gene for accurately predicting species identity among B. pumilus group strains. Finally, principal component analysis was used to classify strains based on the distances between their ybbP genes. The methodologies described could be utilized more broadly to identify other highly phylogenetically related species in metagenomic or epidemiological assessments.
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Affiliation(s)
- Martín Espariz
- Instituto de Biología Molecular de Rosario (IBR-CONICET), Suipacha 590, (S2002LRK) Rosario, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, (S2002LRK) Rosario, Argentina
- * E-mail:
| | - Federico A. Zuljan
- Instituto de Biología Molecular de Rosario (IBR-CONICET), Suipacha 590, (S2002LRK) Rosario, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, (S2002LRK) Rosario, Argentina
| | - Luis Esteban
- Departamento de Fisiología, Facultad de Ciencias Médicas, Universidad Nacional de Rosario (UNR), Santa Fe 3100, (S2002LRK) Rosario, Argentina
| | - Christian Magni
- Instituto de Biología Molecular de Rosario (IBR-CONICET), Suipacha 590, (S2002LRK) Rosario, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, (S2002LRK) Rosario, Argentina
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235
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Garcia EF, Luciano WA, Xavier DE, da Costa WCA, de Sousa Oliveira K, Franco OL, de Morais Júnior MA, Lucena BTL, Picão RC, Magnani M, Saarela M, de Souza EL. Identification of Lactic Acid Bacteria in Fruit Pulp Processing Byproducts and Potential Probiotic Properties of Selected Lactobacillus Strains. Front Microbiol 2016; 7:1371. [PMID: 27625647 PMCID: PMC5003889 DOI: 10.3389/fmicb.2016.01371] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 08/18/2016] [Indexed: 12/17/2022] Open
Abstract
This study aimed to identify lactic acid bacteria (LAB) in byproducts of fruit (Malpighia glabra L., Mangifera indica L., Annona muricata L., and Fragaria vesca L.) pulp processing. Fifty strains of LAB were identified using matrix-assisted laser desorption/ionization–time of flight mass spectrometry (MALDI-TOF MS) and 16S rRNA gene sequence (16S rRNA) analysis. Species belonging to Lactobacillus genus were the predominant LAB in all fruit pulp processing byproducts. The average congruency between the MALDI-TOF MS and 16S rRNA in LAB species identification reached 86%. Isolates of L. plantarum, L. brevis, L. pentosus, L. lactis and L. mesenteroides were identified with 100% congruency. MALDI-TOF MS and 16S rRNA analysis presented 86 and 100% efficiency of LAB species identification, respectively. Further, five selected Lactobacillus strains (L. brevis 59, L. pentosus 129, L. paracasei 108, L. plantarum 49, and L. fermentum 111) were evaluated for desirable probiotic-related properties and growth behavior on two different cultivation media. The exposure to pH 2.0 sharply decreased the counts of the different Lactobacillus strains after a 1 or 2 h incubation, while varied decreases were noted after 3 h of exposure to pH 3.0. Overall, the exposure to pH 5.0 and to bile salts (0.15, 0.30, and 1.00%) did not decrease the counts of the Lactobacillus strains. All tested Lactobacillus strains presented inhibitory activity against Staphylococcus aureus, Salmonella Typhimurium, Salmonella Enteritidis, Listeria monocytogenes and Escherichia coli, and presented variable susceptibility to different antibiotics. The selected Lactobacillus strains presented satisfactory and reproducible growth behavior. In conclusion, MALDI-TOF MS and 16S rRNA analysis revealed high efficiency and congruency for LAB species identification, and the selected Lactobacillus strains may be candidates for further investigation of novel probiotic strains.
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Affiliation(s)
- Estefânia F Garcia
- Laboratório de Microbiologia de Alimentos, Departamento de Nutrição, Universidade Federal da Paraíba João Pessoa, Brazil
| | - Winnie A Luciano
- Laboratório de Microbiologia de Alimentos, Departamento de Nutrição, Universidade Federal da Paraíba João Pessoa, Brazil
| | - Danilo E Xavier
- Laboratório de Microbiologia de Alimentos, Departamento de Nutrição, Universidade Federal da Paraíba João Pessoa, Brazil
| | - Whyara C A da Costa
- Laboratório de Processos Microbianos em Alimentos, Departamento de Engenharia de Alimentos, Universidade Federal da Paraíba João Pessoa, Brazil
| | | | - Octávio L Franco
- Laboratório de Genômica e Proteômica, Universidade Católica de Brasília Brasília, Brazil
| | - Marcos A de Morais Júnior
- Grupo Interdepartamental de Pesquisa em Engenharia Metabólica, Departamento de Genética, Universidade Federal de Pernambuco Recife, Brazil
| | - Brígida T L Lucena
- Grupo Interdepartamental de Pesquisa em Engenharia Metabólica, Departamento de Genética, Universidade Federal de Pernambuco Recife, Brazil
| | - Renata C Picão
- Instituto de Microbiologia Paulo Góes, Universidade Federal do Rio de Janeiro Rio de Janeiro, Brazil
| | - Marciane Magnani
- Laboratório de Processos Microbianos em Alimentos, Departamento de Engenharia de Alimentos, Universidade Federal da Paraíba João Pessoa, Brazil
| | - Maria Saarela
- VTT Technical Research Centre of Finland Espoo, Finland
| | - Evandro L de Souza
- Laboratório de Microbiologia de Alimentos, Departamento de Nutrição, Universidade Federal da Paraíba João Pessoa, Brazil
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236
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Gene content dissimilarity for subclassification of highly similar microbial strains. BMC Genomics 2016; 17:647. [PMID: 27530250 PMCID: PMC4988056 DOI: 10.1186/s12864-016-2991-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 08/03/2016] [Indexed: 11/23/2022] Open
Abstract
Background Identification and classification of highly similar microbial strains is a challenging issue in microbiology, ecology and evolutionary biology. Among various available approaches, gene content analysis is also at the core of microbial taxonomy. However, no threshold has been determined for grouping microorgnisms to different taxonomic levels, and it is still not clear that to what extent genomic fluidity should occur to form a microbial taxonomic group. Results By taking advantage of the eggNOG database for orthologous groups, we calculated gene content dissimilarity among different microbial strains based on the orthologous gene profiles and tested the possibility of applying gene content dissimilarity as a quantitative index in classifying microbial taxonomic groups, as well as its potential application in subclassification of highly similar microbial strains. Evaluation of gene content dissimilarity to completed microbial genomes at different taxonomic levels suggested that cutoffs of 0.2 and 0.4 can be respectively used for species and family delineation, and that 0.2 gene content dissimilarity cutoff approximately corresponded to 98 % 16S rRNA gene identity and 94 % ANI for microbial species delineation. Furthermore, application of gene content dissimilarity to highly similar microbial strains suggested it as an effective approach in classifying closely related microorganisms into subgroups. Conclusions This approach is especially useful in identifying pathogens from commensals in clinical microbiology. It also provides novel insights into how genomic fluidity is linked with microbial taxonomy. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2991-9) contains supplementary material, which is available to authorized users.
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Jensen A, Scholz CFP, Kilian M. Re-evaluation of the taxonomy of the Mitis group of the genus Streptococcus based on whole genome phylogenetic analyses, and proposed reclassification of Streptococcus dentisani as Streptococcus oralis subsp. dentisani comb. nov., Streptococcus tigurinus as Streptococcus oralis subsp. tigurinus comb. nov., and Streptococcus oligofermentans as a later synonym of Streptococcus cristatus. Int J Syst Evol Microbiol 2016; 66:4803-4820. [PMID: 27534397 DOI: 10.1099/ijsem.0.001433] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The Mitis group of the genus Streptococcus currently comprises 20 species with validly published names, including the pathogen S. pneumoniae. They have been the subject of much taxonomic confusion, due to phenotypic overlap and genetic heterogeneity, which has hampered a full appreciation of their clinical significance. The purpose of this study was to critically re-examine the taxonomy of the Mitis group using 195 publicly available genomes, including designated type strains for phylogenetic analyses based on core genomes, multilocus sequences and 16S rRNA gene sequences, combined with estimates of average nucleotide identity (ANI) and in silico and in vitro analyses of specific phenotypic characteristics. Our core genomic phylogenetic analyses revealed distinct clades that, to some extent, and from the clustering of type strains represent known species. However, many of the genomes have been incorrectly identified adding to the current confusion. Furthermore, our data show that 16S rRNA gene sequences and ANI are unsuitable for identifying and circumscribing new species of the Mitis group of the genus Streptococci. Based on the clustering patterns resulting from core genome phylogenetic analysis, we conclude that S. oligofermentans is a later synonym of S. cristatus. The recently described strains of the species Streptococcus dentisani includes one previously referred to as 'S. mitis biovar 2'. Together with S. oralis, S. dentisani and S. tigurinus form subclusters within a coherent phylogenetic clade. We propose that the species S. oralis consists of three subspecies: S. oralis subsp. oralis subsp. nov., S. oralis subsp. tigurinus comb. nov., and S. oralis subsp. dentisani comb. nov.
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Affiliation(s)
- Anders Jensen
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 4, Aarhus 8000, Denmark
| | - Christian F P Scholz
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 4, Aarhus 8000, Denmark
| | - Mogens Kilian
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 4, Aarhus 8000, Denmark
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238
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Biogeographical Patterns of Legume-Nodulating Burkholderia spp.: from African Fynbos to Continental Scales. Appl Environ Microbiol 2016; 82:5099-115. [PMID: 27316955 DOI: 10.1128/aem.00591-16] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 05/24/2016] [Indexed: 12/31/2022] Open
Abstract
UNLABELLED Rhizobia of the genus Burkholderia have large-scale distribution ranges and are usually associated with South African papilionoid and South American mimosoid legumes, yet little is known about their genetic structuring at either local or global geographic scales. To understand variation at different spatial scales, from individual legumes in the fynbos (South Africa) to a global context, we analyzed chromosomal (16S rRNA, recA) and symbiosis (nifH, nodA, nodC) gene sequences. We showed that the global diversity of nodulation genes is generally grouped according to the South African papilionoid or South American mimosoid subfamilies, whereas chromosomal sequence data were unrelated to biogeography. While nodulation genes are structured on a continental scale, a geographic or host-specific distribution pattern was not detected in the fynbos region. In host range experiments, symbiotic promiscuity of Burkholderia tuberum STM678(T) and B phymatum STM815(T) was discovered in selected fynbos species. Finally, a greenhouse experiment was undertaken to assess the ability of mimosoid (Mimosa pudica) and papilionoid (Dipogon lignosus, Indigofera filifolia, Macroptilium atropurpureum, and Podalyria calyptrata) species to nodulate in South African (fynbos) and Malawian (savanna) soils. While the Burkholderia-philous fynbos legumes (D lignosus, I filifolia, and P calyptrata) nodulated only in their native soils, the invasive neotropical species M pudica did not develop nodules in the African soils. The fynbos soil, notably rich in Burkholderia, seems to retain nodulation genes compatible with the local papilionoid legume flora but is incapable of nodulating mimosoid legumes that have their center of diversity in South America. IMPORTANCE This study is the most comprehensive phylogenetic assessment of root-nodulating Burkholderia and investigated biogeographic and host-related patterns of the legume-rhizobial symbiosis in the South African fynbos biome, as well as at global scales, including native species from the South American Caatinga and Cerrado biomes. While a global investigation of the rhizobial diversity revealed distinct nodulation and nitrogen fixation genes among South African and South American legumes, regionally distributed species in the Cape region were unrelated to geographic and host factors.
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239
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Thibodeau G, Walsh DA, Beisner BE. Rapid eco-evolutionary responses in perturbed phytoplankton communities. Proc Biol Sci 2016; 282:rspb.2015.1215. [PMID: 26311667 DOI: 10.1098/rspb.2015.1215] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Biodiversity currently faces unprecedented threats owing to species extinctions. Ecologically, compensatory dynamics can ensure stable community biomass following perturbation. However, whether there is a contribution of genetic diversity to community responses is an outstanding question. To date, the contribution of evolutionary processes through genotype shifts has not been assessed in naturally co-occurring multi-species communities in the field. We examined the mechanisms contributing to the response of a lake phytoplankton community exposed to either a press or pulse acidification perturbation in lake mesocosms. To assess community shifts in the ecological response of morphospecies, we identified taxa microscopically. We also assessed genotype shifts by sequencing the ITS2 region of ribosomal DNA. We observed ecological and genetic contributions to community responses. The ecological response was attributed to compensatory morphospecies dynamics and occurred primarily in the Pulse perturbation treatment. In the Press treatments, in addition to compensatory dynamics, we observed evidence for genotype selection in two species of chlorophytes, Desmodesmus cuneatus and an unidentified Chlamydomonas. Our study demonstrates that while genotype selection may be rare, it is detectable and occurs especially when new environmental conditions are maintained for long enough to force selection processes on standing variation.
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240
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Grabova GY, Dragovoz IV, Zelena LB, Ostapchuk AN, Avdeeva LV. Polyphasic taxonomic analysis of Bacillus sp. strain C6—the antagonist of phytopathogenic microorganisms. CYTOL GENET+ 2016. [DOI: 10.3103/s0095452716040046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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241
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Delamuta JRM, Ribeiro RA, Araújo JLS, Rouws LFM, Zilli JÉ, Parma MM, Melo IS, Hungria M. Bradyrhizobium stylosanthis sp. nov., comprising nitrogen-fixing symbionts isolated from nodules of the tropical forage legume Stylosanthes spp. Int J Syst Evol Microbiol 2016; 66:3078-3087. [DOI: 10.1099/ijsem.0.001148] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jakeline Renata Marçon Delamuta
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, SBN, Quadra 2, BlocoL, Lote 06, Edifício Capes, 70.040-020 Brasília, Distrito Federal, Brazil
| | - Renan Augusto Ribeiro
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001 Brasília, Distrito Federal, Brazil
| | | | | | - Jerri Édson Zilli
- Embrapa Agrobiologia, C.P. 74.505, 23891-000 Seropédica, Rio de Janeiro, Brazil
| | | | | | - Mariangela Hungria
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001 Brasília, Distrito Federal, Brazil
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242
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Porter SS, Chang PL, Conow CA, Dunham JP, Friesen ML. Association mapping reveals novel serpentine adaptation gene clusters in a population of symbiotic Mesorhizobium. ISME JOURNAL 2016; 11:248-262. [PMID: 27420027 PMCID: PMC5315480 DOI: 10.1038/ismej.2016.88] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 05/23/2016] [Accepted: 05/25/2016] [Indexed: 01/18/2023]
Abstract
The genetic variants that underlie microbial environmental adaptation are key components of models of microbial diversification. Characterizing adaptive variants and the pangenomic context in which they evolve remains a frontier in understanding how microbial diversity is generated. The genomics of rhizobium adaptation to contrasting soil environments is ecologically and agriculturally important because these bacteria are responsible for half of all current biologically fixed nitrogen, yet they live the majority of their lives in soil. Our study uses whole-genome sequencing to describe the pan-genome of a focal clade of wild mesorhizobia that show contrasting levels of nickel adaptation despite high relatedness (99.8% identity at 16S). We observe ecotypic specialization within an otherwise genomically cohesive population, rather than finding distinct specialized bacterial lineages in contrasting soil types. This finding supports recent reports that heterogeneous environments impose selection that maintains differentiation only at a small fraction of the genome. Our work further uses a genome-wide association study to propose candidate genes for nickel adaptation. Several candidates show homology to genetic systems involved in nickel tolerance and one cluster of candidates correlates perfectly with soil origin, which validates our approach of ascribing genomic variation to adaptive divergence.
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Affiliation(s)
- Stephanie S Porter
- School of Biological Sciences, Washington State University, Vancouver, WA, USA
| | - Peter L Chang
- Section of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.,Department of Plant Pathology and Nematology, University of California, Davis, CA, USA
| | - Christopher A Conow
- Section of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Joseph P Dunham
- Section of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Maren L Friesen
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
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243
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Bálint M, Bahram M, Eren AM, Faust K, Fuhrman JA, Lindahl B, O'Hara RB, Öpik M, Sogin ML, Unterseher M, Tedersoo L. Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes. FEMS Microbiol Rev 2016; 40:686-700. [DOI: 10.1093/femsre/fuw017] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2016] [Indexed: 11/13/2022] Open
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244
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Okura M, Osaki M, Nomoto R, Arai S, Osawa R, Sekizaki T, Takamatsu D. Current Taxonomical Situation of Streptococcus suis. Pathogens 2016; 5:pathogens5030045. [PMID: 27348006 PMCID: PMC5039425 DOI: 10.3390/pathogens5030045] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 06/09/2016] [Accepted: 06/20/2016] [Indexed: 12/31/2022] Open
Abstract
Streptococcus suis, a major porcine pathogen and an important zoonotic agent, is considered to be composed of phenotypically and genetically diverse strains. However, recent studies reported several “S. suis-like strains” that were identified as S. suis by commonly used methods for the identification of this bacterium, but were regarded as distinct species from S. suis according to the standards of several taxonomic analyses. Furthermore, it has been suggested that some S. suis-like strains can be assigned to several novel species. In this review, we discuss the current taxonomical situation of S. suis with a focus on (1) the classification history of the taxon of S. suis; (2) S. suis-like strains revealed by taxonomic analyses; (3) methods for detecting and identifying this species, including a novel method that can distinguish S. suis isolates from S. suis-like strains; and (4) current topics on the reclassification of S. suis-like strains.
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Affiliation(s)
- Masatoshi Okura
- Division of Bacterial and Parasitic Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan.
| | - Makoto Osaki
- Division of Bacterial and Parasitic Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan.
| | - Ryohei Nomoto
- Department of Infectious Diseases, Kobe Institute of Health, 4-6-5 Minatojima-Nakamachi, Chuo-ku, Kobe, Hyogo 650-0045, Japan.
| | - Sakura Arai
- Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
| | - Ro Osawa
- Organization for Advanced Science and Technology, Kobe University, 1-1 Rokko-dai, Nada-ku, Kobe, Hyogo 657-8501, Japan.
| | - Tsutomu Sekizaki
- Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
| | - Daisuke Takamatsu
- Division of Bacterial and Parasitic Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan.
- The United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan.
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245
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Hanson CA, Marston MF, Martiny JBH. Biogeographic Variation in Host Range Phenotypes and Taxonomic Composition of Marine Cyanophage Isolates. Front Microbiol 2016; 7:983. [PMID: 27446023 PMCID: PMC4919323 DOI: 10.3389/fmicb.2016.00983] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/07/2016] [Indexed: 11/13/2022] Open
Abstract
Despite the important role of phages in marine systems, little is understood about how their diversity is distributed in space. Biogeographic patterns of marine phages may be difficult to detect due to their vast genetic diversity, which may not be accurately represented by conserved marker genes. To investigate the spatial biogeographic structure of marine phages, we isolated over 400 cyanophages on Synechococcus host strain WH7803 at three coastal locations in the United States (Rhode Island, Washington, and southern California). Approximately 90% of the cyanophage isolates were myoviruses, while the other 10% were podoviruses. The diversity of isolates was further characterized in two ways: (i) taxonomically, using conserved marker genes and (ii) phenotypically, by testing isolates for their ability to infect a suite of hosts, or their "host range." Because host range is a highly variable trait even among closely related isolates, we hypothesized that host range phenotypes of cyanophage isolates would vary more strongly among locations than would taxonomic composition. Instead, we found evidence for strong biogeographic variation both in taxonomic composition and host range phenotypes, with little taxonomic overlap among the three coastal regions. For both taxonomic composition and host range phenotypes, cyanophage communities from California and Rhode Island were the most dissimilar, while Washington communities exhibited similarity to each of the other two locations. These results suggest that selection imposed by spatial variation in host dynamics influence the biogeographic distribution of cyanophages.
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Affiliation(s)
- China A Hanson
- School of Biological and Chemical Sciences, Queen Mary University of London, LondonUK; Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CAUSA
| | - Marcia F Marston
- Department of Biology and Marine Biology, Roger Williams University, Bristol, RI USA
| | - Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA USA
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246
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Coutinho FH, Dutilh BE, Thompson CC, Thompson FL. Proposal of fifteen new species of Parasynechococcus based on genomic, physiological and ecological features. Arch Microbiol 2016; 198:973-986. [PMID: 27339259 DOI: 10.1007/s00203-016-1256-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 05/23/2016] [Accepted: 06/07/2016] [Indexed: 01/24/2023]
Abstract
Members of the recently proposed genus Parasynechococcus (Cyanobacteria) are extremely abundant throughout the global ocean and contribute significantly to global primary productivity. However, the taxonomy of these organisms remains poorly characterized. The aim of this study was to propose a new taxonomic framework for Parasynechococcus based on a genomic taxonomy approach that incorporates genomic, physiological and ecological data. Through in silico DNA-DNA hybridization, average amino acid identity, dinucleotide signatures and phylogenetic reconstruction, a total of 15 species of Parasynechococcus could be delineated. Each species was then described on the basis of their gene content, light and nutrient utilization strategies, geographical distribution patterns throughout the oceans and response to environmental parameters.
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Affiliation(s)
- F H Coutinho
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - B E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - C C Thompson
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - F L Thompson
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
- COPPE, SAGE, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
- CCS, IB, BIOMAR, Laboratório de Microbiologia, Cidade Universitária, Av. Carlos Chagas Filho. S/N, BLOCO A (Anexo) A3 - sl 102, Rio de Janeiro, RJ, 21941-599, Brazil.
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247
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Sami D, Mokhtar R, Peter M, Mohamed M. Rhizobium leguminosarum symbiovar trifolii, Ensifer numidicus and Mesorhizobium amorphae symbiovar ciceri (or Mesorhizobium loti) are new endosymbiotic bacteria of Lens culinaris Medik. FEMS Microbiol Ecol 2016; 92:fiw118. [PMID: 27267929 DOI: 10.1093/femsec/fiw118] [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] [Accepted: 05/29/2016] [Indexed: 11/13/2022] Open
Abstract
A total of 142 rhizobial bacteria were isolated from root nodules of Lens culinaris Medik endemic to Tunisia and they belonged to the species Rhizobium leguminosarum, and for the first time to Ensifer and Mesorhizobium, genera never previously described as microsymbionts of lentil. Phenotypically, our results indicate that L. culinaris Medik strains showed heterogenic responses to the different phenotypic features and they effectively nodulated their original host. Based on the concatenation of the 16S rRNA with relevant housekeeping genes (glnA, recA, dnaK), rhizobia that nodulate lentil belonged almost exclusively to the known R. leguminosarum sv. viciae. Interestingly, R. leguminosarum sv. trifolii, Ensifer numidicus (10 isolates) and Mesorhizobium amorphae (or M. loti) (9 isolates) isolates species, not considered, up to now, as a natural symbiont of lentil are reported. The E. numidicus and M. amorphae (or M. loti) strains induced fixing nodules on Medicago sativa and Cicer arietinum host plants, respectively. Symbiotic gene phylogenies showed that the E. numidicus, new symbiont of lentil, markedly diverged from strains of R. leguminosarum, the usual symbionts of lentil, and converged to the symbiovar meliloti so far described within E. meliloti Indeed, the nodC and nodA genes from the M. amorphae showed more than 99% similarity with respect to those from M. mediterraneum, the common chickpea nodulating species, and would be included in the new infrasubspecific division named M. amorphae symbiovar ciceri, or to M. loti, related to the strains able to effectively nodulate C. arietinum host plant. On the basis of these data, R. leguminosarum sv. trifolii (type strain LBg3 (T)), M. loti or M. amorphae sv. ciceri (type strain LB4 (T)) and E. numidicus (type strain LBi2 (T)) are proposed as new symbionts of L. culinaris Medik.
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Affiliation(s)
- Dhaoui Sami
- Research Unit Biodiversity & Valorization of Arid Areas Bioressources, Faculty of Sciences of Gabès, Erriadh-Zrig, Gabes 6072, Tunisia
| | - Rejili Mokhtar
- Research Unit Biodiversity & Valorization of Arid Areas Bioressources, Faculty of Sciences of Gabès, Erriadh-Zrig, Gabes 6072, Tunisia
| | - Mergaert Peter
- Institute for IntegrativeBiology of the Cell, Centre National de la Recherche Scientifique, Avenue de la Terrasse Bât. 34, 91198 Gif-sur-Yvette, France
| | - Mars Mohamed
- Research Unit Biodiversity & Valorization of Arid Areas Bioressources, Faculty of Sciences of Gabès, Erriadh-Zrig, Gabes 6072, Tunisia
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248
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Randle-Boggis RJ, Helgason T, Sapp M, Ashton PD. Evaluating techniques for metagenome annotation using simulated sequence data. FEMS Microbiol Ecol 2016; 92:fiw095. [PMID: 27162180 PMCID: PMC4892715 DOI: 10.1093/femsec/fiw095] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2016] [Indexed: 11/29/2022] Open
Abstract
The advent of next-generation sequencing has allowed huge amounts of DNA sequence data to be produced, advancing the capabilities of microbial ecosystem studies. The current challenge is to identify from which microorganisms and genes the DNA originated. Several tools and databases are available for annotating DNA sequences. The tools, databases and parameters used can have a significant impact on the results: naïve choice of these factors can result in a false representation of community composition and function. We use a simulated metagenome to show how different parameters affect annotation accuracy by evaluating the sequence annotation performances of MEGAN, MG-RAST, One Codex and Megablast. This simulated metagenome allowed the recovery of known organism and function abundances to be quantitatively evaluated, which is not possible for environmental metagenomes. The performance of each program and database varied, e.g. One Codex correctly annotated many sequences at the genus level, whereas MG-RAST RefSeq produced many false positive annotations. This effect decreased as the taxonomic level investigated increased. Selecting more stringent parameters decreases the annotation sensitivity, but increases precision. Ultimately, there is a trade-off between taxonomic resolution and annotation accuracy. These results should be considered when annotating metagenomes and interpreting results from previous studies. The sequence annotation accuracies of metagenomic analysis tools were evaluated using a simulated metagenome.
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Affiliation(s)
| | | | - Melanie Sapp
- Fera Science Ltd, Sand Hutton, York YO41 1LZ, UK
| | - Peter D Ashton
- Department of Biology, University of York, York YO10 5DD, UK
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249
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Jancusova M, Kovacik L, Pereira AB, Dusinsky R, Wilmotte A. Polyphasic characterization of 10 selected ecologically relevant filamentous cyanobacterial strains from the South Shetland Islands, Maritime Antarctica. FEMS Microbiol Ecol 2016; 92:fiw100. [DOI: 10.1093/femsec/fiw100] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2016] [Indexed: 11/14/2022] Open
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250
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Benefit of transferred mutations is better predicted by the fitness of recipients than by their ecological or genetic relatedness. Proc Natl Acad Sci U S A 2016; 113:5047-52. [PMID: 27091964 DOI: 10.1073/pnas.1524988113] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The effect of a mutation depends on its interaction with the genetic background in which it is assessed. Studies in experimental systems have demonstrated that such interactions are common among beneficial mutations and often follow a pattern consistent with declining evolvability of more fit genotypes. However, these studies generally examine the consequences of interactions between a small number of focal mutations. It is not clear, therefore, that findings can be extrapolated to natural populations, where new mutations may be transferred between genetically divergent backgrounds. We build on work that examined interactions between four beneficial mutations selected in a laboratory-evolved population of Escherichia coli to test how they interact with the genomes of diverse natural isolates of the same species. We find that the fitness effect of transferred mutations depends weakly on the genetic and ecological similarity of recipient strains relative to the donor strain in which the mutations were selected. By contrast, mutation effects were strongly inversely correlated to the initial fitness of the recipient strain. That is, there was a pattern of diminishing returns whereby fit strains benefited proportionally less from an added mutation. Our results strengthen the view that the fitness of a strain can be a major determinant of its ability to adapt. They also support a role for barriers of transmission, rather than differential selection of transferred DNA, as an explanation of observed phylogenetically determined patterns of restricted recombination among E. coli strains.
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