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Garavaglia M, Muzlera A, Valverde C. Comparative genomics and informational content analysis uncovered internal regions of the core genes rpoD, pepN and gltX for an MLSA with genome-level resolving power within the genus Pseudomonas. Mol Phylogenet Evol 2023; 179:107663. [PMID: 36372354 DOI: 10.1016/j.ympev.2022.107663] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 08/31/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
Abstract
In the field of prokaryotic taxonomy, there has been a recent transition towards phylogenomics as the gold standard approach. However, genome-based phylogenetics is still restrictive for its cost when managing large amounts of isolates. Fast, cheap, and taxonomically competent alternatives, like multilocus sequence analysis (MLSA) are thus recommendable. Nevertheless, the criteria for selecting the conserved genes for MLSA have not been explicit for different bacterial taxa, including the broadly diverse Pseudomonas genus. Here, we have carried out an unbiased and rational workflow to select internal sequence regions of Pseudomonas core genes (CG) for a MLSA with the best phylogenetic power, and with a resolution comparable to the genome-based ANI approach. A computational workflow was established to inspect 126 complete genomes of representatives from over 60 Pseudomonas species and subspecies, in order to identify the most informative CG internal regions and determine which combinations in sets of three partial CG sequences have comparable phylogenetic resolution to that of the current ANI standard. We found that the rpoD346-1196-pepN1711-2571-gltX86-909 concatenated sequences were the best performing in terms of phylogenetic robustness and resulted highly sensitive and specific when contrasted with ANI. The rpoD-pepN-gltX MLSA was validated in silico and in vitro. Altogether, the results presented here supports the proposal of the rpoD-pepN-gltX MLSA as a fast, affordable, and robust phylogenetic tool for members of the Pseudomonas genus.
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Affiliation(s)
- Matías Garavaglia
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Centro de Bioquímica y Microbiología del Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina
| | - Andrés Muzlera
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Centro de Bioquímica y Microbiología del Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina
| | - Claudio Valverde
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Centro de Bioquímica y Microbiología del Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina.
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Geraerts M, Huyse T, Barson M, Bassirou H, Bilong Bilong CF, Bitja Nyom AR, Chocha Manda A, Cruz-Laufer AJ, Kalombo Kabalika C, Kapepula Kasembele G, Muterezi Bukinga F, Njom S, Artois T, Vanhove MPM. Mosaic or melting pot: The use of monogeneans as a biological tag and magnifying glass to discriminate introduced populations of Nile tilapia in sub-Saharan Africa. Genomics 2022; 114:110328. [PMID: 35276332 DOI: 10.1016/j.ygeno.2022.110328] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 02/10/2022] [Accepted: 03/06/2022] [Indexed: 01/14/2023]
Abstract
The origin of introduced Nile tilapia stocks in sub-Saharan Africa is largely unknown. In this study, the potential of monogeneans as a biological tag and magnifying glass is tested to reveal their hosts' stocking history. The monogenean gill community of different Nile tilapia populations in sub-Saharan Africa was explored, and a phylogeographic analysis was performed based on the mitogenomes of four dactylogyrid species (Cichlidogyrus halli, C. sclerosus, C. thurstonae, and Scutogyrus longicornis). Our results encourage the use of dactylogyrids as biological tags. The magnifying glass hypothesis is only confirmed for C. thurstonae, highlighting the importance of the absence of other potential hosts as prerequisites for a parasite to act as a magnifying glass. With the data generated here, we are the first to extract mitogenomes from individual monogeneans and to perform an upscaled survey of the comparative phylogeography of several monogenean species with unprecedented diagnostic resolution.
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Affiliation(s)
- Mare Geraerts
- UHasselt - Hasselt University, Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Diepenbeek, Belgium.
| | - Tine Huyse
- Department of Biology, Royal Museum for Central Africa, Tervuren, Belgium
| | - Maxwell Barson
- Department of Biological Sciences, University of Zimbabwe, Harare, Zimbabwe; Department of Biological Sciences, University of Botswana, Gaborone, Botswana; Lake Kariba Research Station, University of Zimbabwe, Kariba, Zimbabwe
| | - Hassan Bassirou
- Department of Biological Sciences, University of Ngaoundéré, Ngaoundéré, Cameroon
| | | | - Arnold R Bitja Nyom
- Department of Biological Sciences, University of Ngaoundéré, Ngaoundéré, Cameroon; Department of Management of Fisheries and Aquatic Ecosystems, Institute of Fisheries, University of Douala, Douala, Cameroon
| | - Auguste Chocha Manda
- Unité de Recherche en Biodiversité et Exploitation durable des Zones Humides (BEZHU), Faculté des Sciences Agronomiques, Université de Lubumbashi, Lubumbashi, Democratic Republic of the Congo
| | - Armando J Cruz-Laufer
- UHasselt - Hasselt University, Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Diepenbeek, Belgium
| | - Clément Kalombo Kabalika
- Unité de Recherche en Biodiversité et Exploitation durable des Zones Humides (BEZHU), Faculté des Sciences Agronomiques, Université de Lubumbashi, Lubumbashi, Democratic Republic of the Congo
| | - Gyrhaiss Kapepula Kasembele
- Unité de Recherche en Biodiversité et Exploitation durable des Zones Humides (BEZHU), Faculté des Sciences Agronomiques, Université de Lubumbashi, Lubumbashi, Democratic Republic of the Congo
| | - Fidel Muterezi Bukinga
- Section de Parasitologie, Département de Biologie, Centre de Recherche en Hydrobiologie, Uvira, Democratic Republic of the Congo
| | - Samuel Njom
- Department of Biological Sciences, University of Ngaoundéré, Ngaoundéré, Cameroon
| | - Tom Artois
- UHasselt - Hasselt University, Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Diepenbeek, Belgium
| | - Maarten P M Vanhove
- UHasselt - Hasselt University, Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Diepenbeek, Belgium; Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
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tuf Gene Sequence Variation in Bifidobacterium longum subsp. infantis Detected in the Fecal Microbiota of Chinese Infants. Appl Environ Microbiol 2018; 84:AEM.00336-18. [PMID: 29703739 DOI: 10.1128/aem.00336-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/20/2018] [Indexed: 12/12/2022] Open
Abstract
Members of the bacterial genus Bifidobacterium generally dominate the fecal microbiota of infants. The species Bifidobacterium longum is prevalent, but the B. longum subsp. longum and B. longum subsp. infantis strains that are known to colonize the infant bowel are not usually differentiated in microbiota investigations. These subspecies differ in their capacities to metabolize human milk oligosaccharides (HMO) and may have different ecological and symbiotic roles in humans. Quantitative PCR provides a quick analytical method by which to accurately ascertain the abundances of target species in microbiotas and microcosms. However, amplification targets in DNA extracted from samples need to be dependably differential. We evaluated the tuf gene sequence as a molecular target for quantitative PCR measurements of the abundances of B. longum subsp. infantis and B. longum subsp. longum in fecal microbiotas. This approach resulted in the detection of a tuf gene variant (operational taxonomic unit 49 [OTU49]) in Chinese infants that has sequence similarities to both B. longum subsp. infantis and B. longum subsp. longum We compared the genome sequence and growth and transcriptional characteristics of an OTU49 isolate cultured in HMO medium to those of other B. longum subsp. infantis cultures. We concluded from these studies that OTU49 belongs to B. longum subsp. infantis, that dependable quantitative PCR (qPCR) differentiation between the B. longum subspecies cannot be achieved by targeting tuf gene sequences, and that functional genes involved in carbohydrate metabolism might be better targets because they delineate ecological functions.IMPORTANCE High-throughput DNA sequencing methods and advanced bioinformatics analysis have revealed the composition and biochemical capacities of microbial communities (microbiota and microbiome), including those that inhabit the gut of human infants. However, the microbiology and function of natural ecosystems have received little attention in recent decades, so an appreciation of the dynamics of gut microbiota interactions is lacking. With respect to infants, rapid methodologies, such as quantitative PCR, are needed to determine the prevalences and proportions of different bifidobacterial species in observational and microcosm studies in order to obtain a better understanding of the dynamics of bifidobacterial nutrition and syntrophy, knowledge that might be used to manipulate the microbiota and perhaps ensure the better health of infants.
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Lopes-Santos L, Castro DBA, Ferreira-Tonin M, Corrêa DBA, Weir BS, Park D, Ottoboni LMM, Neto JR, Destéfano SAL. Reassessment of the taxonomic position of Burkholderia andropogonis and description of Robbsia andropogonis gen. nov., comb. nov. Antonie Van Leeuwenhoek 2017; 110:727-736. [PMID: 28190154 DOI: 10.1007/s10482-017-0842-6] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 02/01/2017] [Indexed: 10/20/2022]
Abstract
The phylogenetic classification of the species Burkholderia andropogonis within the Burkholderia genus was reassessed using 16S rRNA gene phylogenetic analysis and multilocus sequence analysis (MLSA). Both phylogenetic trees revealed two main groups, named A and B, strongly supported by high bootstrap values (100%). Group A encompassed all of the Burkholderia species complex, whi.le Group B only comprised B. andropogonis species, with low percentage similarities with other species of the genus, from 92 to 95% for 16S rRNA gene sequences and 83% for conserved gene sequences. Average nucleotide identity (ANI), tetranucleotide signature frequency, and percentage of conserved proteins POCP analyses were also carried out, and in the three analyses B. andropogonis showed lower values when compared to the other Burkholderia species complex, near 71% for ANI, from 0.484 to 0.724 for tetranucleotide signature frequency, and around 50% for POCP, reinforcing the distance observed in the phylogenetic analyses. Our findings provide an important insight into the taxonomy of B. andropogonis. It is clear from the results that this bacterial species exhibits genotypic differences and represents a new genus described herein as Robbsia andropogonis gen. nov., comb. nov.
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Affiliation(s)
- Lucilene Lopes-Santos
- Laboratório de Bacteriologia Vegetal, Instituto Biológico, Rod. Heitor Penteado KM 3, Campinas, SP, CEP 13092-543, Brazil
| | - Daniel Bedo Assumpção Castro
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas - UNICAMP, Campinas, Brazil
| | - Mariana Ferreira-Tonin
- Laboratório de Bacteriologia Vegetal, Instituto Biológico, Rod. Heitor Penteado KM 3, Campinas, SP, CEP 13092-543, Brazil
| | - Daniele Bussioli Alves Corrêa
- Laboratório de Bacteriologia Vegetal, Instituto Biológico, Rod. Heitor Penteado KM 3, Campinas, SP, CEP 13092-543, Brazil
| | | | - Duckchul Park
- Landcare Research, Private Bag 92170, Auckland, New Zealand
| | | | - Júlio Rodrigues Neto
- Laboratório de Bacteriologia Vegetal, Instituto Biológico, Rod. Heitor Penteado KM 3, Campinas, SP, CEP 13092-543, Brazil
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Vollmers J, Voget S, Dietrich S, Gollnow K, Smits M, Meyer K, Brinkhoff T, Simon M, Daniel R. Poles apart: Arctic and Antarctic Octadecabacter strains share high genome plasticity and a new type of xanthorhodopsin. PLoS One 2013; 8:e63422. [PMID: 23671678 PMCID: PMC3646047 DOI: 10.1371/journal.pone.0063422] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 04/03/2013] [Indexed: 12/11/2022] Open
Abstract
The genus Octadecabacter is a member of the ubiquitous marine Roseobacter clade. The two described species of this genus, Octadecabacter arcticus and Octadecabacter antarcticus, are psychrophilic and display a bipolar distribution. Here we provide the manually annotated and finished genome sequences of the type strains O. arcticus 238 and O. antarcticus 307, isolated from sea ice of the Arctic and Antarctic, respectively. Both genomes exhibit a high genome plasticity caused by an unusually high density and diversity of transposable elements. This could explain the discrepancy between the low genome synteny and high 16S rRNA gene sequence similarity between both strains. Numerous characteristic features were identified in the Octadecabacter genomes, which show indications of horizontal gene transfer and may represent specific adaptations to the habitats of the strains. These include a gene cluster encoding the synthesis and degradation of cyanophycin in O. arcticus 238, which is absent in O. antarcticus 307 and unique among the Roseobacter clade. Furthermore, genes representing a new subgroup of xanthorhodopsins as an adaptation to icy environments are present in both Octadecabacter strains. This new xanthorhodopsin subgroup differs from the previously characterized xanthorhodopsins of Salinibacter ruber and Gloeobacter violaceus in phylogeny, biogeography and the potential to bind 4-keto-carotenoids. Biochemical characterization of the Octadecabacter xanthorhodopsins revealed that they function as light-driven proton pumps.
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Affiliation(s)
- John Vollmers
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Sonja Voget
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Sascha Dietrich
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Kathleen Gollnow
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Maike Smits
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Katja Meyer
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
- * E-mail:
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Kim W, Park HK, Hwang WJ, Shin HS. Simultaneous detection of Streptococcus pneumoniae, S. mitis, and S. oralis by a novel multiplex PCR assay targeting the gyrB gene. J Clin Microbiol 2013; 51:835-40. [PMID: 23269740 PMCID: PMC3592088 DOI: 10.1128/jcm.02920-12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 12/17/2012] [Indexed: 01/05/2023] Open
Abstract
A multiplex PCR (mPCR) protocol was developed for simultaneous detection of the gyrB gene in Streptococcus pneumoniae, Streptococcus mitis, and Streptococcus oralis, and the specificity was evaluated using 141 coccus strains. Genomic DNAs purified from S. pneumoniae, S. mitis, and S. oralis strains were efficiently detected with size differences, whereas no PCR products were amplified from any of the reference strains tested. A pilot study of 47 human oral swab specimens was conducted in parallel, and the mPCR assay identified S. pneumoniae in 1 sample, S. mitis in 8 samples, and S. oralis in 2 samples, providing a powerful means for characterization at the level of species compared with traditional culture analysis. Our results suggest that the mPCR protocol presented here is a sensitive and promising tool for the rapid detection and discrimination of S. pneumoniae, S. mitis, and S. oralis from clinical specimens.
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Affiliation(s)
- Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Hee Kuk Park
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Woo-Jin Hwang
- Department of Periodontology, Wonkwang University College of Dentistry, Iksan, Republic of Korea
| | - Hyoung-Shik Shin
- Department of Periodontology, Wonkwang University College of Dentistry, Iksan, Republic of Korea
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Bever JD, Broadhurst LM, Thrall PH. Microbial phylotype composition and diversity predicts plant productivity and plant-soil feedbacks. Ecol Lett 2012; 16:167-74. [PMID: 23216788 DOI: 10.1111/ele.12024] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 06/12/2012] [Accepted: 10/01/2012] [Indexed: 12/01/2022]
Abstract
The relationship between ecological variation and microbial genetic composition is critical to understanding microbial influence on community and ecosystem function. In glasshouse trials using nine native legume species and 40 rhizobial strains, we find that bacterial rRNA phylotype accounts for 68% of amoung isolate variability in symbiotic effectiveness and 79% of host specificity in growth response. We also find that rhizobial phylotype diversity and composition of soils collected from a geographical breadth of sites explains the growth responses of two acacia species. Positive soil microbial feedback between the two acacia hosts was largely driven by changes in diversity of rhizobia. Greater rhizobial diversity accumulated in association with the less responsive host species, Acacia salicina, and negatively affected the growth of the more responsive Acacia stenophylla. Together, this work demonstrates correspondence of phylotype with microbial function, and demonstrates that the dynamics of rhizobia on host species can feed back on plant population performance.
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Affiliation(s)
- James D Bever
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
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Tang L, Liu SL. The 3Cs provide a novel concept of bacterial species: messages from the genome as illustrated by Salmonella. Antonie van Leeuwenhoek 2011; 101:67-72. [PMID: 22113699 DOI: 10.1007/s10482-011-9680-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 11/13/2011] [Indexed: 11/26/2022]
Abstract
A key issue troubling bacterial taxonomy and systematics is the lack of a biological species definition. Criteria to be used for defining bacterial species on genetic and biological bases should be able to reveal clear-cut boundaries among clusters of bacteria. To date, DNA-DNA re-association assays and ribosomal RNA sequence comparison have been useful in determining relative evolutionary distances among bacteria but the data are continuous and thus cannot define bacterial clusters as taxonomic units to be called species. Using Salmonella as models, we have looked for definite genetic and biologic uniqueness of clusters of bacteria. Based on our findings that each Salmonella lineage has a unique genome structure shared by strains of the same lineage but not overlapping with strains of other Salmonella lineages, we conclude that this is a result of genetic isolation following divergence of the bacteria. We propose that there should be genetic boundaries between different species of bacteria at the genomic level, which awaits further genomic information for validation.
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Affiliation(s)
- Le Tang
- Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, China
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Symbiotic effectiveness of rhizobial mutualists varies in interactions with native Australian legume genera. PLoS One 2011; 6:e23545. [PMID: 21887270 PMCID: PMC3162553 DOI: 10.1371/journal.pone.0023545] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Accepted: 07/19/2011] [Indexed: 11/30/2022] Open
Abstract
Background and Objectives Interactions between plants and beneficial soil organisms (e.g. rhizobial bacteria, mycorrhizal fungi) are models for investigating the ecological impacts of such associations in plant communities, and the evolution and maintenance of variation in mutualisms (e.g. host specificity and the level of benefits provided). With relatively few exceptions, variation in symbiotic effectiveness across wild host species is largely unexplored. Methods We evaluated these associations using representatives of several legume genera which commonly co-occur in natural ecosystems in south-eastern Australia and an extensive set of rhizobial strains isolated from these hosts. These strains had been previously assigned to specific phylotypes on the basis of molecular analyses. In the first of two inoculation experiments, the growth responses of each host species was evaluated with rhizobial strains isolated from that species. The second experiment assessed performance across genera and the extent of host specificity using a subset of these strains. Results While host growth responses to their own (sympatric) isolates varied considerably, rhizobial phylotype was a significant predictor of symbiotic performance, indicating that bacterial species designations on the basis of molecular markers have ecological importance. Hosts responded in qualitatively different ways to sympatric and allopatric strains of rhizobia, ranging from species with a clear preference for their own strains, to those that were broad generalists, through to species that grew significantly better with allopatric strains. Conclusion Theory has focused on trade-offs between the provision of benefits and symbiont competitive ability that might explain the persistence of less beneficial strains. However, differences in performance among co-occurring host species could also drive such patterns. Our results thus highlight the likely importance of plant community structure in maintaining variation in symbiotic effectiveness.
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Maughan H, Van der Auwera G. Bacillus taxonomy in the genomic era finds phenotypes to be essential though often misleading. INFECTION GENETICS AND EVOLUTION 2011; 11:789-97. [PMID: 21334463 DOI: 10.1016/j.meegid.2011.02.001] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Revised: 01/31/2011] [Accepted: 02/01/2011] [Indexed: 11/25/2022]
Abstract
Bacillus is a diverse bacterial genus characterized by cells growing aerobically and forming dormant endospores. Although Bacillus species were some of the first bacteria ever characterized, their relationships to one another remain enigmatic. The recent deluge of environmental sequencing projects has further complicated our view of Bacillus taxonomy and diversity. In this review we discuss the current state of Bacillus taxonomy and focus on two examples that highlight the ecological diversity found within identical 16S rDNA-based clusters: the identification of ecologically distinct clusters of B. simplex in Evolution Canyons and the demarcation of species in the industrially and medically important B. cereus group. These examples highlight the difficulties of purely 16S rDNA-based taxonomy, emphasizing the need to interpret the massive amounts of molecular data from environmental sequencing projects in a bacterial ecology framework. Such interpretations are likely to reveal ecological diversity within Bacillus that extends beyond that previously imaginable, providing a true picture of Bacillus ecology and evolution.
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Affiliation(s)
- Heather Maughan
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St, Toronto, ON, Canada M5S 3B2.
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Plant growth-promoting activity in newly isolated Bacillus thioparus (NII-0902) from Western ghat forest, India. World J Microbiol Biotechnol 2010. [DOI: 10.1007/s11274-010-0418-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Peix A, Ramírez-Bahena MH, Velázquez E. Historical evolution and current status of the taxonomy of genus Pseudomonas. INFECTION GENETICS AND EVOLUTION 2009; 9:1132-47. [DOI: 10.1016/j.meegid.2009.08.001] [Citation(s) in RCA: 142] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2009] [Revised: 08/02/2009] [Accepted: 08/18/2009] [Indexed: 10/20/2022]
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Abstract
Variation in gene content has been hypothesized to be the primary mode of adaptive evolution in microorganisms; however, very little is known about the spatial and temporal distribution of variable genes. Through population-scale comparative genomics of 7 Sulfolobus islandicus genomes from 3 locations, we demonstrate the biogeographical structure of the pan-genome of this species, with no evidence of gene flow between geographically isolated populations. The evolutionary independence of each population allowed us to assess genome dynamics over very recent evolutionary time, beginning approximately 910,000 years ago. On this time scale, genome variation largely consists of recent strain-specific integration of mobile elements. Localized sectors of parallel gene loss are identified; however, the balance between the gain and loss of genetic material suggests that S. islandicus genomes acquire material slowly over time, primarily from closely related Sulfolobus species. Examination of the genome dynamics through population genomics in S. islandicus exposes the process of allopatric speciation in thermophilic Archaea and brings us closer to a generalized framework for understanding microbial genome evolution in a spatial context.
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Singh S, Goswami P, Singh R, Heller KJ. Application of molecular identification tools for Lactobacillus, with a focus on discrimination between closely related species: A review. Lebensm Wiss Technol 2009. [DOI: 10.1016/j.lwt.2008.05.019] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Hayward D, van Helden PD, Wiid IJF. Glutamine synthetase sequence evolution in the mycobacteria and their use as molecular markers for Actinobacteria speciation. BMC Evol Biol 2009; 9:48. [PMID: 19245690 PMCID: PMC2667176 DOI: 10.1186/1471-2148-9-48] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2008] [Accepted: 02/26/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although the gene encoding for glutamine synthetase (glnA) is essential in several organisms, multiple glnA copies have been identified in bacterial genomes such as those of the phylum Actinobacteria, notably the mycobacterial species. Intriguingly, previous reports have shown that only one copy (glnA1) is essential for growth in M. tuberculosis, while the other copies (glnA2, glnA3 and glnA4) are not. RESULTS In this report it is shown that the glnA1 and glnA2 encoded glutamine synthetase sequences were inherited from an Actinobacteria ancestor, while the glnA4 and glnA3 encoded GS sequences were sequentially acquired during Actinobacteria speciation. The glutamine synthetase sequences encoded by glnA4 and glnA3 are undergoing reductive evolution in the mycobacteria, whilst those encoded by glnA1 and glnA2 are more conserved. CONCLUSION Different selective pressures by the ecological niche that the organisms occupy may influence the sequence evolution of glnA1 and glnA2 and thereby affecting phylogenies based on the protein sequences they encode. The findings in this report may impact the use of similar sequences as molecular markers, as well as shed some light on the evolution of glutamine synthetase in the mycobacteria.
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Affiliation(s)
- Don Hayward
- DST/NRF Centre for Excellence in Biomedical Tuberculosis Research, US/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences - Stellenbosch University, South Africa.
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Konstantinidis KT, DeLong EF. Genomic patterns of recombination, clonal divergence and environment in marine microbial populations. ISME JOURNAL 2008; 2:1052-65. [PMID: 18580971 DOI: 10.1038/ismej.2008.62] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Microorganisms represent the largest reservoir of biodiversity on Earth, both in numbers and total genetic diversity, but it remains unclear whether this biodiversity is organized in discrete units that correspond to ecologically coherent species. To further explore this question, we examined patterns of genomic diversity in sympatric microbial populations. Analyses of a total of approximately 200 Mb of microbial community genomic DNA sequence recovered from 4000 m depth in the Pacific Ocean revealed discrete sequence-defined populations of Bacteria and Archaea, with intrapopulation genomic sequence divergence ranging from approximately 1% to approximately 6%. The populations appeared to be maintained, at least in part, by intrapopulation genetic exchange (homologous recombination), although the frequency of recombination was estimated to be about three times lower than that observed previously in thermoacidophilic archaeal biofilm populations. Furthermore, the genotypes of a given population were clearly distinguishable from their closest co-occurring relatives based on their relative abundance in situ. The genetic distinctiveness and the matching sympatric abundances imply that these genotypes share similar ecophysiological properties, and therefore may represent fundamental units of microbial diversity in the deep sea. Comparisons to surface-dwelling relatives of the Sargasso Sea revealed that distinct sequence-based clusters were not always detectable, presumably due to environmental variations, further underscoring the important relationship between environmental contexts and genetic mechanisms, which together shape and sustain microbial population structure.
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17
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Volokhov DV, Neverov AA, George J, Kong H, Liu SX, Anderson C, Davidson MK, Chizhikov V. Genetic analysis of housekeeping genes of members of the genus Acholeplasma: Phylogeny and complementary molecular markers to the 16S rRNA gene. Mol Phylogenet Evol 2007; 44:699-710. [PMID: 17267242 DOI: 10.1016/j.ympev.2006.12.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2006] [Revised: 11/29/2006] [Accepted: 12/01/2006] [Indexed: 11/27/2022]
Abstract
The partial nucleotide sequences of the rpoB and gyrB genes as well as the complete sequence of the 16S-23S rRNA intergenic transcribed spacer (ITS) were determined for all known Acholeplasma species. The same genes of Mesoplasma and Entomoplasma species were also sequenced and used to infer phylogenetic relationships among the species within the orders Entomoplasmatales and Acholeplasmatales. The comparison of the ITS, rpoB, and gyrB phylogenetic trees with the 16S rRNA phylogenetic tree revealed a similar branch topology suggesting that the ITS, rpoB, and gyrB could be useful complementary phylogenetic markers for investigation of evolutionary relationships among Acholeplasma species. Thus, the multilocus phylogenetic analysis of Acholeplasma multilocale sequence data (ATCC 49900 (T) = PN525 (NCTC 11723)) strongly indicated that this organism is most closely related to the genera Mesoplasma and Entomoplasma (family Entomoplasmataceae) and form the branch with Mesoplasma seiffertii, Mesoplasma syrphidae, and Mesoplasma photuris. The closest genetic relatedness of this species to the order Entomoplasmatales was additionally supported by the finding that A. multilocale uses UGA as the tryptophan codon in its gyrB and gyrA sequences. Use of the UGA codon for encoding tryptophan was previously reported as a unique genetic feature of Entomoplasmatales and Mycoplasmatales but not of Acholeplasmatales. These data, as well as previously published data on metabolic features of A. multilocale, leads to the proposal to reclassify A. multilocale as a member of the family Entomoplasmataceae.
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Affiliation(s)
- Dmitriy V Volokhov
- Center for Biologics Evaluation and Research, Food and Drug Administration, 1401 Rockville Pike, HFM-470, Rockville, MD 20852, USA.
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18
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Sikorski J. Populations under microevolutionary scrutiny: what will we gain? Arch Microbiol 2007; 189:1-5. [PMID: 17668186 DOI: 10.1007/s00203-007-0294-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2007] [Accepted: 07/15/2007] [Indexed: 10/23/2022]
Abstract
Understanding the evolution of biodiversity and the function of biological systems are burning and linked questions in biology. Evolution of biodiversity begins at the level of microevolution, with the differentiation of individuals in populations. The study of this process splits into two conceptually different approaches (1) the concept of functional biology of testing hypothesis by precisely controlled and forward-directed experiments (digital and experimental evolution), and (2) the concept of a theory-based historical narrative (testing hypothesis on events in the past for their suitability to best explain the present). Here, I discuss and emphasize the benefits of the study of natural bacterial populations for a deeper understanding of prokaryotic biology. Also, I adress current problems in taxonomy at the 'species' level which obviously need discussion and clarification. I exemplify this with a natural model population for such studies, Bacillus simplex from "Evolution Canyon", Israel.
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Affiliation(s)
- Johannes Sikorski
- DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstrasse 7 B, 38124 Braunschweig, Germany.
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19
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Ward DM, Cohan FM, Bhaya D, Heidelberg JF, Kühl M, Grossman A. Genomics, environmental genomics and the issue of microbial species. Heredity (Edinb) 2007; 100:207-19. [PMID: 17551524 DOI: 10.1038/sj.hdy.6801011] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
A microbial species concept is crucial for interpreting the variation detected by genomics and environmental genomics among cultivated microorganisms and within natural microbial populations. Comparative genomic analyses of prokaryotic species as they are presently described and named have led to the provocative idea that prokaryotes may not form species as we think about them for plants and animals. There are good reasons to doubt whether presently recognized prokaryotic species are truly species. To achieve a better understanding of microbial species, we believe it is necessary to (i) re-evaluate traditional approaches in light of evolutionary and ecological theory, (ii) consider that different microbial species may have evolved in different ways and (iii) integrate genomic, metagenomic and genome-wide expression approaches with ecological and evolutionary theory. Here, we outline how we are using genomic methods to (i) identify ecologically distinct populations (ecotypes) predicted by theory to be species-like fundamental units of microbial communities, and (ii) test their species-like character through in situ distribution and gene expression studies. By comparing metagenomic sequences obtained from well-studied hot spring cyanobacterial mats with genomic sequences of two cultivated cyanobacterial ecotypes, closely related to predominant native populations, we can conduct in situ population genetics studies that identify putative ecotypes and functional genes that determine the ecotypes' ecological distinctness. If individuals within microbial communities are found to be grouped into ecologically distinct, species-like populations, knowing about such populations should guide us to a better understanding of how genomic variation is linked to community function.
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Affiliation(s)
- D M Ward
- Department of Land Resources and Environmental Science, Montana State University, Bozeman, MT 59715, USA.
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20
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Pérez-Ibarra BM, Flores ME, García-Varela M. Isolation and characterization ofBacillus thioparussp. nov., chemolithoautotrophic, thiosulfate-oxidizing bacterium. FEMS Microbiol Lett 2007; 271:289-96. [PMID: 17451444 DOI: 10.1111/j.1574-6968.2007.00729.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
A novel bacterium, strain BMP-1(T), was isolated from a continuous wastewater treatment culture system operating with a bacterial consortium. Cells of the isolate were Gram-variable, aerobic, moderately halotolerant, motile and endospore-forming rods. Strain BMP-1(T) grew chemolithoautotrophically by oxidation of thiosulfate to sulfate with a growth yield of 1.07 g protein mol(-1) of thiosulfate consumed. DNA G+C content was 43.8 mol%. Its cell wall had peptidoglycan based on m-diaminopimelic acid, and the major component of fatty acid was C(15 : 0). The 16S rRNA gene analysis showed that strain belongs to the genus Bacillus, sharing a 99.5% of sequence similarity with Bacillus jeotgali CCM 7133(T). DNA-DNA hybridization between the isolate of this study and this strain was 44%. Thus, the inclusion of strain BMP-1(T) in the genus Bacillus is suggested as a novel species and the name Bacillus thioparus sp. nov. (Type strain BMP-1(T)=BM-B-436(T)=CECT 7196(T)) is proposed. The sequence of the 16S rRNA gene has been deposited in GenBank with accession number DQ371431.
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21
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Pontes DS, Lima-Bittencourt CI, Chartone-Souza E, Amaral Nascimento AM. Molecular approaches: advantages and artifacts in assessing bacterial diversity. J Ind Microbiol Biotechnol 2007; 34:463-73. [PMID: 17476541 DOI: 10.1007/s10295-007-0219-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2006] [Accepted: 03/27/2007] [Indexed: 10/23/2022]
Abstract
Bacteria account for a major proportion of Earth's biological diversity. They play essential roles in quite diverse environments and there has been an increasing interest in bacterial biodiversity. Research using novel and efficient tools to identify and characterize bacterial communities has been the key for elucidating biological activities with potential for industrial application. The current approach used for defining bacterial species is based on phenotypic and genomic properties. Traditional and novel DNA-based molecular methods are improving our knowledge of bacterial diversity in nature. Advances in molecular biology have been important for studies of diversity, considerably improving our knowledge of morphological, physiological, and ecological features of bacterial taxa. DNA-DNA hybridization, which has been used for many years, is still considered the golden standard for bacteria species identification. PCR-based methods investigating 16S rRNA gene sequences, and other approaches, such as the metagenome, have been used to study the physiology and diversity of bacteria and to identify novel genes with potential pharmaceutical and other biotechnological applications. We examined the advantages and limitations of molecular methods currently used to analyze bacterial diversity; these are mainly based on the 16S rRNA gene. These methods have allowed us to examine microorganisms that cannot be cultivated by routine methods and have also been useful for phylogenetic studies. We also considered the importance of improvements in microbe culture techniques and how we can combine different methods to allow a more appropriate assessment of bacterial diversity and to determine their real potential for industrial applications.
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Affiliation(s)
- Daniela Santos Pontes
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627 Belo Horizonte, CEP 31.270-901, MG, Brazil
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22
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Abstract
Bacterial systematists face unique challenges when trying to identify ecologically meaningful units of biological diversity. Whereas plant and animal systematists are guided by a theory-based concept of species, microbiologists have yet to agree upon a set of ecological and evolutionary properties that will serve to define a bacterial species. Advances in molecular techniques have given us a glimpse of the tremendous diversity present within the microbial world, but significant work remains to be done in order to understand the ecological and evolutionary dynamics that can account for the origin, maintenance, and distribution of that diversity. We have developed a conceptual framework that uses ecological and evolutionary theory to identify the DNA sequence clusters most likely corresponding to the fundamental units of bacterial diversity. Taking into account diverse models of bacterial evolution, we argue that bacterial systematics should seek to identify ecologically distinct groups with evidence of a history of coexistence, as based on interpretation of sequence clusters. This would establish a theory-based species unit that holds the dynamic properties broadly attributed to species outside of microbiology.
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Affiliation(s)
- Frederick M Cohan
- Department of Biology, Wesleyan University, Middletown, Connecticut 06459-0170, USA.
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23
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Chevalier S, Bodilis J, Jaouen T, Barray S, Feuilloley MGJ, Orange N. Sequence diversity of the OprD protein of environmental Pseudomonas strains. Environ Microbiol 2007; 9:824-35. [PMID: 17298381 DOI: 10.1111/j.1462-2920.2006.01191.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
OprD has been widely described for Pseudomonas aeruginosa at both structural and functional levels. Here, we describe the sequence diversity of the OprD proteins from other fluorescent Pseudomonads. We analysed the sequence of the oprD gene in each of the 49 Pseudomonas isolates, mostly putida and fluorescens species, obtained from various environmental sources, including soil, rhizosphere and hospitals. Phylogeny based on OprD sequences distinguished three well-separated clusters in the P. fluorescens species whereas P. putida isolates formed only one cluster. The OprD sequences were generally well conserved within each cluster whereas on the opposite, they were highly variable from one cluster to another and particularly with regards to the cluster of P. aeruginosa. Predicted secondary structures, based on the topological model elaborated for P. aeruginosa, suggest signatures in the large extracellular loops of OprD, which are linked to the OprD-based clusters. Correlations between these OprD-based clusters and ecological niches, growth on various carbon sources and antibiotic sensitivity were investigated.
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Affiliation(s)
- Sylvie Chevalier
- LMDF (Laboratoire de Microbiologie du Froid), UPRES 2123, Université de Rouen, 55, rue St Germain 27000 Evreux, France.
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Abstract
Marine actinomycetes belonging to the genus Salinispora were cultured from marine sediments collected at six geographically distinct locations. Detailed phylogenetic analyses of both 16S rRNA and gyrB gene sequences reveal that this genus is comprised of three distinct but closely related clades corresponding to the species Salinispora tropica, Salinispora arenicola and a third species for which the name 'Salinispora pacifica' is proposed. Salinispora arenicola was cultured from all locations sampled and provides clear evidence for the cosmopolitan distribution of an individual bacterial species. The co-occurrence of S. arenicola with S. tropica and S. pacifica suggests that ecological differentiation as opposed to geographical isolation is driving speciation within the genus. All Salinispora strains cultured to date share greater than 99% 16S rRNA gene sequence identity and thus comprise what has been described as a microdiverse ribotype cluster. The description of this cluster as a new genus, containing multiple species, provides clear evidence that fine-scale 16S rDNA sequence analysis can be used to delineate among closely related species and that more conservative operational taxonomic unit values may significantly underestimate global species diversity.
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Affiliation(s)
- Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, CA, USA.
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25
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Bodilis J, Hedde M, Orange N, Barray S. OprF polymorphism as a marker of ecological niche in Pseudomonas. Environ Microbiol 2006; 8:1544-51. [PMID: 16913915 DOI: 10.1111/j.1462-2920.2006.01045.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
OprF is the major outer-membrane protein of Pseudomonas sensu stricto (rRNA group I). In addition to playing a role as porin, membrane structural protein and root adhesion, this pleiotropic protein shows a length polymorphism corresponding to two types of OprF, termed OprF type 1 and OprF type 2. In a previous work, all the P. fluorescens isolated from bulk soil (non-rhizospheric) were shown to possess oprF type 1, while all the clinical P. fluorescens isolates and most rhizospheric strains corresponded to type 2. In this study, we further investigated the relation between the OprF polymorphism and the ecological niche by developing a culture-independent approach (a ratio polymerase chain reaction) to measure the percentage of each oprF type in environmental DNA samples, including two different soils and three different cultured plants (flax, wheat and grassland). Although the proportions of oprF type 2 between rhizospheric samples were quite variable, they were always very significantly higher (P<0.001) than the proportions of oprF type 2 of the adjacent bulk soil where the vast majority of oprF (>95%) corresponded to type 1. We discuss the potential applications of this ecological fingerprint in an agronomic and taxonomic point of view.
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Affiliation(s)
- Josselin Bodilis
- LMDF (Laboratoire de Microbiologie Du Froid), UPRES 2123, Université de Rouen, 76821 Mont Saint Aignan, France.
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26
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Whitaker RJ, Banfield JF. Population genomics in natural microbial communities. Trends Ecol Evol 2006; 21:508-16. [PMID: 16859806 DOI: 10.1016/j.tree.2006.07.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2005] [Revised: 05/02/2006] [Accepted: 07/03/2006] [Indexed: 11/24/2022]
Abstract
Little is known about the evolutionary processes that structure and maintain microbial diversity because, until recently, it was difficult to explore individual-level patterns of variation at the microbial scale. Now, community-genomic sequence data enable such variation to be assessed across large segments of microbial genomes. Here, we discuss how population-genomic analysis of these data can be used to determine how selection and genetic exchange shape the evolution of new microbial lineages. We show that once independent lineages have been identified, such analyses enable the identification of genome changes that drive niche differentiation and promote the coexistence of closely related lineages within the same environment. We suggest that understanding the evolutionary ecology of natural microbial populations through population-genomic analyses will enhance our understanding of genome evolution across all domains of life.
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Affiliation(s)
- Rachel J Whitaker
- Ecosystem Sciences, 137 Mulford Hall, University of California, Berkeley, CA 94720-3114, USA.
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27
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Ida T, Kugimiya M, Kogure M, Takahashi R, Tokuyama T. Phylogenetic relationships among ammonia-oxidizing bacteria as revealed by gene sequences of glyceraldehyde 3-phosphate dehydrogenase and phosphoglycerate kinase. J Biosci Bioeng 2005; 99:569-76. [PMID: 16233833 DOI: 10.1263/jbb.99.569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2004] [Accepted: 03/11/2005] [Indexed: 11/17/2022]
Abstract
The three previously recognized genera of 'Nitrosolobus', Nitrosospira and 'Nitrosovibrio' were combined into one genus, Nitrosospira, on the basis of 16S rDNA sequence similarities. However, this classification has been controversial for some time, since the marked differences in their shapes suggest that they are not closely related. In this study, the phylogenetic analyses of the three groups using two genotypical markers, glyceraldehyde-3-phosphate dehydrogenase (GAP, gap), and 3-phosphoglycerate kinase (PGK, pgk), were performed. In the phylogenetic tree inferred from gap and pgk, the three genera appeared as clearly separated clusters. This is the first study of markers that are able to reveal the precise phylogenetic relationship among 'Nitrosolobus', Nitrosospira and 'Nitrosovibrio'.
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Affiliation(s)
- Takeshi Ida
- College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-8510, Japan
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28
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Whitaker RJ, Grogan DW, Taylor JW. Recombination shapes the natural population structure of the hyperthermophilic archaeon Sulfolobus islandicus. Mol Biol Evol 2005; 22:2354-61. [PMID: 16093568 DOI: 10.1093/molbev/msi233] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Although microorganisms make up the preponderance of the biodiversity on Earth, the ecological and evolutionary factors that structure microbial populations are not well understood. We investigated the genetic structure of a thermoacidophilic crenarchaeal species, Sulfolobus islandicus, using multilocus sequence analysis of six variable protein-coding loci on a set of 60 isolates from the Mutnovsky region of Kamchatka, Russia. We demonstrate significant incongruence among gene genealogies and a lack of association between alleles consistent with recombination rates greater than the rate of mutation. The observation of high relative rates of recombination suggests that the structure of this natural population does not fit the periodic selection model often used to describe populations of asexual microorganisms. We propose instead that frequent recombination among closely related individuals prevents periodic selection from purging diversity and provides a fundamental cohesive mechanism within this and perhaps other archaeal species.
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Affiliation(s)
- Rachel J Whitaker
- Department of Plant and Microbial Biology, University of California, Berkeley, USA.
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29
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O'Rourke JL, Solnick JV, Neilan BA, Seidel K, Hayter R, Hansen LM, Lee A. Description of 'Candidatus Helicobacter heilmannii' based on DNA sequence analysis of 16S rRNA and urease genes. Int J Syst Evol Microbiol 2005; 54:2203-2211. [PMID: 15545459 DOI: 10.1099/ijs.0.63117-0] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
While Helicobacter pylori is accepted as the major bacterial agent of gastric disease in humans, some patients and many animals are infected with a larger, tightly helical-shaped bacterium previously referred to as 'Helicobacter heilmannii' or 'Gastrospirillum hominis'. Taxonomic classification of these bacteria has been hampered by the inability to cultivate them in vitro and by the inadequate discriminatory power of 16S rRNA gene sequence analysis. This study describes the detection and phylogenetic analysis of 26 different gastrospirillum isolates from humans and animals, which incorporates sequence data based on the 16S rRNA and urease genes. Fifteen gastrospirilla detected in humans, primates and pigs clustered with 'Candidatus Helicobacter suis', thus expanding the host range for this organism. By comparison, based on 16S rRNA data, the remaining 11 gastrospirilla could not be differentiated from Helicobacter felis, Helicobacter bizzozeronii and Helicobacter salomonis. However, urease gene sequence analysis allowed for the discrimination of this latter group into four discrete clusters, three of which contained the above recognized species. The fourth cluster contained isolates from human and feline hosts, and should provisionally be considered a unique bacterial species, for which the name 'Candidatus Helicobacter heilmannii' is proposed.
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Affiliation(s)
- Jani L O'Rourke
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia, 2052
| | - Jay V Solnick
- Departments of Internal Medicine and Medical Microbiology & Immunology, The Center for Comparative Medicine, University of California, Davis, CA 95616-8645, USA
| | - Brett A Neilan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia, 2052
| | - Karin Seidel
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia, 2052
| | - Robert Hayter
- Departments of Internal Medicine and Medical Microbiology & Immunology, The Center for Comparative Medicine, University of California, Davis, CA 95616-8645, USA
| | - Lori M Hansen
- Departments of Internal Medicine and Medical Microbiology & Immunology, The Center for Comparative Medicine, University of California, Davis, CA 95616-8645, USA
| | - Adrian Lee
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia, 2052
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30
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Jin J, Haga T, Shinjo T, Goto Y. Phylogenetic analysis of Fusobacterium necrophorum, Fusobacterium varium and Fusobacterium nucleatum based on gyrB gene sequences. J Vet Med Sci 2005; 66:1243-5. [PMID: 15528856 DOI: 10.1292/jvms.66.1243] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The nucleotide sequences of the DNA gyrase B subunit gene (gyrB) of Fusobacterium necrophorum subsp. necrophorum, F. necrophorum subsp. funduliforme and F. varium were determined and analyzed together with those of F. nucleatum subsp. nucleatum and F. nucleatum subsp. vincentii. On the phylogenetic tree constructed, the strains of each fusobacterial species formed distinct clusters with deep sublines. The degree of sequence similarity within each cluster was 93.2% or more, whereas similarities between clusters ranged from 70.1 to 72.7%. These clusters were recovered with 100% bootstrap probabilities and are in very good agreement with the species of Fusobacterium. These data suggest that gyrB is an accurate genealogical marker for the classification of the fusobacterial taxa considered in this study.
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Affiliation(s)
- Jinghua Jin
- Department of Veterinary Microbiology, Faculty of Agriculture, Miyazaki University, Japan
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31
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Nercessian O, Bienvenu N, Moreira D, Prieur D, Jeanthon C. Diversity of functional genes of methanogens, methanotrophs and sulfate reducers in deep-sea hydrothermal environments. Environ Microbiol 2005; 7:118-32. [PMID: 15643942 DOI: 10.1111/j.1462-2920.2004.00672.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To contribute to the identification of methanogens, methanotrophs and sulfate-reducing bacteria (SRB) in microbial communities from the 13 degrees N (East Pacific Rise) and Rainbow (Mid-Atlantic Ridge) hydrothermal vent fields, we investigated the diversity of mcrA, pmoA and dsrAB genes sequences. Clone libraries were obtained using DNA isolated from fragments of diffuse vents, sediment and in situ samplers. The clones were categorized by restriction fragment length polymorphism, and representatives of each group were sequenced. Sequences were related to that of hyperthermophilic (order Methanopyrales and family Methanocaldococcaceae), thermophilic and mesophilic (family Methanococcaceae) methanogens, thermophilic (proposed genus 'Methylothermus') and mesophilic type I methanotrophs, and hyperthermophilic (order Archaeoglobales), thermophilic (order Thermodesulfobacteriales) and mesophilic (family Desulfobulbaceae) SRB. Several of the obtained sequences were distantly related to the genes of cultivated organisms, providing evidence of the existence of novel lineages in the three functional groups. This study provides for the first time an insight into the diversity of several functional genes of deep-sea hydrothermal system microorganisms.
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Affiliation(s)
- Olivier Nercessian
- UMR 6539, Laboratoire des Sciences de l'Environnement Marin, Centre National de la Recherche Scientifique, Institut Universitaire Européen de la Mer, Technopôle Brest-Iroise, Place Nicolas Copernic, 29280 Plouzané, France
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32
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Paillard C, Le Roux F, Borrego JJ. Bacterial disease in marine bivalves, a review of recent studies: Trends and evolution. AQUATIC LIVING RESOURCES 2004. [DOI: 10.1051/alr:2004054] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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33
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Stackebrandt E. Will we ever understand? The undescribable diversity of the prokaryotes. Acta Microbiol Immunol Hung 2004; 51:449-62. [PMID: 15704333 DOI: 10.1556/amicr.51.2004.4.5] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
This communication will summarize recent estimations on prokaryotic cell numbers, technical aspects of the exploration of the hidden diversity of the as-yet-uncultured prokaryotes and their function in the environment, recognition of novel major lines of descent, elucidation of novel metabolic pathways and attempts to improve the definition of the taxon species. These are some of recent highlights that will reflect only incompletely recent advances of microbiologist and other aspects of diversity at the genomic level, including the tremendous influence of whole genome sequences on the development of DNA macro- and microarrays for rapid identification of genes and specimen, the annotation of gene sequences to gene function by proteomics and the recognition of the extent of lateral gene transfer in the evolution of the genome, hence of contemporary organisms. As an example of modern trends in systematics three new families will be described for recently described genera, namely Thermoleophilaceae, Solirubrobacteraceae and Conexibacteraceae, which are phylogenetically positioned among environmental clone sequences at the root of the class Actinobacteria.
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Affiliation(s)
- E Stackebrandt
- DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, 38124 Braunschweig, Germany.
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34
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Pretorius AM, Beati L, Birtles RJ. Diversity of bartonellae associated with small mammals inhabiting Free State province, South Africa. Int J Syst Evol Microbiol 2004; 54:1959-1967. [PMID: 15545418 DOI: 10.1099/ijs.0.03033-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The prevalence and diversity of bartonellae infecting the blood of 10 small mammal species inhabiting nine Nature Reserves of the Free State province, South Africa, was assessed using phenotypic, genotypic and phylogenetic methods. Of 86 small mammals sampled, 38 animals belonging to five different species yielded putative bartonellae. Thirty-two isolates were confirmed as bartonellae and were characterized by comparison of partial citrate synthase gene (gltA) sequences. Phylogenetic reconstructions derived from alignment of these sequences with those available for other bartonellae indicated that the South African rodent-associated isolates formed two distinct clades within the radius of the genus Bartonella. One of these clades also included recognized Bartonella species associated with rodents native to Eurasia but not to the New World, whereas the second clade contained exclusively isolates associated with South African rodents. Comparison of gltA sequences delineated the isolates into a number of ecologically distinct populations and provided an indication that a combination of phylogenetics and the identification of sequence clusters in housekeeping protein-encoding genes could be developed as a key criterion in the classification of bartonellae. This study is the first to investigate wildlife-associated bartonellae in Africa, adding support to their ubiquity and broad diversity and to the paradigm that the phylogenetic positions of the Bartonella species encountered today have been influenced by the geographical distribution of their hosts.
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Affiliation(s)
- Anne-Marié Pretorius
- National Health Laboratory Service, Department of Medical Microbiology (G4), School of Medicine, Faculty of Health Sciences, University of the Free State, PO Box 339, Bloemfontein 9300, South Africa
| | - Lorenza Beati
- Department of Epidemiology and Public Health, Yale University School of Medicine, PO Box 208034, 60 College Street, New Haven, CT 06520-8034, USA
| | - Richard J Birtles
- Centre for Comparative Infectious Diseases and Department of Veterinary Pathology, Faculty of Veterinary Science, University of Liverpool, Neston CH64 7TE, UK
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Jaspers E, Overmann J. Ecological significance of microdiversity: identical 16S rRNA gene sequences can be found in bacteria with highly divergent genomes and ecophysiologies. Appl Environ Microbiol 2004; 70:4831-9. [PMID: 15294821 PMCID: PMC492463 DOI: 10.1128/aem.70.8.4831-4839.2004] [Citation(s) in RCA: 217] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2003] [Accepted: 04/14/2004] [Indexed: 11/20/2022] Open
Abstract
A combination of cultivation-based methods with a molecular biological approach was used to investigate whether planktonic bacteria with identical 16S rRNA gene sequences can represent distinct eco- and genotypes. A set of 11 strains of Brevundimonas alba were isolated from a bacterial freshwater community by conventional plating or by using a liquid most-probable-number (MPN) dilution series. These strains had identical 16S rRNA gene sequences and represented the dominant phylotype in the plateable fraction, as well as in the highest positive dilutions of the MPN series. However, internally transcribed spacer and enterobacterial repetitive intergenic consensus PCR fingerprinting analyses, as well as DNA-DNA hybridization analyses, revealed great genetic diversity among the 11 strains. Each strain utilized a specific combination of 59 carbon substrates, and the niche overlap indices were low, suggesting that each strain occupied a different ecological niche. In dialysis cultures incubated in situ, each strain had a different growth rate and cell yield. We thus demonstrated that the B. alba strains represent distinct populations with genetically determined adaptations and probably occupy different ecological niches. Our results have implications for assessment of the diversity and biogeography of bacteria and increase the perception of natural diversity beyond the level of 16S rRNA gene sequences.
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Affiliation(s)
- Elke Jaspers
- Institut für Chemie und Biologie des Meeres, Universität Oldenburg, Oldenburg, Germany
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Ventura M, Canchaya C, Meylan V, Klaenhammer TR, Zink R. Analysis, characterization, and loci of the tuf genes in lactobacillus and bifidobacterium species and their direct application for species identification. Appl Environ Microbiol 2004; 69:6908-22. [PMID: 14602655 PMCID: PMC262312 DOI: 10.1128/aem.69.11.6908-6922.2003] [Citation(s) in RCA: 133] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We analyzed the tuf gene, encoding elongation factor Tu, from 33 strains representing 17 Lactobacillus species and 8 Bifidobacterium species. The tuf sequences were aligned and used to infer phylogenesis among species of lactobacilli and bifidobacteria. We demonstrated that the synonymous substitution affecting this gene renders elongation factor Tu a reliable molecular clock for investigating evolutionary distances of lactobacilli and bifidobacteria. In fact, the phylogeny generated by these tuf sequences is consistent with that derived from 16S rRNA analysis. The investigation of a multiple alignment of tuf sequences revealed regions conserved among strains belonging to the same species but distinct from those of other species. PCR primers complementary to these regions allowed species-specific identification of closely related species, such as Lactobacillus casei group members. These tuf gene-based assays developed in this study provide an alternative to present methods for the identification for lactic acid bacterial species. Since a variable number of tuf genes have been described for bacteria, the presence of multiple genes was examined. Southern analysis revealed one tuf gene in the genomes of lactobacilli and bifidobacteria, but the tuf gene was arranged differently in the genomes of these two taxa. Our results revealed that the tuf gene in bifidobacteria is flanked by the same gene constellation as the str operon, as originally reported for Escherichia coli. In contrast, bioinformatic and transcriptional analyses of the DNA region flanking the tuf gene in four Lactobacillus species indicated the same four-gene unit and suggested a novel tuf operon specific for the genus Lactobacillus.
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Affiliation(s)
- Marco Ventura
- Nestlé Research Center, 1000 Lausanne 26, Switzerland.
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Crosbie ND, Pöckl M, Weisse T. Dispersal and phylogenetic diversity of nonmarine picocyanobacteria, inferred from 16S rRNA gene and cpcBA-intergenic spacer sequence analyses. Appl Environ Microbiol 2003; 69:5716-21. [PMID: 12957969 PMCID: PMC194977 DOI: 10.1128/aem.69.9.5716-5721.2003] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
More than 20 Synechococcus and Cyanobium isolates were obtained from central European subalpine lakes and sequenced for their 16S rRNA gene and part of the phycocyanin operon (cpc), specifically the intergenic spacer (IGS) between cpcB and cpcA, and corresponding flanking regions (cpcBA-IGS). Maximum-likelihood analyses revealed the existence of at least six to seven clusters of nonmarine picocyanobacteria within the picophytoplankton clade and support the conjecture of global dispersal for some closely related picocyanobacterial genotypes.
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Affiliation(s)
- Nicholas D Crosbie
- Institute for Limnology, Austrian Academy of Sciences, A-5310 Mondsee, Austria.
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Ramette A, Frapolli M, Défago G, Moënne-Loccoz Y. Phylogeny of HCN synthase-encoding hcnBC genes in biocontrol fluorescent pseudomonads and its relationship with host plant species and HCN synthesis ability. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2003; 16:525-535. [PMID: 12795378 DOI: 10.1094/mpmi.2003.16.6.525] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Hydrogen cyanide (HCN) is a broad-spectrum antimicrobial compound involved in biological control of root diseases by many plant-associated fluorescent pseudomonads. The HCN synthase is encoded by three biosynthetic genes (hcnA, hcnB, and hcnC), but little is known about the diversity of these genes in fluorescent Pseudomonas spp. and in other bacteria. Here, the partial hcnBC sequence was determined for a worldwide collection of biocontrol fluorescent Pseudomonas spp. Phylogenies based on hcnBC and deduced protein sequences revealed four main bacterial groups, but topological incongruences were found between hcnBC and rrs-based phylogenies, suggesting past lateral transfer of hcnBC among saprophytic root-colonizing pseudomonads. Three of the four groups included isolates from different countries and host plants. Yet, these groups corresponded to distinct, ecologically-adapted populations of HCN-producing biocontrol fluorescent pseudomonads, as indicated by high hcnBC distinctness ratio values and the differences in production levels of HCN in vitro found between groups. This is in accordance with previous results on catabolic properties and biocontrol abilities of these strains. HCN synthase gene diversity may thus reflect the adaptive radiation of HCN+ biocontrol fluorescent pseudomonads. Positive correlations were found between HCN production in vitro and plant protection in the cucumber/Pythium ultimum and tomato/Fusarium oxysporum f. sp. radicis-lycopersici pathosystems.
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Affiliation(s)
- Alban Ramette
- Phytopathology Group, Institute of Plant Sciences, Swiss Federal Institute of Technology (ETH), CH-8092 Zürich, Switzerland
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Abstract
Bacterial systematics has not yet reached a consensus for defining the fundamental unit of biological diversity, the species. The past half-century of bacterial systematics has been characterized by improvements in methods for demarcating species as phenotypic and genetic clusters, but species demarcation has not been guided by a theory-based concept of species. Eukaryote systematists have developed a universal concept of species: A species is a group of organisms whose divergence is capped by a force of cohesion; divergence between different species is irreversible; and different species are ecologically distinct. In the case of bacteria, these universal properties are held not by the named species of systematics but by ecotypes. These are populations of organisms occupying the same ecological niche, whose divergence is purged recurrently by natural selection. These ecotypes can be discovered by several universal sequence-based approaches. These molecular methods suggest that a typical named species contains many ecotypes, each with the universal attributes of species. A named bacterial species is thus more like a genus than a species.
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Affiliation(s)
- Frederick M Cohan
- Department of Biology, Wesleyan University, Middletown, Connecticut 06459-0170, USA.
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Abstract
The recently described genus Pandoraea consists of five named species and four unnamed genomospecies, several of which have been identified in clinical specimens including respiratory secretions from persons with cystic fibrosis. We investigated whether it is possible to distinguish species of the genus Pandoraea by means of restriction fragment length polymorphism (RFLP) analysis and direct sequencing of the gyrB gene. Sixty-seven Pandoraea isolates were included. Species-specific RFLP patterns were obtained following digestion of the PCR-amplified gyrB gene with MspI. Specificity of RFLP groupings was confirmed by direct sequencing of several representative isolates. Our results indicate that RFLP analysis and sequencing of the gyrB gene are useful for the identification of Pandoraea species. We also found that further taxonomic studies within the beta-Proteobacteria using the gyrB gene would benefit from the development of additional primers allowing more efficient amplification of the gyrB gene. Our data also indicate that the taxonomic status of Pandoraea genomospecies 2 should be reinvestigated.
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Affiliation(s)
- Tom Coenye
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, 8301 MSRB III, Box 0646, 1150 W. Med. Ctr. Dr., Ann Arbor, MI 48109-0646, USA.
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