1
|
Lee PW, Chen L, Hsieh K, Traylor A, Wang TH. Harnessing Variabilities in Digital Melt Curves for Accurate Identification of Bacteria. Anal Chem 2023; 95:15522-15530. [PMID: 37812586 DOI: 10.1021/acs.analchem.3c01654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Digital PCR combined with high resolution melt (HRM) is an emerging method for identifying pathogenic bacteria with single cell resolution via species-specific digital melt curves. Currently, the development of such digital PCR-HRM assays entails first identifying PCR primers to target hypervariable gene regions within the target bacteria panel, next performing bulk-based PCR-HRM to examine whether the resulting species-specific melt curves possess sufficient interspecies variability (i.e., variability between bacterial species), and then digitizing the bulk-based PCR-HRM assays with melt curves that have high interspecies variability via microfluidics. In this work, we first report our discovery that the current development workflow can be inadequate because a bulk-based PCR-HRM assay that produces melt curves with high interspecies variability can, in fact, lead to a digital PCR-HRM assay that produces digital melt curves with unwanted intraspecies variability (i.e., variability within the same bacterial species), consequently hampering bacteria identification accuracy. Our subsequent investigation reveals that such intraspecies variability in digital melt curves can arise from PCR primers that target nonidentical gene copies or amplify nonspecifically. We then show that computational in silico HRM opens a window to inspect both interspecies and intraspecies variabilities and thus provides the missing link between bulk-based PCR-HRM and digital PCR-HRM. Through this new development workflow, we report a new digital PCR-HRM assay with improved bacteria identification accuracy. More broadly, this work can serve as the foundation for enhancing the development of future digital PCR-HRM assays toward identifying causative pathogens and combating infectious diseases.
Collapse
Affiliation(s)
- Pei-Wei Lee
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Liben Chen
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Amelia Traylor
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Tza-Huei Wang
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
- Institute of NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| |
Collapse
|
2
|
Xiao Y, Yang C, Yu L, Tian F, Wu Y, Zhao J, Zhang H, Yang R, Chen W, Hill C, Cui Y, Zhai Q. Human gut-derived B. longum subsp. longum strains protect against aging in a D-galactose-induced aging mouse model. MICROBIOME 2021; 9:180. [PMID: 34470652 PMCID: PMC8411540 DOI: 10.1186/s40168-021-01108-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/02/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND Probiotics have been used to regulate the gut microbiota and physiology in various contexts, but their precise mechanisms of action remain unclear. RESULTS By population genomic analysis of 418 Bifidobacterium longum strains, including 143 newly sequenced in this study, three geographically distinct gene pools/populations, BLAsia1, BLAsia2, and BLothers, were identified. Genes involved in cell wall biosynthesis, particularly peptidoglycan biosynthesis, varied considerably among the core genomes of the different populations, but accessory genes that contributed to the carbohydrate metabolism were significantly distinct. Although active transmission was observed inter-host, inter-country, inter-city, intra-community, and intra-family, a single B. longum clone seemed to reside within each individual. A significant negative association was observed between host age and relative abundance of B. longum, while there was a strong positive association between host age and strain genotype [e.g., single nucleotide polymorphisms in the arginine biosynthesis pathway]. Further animal experiments performed with the B. longum isolates via using a D-galactose-induced aging mouse model supported these associations, in which B. longum strains with different genotypes in arginine biosynthesis pathway showed divergent abilities on protecting against host aging possibly via their different abilities to modify the metabolism of gut microbes. CONCLUSIONS This is the first known example of research on the evolutionary history and transmission of this probiotic species. Our results propose a new mechanistic insight for promoting host longevity via the informed use of specific probiotics or molecules. Video abstract.
Collapse
Affiliation(s)
- Yue Xiao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122 People’s Republic of China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
- International Joint Research Laboratory for Probiotics At Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Chao Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
| | - Leilei Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122 People’s Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122 People’s Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Yarong Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122 People’s Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122 People’s Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122 Jiangsu China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, 225004 China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122 People’s Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122 Jiangsu China
- Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, 100048 People’s Republic of China
| | - Colin Hill
- School of Microbiology & APC Microbiome Institute, University College Cork, Cork, T12 YN60 Ireland
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122 People’s Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
- International Joint Research Laboratory for Probiotics At Jiangnan University, Wuxi, 214122 Jiangsu China
| |
Collapse
|
3
|
Brzechffa C, Goffredi SK. Contrasting influences on bacterial symbiont specificity by co-occurring deep-sea mussels and tubeworms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:104-111. [PMID: 33196140 DOI: 10.1111/1758-2229.12909] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/29/2020] [Accepted: 11/13/2020] [Indexed: 06/11/2023]
Abstract
Relationships fueled by sulfide between deep-sea invertebrates and bacterial symbionts are well known, yet the diverse overlapping factors influencing symbiont specificity are complex. For animals that obtain their symbionts from the environment, both host identity and geographic location can impact the ultimate symbiont partner. Bacterial symbionts were analysed for three co-occurring species each of Bathymodiolus mussels and vestimentiferan tubeworms, from three deep methane seeps off the west coast of Costa Rica. The bacterial internal transcribed spacer gene was analysed via direct and barcoded amplicon sequencing to reveal fine-scale symbiont diversity. Each of the three mussel species (B. earlougheri, B. billschneideri and B. nancyschneideri) hosted genetically distinct thiotrophic endosymbionts, despite living nearly side-by-side in their habitat, suggesting that host identity is crucial in driving symbiont specificity. The dominant thiotrophic symbiont of co-occurring tubeworms Escarpia spicata and Lamellibrachia (L. barhami and L. donwalshi), on the other hand, was identical regardless of host species or sample location, suggesting lack of influence by either factor on symbiont selectivity in this group of animals. These findings highlight the specific, yet distinct, influences on the environmental acquisition of symbionts in two foundational invertebrates with similar lifestyles, and provide a rapid, precise method of examining symbiont identities.
Collapse
|
4
|
Okazaki Y, Fujinaga S, Salcher MM, Callieri C, Tanaka A, Kohzu A, Oyagi H, Tamaki H, Nakano SI. Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing. MICROBIOME 2021; 9:24. [PMID: 33482922 PMCID: PMC7825169 DOI: 10.1186/s40168-020-00974-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 12/07/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND Freshwater ecosystems are inhabited by members of cosmopolitan bacterioplankton lineages despite the disconnected nature of these habitats. The lineages are delineated based on > 97% 16S rRNA gene sequence similarity, but their intra-lineage microdiversity and phylogeography, which are key to understanding the eco-evolutional processes behind their ubiquity, remain unresolved. Here, we applied long-read amplicon sequencing targeting nearly full-length 16S rRNA genes and the adjacent ribosomal internal transcribed spacer sequences to reveal the intra-lineage diversities of pelagic bacterioplankton assemblages in 11 deep freshwater lakes in Japan and Europe. RESULTS Our single nucleotide-resolved analysis, which was validated using shotgun metagenomic sequencing, uncovered 7-101 amplicon sequence variants for each of the 11 predominant bacterial lineages and demonstrated sympatric, allopatric, and temporal microdiversities that could not be resolved through conventional approaches. Clusters of samples with similar intra-lineage population compositions were identified, which consistently supported genetic isolation between Japan and Europe. At a regional scale (up to hundreds of kilometers), dispersal between lakes was unlikely to be a limiting factor, and environmental factors or genetic drift were potential determinants of population composition. The extent of microdiversification varied among lineages, suggesting that highly diversified lineages (e.g., Iluma-A2 and acI-A1) achieve their ubiquity by containing a consortium of genotypes specific to each habitat, while less diversified lineages (e.g., CL500-11) may be ubiquitous due to a small number of widespread genotypes. The lowest extent of intra-lineage diversification was observed among the dominant hypolimnion-specific lineage (CL500-11), suggesting that their dispersal among lakes is not limited despite the hypolimnion being a more isolated habitat than the epilimnion. CONCLUSIONS Our novel approach complemented the limited resolution of short-read amplicon sequencing and limited sensitivity of the metagenome assembly-based approach, and highlighted the complex ecological processes underlying the ubiquity of freshwater bacterioplankton lineages. To fully exploit the performance of the method, its relatively low read throughput is the major bottleneck to be overcome in the future. Video abstract.
Collapse
Affiliation(s)
- Yusuke Okazaki
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga, 520-2113, Japan.
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8566, Japan.
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan.
| | - Shohei Fujinaga
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga, 520-2113, Japan
| | - Michaela M Salcher
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 37005, České Budějovice, Czech Republic
- Limnological Station, Institute of Plant and Microbial Biology, University of Zurich, Seestrasse 187, 8802, Kilchberg, Zurich, Switzerland
| | - Cristiana Callieri
- CNR, IRSA Institute of Water Research, Largo Tonolli 50, 28922, Verbania, Italy
| | - Atsushi Tanaka
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Ayato Kohzu
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Hideo Oyagi
- Faculty of Policy Studies, Nanzan University, 18 Yamazato-cho, Showa-ku, Nagoya, Aichi, 466-8673, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8566, Japan
| | - Shin-Ichi Nakano
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga, 520-2113, Japan
| |
Collapse
|
5
|
Lücking R, Aime MC, Robbertse B, Miller AN, Ariyawansa HA, Aoki T, Cardinali G, Crous PW, Druzhinina IS, Geiser DM, Hawksworth DL, Hyde KD, Irinyi L, Jeewon R, Johnston PR, Kirk PM, Malosso E, May TW, Meyer W, Öpik M, Robert V, Stadler M, Thines M, Vu D, Yurkov AM, Zhang N, Schoch CL. Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? IMA Fungus 2020; 11:14. [PMID: 32714773 PMCID: PMC7353689 DOI: 10.1186/s43008-020-00033-z] [Citation(s) in RCA: 178] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.
Collapse
Affiliation(s)
- Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Straße 6–8, 14195 Berlin, Germany
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
| | - M. Catherine Aime
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907 USA
| | - Barbara Robbertse
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892 USA
| | - Andrew N. Miller
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820-6970 USA
| | - Hiran A. Ariyawansa
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Plant Pathology and Microbiology, College of Bio-Resources and Agriculture, National Taiwan University, Taipe City, Taiwan
| | - Takayuki Aoki
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- National Agriculture and Food Research Organization, Genetic Resources Center, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Gianluigi Cardinali
- Department Pharmaceutical Sciences, University of Perugia, Via Borgo 20 Giugno, 74, Perugia, Italy
| | - Pedro W. Crous
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Irina S. Druzhinina
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Microbiology and Applied Genomics Group, Research Area Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - David M. Geiser
- Department of Plant Pathology & Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802 USA
| | - David L. Hawksworth
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Surrey, TW9 3DS UK
- Geography and Environment, University of Southampton, Southampton, SO17 1BJ UK
- Jilin Agricultural University, Changchun, 130118 Jilin Province China
| | - Kevin D. Hyde
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201 Yunnan China
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- World Agroforestry Centre, East and Central Asia, Kunming, 650201 Yunnan China
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Rai, 50150 Thailand
| | - Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Sydney, NSW Australia
| | - Rajesh Jeewon
- Department of Health Sciences, Faculty of Science, University of Mauritius, Reduit, Mauritius
| | - Peter R. Johnston
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Manaaki Whenua – Landcare Research, Private Bag 92170, Auckland, 1142 New Zealand
| | | | - Elaine Malosso
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Universidade Federal de Pernambuco, Centro de Biociências, Departamento de Micologia, Laboratório de Hifomicetos de Folhedo, Avenida da Engenharia, s/n Cidade Universitária, Recife, PE 50.740-600 Brazil
| | - Tom W. May
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne, Victoria 3004 Australia
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Sydney, NSW Australia
| | - Maarja Öpik
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- University of Tartu, 40 Lai Street, 51 005 Tartu, Estonia
| | - Vincent Robert
- Department Pharmaceutical Sciences, University of Perugia, Via Borgo 20 Giugno, 74, Perugia, Italy
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Marc Stadler
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department Microbial Drugs, Helmholtz Centre for Infection Research, and German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Marco Thines
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 9, 60439 Frankfurt (Main); Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt (Main), Germany
| | - Duong Vu
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Andrey M. Yurkov
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Ning Zhang
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901 USA
| | - Conrad L. Schoch
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892 USA
| |
Collapse
|
6
|
Holeva MC, Morán F, Scuderi G, González A, López MM, Llop P. Development of a real-time PCR method for the specific detection of the novel pear pathogen Erwinia uzenensis. PLoS One 2019; 14:e0219487. [PMID: 31291321 PMCID: PMC6619794 DOI: 10.1371/journal.pone.0219487] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/25/2019] [Indexed: 11/24/2022] Open
Abstract
Erwinia uzenensis is a plant-pathogenic bacterium, recently described in Japan, which infects pear trees, causing the ‘bacterial black shoot disease of European pear’ (BBSDP). Like other Erwinia pear pathogens, E. uzenensis causes damp, black lesions on young shoots resembling those of E. amylovora, but not blossom blight, fruitlet blight or wilting of the shoot tip. The distribution of E. uzenensis seems restricted to the country where it was reported up to now, but it may spread to other countries and affect new hosts, as is the current situation with E. piriflorinigrans and E. pyrifoliae. Fast and accurate detection systems for this new pathogen are needed to study its biology and to identify it on pear or other hosts. We report here the development of a specific and sensitive detection protocol based on a real-time PCR with a TaqMan probe for E. uzenensis, and its evaluation. In sensitivity assays, the detection threshold of this protocol was 101 cfu ml-1 on pure bacterial cultures and 102–103 cfu ml-1 on spiked plant material. The specificity of the protocol was evaluated against E. uzenensis and 46 strains of pear-associated Erwinia species different to E. uzenensis. No cross-reaction with the non-target bacterial species or the loss of sensitivity were observed. This specific and sensitive diagnostic tool may reveal a wider distribution and host range of E. uzenensis initially considered restricted to a region and will expand our knowledge of the life cycle and environmental preferences of this pathogen.
Collapse
Affiliation(s)
- Maria C. Holeva
- Laboratory of Bacteriology, Department of Plant Pathology, Benaki Phytopathological Institute, Kifissia, Attica, Greece
| | - Félix Morán
- Laboratory of Bacteriology, Department of Plant Pathology, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Spain
| | - Giuseppe Scuderi
- Laboratory of Biotechnology, Department of Sustainable agriculture, biodiversity and food security, Euro-Mediterranean Institute of Science and Technology (IEMEST), Palermo, Italy
| | - Asier González
- Laboratory of Bacteriology, Department of Plant Pathology, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Spain
| | - María M. López
- Laboratory of Bacteriology, Department of Plant Pathology, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Spain
| | - Pablo Llop
- Laboratory of Bacteriology, Department of Plant Pathology, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Spain
- * E-mail: ,
| |
Collapse
|
7
|
Roscini L, Tristezza M, Corte L, Colabella C, Perrotta C, Rampino P, Robert V, Vu D, Cardinali G, Grieco F. Early Ongoing Speciation of Ogataea uvarum Sp. Nov. Within the Grape Ecosystem Revealed by the Internal Variability Among the rDNA Operon Repeats. Front Microbiol 2018; 9:1687. [PMID: 30123190 PMCID: PMC6085423 DOI: 10.3389/fmicb.2018.01687] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 07/06/2018] [Indexed: 11/13/2022] Open
Abstract
A yeast strain was isolated during a study on vineyard-associated yeast strains from Apulia in Southern Italy. ITS and LSU D1/D2 rDNA sequences showed this strain not to belong to any known species and was described as the type strain of Ogataea uvarum sp. nov., a close relative of O. philodendri. Several secondary peaks appeared in the sequences, suggesting internal heterogeneity among the copies of the rDNA. This hypothesis was tested by sequencing single clones of the marker region. The analyses showed different levels of variability throughout the operon with differences between the rRNA encoding genes and the internally transcribed regions. O. uvarum and O. philodendri share high frequency variants, i.e., variants frequently found in many clones, whereas there is a large variability of the low frequency polymorphisms, suggesting that the mechanism of homogenization is more active with the former than with the latter type of variation. These findings indicate that low frequency variants are detected in Sanger sequencing as secondary peaks whereas in Next Generation Sequencing (NGS) of metagenomics DNA would lead to an overestimate of the alpha diversity. For the first time in our knowledge, this investigation shed light on the variation of the copy number of the rDNA cistron during the yeast speciation process. These polymorphisms can be used to investigate on the processes occurring in these taxonomic markers during the separation of fungal species, it being a genetic process highly frequent in the complex microbial ecosystem existing in grape, must and wine.
Collapse
Affiliation(s)
- Luca Roscini
- Department of Pharmaceutical Sciences – Microbiology, University of Perugia, Perugia, Italy
| | - Mariana Tristezza
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Lecce, Italy
| | - Laura Corte
- Department of Pharmaceutical Sciences – Microbiology, University of Perugia, Perugia, Italy
| | - Claudia Colabella
- Department of Pharmaceutical Sciences – Microbiology, University of Perugia, Perugia, Italy
| | - Carla Perrotta
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Patrizia Rampino
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Vincent Robert
- Bioinformatics Unit, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | - Duong Vu
- Bioinformatics Unit, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
| | - Gianluigi Cardinali
- Department of Pharmaceutical Sciences – Microbiology, University of Perugia, Perugia, Italy
- Centre of Excellence on Nanostructured Innovative Materials (CEMIN), Department of Chemistry Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Francesco Grieco
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Lecce, Italy
| |
Collapse
|
8
|
Benítez-Páez A, Sanz Y. Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinION™ portable nanopore sequencer. Gigascience 2018; 6:1-12. [PMID: 28605506 PMCID: PMC5534310 DOI: 10.1093/gigascience/gix043] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 06/09/2017] [Indexed: 02/07/2023] Open
Abstract
The miniaturized and portable DNA sequencer MinION™ has demonstrated great potential in different analyses such as genome-wide sequencing, pathogen outbreak detection and surveillance, human genome variability, and microbial diversity. In this study, we tested the ability of the MinION™ platform to perform long amplicon sequencing in order to design new approaches to study microbial diversity using a multi-locus approach. After compiling a robust database by parsing and extracting the rrn bacterial region from more than 67000 complete or draft bacterial genomes, we demonstrated that the data obtained during sequencing of the long amplicon in the MinION™ device using R9 and R9.4 chemistries were sufficient to study 2 mock microbial communities in a multiplex manner and to almost completely reconstruct the microbial diversity contained in the HM782D and D6305 mock communities. Although nanopore-based sequencing produces reads with lower per-base accuracy compared with other platforms, we presented a novel approach consisting of multi-locus and long amplicon sequencing using the MinION™ MkIb DNA sequencer and R9 and R9.4 chemistries that help to overcome the main disadvantage of this portable sequencing platform. Furthermore, the nanopore sequencing library, constructed with the last releases of pore chemistry (R9.4) and sequencing kit (SQK-LSK108), permitted the retrieval of the higher level of 1D read accuracy sufficient to characterize the microbial species present in each mock community analysed. Improvements in nanopore chemistry, such as minimizing base-calling errors and new library protocols able to produce rapid 1D libraries, will provide more reliable information in the near future. Such data will be useful for more comprehensive and faster specific detection of microbial species and strains in complex ecosystems.
Collapse
Affiliation(s)
- Alfonso Benítez-Páez
- Microbial Ecology, Nutrition and Health Research Unit. Institute of Agrochemistry and Food Technology (IATA-CSIC). C. Catedràtic Agustín Escardino Benlloch, 7. 46980 Paterna-Valencia, Spain
| | - Yolanda Sanz
- Microbial Ecology, Nutrition and Health Research Unit. Institute of Agrochemistry and Food Technology (IATA-CSIC). C. Catedràtic Agustín Escardino Benlloch, 7. 46980 Paterna-Valencia, Spain
| |
Collapse
|
9
|
Assessment of Bifidobacterium Species Using groEL Gene on the Basis of Illumina MiSeq High-Throughput Sequencing. Genes (Basel) 2017; 8:genes8110336. [PMID: 29160815 PMCID: PMC5704249 DOI: 10.3390/genes8110336] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 11/15/2017] [Indexed: 11/17/2022] Open
Abstract
The next-generation high-throughput sequencing techniques have introduced a new way to assess the gut’s microbial diversity on the basis of 16S rRNA gene-based microbiota analysis. However, the precise appraisal of the biodiversity of Bifidobacterium species within the gut remains a challenging task because of the limited resolving power of the 16S rRNA gene in different species. The groEL gene, a protein-coding gene, evolves quickly and thus is useful for differentiating bifidobacteria. Here, we designed a Bifidobacterium-specific primer pair which targets a hypervariable sequence region within the groEL gene that is suitable for precise taxonomic identification and detection of all recognized species of the genus Bifidobacterium so far. The results showed that the novel designed primer set can specifically differentiate Bifidobacterium species from non-bifidobacteria, and as low as 104 cells of Bifidobacterium species can be detected using the novel designed primer set on the basis of Illumina Miseq high-throughput sequencing. We also developed a novel protocol to assess the diversity of Bifidobacterium species in both human and rat feces through high-throughput sequencing technologies using groEL gene as a discriminative marker.
Collapse
|
10
|
Barcoding the Dendrobium (Orchidaceae) Species and Analysis of the Intragenomic Variation Based on the Internal Transcribed Spacer 2. BIOMED RESEARCH INTERNATIONAL 2017; 2017:2734960. [PMID: 29181391 PMCID: PMC5664236 DOI: 10.1155/2017/2734960] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 08/17/2017] [Accepted: 09/13/2017] [Indexed: 11/17/2022]
Abstract
Many species belonging to the genus Dendrobium are of great commercial value. However, their difficult growth conditions and high demand have caused many of these species to become endangered. Indeed, counterfeit Dendrobium products are common, especially in medicinal markets. This study aims to assess the suitability of the internal transcribed spacer 2 (ITS2) region as a marker for identifying Dendrobium and to evaluate its intragenomic variation in Dendrobium species. In total, 29,624 ITS2 copies from 18 species were obtained using 454 pyrosequencing to evaluate intragenomic variation. In addition, 513 ITS2 sequences from 26 Dendrobium species were used to assess its identification suitability. The highest intragenomic genetic distance was observed in Dendrobium chrysotoxum (0.081). The average intraspecific genetic distances of each species ranged from 0 to 0.032. Phylogenetic trees based on ITS2 sequences showed that most Dendrobium species are monophyletic. The intragenomic and intraspecies divergence analysis showed that greater intragenomic divergence is mostly correlated with larger intraspecific variation. As a major ITS2 variant becomes more common in genome, there are fewer intraspecific variable sites in ITS2 sequences at the species level. The results demonstrated that the intragenomic multiple copies of ITS2 did not affect species identification.
Collapse
|
11
|
Community-like genome in single cells of the sulfur bacterium Achromatium oxaliferum. Nat Commun 2017; 8:455. [PMID: 28878209 PMCID: PMC5587575 DOI: 10.1038/s41467-017-00342-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 06/22/2017] [Indexed: 01/01/2023] Open
Abstract
Polyploid bacteria are common, but the genetic and functional diversity resulting from polyploidy is unknown. Here we use single-cell genomics, metagenomics, single-cell amplicon sequencing, and fluorescence in situ hybridization, to show that individual cells of Achromatium oxaliferum, the world’s biggest known freshwater bacterium, harbor genetic diversity typical of whole bacterial communities. The cells contain tens of transposable elements, which likely cause the unprecedented diversity that we observe in the sequence and synteny of genes. Given the high within-cell diversity of the usually conserved 16S ribosomal RNA gene, we suggest that gene conversion occurs in multiple, separated genomic hotspots. The ribosomal RNA distribution inside the cells hints to spatially differential gene expression. We also suggest that intracellular gene transfer may lead to extensive gene reshuffling and increased diversity. The cells of Achromatium bacteria are remarkably large and contain multiple chromosome copies. Here, Ionescu et al. show that chromosome copies within individual cells display high diversity, similar to that of bacterial communities, and contain tens of transposable elements.
Collapse
|
12
|
Chand Dakal T, Giudici P, Solieri L. Contrasting Patterns of rDNA Homogenization within the Zygosaccharomyces rouxii Species Complex. PLoS One 2016; 11:e0160744. [PMID: 27501051 PMCID: PMC4976873 DOI: 10.1371/journal.pone.0160744] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 07/25/2016] [Indexed: 11/18/2022] Open
Abstract
Arrays of repetitive ribosomal DNA (rDNA) sequences are generally expected to evolve as a coherent family, where repeats within such a family are more similar to each other than to orthologs in related species. The continuous homogenization of repeats within individual genomes is a recombination process termed concerted evolution. Here, we investigated the extent and the direction of concerted evolution in 43 yeast strains of the Zygosaccharomyces rouxii species complex (Z. rouxii, Z. sapae, Z. mellis), by analyzing two portions of the 35S rDNA cistron, namely the D1/D2 domains at the 5’ end of the 26S rRNA gene and the segment including the internal transcribed spacers (ITS) 1 and 2 (ITS regions). We demonstrate that intra-genomic rDNA sequence variation is unusually frequent in this clade and that rDNA arrays in single genomes consist of an intermixing of Z. rouxii, Z. sapae and Z. mellis-like sequences, putatively evolved by reticulate evolutionary events that involved repeated hybridization between lineages. The levels and distribution of sequence polymorphisms vary across rDNA repeats in different individuals, reflecting four patterns of rDNA evolution: I) rDNA repeats that are homogeneous within a genome but are chimeras derived from two parental lineages via recombination: Z. rouxii in the ITS region and Z. sapae in the D1/D2 region; II) intra-genomic rDNA repeats that retain polymorphisms only in ITS regions; III) rDNA repeats that vary only in their D1/D2 domains; IV) heterogeneous rDNA arrays that have both polymorphic ITS and D1/D2 regions. We argue that an ongoing process of homogenization following allodiplodization or incomplete lineage sorting gave rise to divergent evolutionary trajectories in different strains, depending upon temporal, structural and functional constraints. We discuss the consequences of these findings for Zygosaccharomyces species delineation and, more in general, for yeast barcoding.
Collapse
Affiliation(s)
- Tikam Chand Dakal
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122, Reggio Emilia, Italy
| | - Paolo Giudici
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122, Reggio Emilia, Italy
| | - Lisa Solieri
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122, Reggio Emilia, Italy
- * E-mail:
| |
Collapse
|
13
|
Biogeography of sulfur-oxidizing Acidithiobacillus populations in extremely acidic cave biofilms. ISME JOURNAL 2016; 10:2879-2891. [PMID: 27187796 PMCID: PMC5148195 DOI: 10.1038/ismej.2016.74] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 03/17/2016] [Accepted: 03/24/2016] [Indexed: 02/01/2023]
Abstract
Extremely acidic (pH 0–1.5) Acidithiobacillus-dominated biofilms known as snottites are found in sulfide-rich caves around the world. Given the extreme geochemistry and subsurface location of the biofilms, we hypothesized that snottite Acidithiobacillus populations would be genetically isolated. We therefore investigated biogeographic relationships among snottite Acidithiobacillus spp. separated by geographic distances ranging from meters to 1000s of kilometers. We determined genetic relationships among the populations using techniques with three levels of resolution: (i) 16S rRNA gene sequencing, (ii) 16S–23S intergenic transcribed spacer (ITS) region sequencing and (iii) multi-locus sequencing typing (MLST). We also used metagenomics to compare functional gene characteristics of select populations. Based on 16S rRNA genes, snottites in Italy and Mexico are dominated by different sulfur-oxidizing Acidithiobacillus spp. Based on ITS sequences, Acidithiobacillus thiooxidans strains from different cave systems in Italy are genetically distinct. Based on MLST of isolates from Italy, genetic distance is positively correlated with geographic distance both among and within caves. However, metagenomics revealed that At. thiooxidans populations from different cave systems in Italy have different sulfur oxidation pathways and potentially other significant differences in metabolic capabilities. In light of those genomic differences, we argue that the observed correlation between genetic and geographic distance among snottite Acidithiobacillus populations is partially explained by an evolutionary model in which separate cave systems were stochastically colonized by different ancestral surface populations, which then continued to diverge and adapt in situ.
Collapse
|
14
|
Chriki-Adeeb R, Chriki A. Estimating Divergence Times and Substitution Rates in Rhizobia. Evol Bioinform Online 2016; 12:87-97. [PMID: 27168719 PMCID: PMC4856229 DOI: 10.4137/ebo.s39070] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 03/22/2016] [Accepted: 03/26/2016] [Indexed: 11/05/2022] Open
Abstract
Accurate estimation of divergence times of soil bacteria that form nitrogen-fixing associations with most leguminous plants is challenging because of a limited fossil record and complexities associated with molecular clocks and phylogenetic diversity of root nodule bacteria, collectively called rhizobia. To overcome the lack of fossil record in bacteria, divergence times of host legumes were used to calibrate molecular clocks and perform phylogenetic analyses in rhizobia. The 16S rRNA gene and intergenic spacer region remain among the favored molecular markers to reconstruct the timescale of rhizobia. We evaluate the performance of the random local clock model and the classical uncorrelated lognormal relaxed clock model, in combination with four tree models (coalescent constant size, birth-death, birth-death incomplete sampling, and Yule processes) on rhizobial divergence time estimates. Bayes factor tests based on the marginal likelihoods estimated from the stepping-stone sampling analyses strongly favored the random local clock model in combination with Yule process. Our results on the divergence time estimation from 16S rRNA gene and intergenic spacer region sequences are compatible with age estimates based on the conserved core genes but significantly older than those obtained from symbiotic genes, such as nodIJ genes. This difference may be due to the accelerated evolutionary rates of symbiotic genes compared to those of other genomic regions not directly implicated in nodulation processes.
Collapse
Affiliation(s)
- Rim Chriki-Adeeb
- Département de Biologie, Laboratoire de Génétique, Faculté des Sciences de Bizerte, Jarzouna, Tunisie
| | - Ali Chriki
- Département de Biologie, Laboratoire de Génétique, Faculté des Sciences de Bizerte, Jarzouna, Tunisie
| |
Collapse
|
15
|
Ruiz-Estévez M, Ruiz-Ruano FJ, Cabrero J, Bakkali M, Perfectti F, López-León MD, Camacho JPM. Non-random expression of ribosomal DNA units in a grasshopper showing high intragenomic variation for the ITS2 region. INSECT MOLECULAR BIOLOGY 2015; 24:319-330. [PMID: 25565136 DOI: 10.1111/imb.12158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We analyse intragenomic variation of the ITS2 internal transcribed spacer of ribosomal DNA (rDNA) in the grasshopper Eyprepocnemis plorans, by means of tagged PCR 454 amplicon sequencing performed on both genomic DNA (gDNA) and RNA-derived complementary DNA (cDNA), using part of the ITS2 flanking coding regions (5.8S and 28S rDNA) as an internal control for sequencing errors. Six different ITS2 haplotypes (i.e. variants for at least one nucleotide in the complete ITS2 sequence) were found in a single population, one of them (Hap4) being specific to a supernumerary (B) chromosome. The analysis of both gDNA and cDNA from the same individuals provided an estimate of the expression efficiency of the different haplotypes. We found random expression (i.e. about similar recovery in gDNA and cDNA) for three haplotypes (Hap1, Hap2 and Hap5), but significant underexpression for three others (Hap3, Hap4 and Hap6). Hap4 was the most extremely underexpressed and, remarkably, it showed the lowest sequence conservation for the flanking 5.8-28S coding regions in the gDNA reads but the highest conservation (100%) in the cDNA ones, suggesting the preferential expression of mutation-free rDNA units carrying this ITS2 haplotype. These results indicate that the ITS2 region of rDNA is far from complete homogenization in this species, and that the different rDNA units are not expressed at random, with some of them being severely downregulated.
Collapse
Affiliation(s)
- M Ruiz-Estévez
- Departamento de Genética, Universidad de Granada, Granada, Spain
| | | | | | | | | | | | | |
Collapse
|
16
|
Complete Genome Sequence of ER2796, a DNA Methyltransferase-Deficient Strain of Escherichia coli K-12. PLoS One 2015; 10:e0127446. [PMID: 26010885 PMCID: PMC4444293 DOI: 10.1371/journal.pone.0127446] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 04/14/2015] [Indexed: 11/19/2022] Open
Abstract
We report the complete sequence of ER2796, a laboratory strain of Escherichia coli K-12 that is completely defective in DNA methylation. Because of its lack of any native methylation, it is extremely useful as a host into which heterologous DNA methyltransferase genes can be cloned and the recognition sequences of their products deduced by Pacific Biosciences Single-Molecule Real Time (SMRT) sequencing. The genome was itself sequenced from a long-insert library using the SMRT platform, resulting in a single closed contig devoid of methylated bases. Comparison with K-12 MG1655, the first E. coli K-12 strain to be sequenced, shows an essentially co-linear relationship with no major rearrangements despite many generations of laboratory manipulation. The comparison revealed a total of 41 insertions and deletions, and 228 single base pair substitutions. In addition, the long-read approach facilitated the surprising discovery of four gene conversion events, three involving rRNA operons and one between two cryptic prophages. Such events thus contribute both to genomic homogenization and to bacteriophage diversification. As one of relatively few laboratory strains of E. coli to be sequenced, the genome also reveals the sequence changes underlying a number of classical mutant alleles including those affecting the various native DNA methylation systems.
Collapse
|
17
|
Maslunka C, Gürtler V, Seviour R. The impact of horizontal gene transfer on targeting the internal transcribed spacer region (ITS) to identify Acinetobacter junii
strains. J Appl Microbiol 2015; 118:1435-43. [DOI: 10.1111/jam.12800] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 02/24/2015] [Accepted: 03/12/2015] [Indexed: 11/30/2022]
Affiliation(s)
- C. Maslunka
- Biotechnology Research Centre; La Trobe University; Bendigo Vic. Australia
| | - V. Gürtler
- School of Applied Science; RMIT University; Bundoora Vic. Australia
| | - R.J. Seviour
- Biotechnology Research Centre; La Trobe University; Bendigo Vic. Australia
| |
Collapse
|
18
|
Maslunka C, Gürtler V, Seviour R. Unusual features of the sequences of copies of the 16S-23S rRNA internal transcribed spacer regions of Acinetobacter bereziniae, Acinetobacter guillouiae and Acinetobacter baylyi arise from horizontal gene transfer events. MICROBIOLOGY-SGM 2014; 161:322-329. [PMID: 25505188 DOI: 10.1099/mic.0.083600-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The highly variable nature of the internal transcribed spacer region (ITS) has been claimed to represent an ideal target for designing species-specific probes/primers capable of differentiating between closely related Acinetobacter species. However, several Acinetobacter species contain multiple ITS copies of variable lengths, and these include Acinetobacter bereziniae, Acinetobacter guillouiae and Acinetobacter baylyi. This study shows these length variations result from inter-genomic insertion/deletion events (indels) involving horizontal transfer of ITS fragments of other Acinetobacter species and possibly unrelated bacteria, as shown previously by us. In some instances, indel incorporation results in the loss of probe target sites in the recipient cell ITS. In other cases, some indel sequences contain target sites for probes designed from a single ITS sequence to target other Acinetobacter species. Hence, these can generate false positives. The largest of the indels that remove probe sites is 683 bp (labelled bay/i1-0), and it derives from the horizontal transfer of a complete ITS between A. bereziniae BCRC15423(T) and A. baylyi strain ADP1. As a consequence, ITS sequencing or fingerprinting cannot be used to distinguish between the 683 bp ITS in these two strains.
Collapse
Affiliation(s)
- Christopher Maslunka
- Biotechnology Research Centre, La Trobe University, Bendigo, Victoria 3552, Australia
| | - Volker Gürtler
- School of Applied Science, RMIT University, Bundoora, Victoria 3152, Australia
| | - Robert Seviour
- Department of Microbiology, La Trobe University, Bundoora, Victoria 3152, Australia.,Biotechnology Research Centre, La Trobe University, Bendigo, Victoria 3552, Australia
| |
Collapse
|
19
|
Insertions or deletions (Indels) in the rrn 16S-23S rRNA gene internal transcribed spacer region (ITS) compromise the typing and identification of strains within the Acinetobacter calcoaceticus-baumannii (Acb) complex and closely related members. PLoS One 2014; 9:e105390. [PMID: 25141005 PMCID: PMC4139376 DOI: 10.1371/journal.pone.0105390] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Accepted: 07/17/2014] [Indexed: 11/19/2022] Open
Abstract
To determine whether ITS sequences in the rrn operon are suitable for identifying individual Acinetobacter Acb complex members, we analysed length and sequence differences between multiple ITS copies within the genomes of individual strains. Length differences in ITS reported previously between A. nosocomialis BCRC15417T (615 bp) and other strains (607 bp) can be explained by presence of an insertion (indel 13i/1) in the longer ITS variant. The same Indel 13i/1 was also found in ITS sequences of ten strains of A. calcoaceticus, all 639 bp long, and the 628 bp ITS of Acinetobacter strain BENAB127. Four additional indels (13i/2–13i/5) were detected in Acinetobacter strain c/t13TU 10090 ITS length variants (608, 609, 620, 621 and 630 bp). These ITS variants appear to have resulted from horizontal gene transfer involving other Acinetobacter species or in some cases unrelated bacteria. Although some ITS copies in strain c/t13TU 10090 are of the same length (620 bp) as those in Acinetobacter strains b/n1&3, A. pittii (10 strains), A. calcoaceticus and A. oleivorans (not currently acknowledged as an Acb member), their individual ITS sequences differ. Thus ITS length by itself can not by itself be used to identify Acb complex strains. A shared indel in ITS copies in two separate Acinetobacter species compromises the specificity of ITS targeted probes, as shown with the Aun-3 probe designed to target the ITS in A. pitti. The presence of indel 13i/5 in the ITS of Acinetobacter strain c/t13TU means it too responded positively to this probe. Thus, neither ITS sequencing nor the currently available ITS targeted probes can distinguish reliably between Acb member species.
Collapse
|
20
|
Fontanez KM, Cavanaugh CM. Evidence for horizontal transmission from multilocus phylogeny of deep-sea mussel (Mytilidae) symbionts. Environ Microbiol 2014; 16:3608-21. [DOI: 10.1111/1462-2920.12379] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 12/22/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Kristina M. Fontanez
- Department of Organismic and Evolutionary Biology; Harvard University; Cambridge MA 02138 USA
| | - Colleen M. Cavanaugh
- Department of Organismic and Evolutionary Biology; Harvard University; Cambridge MA 02138 USA
| |
Collapse
|
21
|
Lindner DL, Carlsen T, Henrik Nilsson R, Davey M, Schumacher T, Kauserud H. Employing 454 amplicon pyrosequencing to reveal intragenomic divergence in the internal transcribed spacer rDNA region in fungi. Ecol Evol 2013; 3:1751-64. [PMID: 23789083 PMCID: PMC3686207 DOI: 10.1002/ece3.586] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 04/04/2013] [Accepted: 04/09/2013] [Indexed: 11/10/2022] Open
Abstract
The rDNA internal transcribed spacer (ITS) region has been accepted as a DNA barcoding marker for fungi and is widely used in phylogenetic studies; however, intragenomic ITS variability has been observed in a broad range of taxa, including prokaryotes, plants, animals, and fungi, and this variability has the potential to inflate species richness estimates in molecular investigations of environmental samples. In this study 454 amplicon pyrosequencing of the ITS1 region was applied to 99 phylogenetically diverse axenic single-spore cultures of fungi (Dikarya: Ascomycota and Basidiomycota) to investigate levels of intragenomic variation. Three species (one Basidiomycota and two Ascomycota), in addition to a positive control species known to contain ITS paralogs, displayed levels of molecular variation indicative of intragenomic variation; taxon inflation due to presumed intragenomic variation was ≈9%. Intragenomic variability in the ITS region appears to be widespread but relatively rare in fungi (≈3–5% of species investigated in this study), suggesting this problem may have minor impacts on species richness estimates relative to PCR and/or pyrosequencing errors. Our results indicate that 454 amplicon pyrosequencing represents a powerful tool for investigating levels of ITS intragenomic variability across taxa, which may be valuable for better understanding the fundamental mechanisms underlying concerted evolution of repetitive DNA regions.
Collapse
Affiliation(s)
- Daniel L Lindner
- US Forest Service, Northern Research Station, Center for Forest Mycology Research One Gifford Pinchot Drive, Madison, Wisconsin
| | | | | | | | | | | |
Collapse
|
22
|
Kasalický V, Jezbera J, Hahn MW, Šimek K. The diversity of the Limnohabitans genus, an important group of freshwater bacterioplankton, by characterization of 35 isolated strains. PLoS One 2013; 8:e58209. [PMID: 23505469 PMCID: PMC3591437 DOI: 10.1371/journal.pone.0058209] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 01/30/2013] [Indexed: 01/30/2023] Open
Abstract
Bacteria of the genus Limnohabitans, more precisely the R-BT lineage, have a prominent role in freshwater bacterioplankton communities due to their high rates of substrate uptake and growth, growth on algal-derived substrates and high mortality rates from bacterivory. Moreover, due to their generally larger mean cell volume, compared to typical bacterioplankton cells, they contribute over-proportionally to total bacterioplankton biomass. Here we present genetic, morphological and ecophysiological properties of 35 bacterial strains affiliated with the Limnohabitans genus newly isolated from 11 non-acidic European freshwater habitats. The low genetic diversity indicated by the previous studies using the ribosomal SSU gene highly contrasted with the surprisingly rich morphologies and different patterns in substrate utilization of isolated strains. Therefore, the intergenic spacer between 16S and 23S rRNA genes was successfully tested as a fine-scale marker to delineate individual lineages and even genotypes. For further studies, we propose the division of the Limnohabitans genus into five lineages (provisionally named as LimA, LimB, LimC, LimD and LimE) and also additional sublineages within the most diversified lineage LimC. Such a delineation is supported by the morphology of isolated strains which predetermine large differences in their ecology.
Collapse
Affiliation(s)
- Vojtěch Kasalický
- Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic.
| | | | | | | |
Collapse
|
23
|
Nagy LG, Kocsubé S, Csanádi Z, Kovács GM, Petkovits T, Vágvölgyi C, Papp T. Re-mind the gap! Insertion - deletion data reveal neglected phylogenetic potential of the nuclear ribosomal internal transcribed spacer (ITS) of fungi. PLoS One 2012; 7:e49794. [PMID: 23185439 PMCID: PMC3501463 DOI: 10.1371/journal.pone.0049794] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 10/12/2012] [Indexed: 01/09/2023] Open
Abstract
Rapidly evolving, indel-rich phylogenetic markers play a pivotal role in our understanding of the relationships at multiple levels of the tree of life. There is extensive evidence that indels provide conserved phylogenetic signal, however, the range of phylogenetic depths for which gaps retain tree signal has not been investigated in detail. Here we address this question using the fungal internal transcribed spacer (ITS), which is central in many phylogenetic studies, molecular ecology, detection and identification of pathogenic and non-pathogenic species. ITS is repeatedly criticized for indel-induced alignment problems and the lack of phylogenetic resolution above species level, although these have not been critically investigated. In this study, we examined whether the inclusion of gap characters in the analyses shifts the phylogenetic utility of ITS alignments towards earlier divergences. By re-analyzing 115 published fungal ITS alignments, we found that indels are slightly more conserved than nucleotide substitutions, and when included in phylogenetic analyses, improved the resolution and branch support of phylogenies across an array of taxonomic ranges and extended the resolving power of ITS towards earlier nodes of phylogenetic trees. Our results reconcile previous contradicting evidence for the effects of data exclusion: in the case of more sophisticated indel placement, the exclusion of indel-rich regions from the analyses results in a loss of tree resolution, whereas in the case of simpler alignment methods, the exclusion of gapped sites improves it. Although the empirical datasets do not provide to measure alignment accuracy objectively, our results for the ITS region are consistent with previous simulations studies alignment algorithms. We suggest that sophisticated alignment algorithms and the inclusion of indels make the ITS region and potentially other rapidly evolving indel-rich loci valuable sources of phylogenetic information, which can be exploited at multiple taxonomic levels.
Collapse
Affiliation(s)
- László G Nagy
- University of Szeged, Faculty of Science and Informatics, Department of Microbiology, Szeged, Hungary.
| | | | | | | | | | | | | |
Collapse
|
24
|
Čejková D, Zobaníková M, Pospíšilová P, Strouhal M, Mikalová L, Weinstock GM, Šmajs D. Structure of rrn operons in pathogenic non-cultivable treponemes: sequence but not genomic position of intergenic spacers correlates with classification of Treponema pallidum and Treponema paraluiscuniculi strains. J Med Microbiol 2012; 62:196-207. [PMID: 23082031 PMCID: PMC3755535 DOI: 10.1099/jmm.0.050658-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This study examined the sequences of the two rRNA (rrn) operons of pathogenic non-cultivable treponemes, comprising 11 strains of T. pallidum ssp. pallidum (TPA), five strains of T. pallidum ssp. pertenue (TPE), two strains of T. pallidum ssp. endemicum (TEN), a simian Fribourg-Blanc strain and a rabbit T. paraluiscuniculi (TPc) strain. PCR was used to determine the type of 16S–23S ribosomal intergenic spacers in the rrn operons from 30 clinical samples belonging to five different genotypes. When compared with the TPA strains, TPc Cuniculi A strain had a 17 bp deletion, and the TPE, TEN and Fribourg-Blanc isolates had a deletion of 33 bp. Other than these deletions, only 17 heterogeneous sites were found within the entire region (excluding the 16S–23S intergenic spacer region encoding tRNA-Ile or tRNA-Ala). The pattern of nucleotide changes in the rrn operons corresponded to the classification of treponemal strains, whilst two different rrn spacer patterns (Ile/Ala and Ala/Ile) appeared to be distributed randomly across species/subspecies classification, time and geographical source of the treponemal strains. It is suggested that the random distribution of tRNA genes is caused by reciprocal translocation between repetitive sequences mediated by a recBCD-like system.
Collapse
Affiliation(s)
- Darina Čejková
- The Genome Institute, Washington University in St Louis, 4444 Forest Park Avenue, St Louis, MO 63108, USA.,Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 62500 Brno, Czech Republic
| | - Marie Zobaníková
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 62500 Brno, Czech Republic
| | - Petra Pospíšilová
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 62500 Brno, Czech Republic
| | - Michal Strouhal
- The Genome Institute, Washington University in St Louis, 4444 Forest Park Avenue, St Louis, MO 63108, USA.,Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 62500 Brno, Czech Republic
| | - Lenka Mikalová
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 62500 Brno, Czech Republic
| | - George M Weinstock
- The Genome Institute, Washington University in St Louis, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 62500 Brno, Czech Republic
| |
Collapse
|
25
|
Erwin PM, López-Legentil S, Turon X. Ultrastructure, molecular phylogenetics, and chlorophyll a content of novel cyanobacterial symbionts in temperate sponges. MICROBIAL ECOLOGY 2012; 64:771-783. [PMID: 22526400 DOI: 10.1007/s00248-012-0047-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 03/19/2012] [Indexed: 05/31/2023]
Abstract
Marine sponges often harbor photosynthetic symbionts that may enhance host metabolism and ecological success, yet little is known about the factors that structure the diversity, specificity, and nature of these relationships. Here, we characterized the cyanobacterial symbionts in two congeneric and sympatric host sponges that exhibit distinct habitat preferences correlated with irradiance: Ircinia fasciculata (higher irradiance) and Ircinia variabilis (lower irradiance). Symbiont composition was similar among hosts and dominated by the sponge-specific cyanobacterium Synechococcus spongiarum. Phylogenetic analyses of 16S-23S rRNA internal transcribed spacer (ITS) gene sequences revealed that Mediterranean Ircinia spp. host a specific, novel symbiont clade ("M") within the S. spongiarum species complex. A second, rare cyanobacterium related to the ascidian symbiont Synechocystis trididemni was observed in low abundance in I. fasciculata and likewise corresponded to a new symbiont clade. Symbiont communities in I. fasciculata exhibited nearly twice the chlorophyll a concentrations of I. variabilis. Further, S. spongiarum clade M symbionts in I. fasciculata exhibited dense intracellular aggregations of glycogen granules, a storage product of photosynthetic carbon assimilation rarely observed in I. variabilis symbionts. In both host sponges, S. spongiarum cells were observed interacting with host archeocytes, although the lower photosynthetic activity of Cyanobacteria in I. variabilis suggests less symbiont-derived nutritional benefit. The observed differences in clade M symbionts among sponge hosts suggest that ambient irradiance conditions dictate symbiont photosynthetic activity and consequently may mediate the nature of host-symbiont relationships. In addition, the plasticity exhibited by clade M symbionts may be an adaptive attribute that allows for flexibility in host-symbiont interactions across the seasonal fluctuations in light and temperature characteristic of temperate environments.
Collapse
Affiliation(s)
- Patrick M Erwin
- Center for Advanced Studies of Blanes, Accés Cala S. Francesc 14, 17300 Blanes, Girona, Spain.
| | | | | |
Collapse
|
26
|
Thacker RW, Freeman CJ. Sponge-microbe symbioses: recent advances and new directions. ADVANCES IN MARINE BIOLOGY 2012; 62:57-111. [PMID: 22664121 DOI: 10.1016/b978-0-12-394283-8.00002-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Sponges can host abundant and diverse communities of symbiotic microorganisms. In this chapter, we review recent work in the area of sponge-microbe symbioses, focusing on (1) the diversity of these associations, (2) host specificity, (3) modes of symbiont transmission, and (4) the positive and negative impacts of symbionts on their hosts. Over the past 4 years, numerous studies have catalogued the diversity of sponge-microbe symbioses, challenging previous hypotheses of a uniform, vertically transmitted microbial community and supporting a mixed model of symbiont community transmission. We emphasize the need for experimental manipulations of sponge-symbiont interactions coupled with advanced laboratory techniques to determine the identity of metabolically active microbial symbionts, to investigate the physiological processes underlying these interactions, and to elucidate whether symbionts act as mutualists, commensals, or parasites. The amazing diversity of these complex associations continues to offer critical insights into the evolution of symbiosis and the impacts of symbiotic microbes on nutrient cycling and other ecosystem functions.
Collapse
|
27
|
Snyder AK, Adkins KZ, Rio RVM. Use of the Internal Transcribed Spacer (ITS) Regions to Examine Symbiont Divergence and as a Diagnostic Tool for Sodalis-Related Bacteria. INSECTS 2011; 2:515-31. [PMID: 26467831 PMCID: PMC4553445 DOI: 10.3390/insects2040515] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Revised: 11/15/2011] [Accepted: 11/17/2011] [Indexed: 12/11/2022]
Abstract
Bacteria excel in most ecological niches, including insect symbioses. A cluster of bacterial symbionts, established within a broad range of insects, share high 16S rRNA similarities with the secondary symbiont of the tsetse fly (Diptera: Glossinidae), Sodalis glossinidius. Although 16S rRNA has proven informative towards characterization of this clade, the gene is insufficient for examining recent divergence due to selective constraints. Here, we assess the application of the internal transcribed spacer (ITS) regions, specifically the ITS(glu) and ITS(ala,ile), used in conjunction with 16S rRNA to enhance the phylogenetic resolution of Sodalis-allied bacteria. The 16S rRNA + ITS regions of Sodalis and allied bacteria demonstrated significant divergence and were robust towards phylogenetic resolution. A monophyletic clade of Sodalis isolates from tsetse species, distinct from other Enterobacteriaceae, was consistently observed suggesting diversification due to host adaptation. In contrast, the phylogenetic distribution of symbionts isolated from hippoboscid flies and various Hemiptera and Coleoptera were intertwined suggesting either horizontal transfer or a recent establishment from an environmental source. Lineage splitting of Sodalis-allied bacteria into symbiotic and free-living sister groups was also observed. Additionally, we propose an ITS region as a diagnostic marker for the identification of additional Sodalis-allied symbionts in the field. These results expand our knowledge of informative genome regions to assess genetic divergence since splitting from the last common ancestor, of this versatile insect symbiont clade that have become increasingly recognized as valuable towards our understanding of the evolution of symbiosis. These facultative and recently associated symbionts may provide a novel source of traits adaptable to the dynamic ecologies encountered by diverse host backgrounds.
Collapse
Affiliation(s)
- Anna K Snyder
- Department of Biology, West Virginia University, Morgantown, WV 26506, USA.
| | - Kenneth Z Adkins
- Department of Biology, West Virginia University, Morgantown, WV 26506, USA.
| | - Rita V M Rio
- Department of Biology, West Virginia University, Morgantown, WV 26506, USA.
| |
Collapse
|
28
|
López JR, Hamman-Khalifa AM, Navas JI, de la Herran R. Characterization of ISR region and development of a PCR assay for rapid detection of the fish pathogen Tenacibaculum soleae. FEMS Microbiol Lett 2011; 324:181-8. [PMID: 22092820 DOI: 10.1111/j.1574-6968.2011.02404.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Revised: 08/21/2011] [Accepted: 08/26/2011] [Indexed: 11/29/2022] Open
Abstract
The aims of this work were to characterize the 16S-23S internal spacer region of the fish pathogen Tenacibaculum soleae and to develop a PCR assay for its identification and detection. All T. soleae strains tested displayed a single internal spacer region class, containing tRNA(I) (le) and tRNA(A) (la) genes; nevertheless, a considerable intraspecific heterogeneity was observed. However, this region proved to be useful for differentiation of T. soleae from related and non-related species. Species-specific primers were designed targeting the 16S rRNA gene and the internal spacer region region, yielding a 1555-bp fragment. Detection limit was of 1 pg DNA per reaction (< 30 bacterial cells) when using pure cultures. The detection level in the presence of DNA from fish or other bacteria was lower; however, 10 pg were detected at a target/background ratio of 1 : 10(5) . The PCR assay proved to be more sensitive than agar cultivation for the detection of T. soleae from naturally diseased fish, offering a useful tool for diagnosis and for understanding the epidemiology of this pathogen.
Collapse
|
29
|
Lange C, Zerulla K, Breuert S, Soppa J. Gene conversion results in the equalization of genome copies in the polyploid haloarchaeon Haloferax volcanii. Mol Microbiol 2011; 80:666-77. [PMID: 21338422 DOI: 10.1111/j.1365-2958.2011.07600.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Haloferax volcanii is highly polyploid and contains about 20 copies of the major chromosome. A heterozygous strain was constructed that contained two different types of genomes: the leuB locus contained either the wild-type leuB gene or a leuB:trpA gene introduced by gene replacement. As the trpA locus is devoid of the wild-type trpA gene, growth in the absence of both amino acids is only possible when both types of genomes are simultaneously present, exemplifying gene redundancy and the potential to form heterozygous cells as one possible evolutionary advantage of polyploidy. The heterozygous strain was grown (i) in the presence of tryptophan, selecting for the presence of leuB, (ii) in the presence of leucine selecting for leuB:trpA and (iii) in the absence of selection. Both types of genomes were quantified with real-time PCR. The first condition led to a complete loss of leuB:trpA-containing genomes, while under the second condition leuB-containing genomes were lost. Also in the absence of selection gene conversion led to a fast equalization of genomes and resulted in homozygous leuB-containing cells. Gene conversion leading to genome equalization can explain the escape from 'Muller's ratchet' as well as the ease of mutant construction using polyploid haloarchaea.
Collapse
Affiliation(s)
- Christian Lange
- Johann Wolfgang Goethe University, Institute for Molecular Biosciences, Max-von-Laue-Strasse 9, 60438 Frankfurt a.M., Germany
| | | | | | | |
Collapse
|
30
|
Lindner DL, Banik MT. Intragenomic variation in the ITS rDNA region obscures phylogenetic relationships and inflates estimates of operational taxonomic units in genus Laetiporus. Mycologia 2011; 103:731-40. [PMID: 21289107 DOI: 10.3852/10-331] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Regions of rDNA are commonly used to infer phylogenetic relationships among fungal species and as DNA barcodes for identification. These regions occur in large tandem arrays, and concerted evolution is believed to reduce intragenomic variation among copies within these arrays, although some variation still might exist. Phylogenetic studies typically use consensus sequencing, which effectively conceals most intragenomic variation, but cloned sequences containing intragenomic variation are becoming prevalent in DNA databases. To understand effects of using cloned rDNA sequences in phylogenetic analyses we amplified and cloned the ITS region from pure cultures of six Laetiporus species and one Wolfiporia species (Basidiomycota, Polyporales). An average of 66 clones were selected randomly and sequenced from 21 cultures, producing a total of 1399 interpretable sequences. Significant variation (≥ 5% variation in sequence similarity) was observed among ITS copies within six cultures from three species clades (L. cincinnatus, L. sp. clade J, and Wolfiporia dilatohypha) and phylogenetic analyses with the cloned sequences produced different trees relative to analyses with consensus sequences. Cloned sequences from L. cincinnatus fell into more than one species clade and numerous cloned L. cincinnatus sequences fell into entirely new clades, which if analyzed on their own most likely would be recognized as "undescribed" or "novel" taxa. The use of a 95% cut off for defining operational taxonomic units (OTUs) produced seven Laetiporus OTUs with consensus ITS sequences and 20 OTUs with cloned ITS sequences. The use of cloned rDNA sequences might be problematic in fungal phylogenetic analyses, as well as in fungal bar-coding initiatives and efforts to detect fungal pathogens in environmental samples.
Collapse
Affiliation(s)
- Daniel L Lindner
- US Forest Service, Northern Research Station, Center for Forest Mycology Research, One Gifford Pinchot Drive, Madison, Wisconsin 53726, USA.
| | | |
Collapse
|
31
|
Meinersmann RJ, Ladely SR, Lindsey RL. Ribosomal operon intergenic sequence region (ISR) heterogeneity in Campylobacter coli and Campylobacter jejuni. Lett Appl Microbiol 2010; 51:539-45. [PMID: 20849393 DOI: 10.1111/j.1472-765x.2010.02930.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS The intergenic sequence regions (ISR) between the 16S and 23S genes of Campylobacter jejuni and Campylobacter coli are markedly different for each species. However, in the genomic sequence for Camp. coli RM2228, two rRNA operons have an ISR that is characteristic of Camp. coli, and the third operon is characteristic of Camp. jejuni. The aim of this study was to determine the prevalence of ISR heterogeneity in these organisms. METHODS AND RESULTS PCR primers were designed to yield a 327-base pair (bp) product for Camp. coli and 166-bp product for Camp. jejuni. A strain like Camp. coli RM2228 should yield products of both sizes. DNA from a panel of Camp. coli (n=133) and Camp. jejuni (n=134) isolates were tested. All of the isolates yielded products of the predicted size for the species. To verify the data for Camp. coli RM2228, each ribosomal operon from the isolate was individually amplified by PCR and tested with the ISR primer pair. Products of both sizes were produced as predicted. CONCLUSIONS The cross-species heterogeneity of the ISR seen in Camp. coli RM2228 is uncommon. SIGNIFICANCE AND IMPACT OF THE STUDY The heterogeneity must have been caused by horizontal gene transfer at a frequency lower than predicted from housekeeping gene data. Thus, it can be expected that species identification based on the ISR can be confused in rare isolates.
Collapse
|
32
|
Budding AE, Grasman ME, Lin F, Bogaards JA, Soeltan-Kaersenhout DJ, Vandenbroucke-Grauls CMJE, van Bodegraven AA, Savelkoul PHM. IS-pro: high-throughput molecular fingerprinting of the intestinal microbiota. FASEB J 2010; 24:4556-64. [PMID: 20643909 DOI: 10.1096/fj.10-156190] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The human intestinal microbiota is known to play an important role in human health and disease, and with the advent of novel molecular techniques, disease-specific variations in its composition have been found. However, analysis of the intestinal microbiota has not yet been applicable in large-scale clinical research or routine diagnostics because of the complex and expensive nature of the techniques needed. Here, we describe a new PCR-based profiling technique for high-throughput analysis of the human intestinal microbiota, which we have termed IS-pro. This technique combines bacterial species differentiation by the length of the 16S-23S rDNA interspace region with instant taxonomic classification by phylum-specific fluorescent labeling of PCR primers. We validated IS-pro in silico, in vitro, and in vivo, on human colonic biopsies and feces, and introduced a standardized protocol for data analysis. IS-pro is easy to implement in general clinical microbiological laboratories with access to capillary gel electrophoresis, and the high-throughput nature of the test makes analysis of large numbers of samples feasible. This combination renders IS-pro ideally suited for use in clinical research and routine diagnostics.
Collapse
Affiliation(s)
- A E Budding
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands.
| | | | | | | | | | | | | | | |
Collapse
|
33
|
A microarray for screening the variability of 16S-23S rRNA internal transcribed spacer in Pseudomonas syringae. J Microbiol Methods 2010; 82:90-4. [PMID: 20470837 DOI: 10.1016/j.mimet.2010.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Revised: 05/03/2010] [Accepted: 05/07/2010] [Indexed: 11/22/2022]
Abstract
The 16S-23S ribosomal internal transcribed spacer (ITS1) is often used as a subspecies or strain-specific molecular marker for various kinds of bacteria. However, the presence of different copies of ITS1 within a single genome has been reported. Such mosaicism may influence correct typing of many bacteria and therefore knowledge about exact configuration of this region in a particular genome is essential. In order to screen the variability of ITS1 among and within Pseudomonas syringae genomes, an oligonucleotide microarray targeting different configurations of ITS1 was developed. The microarray revealed seven distinct variants in 13 pathovars tested and detected mosaicism within the genomes of P. syringae pv. coronafaciens, pisi, syringae and tabaci. In addition, the findings presented here challenge the using of rRNA analysis for pathovar and strain determination.
Collapse
|
34
|
Baudoin E, Couillerot O, Spaepen S, Moënne-Loccoz Y, Nazaret S. Applicability of the 16S-23S rDNA internal spacer for PCR detection of the phytostimulatory PGPR inoculant Azospirillum lipoferum CRT1 in field soil. J Appl Microbiol 2010; 108:25-38. [PMID: 19583800 DOI: 10.1111/j.1365-2672.2009.04393.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AIMS To assess the applicability of the 16S-23S rDNA internal spacer regions (ISR) as targets for PCR detection of Azospirillum ssp. and the phytostimulatory plant growth-promoting rhizobacteria seed inoculant Azospirillum lipoferum CRT1 in soil. METHODS AND RESULTS Primer sets were designed after sequence analysis of the ISR of A. lipoferum CRT1 and Azospirillum brasilense Sp245. The primers fAZO/rAZO targeting the Azospirillum genus successfully yielded PCR amplicons (400-550 bp) from Azospirillum strains but also from certain non-Azospirillum strains in vitro, therefore they were not appropriate to monitor indigenous Azospirillum soil populations. The primers fCRT1/rCRT1 targeting A. lipoferum CRT1 generated a single 249-bp PCR product but could also amplify other strains from the same species. However, with DNA extracts from the rhizosphere of field-grown maize, both fAZO/rAZO and fCRT1/rCRT1 primer sets could be used to evidence strain CRT1 in inoculated plants by nested PCR, after a first ISR amplification with universal ribosomal primers. In soil, a 7-log dynamic range of detection (10(2)-10(8) CFU g(-1) soil) was obtained. CONCLUSIONS The PCR primers targeting 16S-23S rDNA ISR sequences enabled detection of the inoculant A. lipoferum CRT1 in field soil. SIGNIFICANCE AND IMPACT OF THE STUDY Convenient methods to monitor Azospirillum phytostimulators in the soil are lacking. The PCR protocols designed based on ISR sequences will be useful for detection of the crop inoculant A. lipoferum CRT1 under field conditions.
Collapse
Affiliation(s)
- E Baudoin
- IRD, UMR 113, LSTM, Campus International de Baillarguet, TA-A82/J, 34398 Montpellier cedex5, France
| | | | | | | | | |
Collapse
|
35
|
Philosof A, Sabehi G, Béjà O. Comparative analyses of actinobacterial genomic fragments from Lake Kinneret. Environ Microbiol 2009; 11:3189-200. [DOI: 10.1111/j.1462-2920.2009.02024.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
36
|
Nováková E, Hypša V, Moran NA. Arsenophonus, an emerging clade of intracellular symbionts with a broad host distribution. BMC Microbiol 2009; 9:143. [PMID: 19619300 PMCID: PMC2724383 DOI: 10.1186/1471-2180-9-143] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Accepted: 07/20/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genus Arsenophonus is a group of symbiotic, mainly insect-associated bacteria with rapidly increasing number of records. It is known from a broad spectrum of hosts and symbiotic relationships varying from parasitic son-killers to coevolving mutualists.The present study extends the currently known diversity with 34 samples retrieved mainly from hippoboscid (Diptera: Hippoboscidae) and nycteribiid (Diptera: Nycteribiidae) hosts, and investigates phylogenetic relationships within the genus. RESULTS The analysis of 110 Arsenophonus sequences (incl. Riesia and Phlomobacter), provides a robust monophyletic clade, characterized by unique molecular synapomorphies. On the other hand, unstable inner topology indicates that complete understanding of Arsenophonus evolution cannot be achieved with 16S rDNA. Moreover, taxonomically restricted Sampling matrices prove sensitivity of the phylogenetic signal to sampling; in some cases, Arsenophonus monophyly is disrupted by other symbiotic bacteria. Two contrasting coevolutionary patterns occur throughout the tree: parallel host-symbiont evolution and the haphazard association of the symbionts with distant hosts. A further conspicuous feature of the topology is the occurrence of monophyletic symbiont lineages associated with monophyletic groups of hosts without a co-speciation pattern. We suggest that part of this incongruence could be caused by methodological artifacts, such as intragenomic variability. CONCLUSION The sample of currently available molecular data presents the genus Arsenophonus as one of the richest and most widespread clusters of insect symbiotic bacteria. The analysis of its phylogenetic lineages indicates a complex evolution and apparent ecological versatility with switches between entirely different life styles. Due to these properties, the genus should play an important role in the studies of evolutionary trends in insect intracellular symbionts. However, under the current practice, relying exclusively on 16S rRNA sequences, the phylogenetic analyses are sensitive to various methodological artifacts that may even lead to description of new Arsenophonus lineages as independent genera (e.g. Riesia and Phlomobacter). The resolution of the evolutionary questions encountered within the Arsenophonus clade will thus require identification of new molecular markers suitable for the low-level phylogenetics.
Collapse
Affiliation(s)
- Eva Nováková
- Faculty of Science, University of South Bohemia, Branišovská 31, České Budějovice 37005, Czech Republic
| | - Václav Hypša
- Faculty of Science, University of South Bohemia and Institute of Parasitology, Biology Centre of ASCR, Branišovská 31, České Budějovice 37005, Czech Republic
| | - Nancy A Moran
- Department of Ecology and Evolutionary Biology, The University of Arizona, 1041 E. Lowell St, Tucson, Arizona 85721-0088, USA
| |
Collapse
|
37
|
Yang JC, Madupu R, Durkin AS, Ekborg NA, Pedamallu CS, Hostetler JB, Radune D, Toms BS, Henrissat B, Coutinho PM, Schwarz S, Field L, Trindade-Silva AE, Soares CAG, Elshahawi S, Hanora A, Schmidt EW, Haygood MG, Posfai J, Benner J, Madinger C, Nove J, Anton B, Chaudhary K, Foster J, Holman A, Kumar S, Lessard PA, Luyten YA, Slatko B, Wood N, Wu B, Teplitski M, Mougous JD, Ward N, Eisen JA, Badger JH, Distel DL. The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms). PLoS One 2009; 4:e6085. [PMID: 19568419 PMCID: PMC2699552 DOI: 10.1371/journal.pone.0006085] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Accepted: 05/06/2009] [Indexed: 12/02/2022] Open
Abstract
Here we report the complete genome sequence of Teredinibacter turnerae T7901. T. turnerae is a marine gamma proteobacterium that occurs as an intracellular endosymbiont in the gills of wood-boring marine bivalves of the family Teredinidae (shipworms). This species is the sole cultivated member of an endosymbiotic consortium thought to provide the host with enzymes, including cellulases and nitrogenase, critical for digestion of wood and supplementation of the host's nitrogen-deficient diet. T. turnerae is closely related to the free-living marine polysaccharide degrading bacterium Saccharophagus degradans str. 2–40 and to as yet uncultivated endosymbionts with which it coexists in shipworm cells. Like S. degradans, the T. turnerae genome encodes a large number of enzymes predicted to be involved in complex polysaccharide degradation (>100). However, unlike S. degradans, which degrades a broad spectrum (>10 classes) of complex plant, fungal and algal polysaccharides, T. turnerae primarily encodes enzymes associated with deconstruction of terrestrial woody plant material. Also unlike S. degradans and many other eubacteria, T. turnerae dedicates a large proportion of its genome to genes predicted to function in secondary metabolism. Despite its intracellular niche, the T. turnerae genome lacks many features associated with obligate intracellular existence (e.g. reduced genome size, reduced %G+C, loss of genes of core metabolism) and displays evidence of adaptations common to free-living bacteria (e.g. defense against bacteriophage infection). These results suggest that T. turnerae is likely a facultative intracellular ensosymbiont whose niche presently includes, or recently included, free-living existence. As such, the T. turnerae genome provides insights into the range of genomic adaptations associated with intracellular endosymbiosis as well as enzymatic mechanisms relevant to the recycling of plant materials in marine environments and the production of cellulose-derived biofuels.
Collapse
Affiliation(s)
- Joyce C. Yang
- Ocean Genome Legacy, Inc., Ipswich, Massachusetts, United States of America
| | - Ramana Madupu
- J. Craig Venter Institute, San Diego, California, United States of America
| | - A. Scott Durkin
- J. Craig Venter Institute, San Diego, California, United States of America
| | - Nathan A. Ekborg
- Ocean Genome Legacy, Inc., Ipswich, Massachusetts, United States of America
| | | | | | - Diana Radune
- J. Craig Venter Institute, San Diego, California, United States of America
| | - Bradley S. Toms
- J. Craig Venter Institute, San Diego, California, United States of America
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Universités Aix-Marseille I & II, Case 932, Marseille, France
| | - Pedro M. Coutinho
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Universités Aix-Marseille I & II, Case 932, Marseille, France
| | - Sandra Schwarz
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Lauren Field
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Amaro E. Trindade-Silva
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Ilha do Fundao, CCS, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carlos A. G. Soares
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Ilha do Fundao, CCS, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Sherif Elshahawi
- Department of Environmental and Biomolecular Systems, OGI School of Science & Engineering, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Amro Hanora
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Eric W. Schmidt
- College of Pharmacy, University of Utah, Salt Lake City, Utah, United States of America
| | - Margo G. Haygood
- Department of Environmental and Biomolecular Systems, OGI School of Science & Engineering, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Janos Posfai
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Jack Benner
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | | | - John Nove
- Ocean Genome Legacy, Inc., Ipswich, Massachusetts, United States of America
| | - Brian Anton
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Kshitiz Chaudhary
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Jeremy Foster
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Alex Holman
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Sanjay Kumar
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Philip A. Lessard
- Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Yvette A. Luyten
- Ocean Genome Legacy, Inc., Ipswich, Massachusetts, United States of America
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Barton Slatko
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Nicole Wood
- Ocean Genome Legacy, Inc., Ipswich, Massachusetts, United States of America
| | - Bo Wu
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Max Teplitski
- University of Florida, Gainesville, Florida, United States of America
| | - Joseph D. Mougous
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Naomi Ward
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, United States of America
| | - Jonathan A. Eisen
- UC Davis Genome Center, University of California Davis, Davis, California, United States of America
| | - Jonathan H. Badger
- J. Craig Venter Institute, San Diego, California, United States of America
| | - Daniel L. Distel
- Ocean Genome Legacy, Inc., Ipswich, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
38
|
The extent of migration of the Holliday junction is a crucial factor for gene conversion in Rhizobium etli. J Bacteriol 2009; 191:4987-95. [PMID: 19502410 DOI: 10.1128/jb.00111-09] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Gene conversion, defined as the nonreciprocal transfer of DNA, is one result of homologous recombination. Three steps in recombination could give rise to gene conversion: (i) DNA synthesis for repair of the degraded segment, (ii) Holliday junction migration, leading to heteroduplex formation, and (iii) repair of mismatches in the heteroduplex. There are at least three proteins (RuvAB, RecG, and RadA) that participate in the second step. Their roles have been studied for homologous recombination, but evidence of their relative role in gene conversion is lacking. In this work, we showed the effect on gene conversion of mutations in ruvB, recG, and radA in Rhizobium etli, either alone or in combination, using a cointegration strategy previously developed in our laboratory. The results indicate that the RuvAB system is highly efficient for gene conversion, since its absence provokes smaller gene conversion segments than those in the wild type as well as a shift in the preferred position of conversion tracts. The RecG system possesses a dual role for gene conversion. Inactivation of recG leads to longer gene conversion tracts than those in the wild type, indicating that its activity may hinder heteroduplex extension. However, under circumstances where it is the only migration activity present (as in the ruvB radA double mutant), conversion segments can still be seen, indicating that RecG can also promote gene conversion. RadA is the least efficient system in R. etli but is still needed for the production of detectable gene conversion tracts.
Collapse
|
39
|
Pei A, Nossa CW, Chokshi P, Blaser MJ, Yang L, Rosmarin DM, Pei Z. Diversity of 23S rRNA genes within individual prokaryotic genomes. PLoS One 2009; 4:e5437. [PMID: 19415112 PMCID: PMC2672173 DOI: 10.1371/journal.pone.0005437] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2008] [Accepted: 04/07/2009] [Indexed: 12/23/2022] Open
Abstract
Background The concept of ribosomal constraints on rRNA genes is deduced primarily based on the comparison of consensus rRNA sequences between closely related species, but recent advances in whole-genome sequencing allow evaluation of this concept within organisms with multiple rRNA operons. Methodology/Principal Findings Using the 23S rRNA gene as an example, we analyzed the diversity among individual rRNA genes within a genome. Of 184 prokaryotic species containing multiple 23S rRNA genes, diversity was observed in 113 (61.4%) genomes (mean 0.40%, range 0.01%–4.04%). Significant (1.17%–4.04%) intragenomic variation was found in 8 species. In 5 of the 8 species, the diversity in the primary structure had only minimal effect on the secondary structure (stem versus loop transition). In the remaining 3 species, the diversity significantly altered local secondary structure, but the alteration appears minimized through complex rearrangement. Intervening sequences (IVS), ranging between 9 and 1471 nt in size, were found in 7 species. IVS in Deinococcus radiodurans and Nostoc sp. encode transposases. T. tengcongensis was the only species in which intragenomic diversity >3% was observed among 4 paralogous 23S rRNA genes. Conclusions/Significance These findings indicate tight ribosomal constraints on individual 23S rRNA genes within a genome. Although classification using primary 23S rRNA sequences could be erroneous, significant diversity among paralogous 23S rRNA genes was observed only once in the 184 species analyzed, indicating little overall impact on the mainstream of 23S rRNA gene-based prokaryotic taxonomy.
Collapse
Affiliation(s)
- Anna Pei
- Washington University, College of Arts and Sciences, St. Louis, Missouri, United States of America
| | - Carlos W. Nossa
- Department of Medicine, New York University School of Medicine, New York, New York, United States of America
| | - Pooja Chokshi
- Tufts University College of Arts and Sciences, Medford, Massachusetts, United States of America
| | - Martin J. Blaser
- Department of Medicine, New York University School of Medicine, New York, New York, United States of America
- Department of Microbiology, New York University School of Medicine, New York, New York, United States of America
- Department of Veterans Affairs, New York Harbor Healthcare System, New York, New York, United States of America
| | - Liying Yang
- Department of Medicine, New York University School of Medicine, New York, New York, United States of America
| | - David M. Rosmarin
- Department of Medicine, New York University School of Medicine, New York, New York, United States of America
| | - Zhiheng Pei
- Department of Medicine, New York University School of Medicine, New York, New York, United States of America
- Department of Veterans Affairs, New York Harbor Healthcare System, New York, New York, United States of America
- Department of Pathology, New York University School of Medicine, New York, New York, United States of America
- * E-mail:
| |
Collapse
|
40
|
Stewart FJ, Cavanaugh CM. Pyrosequencing analysis of endosymbiont population structure: co-occurrence of divergent symbiont lineages in a single vesicomyid host clam. Environ Microbiol 2009; 11:2136-47. [PMID: 19397674 DOI: 10.1111/j.1462-2920.2009.01933.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacteria-eukaryote endosymbioses are perhaps the most pervasive co-evolutionary associations in nature. Here, intracellular chemosynthetic symbionts of deep-sea clams (Vesicomyidae) were analysed by amplicon pyrosequencing to explore how symbiont transmission mode affects the genetic diversity of the within-host symbiont population. Vesicomyid symbionts (Gammaproteobacteria) are presumed to be obligately intracellular, to undergo nearly strict vertical transmission between host generations, and to be clonal within a host. However, recent data show that vesicomyid symbionts can be acquired laterally via horizontal transfer between hosts or uptake from the environment, potentially creating opportunities for multiple symbiont strains to occupy the same host. Here, genotype-specific PCR and direct sequencing of the bacterial internal transcribed spacer initially demonstrated the co-occurrence of two symbiont strains, symA and symB (93.5% nt identity), in 8 of 118 Vesicomya sp. clams from 3 of 7 hydrothermal vent sites on the Juan de Fuca Ridge. To confirm multiple strains within individual clams, amplicon pyrosequencing of two symbiont loci was used to obtain deep-coverage measurements (mean: approximately 1500x coverage per locus per clam) of symbiont population structure. Pyrosequencing confirmed symA-symB co-occurrence for two individuals, showing the presence of both genotypes in amplicon pools. However, in the majority of clams, the endosymbiont population was remarkably homogenous, with > 99.5% of sequences collapsing into a single symbiont genotype in each clam. These results support the hypothesis that a predominantly vertical transmission strategy leads to the fixation of a single symbiont strain in most hosts. However, mixed symbiont populations do occur in vesicomyids, potentially facilitating the exchange of genetic material between divergent symbiont lineages.
Collapse
Affiliation(s)
- Frank J Stewart
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | |
Collapse
|
41
|
Stewart FJ, Young CR, Cavanaugh CM. Evidence for homologous recombination in intracellular chemosynthetic clam symbionts. Mol Biol Evol 2009; 26:1391-404. [PMID: 19289597 DOI: 10.1093/molbev/msp049] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Homologous recombination is a fundamental mechanism for the genetic diversification of free-living bacteria. However, recombination may be limited in endosymbiotic bacteria, as these taxa are locked into an intracellular niche and may rarely encounter sources of foreign DNA. This study tested the hypothesis that vertically transmitted endosymbionts of deep-sea clams (Bivalvia: Vesicomyidae) show little or no evidence of recombination. Phylogenetic analysis of 13 loci distributed across the genomes of 14 vesicomyid symbionts revealed multiple, well-supported inconsistencies among gene tree topologies, and maximum likelihood-based tests rejected a hypothesis of shared evolutionary history (linkage) among loci. Further, multiple statistical methods confirmed the presence of recombination by detecting intragenic breakpoints in two symbiont loci. Recombination may be confined to a subset of vesicomyid symbionts, as some clades showed high levels of genomic stability, whereas others showed clear patterns of homologous exchange. Notably, a mosaic genome is present in symB, a symbiont lineage shown to have been acquired laterally (i.e., nonvertically) by Vesicomya sp. JdF clams. The majority of loci analyzed here supported a tight sister clustering of symB with the symbiont of a host species from the Mid-Atlantic Ridge, whereas others placed symB in a clade with symA, the dominant phylotype of V. sp. JdF clams. This result raises the hypothesis that lateral symbiont transfer between hosts may facilitate recombination by bringing divergent symbiont lineages into contact. Together, the data show that homologous recombination contributes to the diversification of vesicomyid clam symbionts, despite the intracellular lifestyle of these bacteria.
Collapse
Affiliation(s)
- Frank J Stewart
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | |
Collapse
|
42
|
Phylogenetic and chemical diversity of three chemotypes of bloom-forming lyngbya species (Cyanobacteria: Oscillatoriales) from reefs of southeastern Florida. Appl Environ Microbiol 2009; 75:2879-88. [PMID: 19270119 DOI: 10.1128/aem.02656-08] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The cyanobacterial genus Lyngbya includes free-living, benthic, filamentous cyanobacteria that form periodic nuisance blooms in lagoons, reefs, and estuaries. Lyngbya spp. are prolific producers of biologically active compounds that deter grazers and help blooms persist in the marine environment. Here, our investigations reveal the presence of three distinct Lyngbya species on nearshore reefs in Broward County, FL, sampled in 2006 and 2007. With a combination of morphological measurements, molecular biology techniques, and natural products chemistry, we associated these three Lyngbya species with three distinct Lyngbya chemotypes. One species, identified as Lyngbya cf. confervoides via morphological measurements and 16S rRNA gene sequencing, produces a diverse array of bioactive peptides and depsipeptides. Our results indicate that the other two Lyngbya species produce either microcolins A and B or curacin D and dragonamides C and D. Results from screening for the biosynthetic capacity for curacin production among the three Lyngbya chemotypes in this study correlated that capacity with the presence of curacin D. Our work on these bloom-forming Lyngbya species emphasizes the significant phylogenetic and chemical diversity of the marine cyanobacteria on southern Florida reefs and identifies some of the genetic components of those differences.
Collapse
|
43
|
Meinersmann RJ, Phillips RW, Ladely SR. Inter- and intra-genomic heterogeneity of the intervening sequence in the 23S ribosomal RNA gene of Campylobacter jejuni and Campylobacter coli. Syst Appl Microbiol 2009; 32:91-100. [PMID: 19201124 DOI: 10.1016/j.syapm.2008.12.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Revised: 12/15/2008] [Accepted: 12/22/2008] [Indexed: 11/30/2022]
Abstract
An intervening sequence (IVS) can be present or absent in the 23S rRNA of Campylobacter jejuni and Campylobacter coli. As part of a survey, we used a polymerase chain reaction (PCR) assay to detect the presence of the IVS in 43 isolates of C. coli and 82 isolates of C. jejuni. An IVS was present in 40 (93.0%) of the C. coli and only 34 (41.5%) of the C. jejuni isolates. Twelve (27.9%) of the C. coli isolates and seven (8.5%) of the C. jejuni isolates resulted in two polymerase chain reaction products, indicating heterogeneity in the presence of the 23S rRNA IVS. Fourteen of the isolates with two products were evaluated by pulse-field gel electrophoresis; 13 different patterns were observed. The total band size of one isolate was substantially greater than the expected 1.7 Mb, possibly indicating a mixed culture. Southern blot analyses demonstrated the expected three rRNA operons in all tested isolates. Nested PCR reactions with operon-specific primers followed by primers for the IVS confirmed that the strains of interest contained either one or two operons carrying the IVS and the remaining operon(s) did not. Sequence analysis of the IVS and flanking regions of the 23S rRNA genes did not discriminate C. jejuni and C. coli as distinct populations. These results indicate horizontal transfer of 23S rRNA genes or portions of the genes between C. jejuni and C. coli. Also, data showing sequence polymorphisms between the three 23S rRNA loci outside of the IVS region suggest that the isolates with intra-genomic heterogeneity appear to be members of clones that have an ancient defect in gene conversion mechanisms needed for concerted evolution of the ribosomal operons.
Collapse
Affiliation(s)
- R J Meinersmann
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, USDA Agricultural Research Service, Athens, Richard J. Russell Research Center, P.O. Box 5677, Athens, GA 30604, USA.
| | | | | |
Collapse
|
44
|
Nazaret S, Assade F, Brothier E, Freydière AM, Bellon G, Cournoyer B. RISA–HPLC analysis of lung bacterial colonizers of cystic fibrosis children. J Microbiol Methods 2009; 76:58-69. [DOI: 10.1016/j.mimet.2008.09.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Revised: 09/05/2008] [Accepted: 09/16/2008] [Indexed: 10/21/2022]
|
45
|
Lee ZMP, Bussema C, Schmidt TM. rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea. Nucleic Acids Res 2008; 37:D489-93. [PMID: 18948294 PMCID: PMC2686494 DOI: 10.1093/nar/gkn689] [Citation(s) in RCA: 288] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
A dramatic exception to the general pattern of single-copy genes in bacterial and archaeal genomes is the presence of 1–15 copies of each ribosomal RNA encoding gene. The original version of the Ribosomal RNA Database (rrnDB) cataloged estimates of the number of 16S rRNA-encoding genes; the database now includes the number of genes encoding each of the rRNAs (5S, 16S and 23S), an internally transcribed spacer region, and the number of tRNA genes. The rrnDB has been used largely by microbiologists to predict the relative rate at which microbial populations respond to favorable growth conditions, and to interpret 16S rRNA-based surveys of microbial communities. To expand the functionality of the rrnDB (http://ribosome.mmg.msu.edu/rrndb/index.php), the search engine has been redesigned to allow database searches based on 16S rRNA gene copy number, specific organisms or taxonomic subsets of organisms. The revamped database also computes average gene copy numbers for any collection of entries selected. Curation tools now permit rapid updates, resulting in an expansion of the database to include data for 785 bacterial and 69 archaeal strains. The rrnDB continues to serve as the authoritative, curated source that documents the phylogenetic distribution of rRNA and tRNA genes in microbial genomes.
Collapse
Affiliation(s)
- Zarraz May-Ping Lee
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | | | | |
Collapse
|
46
|
ERWIN PATRICKM, THACKER ROBERTW. Cryptic diversity of the symbiotic cyanobacterium Synechococcus spongiarum among sponge hosts. Mol Ecol 2008; 17:2937-47. [DOI: 10.1111/j.1365-294x.2008.03808.x] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
47
|
Abstract
Recent evidence suggests that deep-sea vestimentiferan tube worms acquire their endosymbiotic bacteria from the environment each generation; thus, free-living symbionts should exist. Here, free-living tube worm symbiont phylotypes were detected in vent seawater and in biofilms at multiple deep-sea vent habitats by PCR amplification, DNA sequence analysis, and fluorescence in situ hybridization. These findings support environmental transmission as a means of symbiont acquisition for deep-sea tube worms.
Collapse
|