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Colautti A, Comi G, Peterlunger E, Iacumin L. Ancient Roman bacterium against current issues: strain Aquil_B6, Paenisporosarcina quisquiliarum, or Psychrobacillus psychrodurans? Microbiol Spectr 2023; 11:e0068623. [PMID: 37975675 PMCID: PMC10714998 DOI: 10.1128/spectrum.00686-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 10/08/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Since 1988, through the United States government's founding, the National Center for Biotechnology Information (NCBI) has provided an invaluable service to scientific advancement. The universality and total freedom of use if on the one hand allow the use of this database on a global level by all researchers for their valuable work, on the other hand, it has the disadvantage of making it difficult to check the correctness of all the materials present. It is, therefore, of fundamental importance for the correctness and ethics of research to improve the databases at our disposal, identifying and amending the critical issues. This work aims to provide the scientific community with a new sequence for the type strain Paenisporosarcina quisquiliarum SK 55 and broaden the knowledge of the Psychrobacillus psychrodurans species, in particular, considering the ancient strain Aquil_B6 found in an ancient Roman amphora.
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Affiliation(s)
- Andrea Colautti
- Department of Agricultural, Food, Environmental and Animal Science, University of Udine, Udine, Italy
| | - Giuseppe Comi
- Department of Agricultural, Food, Environmental and Animal Science, University of Udine, Udine, Italy
| | - Enrico Peterlunger
- Department of Agricultural, Food, Environmental and Animal Science, University of Udine, Udine, Italy
| | - Lucilla Iacumin
- Department of Agricultural, Food, Environmental and Animal Science, University of Udine, Udine, Italy
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da Silva MBF, da Mota FF, Cypriano J, Abreu F, Seldin L. Psychrobacillus antarcticus sp. nov., a psychrotolerant bioemulsifier producer isolated from King George Island, Antarctica. Int J Syst Evol Microbiol 2023; 73. [PMID: 38009904 DOI: 10.1099/ijsem.0.006181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Abstract
A Gram-stain-positive rod, psychrotolerant, aerobic and bioemulsifier-producing strain, denoted as Val9T, was isolated from soil sampled at Vale Ulman, King George Island, Antarctica. The strain grew at up to 30 °C (optimum, 15 °C), at pH 6-9 (optimum, pH 8) and with up to 5 % w/v NaCl (optimum, 3 %). The strain was motile and positive for catalase, oxidase and H2S. It did not hydrolyse starch, casein or gelatin. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Val9T belonged to the genus Psychrobacillus and was closely related to Psychrobacillus psychrotolerans DSM 11706T (99.9 % similarity), Psychrobacillus psychrodurans DSM 11713T (99.8 %) and Psychrobacillus glaciei PB01T (99.2 %). Digital DNA-DNA hybridization and average nucleotide identity values were lower than 37.3 and 85.5 %, respectively, with the closest phylogenetic neighbours. The DNA G+C content of strain Val9T calculated from the complete genome sequence was 36.6 mol%. The predominant cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 1ω11c. Menaquinone-8 was the major respiratory quinone. The peptidoglycan type was A4β l-Orn-d-glu. The novel strain contained diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol as predominant polar lipids. Based on 16S rRNA phylogenetic and multilocus sequence analyses (recA, rpoB and gyrB), as well as phylogenomic, chemotaxonomic and phenotypic tests, we demonstrate that strain Val9T represents a novel species of the genus Psychrobacillus, for which the name Psychrobacillus antarcticus sp. nov. is proposed. The type strain is Val9T (=DSM 115096T=CCGB 1952T=NRRL B-65674T).
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Affiliation(s)
| | - Fabio Faria da Mota
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Jefferson Cypriano
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Fernanda Abreu
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Lucy Seldin
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Genomic analyses of a novel bioemulsifier-producing Psychrobacillus strain isolated from soil of King George Island, Antarctica. Polar Biol 2022. [DOI: 10.1007/s00300-022-03028-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Choi JY, Kim SC, Lee PC. Comparative Genome Analysis of Psychrobacillus Strain PB01, Isolated from an Iceberg. J Microbiol Biotechnol 2020; 30:237-243. [PMID: 31838800 PMCID: PMC9728334 DOI: 10.4014/jmb.1909.09008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A novel psychrotolerant Psychrobacillus strain PB01, isolated from an Antarctic iceberg, was comparatively analyzed with five related strains. The complete genome of strain PB01 consists of a single circular chromosome (4.3 Mb) and a plasmid (19 Kb). As potential low-temperature adaptation strategies, strain PB01 has four genes encoding cold-shock proteins, two genes encoding DEAD-box RNA helicases, and eight genes encoding transporters for glycine betaine, which can serve as a cryoprotectant, on the genome. The pan-genome structure of the six Psychrobacillus strains suggests that strain PB01 might have evolved to adapt to extreme environments by changing its genome content to gain higher capacity for DNA repair, translation, and membrane transport. Notably, strain PB01 possesses a complete TCA cycle consisting of eight enzymes as well as three additional Helicobacter pylori-type enzymes: ferredoxin-dependent 2-oxoglutarate synthase, succinyl-CoA/acetoacetyl-CoA transferase, and malate/quinone oxidoreductase. The co-existence of the genes for TCA cycle enzymes has also been identified in the other five Psychrobacillus strains.
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Affiliation(s)
- Jun Young Choi
- Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon 6499, Republic of Korea
| | - Sun Chang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Pyung Cheon Lee
- Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon 6499, Republic of Korea,Corresponding author Phone: +82-31-219-2461 Fax: +82-31-219-1610 E-mail:
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Rodríguez M, Reina JC, Béjar V, Llamas I. Psychrobacillus vulpis sp. nov., a new species isolated from faeces of a red fox in Spain. Int J Syst Evol Microbiol 2019; 70:882-888. [PMID: 31833832 DOI: 10.1099/ijsem.0.003840] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A facultative anaerobic, chemoheterotrophic, endospore-forming, Gram-stain-positive rod, designated as strain Z8T, was isolated from red fox (Vulpes vulpes) faeces sampled at Tablas de Daimiel National Park, Ciudad Real, Spain. Strain Z8T grew at 0-37 °C (optimum, 28 °C), in the presence of 0-5.5 % (w/v) NaCl (2.5 %, w/v) and at pH 6-10 (pH 7). The strain was motile and positive for catalase, oxidase, H2S and siderophore production, acid and alkaline phosphatases, and N-acetylglucosamine, adipic acid and malate assimilation. It hydrolysed starch, DNA, l-tyrosine, Tween 20, Tween 80 and lecithovitellin. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain Z8T is a member of the genus Psychrobacillus, showing high sequence similarity to Psychrobacillus lasiicapitis NEAU-3TGS17T (99.2 %) and Psychrobacillus soli NHI-2TT (99.1 %), and around 98 % to other known species of the genus Psychrobacillus. Digital DNA-DNA hybridization and average nucleotide identity values were lower than 24 and 79 %, respectively, with the most related species. In silico G+C content was 35.9 mol%. The major cellular fatty acids of strain Z8T were iso-C14 : 0, iso-C15 : 0 and anteiso-C15 : 0. The novel strain contained diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol as predominant polar lipids, and the main respiratory isoprenoid quinone was MK-8. Based on the 16S rRNA phylogenetic analysis, together with MLSA (recA, rpoB and gyrB), phylogenomic, chemotaxonomic and phenotypic results, we demonstrate that strain Z8T represents a novel species of the genus Psychrobacillus, for which the name Psychrobacillus vulpis sp. nov., is proposed. The type strain is Z8T (=CECT 9721T=LMG 31001T).
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Affiliation(s)
- Miguel Rodríguez
- Biomedical Research Center (CIBM), Biotechnology Institute, Parque Tecnológico Ciencias de la Salud (PTS), Avenida del Conocimiento s/n, 18100, Armilla, Granada, Spain.,Microbial Exopolysaccharide Research Group, Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus Universitario Cartuja s/n, 18071 Granada, Spain
| | - José Carlos Reina
- Biomedical Research Center (CIBM), Biotechnology Institute, Parque Tecnológico Ciencias de la Salud (PTS), Avenida del Conocimiento s/n, 18100, Armilla, Granada, Spain.,Microbial Exopolysaccharide Research Group, Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus Universitario Cartuja s/n, 18071 Granada, Spain
| | - Victoria Béjar
- Biomedical Research Center (CIBM), Biotechnology Institute, Parque Tecnológico Ciencias de la Salud (PTS), Avenida del Conocimiento s/n, 18100, Armilla, Granada, Spain.,Microbial Exopolysaccharide Research Group, Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus Universitario Cartuja s/n, 18071 Granada, Spain
| | - Inmaculada Llamas
- Biomedical Research Center (CIBM), Biotechnology Institute, Parque Tecnológico Ciencias de la Salud (PTS), Avenida del Conocimiento s/n, 18100, Armilla, Granada, Spain.,Microbial Exopolysaccharide Research Group, Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus Universitario Cartuja s/n, 18071 Granada, Spain
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Yu L, Tang X, Wei S, Qiu Y, Xu X, Xu G, Wang Q, Yang Q. Two novel species of the family Bacillaceae: Oceanobacillus piezotolerans sp. nov. and Bacillus piezotolerans sp. nov., from deep-sea sediment samples of Yap Trench. Int J Syst Evol Microbiol 2019; 69:3022-3030. [DOI: 10.1099/ijsem.0.003559] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Libo Yu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, PR China
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, PR China
| | - Xixiang Tang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, PR China
| | - Shiping Wei
- School of Ocean Sciences, China university of Geosciences (Beijing), Beijing, 100083, PR China
| | - Yinkun Qiu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102, PR China
| | - Xiashutong Xu
- School of Ocean Sciences, China university of Geosciences (Beijing), Beijing, 100083, PR China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, PR China
| | - Guangxin Xu
- School of Ocean Sciences, China university of Geosciences (Beijing), Beijing, 100083, PR China
| | - Qilin Wang
- School of Ocean Sciences, China university of Geosciences (Beijing), Beijing, 100083, PR China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, PR China
| | - Qian Yang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, PR China
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Montaño-Salazar SM, Lizarazo-Marriaga J, Brandão PFB. Isolation and Potential Biocementation of Calcite Precipitation Inducing Bacteria from Colombian Buildings. Curr Microbiol 2017; 75:256-265. [PMID: 29043388 DOI: 10.1007/s00284-017-1373-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/10/2017] [Indexed: 10/18/2022]
Abstract
Microbiological induced calcium carbonate or calcite precipitation (MICP) has become a highly researched issue due to its multiple applications in the construction industry, being a promising alternative with a great biotechnological importance. In this work, potential calcite precipitation inducing bacteria were isolated from mortar and concrete samples of different buildings at the National University of Colombia. Eighteen crystal-precipitating strains were recovered in Urea-CaCl2 solid medium. The 16S rRNA gene sequencing identified isolates as Arthrobacter, Psychrobacillus and Rhodococcus genera. It is reported, for the first time, the calcite precipitation by P. psycrodurans and R. qingshengii. Optical microscopy and Scanning Electron Microscopy showed crystals with irregular and spherical shapes, and beige and white colours. Furthermore, crystals formation appeared to be strain-specific. X-Ray diffraction analysis confirmed crystals composition as CaCO3. Biocementation tests showed that MICP treatments of mortar cubes using P. psycrodurans caused an increase in their compressive strength compared to control samples. The positive action of a native MICP strain in mortar blocks biomineralization is shown, which is of great interest and potential for the construction industry.
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Affiliation(s)
- Sandra M Montaño-Salazar
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Juan Lizarazo-Marriaga
- Grupo de Investigación en Análisis, Diseño y Materiales - GIES, Facultad de Ingeniería, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Pedro F B Brandão
- Grupo de Estudios para la Remediación y Mitigación de Impactos Negativos al Ambiente (G.E.R.M.I.N.A.), Laboratorio de Microbiología Ambiental y Aplicada, Departamento de Química, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia.
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Kolsal F, Akbal Z, Liaqat F, Gök O, Sponza DT, Eltem R. Hydrocarbon degradation abilities of psychrotolerant Bacillus strains. AIMS Microbiol 2017; 3:467-482. [PMID: 31294171 PMCID: PMC6604985 DOI: 10.3934/microbiol.2017.3.467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 06/07/2017] [Indexed: 11/24/2022] Open
Abstract
Biodegradation requires identification of hydrocarbon degrading microbes and the investigation of psychrotolerant hydrocarbon degrading microbes is essential for successful biodegradation in cold seawater. In the present study, a total of 597 Bacillus isolates were screened to select psychrotolerant strains and 134 isolates were established as psychrotolerant on the basis of their ability to grow at 7 °C. Hydrocarbon degradation capacities of these 134 psychrotolerant isolate were initially investigated on agar medium containing different hydrocarbons (naphthalene, n-hexadecane, mineral oil) and 47 positive isolates were grown in broth medium containing hydrocarbons at 20 °C under static culture. Bacterial growth was estimated in terms of viable cell count (cfu ml-1). Isolates showing the best growth in static culture were further grown in presence of crude oil under shaking culture and viable cell count was observed between 8.3 × 105-7.4 × 108 cfu ml-1. In the final step, polycyclic aromatic hydrocarbon (PAH) (chrysene and naphthalene) degradation yield of two most potent isolates was determined by GC-MS along with the measurement of pH, biomass and emulsification activities. Results showed that isolates Ege B.6.2i and Ege B.1.4Ka have shown 60% and 36% chrysene degradation yield, respectively, while 33% and 55% naphthalene degradation yield, respectively, with emulsification activities ranges between 33-50%. These isolates can be used to remove hydrocarbon contamination from different environments, particularly in cold regions.
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Affiliation(s)
- Fulya Kolsal
- Department of Bioengineering, Faculty of Engineering, Ege University, 35100, İzmir, Turkey
| | - Zeynep Akbal
- Department of Bioengineering, Faculty of Engineering, Ege University, 35100, İzmir, Turkey
| | - Fakhra Liaqat
- Department of Biotechnology, Graduate School of Natural and Applied Sciences, Ege University, 35100, İzmir, Turkey
| | - Oğuzhan Gök
- Department of Environmental Engineering, Engineering Faculty, Aksaray University, Aksaray, Turkey
| | - Delia Teresa Sponza
- Department of Environmental Engineering, Engineering Faculty, Dokuz Eylül University, Buca, Kaynaklar Campus, 35160, İzmir, Turkey
| | - Rengin Eltem
- Department of Bioengineering, Faculty of Engineering, Ege University, 35100, İzmir, Turkey
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Abstract
Formation of heat-resistant endospores is a specific property of the members of the phylum Firmicutes (low-G+C Gram-positive bacteria). It is found in representatives of four different classes of Firmicutes, Bacilli, Clostridia, Erysipelotrichia, and Negativicutes, which all encode similar sets of core sporulation proteins. Each of these classes also includes non-spore-forming organisms that sometimes belong to the same genus or even species as their spore-forming relatives. This chapter reviews the diversity of the members of phylum Firmicutes, its current taxonomy, and the status of genome-sequencing projects for various subgroups within the phylum. It also discusses the evolution of the Firmicutes from their apparently spore-forming common ancestor and the independent loss of sporulation genes in several different lineages (staphylococci, streptococci, listeria, lactobacilli, ruminococci) in the course of their adaptation to the saprophytic lifestyle in a nutrient-rich environment. It argues that the systematics of Firmicutes is a rapidly developing area of research that benefits from the evolutionary approaches to the ever-increasing amount of genomic and phenotypic data and allows arranging these data into a common framework.
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Piñar G, Kraková L, Pangallo D, Piombino-Mascali D, Maixner F, Zink A, Sterflinger K. Halophilic bacteria are colonizing the exhibition areas of the Capuchin Catacombs in Palermo, Italy. Extremophiles 2014; 18:677-91. [PMID: 24863363 PMCID: PMC4065341 DOI: 10.1007/s00792-014-0649-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 04/27/2014] [Indexed: 01/11/2023]
Abstract
The Capuchin Catacombs of Palermo, Italy, contain over 1800 mummies dating from the 16th to 20th centuries AD. Their environment is not conducive to the conservation of the remains due to, among other factors, water infiltration, which is producing salt efflorescences on the walls. A multiphasic approach was applied to investigate the halophilic microbiota present in the Catacombs. Enrichment cultures were conducted on media containing different NaCl concentrations, ranging from 3 to 20 %. For screening of the strains, the following two PCR-based methods were used and compared: fluorescence internal transcribed spacer PCR (f-ITS) and random amplification of polymorphic DNA (RAPD) analyses. Results derived from RAPD profiles were shown to be slightly more discriminative than those derived from f-ITS. In addition, the proteolytic and cellulolytic abilities were screened through the use of plate assays, gelatin agar and Ostazin Brilliant Red H-3B (OBR-HEC), respectively. Many of the strains isolated from the wall samples displayed proteolytic activities, such as all strains belonging to the genera Bacillus, Virgibacillus and Arthrobacter, as well as some strains related to the genera Oceanobacillus, Halobacillus and Idiomarina. In addition, many of the strains isolated from materials employed to stuff the mummies showed cellulolytic activities, such as those related to species of the genera Chromohalobacter and Nesterenkonia, as well as those identified as Staphylococcus equorum and Halomonas sp. Furthermore, many of the strains were pigmented ranging from yellow to a strong pink color, being directly related to the discoloration displayed by the materials.
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Affiliation(s)
- G Piñar
- VIBT-Vienna Institute of BioTechnology, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 11, 1190, Vienna, Austria,
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Ashcroft JW, Zalinger ZB, Bevier CR, Fekete FA. Antimicrobial properties of two purified skin peptides from the mink frog (Rana septentrionalis) against bacteria isolated from the natural habitat. Comp Biochem Physiol C Toxicol Pharmacol 2007; 146:325-30. [PMID: 17499556 PMCID: PMC4688893 DOI: 10.1016/j.cbpc.2007.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2007] [Revised: 04/07/2007] [Accepted: 04/10/2007] [Indexed: 11/29/2022]
Abstract
Numerous peptides exhibiting antimicrobial properties have been isolated from the skins of many amphibian species. These peptides offer an innate chemical defense system against various microbial agents that exist in the amphibian's environment. Amphibian skin peptides are typically tested for antimicrobial activity against microbial strains that are pathogenic to humans, but not on potential pathogenic or opportunistic bacteria that exist in the organism's habitat. Two peptides, a brevinin-2-related peptide and temporin-1SPb previously isolated from secretions of the mink frog, Rana septentrionalis, were tested for antimicrobial activity on bacterial isolates endemic to the frog's habitat. Ten isolates were identified, using 16S rRNA gene sequencing techniques, in the genera Pseudomonas, Serratia, Bacillus, Aeromonas, Burkholderia, Microbacterium, and Delftia. Bacterial isolates were tested with peptides at concentrations ranging from 0.8 microM to 1000 microM to determine the minimum inhibitory concentration (MIC) to inhibit growth. Growth of four of the isolates was inhibited by temporin-1SPb at the concentrations used, but all of the isolates were inhibited by the brevinin-2-related within the range of peptide concentrations used. This demonstrates the efficacy of both peptides as a component of the frog's innate chemical defense system.
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Blackwood KS, Turenne CY, Harmsen D, Kabani AM. Reassessment of sequence-based targets for identification of bacillus species. J Clin Microbiol 2004; 42:1626-30. [PMID: 15071016 PMCID: PMC387569 DOI: 10.1128/jcm.42.4.1626-1630.2004] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2003] [Revised: 10/07/2003] [Accepted: 12/14/2003] [Indexed: 11/20/2022] Open
Abstract
The Bacillus genus is a large heterogeneous group in need of an efficient method for species differentiation. To determine the current validity of a sequence-based method for identification and provide contemporary data, PCR and sequencing of a 500-bp product encompassing the V1 to V3 regions of the 16S rRNA gene were undertaken using 65 of the 83 type strains of this genus. This region proved discriminatory between most species (70.0 to 100% similarity), the exceptions being clinically relevant B. cereus and B. anthracis as well as nonpathogenic B. psychrotolerans and B. psychrodurans. Consequently, 27 type and clinical strains from the B. cereus group were used to test alternate targets (rpoB, vrrA, and the 16S-23S spacer region) for identification. The rpoB gene proved the best alternate target, with a conserved 4-nucleotide difference between B. cereus and B. anthracis. The high 16S rRNA gene sequence similarities between some strains demonstrated the need for a polyphasic approach to the systematics of this genus. This approach is one focus of the Ribosomal Differentiation of Medical Microorganisms mandate. Accordingly, the 16S rRNA gene sequences generated in this study have been submitted for inclusion into its publicly accessible, quality-controlled database at http://www.ridom_rdna.de/.
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Affiliation(s)
- K S Blackwood
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Population and Public Health Branch, Health Canada.
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Artursson V, Jansson JK. Use of bromodeoxyuridine immunocapture to identify active bacteria associated with arbuscular mycorrhizal hyphae. Appl Environ Microbiol 2003; 69:6208-15. [PMID: 14532082 PMCID: PMC201251 DOI: 10.1128/aem.69.10.6208-6215.2003] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2003] [Accepted: 07/04/2003] [Indexed: 11/20/2022] Open
Abstract
Arbuscular mycorrhizae are beneficial for crops grown under low-till management systems. Increasingly, it is becoming apparent that bacteria associated with mycorrhizae can enhance the beneficial relationship between mycorrhizae and plants. However, it has been difficult to study these relationships by conventional techniques. In this study actively growing bacteria were identified in soil from an undisturbed fallow field known to contain arbuscular mycorrhizae by using molecular tools to eliminate the need for cultivation. A thymidine analog, bromodeoxyuridine (BrdU), was added to the soil and incubated for 2 days. DNA was extracted, and the newly synthesized DNA was isolated by immunocapture of the BrdU-containing DNA. The active bacteria in the community were identified by 16S rRNA gene PCR amplification and DNA sequence analysis. Based on 16S rRNA gene sequence information, a selective medium was chosen to isolate the corresponding active bacteria. Bacillus cereus strain VA1, one of the bacteria identified by the BrdU method, was isolated from the soil and tagged with green fluorescent protein. By using confocal microscopy, this bacterium was shown to clearly attach to arbuscular mycorrhizal hyphae. This study was the first to use this combination of molecular and traditional approaches to isolate, identify, and visualize a specific bacterium that is active in fallow soil and associates with arbuscular mycorrhizal hyphae.
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Affiliation(s)
- Veronica Artursson
- Department of Microbiology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
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