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Rolon ML, Voloshchuk O, Bartlett KV, LaBorde LF, Kovac J. Multi-species biofilms of environmental microbiota isolated from fruit packing facilities promoted tolerance of Listeria monocytogenes to benzalkonium chloride. Biofilm 2024; 7:100177. [PMID: 38304489 PMCID: PMC10832383 DOI: 10.1016/j.bioflm.2024.100177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/06/2024] [Accepted: 01/08/2024] [Indexed: 02/03/2024] Open
Abstract
Listeria monocytogenes may survive and persist in food processing environments due to formation of complex multi-species biofilms of environmental microbiota that co-exists in these environments. This study aimed to determine the effect of selected environmental microbiota on biofilm formation and tolerance of L. monocytogenes to benzalkonium chloride in formed biofilms. The studied microbiota included bacterial families previously shown to co-occur with L. monocytogenes in tree fruit packing facilities, including Pseudomonadaceae, Xanthomonadaceae, Microbacteriaceae, and Flavobacteriaceae. Biofilm formation ability and the effect of formed biofilms on the tolerance of L. monocytogenes to benzalkonium chloride was measured in single- and multi-family assemblages. Biofilms were grown statically on polystyrene pegs submerged in a R2A broth. Biofilm formation was quantified using a crystal violet assay, spread-plating, confocal laser scanning microscopy, and its composition was assessed using amplicon sequencing. The concentration of L. monocytogenes in biofilms was determined using the most probable number method. Biofilms were exposed to the sanitizer benzalkonium chloride, and the death kinetics of L. monocytogenes were quantified using a most probable number method. A total of 8, 8, 6, and 3 strains of Pseudomonadaceae, Xanthomonadaceae, Microbacteriaceae, and Flavobacteriaceae, respectively, were isolated from the environmental microbiota of tree fruit packing facilities and were used in this study. Biofilms formed by Pseudomonadaceae, Xanthomonadaceae, and all multi-family assemblages had significantly higher concentration of bacteria, as well as L. monocytogenes, compared to biofilms formed by L. monocytogenes alone. Furthermore, multi-family assemblage biofilms increased the tolerance of L. monocytogenes to benzalkonium chloride compared to L. monocytogenes mono-species biofilms and planktonic multi-family assemblages. These findings suggest that L. monocytogenes control strategies should focus not only on assessing the efficacy of sanitizers against L. monocytogenes, but also against biofilm-forming microorganisms that reside in the food processing built environment, such as Pseudomonadaceae or Xanthomonadaceae.
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Affiliation(s)
- M. Laura Rolon
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
- One Health Microbiome Center, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Olena Voloshchuk
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Katelyn V. Bartlett
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Luke F. LaBorde
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Jasna Kovac
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
- One Health Microbiome Center, The Pennsylvania State University, University Park, PA, 16802, USA
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Liu L, Geng K, Lv Y, Zhang Q, Chen G, Cheng D, Shao J, He J, Shen Q. Ruicaihuangia caeni gen. nov., sp. nov., a novel taxon within the family Microbacteriaceae isolated from sludge. Int J Syst Evol Microbiol 2024; 74. [PMID: 38530752 DOI: 10.1099/ijsem.0.006302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024] Open
Abstract
A Gram-stain-positive bacterium, designated YN-L-19T, was isolated from a sludge sample collected from a pesticide-manufacturing plant. Cells of YN-L-19T were strictly aerobic, non-spore-forming, non-motile and ovoid-shaped. Colonies were small, smooth and yellow. Growth occurred at 10-37 °C (optimum, 30 °C), pH 5.0-9.0 (optimum, 7.0) and 0-3.0 % (w/v) NaCl (optimum 0.5 %). Phylogenetic analysis based on genome and 16S rRNA gene sequences indicated that YN-L-19T was affiliated to the family Microbacteriaceae and most closely related to Diaminobutyricimonas aenilata, Terrimesophilobacter mesophilus, Planctomonas deserti and Curtobacterium luteum. The major cellular fatty acids of YN-L-19T were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and C16 : 0. The predominant menaquinone was MK-7. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, glycolipid and one unidentified lipid. The average amino acid identity values between strain YN-L-19T and the related strains were 57.9-61.9 %, which were below the genus boundary (70 %). On the basis of the evidence presented in this study, strain YN-L-19T represents a novel species of a new genus in the family Microbacteriaceae, for which the name Ruicaihuangia caeni gen. nov., sp. nov. (type strain YN-L-19T=CCTCC AB 2022401T= KCTC 49935T) is proposed.
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Affiliation(s)
- Le Liu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
- Agricultural Microbial Resources Protection and Germplasm Innovation and Utilization Center of Jiangsu Province, Nanjing, Jiangsu 210095, PR China
| | - Keke Geng
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Yu Lv
- Agricultural Microbial Resources Protection and Germplasm Innovation and Utilization Center of Jiangsu Province, Nanjing, Jiangsu 210095, PR China
| | - Qi Zhang
- Agricultural Microbial Resources Protection and Germplasm Innovation and Utilization Center of Jiangsu Province, Nanjing, Jiangsu 210095, PR China
| | - Gang Chen
- An hui Neotec Co., Ltd., Huaibei, An hui 235100, PR China
| | - Dan Cheng
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Jiahui Shao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
- Agricultural Microbial Resources Protection and Germplasm Innovation and Utilization Center of Jiangsu Province, Nanjing, Jiangsu 210095, PR China
| | - Jian He
- Agricultural Microbial Resources Protection and Germplasm Innovation and Utilization Center of Jiangsu Province, Nanjing, Jiangsu 210095, PR China
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Qirong Shen
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
- Agricultural Microbial Resources Protection and Germplasm Innovation and Utilization Center of Jiangsu Province, Nanjing, Jiangsu 210095, PR China
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Osdaghi E, Taghavi SM, Hamidizade M, Kariminejhad M, Fazliarab A, Hajian Maleki H, Baeyen S, Taghouti G, Jacques MA, Van Vaerenbergh J, Portier P. Multiphasic investigations imply transfer of orange-/red-pigmented strains of the bean pathogen Curtobacterium flaccumfaciens pv. flaccumfaciens to a new species as C. aurantiacum sp. nov., elevation of the poinsettia pathogen C. flaccumfaciens pv. poinsettiae to the species level as C. Poinsettiae sp. nov., and synonymy of C. albidum with C. citreum. Syst Appl Microbiol 2024; 47:126489. [PMID: 38325043 DOI: 10.1016/j.syapm.2024.126489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/09/2024]
Abstract
Curtobacterium flaccumfaciens (Microbacteriaceae), a plant-pathogenic coryneform species includes five pathovars with valid names and a number of proposed - but unvalidated - new members. In this study, phenotypic features and DNA similarity indexes were investigated among all C. flaccumfaciens members. Results showed that the C. flaccumfaciens pv. poinsettiae strains causing bacterial canker of Euphorbia pulcherrima in the USA as well as the orange-/red-pigmented strains of C. flaccumfaciens pv. flaccumfaciens pathogenic on dry beans in Iran are too distinct from each other and from the type strain of the species to be considered members of C. flaccumfaciens. Hence, the latter two groups were elevated at the species level as C. poinsettiae sp. nov. (ATCC 9682T = CFBP 2403T = ICMP 2566T = LMG 3715T = NCPPB 854T as type strain), and C. aurantiacum sp. nov. (50RT = CFBP 8819T = ICMP 22071T as type strain). Within the emended species C. flaccumfaciens comb. nov., yellow-pigmented strains causing bacterial wilt of dry beans and those causing bacterial canker of Euphorbia pulcherrima in Europe were retained as C. flaccumfaciens pv. flaccumfaciens and C. flaccumfaciens pv. poinsettiae, respectively; while taxonomic position of the sugar beet pathogen C. flaccumfaciens pv. beticola ATCC BAA144PT was confirmed. The newly described onion pathogen C. allii was also reclassified as C. flaccumfaciens pv. allii with the pathotype strain LMG 32517PT. Furthermore, C. flaccumfaciens pv. basellae causing bacterial leaf spot of malabar spinach (Basella rubra) was transferred to C. citreum pv. basellae with ATCC BAA143PT as pathotype.
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Affiliation(s)
- Ebrahim Osdaghi
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran.
| | - S Mohsen Taghavi
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Mozhde Hamidizade
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran; Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Mehdi Kariminejhad
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran
| | - Amal Fazliarab
- Iranian Sugarcane Research and Training Institute (ISCRTI), Ahvaz, Khuzestan, Iran
| | - Habibeh Hajian Maleki
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran
| | - Steve Baeyen
- Flanders' Research Institute for Agriculture, Fisheries and Food (ILVO), Unit Plant Sciences, EU Reference Laboratory for Plant Health - on bacteria, Burgemeester van Gansberghelaan 96, 9820 Merelbeke, Belgium
| | - Geraldine Taghouti
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Marie-Agnes Jacques
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Johan Van Vaerenbergh
- Flanders' Research Institute for Agriculture, Fisheries and Food (ILVO), Unit Plant Sciences, EU Reference Laboratory for Plant Health - on bacteria, Burgemeester van Gansberghelaan 96, 9820 Merelbeke, Belgium
| | - Perrine Portier
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France.
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Santos JDND, Klimek D, Calusinska M, Lobo-da-Cunha A, Catita J, Gonçalves H, González I, Lage OM. Microbacterium memoriense sp. nov., a member of the Actinomycetota from marine beach sediment of the north coast of Portugal. Int J Syst Evol Microbiol 2024; 74. [PMID: 38189368 DOI: 10.1099/ijsem.0.006230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024] Open
Abstract
The oceans harbour a myriad of unknown micro-organisms that remain unstudied because of a failure to establish the right growth conditions under laboratory conditions. To overcome this limitation, an isolation effort inspired by the iChip was performed using marine sediments from Memória beach, Portugal. A novel strain, PMIC_1C1BT, was obtained and subjected to a polyphasic study. Cells of strain PMIC_1C1BT were Gram-positive, rod-shaped, divided by binary fission and formed colonies that were shiny light-yellow. Based on its full 16S rRNA gene sequence, strain PMIC_1C1BT was phylogenetically associated to the genus Microbacterium and its closest relatives were Microbacterium aurum KACC 15219T (98.55 %), Microbacterium diaminobutyricum RZ63T (98.48 %) and Microbacterium hatanonis JCM 14558T (98.13 %). Strain PMIC_1C1BT had a genome size of 2 761 607 bp with 67.71 mol% of G+C content and 2582 coding sequences, which is lower than the genus average. Strain PMIC_1C1BT grew from 15 to 30 °C, optimally at 25 °C, at pH 6.0 to 11.0, optimally between pH 6.0 and 8.0, and from 0 to 5 % (w/v) NaCl, optimally between 2.0 and 3.0 %. It grew with casamino acids, glutamine, methionine, N-acetylglucosamine, sodium nitrate, tryptophan, urea and valine as sole nitrogen sources, and arabinose and cellobiose as sole carbon sources. The major cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0 and iso-C17 : 0. Genome mining revealed the presence of four biosynthetic gene clusters (BGCs) with low similarities to other known BCGs. Based on the polyphasic data, strain PMIC_1C1BT is proposed to represent a novel species, for which the name Microbacterium memoriense sp. nov. (=CECT 30366T=LMG 32350T) is proposed.
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Affiliation(s)
- José Diogo Neves Dos Santos
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/no., 4169-007 Porto, Portugal
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Dominika Klimek
- Environmental Research and Innovation Department (ERIN), Luxembourg Institute of Science and Technology (LIST), Belvaux, Luxembourg
- The Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, Esch-Belval Esch-sur-Alzette, Luxembourg
| | - Magdalena Calusinska
- Environmental Research and Innovation Department (ERIN), Luxembourg Institute of Science and Technology (LIST), Belvaux, Luxembourg
| | - Alexandre Lobo-da-Cunha
- Department of Microscopy, School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - José Catita
- Paralab, SA, Valbom, Portugal
- FP-I3ID, FP-BHS, Faculdade de Ciências da Saúde, Universidade Fernando Pessoa, Rua Carlos da Maia, 296, 4200-150 Porto, Portugal
| | | | - Ignacio González
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de la Salud, 18016 Granada, Spain
| | - Olga Maria Lage
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/no., 4169-007 Porto, Portugal
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
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Lee SD, Yang HL, Kim IS. Four new Microbacterium species isolated from seaweeds and reclassification of five Microbacterium species with a proposal of Paramicrobacterium gen. nov. under a genome-based framework of the genus Microbacterium. Front Microbiol 2023; 14:1299950. [PMID: 38164402 PMCID: PMC10757982 DOI: 10.3389/fmicb.2023.1299950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 11/15/2023] [Indexed: 01/03/2024] Open
Abstract
The taxonomic relationships of 10 strains isolated from seaweeds collected from two beaches in Republic of Korea were studied by sequencing and analyses of 16S rRNA genes and whole genomes. For the construction of a more reliable and robust 16S rRNA gene phylogeny, the authentic and nearly complete 16S rRNA gene sequences of all the Microbacterium type strains were selected through pairwise comparison of the sequences contained in several public databases including the List of Prokaryotic names with Standing in Nomenclature (LPSN). The clustering of the ten study strains into five distinct groups was apparent in this single gene-based phylogenetic tree. In addition, the 16S rRNA gene sequences of a few type strains were shown to be incorrectly listed in LPSN. An overall phylogenomic clustering of the genus Microbacterium was performed with a total of 113 genomes by core genome analysis. As a result, nine major (≥ three type strains) and eight minor (two type strains) clusters were defined mostly at gene support index of 92 and mean intra-cluster OrthoANIu of >80.00%. All of the study strains were assigned to a Microbacterium liquefaciens clade and distributed further into four subclusters in the core genome-based phylogenetic tree. In vitro phenotypic assays for physiological, biochemical, and chemotaxonomic characteristics were also carried out with the ten study strains and seven closely related type strains. Comparison of the overall genomic relatedness indices (OGRI) including OrthoANIu and digital DNA-DNA hybridization supported that the study strains constituted four new species of the genus Microbacterium. In addition, some Microbacterium type strains were reclassified as members of preexisting species. Moreover, some of them were embedded in a new genus of the family Microbacteriaceae based on their distinct separation in the core genome-based phylogenetic tree and amino acid identity matrices. Based on the results here, four new species, namely, Microbacterium aurugineum sp. nov., Microbacterium croceum sp. nov., Microbacterium galbinum sp. nov., and Microbacterium sufflavum sp. nov., are described, along with the proposal of Paramicrobacterium gen. nov. containing five reclassified Microbacterium species from the "Microbacterium agarici clade", with Paramicrobacterium agarici gen. nov., comb. nov. as the type species.
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Affiliation(s)
- Soon Dong Lee
- Institute of Jeju Microbial Resources, BioPS Co., Ltd., Jeju, Republic of Korea
| | - Hong Lim Yang
- Institute of Jeju Microbial Resources, BioPS Co., Ltd., Jeju, Republic of Korea
| | - In Seop Kim
- Department of Biological Sciences and Biotechnology, Hannam University, Daejon, Republic of Korea
- BioPS Co., Ltd., Daejeon, Republic of Korea
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Toumi M, Whitman WB, Kyrpides NC, Woyke T, Wolf J, Neumann-Schaal M, Abbaszade G, Károly B, Tóth E. Antiquaquibacter oligotrophicus gen. nov., sp. nov., a novel oligotrophic bacterium from groundwater. Int J Syst Evol Microbiol 2023; 73. [PMID: 38108591 DOI: 10.1099/ijsem.0.006205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023] Open
Abstract
In this study, a Gram-stain-positive, non-motile, oxidase- and catalase-negative, rod-shaped, bacterial strain (SG_E_30_P1T) that formed light yellow colonies was isolated from a groundwater sample of Sztaravoda spring, Hungary. Based on 16S rRNA phylogenetic and phylogenomic analyses, the strain was found to form a distinct linage within the family Microbacteriaceae. Its closest relatives in terms of near full-length 16S rRNA gene sequences are Salinibacterium hongtaonis MH299814 (97.72 % sequence similarity) and Leifsonia psychrotolerans GQ406810 (97.57 %). The novel strain grows optimally at 20-28 °C, at neutral pH and in the presence of NaCl (1-2 w/v%). Strain SG_E_30_P1T contains MK-7 and B-type peptidoglycan with diaminobutyrate as the diagnostic amino acid. The major cellular fatty acids are anteiso-C15 : 0, iso-C16 : 0 and iso-C14 : 0, and the polar lipid profile is composed of diphosphatidylglycerol and phosphatidylglycerol, as well as an unidentified aminoglycolipid, aminophospholipid and some unidentified phospholipids. The assembled draft genome is a contig with a total length of 2 897 968 bp and a DNA G+C content of 65.5 mol%. Amino acid identity values with it closest relatives with sequenced genomes of <62.54 %, as well as other genome distance results, indicate that this bacterium represents a novel genus within the family Microbacteriaceae. We suggest that SG_E_30_P1T (=DSM 111415T=NCAIM B.02656T) represents the type strain of a novel genus and species for which the name Antiquaquibacter oligotrophicus gen. nov., sp. nov. is proposed.
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Affiliation(s)
- Marwene Toumi
- Department of Microbiology, Faculty of Science, Eötvös Loránd University, Pázmány Péter stny, 1/C, H-1117 Budapest, Hungary
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Nikos C Kyrpides
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Jacqueline Wolf
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124, Braunschweig, Germany
| | - Gorkhmaz Abbaszade
- Department of Microbiology, Faculty of Science, Eötvös Loránd University, Pázmány Péter stny, 1/C, H-1117 Budapest, Hungary
| | - Bóka Károly
- Department of plant anatomy, Faculty of Science, Eötvös Loránd University, Pázmány Péter stny, 1/C, H-1117 Budapest, Hungary
| | - Erika Tóth
- Department of Microbiology, Faculty of Science, Eötvös Loránd University, Pázmány Péter stny, 1/C, H-1117 Budapest, Hungary
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Molina Ayala KM, Kim SB. Description of Microcella humidisoli sp. nov. and Microcella daejeonensis sp. nov., isolated from riverside soil, reclassification of Marinisubtilis pacificus as Microcella pacifica comb. nov., and emended description of the genus Microcella. Int J Syst Evol Microbiol 2023; 73. [PMID: 37930354 DOI: 10.1099/ijsem.0.006150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023] Open
Abstract
Three Gram-positive, aerobic and rod shaped actinobacteria, designated strains MMS21-STM10T, MMS21-STM12T and MMS21-STM26, were isolated from riverside soil and subjected to polyphasic taxonomic analysis. The strains grew optimally at mesophilic temperatures (25-30 °C) and neutral to slightly alkaline pH (7-8), and NaCl was not required for growth. Best growth was observed on nutrient agar or marine agar media. The strains contained diphosphatidylglycerol, phosphatidylglycerol and a series of unidentified phospholipids, glycolipids and aminolipids, and anteiso-C15 : 0 and iso-C16 : 0 as the main fatty acids in common. The genome sizes ranged between 2.65 and 2.78 Mbp, and the DNA G+C contents between 70.4 and 72.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MMS21-STM10T showed highest sequence similarity of 98.3 % to Microcella putealis CV-2T, and MMS21-STM12T and MMS21-STM26 of 99.2-99.3 % to Microcella flavibacter WY83T, respectively. In the whole genome-based comparison using the orthologous average nucleotide identity and digital DNA-DNA hybridization, each of strains MMS21-STM10T and MMS21-STM12T could be separated from other species of Microcella. The genome analysis also indicated that both strains contained gene clusters involved in the biosynthesis of alkylresorcinol, microansamycin and carotenoids. The phenotypic characteristics again differentiated the strains from related species, and two new species of Microcella, Microcella humidisoli sp. nov. (type strain, MMS21-STM10T=KCTC 49773T=LMG 32522T) and Microcella daejeonensis sp. nov. (type strain, MMS21-STM12T=KCTC 49750T=LMG 32523T) are proposed accordingly. It was also evident that Marinisubtilis pacificus KN1116T should be reclassified as a new species of Microcella, and Microcella pacifica comb. nov. (type strain, KN1116T=CGMCC 1.17143T=KCTC 49299T) is proposed. In addition, an emended description of Microcella is proposed based on this study.
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Affiliation(s)
- Katya Michelle Molina Ayala
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99 Daehak-ro, Yuseong, Daejeon 34134, Republic of Korea
| | - Seung Bum Kim
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99 Daehak-ro, Yuseong, Daejeon 34134, Republic of Korea
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Osdaghi E, Taghavi SM, Hamidizade M, Fazliarab A, Hajian Maleki H, Li X, Jacques MA, Portier P. Clavibacter lycopersici sp. nov.: a peach-colored actinobacterium isolated from symptomless tomato plant. Int J Syst Evol Microbiol 2023; 73. [PMID: 37737062 DOI: 10.1099/ijsem.0.006022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023] Open
Abstract
In 2015, Gram-positive peach-coloured actinobacterial strains were isolated from symptomless tomato phyllosphere in Iran. Biochemical and physiological characteristics, as well as 16S rRNA phylogeny showed that the strains belong to Clavibacter sp., while they were non-pathogenic on the host of isolation, and morphologically distinct from the tomato pathogen C. michiganensis and other plant-associated bacteria. Multilocus sequence analysis of five housekeeping genes showed that the two peach-coloured strains CFBP 8615T (Tom532T) and CFBP 8616 (Tom495) were phylogenetically distinct from all validly described Clavibacter species. Whole genome sequence-based indices, i.e. average nucleotide identity (orthoANI) and digital DNA-DNA hybridization (dDDH), showed that the two peach-colored strains share nearly 100 % orthoANI value with one another, while they differ from all validly described Clavibacter species with the orthoANI/dDDH values <93 % and <50 %, respectively. Thus, based on both phenotypic features and orthoANI/dDDH indices the peach-coloured strains could belong to a new species within Clavibacter. In this study, we provide a formal species description for the peach-coloured tomato-associated Clavibacter strains. Clavibacter lycopersici sp. nov. is proposed for the new species with Tom532T = CFBP 8615T = ICMP 22100T as type strain.
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Affiliation(s)
- Ebrahim Osdaghi
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran
| | - S Mohsen Taghavi
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Mozhde Hamidizade
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Amal Fazliarab
- Iranian Sugarcane Research and Training Institute (ISCRTI), Ahvaz, Khuzestan, Iran
| | - Habibeh Hajian Maleki
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran
| | - Xiang Li
- Canadian Food Inspection Agency (CFIA), Charlottetown Laboratory, 93 Mount Edward Road, Charlottetown, PE C1A 5T1, Canada
| | - Marie-Agnes Jacques
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Perrine Portier
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
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9
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Stoll DA, Grimmler C, Hetzer B, Kulling SE, Huch M. Rathayibacter rubneri sp. nov. isolated from Allium cepa var. Rijnsburger, an onion landrace. Int J Syst Evol Microbiol 2023; 73. [PMID: 37040159 DOI: 10.1099/ijsem.0.005811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023] Open
Abstract
The novel, aerobic, Gram-stain-positive, rod-shaped bacterial strain, ZW T2_19T, was isolated from an onion sample (Allium cepa var. Rijnsburger). Analyses of the 16S rRNA gene sequence revealed that ZW T2_19T represented a member of the genus Rathayibacter but may represent a novel species of this genus. Analyses of the whole draft genome sequences, i.e. digital DNA-DNA hybridisation (dDDH) and average nucleotide identity (ANI) of ZW T2_19T and all type strains of species of the genus Rathayibacter confirmed that ZW T2_19T represents a novel species of the genus Rathayibacter. The genome size of ZW T2_19T is 4.01 Mbp and the DNA G+C content is 71.8 mol%. Glucose, mannose, rhamnose and ribose were detected as whole-cell sugars of ZW T2_19T. The major respiratory quinone of ZW T2_19T is menaquinone MK-10, at 78.9 %. The detected peptidoglycan type in ZW T2_19T is a variant of type B2γ with {Gly} [l-diaminobutyric acid (l-DAB)/l-homoserine (l-Hse)] d-Glu-l-DAB. Polar lipids in ZW T2_19T consisted of one diphosphatidylglycerol, one phosphatidylglycerol, seven glycolipids, one phospholipid and one lipid. The fatty acid profile of ZW T2_19T predominantly consisted of anteiso-C15 : 0 (53 %), iso-C16 : 0 (21 %) and anteiso-C17 : 0 (18 %). In addition, API 20NE, API 50CH, API Coryne, API ZYM, antibiotic susceptibility, haemolysis and growth at different temperatures and with different supplements was investigated. On the basis of the results obtained using this polyphasic approach, including molecular, phenotypic and biochemical analyses, we propose the novel species Rathayibacter rubneri with the type and only strain ZW T2_19T (= DSM 114294T = LMG 32700T).
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Affiliation(s)
- Dominic A Stoll
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131 Karlsruhe, Germany
| | - Christina Grimmler
- Department of Safety and Quality of Meat, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, E.-C.-Baumann-Straße 20, 95326 Kulmbach, Germany
| | - Birgit Hetzer
- Department of Food Technology and Bioprocess Engineering, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131 Karlsruhe, Germany
| | - Sabine E Kulling
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131 Karlsruhe, Germany
| | - Melanie Huch
- Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131 Karlsruhe, Germany
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10
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Kim YS, Kim SB. Agromyces seonyuensis sp. nov., isolated from island soil. Int J Syst Evol Microbiol 2023; 73. [PMID: 36748535 DOI: 10.1099/ijsem.0.005689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A Gram-positive, non-motile, pale yellow coloured actinobacterial strain designated MMS17-SY077T was isolated from island soil, and its taxonomic position was investigated using a polyphasic approach. Strain MMS17-SY077T grew optimally at 30 °C, at pH 7 and in the absence of NaCl on Reasoner's 2A agar. Based on the 16S rRNA gene sequence analysis, the strain was assigned to the genus Agromyces of the family Microbacteriaceae, and the most related species were Agromyces italicus DSM 16388T (98.8 % sequence similarity), Agromyces allii UMS-62T (98.1 %) and Agromyces terreus DS-10T (97.8 %). Strain MMS17-SY077T formed a distinct cluster within the Agromyces clade in the phylogenetic tree. Genome-based comparative analyses confirmed a clear distinction between the strain and neighbouring species, as the highest orthologous average nucleotide identity and digital DNA-DNA hybridization values with other related species were 77.2 and 21.4% respectively, which were far below the cutoffs for species distinction. The diagnostic polar lipids of MMS17-SY077T were diphosphatidylglycerol and phosphatidylglycerol, and unidentified glycolipids and an unidentified aminolipid were also present. The main isoprenoid quinones were menaquinones with 11 and 12 isoprene units (MK-11 and MK-12), and main fatty acids were anteiso-C15 : 0 (34.4 %) and iso-C16 : 0 (33.2 %). The whole-cell hydrolysates contained rhamnose, ribose and galactose as diagnostic sugars, and l-2,4-diaminobutyric acid as the major diamino acid. The DNA G+C content was 72.1 mol %. Based on phenotypic, chemotaxnomic and phylogenetic characterization, strain MMS17-SY077T should be classified as representing a new species of the genus Agromyces, for which the name Agromyces seonyunensis sp. nov. is proposed (type strain MMS17-SY077T=KCTC 49423T=LMG 31762T).
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Affiliation(s)
- Yeong Seok Kim
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99, Daehak-ro, Yuseong, Daejeon 34134, Republic of Korea
- Center for Eco-friendly New Materials, Korea Research Institute of Chemical Technology, 141, Gajeong-ro, Yuseong, Daejeon 34114, Republic of Korea
- Department of Medicinal Chemistry and Pharmacology, University of Science and Technology, 217, Gajeong-ro, Yuseong, Daejeon 34113, Republic of Korea
| | - Seung Bum Kim
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99, Daehak-ro, Yuseong, Daejeon 34134, Republic of Korea
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11
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Osdaghi E, Taghouti G, Dutrieux C, Taghavi SM, Fazliarab A, Briand M, Le Saux MF, Portier P, Jacques MA. Whole Genome Resources of 17 Curtobacterium flaccumfaciens Strains Including Pathotypes of C. flaccumfaciens pv. betae, C. flaccumfaciens pv. oortii, and C. flaccumfaciens pv. poinsettiae. Mol Plant Microbe Interact 2022; 35:352-356. [PMID: 35021852 DOI: 10.1094/mpmi-11-21-0282-a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Ebrahim Osdaghi
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran
| | - Geraldine Taghouti
- University of Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Cecile Dutrieux
- University of Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - S Mohsen Taghavi
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Amal Fazliarab
- Iranian Sugarcane Research and Training Institute (ISCRTI), Ahvaz, Khuzestan, Iran
| | - Martial Briand
- University of Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Marion Fischer Le Saux
- University of Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Perrine Portier
- University of Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Marie-Agnes Jacques
- University of Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
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12
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Abstract
A novel Gram-stain-positive, strictly aerobic, short rod-shaped bacterium, designated 2CT, was isolated from freshly packaged microfiltered milk. This strain was able to grow within the NaCl concentration range of 0-5 % (w/v), temperature range of 8-37 °C (optimally at 30 °C) and at pH 6.0-10.0. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 2CT was closely related to species of the genus Microbacterium, with the highest sequence similarity (99.2 %) to Microbacterium lacticum DSM 20427T as well as Microbacterium flavum DSM 18909T (=YM18-098T). The phylogenetic tree based on 16S rRNA genes showed that strain 2CT clustered with M. flavum DSM 18909T. However, the phylogenetic tree based on concatenated 16S rRNA and four housekeeping genes showed that strain 2CT clustered with M. lacticum DSM 20427T. Furthermore, the phylogenomic tree showed that strain 2CT clustered with M. lacticum DSM 20427T and M. flavum DSM 18909T. The major respiratory quinones were MK-10, MK-11 and MK-12. The predominant cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The polar lipid composition of strain 2CT consisted of diphosphatidylglycerol, phosphatidylglycerol, three unidentified glycolipids and two unidentified lipids. The cell-wall peptidoglycan type was a variant of B1α {Gly} [l-Lys] d-Glu-l-Lys, with the amino acids lysine, glycine, alanine and glutamic acid. The whole-cell sugars consisted of galactose, glucose, ribose and minor amounts of rhamnose. In addition, strain 2CT showed a glycolyl-type cell wall. The genomic DNA G+C content was 69.8mol%, while the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values with the closely related Microbacterium species were below the recognized thresholds of 95-96 % ANI and 70 % DDH for species definition. Based on the phenotypic and genotypic data, strain 2CT (=LMG 32277T=CECT 30329T) is considered to represent a new species, for which the name Microbacterium paulum sp. nov. is proposed.
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Affiliation(s)
- Paolo Bellassi
- Department for Sustainable Food Process (DiSTAS), Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Alessandra Fontana
- Department for Sustainable Food Process (DiSTAS), Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Maria Luisa Callegari
- Department for Sustainable Food Process (DiSTAS), Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Fabrizio Cappa
- Department for Sustainable Food Process (DiSTAS), Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Lorenzo Morelli
- Department for Sustainable Food Process (DiSTAS), Università Cattolica del Sacro Cuore, Piacenza, Italy
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Vaghefi N, Adorada DL, Huth L, Kelly LA, Poudel B, Young A, Sparks AH. Whole-Genome Data from Curtobacterium flaccumfaciens pv. flaccumfaciens Strains Associated with Tan Spot of Mungbean and Soybean Reveal Diverse Plasmid Profiles. Mol Plant Microbe Interact 2021; 34:1216-1222. [PMID: 34185567 DOI: 10.1094/mpmi-05-21-0116-a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Despite the substantial economic impact of Curtobacterium flaccumfaciens pv. flaccumfaciens on legume production worldwide, the genetic basis of its pathogenicity and potential host association is poorly understood. The production of high-quality reference genome assemblies of C. flaccumfaciens pv. flaccumfaciens strains associated with different hosts sheds light on the genetic basis of its pathogenic variability and host association. Moreover, the study of recent outbreaks of bacterial wilt and microevolution of the pathogen in Australia requires access to high-quality reference genomes that are sufficiently closely related to the population being studied within Australia. We provide the first genome assemblies of C. flaccumfaciens pv. flaccumfaciens strains associated with mungbean and soybean, which revealed high variability in their plasmid composition. The analysis of C. flaccumfaciens pv. flaccumfaciens genomes revealed an extensive suite of carbohydrate-active enzymes potentially associated with pathogenicity, including four carbohydrate esterases, 50 glycoside hydrolases, 23 glycosyl transferases, and a polysaccharide lyase. We also identified 11 serine peptidases, three of which were located within a linear plasmid, pCff119. These high-quality assemblies and annotations will provide a foundation for population genomics studies of C. flaccumfaciens pv. flaccumfaciens in Australia and for answering fundamental questions regarding pathogenicity factors and adaptation of C. flaccumfaciens pv. flaccumfaciens to various hosts worldwide and, at a broader scale, contribute to unraveling genomic features of gram-positive, xylem-inhabiting bacterial pathogens.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Niloofar Vaghefi
- Centre for Crop Health, University of Southern Queensland, Australia
| | - Dante L Adorada
- Centre for Crop Health, University of Southern Queensland, Australia
| | - Lauren Huth
- Centre for Crop Health, University of Southern Queensland, Australia
| | - Lisa A Kelly
- Centre for Crop Health, University of Southern Queensland, Australia
- Department of Agriculture and Fisheries, Queensland, Australia
| | - Barsha Poudel
- Centre for Crop Health, University of Southern Queensland, Australia
| | - Anthony Young
- School of Agriculture and Food Sciences, The University of Queensland, Australia
| | - Adam H Sparks
- Centre for Crop Health, University of Southern Queensland, Australia
- Department of Primary Industries and Regional Development, Perth, WA 6983, Australia
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14
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Pitt A, Schmidt J, Koll U, Hahn MW. Aquiluna borgnonia gen. nov., sp. nov., a member of a Microbacteriaceae lineage of freshwater bacteria with small genome sizes. Int J Syst Evol Microbiol 2021; 71. [PMID: 33999796 DOI: 10.1099/ijsem.0.004825] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The actinobacterial strain 15G-AUS-rotT was isolated from an artificial pond located near Salzburg, Austria. The strain showed 16S rRNA gene sequence similarities of 98.7 % to Candidatus Aquiluna rubra and of 96.6 and 96.7 % to the two validly described species of the genus Rhodoluna. Phylogenetic reconstructions based on 16S rRNA gene sequences and genome-based on amino acid sequences of 118 single copy genes referred strain 15G-AUS-rotT to the family Microbacteriaceae and therein to the so-called subcluster Luna-1. The genome-based phylogenetic tree showed that the new strain represents a putative new genus. Cultures of strain 15G-AUS-rotT were light red pigmented and comprised very small, rod-shaped cells. They metabolized a broad variety of substrates. Major fatty acids (>10 %) of cells were iso-C16 : 0, antiso-C15 : 0 and iso-C14 : 0. The major respiratory quinone was MK-11 and a minor component was MK-10. The peptidoglycan structure belonged to an unusual B type. The closed genome sequence of the strain was very small (1.4 Mbp) and had a DNA G+C content of 54.8 mol%. An interesting feature was the presence of genes putatively encoding the complete light-driven proton pumping actinorhodopsin/retinal system, which were located at three different positions of the genome. Based on the characteristics of the strain, a new genus and a new species termed Aquiluna borgnonia is proposed for strain 15G-AUS-rotT (=DSM 107803T=JCM 32974T).
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Affiliation(s)
- Alexandra Pitt
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Johanna Schmidt
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Ulrike Koll
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Martin W Hahn
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
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15
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Chen G, Khojasteh M, Taheri-Dehkordi A, Taghavi SM, Rahimi T, Osdaghi E. Complete Genome Sequencing Provides Novel Insight Into the Virulence Repertories and Phylogenetic Position of Dry Beans Pathogen Curtobacterium flaccumfaciens pv. flaccumfaciens. Phytopathology 2021; 111:268-280. [PMID: 32716255 DOI: 10.1094/phyto-06-20-0243-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Bacterial wilt of dry beans (family Fabaceae) caused by the actinobacterial agent Curtobacterium flaccumfaciens pv. flaccumfaciens is one of the most important diseases threatening edible legume production around the globe. Despite the economic losses due to the bacterial wilt disease, the pathogen has not so far been investigated for its genomic features, pathogenicity determinants, and virulence strategies. Here we present the first complete genome sequence of a highly virulent bacteriocin-producing C. flaccumfaciens pv. flaccumfaciens strain P990. The bacterium has a circular chromosome consisting of 3,736 kbp with the G+C% content of 71.0%. Furthermore, a 147-kbp circular plasmid (pCff1) with 66.1% G+C% content as well as two circular plasmid-like DNAs with sizes of 25 and 22 kbp were detected within the genomic contents of C. flaccumfaciens pv. flaccumfaciens. Phylogenetic analyses revealed that only a few number of Curtobacterium sp. strains deposited in the public databases could be classified within the species C. flaccumfaciens. Comparative genomics of C. flaccumfaciens pv. flaccumfaciens using the genome sequences of actinobacterial plant pathogens revealed the presence of a set of unique low G+C% content genomic islands in the C. flaccumfaciens pv. flaccumfaciens genome. Homologs of pathogenicity-determinant loci capable of producing 1,4-beta-xylanase (xysA), pectate lyase (pelA1 and pelA2), serine protease (chpC, chpG, and pat-1), and sortase (srtA) were detected in C. flaccumfaciens pv. flaccumfaciens genome. The genomic data presented here extend our understanding of the C. flaccumfaciens pv. flaccumfaciens genomic features and pave the ways of research on functional and interaction genetics to combat the risk of bacterial wilt disease in the 21st century's dry bean industry.
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Affiliation(s)
- Gongyou Chen
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Moein Khojasteh
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
- Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Ayat Taheri-Dehkordi
- Department of Horticultural Science, College of Agriculture & Natural Resources, University of Tehran, Karaj 31587-77871, Iran
| | - S Mohsen Taghavi
- Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Touraj Rahimi
- Department of Agronomy and Plant Breeding, Shahr-e-Qods Branch, Islamic Azad University, Tehran, Iran
| | - Ebrahim Osdaghi
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran
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Li XJ, Wang CM, Feng XM, Liu SW, Qiao HX, Chang YL, Sun CH. Planctomonas psychrotolerans sp. nov., isolated from rhizosphere soil of Suaeda salsa. Int J Syst Evol Microbiol 2020; 70:5271-5279. [PMID: 32833615 DOI: 10.1099/ijsem.0.004408] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A psychrotolerant actinobacterium, designated strain J5903T, was isolated from an alkaline soil sample from the rhizosphere of Suaeda salsa collected in desertification land surrounding Jiuliancheng Nur in Hebei Province, PR China. Cells of the isolate were Gram-stain-positive, aerobic, non-motile and non-spore-forming cocci. Strain J5903T grew optimally at 20‒25 °C, at pH 7.0‒7.5 and with <1 % (w/v) NaCl. The cell-wall peptidoglycan type was B2γ with d-2,4-diaminobutyric acid and l-2,4-diaminobutyric acid as diagnostic amino acids. The muramyl residue was acetyl type. The menaquinones were MK-11, MK-12, MK-10 and MK-13. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and one unidentified glycolipid. The major whole-cell fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The genomic DNA G+C content was 69.1 mol%. It shared the highest average nucleotide identity and digital DNA-DNA hybridization values with Planctomonas deserti 13S1-3T. Phylogenies based on genome sequence showed that strain J5903T and P. deserti 13S1-3T formed a robust cluster with high bootstrap support. Strain J5903T shared typical chemotaxonomic characteristics with P. deserti 13S1-3T. Combining the polyphasic taxonomic evidence, strain J5903T represents a novel species of the genus Planctomonas, for which the name Planctomonas psychrotolerans sp. nov. is proposed. The type strain is J5903T (=DSM 101894T=CGMCC 1.15523T).
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Affiliation(s)
- Xiao-Jun Li
- College of Lab Medicine, Hebei North University, Zhangjiakou 075000, PR China
| | - Chun-Miao Wang
- College of Lab Medicine, Hebei North University, Zhangjiakou 075000, PR China
| | - Xue-Mei Feng
- College of Lab Medicine, Hebei North University, Zhangjiakou 075000, PR China
| | - Shao-Wei Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Hai-Xia Qiao
- College of Lab Medicine, Hebei North University, Zhangjiakou 075000, PR China
| | - Yue-Li Chang
- College of Lab Medicine, Hebei North University, Zhangjiakou 075000, PR China
| | - Cheng-Hang Sun
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
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Hamidizade M, Taghavi SM, Martins SJ, Herschlag RA, Hockett KL, Bull CT, Osdaghi E. Bacterial Brown Pit, a New Disease of Edible Mushrooms Caused by Mycetocola sp. Plant Dis 2020; 104:1445-1454. [PMID: 32181723 DOI: 10.1094/pdis-10-19-2176-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
From September to December 2018, commercial button mushroom (Agaricus bisporus) farms in central Iran were surveyed to monitor the causal agent(s) of browning and blotch symptoms on mushroom caps. In addition to dozens of pseudomonads (i.e., Pseudomonas tolaasii and Pseudomonas reactans), six slow-growing gram-positive bacterial strains were isolated from blotched mushroom caps. These bacteria presented as creamy white, circular, smooth, nonfluorescent, and shiny colonies with whole margins resembling members of Microbacteriaceae (Actinobacteria). All of the actinobacterial strains were aggressively pathogenic on cut cap surface of two edible mushrooms (i.e., A. bisporus and Pleurotus eryngii), inducing brown pit symptoms 48 h postinoculation. The strains did not induce symptoms on the vegetables tested (i.e., carrot, cucumber, and potato), and they did not affect the growth of mycelium of tested plant-pathogenic fungi (i.e., Acremonium sp., Fusarium spp., and Phytopythium sp.). Phylogeny of 16S ribosomal RNA and multilocus sequence analysis of six housekeeping genes (i.e., atpD, dnaK, gyrB, ppK, recA, and rpoB) revealed that the bacterial strains belong to the actinobacterial genus Mycetocola spp., whereas the species status of the strains remains undetermined. Mushroom-associated Mycetocola species were previously reported to be capable of detoxifying tolaasin, a toxin produced by P. tolaasii, whereas the strains isolated in this study did not show tolaasin detoxification activities. Altogether, this is the first report of a mushroom disease caused by an actinobacterial species, and "bacterial brown pit" was assigned as the common name of the disease.
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Affiliation(s)
- Mozhde Hamidizade
- Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - S Mohsen Taghavi
- Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Samuel J Martins
- Plant Pathology & Environmental Microbiology Department, The Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Rachel A Herschlag
- Plant Pathology & Environmental Microbiology Department, The Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Kevin L Hockett
- Plant Pathology & Environmental Microbiology Department, The Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Carolee T Bull
- Plant Pathology & Environmental Microbiology Department, The Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Ebrahim Osdaghi
- Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
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18
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Liu SW, Li FN, Zheng HY, Qi X, Huang DL, Xie YY, Sun CH. Planctomonas deserti gen. nov., sp. nov., a new member of the family Microbacteriaceae isolated from soil of the Taklamakan desert. Int J Syst Evol Microbiol 2018; 69:616-624. [PMID: 30387709 DOI: 10.1099/ijsem.0.003095] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-positive, aerobic, irregular coccoid- to ovoid-shaped, non-spore-forming and motile bacterium, designated strain 13S1-3T, was isolated from a soil sample from the rhizosphere of Tamarix collected in the Taklamakan desert in Xinjiang Uygur Autonomous Region, PR China. The strain was examined by a polyphasic approach to clarify its taxonomic position. Strain 13S1-3T grew optimally at 28-30 °C, pH 7.0 and with 0-1 % (w/v) NaCl. The cell-wall peptidoglycan was of the B2γ type and contained d-alanine, d-glutamic acid, glycine, d-2,4-diaminobutyric acid and l-2,4-diaminobutyric acid. Ribose, xylose, glucose and galactose were detected as cell-wall sugars. The acyl type of the muramic acid was acetyl. The predominant menaquinones were MK-12, MK-11, MK-13 and MK-10. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids and one unidentified phospholipid. The major whole-cell fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The DNA G+C content was 70.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that 13S1-3T represented a member of the family Microbacteriaceae and showed the highest level of 16S rRNA gene sequence similarity with Frondihabitans australicus E1HC-02T (97.11 %). Phylogenetic trees revealed that 13S1-3T formed a distinct lineage with respect to closely related genera within the family Microbacteriaceae. On the basis of the results of phylogenetic, phenotypic and chemotaxonomic analyses, 13S1-3T is distinguishable from phylogenetically related genera in the family Microbacteriaceae, and represents a novel species of a new genus, for which the name Planctomonas deserti gen. nov., sp. nov. is proposed. The type strain is 13S1-3T (=KCTC 49115T=CGMCC 1.16554T).
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Affiliation(s)
- Shao-Wei Liu
- 1Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Fei-Na Li
- 1Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Hong-Yun Zheng
- 1Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China.,2College of Basic Medical Sciences, Guilin Medical University, Guilin 541004, PR China
| | - Xin Qi
- 1Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Da-Lin Huang
- 2College of Basic Medical Sciences, Guilin Medical University, Guilin 541004, PR China
| | - Yun-Ying Xie
- 1Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Cheng-Hang Sun
- 1Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
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19
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Cho BC, Hardies SC, Jang GI, Hwang CY. Complete genome of streamlined marine actinobacterium Pontimonas salivibrio strain CL-TW6 T adapted to coastal planktonic lifestyle. BMC Genomics 2018; 19:625. [PMID: 30134835 PMCID: PMC6106888 DOI: 10.1186/s12864-018-5019-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 08/14/2018] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Pontimonas salivibrio strain CL-TW6T (=KCCM 90105 = JCM18206) was characterized as the type strain of a new genus within the Actinobacterial family Microbacteriaceae. It was isolated from a coastal marine environment in which members of Microbactericeae have not been previously characterized. RESULTS The genome of P. salivibrio CL-TW6T was a single chromosome of 1,760,810 bp. Genomes of this small size are typically found in bacteria growing slowly in oligotrophic zones and said to be streamlined. Phylogenetic analysis showed it to represent a lineage originating in the Microbacteriaceae radiation occurring before the snowball Earth glaciations, and to have a closer relationship with some streamlined bacteria known through metagenomic data. Several genomic characteristics typical of streamlined bacteria are found: %G + C is lower than non-streamlined members of the phylum; there are a minimal number of rRNA and tRNA genes, fewer paralogs in most gene families, and only two sigma factors; there is a noticeable absence of some nonessential metabolic pathways, including polyketide synthesis and catabolism of some amino acids. There was no indication of any phage genes or plasmids, however, a system of active insertion elements was present. P. salivibrio appears to be unusual in having polyrhamnose-based cell wall oligosaccharides instead of mycolic acid or teichoic acid-based oligosaccharides. Oddly, it conducts sulfate assimilation apparently for sulfating cell wall components, but not for synthesizing amino acids. One gene family it has more of, rather than fewer of, are toxin/antitoxin systems, which are thought to down-regulate growth during nutrient deprivation or other stressful conditions. CONCLUSIONS Because of the relatively small number of paralogs and its relationship to the heavily characterized Mycobacterium tuberculosis, we were able to heavily annotate the genome of P. salivibrio CL-TW6T. Its streamlined status and relationship to streamlined metagenomic constructs makes it an important reference genome for study of the streamlining concept. The final evolutionary trajectory of CL-TW6 T was to adapt to growth in a non-oligotrophic coastal zone. To understand that adaptive process, we give a thorough accounting of gene content, contrasting with both oligotrophic streamlined bacteria and large genome bacteria, and distinguishing between genes derived by vertical and horizontal descent.
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Affiliation(s)
- Byung Cheol Cho
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Gwanak-gu, Seoul, Republic of Korea
| | - Stephen C. Hardies
- Department of Biochemistry, The University of Texas Health Science Center at San Antonio, San Antonio, TX USA
| | - Gwang Il Jang
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Gwanak-gu, Seoul, Republic of Korea
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Chung Yeon Hwang
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea
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20
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Nandi M, Macdonald J, Liu P, Weselowski B, Yuan Z. Clavibacter michiganensis ssp. michiganensis: bacterial canker of tomato, molecular interactions and disease management. Mol Plant Pathol 2018; 19:2036-2050. [PMID: 29528201 PMCID: PMC6638088 DOI: 10.1111/mpp.12678] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/06/2018] [Accepted: 03/07/2018] [Indexed: 05/11/2023]
Abstract
Bacterial canker disease is considered to be one of the most destructive diseases of tomato (Solanum lycopersicum), and is caused by the seed-borne Gram-positive bacterium Clavibacter michiganensis ssp. michiganensis (Cmm). This vascular pathogen generally invades and proliferates in the xylem through natural openings or wounds, causing wilt and canker symptoms. The incidence of symptomless latent infections and the invasion of tomato seeds by Cmm are widespread. Pathogenicity is mediated by virulence factors and transcriptional regulators encoded by the chromosome and two natural plasmids. The virulence factors include serine proteases, cell wall-degrading enzymes (cellulases, xylanases, pectinases) and others. Mutational analyses of these genes and gene expression profiling (via quantitative reverse transcription-polymerase chain reaction, transcriptomics and proteomics) have begun to shed light on their roles in colonization and virulence, whereas the expression of tomato genes in response to Cmm infection suggests plant factors involved in the defence response. These findings may aid in the generation of target-specific bactericides or new resistant varieties of tomato. Meanwhile, various chemical and biological controls have been researched to control Cmm. This review presents a detailed investigation regarding the pathogen Cmm, bacterial canker infection, molecular interactions between Cmm and tomato, and current perspectives on improved disease management.
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Affiliation(s)
- Munmun Nandi
- Department of Microbiology & Immunology, Schulich School of Medicine & DentistryUniversity of Western OntarioLondonONCanada, N6A 5C1
| | - Jacqueline Macdonald
- Department of Microbiology & Immunology, Schulich School of Medicine & DentistryUniversity of Western OntarioLondonONCanada, N6A 5C1
| | - Peng Liu
- Department of Microbiology & Immunology, Schulich School of Medicine & DentistryUniversity of Western OntarioLondonONCanada, N6A 5C1
| | - Brian Weselowski
- London Research and Development Centre, Agriculture & Agri‐Food CanadaLondonONCanada, N5V 4T3
| | - Ze‐Chun Yuan
- Department of Microbiology & Immunology, Schulich School of Medicine & DentistryUniversity of Western OntarioLondonONCanada, N6A 5C1
- London Research and Development Centre, Agriculture & Agri‐Food CanadaLondonONCanada, N5V 4T3
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21
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Villalobos AS, Wiese J, Aguilar P, Dorador C, Imhoff JF. Subtercola vilae sp. nov., a novel actinobacterium from an extremely high-altitude cold volcano lake in Chile. Antonie Van Leeuwenhoek 2017; 111:955-963. [PMID: 29214367 PMCID: PMC5945732 DOI: 10.1007/s10482-017-0994-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 12/01/2017] [Indexed: 11/08/2022]
Abstract
A novel actinobacterium, strain DB165T, was isolated from cold waters of Llullaillaco Volcano Lake (6170 m asl) in Chile. Phylogenetic analysis based on 16S rRNA gene sequences identified strain DB165T as belonging to the genus Subtercola in the family Microbacteriaceae, sharing 97.4% of sequence similarity with Subtercola frigoramans DSM 13057T, 96.7% with Subtercola lobariae DSM 103962T, and 96.1% with Subtercola boreus DSM 13056T. The cells were observed to be Gram-positive, form rods with irregular morphology, and to grow best at 10–15 °C, pH 7 and in the absence of NaCl. The cross-linkage between the amino acids in its peptidoglycan is type B2γ; 2,4-diaminobutyric acid is the diagnostic diamino acid; the major respiratory quinones are MK-9 and MK-10; and the polar lipids consist of phosphatidylglycerol, diphosphatidylglycerol, 5 glycolipids, 2 phospholipids and 5 additional polar lipids. The fatty acid profile of DB165T (5% >) contains iso-C14:0, iso-C16:0, anteiso-C15:0, anteiso-C17:0, and the dimethylacetal iso-C16:0 DMA. The genomic DNA G+C content of strain DB165T was determined to be 65 mol%. Based on the phylogenetic, phenotypic, and chemotaxonomic analyses presented in this study, strain DB165T (= DSM 105013T = JCM 32044T) represents a new species in the genus Subtercola, for which the name Subtercola vilae sp. nov. is proposed.
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Affiliation(s)
- Alvaro S Villalobos
- Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105, Kiel, Germany
| | - Jutta Wiese
- Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105, Kiel, Germany
| | - Pablo Aguilar
- Laboratorio de Complejidad Microbiana y Ecología Funcional and Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile.,Lake and Glacier Ecology Research Group, Institute of Ecology, University of Innsbruck, Techniker Str. 25, 6020, Innsbruck, Austria
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional and Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile.,Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
| | - Johannes F Imhoff
- Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105, Kiel, Germany.
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22
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Chase AB, Karaoz U, Brodie EL, Gomez-Lunar Z, Martiny AC, Martiny JBH. Microdiversity of an Abundant Terrestrial Bacterium Encompasses Extensive Variation in Ecologically Relevant Traits. mBio 2017; 8:e01809-17. [PMID: 29138307 DOI: 10.1128/mBio.01809-17] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Much genetic diversity within a bacterial community is likely obscured by microdiversity within operational taxonomic units (OTUs) defined by 16S rRNA gene sequences. However, it is unclear how variation within this microdiversity influences ecologically relevant traits. Here, we employ a multifaceted approach to investigate microdiversity within the dominant leaf litter bacterium, Curtobacterium, which comprises 7.8% of the bacterial community at a grassland site undergoing global change manipulations. We use cultured bacterial isolates to interpret metagenomic data, collected in situ over 2 years, together with lab-based physiological assays to determine the extent of trait variation within this abundant OTU. The response of Curtobacterium to seasonal variability and the global change manipulations, specifically an increase in relative abundance under decreased water availability, appeared to be conserved across six Curtobacterium lineages identified at this site. Genomic and physiological analyses in the lab revealed that degradation of abundant polymeric carbohydrates within leaf litter, cellulose and xylan, is nearly universal across the genus, which may contribute to its high abundance in grassland leaf litter. However, the degree of carbohydrate utilization and temperature preference for this degradation varied greatly among clades. Overall, we find that traits within Curtobacterium are conserved at different phylogenetic depths. We speculate that similar to bacteria in marine systems, diverse microbes within this taxon may be structured in distinct ecotypes that are key to understanding Curtobacterium abundance and distribution in the environment. Despite the plummeting costs of sequencing, characterizing the fine-scale genetic diversity of a microbial community—and interpreting its functional importance—remains a challenge. Indeed, most studies, particularly studies of soil, assess community composition at a broad genetic level by classifying diversity into taxa (OTUs) defined by 16S rRNA sequence similarity. However, these classifications potentially obscure variation in traits that result in fine-scale ecological differentiation among closely related strains. Here, we investigated “microdiversity” in a highly diverse and poorly characterized soil system (leaf litter in a southern Californian grassland). We focused on the most abundant bacterium, Curtobacterium, which by standard methods is grouped into only one OTU. We find that the degree of carbohydrate usage and temperature preference vary within the OTU, whereas its responses to changes in precipitation are relatively uniform. These results suggest that microdiversity may be key to understanding how soil bacterial diversity is linked to ecosystem functioning.
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23
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Corretto E, Antonielli L, Sessitsch A, Compant S, Höfer C, Puschenreiter M, Brader G. Complete genome sequence of the heavy metal resistant bacterium Agromyces aureus AR33 T and comparison with related Actinobacteria. Stand Genomic Sci 2017; 12:2. [PMID: 28074120 PMCID: PMC5217419 DOI: 10.1186/s40793-016-0217-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 12/06/2016] [Indexed: 11/17/2022] Open
Abstract
Agromyces aureus AR33T is a Gram-positive, rod-shaped and motile bacterium belonging to the Microbacteriaceae family in the phylum Actinobacteria that was isolated from a former zinc/lead mining and processing site in Austria. In this study, the whole genome was sequenced and assembled combining sequences obtained from Illumina MiSeq and Sanger sequencing. The assembly resulted in the complete genome sequence which is 4,373,124 bp long and has a GC content of 70.1%. Furthermore, we performed a comparative genomic analysis with other related organisms: 6 Agromyces spp., 4 Microbacteriaceae spp. and 2 other members of the class Actinobacteria.
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Affiliation(s)
- Erika Corretto
- AIT Austrian Institute of Technology, Health and Environment Department, Konrad-Lorenz-Straße 24, A-3430 Tulln, Austria
| | - Livio Antonielli
- AIT Austrian Institute of Technology, Health and Environment Department, Konrad-Lorenz-Straße 24, A-3430 Tulln, Austria
| | - Angela Sessitsch
- AIT Austrian Institute of Technology, Health and Environment Department, Konrad-Lorenz-Straße 24, A-3430 Tulln, Austria
| | - Stéphane Compant
- AIT Austrian Institute of Technology, Health and Environment Department, Konrad-Lorenz-Straße 24, A-3430 Tulln, Austria
| | - Christoph Höfer
- Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences (BOKU), Konrad-Lorenz-Straβe 24, A-3430 Tulln, Austria
| | - Markus Puschenreiter
- Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences (BOKU), Konrad-Lorenz-Straβe 24, A-3430 Tulln, Austria
| | - Günter Brader
- AIT Austrian Institute of Technology, Health and Environment Department, Konrad-Lorenz-Straße 24, A-3430 Tulln, Austria
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24
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Chase AB, Arevalo P, Polz MF, Berlemont R, Martiny JBH. Evidence for Ecological Flexibility in the Cosmopolitan Genus Curtobacterium. Front Microbiol 2016; 7:1874. [PMID: 27920771 PMCID: PMC5118839 DOI: 10.3389/fmicb.2016.01874] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 11/07/2016] [Indexed: 12/30/2022] Open
Abstract
Assigning ecological roles to bacterial taxa remains imperative to understanding how microbial communities will respond to changing environmental conditions. Here we analyze the genus Curtobacterium, as it was found to be the most abundant taxon in a leaf litter community in southern California. Traditional characterization of this taxon predominantly associates it as the causal pathogen in the agricultural crops of dry beans. Therefore, we sought to investigate whether the abundance of this genus was because of its role as a plant pathogen or another ecological role. By collating >24,000 16S rRNA sequences with 120 genomes across the Microbacteriaceae family, we show that Curtobacterium has a global distribution with a predominant presence in soil ecosystems. Moreover, this genus harbors a high diversity of genomic potential for the degradation of carbohydrates, specifically with regards to structural polysaccharides. We conclude that Curtobacterium may be responsible for the degradation of organic matter within litter communities.
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Affiliation(s)
- Alexander B. Chase
- Department of Ecology and Evolutionary Biology, University of California, IrvineIrvine, CA, USA
| | - Philip Arevalo
- Parsons Laboratory for Environmental Science and Engineering, Massachusetts Institute of TechnologyCambridge, MA, USA
| | - Martin F. Polz
- Parsons Laboratory for Environmental Science and Engineering, Massachusetts Institute of TechnologyCambridge, MA, USA
| | - Renaud Berlemont
- Department of Biological Sciences, California State University Long BeachLong Beach, CA, USA
| | - Jennifer B. H. Martiny
- Department of Ecology and Evolutionary Biology, University of California, IrvineIrvine, CA, USA
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25
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Abstract
A novel actinobacterial strain, designated R1-20T, was isolated during a study of the bacterial diversity of the soil at a white heron nesting site. The isolate was non-motile, Gram-stain-positive and short rod-shaped. Colonies were dull white and convex with entire margin during the early stages of growth, and gradually became yellow. 16S rRNA gene sequence analysis indicated that the isolate belongs to the genus Humibacter of the family Microbacteriaceae, as sequence similarity with its nearest neighbours was 97.16 % with Humibacter antriD7-27Tand 96.44 % with Humibacter albusDSM 18994T. However, the combination of cultural and physiological as well as chemotaxonomic properties clearly distinguished strain R1-20T from other Humibacter species. The DNA G+C content of strain R1-20T was 65.5 mol%, and the major respiratory isoprenoid quinone was menaquinone MK-11. The acyl group of the peptidoglycan was of acetyl type, and the diagnostic diamino acid was 2,4-diaminobutyric acid. Glutamic acid, alanine and glycine were also present in the cell wall. The major fatty acids of strain R1-20T were anteiso-C17 : 0, iso-C16 : 0 and anteiso-C15 : 0. On the basis of phylogenetic, phenotypic and chemotaxonomic analysis, strain R1-20T merits recognition as a representative of a novel species of the genus Humibacter, for which the name Humibacter soli sp. nov. is proposed. The type strain is R1-20T (=KCTC 39614T=JCM 31015T).
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Affiliation(s)
- Jisun Park
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, South Korea
| | - Yu Ri Kim
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, South Korea
| | - Min-Kyeong Kim
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, South Korea
| | - Jung Hun Jo
- Department of Biotechnology, Hankyoung National University, Anseong, South Korea
| | - Wan-Taek Im
- Department of Biotechnology, Hankyoung National University, Anseong, South Korea
| | - Seung Bum Kim
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, South Korea
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26
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Laviad S, Lapidus A, Copeland A, Reddy T, Huntemann M, Pati A, Ivanova NN, Markowitz VM, Pukall R, Klenk HP, Woyke T, Kyrpides NC, Halpern M. High quality draft genome sequence of Leucobacter chironomi strain MM2LB(T) (DSM 19883(T)) isolated from a Chironomus sp. egg mass. Stand Genomic Sci 2015. [PMID: 26203333 PMCID: PMC4511665 DOI: 10.1186/s40793-015-0003-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Leucobacter chironomi strain MM2LBT (Halpern et al., Int J
Syst Evol Microbiol 59:665-70 2009) is a Gram-positive, rod shaped, non-motile,
aerobic, chemoorganotroph bacterium. L. chironomi belongs to the family
Microbacteriaceae, a family within the class Actinobacteria.
Strain MM2LBT was isolated from a chironomid (Diptera;
Chironomidae) egg mass that was sampled from a waste stabilization pond in
northern Israel. In a phylogenetic tree based on 16S rRNA gene sequences, strain
MM2LBT formed a distinct branch within the radiation encompassing the
genus Leucobacter. Here we describe the features of this organism, together
with the complete genome sequence and annotation. The DNA GC content is 69.90%. The
chromosome length is 2,964,712 bp. It encodes 2,690 proteins and 61 RNA genes. L.
chironomi genome is part of the Genomic Encyclopedia of Type Strains, Phase
I: the one thousand microbial genomes (KMG) project.
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Affiliation(s)
- Sivan Laviad
- Dept. of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Alla Lapidus
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia ; Algorithmic Biology Lab. St. Petersburg Academic University, St. Petersburg, Russia
| | - Alex Copeland
- Dept. of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, USA
| | - Tbk Reddy
- Dept. of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, USA
| | - Marcel Huntemann
- Dept. of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, USA
| | - Amrita Pati
- Dept. of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, USA
| | - Natalia N Ivanova
- Dept. of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, USA
| | - Victor M Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Rüdiger Pukall
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- Dept. of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, USA
| | - Nikos C Kyrpides
- Dept. of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, USA ; Dept. of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Malka Halpern
- Dept. of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel ; Dept. of Biology and Environment, Faculty of Natural Sciences, University of Haifa, Oranim, Kiryat Tivon, Israel
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27
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Abstract
Leucobacter salsicius M1-8(T) is a member of the Microbacteriaceae family within the class Actinomycetales. This strain is a Gram-positive, rod-shaped bacterium and was previously isolated from a Korean fermented food. Most members of the genus Leucobacter are chromate-resistant and this feature could be exploited in biotechnological applications. However, the genus Leucobacter is poorly characterized at the genome level, despite its potential importance. Thus, the present study determined the features of Leucobacter salsicius M1-8(T), as well as its genome sequence and annotation. The genome comprised 3,185,418 bp with a G+C content of 64.5%, which included 2,865 protein-coding genes and 68 RNA genes. This strain possessed two predicted genes associated with chromate resistance, which might facilitate its growth in heavy metal-rich environments.
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Affiliation(s)
- Ji-Hyun Yun
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, South Korea
| | - Yong-Joon Cho
- ChunLab Inc., Seoul National University, Seoul, South Korea
| | - Jongsik Chun
- ChunLab Inc., Seoul National University, Seoul, South Korea
| | - Dong-Wook Hyun
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, South Korea
| | - Jin-Woo Bae
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, South Korea
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