1
|
Thite S, Tarwadge K, Mengade P, Lodha T, Joseph N, Thakkar L, Joshi A. Taxogenomics of Alkalihalobacterium chitinilyticum sp. nov.: an alkaliphilic chitin degrading bacterial strain isolated from Lonar Lake, India, with potential biotechnological applications. Antonie Van Leeuwenhoek 2023; 116:1103-1112. [PMID: 37615744 DOI: 10.1007/s10482-023-01872-7] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/09/2023] [Indexed: 08/25/2023]
Abstract
A novel chitin degrading alkaliphilic bacterial strain (MEB 203 T) was isolated from sediment collected from Lonar lake, India. The strain exhibited its maximum growth at a temperature of 37 °C, with an optimal pH of 10 and a NaCl concentration of 2%. 16S rRNA gene based phylogenetic tree showed that strain was closely related to Alkalihalobacterium elongatum MCC 2982 T (98.64% similarity) followed by A. alkalinitrilicum DSM 22532 T (97.84% similarity). The genome size was 4.9 Mb with DNA G + C content of 37.7%. The dDDH value between strain MEB 203 T and A. elongatum MCC 2982 T was 26.4 ± 2.4% while OrthoANI value was 82.1%. Genome analysis revealed the presence of genes responsible for L-ectoine and cation/proton antiporter which may facilitate growth of strain in alkaline-saline habitat of Lonar lake. Strain MEB 203 T was able to utilize complex sugars such as chitin, cellulose, and starch as a carbon source at alkaline conditions which was also corroborated from the genomic presence of carbohydrate active enzymes (CAZymes). It was also able to produce biotechnologically important enzymes such as lipases and proteases which were stable at pH (9-10). The bacterium is majorly composed of C15:0 iso, C16:0 iso, and C17:0 iso (> 10%) fatty acids while diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and unidentified phospholipid (PL3) were identified as the predominant polar lipids. Based on differential physiological, biochemical, and genomic features of strain MEB 203 T, a novel species Alkalihalobacterium chitinilyticum sp. nov. (Type strain MEB 203 T = MCC 3920 T = NCIMB 15407 T = JCM 35078 T) is proposed.
Collapse
Affiliation(s)
- Sonia Thite
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, Sai Trinity Complex, Sus Road, Pashan, Pune, Maharashtra, 411021, India
| | - Kamakshi Tarwadge
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, Sai Trinity Complex, Sus Road, Pashan, Pune, Maharashtra, 411021, India
| | - Purva Mengade
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, Sai Trinity Complex, Sus Road, Pashan, Pune, Maharashtra, 411021, India
| | - Tushar Lodha
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, Sai Trinity Complex, Sus Road, Pashan, Pune, Maharashtra, 411021, India
- Bioenergy Group, Agharkar Research Institute, Gopal Ganesh Agarkar Road, Pune, Maharashtra, 411004, India
| | - Neetha Joseph
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, Sai Trinity Complex, Sus Road, Pashan, Pune, Maharashtra, 411021, India
| | - Lucky Thakkar
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, Sai Trinity Complex, Sus Road, Pashan, Pune, Maharashtra, 411021, India
| | - Amaraja Joshi
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, Sai Trinity Complex, Sus Road, Pashan, Pune, Maharashtra, 411021, India.
| |
Collapse
|
2
|
Shi H, Ambika Manirajan B, Ratering S, Geissler-Plaum R, Schnell S. Robbsia betulipollinis sp. nov., Isolated from Pollen of Birch (Betula pendula). Curr Microbiol 2023; 80:234. [PMID: 37278851 DOI: 10.1007/s00284-023-03344-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 05/23/2023] [Indexed: 06/07/2023]
Abstract
One gram-negative strain designated Bb-Pol-6 T was isolated from birch (Betula pendula) pollen at Giessen area, Germany. The analysis of 16S rRNA gene-based phylogenies indicated the next-relative genera were Robbsia, Chitinasiproducens, Pararobbsia and Paraburkholderia (96-95.6%). Further comparative genome analysis and phylogenetic tree-based methods revealed its phylogenetic position under the genus Robbsia. The genome of strain Bb-Pol-6 T was 5.04 Mbp with 4401 predicted coding sequences and a G + C content of 65.31 mol%. Average amino acid identity, average nucleotide identity, digital DNA-DNA hybridization and percentage of conserved proteins values to Robbsia andropogonis DSM 9511 T were 68.0, 72.5, 22.7 and 65.85%, respectively. Strain Bb-Pol-6 T was rod-shaped, non-motile, facultative anaerobic and grew optimally at 28 °C and pH 6-7. Ubiquinone 8 was the major respiratory quinone and the major cellular fatty acids were C16:0, C19:0 cyclo ω7c, C17:0 cyclo ω7c and C17:1 ω6c. The dominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. Based on the genomic physiological and phenotypic characteristics, strain Bb-Pol-6 T was considered a novel species under the genus Robbsia, for which the name Robbsia betulipollinis sp. nov. was proposed. The type strain is Bb-Pol-6 T (= LMG 32774 T = DSM 114812 T).
Collapse
Affiliation(s)
- Haoran Shi
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig University Giessen, 35392, Giessen, Germany
| | - Binoy Ambika Manirajan
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig University Giessen, 35392, Giessen, Germany
- School of Biosciences, Mahatma Gandhi University, Kerala, India
| | - Stefan Ratering
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig University Giessen, 35392, Giessen, Germany.
| | - Rita Geissler-Plaum
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig University Giessen, 35392, Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Research Center for BioSystems, Land Use, and Nutrition (IFZ), Justus-Liebig University Giessen, 35392, Giessen, Germany
| |
Collapse
|
3
|
Korponai K, Szuróczki S, Márton Z, Szabó A, Morais PV, Proença DN, Tóth E, Boros E, Márialigeti K, Felföldi T. Habitat distribution of the genus Belliella in continental waters and the description of Belliella alkalica sp. nov., Belliella calami sp. nov. and Belliella filtrata sp. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 37326610 DOI: 10.1099/ijsem.0.005928] [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: 06/17/2023] Open
Abstract
The genus Belliella belongs to the family Cyclobacteriaceae (order Cytophagales, phylum Bacteroidota) and harbours aerobic chemoheterotrophic bacteria. Members of this genus were isolated from various aquatic habitats, and our analysis based on global amplicon sequencing data revealed that their relative abundance can reach up to 5-10 % of the bacterioplankton in soda lakes and pans. Although a remarkable fraction of the most frequent genotypes that we identified from continental aquatic habitats is still uncultured, five new alkaliphilic Belliella strains were characterized in detail in this study, which were isolated from three different soda lakes and pans of the Carpathian Basin (Hungary). Cells of all strains were Gram-stain-negative, obligate aerobic, rod-shaped, non-motile and non-spore-forming. The isolates were oxidase- and catalase-positive, red-coloured, but did not contain flexirubin-type pigments; they formed bright red colonies that were circular, smooth and convex. Their major isoprenoid quinone was MK-7 and the predominant fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 containing C16 : 1 ω6c and/or C16 : 1 ω7c. The polar lipid profiles contained phosphatidylethanolamine, an unidentified aminophospholipid, an unidentified glycolipid, and several unidentified lipids and aminolipids. Based on whole-genome sequences, the DNA G+C content was 37.0, 37.1 and 37.8 mol % for strains R4-6T, DMA-N-10aT and U6F3T, respectively. The distinction of three new species was confirmed by in silico genomic comparison. Orthologous average nucleotide identity (<85.4 %) and digital DNA-DNA hybridization values (<38.9 %) supported phenotypic, chemotaxonomic and 16S rRNA gene sequence data and, therefore, the following three novel species are proposed: Belliella alkalica sp. nov. (represented by strains R4-6T=DSM 111903T=JCM 34281T=UCCCB122T and S4-10), Belliella calami sp. nov. (DMA-N-10aT=DSM 107340T=JCM 34280T=UCCCB121T) and Belliella filtrata sp. nov. (U6F3T=DSM 111904T=JCM 34282T=UCCCB123T and U6F1). Emended descriptions of species Belliella aquatica, Belliella baltica, Belliella buryatensis, Belliella kenyensis and Belliella pelovolcani are also presented.
Collapse
Affiliation(s)
- Kristóf Korponai
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
- Agricultural Institute, Centre for Agricultural Research, Brunszvik utca 2, 2462 Martonvásár, Hungary
| | - Sára Szuróczki
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
| | - Zsuzsanna Márton
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
- Institute of Aquatic Ecology, Centre for Ecological Research, Karolina út 29, 1113 Budapest, Hungary
| | - Attila Szabó
- Institute of Aquatic Ecology, Centre for Ecological Research, Karolina út 29, 1113 Budapest, Hungary
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Lennart Hjelms Vag 9, 750 07 Uppsala, Sweden
| | - Paula V Morais
- Department of Life Sciences, Centre for Mechanical Engineering, Materials and Processes, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Diogo Neves Proença
- Department of Life Sciences, Centre for Mechanical Engineering, Materials and Processes, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Erika Tóth
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
| | - Emil Boros
- Institute of Aquatic Ecology, Centre for Ecological Research, Karolina út 29, 1113 Budapest, Hungary
| | - Károly Márialigeti
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
| | - Tamás Felföldi
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
- Institute of Aquatic Ecology, Centre for Ecological Research, Karolina út 29, 1113 Budapest, Hungary
| |
Collapse
|
4
|
Cuellar-Gaviria TZ, García-Botero C, Ju KS, Villegas-Escobar V. The genome of Bacillus tequilensis EA-CB0015 sheds light into its epiphytic lifestyle and potential as a biocontrol agent. Front Microbiol 2023; 14:1135487. [PMID: 37051516 PMCID: PMC10083409 DOI: 10.3389/fmicb.2023.1135487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 03/06/2023] [Indexed: 03/29/2023] Open
Abstract
Different Bacillus species have successfully been used as biopesticides against a broad range of plant pathogens. Among these, Bacillus tequilensis EA-CB0015 has shown to efficiently control Black sigatoka disease in banana plants, presumably by mechanisms of adaptation that involve modifying the phyllosphere environment. Here, we report the complete genome of strain EA-CB0015, its precise taxonomic identity, and determined key genetic features that may contribute to its effective biocontrol of plant pathogens. We found that B. tequilensis EA-CB0015 harbors a singular 4 Mb circular chromosome, with 3,951 protein-coding sequences. Multi-locus sequence analysis (MLSA) and average nucleotide identity (ANI) analysis classified strain EA-CB0015 as B. tequilensis. Encoded within its genome are biosynthetic gene clusters (BGCs) for surfactin, iturin, plipastatin, bacillibactin, bacilysin, subtilosin A, sporulation killing factor, and other natural products that may facilitate inter-microbial warfare. Genes for indole-acetic acid (IAA) synthesis, the use of diverse carbon sources, and a multicellular lifestyle involving motility, biofilm formation, quorum sensing, competence, and sporulation suggest EA-CB0015 is adept at colonizing plant surfaces. Defensive mechanisms to survive invading viral infections and preserve genome integrity include putative type I and type II restriction modification (RM) and toxin/antitoxin (TA) systems. The presence of bacteriophage sequences, genomic islands, transposable elements, virulence factors, and antibiotic resistance genes indicate prior occurrences of genetic exchange. Altogether, the genome of EA-CB0015 supports its function as a biocontrol agent against phytopathogens and suggest it has adapted to thrive within phyllosphere environments.
Collapse
Affiliation(s)
- Tatiana Z. Cuellar-Gaviria
- CIBIOP Group, Department of Biological Sciences, Universidad EAFIT, Medellin, Colombia
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
- Banana Research Center, Augura, Conjunto Residencial Los Almendros, Carepa, Colombia
| | - Camilo García-Botero
- CIBIOP Group, Department of Biological Sciences, Universidad EAFIT, Medellin, Colombia
| | - Kou-San Ju
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, Columbus, OH, United States
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, United States
- Infectious Diseases Institute, The Ohio State University, Columbus, OH, United States
- *Correspondence: Kou-San Ju, ; Valeska Villegas-Escobar,
| | - Valeska Villegas-Escobar
- CIBIOP Group, Department of Biological Sciences, Universidad EAFIT, Medellin, Colombia
- *Correspondence: Kou-San Ju, ; Valeska Villegas-Escobar,
| |
Collapse
|
5
|
Taylor M, Janasky L, Vega N. Convergent structure with divergent adaptations in combinatorial microbiome communities. FEMS Microbiol Ecol 2022; 98:6726631. [PMID: 36170949 DOI: 10.1093/femsec/fiac115] [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: 06/13/2022] [Revised: 09/13/2022] [Accepted: 09/26/2022] [Indexed: 01/21/2023] Open
Abstract
Adaptation of replicate microbial communities frequently produces shared trajectories of community composition and structure. However, divergent adaptation of individual community members can occur and is associated with community-level divergence. The extent to which community-based adaptation of microbes should be convergent when community members are similar but not identical is, therefore, not well-understood. In these experiments, adaptation of combinatorial minimal communities of bacteria with the model host Caenorhabditis elegans produces structurally similar communities over time, but with divergent adaptation of member taxa and differences in community-level resistance to invasion. These results indicate that community-based adaptation from taxonomically similar starting points can produce compositionally similar communities that differ in traits of member taxa and in ecological properties.
Collapse
Affiliation(s)
- Megan Taylor
- Biology Department, Emory University, Atlanta, GA, 30322, United States
| | - Lili Janasky
- Biology Department, Emory University, Atlanta, GA, 30322, United States
| | - Nic Vega
- Biology Department, Emory University, Atlanta, GA, 30322, United States.,Physics Department, Emory University, Atlanta, GA, 30322, United States
| |
Collapse
|
6
|
Kurniyati K, Chang Y, Liu J, Li C. Identification and Characterization of the Alternative σ(28) Factor in Treponema denticola. J Bacteriol 2022; 204:e0024822. [PMID: 36043861 DOI: 10.1128/jb.00248-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
FliA (also known as σ28), a member of the bacterial σ70 family of transcription factors, directs RNA polymerase to flagellar late (class 3) promoters and initiates transcription. FliA has been studied in several bacteria, yet its role in spirochetes has not been established. In this report, we identify and functionally characterize a FliA homolog (TDE2683) in the oral spirochete Treponema denticola. Computational, genetic, and biochemical analyses demonstrated that TDE2683 has a structure similar to that of the σ28 of Escherichia coli, binds to σ28-dependent promoters, and can functionally replace the σ28 of E. coli. However, unlike its counterparts from other bacteria, TDE2683 cannot be deleted, suggesting its essential role in the survival of T. denticola. In vitro site-directed mutagenesis revealed that E221 and V231, two conserved residues in the σ4 region of σ28, are indispensable for the binding activity of TDE2683 to the σ28-dependent promoter. We then mutated these two residues in T. denticola and found that the mutations impair the expression of flagellin and chemotaxis genes and bacterial motility as well. Cryo-electron tomography analysis further revealed that the mutations disrupt the flagellar symmetry (i.e., number and placement) of T. denticola. Collectively, these results indicate that TDE2683 is a σ28 transcription factor that regulates the class 3 gene expression and controls the flagellar symmetry of T. denticola. To the best of our knowledge, this is the first report establishing the functionality of FliA in spirochetes. IMPORTANCE Spirochetes are a group of medically important but understudied bacteria. One of the unique aspects of spirochetes is that they have periplasmic flagella (PF, also known as endoflagella) which give rise to their unique spiral shape and distinct swimming behaviors and play a critical role in the pathophysiology of spirochetes. PF are structurally similar to external flagella, but the underpinning mechanism that regulates PF biosynthesis and assembly remains largely unknown. By using the oral spirochete Treponema denticola as a model, this report provides several lines of evidence that FliA, a σ28 transcriptional factor, regulates the late flagellin gene (class 3) expression, PF assembly, and flagellar symmetry as well, which provides insights into flagellar regulation and opens an avenue to investigate the role of σ28 in spirochetes.
Collapse
|
7
|
Chauhan NS, Joseph N, Shaligram S, Chavan N, Joshi A, Dhotre D, Lodha T, Shouche Y. Paenibacillus oleatilyticus sp. nov., isolated from soil. Arch Microbiol 2022; 204:516. [DOI: 10.1007/s00203-022-03116-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 11/24/2022]
|
8
|
Leonard H, Jiang X, Arshavsky-Graham S, Holtzman L, Haimov Y, Weizman D, Halachmi S, Segal E. Shining light in blind alleys: deciphering bacterial attachment in silicon microstructures. Nanoscale Horiz 2022; 7:729-742. [PMID: 35616534 DOI: 10.1039/d2nh00130f] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
With new advances in infectious disease, antifouling surfaces, and environmental microbiology research comes the need to understand and control the accumulation and attachment of bacterial cells on a surface. Thus, we employ intrinsic phase-shift reflectometric interference spectroscopic measurements of silicon diffraction gratings to non-destructively observe the interactions between bacterial cells and abiotic, microstructured surfaces in a label-free and real-time manner. We conclude that the combination of specific material characteristics (i.e., substrate surface charge and topology) and characteristics of the bacterial cells (i.e., motility, cell charge, biofilm formation, and physiology) drive bacteria to adhere to a particular surface, often leading to a biofilm formation. Such knowledge can be exploited to predict antibiotic efficacy and biofilm formation, and enhance surface-based biosensor development, as well as the design of anti-biofouling strategies.
Collapse
Affiliation(s)
- Heidi Leonard
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 3200003, Israel.
| | - Xin Jiang
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 3200003, Israel.
| | - Sofia Arshavsky-Graham
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 3200003, Israel.
| | - Liran Holtzman
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 3200003, Israel.
| | - Yuri Haimov
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 3200003, Israel.
| | - Daniel Weizman
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 3200003, Israel.
| | - Sarel Halachmi
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
- Department of Urology, Bnai Zion Medical Center, Haifa, 3104800, Israel
| | - Ester Segal
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 3200003, Israel.
| |
Collapse
|
9
|
Riborg A, Colquhoun DJ, Gulla S. Biotyping reveals loss of motility in two distinct Yersinia ruckeri lineages exclusive to Norwegian aquaculture. J Fish Dis 2022; 45:641-653. [PMID: 35180320 PMCID: PMC9304254 DOI: 10.1111/jfd.13590] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 05/26/2023]
Abstract
Non-motile strains of Yersinia ruckeri, known as Y. ruckeri biotype 2, now dominate amongst clinical isolates retrieved from rainbow trout internationally. Due to an acute increase in the number of yersiniosis cases in Norway in recent years, followed by introduction of widespread intraperitoneal vaccination against the disease, an investigation on the prevalence of Y. ruckeri biotype 2 in Norwegian aquaculture was conducted. We biotyped 263 Y. ruckeri isolates recovered from diseased salmonids in Norway between 1985 and 2020. A total of seven biotype 2 isolates were identified, four of which were collected between 1985 and 1987, and three of which belong to the current epizootic clone, isolated from two different sea-farms in 2017. Whole-genome sequencing revealed single non-synonymous nucleotide polymorphisms in the flagellar genes flhC in isolates from the 1980s, and in fliP in isolates from 2017. In both variants, motility was restored both by complementation with wild-type alleles in trans and via spontaneous mutation-driven reversion following prolonged incubation on motility agar. While biotype 2 strains do not yet seem to have become broadly established in Norwegian aquaculture, the seven isolates described here serve to document a further two independent cases of Y. ruckeri biotype 2 emergence in salmonid aquaculture.
Collapse
Affiliation(s)
- Andreas Riborg
- Norwegian Veterinary InstituteÅsNorway
- Vaxxinova Norway ASBergenNorway
| | | | | |
Collapse
|
10
|
Abstract
A Gram-stain-negative, aerobic, yellow-pigmented and non-motile rod-shaped bacterium, designated as GrpM-11T, was isolated from coastal seawater collected from the East Sea, Republic of Korea. Strain GrpM-11T could grow at 10-40 °C (optimum, 35 °C), at pH 5.5-9.5 (optimum, pH 7.0) and in the presence of 0-8 % (w/v) NaCl (optimum, 3-4 %). Cells hydrolysed aesculin, gelatin and casein, but could not reduce nitrate to nitrite. The 16S rRNA gene sequence analysis showed that this strain formed a distinct phylogenic lineage with Parasphingopyxis algicola ATAX6-5T (96.2 % sequence identity) and Parasphingopyxis lamellibrachiae DSM 26725T (96.2 % identity) and belonged to the genus Parasphingopyxis. The predominant isoprenoid quinone was ubiquinone-10. The polar lipid profile of strain GrpM-11T consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid and three unknown glycolipids. Cellular fatty acid analysis indicated that summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c; 42.8 %), C16 : 0 (19.0 %), C18 : 1 ω7c 11-methyl (13.3 %) and C18 : 1 ω7c (8.0 %) were the major fatty acids. The DNA G+C content of strain GrpM-11T was 63.7 mol%. Through whole genome sequence comparisons, the digital DNA-DNA hybridization and average nucleotide identity values between strain GrpM-11T and two species of the genus Parasphingopyxis were revealed to be in the ranges of 19.0-22.0 % and 76.3-79.7 %, respectively. Based on the results of polyphasic analysis, strain GrpM-11T represents a novel species of the genus Parasphingopyxis, for which the name Parasphingopyxis marina sp. nov. is proposed. The type strain is GrpM-11T (KCCM 43343T=JCM 34665T).
Collapse
Affiliation(s)
- Soo-Yeon Choi
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju 28644, Chungbuk, Republic of Korea
| | - Ji-Sung Oh
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju 28644, Chungbuk, Republic of Korea
| | - Dong-Hyun Roh
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju 28644, Chungbuk, Republic of Korea
| |
Collapse
|
11
|
Reuter M, Ultee E, Toseafa Y, Tan A, van Vliet AHM. Inactivation of the core cheVAWY chemotaxis genes disrupts chemotactic motility and organised biofilm formation in Campylobacter jejuni. FEMS Microbiol Lett 2021; 367:6017310. [PMID: 33264398 DOI: 10.1093/femsle/fnaa198] [Citation(s) in RCA: 5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 11/30/2020] [Indexed: 12/13/2022] Open
Abstract
Flagellar motility plays a central role in the bacterial foodborne pathogen Campylobacter jejuni, as flagellar motility is required for reaching the intestinal epithelium and subsequent colonisation or disease. Flagellar proteins also contribute strongly to biofilm formation during transmission. Chemotaxis is the process directing flagellar motility in response to attractant and repellent stimuli, but its role in biofilm formation of C. jejuni is not well understood. Here we show that inactivation of the core chemotaxis genes cheVAWY in C. jejuni strain NCTC 11168 affects both chemotactic motility and biofilm formation. Inactivation of any of the core chemotaxis genes (cheA, cheY, cheV or cheW) impaired chemotactic motility but did not affect flagellar assembly or growth. The ∆cheY mutant swam in clockwise loops, while complementation restored normal motility. Inactivation of the core chemotaxis genes interfered with the ability to form a discrete biofilm at the air-media interface, and the ∆cheY mutant displayed reduced dispersal/shedding of bacteria into the planktonic fraction. This suggests that while the chemotaxis system is not required for biofilm formation per se, it is necessary for organized biofilm formation. Hence interference with the Campylobacter chemotaxis system at any level disrupts optimal chemotactic motility and transmission modes such as biofilm formation.
Collapse
Affiliation(s)
- Mark Reuter
- Gut Health and Food Safety Programme, Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Eveline Ultee
- Gut Health and Food Safety Programme, Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Yasmin Toseafa
- Gut Health and Food Safety Programme, Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Andrew Tan
- Gut Health and Food Safety Programme, Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Arnoud H M van Vliet
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Daphne Jackson Road, Guildford GU2 7AL, UK
| |
Collapse
|
12
|
Hook JC, Blagotinsek V, Pané-Farré J, Mrusek D, Altegoer F, Dornes A, Schwan M, Schier L, Thormann KM, Bange G. A Proline-Rich Element in the Type III Secretion Protein FlhB Contributes to Flagellar Biogenesis in the Beta- and Gamma-Proteobacteria. Front Microbiol 2020; 11:564161. [PMID: 33384667 PMCID: PMC7771051 DOI: 10.3389/fmicb.2020.564161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 05/20/2020] [Accepted: 10/26/2020] [Indexed: 11/24/2022] Open
Abstract
Flagella are bacterial organelles of locomotion. Their biogenesis is highly coordinated in time and space and relies on a specialized flagellar type III secretion system (fT3SS) required for the assembly of the extracellular hook, rod, and filament parts of this complex motor device. The fT3SS protein FlhB switches secretion substrate specificity once the growing hook reaches its determined length. Here we present the crystal structure of the cytoplasmic domain of the transmembrane protein FlhB. The structure visualizes a so-far unseen proline-rich region (PRR) at the very C-terminus of the protein. Strains lacking the PRR show a decrease in flagellation as determined by hook- and filament staining, indicating a role of the PRR during assembly of the hook and filament structures. Phylogenetic analysis shows that the PRR is a primary feature of FlhB proteins of flagellated beta- and gamma-proteobacteria. Taken together, our study adds another layer of complexity and organismic diversity to the process of flagella biogenesis.
Collapse
Affiliation(s)
- John C Hook
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität, Giessen, Germany
| | - Vitan Blagotinsek
- SYNMIKRO Research Center, Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Jan Pané-Farré
- SYNMIKRO Research Center, Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Devid Mrusek
- SYNMIKRO Research Center, Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Florian Altegoer
- SYNMIKRO Research Center, Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Anita Dornes
- SYNMIKRO Research Center, Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Meike Schwan
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität, Giessen, Germany
| | - Lukas Schier
- SYNMIKRO Research Center, Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Kai M Thormann
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität, Giessen, Germany
| | - Gert Bange
- SYNMIKRO Research Center, Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| |
Collapse
|
13
|
Molina-Menor E, Gimeno-Valero H, Pascual J, Peretó J, Porcar M. Kineococcus vitellinus sp. nov., Kineococcus indalonis sp. nov. and Kineococcus siccus sp. nov., Isolated Nearby the Tabernas Desert (Almería, Spain). Microorganisms 2020; 8:E1547. [PMID: 33036385 PMCID: PMC7601052 DOI: 10.3390/microorganisms8101547] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/25/2020] [Accepted: 10/02/2020] [Indexed: 11/16/2022] Open
Abstract
Three novel Gram-positive, aerobic, chemoheterotrophic, motile, non-endospore-forming, orange-pigmented bacteria designated strains T13T, T90T and R8T were isolated from the Tabernas Desert biocrust (Almería, Spain). Cells of the three strains were coccus-shaped and occurred singly, in pairs or clusters. The three strains were oxidase-negative and catalase-positive, and showed a mesophilic, neutrophilic and non-halophilic metabolism. Based on the 16S rRNA gene sequences, the closest neighbours of strains T13T, T90T and R8T were Kineococcus aurantiacus IFO 15268T, Kineococcus gypseus YIM 121300T and Kineococcus radiotolerans SRS 30216T (98.5%, 97.1% and 97.9% gene sequence similarity, respectively). The genomes were sequenced, and have been deposited in the GenBank/EMBL/DDBJ databases under the accession numbers JAAALL000000000, JAAALM000000000 and JAAALN000000000, respectively, for strains T13T, T90T and R8T. The average nucleotide identity (ANIb) and digital DNA-DNA hybridization (dDDH) values confirmed their adscription to three new species within the genus Kineococcus. The genomic G + C content of strains T13T, T90T and R8T ranged from 75.1% to 76.3%. The predominant fatty acid of all three strains was anteiso-C15:0. According to a polyphasic study, strains T13T, T90T and R8T are representatives of three new species in the genus Kineococcus, for which names Kineococcus vitellinus sp. nov. (type strain T13T = CECT 9936T = DSM 110024T), Kineococcus indalonis sp. nov. (type strain T90T = CECT 9938T = DSM 110026T) and Kineococcus siccus sp. nov. (type strain R8T = CECT 9937T = DSM 110025T) are proposed.
Collapse
Affiliation(s)
- Esther Molina-Menor
- Institute for Integrative Systems Biology I2SysBio (Universitat de València-CSIC), Calle del Catedràtic Agustin Escardino Benlloch 9, 46980 Paterna, Spain; (E.M.-M.); (J.P.)
| | - Helena Gimeno-Valero
- Darwin Bioprospecting Excellence SL. Parc Científic Universitat de València, Calle del Catedràtic Agustin Escardino Benlloch 9, 46980 Paterna, Spain; (H.G.-V.); (J.P.)
| | - Javier Pascual
- Darwin Bioprospecting Excellence SL. Parc Científic Universitat de València, Calle del Catedràtic Agustin Escardino Benlloch 9, 46980 Paterna, Spain; (H.G.-V.); (J.P.)
| | - Juli Peretó
- Institute for Integrative Systems Biology I2SysBio (Universitat de València-CSIC), Calle del Catedràtic Agustin Escardino Benlloch 9, 46980 Paterna, Spain; (E.M.-M.); (J.P.)
- Darwin Bioprospecting Excellence SL. Parc Científic Universitat de València, Calle del Catedràtic Agustin Escardino Benlloch 9, 46980 Paterna, Spain; (H.G.-V.); (J.P.)
- Departament de Bioquimica i Biologia Molecular, Universitat de València, Calle del Dr. Moliner 50, 46100 Burjassot, Spain
| | - Manuel Porcar
- Institute for Integrative Systems Biology I2SysBio (Universitat de València-CSIC), Calle del Catedràtic Agustin Escardino Benlloch 9, 46980 Paterna, Spain; (E.M.-M.); (J.P.)
- Darwin Bioprospecting Excellence SL. Parc Científic Universitat de València, Calle del Catedràtic Agustin Escardino Benlloch 9, 46980 Paterna, Spain; (H.G.-V.); (J.P.)
| |
Collapse
|
14
|
Blagotinsek V, Schwan M, Steinchen W, Mrusek D, Hook JC, Rossmann F, Freibert SA, Kratzat H, Murat G, Kressler D, Beckmann R, Beeby M, Thormann KM, Bange G. An ATP-dependent partner switch links flagellar C-ring assembly with gene expression. Proc Natl Acad Sci U S A 2020; 117:20826-35. [PMID: 32788349 DOI: 10.1073/pnas.2006470117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Bacterial flagella differ in their number and spatial arrangement. In many species, the MinD-type ATPase FlhG (also YlxH/FleN) is central to the numerical control of bacterial flagella, and its deletion in polarly flagellated bacteria typically leads to hyperflagellation. The molecular mechanism underlying this numerical control, however, remains enigmatic. Using the model species Shewanella putrefaciens, we show that FlhG links assembly of the flagellar C ring with the action of the master transcriptional regulator FlrA (named FleQ in other species). While FlrA and the flagellar C-ring protein FliM have an overlapping binding site on FlhG, their binding depends on the ATP-dependent dimerization state of FlhG. FliM interacts with FlhG independent of nucleotide binding, while FlrA exclusively interacts with the ATP-dependent FlhG dimer and stimulates FlhG ATPase activity. Our in vivo analysis of FlhG partner switching between FliM and FlrA reveals its mechanism in the numerical restriction of flagella, in which the transcriptional activity of FlrA is down-regulated through a negative feedback loop. Our study demonstrates another level of regulatory complexity underlying the spationumerical regulation of flagellar biogenesis and implies that flagellar assembly transcriptionally regulates the production of more initial building blocks.
Collapse
|
15
|
Lu YJ, Morimoto Y, Tohya M, Hishinuma T, Hiramatsu K, Kirikae T, Baba T. Pseudomonas izuensis sp. nov., a novel species isolated from Izu Oshima, Japan. Int J Syst Evol Microbiol 2020; 70:4212-4216. [PMID: 32553034 DOI: 10.1099/ijsem.0.004271] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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
An aerobic, Gram-stain-negative, rod-shaped bacterial strain, IzPS43_3003T, was isolated from Izu Oshima, an active volcanic island located 22 km east of the Izu Peninsula, Japan. The sequence of its 16S rRNA gene indicated that IzPS43_3003T belongs to the Pseudomonas fluorescens lineage, with its sequence being most similar to that of Pseudomonas vancouverensis DhA-51T (99.79 %). Phylogenetic analysis based on whole genome sequences showed that IzPS43_3003T was a member of the Pseudomonas jessenii subgroup. The average nucleotide identity values and genome-to genome distances between the whole genome sequences of IzPS43_3003T and other type strains showed that the highest correlations were with Pseudomonas moorei DSM 12647T (87.3 and 33.5% respectively). These genotypic and phenotypic analyses indicated that IzPS43_3003T belongs to a novel species, Pseudomonas izuensis sp. nov. Its type strain is IzPS43_3003T (=LMG 31527T,=CECT 9963T).
Collapse
Affiliation(s)
- Yu Jie Lu
- Center of Excellence for Infection Control Science, Graduate School of Medicine, Juntendo University, 2-1-1 Hongo Bunkyo-ku Tokyo, Japan
| | - Yuh Morimoto
- Center of Excellence for Infection Control Science, Graduate School of Medicine, Juntendo University, 2-1-1 Hongo Bunkyo-ku Tokyo, Japan
| | - Mari Tohya
- Department of Microbiology, Faculty of Medicine, Juntendo University, 2-1-1 Hongo Bunkyo-ku Tokyo, Japan
| | - Tomomi Hishinuma
- Department of Microbiology, Faculty of Medicine, Juntendo University, 2-1-1 Hongo Bunkyo-ku Tokyo, Japan
| | - Keiichi Hiramatsu
- Center of Excellence for Infection Control Science, Graduate School of Medicine, Juntendo University, 2-1-1 Hongo Bunkyo-ku Tokyo, Japan
| | - Teruo Kirikae
- Department of Microbiology, Faculty of Medicine, Juntendo University, 2-1-1 Hongo Bunkyo-ku Tokyo, Japan
| | - Tadashi Baba
- Center of Excellence for Infection Control Science, Graduate School of Medicine, Juntendo University, 2-1-1 Hongo Bunkyo-ku Tokyo, Japan
| |
Collapse
|
16
|
Lucena T, Arahal DR, Sanz-Sáez I, Acinas SG, Sánchez O, Aznar R, Pedrós-Alió C, Pujalte MJ. Thalassocella blandensis gen. nov., sp. nov., a novel member of the family Cellvibrionaceae. Int J Syst Evol Microbiol 2020; 70:1231-1239. [PMID: 31793854 DOI: 10.1099/ijsem.0.003906] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [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
Strain ISS155T, isolated from surface Mediterranean seawater, has cells that are Gram-reaction-negative, motile, strictly aerobic chemoorganotrophic, oxidase-positive, unable to reduce nitrate to nitrite, and able to grow with cellulose as the sole carbon and energy source. It is mesophilic, neutrophilic, slightly halophilic and has a requirement for sodium and magnesium ions. Its 16S rRNA gene sequence places the strain among members of Cellvibrionaceae, in the Gammaproteobacteria, with Agarilytica rhodophyticola 017T as closest relative (94.3 % similarity). Its major cellular fatty acids are C18 : 1, C16 : 0 and C16 : 1; major phospholipids are phosphatidyl glycerol, phosphatidyl ethanolamine and an unidentified lipid, and the major respiratory quinone is Q8. The genome size is 6.09 Mbp and G+C content is 45.2 mol%. A phylogenomic analysis using UBCG merges strain ISS155T in a clade with A. rhodophyticola, Teredinibacter turnerae, Saccharophagus degradans and Agaribacterium haliotis type strain genomes, all of them possessing a varied array of carbohydrate-active enzymes and the potential for polysaccharide degradation. Average amino acid identity indexes determined against available Cellvibrionaceae type strain genomes show that strain ISS155T is related to them by values lower than 60 %, with a maximum of 58 % to A. rhodophyticola 017T and 57 % to T. turnerae T7902T and S. degradans 2-40T. These results, together with the low 16S rRNA gene sequence similarities and differences in phenotypic profiles, indicate that strain ISS155T represents a new genus and species in Cellvibrionaceae, for which we propose the name Thalassocella blandensis gen. nov., sp. nov., and strain ISS155T (=CECT 9533T=LMG 31237T) as the type strain.
Collapse
Affiliation(s)
- Teresa Lucena
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain
| | - David R Arahal
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain
| | - Isabel Sanz-Sáez
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Spain
| | - Silvia G Acinas
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Spain
| | - Olga Sánchez
- Departament de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Rosa Aznar
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain
| | - Carlos Pedrós-Alió
- Department of Systems Biology, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - María J Pujalte
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain
| |
Collapse
|
17
|
Albuquerque L, Castelhano N, Raposo P, Froufe HJC, Tiago I, Severino R, Roxo I, Gregório I, Barroso C, Egas C, da Costa MS. Comparative genome sequence analysis of several species in the genus Tepidimonas and the description of a novel species Tepidimonas charontis sp. nov. Int J Syst Evol Microbiol 2020; 70:1596-1604. [PMID: 32228748 PMCID: PMC7386788 DOI: 10.1099/ijsem.0.003942] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/22/2019] [Accepted: 12/06/2019] [Indexed: 11/18/2022] Open
Abstract
We performed high-quality genome sequencing of eight strains of the species of the genus Tepidimonas and examined the genomes of closely related strains from the databases to understand why Tepidimonas taiwanensis is the only strain of this genus that utilizes glucose and fructose for growth. We found that the assimilation of these hexoses by T. taiwanensis was due to the presence of two transporters that are absent in all other genomes of strains of members of the genus Tepidimonas examined. Some strains lack genes coding for glucokinase, but the Embden-Meyerhof-Parnas pathway appears to be otherwise complete. The pentose phosphate pathway has a complete set of genes, but genes of the Entner-Doudoroff pathway were not identified in the genomes of any of the strains examined. Genome analysis using average nucleotide identity (ANIb), digital DNA-DNA hybridization (dDDH), average amino acid identity (AAI) and phylogenetic analysis of 400 conserved genes was performed to assess the taxonomic classification of the organisms. Two isolates of the genus Tepidimonas from the hot spring at São Pedro do Sul, Portugal, designated SPSP-6T and SPSPC-18 were also examined in this study. These organisms are mixotrophic, have an optimum growth temperature of about 50 ºC, utilize several organic acids and amino acids for growth but do not grow on sugars. Distinctive phenotypic, 16S rRNA gene sequence and genomic characteristics of strains SPSP-6T and SPSPC-18 lead us to propose a novel species based on strain SPSP-6T for which we recommend the name Tepidimonas charontis sp. nov. (=CECT 9683T=LMG 30884T).
Collapse
Affiliation(s)
- Luciana Albuquerque
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Nadine Castelhano
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Pedro Raposo
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Hugo J. C. Froufe
- Next Generation Sequencing Unit, Biocant, BiocantPark, Núcleo 04, Lote 8, 3060-197 Cantanhede, Portugal
| | - Igor Tiago
- Center for Functional Ecology, University of Coimbra, 3000-456, Coimbra, Portugal
| | - Rita Severino
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Inês Roxo
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Inês Gregório
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Cristina Barroso
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
- Next Generation Sequencing Unit, Biocant, BiocantPark, Núcleo 04, Lote 8, 3060-197 Cantanhede, Portugal
| | - Conceição Egas
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
- Next Generation Sequencing Unit, Biocant, BiocantPark, Núcleo 04, Lote 8, 3060-197 Cantanhede, Portugal
| | - Milton S. da Costa
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| |
Collapse
|
18
|
Joshi A, Thite S, Dhotre D, Moorthy M, Joseph N, Ramana VV, Shouche Y. Nitrincola tapanii sp. nov., a novel alkaliphilic bacterium from An Indian Soda Lake. Int J Syst Evol Microbiol 2019; 70:1106-1111. [PMID: 31751193 DOI: 10.1099/ijsem.0.003883] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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 novel Gram-stain-negative bacterial strain designated as MEB193T was isolated from a sediment sample collected from Lonar Lake, India. The cells were motile, non-spore-forming and rod-shaped. The strain was oxidase- and catalase-positive. It grew optimally at pH 9.0 and at 1 % (w/v) NaCl concentration at 30 °C. Based on 16S rRNA gene sequence similarity, MEB193T belongs to genus Nitrincola, with Nitrincola alkalilacustris ZV-19T (95.89 %) and Nitrincola lacisaponensis 4CAT (95.87 %) as its closest neighbours. The major fatty acid was summed feature 8 comprising C18:1ω7c/C18:1ω6c (52 %) followed by C16 : 0 (25 %). Phosphatidylglycerol (PG) and diphosphatidylglycerol (DPG) were present as the major polar lipids. The draft genome obtained in this study was 2 793 747 bp and the G+C content was 50.79 mol%. Average nucleotide identity (71.76 %) and DNA-DNA hybridization (<20 %) values between strain MEB193T and Nitrincola lacisaponensis 4CAT confirmed the novelty of this new species. Based on phenotypic including chemotaxonomic and genotypic characterization data, strain MEB193T represents a new species of the genus Nitrincola for which the name Nitrincola tapanii sp. nov. is proposed. The type strain is MEB193T (=MCC 2863T=JCM 31570 T=KCTC 52390 T).
Collapse
Affiliation(s)
- Amaraja Joshi
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, Sai Trinity Complex, Sus road, Pashan, Pune, 411021, Maharashtra, India
| | - Sonia Thite
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, Sai Trinity Complex, Sus road, Pashan, Pune, 411021, Maharashtra, India
| | - Dhiraj Dhotre
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, Sai Trinity Complex, Sus road, Pashan, Pune, 411021, Maharashtra, India
| | - Manju Moorthy
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, Sai Trinity Complex, Sus road, Pashan, Pune, 411021, Maharashtra, India
| | - Neetha Joseph
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, Sai Trinity Complex, Sus road, Pashan, Pune, 411021, Maharashtra, India
| | - V Venkata Ramana
- Present address: Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh - 160036, India.,National Centre for Microbial Resource (NCMR), National Centre for Cell Science, Sai Trinity Complex, Sus road, Pashan, Pune, 411021, Maharashtra, India
| | - Yogesh Shouche
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, Sai Trinity Complex, Sus road, Pashan, Pune, 411021, Maharashtra, India
| |
Collapse
|
19
|
Felföldi T, Szabó A, Tóth E, Schumann P, Kéki Z, Márialigeti K, Máthé I. Sapientia aquatica gen. nov., sp. nov., isolated from a crater lake. Int J Syst Evol Microbiol 2019; 70:346-351. [PMID: 31592761 DOI: 10.1099/ijsem.0.003761] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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 new aerobic betaproteobacterium, strain SA-152T, was isolated from the water of a crater lake. 16S rRNA gene sequence analysis revealed that strain SA-152T belonged to the family Oxalobacteraceae (order Burkholderiales) and was phylogenetically related to Solimicrobium silvestre S20-91T with 97.09 % and to Herminiimonas arsenicoxydans ULPAs1T with 96.00 % 16S rRNA gene pairwise sequence similarity. Cells of strain SA-152T were rod-shaped, non-motile, oxidase-negative and catalase-positive. Its fatty acid profile was dominated by two fatty acids, C16 : 1 ω7c and C16 : 0, the major respiratory quinones were Q-8 and Q-7, and the main polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The G+C content of the genomic DNA of strain SA-152T was 48.3 mol%. The new bacterium can be distinguished from closely related genera Solimicrobium, Herminiimonas, Rugamonas and Undibacterium based on its non-motile and oxidase-negative cells. On the basis of the phenotypic, chemotaxonomic and genomic data, strain SA-152T is considered to represent a novel species of a new genus, for which the name Sapientia aquatica gen. nov., sp. nov. is proposed. The type strain of Sapientia aquatica is SA-152T (=DSM 29805T=NCAIM B.02613T).
Collapse
Affiliation(s)
- Tamás Felföldi
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary.,Department of Bioengineering, Sapientia Hungarian University of Transylvania, Piaţa Libertăţii 1, 530104 Miercurea Ciuc, Romania
| | - Attila Szabó
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - Erika Tóth
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - Peter Schumann
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Zsuzsa Kéki
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - Károly Márialigeti
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - István Máthé
- Department of Bioengineering, Sapientia Hungarian University of Transylvania, Piaţa Libertăţii 1, 530104 Miercurea Ciuc, Romania
| |
Collapse
|
20
|
Keshavarz-Tohid V, Vacheron J, Dubost A, Prigent-Combaret C, Taheri P, Tarighi S, Taghavi SM, Moënne-Loccoz Y, Muller D. Genomic, phylogenetic and catabolic re-assessment of the Pseudomonas putida clade supports the delineation of Pseudomonas alloputida sp. nov., Pseudomonas inefficax sp. nov., Pseudomonas persica sp. nov., and Pseudomonas shirazica sp. nov. Syst Appl Microbiol 2019; 42:468-480. [DOI: 10.1016/j.syapm.2019.04.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/15/2019] [Accepted: 04/21/2019] [Indexed: 12/21/2022]
|
21
|
Felföldi T, Márton Z, Szabó A, Mentes A, Bóka K, Márialigeti K, Máthé I, Koncz M, Schumann P, Tóth E. Siculibacillus lacustris gen. nov., sp. nov., a new rosette-forming bacterium isolated from a freshwater crater lake (Lake St. Ana, Romania). Int J Syst Evol Microbiol 2019; 69:1731-1736. [PMID: 30950779 DOI: 10.1099/ijsem.0.003385] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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 new aerobic alphaproteobacterium, strain SA-279T, was isolated from a water sample of a crater lake. The 16S rRNA gene sequence analysis revealed that strain SA-279T formed a distinct lineage within the family Ancalomicrobiaceae and shared the highest pairwise similarity values with Pinisolibacterravus E9T (96.4 %) and Ancalomicrobiumadetum NBRC 102456T (94.2 %). Cells of strain SA-279T were rod-shaped, motile, oxidase and catalase positive, and capable of forming rosettes. Its predominant fatty acids were C18 : 1ω7c (69.0 %) and C16 : 1ω7c (22.7 %), the major respiratory quinone was Q-10, and the main polar lipids were phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, phosphatidylglycerol, an unidentified aminophospholipid and an unidentified lipid. The G+C content of the genomic DNA of strain SA-279T was 69.2 mol%. On the basis of the phenotypic, chemotaxonomic and molecular data, strain SA-279T is considered to represent a new genus and species within the family Ancalomicrobiaceae, for which the name Siculibacillus lacustris gen. nov., sp. nov. is proposed. The type strain is SA-279T (=DSM 29840T=JCM 31761T).
Collapse
Affiliation(s)
- Tamás Felföldi
- 2Department of Bioengineering, Sapientia Hungarian University of Transylvania, Piaţa Libertăţii 1, 530104 Miercurea Ciuc, Romania.,1Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - Zsuzsanna Márton
- 1Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - Attila Szabó
- 1Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - Anikó Mentes
- 1Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - Károly Bóka
- 3Department of Plant Anatomy, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - Károly Márialigeti
- 1Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - István Máthé
- 2Department of Bioengineering, Sapientia Hungarian University of Transylvania, Piaţa Libertăţii 1, 530104 Miercurea Ciuc, Romania
| | - Mihály Koncz
- 2Department of Bioengineering, Sapientia Hungarian University of Transylvania, Piaţa Libertăţii 1, 530104 Miercurea Ciuc, Romania.,†Present address: Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Temesvári krt. 62, 6726 Szeged, Hungary
| | - Peter Schumann
- 4Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Erika Tóth
- 1Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| |
Collapse
|
22
|
Le Moine Bauer S, Sjøberg AG, L'Haridon S, Stokke R, Roalkvam I, Steen IH, Dahle H. Profundibacter amoris gen. nov., sp. nov., a new member of the Roseobacter clade isolated from Loki’s Castle Vent Field on the Arctic Mid-Ocean Ridge. Int J Syst Evol Microbiol 2019; 69:975-981. [DOI: 10.1099/ijsem.0.003234] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain, designated BAR1T, was isolated from a microbial mat growing on the surface of a barite chimney at the Loki’s Castle Vent Field, at a depth of 2216 m. Cells of strain BAR1T were rod-shaped, Gram-reaction-negative and grew on marine broth 2216 at 10–37 °C (optimum 27–35 °C), pH 5.5–8.0 (optimum pH 6.5–7.5) and 0.5–5.0 % NaCl (optimum 2 %). The DNA G+C content was 57.38 mol%. The membrane-associated major ubiquinone was Q-10, the fatty acid profile was dominated by C18 : 1ω7c (91 %), and the polar lipids detected were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid, one unidentified lipid and one unidentified phospholipid. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain BAR1T clustered together with Rhodobacterales bacterium PRT1, as well as the genera
Halocynthiibacter
and Pseudohalocynthiibacter in a polyphyletic clade within the
Roseobacter
clade. Several characteristics differentiate strain BAR1T from the aforementioned genera, including its motility, its piezophilic behaviour and its ability to grow at 35 °C and under anaerobic conditions. Accordingly, strain BAR1T is considered to represent a novel genus and species within the Roseobacter clade, for which the name Profundibacter amoris gen. nov., sp. nov. is proposed. The type strain is Profundibacter amoris BAR1T (=JCM 31874T=DSM 104147T).
Collapse
Affiliation(s)
- Sven Le Moine Bauer
- Department of Biological Sciences and K.G. Jebsen Center for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway
| | - Andreas Gilje Sjøberg
- Department of Biological Sciences and K.G. Jebsen Center for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway
| | - Stéphane L'Haridon
- Université de Brest (UBO), Institut Universitaire Européen de la Mer (IUEM) - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Plouzané, France
- CNRS, IUEM-UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Plouzané, France
- Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Plouzané, France
| | - Runar Stokke
- Department of Biological Sciences and K.G. Jebsen Center for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway
| | - Irene Roalkvam
- Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway
| | - Ida Helene Steen
- Department of Biological Sciences and K.G. Jebsen Center for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway
| | - Håkon Dahle
- Department of Biological Sciences and K.G. Jebsen Center for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway
| |
Collapse
|
23
|
Ward E, Kim EA, Panushka J, Botelho T, Meyer T, Kearns DB, Ordal G, Blair DF. Organization of the Flagellar Switch Complex of Bacillus subtilis. J Bacteriol 2019; 201:e00626-18. [PMID: 30455280 DOI: 10.1128/JB.00626-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 11/14/2018] [Indexed: 01/12/2023] Open
Abstract
While the protein complex responsible for controlling the direction (clockwise [CW] or counterclockwise [CCW]) of flagellar rotation has been fairly well studied in Escherichia coli and Salmonella, less is known about the switch complex in Bacillus subtilis or other Gram-positive species. Two component proteins (FliG and FliM) are shared between E. coli and B. subtilis, but in place of the protein FliN found in E. coli, the B. subtilis complex contains the larger protein FliY. Notably, in B. subtilis the signaling protein CheY-phosphate induces a switch from CW to CCW rotation, opposite to its action in E. coli Here, we have examined the architecture and function of the switch complex in B. subtilis using targeted cross-linking, bacterial two-hybrid protein interaction experiments, and characterization of mutant phenotypes. In major respects, the B. subtilis switch complex appears to be organized similarly to that in E. coli The complex is organized around a ring built from the large middle domain of FliM; this ring supports an array of FliG subunits organized in a similar way to that of E. coli, with the FliG C-terminal domain functioning in the generation of torque via conserved charged residues. Key differences from E. coli involve the middle domain of FliY, which forms an additional, more outboard array, and the C-terminal domains of FliM and FliY, which are organized into both FliY homodimers and FliM heterodimers. Together, the results suggest that the CW and CCW conformational states are similar in the Gram-negative and Gram-positive switches but that CheY-phosphate drives oppositely directed movements in the two cases.IMPORTANCE Flagellar motility plays key roles in the survival of many bacteria and in the harmful action of many pathogens. Bacterial flagella rotate; the direction of flagellar rotation is controlled by a multisubunit protein complex termed the switch complex. This complex has been extensively studied in Gram-negative model species, but little is known about the complex in Bacillus subtilis or other Gram-positive species. Notably, the switch complex in Gram-positive species responds to its effector CheY-phosphate (CheY-P) by switching to CCW rotation, whereas in E. coli or Salmonella CheY-P acts in the opposite way, promoting CW rotation. In the work here, the architecture of the B. subtilis switch complex has been probed using cross-linking, protein interaction measurements, and mutational approaches. The results cast light on the organization of the complex and provide a framework for understanding the mechanism of flagellar direction control in B. subtilis and other Gram-positive species.
Collapse
|
24
|
Kaminski MA, Sobczak A, Spolnik G, Danikiewicz W, Dziembowski A, Lipinski L. Sphingopyxis lindanitolerans sp. nov. strain WS5A3pT enriched from a pesticide disposal site. Int J Syst Evol Microbiol 2018; 68:3935-41. [DOI: 10.1099/ijsem.0.003094] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
25
|
Schouw A, Vulcano F, Roalkvam I, Hocking WP, Reeves E, Stokke R, Bødtker G, Steen IH. Genome Analysis of Vallitalea guaymasensis Strain L81 Isolated from a Deep-Sea Hydrothermal Vent System. Microorganisms 2018; 6:E63. [PMID: 29973550 PMCID: PMC6163223 DOI: 10.3390/microorganisms6030063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 06/13/2018] [Revised: 06/28/2018] [Accepted: 06/29/2018] [Indexed: 12/21/2022] Open
Abstract
Abyssivirga alkaniphila strain L81T, recently isolated from a black smoker biofilm at the Loki’s Castle hydrothermal vent field, was previously described as a mesophilic, obligately anaerobic heterotroph able to ferment carbohydrates, peptides, and aliphatic hydrocarbons. The strain was classified as a new genus within the family Lachnospiraceae. Herein, its genome is analyzed and A. alkaniphila is reassigned to the genus Vallitalea as a new strain of V. guaymasensis, designated V. guaymasensis strain L81. The 6.4 Mbp genome contained 5651 protein encoding genes, whereof 4043 were given a functional prediction. Pathways for fermentation of mono-saccharides, di-saccharides, peptides, and amino acids were identified whereas a complete pathway for the fermentation of n-alkanes was not found. Growth on carbohydrates and proteinous compounds supported methane production in co-cultures with Methanoplanus limicola. Multiple confurcating hydrogen-producing hydrogenases, a putative bifurcating electron-transferring flavoprotein—butyryl-CoA dehydrogenase complex, and a Rnf-complex form a basis for the observed hydrogen-production and a putative reverse electron-transport in V. guaymasensis strain L81. Combined with the observation that n-alkanes did not support growth in co-cultures with M. limicola, it seemed more plausible that the previously observed degradation patterns of crude-oil in strain L81 are explained by unspecific activation and may represent a detoxification mechanism, representing an interesting ecological function. Genes encoding a capacity for polyketide synthesis, prophages, and resistance to antibiotics shows interactions with the co-occurring microorganisms. This study enlightens the function of the fermentative microorganisms from hydrothermal vents systems and adds valuable information on the bioprospecting potential emerging in deep-sea hydrothermal systems.
Collapse
Affiliation(s)
- Anders Schouw
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Francesca Vulcano
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Irene Roalkvam
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - William Peter Hocking
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Eoghan Reeves
- Department of Earth Science and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Runar Stokke
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Gunhild Bødtker
- Centre for Integrated Petroleum Research (CIPR), Uni Research AS, Nygårdsgaten 112, N-5008 Bergen, Norway.
| | - Ida Helene Steen
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| |
Collapse
|
26
|
Abstract
Bacterial motion is strongly affected by the presence of a surface. One of the hallmarks of swimming near a surface is a defined curvature of bacterial trajectories, underlining the importance of counter rotations of the cell body and flagellum for locomotion of the microorganism. We find that there is another mode of bacterial motion on solid surfaces, i.e., self trapping due to fluid flows created by a rotating flagellum perpendicular to the surface. For a rod-like bacterium, such as Escherichia coli, this creates a peculiar situation in that the bacterium appears to swim along a minor axis of the cell body and is pressed against the surface. Although a full hydrodynamic theory is still lacking to explain the self-trapping phenomenon, the effect is intriguing and can be exploited to study a variety of biophysical phenomena of swimming bacteria. In particular, we showed that self-trapped E. coli cells display a chemotaxis response that is identical to the classical rotation assay in which antibodies are used to physically "glue" a flagellum to the surface.
Collapse
Affiliation(s)
- Corey N Dominick
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Xiao-Lun Wu
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, Pennsylvania.
| |
Collapse
|
27
|
Máthé I, Tóth E, Mentes A, Szabó A, Márialigeti K, Schumann P, Felföldi T. A new Rhizobium species isolated from the water of a crater lake, description of Rhizobium aquaticum sp. nov. Antonie van Leeuwenhoek 2018; 111:2175-2183. [DOI: 10.1007/s10482-018-1110-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 06/01/2018] [Indexed: 11/28/2022]
|
28
|
Furmanczyk EM, Kaminski MA, Lipinski L, Dziembowski A, Sobczak A. Pseudomonas laurylsulfatovorans sp. nov., sodium dodecyl sulfate degrading bacteria, isolated from the peaty soil of a wastewater treatment plant. Syst Appl Microbiol 2018; 41:348-354. [PMID: 29752019 DOI: 10.1016/j.syapm.2018.03.009] [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] [Received: 11/14/2017] [Revised: 03/26/2018] [Accepted: 03/30/2018] [Indexed: 10/17/2022]
Abstract
Pseudomonas are known from their flexible degradation capabilities and their engagement in xenobiotic biotransformation and bioremediation in habitats like soil, active sludge, plant surfaces, and freshwater or marine environments. Here we present taxonomic characterization of three efficient sodium dodecyl sulfate degrading strains: AP3_10, AP3_20 and AP3_22T belonging to the genus Pseudomonas, recently isolated from peaty soil used in a biological wastewater treatment plant. Sequence analyses of 16S rRNA and housekeeping genes: gyrB, rpoD and rpoB showed that the three closely related isolates classify within the Pseudomonas jessenii subgroup. ANIb or dDDH genomic comparisons of AP3_22T (type strain DSM 105098T=PCM 2904T) supported by biochemical tests showed that the isolates differ significantly from their closest relatives. The combined genotypic, phenotypic and chemotaxonomic data strongly support the classification of the three strains: AP3_10, AP3_20 and AP3_22T as a novel species of Pseudomonas, for which we propose the name Pseudomonas laurylsulfatovorans sp. nov. with AP3_22T as the type strain.
Collapse
Affiliation(s)
- Ewa M Furmanczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Michal A Kaminski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Leszek Lipinski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Andrzej Dziembowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Adam Sobczak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland.
| |
Collapse
|
29
|
Abstract
We describe labeling of bacteria with amino-specific or sulfhydryl-specific Alexa Fluor dyes, methods that allow visualization of flagellar filaments, even in swimming cells. Bacterial flagellar filaments are long (~10 μm), but of small diameter (~20 nm), and their rotation rates are high (>100 Hz), so visualization is difficult. Dark-field microscopy works well with isolated filaments, but visualization in situ is hampered by light scattered from cell bodies, which obscures short filaments or the proximal ends of long filaments. Differential interference contrast microscopy also works, but is technically difficult and suffers from a narrow depth of field and low image contrast; background subtraction and contrast enhancement are necessary. If filaments are fluorescent, they can be imaged in their entirety using standard fluorescence microscopes. For imaging in vivo, blurring can be prevented by strobing the light source or by using a camera with a fast shutter. The former method is preferred, since it minimizes bleaching.
Collapse
|
30
|
Kaminski MA, Furmanczyk EM, Sobczak A, Dziembowski A, Lipinski L. Pseudomonas silesiensis sp. nov. strain A3 T isolated from a biological pesticide sewage treatment plant and analysis of the complete genome sequence. Syst Appl Microbiol 2018; 41:13-22. [DOI: 10.1016/j.syapm.2017.09.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 08/30/2017] [Accepted: 09/01/2017] [Indexed: 11/15/2022]
|
31
|
Borsodi AK, Korponai K, Schumann P, Spröer C, Felföldi T, Márialigeti K, Szili-Kovács T, Tóth E. Nitrincola alkalilacustris sp. nov. and Nitrincola schmidtii sp. nov., alkaliphilic bacteria isolated from soda pans, and emended description of the genus Nitrincola. Int J Syst Evol Microbiol 2017; 67:5159-5164. [DOI: 10.1099/ijsem.0.002437] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Andrea K. Borsodi
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - Kristóf Korponai
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - Peter Schumann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7 B, 38124 Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7 B, 38124 Braunschweig, Germany
| | - Tamás Felföldi
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - Károly Márialigeti
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - Tibor Szili-Kovács
- Institute for Soil Sciences and Agricultural Chemistry, Agricultural Research Center, Hungarian Academy of Sciences, Herman Ottó út 15, H-1022 Budapest, Hungary
| | - Erika Tóth
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| |
Collapse
|
32
|
Felföldi T, Fikó RD, Mentes A, Kovács E, Máthé I, Schumann P, Tóth E. Quisquiliibacterium transsilvanicum gen. nov., sp. nov., a novel betaproteobacterium isolated from a waste-treating bioreactor. Int J Syst Evol Microbiol 2017; 67:4742-4746. [PMID: 28950929 DOI: 10.1099/ijsem.0.002368] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [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 new betaproteobacterium, CGI-09T, was isolated from an activated sludge bioreactor which treated landfill leachate. Based on 16S rRNA gene sequence analysis, the new strain shared the highest pairwise similarity values with members of the order Burkholderiales: Derxia gummosa IAM 13946T (family Alcaligenaceae), 93.7 % and Lautropia mirabilis DSM 11362T (family Burkholderiaceae), 93.6 %. Cells of strain CGI-09T were rod-shaped and non-motile. The new strain was oxidase and catalase positive and capable of reducing nitrate to nitrite. The predominant fatty acids were C16 : 1 ω7c, C16 : 0, cycloC17 : 0 and C18 : 1 ω7c, the major respiratory quinone was Q-8, and the detected polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and an unknown phospholipid. The G+C content of the genomic DNA of strain CGI-09T was 70.2 mol%. The new bacterium can be distinguished from the members of genera Derxia and Lautropia based on its non-motile cells, arginine dihydrolase activity, its high cyclo C17 : 0 fatty acid content and the lack of hydroxy fatty acids. On the basis of the phenotypic, chemotaxonomic and molecular data, strain CGI-09T is considered to represent a new genus and species within the family Burkholderiaceae, for which the name Quisquiliibacterium transsilvanicum gen. nov., sp. nov. is proposed. The type strain is CGI-09T (=DSM 29781T=JCM 31785T).
Collapse
Affiliation(s)
- Tamás Felföldi
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary.,Department of Bioengineering, Sapientia Hungarian University of Transylvania, Piaţa Libertăţii 1, 530104 Miercurea Ciuc, Romania
| | - Róbert Dezső Fikó
- Department of Bioengineering, Sapientia Hungarian University of Transylvania, Piaţa Libertăţii 1, 530104 Miercurea Ciuc, Romania
| | - Anikó Mentes
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - Erika Kovács
- Department of Bioengineering, Sapientia Hungarian University of Transylvania, Piaţa Libertăţii 1, 530104 Miercurea Ciuc, Romania
| | - István Máthé
- Department of Bioengineering, Sapientia Hungarian University of Transylvania, Piaţa Libertăţii 1, 530104 Miercurea Ciuc, Romania
| | - Peter Schumann
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Erika Tóth
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| |
Collapse
|
33
|
Suarez C, Ratering S, Schäfer J, Schnell S. Ancylobacter pratisalsi sp. nov. with plant growth promotion abilities from the rhizosphere of Plantago winteri Wirtg. Int J Syst Evol Microbiol 2017; 67:4500-4506. [PMID: 28945527 DOI: 10.1099/ijsem.0.002320] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [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-negative bacterium, designated E130T, was isolated from rhizospheric soil of Plantago winteri Wirtg. from a natural salt meadow as part of an investigation on rhizospheric bacteria from salt-resistant plant species and evaluation of their plant growth-promoting abilities. Cells were rods, non-motile, aerobic, and oxidase and catalase positive, grew in a temperature range of between 4 and 37 °C, and in the presence of 0.5-5 % NaCl (w/v). Based on 16S rRNA gene sequence analysis, strain E130T is affiliated within the genus Ancylobacter, sharing the highest similarity with Ancylobacter rudongensis DSM 17131T (97.6 %), Ancylobacter defluvii CCUG 63806T (97.5 %) and Ancylobacter dichloromethanicus DSM 21507T (97.4 %). The DNA G+C content of strain E130T was 65.1 mol%. Its respiratory quinones were Q-9 and Q-10 and its major polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and unidentified phospholipid. Major fatty acids of the strains E130T were C12 : 0, C16 : 0, C18 : 1ω7c and C19 : 0cycloω8c. The DNA-DNA relatedness of E130T to A. rudongensis DSM 17131T, A. defluvii CCUG 63806T and A. dichloromethanicus DSM 21507T was 29.2, 21.2 and 32.2 % respectively. On the basis of our polyphasic taxonomic study the new isolate represents a novel species, for which the name Ancylobacter pratisalsi sp. nov. is proposed. The type strain is E130T (LMG 29367T=DSM 102029T).
Collapse
Affiliation(s)
- Christian Suarez
- Institute of Applied Microbiology, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Stefan Ratering
- Institute of Applied Microbiology, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Johanna Schäfer
- Institute of Applied Microbiology, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Justus-Liebig University Giessen, 35392 Giessen, Germany
| |
Collapse
|
34
|
Felföldi T, Schumann P, Mentes A, Kéki Z, Máthé I, Tóth EM. Caenimicrobium hargitense gen. nov., sp. nov., a new member of the family Alcaligenaceae (Betaproteobacteria) isolated from activated sludge. Int J Syst Evol Microbiol 2016; 67:627-632. [PMID: 27902326 DOI: 10.1099/ijsem.0.001674] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A new betaproteobacterium, CGII-59m2T, was isolated from an activated sludge bioreactor which treated landfill leachate. The 16S rRNA gene sequence analysis revealed that strain CGII-59m2T belonged to the family Alcaligenaceae and shared the highest pairwise similarity values with Parapusillimonas granuli LMG 24012T (97.7 %), various species of the genus Bordetella (97.3-97.0 %) and Candidimonas nitroreducens LMG 24812T (97.0 %). Cells of strain CGII-59m2T were rod-shaped, non-motile, and oxidase- and catalase-positive. The predominant fatty acids were C16 : 1ω7c, C16 : 0, cyclo C17 : 0 and C18 : 1ω7c, the major respiratory quinone was Q-8, and the main polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unknown phospholipid. The G+C content of the genomic DNA of strain CGII-59m2T was 62.3 mol%. The new bacterium can be distinguished from the closely related type strains based on its non-motile cells and its high C16 : 1ω7c fatty acid content. On the basis of the phenotypic, chemotaxonomic and molecular data, strain CGII-59m2T is considered to represent a novel species of a new genus, for which the name Caenimicrobium hargitense gen. nov., sp. nov. is proposed. The type strain is CGII-59m2T (=DSM 29806T=NCAIM B.02615T).
Collapse
Affiliation(s)
- Tamás Felföldi
- Department of Bioengineering, Sapientia Hungarian University of Transylvania, Piaţa Libertăţii 1, 530104 Miercurea Ciuc, Romania.,Department of Microbiology, Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - Peter Schumann
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Anikó Mentes
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - Zsuzsa Kéki
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - István Máthé
- Department of Bioengineering, Sapientia Hungarian University of Transylvania, Piaţa Libertăţii 1, 530104 Miercurea Ciuc, Romania
| | - Erika M Tóth
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| |
Collapse
|
35
|
Kumar B, Cardona ST. Synthetic Cystic Fibrosis Sputum Medium Regulates Flagellar Biosynthesis through the flhF Gene in Burkholderia cenocepacia. Front Cell Infect Microbiol 2016; 6:65. [PMID: 27379216 PMCID: PMC4905959 DOI: 10.3389/fcimb.2016.00065] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [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: 02/26/2016] [Accepted: 05/30/2016] [Indexed: 12/03/2022] Open
Abstract
Burkholderia cenocepacia belongs to the Burkholderia cepacia complex (Bcc), a group of at least 18 distinct species that establish chronic infections in the lung of people with the genetic disease cystic fibrosis (CF). The sputum of CF patients is rich in amino acids and was previously shown to increase flagellar gene expression in B. cenocepacia. We examined flagellin expression and flagellar morphology of B. cenocepacia grown in synthetic cystic fibrosis sputum medium (SCFM) compared to minimal medium. We found that CF nutritional conditions induce increased motility and flagellin expression. Individual amino acids added at the same concentrations as found in SCFM also increased motility but not flagellin expression, suggesting a chemotactic effect of amino acids. Electron microscopy and flagella staining demonstrated that the increase in flagellin corresponds to a change in the number of flagella per cell. In minimal medium, the ratio of multiple: single: aflagellated cells was 2:3.5:4.5; while under SCFM conditions, the ratio was 7:2:1. We created a deletion mutant, ΔflhF, to study whether this putative GTPase regulates the flagellation pattern of B. cenocepacia K56-2 during growth in CF conditions. The ΔflhF mutant exhibited 80% aflagellated, 14% single and 6% multiple flagellated bacterial subpopulations. Moreover, the ratio of multiple to single flagella in WT and ΔflhF was 3.5 and 0.43, respectively in CF conditions. The observed differences suggest that FlhF positively regulates flagellin expression and the flagellation pattern in B. cenocepacia K56-2 during CF nutritional conditions.
Collapse
Affiliation(s)
- Brijesh Kumar
- Department of Microbiology, University of Manitoba Winnipeg, MB, Canada
| | - Silvia T Cardona
- Department of Microbiology, University of ManitobaWinnipeg, MB, Canada; Department of Medical Microbiology and Infectious Diseases, University of ManitobaWinnipeg, MB, Canada
| |
Collapse
|
36
|
Le MT, van Veldhuizen M, Porcelli I, Bongaerts RJ, Gaskin DJH, Pearson BM, van Vliet AHM. Conservation of σ28-Dependent Non-Coding RNA Paralogs and Predicted σ54-Dependent Targets in Thermophilic Campylobacter Species. PLoS One 2015; 10:e0141627. [PMID: 26512728 PMCID: PMC4626219 DOI: 10.1371/journal.pone.0141627] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 10/09/2015] [Indexed: 12/28/2022] Open
Abstract
Assembly of flagella requires strict hierarchical and temporal control via flagellar sigma and anti-sigma factors, regulatory proteins and the assembly complex itself, but to date non-coding RNAs (ncRNAs) have not been described to regulate genes directly involved in flagellar assembly. In this study we have investigated the possible role of two ncRNA paralogs (CjNC1, CjNC4) in flagellar assembly and gene regulation of the diarrhoeal pathogen Campylobacter jejuni. CjNC1 and CjNC4 are 37/44 nt identical and predicted to target the 5' untranslated region (5' UTR) of genes transcribed from the flagellar sigma factor σ54. Orthologs of the σ54-dependent 5' UTRs and ncRNAs are present in the genomes of other thermophilic Campylobacter species, and transcription of CjNC1 and CNC4 is dependent on the flagellar sigma factor σ28. Surprisingly, inactivation and overexpression of CjNC1 and CjNC4 did not affect growth, motility or flagella-associated phenotypes such as autoagglutination. However, CjNC1 and CjNC4 were able to mediate sequence-dependent, but Hfq-independent, partial repression of fluorescence of predicted target 5' UTRs in an Escherichia coli-based GFP reporter gene system. This hints towards a subtle role for the CjNC1 and CjNC4 ncRNAs in post-transcriptional gene regulation in thermophilic Campylobacter species, and suggests that the currently used phenotypic methodologies are insufficiently sensitive to detect such subtle phenotypes. The lack of a role of Hfq in the E. coli GFP-based system indicates that the CjNC1 and CjNC4 ncRNAs may mediate post-transcriptional gene regulation in ways that do not conform to the paradigms obtained from the Enterobacteriaceae.
Collapse
Affiliation(s)
- My Thanh Le
- Gut Health and Food Safety Programme, Institute of Food Research, Norwich Research Park, Norwich, United Kingdom
| | - Mart van Veldhuizen
- Gut Health and Food Safety Programme, Institute of Food Research, Norwich Research Park, Norwich, United Kingdom
| | - Ida Porcelli
- Gut Health and Food Safety Programme, Institute of Food Research, Norwich Research Park, Norwich, United Kingdom
| | - Roy J. Bongaerts
- Gut Health and Food Safety Programme, Institute of Food Research, Norwich Research Park, Norwich, United Kingdom
| | - Duncan J. H. Gaskin
- Gut Health and Food Safety Programme, Institute of Food Research, Norwich Research Park, Norwich, United Kingdom
| | - Bruce M. Pearson
- Gut Health and Food Safety Programme, Institute of Food Research, Norwich Research Park, Norwich, United Kingdom
| | - Arnoud H. M. van Vliet
- Gut Health and Food Safety Programme, Institute of Food Research, Norwich Research Park, Norwich, United Kingdom
- * E-mail:
| |
Collapse
|
37
|
Reuter M, Periago PM, Mulholland F, Brown HL, van Vliet AHM. A PAS domain-containing regulator controls flagella-flagella interactions in Campylobacter jejuni. Front Microbiol 2015; 6:770. [PMID: 26284050 PMCID: PMC4519771 DOI: 10.3389/fmicb.2015.00770] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [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: 03/11/2015] [Accepted: 07/14/2015] [Indexed: 01/09/2023] Open
Abstract
The bipolar flagella of the foodborne bacterial pathogen Campylobacter jejuni confer motility, which is essential for virulence. The flagella of C. jejuni are post-translationally modified, but how this process is controlled is not well understood. In this work, we have identified a novel PAS-domain containing regulatory system, which modulates flagella-flagella interactions in C. jejuni. Inactivation of the cj1387c gene, encoding a YheO-like PAS6 domain linked to a helix-turn-helix domain, resulted in the generation of a tightly associated “cell-train” morphotype, where up to four cells were connected by their flagella. The morphotype was fully motile, resistant to vortexing, accompanied by increased autoagglutination, and was not observed in aflagellated cells. The Δcj1387c mutant displayed increased expression of the adjacent Cj1388 protein, which comprises of a single endoribonuclease L-PSP domain. Comparative genomics showed that cj1387c (yheO) orthologs in bacterial genomes are commonly linked to an adjacent cj1388 ortholog, with some bacteria, including C. jejuni, containing another cj1388-like gene (cj0327). Inactivation of the cj1388 and cj0327 genes resulted in decreased autoagglutination in Tween-20-supplemented media. The Δcj1388 and Δcj0327 mutants were also attenuated in a Galleria larvae-based infection model. Finally, substituting the sole cysteine in Cj1388 for serine prevented Cj1388 dimerization in non-reducing conditions, and resulted in decreased autoagglutination in the presence of Tween-20. We hypothesize that Cj1388 and Cj0327 modulate post-translational modification of the flagella through yet unidentified mechanisms, and propose naming Cj1387 the Campylobacter Flagella Interaction Regulator CfiR, and the Cj1388 and Cj0327 protein as CfiP and CfiQ, respectively.
Collapse
Affiliation(s)
- Mark Reuter
- Institute of Food Research, Gut Health and Food Safety Programme Norwich, UK
| | - Paula M Periago
- Departamento Ingeniería de Alimentos y del Equipamiento Agrícola, Campus de Excelencia Internacional Regional "Campus Mare Nostrum," Escuela Técnica Superior de Ingeniería Agronómica, Universidad Politécnica de Cartagena Cartagena, Spain ; Instituto de Biotecnología Vegetal, Campus de Excelencia Internacional Regional "Campus Mare Nostrum," Universidad Politécnica de Cartagena Cartagena, Spain
| | - Francis Mulholland
- Institute of Food Research, Gut Health and Food Safety Programme Norwich, UK
| | - Helen L Brown
- Institute of Food Research, Gut Health and Food Safety Programme Norwich, UK ; Cardiff School of Health Sciences, Cardiff Metropolitan University Cardiff, UK
| | | |
Collapse
|
38
|
Hingston PA, Piercey MJ, Truelstrup Hansen L. Genes Associated with Desiccation and Osmotic Stress in Listeria monocytogenes as Revealed by Insertional Mutagenesis. Appl Environ Microbiol 2015; 81:5350-62. [PMID: 26025900 DOI: 10.1128/AEM.01134-15] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 05/22/2015] [Indexed: 12/29/2022] Open
Abstract
Listeria monocytogenes is a foodborne pathogen whose survival in food processing environments may be associated with its tolerance to desiccation. To probe the molecular mechanisms used by this bacterium to adapt to desiccation stress, a transposon library of 11,700 L. monocytogenes mutants was screened, using a microplate assay, for strains displaying increased or decreased desiccation survival (43% relative humidity, 15°C) in tryptic soy broth (TSB). The desiccation phenotypes of selected mutants were subsequently assessed on food-grade stainless steel (SS) coupons in TSB plus 1% glucose (TSB-glu). Single transposon insertions in mutants exhibiting a change in desiccation survival of >0.5 log CFU/cm(2) relative to that of the wild type were determined by sequencing arbitrary PCR products. Strain morphology, motility, and osmotic stress survival (in TSB-glu plus 20% NaCl) were also analyzed. The initial screen selected 129 desiccation-sensitive (DS) and 61 desiccation-tolerant (DT) mutants, out of which secondary screening on SS confirmed 15 DT and 15 DS mutants. Among the DT mutants, seven immotile and flagellum-less strains contained transposons in genes involved in flagellum biosynthesis (fliP, flhB, flgD, flgL) and motor control (motB, fliM, fliY), while others harbored transposons in genes involved in membrane lipid biosynthesis, energy production, potassium uptake, and virulence. The genes that were interrupted in the 15 DS mutants included those involved in energy production, membrane transport, protein metabolism, lipid biosynthesis, oxidative damage control, and putative virulence. Five DT and 14 DS mutants also demonstrated similar significantly (P < 0.05) different survival relative to that of the wild type when exposed to osmotic stress, demonstrating that some genes likely have similar roles in allowing the organism to survive the two water stresses.
Collapse
|
39
|
Goyal G, Mulero R, Ali J, Darvish A, Kim MJ. Low aspect ratio micropores for single-particle and single-cell analysis. Electrophoresis 2015; 36:1164-71. [DOI: 10.1002/elps.201400570] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 02/13/2015] [Accepted: 02/14/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Gaurav Goyal
- School of Biomedical Engineering, Science and Health Systems; Drexel University; Philadelphia PA USA
| | - Rafael Mulero
- Department of Mechanical Engineering and Mechanics; Drexel University; Philadelphia PA USA
| | - Jamel Ali
- Department of Mechanical Engineering and Mechanics; Drexel University; Philadelphia PA USA
| | - Armin Darvish
- School of Biomedical Engineering, Science and Health Systems; Drexel University; Philadelphia PA USA
| | - Min Jun Kim
- School of Biomedical Engineering, Science and Health Systems; Drexel University; Philadelphia PA USA
- Department of Mechanical Engineering and Mechanics; Drexel University; Philadelphia PA USA
| |
Collapse
|
40
|
Anders H, Power JF, MacKenzie AD, Lagutin K, Vyssotski M, Hanssen E, Moreau JW, Stott MB. Limisphaera ngatamarikiensis gen. nov., sp. nov., a thermophilic, pink-pigmented coccus isolated from subaqueous mud of a geothermal hotspring. Int J Syst Evol Microbiol 2015; 65:1114-1121. [DOI: 10.1099/ijs.0.000063] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterial strain, NGM72.4T, was isolated from a hot spring in the Ngatamariki geothermal field, New Zealand. Phylogenetic analysis based on 16S rRNA gene sequences grouped it into the phylum
Verrucomicrobia
and class level group 3 (also known as OPB35 soil group). NGM72.4T stained Gram-negative, and was catalase- and oxidase-positive. Cells were small cocci, 0.5–0.8 µm in diameter, which were motile by means of single flagella. Transmission electron micrograph (TEM) imaging showed an unusual pirellulosome-like intracytoplasmic membrane. The peptidoglycan content was very small with only trace levels of diaminopimelic acid detected. No peptidoglycan structure was visible in TEM imaging. The predominant isoprenoid quinone was MK-7 (92 %). The major fatty acids (>15 %) were C16 : 0, anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. Major phospholipids were phosphatidylethanolamine (PE), phosphatidylmonomethylethanolamine (PMME) and cardiolipin (CL), and a novel analogous series of phospholipids where diacylglycerol was replaced with diacylserinol (sPE, sPMME, sCL). The DNA G+C content was 65.6 mol%. Cells displayed an oxidative chemoheterotrophic metabolism. NGM72.4T is a strictly aerobic thermophile (growth optimum 60–65 °C), has a slightly alkaliphilic pH growth optimum (optimum pH 8.1–8.4) and has a NaCl tolerance of up to 8 g l−1. Colonies were small, circular and pigmented pale pink. The distinct phylogenetic position and phenotypic traits of strain NGM72.4T distinguish it from all other described species of the phylum
Verrucomicrobia
and, therefore, it is considered to represent a novel species in a new genus for which we propose the name Limisphaera ngatamarikiensis gen. nov., sp. nov. The type strain is NGM72.4T ( = ICMP 20182T = DSM 27329T).
Collapse
Affiliation(s)
- Heike Anders
- Lehrstuhl für Tierhygiene, Technische Universität München, Weihenstephaner Berg 3 0D-85354, Freising, Germany
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupō 3352, New Zealand
| | - Jean F. Power
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupō 3352, New Zealand
| | | | - Kirill Lagutin
- Callaghan Innovation, PO Box 31310, Lower Hutt 5040, New Zealand
| | | | - Eric Hanssen
- University of Melbourne, 30 Flemington Road, Victoria 3010, Australia
| | - John W. Moreau
- University of Melbourne, 30 Flemington Road, Victoria 3010, Australia
| | - Matthew B. Stott
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupō 3352, New Zealand
| |
Collapse
|
41
|
Lefèvre CT, Bennet M, Klumpp S, Faivre D. Positioning the flagellum at the center of a dividing cell to combine bacterial division with magnetic polarity. mBio 2015; 6:e02286. [PMID: 25714711 DOI: 10.1128/mBio.02286-14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Faithful replication of all structural features is a sine qua non condition for the success of bacterial reproduction by binary fission. For some species, a key challenge is to replicate and organize structures with multiple polarities. Polarly flagellated magnetotactic bacteria are the prime example of organisms dealing with such a dichotomy; they have the challenge of bequeathing two types of polarities to their daughter cells: magnetic and flagellar polarities. Indeed, these microorganisms align and move in the Earth’s magnetic field using an intracellular chain of nano-magnets that imparts a magnetic dipole to the cell. The paradox is that, after division occurs in cells, if the new flagellum is positioned opposite to the old pole devoid of a flagellum during cell division, the two daughter cells will have opposite magnetic polarities with respect to the positions of their flagella. Here we show that magnetotactic bacteria of the class Gammaproteobacteria pragmatically solve this problem by synthesizing a new flagellum at the division site. In addition, we model this particular structural inheritance during cell division. This finding opens up new questions regarding the molecular aspects of the new division mechanism, the way other polarly flagellated magnetotactic bacteria control the rotational direction of their flagella, and the positioning of organelles. Magnetotactic bacteria produce chains of magnetic nanoparticles that endow the cells with a magnetic dipole, a “compass” used for navigation. This feature, however, also drastically complicates cellular division in the case of polarly flagellated bacteria. In this case, the bacteria have to pass on to their daughter cells two types of cellular polarities simultaneously, their magnetic polarity and the polarity of their motility apparatus. We show here that magnetotactic bacteria of the Gammaproteobacteria class pragmatically solve this problem by synthesizing the new flagellum at the division site, a division scheme never observed so far in bacteria. Even though the molecular mechanisms behind this scheme cannot be resolved at the moment due to the lack of genetic tools, this discovery provides a new window into the organizational complexity of simple organisms.
Collapse
|
42
|
Bang BH, Rhee MS, Chang DH, Park DS, Kim BC. Erysipelothrix larvae sp. nov., isolated from the larval gut of the rhinoceros beetle, Trypoxylus dichotomus (Coleoptera: Scarabaeidae). Antonie Van Leeuwenhoek 2014; 107:443-51. [PMID: 25534074 DOI: 10.1007/s10482-014-0342-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Accepted: 11/19/2014] [Indexed: 10/24/2022]
Abstract
A novel, Gram-stain positive, facultative anaerobic, non-motile and straight to curve rod shaped bacterium, strain LV19(T) was isolated from the larval gut of the rhinoceros beetle, Trypoxylus dichotomus, which was collected from Yeong-dong, Chuncheongbuk-do, South Korea. The colonies of the new isolate were convex, circular, cream white in color and 1-2 mm in diameter after 3 days incubation on Tryptic Soy Agar at 37 °C. Based on the 16S rRNA gene sequence similarity, the new isolate was most closely related to Erysipelothrix inopinata MF-EP02(T), E. rhusiopathiae ATCC 19414 (T) and E. tonsillarum T-305(T) (94.8, 93.8 and 93.7 % similarity, respectively). Strain LV19(T) grew optimally at 37 °C, at pH 8.0 and in the presence of 0.5 % (w/v) NaCl. Oxidase activity and catalase activity were negative. The major cellular fatty acids (>10 %) were C18:2 cis-9,12 (28.9 %), C18:1 cis-9 (22.3 %), C16:0 (22.2 %) and C18:0 (18.5 %). The cell-wall hydrolysates contained ribose as a major sugar. Major polar lipids were phosphatidylglycerol and three unidentified glycolipids. No quinone was detected. The G+C content of the genomic DNA was 36.3 mol%. The levels of DNA-DNA relatedness between strain LV19(T) and all the reference strains were less than 20 %. On the basis of polyphasic evidence from this study, the isolate is considered to represent a novel species of the genus Erysipelothrix, for which the name Erysipelothrix larvae sp. nov. is proposed; the type strain is LV19(T) (=KCTC 33523(T) = DSM 28480(T)).
Collapse
Affiliation(s)
- Byung-Ho Bang
- Department of Food and Nutrition Science, Eulji University, 553 Sanseong-Daero, Sujeong-gu, Seongnam-si, Gyeonggi-do, 461-832, Republic of Korea
| | | | | | | | | |
Collapse
|
43
|
Pascual J, García-López M, Bills GF, Genilloud O. Pseudomonas granadensis sp. nov., a new bacterial species isolated from the Tejeda, Almijara and Alhama Natural Park, Granada, Spain. Int J Syst Evol Microbiol 2014; 65:625-632. [PMID: 25410940 DOI: 10.1099/ijs.0.069260-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
During the course of screening bacterial isolates as sources of as-yet unknown bioactive compounds with pharmaceutical applications, a chemo-organotrophic, Gram-negative bacterium was isolated from a soil sample taken from the Tejeda, Almijara and Alhama Natural Park, Granada, Spain. Strain F-278,770(T) was oxidase- and catalase-positive, aerobic, with a respiratory type of metabolism with oxygen as the terminal electron acceptor, non-spore-forming and motile by one polar flagellum, although some cells had two polar flagella. Phylogenetic analysis of the 16S rRNA, gyrB, rpoB and rpoD genes revealed that strain F-278,770(T) belongs to the Pseudomonas koreensis subgroup (Pseudomonas fluorescens lineage), with Pseudomonas moraviensis, P. koreensis, P. baetica and P. helmanticensis as its closest relatives. Chemotaxonomic traits such as polar lipid and fatty acid compositions and G+C content of genomic DNA corroborated the placement of strain F-278,770(T) in the genus Pseudomonas. DNA-DNA hybridization assays and phenotypic traits confirmed that this strain represents a novel species of the genus Pseudomonas, for which the name Pseudomonas granadensis sp. nov. is proposed. The type strain is F-278,770(T) ( = DSM 28040(T) = LMG 27940(T)).
Collapse
Affiliation(s)
- Javier Pascual
- Fundación MEDINA, Avenida del Conocimiento, 3. Health Sciences Technology Park, 18016 Granada, Spain
| | - Marina García-López
- Fundación MEDINA, Avenida del Conocimiento, 3. Health Sciences Technology Park, 18016 Granada, Spain
| | - Gerald F Bills
- Fundación MEDINA, Avenida del Conocimiento, 3. Health Sciences Technology Park, 18016 Granada, Spain
| | - Olga Genilloud
- Fundación MEDINA, Avenida del Conocimiento, 3. Health Sciences Technology Park, 18016 Granada, Spain
| |
Collapse
|
44
|
Suarez C, Ratering S, Geissler-Plaum R, Schnell S. Hartmannibacter diazotrophicus gen. nov., sp. nov., a phosphate-solubilizing and nitrogen-fixing alphaproteobacterium isolated from the rhizosphere of a natural salt-meadow plant. Int J Syst Evol Microbiol 2014; 64:3160-3167. [DOI: 10.1099/ijs.0.064154-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A phosphate-mobilizing, Gram-negative bacterium was isolated from rhizospheric soil of Plantago winteri from a natural salt meadow as part of an investigation of rhizospheric bacteria from salt-resistant plant species and evaluation of their plant-growth-promoting abilities. Cells were rods, motile, strictly aerobic, oxidase-positive and catalase-negative. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain E19T was distinct from other taxa within the class
Alphaproteobacteria
. Strain E19T showed less than 93.5 % 16S rRNA gene sequence similarity with members of the genera
Rhizobium
(≤93.5 %),
Labrenzia
(≤93.1 %),
Stappia
(≤93.1 %),
Aureimonas
(≤93.1 %) and
Mesorhizobium
(≤93.0 %) and was most closely related to
Rhizobium rhizoryzae
(93.5 % 16S rRNA gene sequence similarity to the type strain). The sole respiratory quinone was Q-10, and the polar lipids comprised phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, an aminolipid and an unidentified phospholipid. Major fatty acids were C18 : 1ω7c (71.4 %), summed feature 2 (C14 : 0 3-OH and/or iso-C16 : 1; 8.3 %), C20 : 0 (7.9 %) and C16 : 0 (6.1 %). The DNA G+C content of strain E19T was 59.9±0.7 mol%. The capacity for nitrogen fixation was confirmed by the presence of the nifH gene and the acetylene reduction assay. On the basis of the results of our polyphasic taxonomic study, the new isolate represents a novel genus and species, for which the name Hartmannibacter diazotrophicus gen. nov., sp. nov. is proposed. The type strain of Hartmannibacter diazotrophicus is E19T ( = LMG 27460T = KACC 17263T).
Collapse
Affiliation(s)
- Christian Suarez
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Stefan Ratering
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Rita Geissler-Plaum
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| |
Collapse
|
45
|
Pascual J, García-lópez M, Carmona C, Sousa TDS, de Pedro N, Cautain B, Martín J, Vicente F, Reyes F, Bills GF, Genilloud O. Pseudomonas soli sp. nov., a novel producer of xantholysin congeners. Syst Appl Microbiol 2014; 37:412-6. [DOI: 10.1016/j.syapm.2014.07.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 07/03/2014] [Accepted: 07/11/2014] [Indexed: 11/19/2022]
|
46
|
Hoefman S, van der Ha D, Iguchi H, Yurimoto H, Sakai Y, Boon N, Vandamme P, Heylen K, De Vos P. Methyloparacoccus murrellii gen. nov., sp. nov., a methanotroph isolated from pond water. Int J Syst Evol Microbiol 2014; 64:2100-2107. [DOI: 10.1099/ijs.0.057760-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel methanotrophic strains, R-49797T and OS501, were isolated from pond water in South Africa and Japan, respectively. Strains R-49797T and OS501 shared 99.7 % 16S rRNA gene sequence similarity. Cells were Gram-stain-negative, non-motile cocci with a diplococcoid tendency and contained type I methanotroph intracytoplasmic membranes. The pmoA gene encoding particulate methane monooxygenase was present. Soluble methane monoooxygenase (sMMO) activity, the mmoX gene encoding sMMO and the nifH gene encoding nitrogenase were not detected. Methane and methanol were utilized as sole carbon source. The strains grew optimally at 25–33 °C (range 20–37 °C) and at pH 6.3–6.8 (range 5.8–9.0). The strains did not support growth in media supplemented with 1 % (w/v) NaCl. For both strains, the two major fatty acids were C16 : 1ω7c and C16 : 0 and the DNA G+C content was 65.6 mol%. The isolates belong to the family
Methylococcaceae
of the class
Gammaproteobacteria
and cluster most closely among the genera
Methylocaldum
,
Methylococcus
and
Methylogaea
, with a 16S rRNA gene sequence similarity of 94.2 % between strain R-49797T and its closest related type strain (
Methylocaldum gracile
VKM 14LT). Based on the low 16S rRNA gene sequence similarities with its nearest phylogenetic neighbouring genera, the formation of a separate lineage based on 16S rRNA and pmoA gene phylogenetic analysis, and the unique combination of phenotypic characteristics of the two isolated strains compared with the genera
Methylocaldum
,
Methylococcus
and
Methylogaea
, we propose to classify these strains as representing a novel species of a new genus, Methyloparacoccus murrellii gen. nov., sp. nov., within the family
Methylococcaceae
. The type strain of Methyloparacoccus murrellii is R-49797T ( = LMG 27482T = JCM 19379T).
Collapse
Affiliation(s)
- Sven Hoefman
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - David van der Ha
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Hiroyuki Iguchi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hiroya Yurimoto
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yasuyoshi Sakai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Nico Boon
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - Kim Heylen
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - Paul De Vos
- BCCM/LMG Bacteria Collection, Gent, Belgium
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| |
Collapse
|
47
|
Suarez C, Ratering S, Geissler-Plaum R, Schnell S. Rheinheimera hassiensis sp. nov. and Rheinheimera muenzenbergensis sp. nov., two species from the rhizosphere of Hordeum secalinum. Int J Syst Evol Microbiol 2014; 64:1202-1209. [DOI: 10.1099/ijs.0.061200-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two motile, Gram-staining-negative, aerobic, rod-shaped bacteria designated strains E48T and E49T were isolated from the rhizosphere of Hordeum secalinum from a natural salt meadow near Münzenberg, Germany. 16S rRNA gene sequence similarity analysis revealed that strains E48T and E49T shared similarities of 97.6 % with
Rheinheimera pacifica
KMM 1406T and 98.5 % with
Rheinheimera nanhaiensis
E407-8T, respectively. Major fatty acids of strain E48T were C16 : 0, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C17 : 1ω8c, and of strain E49T were C16 : 0, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C18 : 1ω7c. The DNA G+C contents were 50.5 mol% (E48T) and 50.0 mol% (E49T). Strains E48T and E49T grew at 4–37 °C (optimum 28 °C) and with 0–6 % NaCl (optimum 0–3 %) and 0–5 % NaCl (optimum 0–3 %), respectively. The potential for nitrogen fixation by strains E48T and E49T was evaluated by molecular techniques and the acetylene reduction assay. The DNA–DNA hybridization, physiological and molecular data demonstrated that strains E48T and E49T represent two novel species of the genus
Rheinheimera
, and therefore the names Rheinheimera hassiensis sp. nov. (type strain E48T = LMG 27268T = KACC 17070T) and Rheinheimera muenzenbergensis sp. nov. (type strain E49T = LMG 27269T = KACC 17071T) are proposed.
Collapse
Affiliation(s)
- Christian Suarez
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Stefan Ratering
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Rita Geissler-Plaum
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| |
Collapse
|
48
|
Felföldi T, Vengring A, Márialigeti K, András J, Schumann P, Tóth EM. Hephaestia caeni gen. nov., sp. nov., a novel member of the family Sphingomonadaceae isolated from activated sludge. Int J Syst Evol Microbiol 2014; 64:738-44. [DOI: 10.1099/ijs.0.053736-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative, rod-shaped and motile bacterium, designated strain ERB1-3T, was isolated from a laboratory-scale activated sludge system treating coke plant effluent using thiocyanate-supplemented growth medium. Strain ERB1-3T was oxidase-positive and weakly catalase-positive. The predominant fatty acids were C18 : 1ω7c (35.6 %) and C17 : 1ω6c (29.2 %), and the major respiratory quinone was Q-10. Polar lipids were dominated by sphingoglycolipid and phosphatidylglycerol. Major polyamines were spermidine and sym-homospermidine. The G+C content of the genomic DNA of strain ERB1-3T was 66.4 mol%. Based on the 16S rRNA gene, strain ERB1-3T exhibited the highest sequence similarity values to
Sphingomonas sanxanigenens
DSM 19645T (96.1 %),
Sphingobium scionense
DSM 19371T (95.1 %) and
Stakelama pacifica
LMG 24686T (94.8 %) within the family
Sphingomonadaceae
. The novel isolate had some unique chemotaxonomic features that differentiated it from these closely related strains, contained much more C17 : 1ω6c, C15 : 0 2-OH, C17 : 0 and C17 : 1ω8c fatty acids and possessed diphosphatidylglycerol only in trace amounts. On the basis of the phenotypic, chemotaxonomic and molecular data, strain ERB1-3T is considered to represent a novel genus and species, for which the name Hephaestia caeni gen. nov., sp. nov. is proposed. The type strain is ERB1-3T ( = DSM 25527T = NCAIM B 02511T).
Collapse
|
49
|
Felföldi T, Vengring A, Kéki Z, Márialigeti K, Schumann P, Tóth EM. Eoetvoesia caeni gen. nov., sp. nov., isolated from an activated sludge system treating coke plant effluent. Int J Syst Evol Microbiol 2014; 64:1920-1925. [PMID: 24585374 DOI: 10.1099/ijs.0.058875-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterium, PB3-7B(T), was isolated on phenol-supplemented inorganic growth medium from a laboratory-scale wastewater purification system that treated coke plant effluent. 16S rRNA gene sequence analysis revealed that strain PB3-7B(T) belonged to the family Alcaligenaceae and showed the highest pairwise sequence similarity to Parapusillimonas granuli Ch07(T) (97.5%), Candidimonas bauzanensis BZ59(T) (97.3%) and Pusillimonas noertemannii BN9(T) (97.2%). Strain PB3-7B(T) was rod-shaped, motile and oxidase- and catalase-positive. The predominant fatty acids were C(16 : 0), C(17 : 0) cyclo, C(19 : 0) cyclo ω8c and C(14 : 0) 3-OH, and the major respiratory quinone was Q-8. The G+C content of the genomic DNA of strain PB3-7B(T) was 59.7 mol%. The novel bacterium can be distinguished from closely related type strains based on its urease activity and the capacity for assimilation of glycerol and amygdalin. On the basis of the phenotypic, chemotaxonomic and molecular data, strain PB3-7B(T) is considered to represent a new genus and species, for which the name Eoetvoesia caeni gen. nov., sp. nov. is proposed. The type strain of Eoetvoesia caeni is PB3-7B(T) ( = DSM 25520(T) = NCAIM B 02512(T)).
Collapse
Affiliation(s)
- Tamás Felföldi
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - Anita Vengring
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - Zsuzsa Kéki
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - Károly Márialigeti
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| | - Peter Schumann
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Erika M Tóth
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter stny. 1/c, 1117 Budapest, Hungary
| |
Collapse
|
50
|
Doerges L, Kutschera U. Assembly and loss of the polar flagellum in plant-associated methylobacteria. Naturwissenschaften 2014; 101:339-46. [PMID: 24566997 DOI: 10.1007/s00114-014-1162-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 02/10/2014] [Accepted: 02/12/2014] [Indexed: 01/14/2023]
Abstract
On the leaf surfaces of numerous plant species, inclusive of sunflower (Helianthus annuus L.), pink-pigmented, methanol-consuming, phytohormone-secreting prokaryotes of the genus Methylobacterium have been detected. However, neither the roles, nor the exact mode of colonization of these epiphytic microbes have been explored in detail. Using germ-free sunflower seeds, we document that, during the first days of seedling development, methylobacteria exert no promotive effect on organ growth. Since the microbes are evenly distributed over the outer surface of the above-ground phytosphere, we analyzed the behavior of populations taken from two bacterial strains that were cultivated as solid, biofilm-like clones on agar plates in different aqueous environments (Methylobacterium mesophilicum and M. marchantiae, respectively). After transfer into liquid medium, the rod-shaped, immobile methylobacteria assembled a flagellum and developed into planktonic microbes that were motile. During the linear phase of microbial growth in liquid cultures, the percentage of swimming, flagellated bacteria reached a maximum, and thereafter declined. In stationary populations, living, immotile bacteria, and isolated flagella were observed. Hence, methylobacteria that live in a biofilm, transferred into aqueous environments, assemble a flagellum that is lost when cell density has reached a maximum. This swimming motility, which appeared during ontogenetic development within growing microbial populations, may be a means to colonize the moist outer surfaces of leaves.
Collapse
Affiliation(s)
- L Doerges
- Institute of Biology, University of Kassel, Heinrich-Plett-Str. 40, 34123, Kassel, Germany
| | | |
Collapse
|