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Reiß F, Kiefer N, Purahong W, Borken W, Kalkhof S, Noll M. Active soil microbial composition and proliferation are directly affected by the presence of biocides from building materials. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168689. [PMID: 38000743 DOI: 10.1016/j.scitotenv.2023.168689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/20/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023]
Abstract
Combinations of biocides are commonly added to building materials to prevent microbial growth and thereby cause degradation of the façades. These biocides reach the environment by leaching from façades posing an environmental risk. Although ecotoxicity to the aquatic habitat is well established, there is hardly any data on the ecotoxicological effects of biocides on the soil habitat. This study aimed to characterize the effect of the biocides terbutryn, isoproturon, octhilinone, and combinations thereof on the total and metabolically active soil microbial community composition and functions. Total soil microbial community was retrieved directly from the nucleic acid extracts, while the DNA of the active soil microbial community was separated after bromodeoxyuridine labeling. Bacterial 16S rRNA gene and fungal internal transcribed spacer region gene-based amplicon sequencing was carried out for both active and total, while gene copy numbers were quantified only for the total soil microbial community. Additionally, soil respiration and physico-chemical parameters were analyzed to investigate overall soil microbial activity. The bacterial and fungal gene copy numbers were significantly affected by single biocides and combined biocide soil treatment but not soil respiration and physico-chemical parameters. While the total soil microbiome experienced only minor effects from single and combined biocide treatment, the active soil microbiome was significantly impacted in its diversity, richness, composition, and functional patterns. The active bacterial richness was more sensitive than fungal richness. However, the adverse effects of the biocide combination treatments on soil bacterial richness were highly dependent on the identities of the biocide combination. Our results demonstrate that the presence of biocides frequently used in building materials affects the active soil microbiome. Thereby, the approach described herein can be used as an ecotoxicological measure for the effect on complex soil environments in future studies.
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Affiliation(s)
- Fabienne Reiß
- Institute for Bioanalysis, Department of Applied Natural Sciences and Health, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Nadine Kiefer
- Institute for Bioanalysis, Department of Applied Natural Sciences and Health, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Witoon Purahong
- Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany
| | - Werner Borken
- Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Stefan Kalkhof
- Institute for Bioanalysis, Department of Applied Natural Sciences and Health, Coburg University of Applied Sciences and Arts, Coburg, Germany; Proteomics Unit, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Matthias Noll
- Institute for Bioanalysis, Department of Applied Natural Sciences and Health, Coburg University of Applied Sciences and Arts, Coburg, Germany; Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany.
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2
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Zhang X, Feng G, Liu Y, Li J, Deng X, Yao Q, Zhu H. Characterization of phytopathogen-preying Hyalangium versicolor sp. nov., and proposal for the reclassification of Cystobacter gracilis as Hyalangium gracile comb. Nov. Arch Microbiol 2023; 205:198. [PMID: 37067626 DOI: 10.1007/s00203-023-03512-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/11/2023] [Accepted: 03/23/2023] [Indexed: 04/18/2023]
Abstract
A Gram-staining-negative, aerobic, and rod-shaped with tapered end myxobacterium, designed as strain H56D21T, was isolated from forest soil sampled from the Diaoluo Mountain National Nature Reserve located in Hainan Province, PR China. It showed prey ability on two kinds of phytopathogens including both fungi (Fusarium solani, Fusarium graminearum, and Fusarium oxysporum) and bacteria (Ralstonia solanacearum and Xanthomonas campestris). Phylogenetic analyses based on the 16S rRNA gene and core genes sequences revealed that strain H56D21T belonged to the genus Hyalangium and was most closely related to Cystobacter gracilis DSM 14753 T and Hyalangium minutum DSM 14724 T. Genome comparison showed 85.6% and 82.3% of average nucleotide identity between strain H56D21T and the above two type strains and 29.8% and 25.1% of digital DNA-DNA hybridization , respectively. The novel strain had a large genome size of 13.56 Mbp and a high DNA G + C content of 67.1%. Genome annotation identified 46 secondary metabolite biosynthesis gene clusters and 187 CAZymes-encoding genes. The major fatty acids contained iso-C15:0, iso-C15:0 DMA, C16:1 ω5c, and iso-C17:0. The dominant respiratory quinone was menaquinone 8. Based on the phenotypic, chemotaxonomic and phylogenetic analyses, we suggested that strain H56D21T should represent a novel species of the genus Hyalangium with a proposed name of Hyalangium versicolor sp. nov. (type strain H56D21T = GDMCC 1.1944 T = KCTC 82613 T) and Cystobacter gracilis should be reclassified as Hyalangium gracile comb. nov.
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Affiliation(s)
- Xianjiao Zhang
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
- College of Horticulture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Guangda Feng
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Yang Liu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Jiali Li
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Xiaoqin Deng
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Qing Yao
- College of Horticulture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
| | - Honghui Zhu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China.
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3
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Phillips KE, Akbar S, Stevens DC. Concepts and conjectures concerning predatory performance of myxobacteria. Front Microbiol 2022; 13:1031346. [PMID: 36246230 PMCID: PMC9556981 DOI: 10.3389/fmicb.2022.1031346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/14/2022] [Indexed: 01/28/2023] Open
Abstract
Myxobacteria are excellent model organisms for investigation of predator-prey interactions and predatory shaping of microbial communities. This review covers interdisciplinary topics related to myxobacterial predation and provides current concepts and challenges for determining predatory performance. Discussed topics include the role of specialized metabolites during predation, genetic determinants for predatory performance, challenges associated with methodological differences, discrepancies between sequenced and environmental myxobacteria, and factors that influence predation.
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Affiliation(s)
- Kayleigh E. Phillips
- Department of BioMolecular Sciences, The University of Mississippi, Oxford, MS, United States
| | - Shukria Akbar
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, United States,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - D. Cole Stevens
- Department of BioMolecular Sciences, The University of Mississippi, Oxford, MS, United States,*Correspondence: D. Cole Stevens,
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Wang L, Wang M, Li Q, Zhang J, Li C, Yuan Y, Tan P, Liu H. Dynamics of soil properties and bacterial community structure by mulched fertigation system in semi-arid area of Northeast China. PeerJ 2022; 10:e14044. [PMID: 36168430 PMCID: PMC9509672 DOI: 10.7717/peerj.14044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 08/21/2022] [Indexed: 01/19/2023] Open
Abstract
The agricultural irrigation and fertigation systems have a non-negligible impact on the soil microenvironment in arid and semi-arid areas. Therefore, studying the processes and changes of soil microenvironment under different plastic mulch drip irrigation systems can reveal the "soil-microbe" mechanism and provide a theoretical support for the optimal irrigation and nutrition management of maize in the semi-arid area of Northeast China. Three treatments were used for this study in the semi-arid area of northeast China, namely; mulched fertigation system (MF), drip irrigation system (DI), and farmers' practices system (FP). We used high-throughput sequencing to study the soil bacterial community structure targeting the 16S rRNA gene. The agricultural irrigation and fertigation systems significantly affected soil properties. MF significantly increased bacterial abundance and bacterial diversity and richness. Moreover, MF and DI markedly increased some relative abundance of beneficial bacterial. The bacterial network in MF was more conducive to the health and stability of the agroecosystem and the relationships among species in MF bacterial network were more complex. The agricultural irrigation and fertigation systems had indirect effects on community composition and bacterial diversity through soil organic carbon (SOC), ammonium nitrogen ( NH 4 + -N), nitrate nitrogen ( NO 3 - -N), pH, moisture, NH 4 + -N and NO 3 - -N had indirect effects on yield through bacterial community composition, bacterial diversity and bacterial abundance. These findings suggested that MF was the most effective treatment to improve soil bacterial abundance and diversity, and stabilize the functional quality of soil biological processes.
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Affiliation(s)
- Ling Wang
- Key Laboratory of Soil Resource Sustainable Utilization for Commodity Grain Bases of Jilin Province, College of Resource and Environmental Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Meng Wang
- Institute of Agricultural Environment and Resources Research, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Qian Li
- Institute of Agricultural Environment and Resources Research, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Jinjing Zhang
- Key Laboratory of Soil Resource Sustainable Utilization for Commodity Grain Bases of Jilin Province, College of Resource and Environmental Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Cuilan Li
- Key Laboratory of Soil Resource Sustainable Utilization for Commodity Grain Bases of Jilin Province, College of Resource and Environmental Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Yuhan Yuan
- Key Laboratory of Soil Resource Sustainable Utilization for Commodity Grain Bases of Jilin Province, College of Resource and Environmental Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Pan Tan
- Key Laboratory of Soil Resource Sustainable Utilization for Commodity Grain Bases of Jilin Province, College of Resource and Environmental Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Hang Liu
- Key Laboratory of Soil Resource Sustainable Utilization for Commodity Grain Bases of Jilin Province, College of Resource and Environmental Science, Jilin Agricultural University, Changchun, Jilin, China
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Judicial Opinions 112–122. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Opinion 112 denies the request to place
Seliberia
Aristovskaya and Parinkina 1963 (Approved Lists 1980) on the list of rejected names because the information provided is insufficient. For the same reason, Opinion 113 denies the request to reject
Shewanella irciniae
Lee et al. 2006 and Opinion 114 denies the request to reject the name
Enterobacter siamensis
Khunthongpan et al. 2014. Opinion 115 rejects the epithet of
Moorella thermoautotrophica
(Wiegel et al. 1981) Collins et al. 1994, which is regarded as a nomen confusum. To assess the consequences of Rule 8, Opinion 116 revisits names of taxa above the rank of genus which should comprise the stem of the name of a nomenclatural type and a category-specific ending but fail to do so. Such names should be orthographically corrected if the sole error is the inadvertent usage of an incorrect stem or be regarded as illegitimate if otherwise. The necessary corrections are made for a number of names. In Opinion 117, the request to designate
Methylothermus subterraneus
Hirayama et al. 2011 as the type species of the genus
Methylothermus
is denied because an equivalent action compatible with the Code was already conducted. In Opinion 118, the possible orthographical correction of the name
Flaviaesturariibacter
is treated, as are the analogous cases of
Fredinandcohnia
and
Hydrogeniiclostidium
. The genus names are corrected to Flaviaestuariibacter, Ferdinandcohnia and
Hydrogeniiclostridium
, respectively. Opinion 119 concludes that assigning
Actinomycetales
Buchanan 1917 (Approved Lists 1980) as nomenclatural type of the class
Actinobacteria
Stackebrandt et al. 1997 would not render that name legitimate if Rule 8 remained retroactive. The request is granted but
Actinomycetales
is also assigned as type of
Actinomycetes
Krassilnikov 1949 (Approved Lists 1980). In Opinion 120, the possible orthographical correction of the name
Amycolatopsis albidoflavus
is treated. It is grammatically corrected to Amycolatopsis albidoflava. Six names which could according to Rule 61 be grammatically corrected by anyone are also corrected. Opinion 121 denies the request to revise Opinion 69 and notes that Opinion 69 does not have the undesirable consequences emphasized in the request. In Opinion 122, the request to reject various taxon names of
Mollicutes
proposed in 2018 is denied because it is based on misinterpretations of the Code, which are clarified. Alternative ways to solve the perceived problems are outlined. These Opinions were ratified by the voting members of the International Committee on Systematics of Prokaryotes.
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Babadi ZK, Garcia R, Ebrahimipour GH, Risdian C, Kämpfer P, Jarek M, Müller R, Wink J. Corallococcus soli sp. Nov., a Soil Myxobacterium Isolated from Subtropical Climate, Chalus County, Iran, and Its Potential to Produce Secondary Metabolites. Microorganisms 2022; 10:microorganisms10071262. [PMID: 35888982 PMCID: PMC9323933 DOI: 10.3390/microorganisms10071262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/24/2022] [Accepted: 06/15/2022] [Indexed: 11/16/2022] Open
Abstract
A novel myxobacterial strain ZKHCc1 1396T was isolated in 2017 from a soil sample collected along Chalus Road connecting Tehran and Mazandaran, Iran. It was a Gram-negative, rod-shaped bacterial strain that displayed the general features of Corallococcus, including gliding and fruiting body formation on agar and microbial lytic activity. Strain ZKHCc1 1396T was characterized as an aerobic, mesophilic, and chemoheterotrophic bacterium resistant to many antibiotics. The major cellular fatty acids were branched-chain iso-C17:0 2-OH, iso-C15:0, iso-C17:1, and iso-C17:0. The strain showed the highest 16S rRNA gene sequence similarity to Corallococcusterminator CA054AT (99.67%) and C. praedator CA031BT (99.17%), and formed a novel branch both in the 16S rRNA gene sequence and phylogenomic tree. The genome size was 9,437,609 bp, with a DNA G + C content of 69.8 mol%. The strain had an average nucleotide identity (ANI) value lower than the species cut-off (95%), and with the digital DNA–DNA hybridization (dDDH) below the 70% threshold compared to the closest type strains. Secondary metabolite and biosynthetic gene cluster analyses revealed the strain’s potential to produce novel compounds. Based on polyphasic taxonomic characterization, we propose that strain ZKHCc1 1396T represents a novel species, Corallococcus soli sp. nov. (NCCB 100659T = CIP 111634T).
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Affiliation(s)
- Zahra Khosravi Babadi
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University GC, Tehran 1983969411, Iran;
- Microbial Strain Collection, Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany;
- Correspondence: (Z.K.B.); (J.W.); Tel.: +98-021-29905901 (Z.K.B.); +49-531-61814223 (J.W.); Fax: +98-021-22431664 (Z.K.B.); +49-531-61819499 (J.W.)
| | - Ronald Garcia
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany; (R.G.); (R.M.)
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Gholam Hossein Ebrahimipour
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University GC, Tehran 1983969411, Iran;
| | - Chandra Risdian
- Microbial Strain Collection, Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany;
- Research Unit for Clean Technology, National Research and Innovation Agency (BRIN), Bandung 40135, Indonesia
| | - Peter Kämpfer
- Department of Applied Microbiology, Justus Liebig University Gießen, 35392 Gießen, Germany;
| | - Michael Jarek
- Genome Analytics, Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany;
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany; (R.G.); (R.M.)
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Joachim Wink
- Microbial Strain Collection, Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany;
- Correspondence: (Z.K.B.); (J.W.); Tel.: +98-021-29905901 (Z.K.B.); +49-531-61814223 (J.W.); Fax: +98-021-22431664 (Z.K.B.); +49-531-61819499 (J.W.)
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7
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Corona Ramírez A, Cailleau G, Fatton M, Dorador C, Junier P. Diversity of Lysis-Resistant Bacteria and Archaea in the Polyextreme Environment of Salar de Huasco. Front Microbiol 2022; 13:826117. [PMID: 36687602 PMCID: PMC9847572 DOI: 10.3389/fmicb.2022.826117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/07/2022] [Indexed: 01/25/2023] Open
Abstract
The production of specialized resting cells is a remarkable strategy developed by several organisms to survive unfavorable environmental conditions. Spores are specialized resting cells that are characterized by low to absent metabolic activity and higher resistance. Spore-like cells are known from multiple groups of bacteria, which can form spores under suboptimal growth conditions (e.g., starvation). In contrast, little is known about the production of specialized resting cells in archaea. In this study, we applied a culture-independent method that uses physical and chemical lysis, to assess the diversity of lysis-resistant bacteria and archaea and compare it to the overall prokaryotic diversity (direct DNA extraction). The diversity of lysis-resistant cells was studied in the polyextreme environment of the Salar de Huasco. The Salar de Huasco is a high-altitude athalassohaline wetland in the Chilean Altiplano. Previous studies have shown a high diversity of bacteria and archaea in the Salar de Huasco, but the diversity of lysis-resistant microorganisms has never been investigated. The underlying hypothesis was that the combination of extreme abiotic conditions might favor the production of specialized resting cells. Samples were collected from sediment cores along a saline gradient and microbial mats were collected in small surrounding ponds. A significantly different diversity and composition were found in the sediment cores or microbial mats. Furthermore, our results show a high diversity of lysis-resistant cells not only in bacteria but also in archaea. The bacterial lysis-resistant fraction was distinct in comparison to the overall community. Also, the ability to survive the lysis-resistant treatment was restricted to a few groups, including known spore-forming phyla such as Firmicutes and Actinobacteria. In contrast to bacteria, lysis resistance was widely spread in archaea, hinting at a generalized resistance to lysis, which is at least comparable to the resistance of dormant cells in bacteria. The enrichment of Natrinema and Halarchaeum in the lysis-resistant fraction could hint at the production of cyst-like cells or other resistant cells. These results can guide future studies aiming to isolate and broaden the characterization of lysis-resistant archaea.
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Affiliation(s)
- Andrea Corona Ramírez
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Guillaume Cailleau
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Mathilda Fatton
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Cristina Dorador
- Department of Biotechnology, University of Antofagasta, Antofagasta, Chile
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland,*Correspondence: Pilar Junier,
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8
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Shah AM, Yang W, Mohamed H, Zhang Y, Song Y. Microbes: A Hidden Treasure of Polyunsaturated Fatty Acids. Front Nutr 2022; 9:827837. [PMID: 35369055 PMCID: PMC8968027 DOI: 10.3389/fnut.2022.827837] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/21/2022] [Indexed: 12/26/2022] Open
Abstract
Microbes have gained a lot of attention for their potential in producing polyunsaturated fatty acids (PUFAs). PUFAs are gaining scientific interest due to their important health-promoting effects on higher organisms including humans. The current sources of PUFAs (animal and plant) have associated limitations that have led to increased interest in microbial PUFAs as most reliable alternative source. The focus is on increasing the product value of existing oleaginous microbes or discovering new microbes by implementing new biotechnological strategies in order to compete with other sources. The multidisciplinary approaches, including metabolic engineering, high-throughput screening, tapping new microbial sources, genome-mining as well as co-culturing and elicitation for the production of PUFAs, have been considered and discussed in this review. The usage of agro-industrial wastes as alternative low-cost substrates in fermentation for high-value single-cell oil production has also been discussed. Multidisciplinary approaches combined with new technologies may help to uncover new microbial PUFA sources that may have nutraceutical and biotechnological importance.
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Affiliation(s)
- Aabid Manzoor Shah
- Colin Ratledge Center of Microbial Lipids, School of Agriculture Engineering and Food Sciences, Shandong University of Technology, Zibo, China
| | - Wu Yang
- Colin Ratledge Center of Microbial Lipids, School of Agriculture Engineering and Food Sciences, Shandong University of Technology, Zibo, China
| | - Hassan Mohamed
- Colin Ratledge Center of Microbial Lipids, School of Agriculture Engineering and Food Sciences, Shandong University of Technology, Zibo, China
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assiut, Egypt
| | - Yingtong Zhang
- Institute of Agricultural Facilities and Equipment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yuanda Song
- Colin Ratledge Center of Microbial Lipids, School of Agriculture Engineering and Food Sciences, Shandong University of Technology, Zibo, China
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9
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Corallococcus silvisoli sp. nov., a novel myxobacterium isolated from subtropical forest soil. Arch Microbiol 2022; 204:141. [PMID: 35041085 DOI: 10.1007/s00203-021-02725-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/26/2021] [Accepted: 12/13/2021] [Indexed: 01/26/2023]
Abstract
An orange-pigmented myxobacterium, designated strain c25j21T, was isolated from subtropical forest soil collected from the Chebaling National Nature Reserve in Guangdong Province, China. Phylogenetic analysis based on the 16S rRNA gene and core genes clearly showed that the novel strain was affiliated within the genus Corallococcus and most closely related to Corallococcus aberystwythensis DSM 108846T (99.3% 16S rRNA gene sequence similarity), while C. exercitus DSM 108849T (99.2%) and C. carmarthensis DSM 108842T (99.0%) were the next most closely related type strains. The draft genome sequence of strain c25j21T was 9.23 Mb in length with a G + C content of 70.7 mol%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain c25j21T and its closely related type strains were 88.1-89.1 and 34.1-36.3%, respectively. The major fatty acids contained iso-C15:0, iso-C17:0, iso-C17:1ω5c and iso-C17:0 2-OH. The predominant respiratory quinone was menaquinone 7. Based on phylogenetic, phenotypic and chemotaxonomic analysis, strain c25j21T represents a novel species of the genus Corallococcus, for which the name Corallococcus silvisoli sp. nov. is proposed. The type strain is c25j21T (= GDMCC 1.1387T = KCTC 62437T).
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10
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Shrivastava A, Sharma RK. Myxobacteria and their products: current trends and future perspectives in industrial applications. Folia Microbiol (Praha) 2021; 66:483-507. [PMID: 34060028 DOI: 10.1007/s12223-021-00875-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 05/13/2021] [Indexed: 12/12/2022]
Abstract
Myxobacteria belong to a group of bacteria that are known for their well-developed communication system and synchronized or coordinated movement. This typical behavior of myxobacteria is mediated through secondary metabolites. They are capable of producing secondary metabolites belonging to several chemical classes with unique and wide spectrum of bioactivities. It is predominantly significant that myxobacteria specialize in mechanisms of action that are very rare with other producers. Most of the metabolites have been explored for their medical and pharmaceutical values while a lot of them are still unexplored. This review is an attempt to understand the role of potential metabolites produced by myxobacteria in different applications. Different myxobacterial metabolites have demonstrated antibacterial, antifungal, and antiviral properties along with cytotoxic activity against various cell lines. Beside their metabolites, these myxobacteria have also been discussed for better exploitation and implementation in different industrial sectors.
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Affiliation(s)
- Akansha Shrivastava
- Department of Biosciences, Manipal University Jaipur, Rajasthan, 303007, Jaipur, India
| | - Rakesh Kumar Sharma
- Department of Biosciences, Manipal University Jaipur, Rajasthan, 303007, Jaipur, India.
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11
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Jovanovic S, Dietrich D, Becker J, Kohlstedt M, Wittmann C. Microbial production of polyunsaturated fatty acids - high-value ingredients for aquafeed, superfoods, and pharmaceuticals. Curr Opin Biotechnol 2021; 69:199-211. [PMID: 33540327 DOI: 10.1016/j.copbio.2021.01.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 01/01/2021] [Accepted: 01/10/2021] [Indexed: 12/26/2022]
Abstract
Polyunsaturated fatty acids (PUFAs), primarily docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), have received worldwide attention in recent years due to an increasing awareness of their uniqueness in improving diet and human health and their apparently inevitable shortage in global availability. Microbial cell factories are a major solution to supplying these precious molecules in sufficient amounts and providing PUFA-rich aquafeed, superfoods, and medical formulations. This review assesses the PUFA world markets and highlights recent advances in upgrading and streamlining microalgae, yeasts, fungi, and bacteria for high-level PUFA production and broadening of the PUFA spectrum.
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Affiliation(s)
- Sofija Jovanovic
- Institute of Systems Biotechnology, Universität des Saarlandes, Germany
| | - Demian Dietrich
- Institute of Systems Biotechnology, Universität des Saarlandes, Germany
| | - Judith Becker
- Institute of Systems Biotechnology, Universität des Saarlandes, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Universität des Saarlandes, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Universität des Saarlandes, Germany.
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12
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Garcia R, Müller R. Simulacricoccus ruber gen. nov., sp. nov., a microaerotolerant, non-fruiting, myxospore-forming soil myxobacterium and emended description of the family Myxococcaceae. Int J Syst Evol Microbiol 2018; 68:3101-3110. [PMID: 30113300 DOI: 10.1099/ijsem.0.002936] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
A non-fruiting group of myxobacteria was previously speculated to exist in nature based on metagenomics data containing uncultured members of the order Myxococcales. Here, we describe a myxobacterial strain, designated MCy10636T, which was isolated from a German soil sample collected in 2013. It exhibits swarming characteristics but atypically produces myxospores in the absence of fruiting bodies. The novel strain stains Gram-negative and Congo-red-negative and is characterized mesophilic, neutrophilic, chemoheterotrophic and microaerotolerant. Branched-chain fatty acids are the predominant cellular fatty acids over the straight-chain type, and contain the major fatty acids iso-C17 : 0 2-OH, C16 : 1, iso-C17 : 0 and iso-C15 : 0. Based on blastn results, the 16S rRNA gene sequence reveals similarity (97 %) to Aggregicoccus edonensis MCy1366T, (97 %) Myxococcus macrosporus DSM 14697T, (96 %) Corallococcus coralloides DSM2259T and Corallococcus exiguus Cc e167T. Phylogenetic analysis showed a novel lineage of MCy10636T in the family Myxococcaceae, suborder Cystobacterineae. Based on polyphasic taxonomic characterization, we propose that this unusual, non-fruiting, myxospore-forming and microaerotolerant myxobacterial strain, MCy10636T, represents a novel genus and species, Simulacricoccus ruber gen. nov., sp. nov. (DSM 106554T=NCCB 100651T).
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Affiliation(s)
- Ronald Garcia
- 1Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Saarland University Campus Building E8 1, 66123 Saarbrücken, Germany.,2German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Rolf Müller
- 1Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Saarland University Campus Building E8 1, 66123 Saarbrücken, Germany.,2German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, 38124 Braunschweig, Germany.,3Department of Pharmacy, Saarland University, Building E8 1, 66123 Saarbrücken, Germany
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13
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Mohr KI, Moradi A, Glaeser SP, Kämpfer P, Gemperlein K, Nübel U, Schumann P, Müller R, Wink J. Nannocystis konarekensis sp. nov., a novel myxobacterium from an Iranian desert. Int J Syst Evol Microbiol 2018; 68:721-729. [DOI: 10.1099/ijsem.0.002569] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Kathrin I. Mohr
- Microbial Drugs, Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany
| | - Azam Moradi
- Department of Microbiology, Faculty of Biological Sciences, Shahid Beheshti University, Tehran, Iran
| | - Stefanie P. Glaeser
- Department of Applied Microbiology, Justus-Liebig University Gießen, 35392 Gießen, Germany
| | - Peter Kämpfer
- Department of Applied Microbiology, Justus-Liebig University Gießen, 35392 Gießen, Germany
| | - Katja Gemperlein
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) – Helmholtz Centre for Infection Research (HZI), Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
- Department of Pharmaceutical Biotechnology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Ulrich Nübel
- Microbial Genome Research, Leibniz Institute DSMZ-German Collection of Microrganisms and Cell Cultures, Braunschweig, Germany
- German Center of Infection Research (DZIF), Braunschweig, Germany
| | - Peter Schumann
- Department Central Services, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) – Helmholtz Centre for Infection Research (HZI), Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
- Department of Pharmaceutical Biotechnology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Joachim Wink
- Microbial Strain Collection, Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany
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14
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Affiliation(s)
- Silke C. Wenzel
- Saarland University; Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Pharmaceutical Biotechnology; Saarland University Campus, Building E8.1 66123 Saarbrücken Germany
| | - Rolf Müller
- Saarland University; Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Pharmaceutical Biotechnology; Saarland University Campus, Building E8.1 66123 Saarbrücken Germany
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15
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Garcia R, Stadler M, Gemperlein K, Müller R. Aetherobacter fasciculatus gen. nov., sp. nov. and Aetherobacter rufus sp. nov., novel myxobacteria with promising biotechnological applications. Int J Syst Evol Microbiol 2016; 66:928-938. [DOI: 10.1099/ijsem.0.000813] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Affiliation(s)
- Ronald Garcia
- Department of Microbial Natural Products (MINS),Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) – Helmholtz Centre for Infection Research (HZI) and Department of Pharmaceutical Biotechnology of Saarland University, Saarland University Campus Building E8 1, D-66123, Saarbrücken,Germany
- German Center for Infection Research (DZIF),Partner Site Hannover–Braunschweig, D-38124, Braunschweig,Germany
| | - Marc Stadler
- German Center for Infection Research (DZIF),Partner Site Hannover–Braunschweig, D-38124, Braunschweig,Germany
- Department of Microbial Drugs,Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, D-38124, Braunschweig,Germany
| | - Katja Gemperlein
- Department of Microbial Natural Products (MINS),Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) – Helmholtz Centre for Infection Research (HZI) and Department of Pharmaceutical Biotechnology of Saarland University, Saarland University Campus Building E8 1, D-66123, Saarbrücken,Germany
| | - Rolf Müller
- Department of Microbial Natural Products (MINS),Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) – Helmholtz Centre for Infection Research (HZI) and Department of Pharmaceutical Biotechnology of Saarland University, Saarland University Campus Building E8 1, D-66123, Saarbrücken,Germany
- German Center for Infection Research (DZIF),Partner Site Hannover–Braunschweig, D-38124, Braunschweig,Germany
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16
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Approach to analyze the diversity of myxobacteria in soil by semi-nested PCR-denaturing gradient gel electrophoresis (DGGE) based on taxon-specific gene. PLoS One 2014; 9:e108877. [PMID: 25280065 PMCID: PMC4184826 DOI: 10.1371/journal.pone.0108877] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 08/27/2014] [Indexed: 11/19/2022] Open
Abstract
The genotypic diversity of insoluble macromolecules degraded myxobacteria, provided an opportunity to discover new bacterial resources and find new ecological functions. In this study, we developed a semi-nested-PCR-denaturing gradient gel electrophoresis (DGGE) strategy to determine the presence and genotypic diversity of myxobacteria in soil. After two rounds of PCR with myxobacteria-specific primers, an 194 bp fragment of mglA, a key gene involved in gliding motility, suitable for DGGE was obtained. A large number of bands were observed in DGGE patterns, indicating diverse myxobacteria inhabiting in soils. Furthermore, sequencing and BLAST revealed that most of the bands belonged to the myxobacteria-group, and only three of the twenty-eight bands belonged to other group, i.e., Deinococcus maricopensis. The results verified that myxobacterial strains with discrepant sequence compositions of gene mglA could be discriminated by DGGE with myxobacteria-specific primers. Collectively, the developed semi-nested-PCR-DGGE strategy is a useful tool for studying the diversity of myxobacteria.
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17
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Garcia R, Gemperlein K, Müller R. Minicystis rosea gen. nov., sp. nov., a polyunsaturated fatty acid-rich and steroid-producing soil myxobacterium. Int J Syst Evol Microbiol 2014; 64:3733-3742. [PMID: 25114157 DOI: 10.1099/ijs.0.068270-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A bacterial strain designated SBNa008(T) was isolated from a Philippine soil sample. It exhibited the general characteristics associated with myxobacteria, such as swarming of Gram-negative vegetative rod cells, fruiting body and myxospore formation and predatory behaviour in lysing micro-organisms. The novel strain was characterized as mesophilic, chemoheterotrophic and aerobic. The major fatty acids were C(20:4)ω6,9,12,15 all cis (arachidonic acid), iso-C(15 : 0), C(17 : 1) 2-OH and iso-C(15 : 0) dimethylacetal. Interestingly, SBNa008(T) contained diverse fatty acids belonging to the commercially valuable polyunsaturated omega-6 and omega-3 families, and a highly conjugated dihydroxylated C28 steroid. The G+C content of the genomic DNA was 67.3 mol%. The 16S rRNA gene sequence revealed 95-96% similarity to sequences derived from clones of uncultured bacteria and 94-95% similarity to cultured members of the suborder Sorangiineae. Phylogenetic analysis revealed that strain SBNa008(T) formed a novel lineage in the suborder Sorangiineae. Based on a polyphasic taxonomic characterization, we propose that strain SBNa008(T) represents a novel genus and species, Minicystis rosea gen. nov., sp. nov. The type strain of Minicystis rosea is SBNa008(T) ( =DSM 24000(T) =NCCB 100349(T)).
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Affiliation(s)
- Ronald Garcia
- German Center for Infection Research (DZIF), Partner site Hannover, 38124 Braunschweig, Germany.,Department of Pharmaceutical Biotechnology, Saarland University, Building C2 3, 66123 Saarbrücken, Germany.,Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Saarland University Campus Building C2 3, 66123 Saarbrücken, Germany
| | - Katja Gemperlein
- Department of Pharmaceutical Biotechnology, Saarland University, Building C2 3, 66123 Saarbrücken, Germany.,Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Saarland University Campus Building C2 3, 66123 Saarbrücken, Germany
| | - Rolf Müller
- German Center for Infection Research (DZIF), Partner site Hannover, 38124 Braunschweig, Germany.,Department of Pharmaceutical Biotechnology, Saarland University, Building C2 3, 66123 Saarbrücken, Germany.,Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Saarland University Campus Building C2 3, 66123 Saarbrücken, Germany
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18
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Yamamoto E, Muramatsu H, Nagai K. Vulgatibacter incomptus gen. nov., sp. nov. and Labilithrix luteola gen. nov., sp. nov., two myxobacteria isolated from soil in Yakushima Island, and the description of Vulgatibacteraceae fam. nov., Labilitrichaceae fam. nov. and Anaeromyxobacteraceae fam. nov. Int J Syst Evol Microbiol 2014; 64:3360-3368. [PMID: 25048208 DOI: 10.1099/ijs.0.063198-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two myxobacterial strains (designated B00001(T) and B00002(T)) were isolated from forest soil samples collected from Yakushima Island, Kagoshima, Japan. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains B00001(T) and B00002(T) respectively formed independent branches within the suborders Cystobacterineae and Sorangiineae and were most closely related to Cystobacter armeniaca DSM 14710(T) (90.4% similarity) and Byssovorax cruenta DSM 14553(T) (91.3%). Neither strain showed typical features of myxobacteria such as bacteriolytic action or fruiting body formation, but both had high DNA G+C contents (66.3-68.3 mol%). Swarming motility was observed in strain B00002(T) only. Cells of both strains were vegetative, chemoheterotrophic, mesophilic, strictly aerobic, Gram-negative, motile rods, and both strains exhibited esterase lipase (C8), leucine arylamidase, naphthol-AS-BI-phosphohydrolase and β-galactosidase activities. Strain B00001(T) contained MK-7 as the predominant respiratory quinone and the major fatty acid was iso-C15:0. In contrast, strain B00002(T) contained MK-8 as the major cellular quinone and the major fatty acids were C16 : 1ω5c and iso-C17 : 0. Based on the phenotypic and genotypic data presented, strains B00001(T) and B00002(T) represent novel genera and species, for which we propose the names Vulgatibacter incomptus gen. nov., sp. nov. and Labilithrix luteola gen. nov., sp. nov., respectively. The type strains of Vulgatibacter incomptus and Labilithrix luteola are B00001(T) ( = NBRC 109945(T) = DSM 27710(T)) and B00002(T) ( = NBRC 109946(T) = DSM 27648(T)), respectively. The new genera are assigned to the new families Vulgatibacteraceae fam. nov. and Labilitrichaceae fam. nov., respectively. In addition, Anaeromyxobacteraceae fam. nov., is proposed to accommodate the genus Anaeromyxobacter, which is related to the genus Vulgatibacter.
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Affiliation(s)
- Eisaku Yamamoto
- Fermentation Research Division, Astellas Research Technologies Co., Ltd, Tsukuba, Ibaraki, Japan
| | - Hideyuki Muramatsu
- Fermentation Research Division, Astellas Research Technologies Co., Ltd, Tsukuba, Ibaraki, Japan
| | - Koji Nagai
- Fermentation Research Division, Astellas Research Technologies Co., Ltd, Tsukuba, Ibaraki, Japan
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19
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A multifunctional enzyme is involved in bacterial ether lipid biosynthesis. Nat Chem Biol 2014; 10:425-7. [DOI: 10.1038/nchembio.1526] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Accepted: 04/14/2014] [Indexed: 11/09/2022]
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20
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Sood S, Awal RP, Wink J, Mohr KI, Rohde M, Stadler M, Kämpfer P, Glaeser SP, Schumann P, Garcia R, Müller R. Aggregicoccus edonensis gen. nov., sp. nov., an unusually aggregating myxobacterium isolated from a soil sample. Int J Syst Evol Microbiol 2014; 65:745-753. [PMID: 24591423 DOI: 10.1099/ijs.0.061176-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel myxobacterium, MCy1366(T) (Ar1733), was isolated in 1981 from a soil sample collected from a region near Tokyo, Japan. It displayed general myxobacterial features like Gram-negative-staining, rod-shaped vegetative cells, gliding on solid surfaces, microbial lytic activity, fruiting-body-like aggregates and myxospore-like structures. The strain was mesophilic, aerobic and showed a chemoheterotrophic mode of nutrition. It was resistant to many antibiotics such as cephalosporin C, kanamycin, gentamicin, hygromycin B, polymyxin and bacitracin, and the key fatty acids of whole cell hydrolysates were iso-C15 : 0, iso-C17 : 0 and iso-C17 : 0 2-OH. The genomic DNA G+C content of the novel strain was 65.6 mol%. The 16S rRNA gene sequence showed highest similarity (97.60 %) to 'Stigmatella koreensis' strain KYC-1019 (GenBank accession no. EF112185). Phylogenetic analysis based on 16S rRNA gene sequences and MALDI-TOF MS data revealed a novel branch in the family Myxococcaceae. DNA-DNA hybridization showed only 28 % relatedness between the novel strain and the closest recognized species, Corallococcus exiguus DSM 14696(T) (97 % 16S rRNA gene sequence similarity). A recent isolate from a soil sample collected in Switzerland, MCy10622, displayed 99.9 % 16S rRNA gene sequence similarity with strain MCy1366(T) and showed almost the same characteristics. Since some morphological features like fruiting-body-like aggregates were barely reproducible in the type strain, the newly isolated strain, MCy10622, was also intensively studied. On the basis of a comprehensive taxonomic study, we propose a novel genus and species, Aggregicoccus edonensis gen. nov., sp. nov., for strains MCy1366(T) and MCy10622. The type strain of the type species is MCy1366(T) ( = DSM 27872(T) = NCCB 100468(T)).
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Affiliation(s)
- Sakshi Sood
- Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University, Grisebachstraße 8, 37077 Göttingen, Germany.,Department of Microbial Drugs, Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, D-38124 Braunschweig, Germany
| | - Ram Prasad Awal
- Department of Pharmaceutical Biotechnology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany.,Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Joachim Wink
- Department of Microbial Drugs, Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, D-38124 Braunschweig, Germany
| | - Kathrin I Mohr
- Department of Microbial Drugs, Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, D-38124 Braunschweig, Germany
| | - Manfred Rohde
- Department of Medical Microbiology, Central Facility for Microscopy, Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, D-38124 Braunschweig, Germany
| | - Marc Stadler
- Department of Microbial Drugs, Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, D-38124 Braunschweig, Germany
| | - Peter Kämpfer
- Department of Applied Microbiology, Justus Liebig University Gießen, Heinrich-Buff-Ring 26, D-35392 Gießen, Germany
| | - Stefanie P Glaeser
- Department of Applied Microbiology, Justus Liebig University Gießen, Heinrich-Buff-Ring 26, D-35392 Gießen, Germany
| | - Peter Schumann
- Central Services, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Ronald Garcia
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Rolf Müller
- Department of Pharmaceutical Biotechnology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany.,Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
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Iizuka T, Jojima Y, Hayakawa A, Fujii T, Yamanaka S, Fudou R. Pseudenhygromyxa salsuginis gen. nov., sp. nov., a myxobacterium isolated from an estuarine marsh. Int J Syst Evol Microbiol 2013; 63:1360-1369. [DOI: 10.1099/ijs.0.040501-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A myxobacterial strain, designated SYR-2T, was obtained from a mud sample from an estuarine marsh alongside the Yoshino River, Shikoku, Japan. It had rod-shaped vegetative cells and formed bacteriolytic enlarging colonies or so-called ‘swarms’ in the agar media. Fruiting-body-like globular to polyhedral cell aggregates and myxospore-like spherical to ellipsoidal cells within them were observed. Those features coincided with the general characteristics of myxobacteria. The strain was mesophilic and strictly aerobic. Growth of SYR-2T was observed at 18–40 °C (optimum, 30–35 °C), pH 5.5–8.3 (optimum, pH 7.0–7.5) and with 0.0–2.5 % (w/v) NaCl (optimum, 0.2–1.0 %). Both Mg2+ and Ca2+ were essential cations for the growth. The predominant fatty acids were iso-C15 : 0 (43.8 %), iso-C17 : 0 (22.4 %) and iso-C16 : 0 (9.6 %). A C20 : 4 fatty acid [arachidonic acid (4.3 %)], iso-C19 : 0 (1.5 %) and anteiso-acids [ai-C15 : 0 (0.5 %), ai-C17 : 0 (0.3 %)] were also detected. The G+C content of the DNA was 69.7 mol%. The strain contained menaquinone-7 (MK-7) as the major respiratory quinone. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SYR-2T belonged to the suborder
Nannocystineae
, order
Myxococcales
in the class
Deltaproteobacteria
, and the strain was most closely related to two type strains of marine myxobacteria,
Enhygromyxa salina
SHK-1T and
Plesiocystis pacifica
SIR-1T, with 96.5 % and 96.0 % similarities, respectively. These characteristics determined in this polyphasic study suggested that strain SYR-2T represents a novel species in a new genus of myxobacteria. The name Pseudenhygromyxa salsuginis gen. nov., sp. nov. is proposed to accommodate this isolate, and the type strain of Pseudenhygromyxa salsuginis is SYR-2T ( = NBRC 104351T = DSM 21377T).
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Affiliation(s)
- Takashi Iizuka
- Frontier Research Labs, Institute for Innovation, Ajinomoto Co. Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki 210-8681, Japan
| | - Yasuko Jojima
- Frontier Research Labs, Institute for Innovation, Ajinomoto Co. Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki 210-8681, Japan
| | - Atsushi Hayakawa
- Frontier Research Labs, Institute for Innovation, Ajinomoto Co. Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki 210-8681, Japan
| | - Takayoshi Fujii
- Frontier Research Labs, Institute for Innovation, Ajinomoto Co. Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki 210-8681, Japan
| | - Shigeru Yamanaka
- Faculty of Textile Science and Technology, Shinshu University, Ueda 386-8567, Japan
| | - Ryosuke Fudou
- Frontier Research Labs, Institute for Innovation, Ajinomoto Co. Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki 210-8681, Japan
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Li SG, Zhou XW, Li PF, Han K, Li W, Li ZF, Wu ZH, Li YZ. The existence and diversity of myxobacteria in lake mud - a previously unexplored myxobacteria habitat. ENVIRONMENTAL MICROBIOLOGY REPORTS 2012; 4:587-595. [PMID: 23760929 DOI: 10.1111/j.1758-2229.2012.00373.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 07/22/2012] [Indexed: 06/02/2023]
Abstract
Myxobacteria are widely distributed in soil and oceanic sediment with a phylogeographic separation at high levels of classification. However, it is unclear whether freshwater environments, from which there has been no isolation report of myxobacteria since 1981, are habitats for myxobacteria. In this study, we investigated the presence of myxobacteria in lake mud using a two-step strategy. First, we constructed two universal bacterial libraries from the V3-V4 (V34) and V6-V8 (V678) hypervariable regions of 16S rRNA gene sequences. High-throughput 454 pyrosequencing revealed that myxobacteria were one of the major bacterial groups in the lake mud. They accounted for 5.77% of the total sequences and 7.52% of the total operational taxonomic units (OTUs) at a phylogenetic distance of 0.03. The community composition and taxonomic structure of the mud myxobacterial community were further analysed using myxobacteria-enriched libraries targeting the V34 and V678 regions, which were amplified with Cystobacterineae- and Sorangineae-specific primer pairs respectively. Phylogenetic analysis showed that the limnetic myxobacteria exhibited closer relationships to their soil than their marine relatives, but there were also exclusive taxa of limnetic myxobacteria detected. These results, together with a survey on available GenBank data, indicate that lake mud is a primary habitat for myxobacteria.
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Affiliation(s)
- Shu-Guang Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China
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23
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Mohr KI, Garcia RO, Gerth K, Irschik H, Müller R. Sandaracinus amylolyticus gen. nov., sp. nov., a starch-degrading soil myxobacterium, and description of Sandaracinaceae fam. nov. Int J Syst Evol Microbiol 2012; 62:1191-1198. [DOI: 10.1099/ijs.0.033696-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A novel starch-degrading myxobacterium designated NOSO-4T (new organism of the
Sorangiineae
strain 4) was isolated in 1995 from a soil sample containing plant residues, collected in Lucknow, Uttar Pradesh, India. The novel bacterium shows typical myxobacterial characteristics such as Gram-negative, rod-shaped vegetative cells, swarming colonies, fruiting body-like aggregates and bacteriolytic activity. The strain is mesophilic, strictly aerobic and chemoheterotrophic. Based on 16S rRNA gene sequences, NOSO-4T shows highest similarity (96.2 %) with the unidentified bacterial strain O29 (accession no. FN554397), isolated from leek (Allium porrum) rhizosphere, and to the myxobacteria
Jahnella thaxteri
(88.9 %) and
Chondromyces pediculatus
(88.5 %). Major fatty acids are C17 : 1 2-OH, C20 : 4ω6 (arachidonic acid), and the straight-chain fatty acids C17 : 0, C15 : 0 and C16 : 0. The genomic DNA G+C content of the novel isolate is 66.8 mol%. It is proposed that strain NOSO-4T represents a novel species in a new genus, i.e. Sandaracinus amylolyticus gen. nov., sp. nov., but also belongs to a new family, Sandaracinaceae fam. nov. The type strain of the type species, S. amylolyticus sp. nov., is NOSO-4T ( = DSM 53668T = NCCB 100362T).
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Affiliation(s)
- Kathrin I. Mohr
- Department of Microbial Drugs, Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, D-38124 Braunschweig, Germany
| | - Ronald O. Garcia
- Department of Pharmaceutical Biotechnology, Saarland University, Campus C2 3 66123 Saarbrücken, Germany
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) – Helmholtz Centre for Infection Research (HZI), Saarland University, Campus C2 3 66123 Saarbrücken, Germany
| | - Klaus Gerth
- Department of Microbial Drugs, Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, D-38124 Braunschweig, Germany
| | - Herbert Irschik
- Department of Microbial Drugs, Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, D-38124 Braunschweig, Germany
| | - Rolf Müller
- Department of Pharmaceutical Biotechnology, Saarland University, Campus C2 3 66123 Saarbrücken, Germany
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) – Helmholtz Centre for Infection Research (HZI), Saarland University, Campus C2 3 66123 Saarbrücken, Germany
- Department of Microbial Drugs, Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, D-38124 Braunschweig, Germany
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Gawas D, Garcia R, Huch V, Müller R. A highly conjugated dihydroxylated C28 steroid from a myxobacterium. JOURNAL OF NATURAL PRODUCTS 2011; 74:1281-1283. [PMID: 21513291 DOI: 10.1021/np100682c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In the course of our search for novel secondary metabolites, the CHCl3-MeOH extract of the novel myxobacterial strain Sorangiineae SBNa008 was shown to be active against human SW480 colon adinocarcinoma cells. Bioassay-guided fractionation of the extract yielded a highly conjugated novel, sterol 9α,11α-dihydroxyergosta-4,6,8(14),22-tetraen-3-one, 1. The structure and the relative stereochemistry of 1 were established from interpretation of spectroscopic data and X-ray crystallography.
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Affiliation(s)
- Dnyaneshwar Gawas
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
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25
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Fatty acid-related phylogeny of myxobacteria as an approach to discover polyunsaturated omega-3/6 Fatty acids. J Bacteriol 2011; 193:1930-42. [PMID: 21317327 DOI: 10.1128/jb.01091-10] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In an analysis of 47 aerobic myxobacterial strains, representing 19 genera in suborders Cystobacterineae, Nannocystineae, Sorangiineae, and a novel isolate, "Aetherobacter" SBSr008, an enormously diverse array of fatty acids (FAs) was found. The distribution of straight-chain fatty acids (SCFAs) and branched-chain fatty acids (BCFAs) supports the reported clustering of strains in the phylogenetic tree based on 16S rRNA genes. This finding additionally allows the prediction and assignment of the novel isolate SBSr008 into its corresponding taxon. Sorangiineae predominantly contains larger amounts of SCFA (57 to 84%) than BCFA. On the other hand, Cystobacterineae exhibit significant BCFA content (53 to 90%), with the exception of the genus Stigmatella. In Nannocystineae, the ratio of BCFA and SCFA seems dependent on the taxonomic clade. Myxobacteria could also be identified and classified by using their specific and predominant FAs as biomarkers. Nannocystineae is remarkably unique among the suborders for its absence of hydroxy FAs. After the identification of arachidonic (AA) FA in Phaselicystidaceae, eight additional polyunsaturated fatty acids (PUFAs) belonging to the omega-6 and omega-3 families were discovered. Here we present a comprehensive report of FAs found in aerobic myxobacteria. Gliding bacteria belonging to Flexibacter and Herpetosiphon were chosen for comparative analysis to determine their FA profiles in relation to the myxobacteria.
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26
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Garcia R, Gerth K, Stadler M, Dogma IJ, Müller R. Expanded phylogeny of myxobacteria and evidence for cultivation of the 'unculturables'. Mol Phylogenet Evol 2010; 57:878-87. [PMID: 20807581 DOI: 10.1016/j.ympev.2010.08.028] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Revised: 08/10/2010] [Accepted: 08/12/2010] [Indexed: 10/19/2022]
Abstract
An expanded neighbour-joining tree of myxobacteria is presented based on the analysis of 16S rRNA gene sequences of 101 strains (including types) representing 3 suborders, 6 families, 20 genera, 46 species, and 12 other novel taxa. The distinctions amongst members of the three suborders (Sorangiineae, Cytobacterineae and Nannocystineae) are reaffirmed. The positions of anaerobic myxobacteria, novel groups (Pyxidicoccus and several Cystobacter species) in Cystobacterineae, the marine genera (Plesiocystis, Haliangium, Enhygromyxa), and two additional novel taxa ('Paraliomyxa miuraensis', brackish-water isolate) were together revealed for the first time. Changes in the nomenclature of several isolates (Polyangium vitellinum Pl vt1(T), Polyangium thaxteri Pl t3, Polyangium cellulosum, NOSO-1, NOCB-2, NOCB-4) are also highlighted. Suborders Sorangiineae and Nannocystineae hold great promise for novel strain discovery. In Sorangiineae, the new family Phaselicystidaceae, with a monotypic genus, was added. Nine additional novel taxa were discovered in this suborder for which new genera or even families may be erected in the near future. These taxa appear to represent the so-called viable but not culturable (VBNC) group of myxobacteria. Based on at least 4% phylogenetic distance, new clades were formed comprising of novel Nannocystineae and Sorangiineae isolates. Overall, the myxobacteria, on the basis of bracket distance, could be divided into 16 clusters, as supported by tree topology and a morphology-based approach.
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Affiliation(s)
- Ronald Garcia
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
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27
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Ring MW, Schwär G, Bode HB. Biosynthesis of 2-hydroxy and iso-even fatty acids is connected to sphingolipid formation in myxobacteria. Chembiochem 2009; 10:2003-10. [PMID: 19575369 DOI: 10.1002/cbic.200900164] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
2-Hydroxy fatty acids can be found in several different organisms, including bacteria. In this study, we have studied the biosynthesis of 2-hydroxy fatty acids in the myxobacteria Myxococcus xanthus and Stigmatella aurantiaca, resulting in the identification of a family of stereospecific fatty acid alpha-hydroxylases. Although the stereospecificities of the hydroxylases differ between these two species, they share a common function in supporting fatty acid alpha-oxidation; that is, the oxidative shortening of fatty acids. Whereas in S. aurantiaca this process takes place during normal vegetative growth, in M. xanthus it takes place only under developmental conditions. We were also able to identify serine palmitoyltransferase encoding genes involved in sphingolipid biosynthesis as well as sphingolipids themselves in both types of myxobacteria, and were able to show that the alpha-hydroxylation reaction is in fact dependent on the presence of fatty acids bound to sphingolipids.
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Affiliation(s)
- Michael W Ring
- Institut für Pharmazeutische Biotechnologie, Universität des Saarlandes, 66041 Saarbrücken (Germany)
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28
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Garcia RO, Krug D, Müller R. Chapter 3. Discovering natural products from myxobacteria with emphasis on rare producer strains in combination with improved analytical methods. Methods Enzymol 2009; 458:59-91. [PMID: 19374979 DOI: 10.1016/s0076-6879(09)04803-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Myxobacteria produce a range of structurally novel natural products which exhibit unusual or unique modes of action, attracting significant interest from both the academic and drug discovery communities. Efforts to discover new strains with the potential to biosynthesize novel molecules have revealed that myxobacterial diversity and natural products are far from exhausted. We describe here a general, nonselective approach to unearth further myxobacterial strains, in order to mine them for compounds with potential as medicines. Sample collection from locations world-wide has shown that environments which exhibit significant biological complexity yield the highest probability of isolating novel myxobacterial strains. Here, we illustrate the details of simple and efficient strain purification techniques, which lead systematically to the identification of new and promising myxobacteria. Compound identification is then facilitated by molecular biological approaches, coupled with sophisticated high resolution mass spectrometry, statistical analysis, and bioassays.
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Affiliation(s)
- Ronald O Garcia
- Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
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