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Wielgoss S, Van Dyken JD, Velicer GJ. Mutation Rate and Effective Population Size of the Model Cooperative Bacterium Myxococcus xanthus. Genome Biol Evol 2024; 16:evae066. [PMID: 38526062 PMCID: PMC11069108 DOI: 10.1093/gbe/evae066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 03/26/2024] Open
Abstract
Intrinsic rates of genetic mutation have diverged greatly across taxa and exhibit statistical associations with several other parameters and features. These include effective population size (Ne), genome size, and gametic multicellularity, with the latter being associated with both increased mutation rates and decreased effective population sizes. However, data sufficient to test for possible relationships between microbial multicellularity and mutation rate (µ) are lacking. Here, we report estimates of two key population-genetic parameters, Ne and µ, for Myxococcus xanthus, a bacterial model organism for the study of aggregative multicellular development, predation, and social swarming. To estimate µ, we conducted an ∼400-day mutation accumulation experiment with 46 lineages subjected to regular single colony bottlenecks prior to clonal regrowth. Upon conclusion, we sequenced one clonal-isolate genome per lineage. Given collective evolution for 85,323 generations across all lines, we calculate a per base-pair mutation rate of ∼5.5 × 10-10 per site per generation, one of the highest mutation rates among free-living eubacteria. Given our estimate of µ, we derived Ne at ∼107 from neutral diversity at four-fold degenerate sites across two dozen M. xanthus natural isolates. This estimate is below average for eubacteria and strengthens an already clear negative correlation between µ and Ne in prokaryotes. The higher and lower than average mutation rate and Ne for M. xanthus, respectively, amplify the question of whether any features of its multicellular life cycle-such as group-size reduction during fruiting-body development-or its highly structured spatial distribution have significantly influenced how these parameters have evolved.
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Affiliation(s)
- Sébastien Wielgoss
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland
| | - James David Van Dyken
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA
| | - Gregory J Velicer
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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Wang J, Ran Q, Du X, Wu S, Wang J, Sheng D, Chen Q, Du Z, Li YZ. Two new Polyangium species, P. aurulentum sp. nov. and P. jinanense sp. nov., isolated from a soil sample. Syst Appl Microbiol 2021; 44:126274. [PMID: 34763291 DOI: 10.1016/j.syapm.2021.126274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/01/2021] [Accepted: 10/04/2021] [Indexed: 11/18/2022]
Abstract
Polyangium belongs to Polyangiaceae family of Myxococcales, a taxonomic group well-known for their extraordinary social lifestyle and diverse novel gene clusters of secondary metabolites. A yellow-golden strain, designated SDU3-1T, and two rose pink strains, designated SDU13 and SDU14T, were isolated from a soil sample. These three strains were aerobic, mesophilic, not salt-tolerant and were able to prey on living microorganisms. SDU13 and SDU14T formed solitary sporangioles under starvation conditions, while SDU3-1T had no fruiting body structures. They showed 95.9-97.0% (SDU3-1T) or 98.7-98.9% (SDU13 and SDU14T) 16S rRNA gene similarity with the type strains of Polyangium, but were phylogenetically separate from them based on the 16S rRNA gene and genome sequences. Their genomes were 12.3 Mbp (SDU3-1T), 13.9 Mbp (SDU13) and 13.8 Mbp (SDU14T) with the G + C content range of 68.3-69.4 mol%. The average nucleotide identity and DNA-DNA hybridization analyses of genomes further indicated that these three strains belonged to two new species in Polyangium. Their major fatty acids were C18:1ω9c, C16:0 and C18:0. The polyphasic taxonomic characterization suggest that the three strains represent two novel species in the genus Polyangium, for which the names Polyangium aurulentum sp. nov. and Polyangium jinanense sp. nov. are proposed, and the type strains are SDU3-1T (=CGMCC 1.16875T = KCTC 72136T) and SDU14T (=CCTCC AB 2021123T = KCTC 82625T), respectively.
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Affiliation(s)
- Jingjing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Qi Ran
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Xinran Du
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Shuge Wu
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Jianing Wang
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Duohong Sheng
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Qi Chen
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China
| | - Zongjun Du
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China; College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbiology Technology, Shandong University, Qingdao 266237, PR China.
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Abstract
Bacteria are globally distributed in various environments on earth, but a global view of the geographic diversity and distribution of a single taxon is lacking. The Earth Microbiome Project (EMP) has established a global collection of microbial communities, providing the possibility for such a survey. Myxococcales is a bacterial order with a potent ability to produce diverse natural products and have wide application potential in agriculture, biomedicine, and environmental protection. In this study, through a comparative analysis of the EMP data and public information, we determined that myxobacteria account for 2.34% of the total bacterial operational taxonomic units (OTUs), and are one of the most diverse bacterial groups on Earth. Myxococcales OTUs are globally distributed and prefer nonsaline soil and sediments, followed by saline environments, but rarely appear in host-associated environments. Myxobacteria are among the least-investigated bacterial groups. The presently cultured and genome-sequenced myxobacteria are most likely environmentally widespread and abundant taxa, and account for approximately 10% and 7% of the myxobacterial community (>97% similarity), respectively. This global panoramic view of the geographic distribution and diversity of myxobacteria, as well as their cultured and genome-sequenced information, will enable us to explore these important bioresources more reasonably and efficiently. The diversity and distribution of myxobacteria beyond the EMP data are further discussed. IMPORTANCE The diversity and distribution of bacteria are crucial for our understanding of their ecological importance and application potential. Myxobacteria are fascinating prokaryotes with multicellular behaviors and a potent capacity for producing secondary metabolites, and have a wide range of potential applications. The ecological importance of myxobacteria in major ecosystems is becoming established, but the global geographic diversity and distribution remain unclear. From a global survey we revealed that Myxococcales OTUs are globally distributed and prefer nonsaline soil and sediments, followed by saline environments, but rarely appear in host-associated environments. The global panoramic view of the geographic distribution and diversity of myxobacteria, as well as their cultured and genome-sequenced information, will enable us to explore these important bioresources more reasonably and efficiently.
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Whitfield DL, Sharma G, Smaldone GT, Singer M. Peripheral rods: a specialized developmental cell type in Myxococcus xanthus. Genomics 2019; 112:1588-1597. [PMID: 31605730 DOI: 10.1016/j.ygeno.2019.09.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/13/2019] [Accepted: 09/11/2019] [Indexed: 01/08/2023]
Abstract
In response to nutrient deprivation, the ubiquitous Gram-negative soil bacterium Myxococcus xanthus undergoes a well-characterized developmental response, resulting in the formation of a multicellular fruiting body. The center of the fruiting body consists of myxospores; surrounding this structure are rod-shaped peripheral cells. Unlike spores, the peripheral rods are a metabolically active cell type that inhabits nutrient-deprived environments. The survival characteristics exhibited by peripheral rods, protection from oxidative stress and heat shock, are common survival characteristics exhibited by cells in stationary phase including modifications to morphology and metabolism. Vegetative M. xanthus cells undergo a number of physiological changes during the transition into stationary phase similar to other proteobacteria. In M. xanthus, stationary-phase cells are not considered a component of the developmental response and occur when cells are grown on nutrient-rich plates or in dispersed aqueous media. However, this cell type is not routinely studied and little of its physiology is known. Similarities between these two stress-induced cell types led to the question of whether peripheral rods are actually a distinct developmental cell type or simply cells in stationary phase. In this study, we examine the transcriptome of peripheral rods and its relationship to development. This work demonstrates that peripheral rods are in fact a distinct developmentally differentiated cell type. Although peripheral rods and stationary phase cells display similar characteristics, each transcriptomic pattern is unique and quite different from that of any other M. xanthus cell type.
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Affiliation(s)
- Damion L Whitfield
- Dept. of Microbiology and Molecular Genetics, University of California, Davis, CA, USA.
| | - Gaurav Sharma
- Dept. of Microbiology and Molecular Genetics, University of California, Davis, CA, USA
| | - Gregory T Smaldone
- Dept. of Microbiology and Molecular Genetics, University of California, Davis, CA, USA
| | - Mitchell Singer
- Dept. of Microbiology and Molecular Genetics, University of California, Davis, CA, USA.
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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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6
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Mohr KI. Diversity of Myxobacteria-We Only See the Tip of the Iceberg. Microorganisms 2018; 6:E84. [PMID: 30103481 PMCID: PMC6164225 DOI: 10.3390/microorganisms6030084] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/06/2018] [Accepted: 08/08/2018] [Indexed: 11/20/2022] Open
Abstract
The discovery of new antibiotics is mandatory with regard to the increasing number of resistant pathogens. One approach is the search for new antibiotic producers in nature. Among actinomycetes, Bacillus species, and fungi, myxobacteria have been a rich source for bioactive secondary metabolites for decades. To date, about 600 substances could be described, many of them with antibacterial, antifungal, or cytostatic activity. But, recent cultivation-independent studies on marine, terrestrial, or uncommon habitats unequivocally demonstrate that the number of uncultured myxobacteria is much higher than would be expected from the number of cultivated strains. Although several highly promising myxobacterial taxa have been identified recently, this so-called Great Plate Count Anomaly must be overcome to get broader access to new secondary metabolite producers. In the last years it turned out that especially new species, genera, and families of myxobacteria are promising sources for new bioactive metabolites. Therefore, the cultivation of the hitherto uncultivable ones is our biggest challenge.
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Affiliation(s)
- Kathrin I Mohr
- Microbial Drugs (MWIS), Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany.
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7
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Bacteriophages of Myxococcus xanthus, a Social Bacterium. Viruses 2018; 10:v10070374. [PMID: 30021959 PMCID: PMC6070905 DOI: 10.3390/v10070374] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/12/2018] [Accepted: 07/16/2018] [Indexed: 01/21/2023] Open
Abstract
Bacteriophages have been used as molecular tools in fundamental biology investigations for decades. Beyond this, however, they play a crucial role in the eco-evolutionary dynamics of bacterial communities through their demographic impact and the source of genetic information they represent. The increasing interest in describing ecological and evolutionary aspects of bacteria–phage interactions has led to major insights into their fundamental characteristics, including arms race dynamics and acquired bacterial immunity. Here, we review knowledge on the phages of the myxobacteria with a major focus on phages infecting Myxococcus xanthus, a bacterial model system widely used to study developmental biology and social evolution. In particular, we focus upon the isolation of myxophages from natural sources and describe the morphology and life cycle parameters, as well as the molecular genetics and genomics of the major groups of myxophages. Finally, we propose several interesting research directions which focus on the interplay between myxobacterial host sociality and bacteria–phage interactions.
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8
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Mohr KI, Zindler T, Wink J, Wilharm E, Stadler M. Myxobacteria in high moor and fen: An astonishing diversity in a neglected extreme habitat. Microbiologyopen 2017; 6. [PMID: 28401707 PMCID: PMC5552953 DOI: 10.1002/mbo3.464] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 01/25/2017] [Accepted: 02/02/2017] [Indexed: 02/05/2023] Open
Abstract
Increasing antibiotic resistances of numerous pathogens mean that myxobacteria, well known producers of new antibiotics, are becoming more and more interesting. More than 100 secondary metabolites, most of them with bioactivity, were described from the order Myxococcales. Especially new myxobacterial genera and species turned out to be reliable sources for novel antibiotics and can be isolated from uncommon neglected habitats like, for example, acidic soils. Almost nothing is known about the diversity of myxobacteria in moors, except some information from cultivation studies of the 1970s. Therefore, we evaluated the myxobacterial community composition of acidic high moor and fen both with cultivation‐independent 16S rRNA clone bank analysis and with cultivation. Phylogenetic analyses of clone sequences revealed a great potential of undescribed myxobacteria in high moor and fen, whereby all sequences represent unknown taxa and were detected exclusively by cultivation‐independent analyses. However, many clones were assigned to sequences from other cultivation‐independent studies of eubacterial diversity in acidic habitats. Cultivation revealed different strains exclusively from the genus Corallococcus. Our study shows that the neglected habitat moor is a promising source and of high interest with regard to the cultivation of prospective new bioactive secondary metabolite producing myxobacteria.
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Affiliation(s)
- Kathrin I Mohr
- Microbial Drugs, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Tanja Zindler
- Department of Supply Engineering, Ostfalia, Wolfenbüttel, Germany
| | - Joachim Wink
- Microbial Strain Collection, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Elke Wilharm
- Department of Supply Engineering, Ostfalia, Wolfenbüttel, Germany
| | - Marc Stadler
- Microbial Drugs, Helmholtz Centre for Infection Research, Braunschweig, Germany
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9
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Mohr KI, Stechling M, Wink J, Wilharm E, Stadler M. Comparison of myxobacterial diversity and evaluation of isolation success in two niches: Kiritimati Island and German compost. Microbiologyopen 2015; 5:268-78. [PMID: 26669488 PMCID: PMC4831471 DOI: 10.1002/mbo3.325] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 11/08/2015] [Accepted: 11/09/2015] [Indexed: 02/05/2023] Open
Abstract
Myxobacteria harbor an enormous potential for new bioactive secondary metabolites and therefore the isolation of in particular new groups is of great interest. The diversity of myxobacteria present in two ecological habitats, namely sand from Kiritimati Island and German compost, was evaluated by both cultivation‐based and cultivation‐independent methods. Phylogenetic analyses of the strains in comparison with 16S rRNA gene sequences from cultured and uncultured material in GenBank revealed a great potential of undescribed myxobacteria in both sampling sites. Several OTUs (operational taxonomic units) represent unknown taxa and were detected by clone bank analyses, but not by cultivation. Clone bank analyses indicated that the myxobacterial community is predominantly indigenous. The 16S rDNA libraries from the two samples were generated from total community DNA with myxobacterial specific forward and universal reverse primer sets. The clones were partially sequenced. Cultivation was successful for exclusively bacteriolytic, but not for cellulolytic myxobacteria and revealed 42 strains from the genera Corallococcus, Myxococcus, and Polyangium. The genera of Myxococcaceae family were represented by both approaches. But, even in this well studied family, as well as in the suborders Sorangiineae and Nannocystineae, a considerable number of clones were assigned to, if any, uncultivated organisms. Our study shows an overrepresentation of the genera Myxococcus spp. and Corallococcus spp. with standard cultivation methods. However, high deficits are demonstrated in the cultivation success of the myxobacterial diversity detected by exclusively cultivation‐independent approaches. Especially, clades which are exclusively represented by clones are of high interest with regard to the cultivation of new bioactive secondary metabolite producers.
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Affiliation(s)
- Kathrin I Mohr
- Microbial Drugs, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, Braunschweig, D-38124, Germany
| | - Marc Stechling
- Microbial Strain Collection, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, Braunschweig, D-38124, Germany.,Department of Supply Engineering, Ostfalia, Salzdahlumer Straße 46/48, Wolfenbüttel, D-38302, Germany
| | - Joachim Wink
- Microbial Strain Collection, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, Braunschweig, D-38124, Germany
| | - Elke Wilharm
- Department of Supply Engineering, Ostfalia, Salzdahlumer Straße 46/48, Wolfenbüttel, D-38302, Germany
| | - Marc Stadler
- Microbial Drugs, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, Braunschweig, D-38124, Germany
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11
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Zhou XW, Li SG, Li W, Jiang DM, Han K, Wu ZH, Li YZ. Myxobacterial community is a predominant and highly diverse bacterial group in soil niches. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:45-56. [PMID: 24596262 DOI: 10.1111/1758-2229.12107] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 09/10/2013] [Indexed: 06/03/2023]
Abstract
Although many molecular ecological surveys have been conducted, there is little concerning the details of specific bacterial groups, resulting in an incomplete understanding of the microorganismal composition and community structures in the environment. Myxobacteria are micropredators that are metabolically active in the soil microbial food web and have typically been considered minority components of soil bacterial communities. In this study, we surveyed the percentage of myxobacteria in a single soil sample via pyrosequencing on combined universal libraries of the V3-V4 and V6-V8 hypervariable regions of the 16S rRNA gene. Surprisingly, myxobacteria accounted for 4.10% of the bacterial community and 7.5% of the total operational taxonomic units at the 3% similarity level in the soil, containing almost all of the cultivated myxobacterial families or genera. To testify the appearance of myxobacteria in soil niches, we retrieved myxobacteria-related 16S rRNA gene sequences of 103 high-throughput sequencing data sets obtained from public databases. The results indicated that myxobacteria-related sequences were among the predominant groups in these data sets accounting for 0.4-4.5% of bacterial communities. The abundance of myxobacterial communities were correlated with site temperature, carbon-to-nitrogen ratio and pH values. Based on these results, we discussed the survival strategies of myxobacterial community in soil.
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Affiliation(s)
- Xiu-wen Zhou
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100, China
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Li SG, Zhao L, Han K, Li PF, Li ZF, Hu W, Liu H, Wu ZH, Li YZ. Diversity of epothilone producers among Sorangium strains in producer-positive soil habitats. Microb Biotechnol 2013; 7:130-41. [PMID: 24308800 PMCID: PMC3937717 DOI: 10.1111/1751-7915.12103] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 10/24/2013] [Accepted: 10/30/2013] [Indexed: 11/29/2022] Open
Abstract
Large-scale surveys show that the anti-tumour compounds known as epothilones are produced by only a small proportion of Sorangium strains, thereby greatly hampering the research and development of these valuable compounds. In this study, to investigate the niche diversity of epothilone-producing Sorangium strains, we re-surveyed four soil samples where epothilone producers were previously found. Compared with the < 2.5% positive strains collected from different places, epothilone producers comprised 25.0-75.0% of the Sorangium isolates in these four positive soil samples. These sympatric epothilone producers differed not only in their 16S rRNA gene sequences and morphologies but also in their production of epothilones and biosynthesis genes. A further exploration of 14 soil samples collected from a larger area around a positive site showed a similar high positive ratio of epothilone producers among the Sorangium isolates. The present results suggest that, in an area containing epothilone producers, the long-term genetic variations and refinements resulting from selective pressure form a large reservoir of epothilone-producing Sorangium strains with diverse genetic compositions.
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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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13
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Li PF, Li SG, Li ZF, Zhao L, Wang T, Pan HW, Liu H, Wu ZH, Li YZ. Co-cultivation ofSorangium cellulosumstrains affects cellular growth and biosynthesis of secondary metabolite epothilones. FEMS Microbiol Ecol 2013; 85:358-68. [DOI: 10.1111/1574-6941.12125] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 03/18/2013] [Accepted: 03/24/2013] [Indexed: 12/18/2022] Open
Affiliation(s)
- Peng-fei Li
- State Key Laboratory of Microbial Technology; School of Life Science; Shandong University; Jinan; China
| | - Shu-guang Li
- State Key Laboratory of Microbial Technology; School of Life Science; Shandong University; Jinan; China
| | - Zhi-feng Li
- State Key Laboratory of Microbial Technology; School of Life Science; Shandong University; Jinan; China
| | - Lin Zhao
- State Key Laboratory of Microbial Technology; School of Life Science; Shandong University; Jinan; China
| | - Ting Wang
- State Key Laboratory of Microbial Technology; School of Life Science; Shandong University; Jinan; China
| | - Hong-wei Pan
- State Key Laboratory of Microbial Technology; School of Life Science; Shandong University; Jinan; China
| | - Hong Liu
- State Key Laboratory of Microbial Technology; School of Life Science; Shandong University; Jinan; China
| | - Zhi-hong Wu
- State Key Laboratory of Microbial Technology; School of Life Science; Shandong University; Jinan; China
| | - Yue-zhong Li
- State Key Laboratory of Microbial Technology; School of Life Science; Shandong University; Jinan; China
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14
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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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Jiang DM, Kato C, Zhou XW, Wu ZH, Sato T, Li YZ. Phylogeographic separation of marine and soil myxobacteria at high levels of classification. ISME JOURNAL 2010; 4:1520-30. [DOI: 10.1038/ismej.2010.84] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Affiliation(s)
| | - Michiel Vos
- Department of Terrestrial Microbial Ecology, NIOO KNAW Centre for Terrestrial Ecology, Heteren 6666 GA, The Netherlands
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