DOCSLIB.ORG

Molecular and Functional Characterization of Myxobacteria Isolated from Soil in India

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Molecular and Functional Characterization of Myxobacteria Isolated from Soil in India 3 Biotech (2017) 7:112 DOI 10.1007/s13205-017-0722-9 ORIGINAL ARTICLE Molecular and functional characterization of myxobacteria isolated from soil in India 1 1 1 1,2 Shiv Kumar • Arun Kumar Yadav • Priyanka Chambel • Ramandeep Kaur Received: 6 December 2016 / Accepted: 6 April 2017 / Published online: 31 May 2017 Ó Springer-Verlag Berlin Heidelberg 2017 Abstract This study reports the isolation of myxobacteria Introduction from soil collected from plains in north India. Based on the morphology and 16S rDNA sequence, the isolated For decades, microbes have been the major contributor to myxobacteria were identified as Corallococcus sp., Pyxi- natural products for drug discovery and development. dicoccus sp., Myxococcus sp., Cystobacter sp. and Ar- The microbial natural products being used as drugs are: changium sp. The myxobacteria were functionally antibacterial agents, such as the penicillins, cephalos- characterized to assess their ability to produce antibacterial porins, aminoglycosides, tetracyclines and various and anticancer metabolites. The isolates were found to be polyketides; cholesterol lowering agents, such as mevas- functionally versatile as they produced extracellular tatin and lovastatin; immunosuppressive agents, such as bioactive molecules that exhibited high frequency of the cyclosporins and rapamycin; and anthelmintics and activities against Bacillus cereus, Mycobacterium smeg- antiparasitic drugs, such as the ivermectins (Buss and matis, Enterobacter cloacae and Pseudomonas syringae. Waigh 1995). The emergence of antibiotic-resistant The strains also showed cytotoxic activity against the pathogenic microorganisms and rapid development of human cancer cell lines of liver, pancreas, prostrate, bone resistance to chemotherapeutic drugs have necessitated and cervix. These results indicate the importance of iso- the discovery of structurally diverse and mechanistically lating diverse strains of myxobacteria from unexplored distinct antimicrobial and anticancer compounds. Most of habitats to find novel bioactive compounds. Moreover, the the microbial bioactive compounds discovered so far bioactive molecules explored in this study are predomi- originated from actinomycetes, but the focus is currently nantly hydrophilic compounds, obviating the limitations of on the less exploited microbes as viable sources of sec- solubility-related aspect of drug discovery. ondary metabolites; viz., marine bacteria, cyanobacteria, endosymbionts and myxobacteria. Myxobacteria are aer- Keywords Myxobacteria Á Functional characterization Á obic Gram-negative, unicellular, rod-shaped d-proteobac- Antibacterial Á Anticancer teria, distributed in a wide range of habitats including soil, bark of trees, decaying plant materials, and fresh- water and marine environment (Ravenschlag et al. 1999; Electronic supplementary material The online version of this Reichenbach 1999; Garcia et al. 2009; Dawid 2000). article (doi:10.1007/s13205-017-0722-9) contains supplementary material, which is available to authorized users. They have a very large genome size compared to other bacteria, and a number of structurally unique biologically & Ramandeep Kaur active secondary metabolites are produced by this group [email protected] of bacteria (Wenzel and Muller 2009; Han et al. 2013; Reichenbach 2001). Many compounds isolated from 1 Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab 143005, India myxobacteria act on unique cellular targets, which, at the time of their discovery, were not targeted by other sec- 2 Department cum National Centre for Human Genome Studies and Research, Punjab University, Sector 14, Chandigarh, ondary metabolites (Bode and Muller 2006; Herrmann India et al. 2017). 123 112 Page 2 of 9 3 Biotech (2017) 7:112 Myxobacteria have been the source of several new to investigate myxobacteria to assess them as source of antibacterials, e.g., thuggacins from Sorangium cellulosum novel pharmaceutically active molecules. (active against Mycobacterium tuberculosis), crocacin Our study shows that myxobacteria isolated from soil in from Chondromyces crocatus (active against Gram-posi- India inhibit Bacillus cereus, Mycobacterium smegmatis tive bacteria), indiacens from Sandaracinus amylolyticus and Gram-negative bacteria (Pseudomonas syringae and (mildly inhibit Gram-positive and Gram-negative bacteria), Enterobacter cloacae) suggesting their potential to be disciformycins from Pyxidicoccus fallax (active against exploited as a source of antimicrobial compounds. The methicillin- and vancomycin-resistant Staphylococcus extracted molecules also showed antiproliferative activity aureus), Coralmycins (potent activity against Gram-nega- against the cancer cell lines of cervix, liver, pancreas, tive bacteria), etc. (Irschik et al. 2007; Kunze et al. 1994; prostate and bone. Most of the compounds tested in labo- Steinmetz et al. 2012; Surup et al. 2014; Kim et al. 2016). ratories fail to make it to the clinic because of bioavail- Several new antifungal compounds have also been reported ability limitations. To address this constraint, in this study, from myxobacteria: pedein A and B, miuraenamides, we focused on the assessment of bioactive potential of aurafurons A and B and cyrmenins (Kunze et al. water-soluble compounds secreted by myxobacteria. 2005, 2008; Iizuka et al. 2006; Sasse et al. 2003). A recent assessment of the antibacterial compounds form myxobacteria has revealed that most of these compounds Materials and methods are active against Gram-positive bacteria (Schaberle et al. 2014). All chemicals and media components were procured from Several secondary metabolites produced by myxobac- HiMedia, Sisco Research Laboratory, Lobachemie, Genei- teria are promising anticancer agents. Epothilone, a pacli- Merck or Sigma-Aldrich. All plastic wares and glass wares taxel mimetic, obtained from Sorangium cellulosum So were purchased from HiMedia, Tarsons or Borosil. ce56, has been approved for breast cancer treatment (Burris 2008). In 2007, ixabepilone, an analog of epothilone B, Isolation, purification and taxonomy was approved by FDA for the treatment of metastatic or of myxobacteria locally advanced taxane-resistant breast cancer (Tan and Toppmeyer 2008). Tubulysins, produced by Archangium Myxobacteria were isolated by baiting technique from the gephyra Ar 315, Angiococcus disciformis An d48 and soil samples collected near decaying plants and animals in Cystobacter sp. SBCb004, are potent growth inhibitors the plains of north India (Reichenbach and Hofle 1999). compared to taxol, epothilone and vincristine and are Escherichia coli and/or autoclaved baker’s yeast was effective in multidrug-resistant cell lines (Sasse et al. 2000; streaked on cycloheximide (100 lg/ml) incorporated water Steinmetz et al. 2004; Chai et al. 2010). Argyrin A and CleriGel plate as three parallel streaks, cross streak or dot. cruentaren A produced by Archangium gephyra and Cycloheximide (100 lg/ml)-treated soil samples were Byssovorax cruenta, respectively, are highly cytotoxic placed on E. coli/autoclaved yeast and incubated at 30 °C against various human tumor cell lines (Nickeleit et al. for 3–20 days. For purification, colony morphology and/or 2008; Kunze et al. 2007). Recently, nannocystin from fruiting bodies were viewed under stereomicroscope to Nannocystis sp. has been found to show activity against confirm the identity of myxobacteria according to the cri- various cancer cell lines by targeting eukaryotic translation teria indicated by Reichenbach and Dworkin (1992). The (Krastel et al. 2015). fruiting bodies and cells from the edge of the swarms were Although myxobacteria are an attractive source of new picked up and streaked on CY agar (g/l: Casitone, 10; yeast chemical class of compounds, they have not been fully extract, 1; CaCl2Á2H2O, 1; agar 20) or SP agar (DSZM exploited in the quest for new bioactive compounds, medium 222) and incubated at 30 °C. This step was because their isolation and purification are tedious. The repeated till the isolates were obtained in pure culture. fact that they are very sensitive to mechanical stress and Thereafter, the isolates were maintained on SP medium. are prone to lysis make their handling very difficult (Re- ichenbach and Dworkin 1992). The ability of myxobacteria Molecular characterization of myxobacteria to synthesize a particular compound is specific to a strain, which makes myxobacteria an attractive proposition for Genomic DNA isolation bioprospection (Reichenbach and Hofle 1999). In view of their immense potential as a source of natural compounds Myxobacteria were grown in SP medium at 30 °C for 48 h having new chemical structures with unique mechanism of on a rotary shaker. Genomic DNA was extracted using action and no report on functional diversity of myxobac- HiYieldTM Genomic DNA Mini Kit (Real Biotech Cor- teria from Indian habitats, the present study was undertaken poration, Taiwan). 123 3 Biotech (2017) 7:112 Page 3 of 9 112 PCR amplification of 16S rDNA extract (WE). The insoluble residual matter was dissolved in 250 ll DMSO and designated as DMSO extract (DE). Genomic DNA of myxobacterial isolates was used as To prepare extracts for checking the anticancer activity, template for PCR amplification of 16S rRNA gene with myxobacteria were grown in 300 ml of CY broth at 30 °C bacterial universal forward primer 8-27F (50-AGAGTT for 36 h in an incubator shaker. Thereafter, 300 ml of ethyl TGATCCTGGCTCAG-30) and reverse primer 1492R acetate was added to each flask and extraction was carried
Load more

Recommended publications
  • DDDC 2019 Organizing Committee
    Conference Sponsors 2 Drug Discovery and Development Colloquium 2018 VI Annual Conference June 13 - 15, 2019 DDDC 2019 Organizing Committee Skylar Connor, Conference Co-chair, SHraddHa THakkar, PH.D., Conference Co-chair, UAMS AAPS Student CHapter President, Student UAMS AAPS Student CHapter Sponsor, Faculty University of Arkansas for Medical Sciences • FDA National Center for Toxicological Research University of Arkansas Little Rock Ujwani Nukala, Organizing Committee, UAMS Cesar M. Compadre, PH.D., Conference Co-chair, AAPS Student CHapter Past-President, Student UAMS AAPS Student CHapter Co-Sponsor, University of Arkansas for Medical Sciences Faculty University of Arkansas Little Rock University of Arkansas for Medical Sciences Ting Lee, Organizing Committee, UAMS AAPS David Mery, Organizing Committee, UAMS Student CHapter Treasurer, Student AAPS Student CHapter CHair Elect, Student University of Arkansas for Medical Sciences. University of Arkansas for Medical Sciences University of Arkansas Little Rock Cord Carter, Organizing Committee, UAMS AAPS Pankaj Patyal, Organizing Committee, UAMS Student CHapter Secretary, Student AAPS Student CHapter Vice President, Student University of Arkansas for Medical Sciences University of Arkansas for Medical Sciences Taylor Connor, Organizing Committee, UAMS Nemu Saumyadip, Organizing Committee, AAPS Student Chapter Member, Student UAMS AAPS Student CHapter Member, Student University of Arkansas for Medical Sciences University of Arkansas for Medical Sciences PHuc Tran, Organizing Committee, UAMS AAPS Edward Selvik, Organizing Committee, UAMS Student CHapter Member, Student AAPS Student CHapter Member, Student University of Arkansas for Medical Sciences University of Arkansas for Medical Sciences University of Arkansas Little Rock Table of Contents DDDC 2019 Agenda 5 List of Poster Presenters 10 Speakers and Organizers Bios 11 Abstracts 23 3 Drug Discovery and Development Colloquium 2019 University of Arkansas for Medical Sciences I.
    [Show full text]
  • Novel Myxobacteria As a Potential Source of Natural Products and Description of Inter-Species Nature of C-Signal
    Novel myxobacteria as a potential source of natural products and description of inter-species nature of C-signal Dissertation zur Erlangung des Grades des Doktors der Naturwissenschaften der Naturwissenschaftlich-Technischen Fakultät III Chemie, Pharmazie, Bio- und Werkstoffwissenschaften der Universität des Saarlandes von Ram Prasad Awal (M. Sc. in Medical Microbiology) Saarbrücken 2016 Tag des Kolloquiums: ......19.12.2016....................................... Dekan: ......Prof. Dr. Guido Kickelbick.............. Berichterstatter: ......Prof. Dr. Rolf Müller...................... ......Prof. Dr. Manfred J. Schmitt........... ............................................................... Vositz: ......Prof. Dr. Uli Kazmaier..................... Akad. Mitarbeiter: ......Dr. Jessica Stolzenberger.................. iii Diese Arbeit entstand unter der Anleitung von Prof. Dr. Rolf Müller in der Fachrichtung 8.2, Pharmazeutische Biotechnologie der Naturwissenschaftlich-Technischen Fakultät III der Universität des Saarlandes von Oktober 2012 bis September 2016. iv Acknowledgement Above all, I would like to express my special appreciation and thanks to my advisor Professor Dr. Rolf Müller. It has been an honor to be his Ph.D. student and work in his esteemed laboratory. I appreciate for his supervision, inspiration and for allowing me to grow as a research scientist. Your guidance on both research as well as on my career have been invaluable. I would also like to thank Professor Dr. Manfred J. Schmitt for his scientific support and suggestions to my research work. I am thankful for my funding sources that made my Ph.D. work possible. I was funded by Deutscher Akademischer Austauschdienst (DAAD) for 3 and half years and later on by Helmholtz-Institute. Many thanks to my co-advisors: Dr. Carsten Volz, who supported and guided me through the challenging research and Dr. Ronald Garcia for introducing me to the wonderful world of myxobacteria.
    [Show full text]
  • The Correlation Between Morphological and Phylogenetic Classification of Myxobacteria
    International Journal of Systematic Bacteriology (1 999), 49, 1255-1 262 Printed in Great Britain The correlation between morphological and phylogenetic classification of myxobacteria Cathrin Sproer,’ Hans Reichenbach’ and Erko Stackebrandtl Author for correspondence: Erko Stackebrandt.Tel: +49 531 2616 352. Fax: +49 531 2616 418. e-mail : [email protected] DSMZ-Deutsche Sammlung In order to determine whether morphological criteria are suitable to affiliate von Mikroorganismen und myxobacterial strains to species, a phylogenetic analysis of 16s rDNAs was Zellkulturen GmbH1 and G BF-Gesel Isc haft fur performed on 54 myxobacterial strains that represented morphologically 21 Biotechnologische species of the genera Angiococcus, Archangium, Chondromyces, Cystobacter, Forschung mbH*, 381 24 Melittangium, Myxococcus, Polyangium and Stigmatella, five invalid species Braunschweig, Germany and three unclassified isolates. The analysis included 12 previously published sequences. The branching pattern confirmed the deep trifurcation of the order Myxococcales. One lineage is defined by the genera Cystobacter, Angiococcus, Archangium, Melittangium, Myxococcus and Stigmatella. The study confirms the genus status of Corallococcus’, previously ‘Chondrococcus’,within the family Myxococcaceae. The second lineage contains the genus Chondromyces and the species Polyangium (‘Sorangium’) cellulosum, while the third lineage is comprised of Nannocystis and a strain identified as Polyangium vitellinum. With the exception of a small number of strains that did not cluster phylogenetically with members of the genus to which they were assigned by morphological criteria (‘Polyangium thaxteri’ PI t3, Polyangium cellulosum ATCC 25531T, Melittangium lichenicola ATCC 25947Tand Angiococcus disciformis An dl), the phenotypic classification should provide a sound basis for the description of neotype species in those cases where original strain material is not available or is listed as reference material.
    [Show full text]
  • Niranjan Parajuli Et Al Paper
    Journal of Institute of Science and Technology, 24(2), 7-16 (2019) ISSN: 2469-9062 (print), 2467-9240 (e) © IOST, Tribhuvan University Doi: http://doi.org/10.3126/jist.v24i2.27246 Research Article ISOLATION AND CHARACTERIZATION OF SOIL MYXOBACTERIA FROM NEPAL Nabin Rana1, Saraswoti Khadka1, Bishnu Prasad Marasini1, Bishnu Joshi1, Pramod Poudel2, Santosh Khanal1, Niranjan Parajuli3 1Department of Biotechnology, National College, Tribhuvan University, Naya Bazar, Kathmandu, Nepal 2Research Division, University Grant Commission (UGC-Nepal), Sanothimi, Bhaktapur, Nepal 3Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal *Corresponding author: [email protected] (Received: May 22, 2019; Revised: October 26, 2019; Accepted: November 1, 2019) ABSTRACT Realizing myxobacteria as a potential source of antimicrobial metabolites, we pursued research to isolate myxobacteria showing antimicrobial properties. We have successfully isolated three strains (NR-1, NR-2, NR-3) using the Escherichia coli baiting technique. These isolates showed typical myxobacterial growth characteristics. Phylogenetic analysis showed that all the strains (NR-1, NR-2, NR-3) belong to the family Archangiaceae, suborder Cystobacterineae, and order Myxococcales. Furthermore, 16S rRNA gene sequence similarity searched through BLAST revealed that strain NR-1 showed the closest similarity (91.8 %) to the type strain Vitiosangium cumulatum (NR-156939), NR-2 showed (98.8 %) to the type of Cystobacter badius (NR-043940), and NR-3 showed the closest similarity (83.5 %) to the type of strain Cystobacter fuscus (KP-306730). All isolates showed better growth in 0.5-1 % NaCl and pH around 7.0, whereas no growth was observed at pH 9.0 and below 5.0. All strains showed better growth at 32° C and hydrolyzed starch, whereas casein was efficiently hydrolyzed by NR-1 and NR-2.
    [Show full text]
  • A Recent Evolutionary Origin of a Bacterial Small RNA That Controls
    Molecular Phylogenetics and Evolution 73 (2014) 1–9 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev A recent evolutionary origin of a bacterial small RNA that controls multicellular fruiting body development q ⇑ I-Chen Kimberly Chen a,b, , Brad Griesenauer a, Yuen-Tsu Nicco Yu b, Gregory J. Velicer a,b a Department of Biology, Indiana University, Bloomington, IN 47405, USA b Institute of Integrative Biology (IBZ), ETH Zurich, CH-8092 Zurich, Switzerland article info abstract Article history: In animals and plants, non-coding small RNAs regulate the expression of many genes at the post-tran- Received 26 August 2013 scriptional level. Recently, many non-coding small RNAs (sRNAs) have also been found to regulate a vari- Revised 30 December 2013 ety of important biological processes in bacteria, including social traits, but little is known about the Accepted 2 January 2014 phylogenetic or mechanistic origins of such bacterial sRNAs. Here we propose a phylogenetic origin of Available online 10 January 2014 the myxobacterial sRNA Pxr, which negatively regulates the initiation of fruiting body development in Myxococcus xanthus as a function of nutrient level, and also examine its diversification within the Keywords: Myxococcocales order. Homologs of pxr were found throughout the Cystobacterineae suborder (with a Bacterial development few possible losses) but not outside this clade, suggesting a single origin of the Pxr regulatory system Multicellularity Myxobacteria in the basal Cystobacterineae lineage. Rates of pxr sequence evolution varied greatly across Cystobacte- Non-coding small RNAs rineae sub-clades in a manner not predicted by overall genome divergence.
    [Show full text]
  • The Existence and Diversity of Myxobacteria in Lake Mud A
    bs_bs_banner Environmental Microbiology Reports (2012) doi:10.1111/j.1758-2229.2012.00373.x The existence and diversity of myxobacteria in lake mud – a previously unexplored myxobacteria habitat Shu-guang Li,† Xiu-wen Zhou,† Peng-fei Li, Kui Han, et al., 2003). Using fruiting body-dependent techniques, Wei Li, Zhi-feng Li, Zhi-hong Wu and Yue-zhong Li* myxobacteria have been isolated from various soil-related State Key Laboratory of Microbial Technology, School of samples, including soil, rotting wood, bark from dead or Life Science, Shandong University, Jinan 250100, living trees and dung of herbivorous mammals, but rarely China. from aquatic environments (Reichenbach, 1999; Dawid, 2000). Accordingly, myxobacteria are widely recognized as typical soil bacteria (Reichenbach, 1999). Recently, Summary halophilic (Iizuka et al., 1998; 2003; Fudou et al., 2002) Myxobacteria are widely distributed in soil and and halotolerant (Li et al., 2002) myxobacterial strains oceanic sediment with a phylogeographic separation have been isolated from coastal areas. They have been at high levels of classification. However, it is unclear shown to exhibit certain characteristics that differ from whether freshwater environments, from which there their soil-dwelling relatives (Zhang et al., 2005; Wang has been no isolation report of myxobacteria since et al., 2007a). Molecular surveys have indicated that 1981, are habitats for myxobacteria. In this study, we myxobacteria-related 16S rRNA gene sequences are also investigated the presence of myxobacteria in lake widely distributed in marine sediments at different depths mud using a two-step strategy. First, we constructed and sites, but they are distantly related to those of soil two universal bacterial libraries from the V3–V4 (V34) myxobacteria (Jiang et al., 2010; Brinkhoff et al., 2012).
    [Show full text]
  • Their Classification (16S Rrna/8 Purple Bacteria/Rrna Gnatwe/R D Evolution) L
    Proc. Nati. Acad. Sci. USA Vol. 89, pp. 9459-9463, October 1992 Evolution A phylogenetic analysis of the myxobacteria: Basis for their classification (16S rRNA/8 purple bacteria/rRNA gnatWe/r d evolution) L. SHIMKETS* AND C. R. WOESEt *Department of Microbiology, University of Georgia, Athens, GA 30602; and tDepartment of Microbiology, University of Illinois, 131 Burrill Hall, Urbana, IL 61801 Contributed by C. R. Woese, June 16, 1992 ABSTRACT The primary sequence and secondary struc- and available type or reference strains further complicates tural features of the 16S rRNA were compared for 12 different taxonomic placement (6, 7). The present study was severely myxobacteria representing all the known cultivated genera. limited in that reference strains listed in Bergey's Manual (6) Analysis of these data show the myxobacteria to form a were not made available by the authors. The placement of monophyletic grouping consisting of three distinct famiies, reference cultures in accessible collections, such as the which lies within the 6 subdivision of the purple baerial American Type Culture Collection, needs to be an estab- phylum. The composition of the familes is consitent with lished practice. differences in cell and spore morphology, cell behavior, and The use of molecular taxonomic approaches may help pigment and secondary metabolite production but is not cor- alleviate some of these problems, gradually replacing fruit- related with the morphological complexity of the fruiting ing-body morphology as the ultimate taxonomic criterion and bodies. The Nannocysts exedens lineage has evolved at an paving the way for modern myxobacterial systematics rooted unusually rapid pace and its rRNA shows numerous primary in the genetic lineages of the organisms (8, 9).
    [Show full text]
  • Current Trends in Myxobacteria Research
    Ann Microbiol (2016) 66:17–33 DOI 10.1007/s13213-015-1104-3 REVIEW ARTICLE Current trends in myxobacteria research Wioletta Wrótniak-Drzewiecka1 & Anna Joanna Brzezińska1 & Hanna Dahm1 & Avinash P. Ingle 2 & Mahendra Rai 2 Received: 5 March 2015 /Accepted: 19 May 2015 /Published online: 12 June 2015 # Springer-Verlag Berlin Heidelberg and the University of Milan 2015 Abstract Myxobacteria are fascinating Gram-negative bacte- Keywords Myxobacteria . Ecology . Cytology . Enzymatic ria whose life cycle includes the formation of multicellular activity . Secondary metabolism . Social interactions fruiting bodies that contain about 100,000 cells differentiated as asexual spores for their long-term survival. They move by gliding on surfaces, an activity that helps them carry out their Introduction primitive kind of multicellular development. Myxobacteria have multiple traits that are clearly social in nature; they move Myxobacteria (slime bacteria) are rod-shaped Gram-negative and feed socially. These processes require specific intercellu- bacteria that move by gliding. They typically travel in swarms, lar signals, thereby exhibiting a sophisticated level of the inter- containing many cells kept together by intercellular molecular organismal communication. Myxobacteria are predators. signals. Bacterial gliding is a process whereby a bacterium can Predation is social not only with respect to searching for prey move under its own power. For many bacteria, the mechanism (motility) but also in the killing of prey. Swarming groups of of gliding is unknown or only partially known, and different cells secrete antibiotics and bacteriolytic compounds that kill bacteria (cyanobacteria, cytophaga-flavobacteria) have dis- and lyse their prey, and food is thereby released. Since the last tinct mechanisms of movement.
    [Show full text]
  • Maxbin: an Automated Binning Method to Recover Individual
    Wu et al. Microbiome 2014, 2:26 http://www.microbiomejournal.com/content/2/1/26 METHODOLOGY Open Access MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm Yu-Wei Wu1,2*, Yung-Hsu Tang1,3, Susannah G Tringe4,5, Blake A Simmons1,6 and Steven W Singer1,7 Abstract Background: Recovering individual genomes from metagenomic datasets allows access to uncultivated microbial populations that may have important roles in natural and engineered ecosystems. Understanding the roles of these uncultivated populations has broad application in ecology, evolution, biotechnology and medicine. Accurate binning of assembled metagenomic sequences is an essential step in recovering the genomes and understanding microbial functions. Results: We have developed a binning algorithm, MaxBin, which automates the binning of assembled metagenomic scaffolds using an expectation-maximization algorithm after the assembly of metagenomic sequencing reads. Binning of simulated metagenomic datasets demonstrated that MaxBin had high levels of accuracy in binning microbial genomes. MaxBin was used to recover genomes from metagenomic data obtained through the Human Microbiome Project, which demonstrated its ability to recover genomes from real metagenomic datasets with variable sequencing coverages. Application of MaxBin to metagenomes obtained from microbial consortia adapted to grow on cellulose allowed genomic analysis of new, uncultivated, cellulolytic bacterial populations, including an abundant myxobacterial population distantly related to Sorangium cellulosum that possessed a much smaller genome (5 MB versus 13 to 14 MB) but has a more extensive set of genes for biomass deconstruction. For the cellulolytic consortia, the MaxBin results were compared to binning using emergent self-organizing maps (ESOMs) and differential coverage binning, demonstrating that it performed comparably to these methods but had distinct advantages in automation, resolution of related genomes and sensitivity.
    [Show full text]
  • Their Classification (16S Rrna/8 Purple Bacteria/Rrna Gnatwe/R D Evolution) L
    Proc. Nati. Acad. Sci. USA Vol. 89, pp. 9459-9463, October 1992 Evolution A phylogenetic analysis of the myxobacteria: Basis for their classification (16S rRNA/8 purple bacteria/rRNA gnatWe/r d evolution) L. SHIMKETS* AND C. R. WOESEt *Department of Microbiology, University of Georgia, Athens, GA 30602; and tDepartment of Microbiology, University of Illinois, 131 Burrill Hall, Urbana, IL 61801 Contributed by C. R. Woese, June 16, 1992 ABSTRACT The primary sequence and secondary struc- and available type or reference strains further complicates tural features of the 16S rRNA were compared for 12 different taxonomic placement (6, 7). The present study was severely myxobacteria representing all the known cultivated genera. limited in that reference strains listed in Bergey's Manual (6) Analysis of these data show the myxobacteria to form a were not made available by the authors. The placement of monophyletic grouping consisting of three distinct famiies, reference cultures in accessible collections, such as the which lies within the 6 subdivision of the purple baerial American Type Culture Collection, needs to be an estab- phylum. The composition of the familes is consitent with lished practice. differences in cell and spore morphology, cell behavior, and The use of molecular taxonomic approaches may help pigment and secondary metabolite production but is not cor- alleviate some of these problems, gradually replacing fruit- related with the morphological complexity of the fruiting ing-body morphology as the ultimate taxonomic criterion and bodies. The Nannocysts exedens lineage has evolved at an paving the way for modern myxobacterial systematics rooted unusually rapid pace and its rRNA shows numerous primary in the genetic lineages of the organisms (8, 9).
    [Show full text]
  • SPATIAL VARIATION of BACTERIAL COMMUNITIES on the LEAVES of a SOUTHERN MAGNOLIA TREE by Emily Nguyen a Thesis Submitted To
    SPATIAL VARIATION OF BACTERIAL COMMUNITIES ON THE LEAVES OF A SOUTHERN MAGNOLIA TREE By Emily Nguyen A thesis submitted to the faculty of The University of Mississippi in partial fulfillment of the requirements of the Sally McDonnell Barksdale Honors College. Oxford May 2016 Approved by ____________________________________ Advisor: Dr. Colin Jackson ____________________________________ Reader: Dr. Ryan Garrick _____________________________________ Reader: Dr. Stephen Brewer i Abstract: The leaf surface, or phylloplane, is a dynamic environment for its microbial inhabitants, which can be subjected to many environmental factors. Existing phylloplane studies have focused on differences in bacterial community structure between trees of the same species, in different geographical locations, or between trees of different species. Few studies have examined the spatial distribution of bacterial communities on the leaves of a single tree. In this study, leaf samples from different areas of the canopy were obtained from a single Magnolia grandiflora tree. Samples were taken from the high (3.5-4.0 m above the ground), middle (1.5 m), inner middle (1.5 m but close to the trunk), and low (0.5 m) portions of the tree canopy, following cardinal directions (north, south, east, west). Following DNA extraction procedures, dual index barcoding was used to sequence the V4 region of the 16S ribosomal RNA gene. Phylloplane communities were dominated by Alphaproteobacteria, Actinobacteria, and Bacteroidetes, which are common inhabitants of plants. Patterns in alpha and beta diversity suggested that the height from which the sample was taken had a strong influence on the shaping of communities, while cardinal direction was not a significant predictor of diversity.
    [Show full text]
  • Morphologies and Phylogenetic Classification of Cellulolytic Myxobacteria
    http://www.paper.edu.cn System. Appl. Microbiol. 26, 104–109 (2003) © Urban & Fischer Verlag http://www.urbanfischer.de/journals/sam Morphologies and Phylogenetic Classification of Cellulolytic Myxobacteria Zhang-Cai Yan, Bing Wang, Yue-Zhong Li, Xun Gong, Huai-Qiang Zhang, and Pei-Ji Gao State Key Laboratory of Microbial Technology, College of Life Science, Shandong University, Jinan, China Received: September 15, 2002 Summary The evolutionary distances of the 16S rDNA sequences in cellulolytic myxobacteria are less than 3%, which units all the strains into a single genus, Sorangium. The size of myxospores and the shape of spo- rangioles, rather than fruiting body colors or swarm morphologies are consistent with the changes of the 16S rDNA sequences. It is suggested that there are at least two species in the genus Sorangium: one in- cludes strains with small myxospores and spherical sporangioles, and the color of the fruiting bodies is normally orange or brown, though sometimes yellow or black. The second species has large myxospores, polyhedral sporangioles with many inter-cystic substrates, and normally deep brown to black color. Key words: cellulolytic – myxobacteria – Sorangium – morphologies – 16S rDNA – Classification Introduction Myxobacteria are unique among bacteria for their lulosum, but suggested that there were at least two complicated multicellular morphogenesis, which also species in the genus considering the differences of their forms the primary basis for myxobacterial taxonomy fruiting body colors. [7, 10]. Phylogenetically, the Myxobacterales are located In 1992, Shimkets and Woese [12] phylogenetically in the δ-division of Proteobacteria depending on the analyzed 12 representative strains from 10 myxobacteri- analysis of their 16S rDNA sequences [8, 14], but classi- al genera, including one cellulose-degrader.
    [Show full text]