Molecular Phylogenetics and Evolution 57 (2010) 878–887

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Molecular Phylogenetics and Evolution

journal homepage: www.elsevier .com/locate /ympev

Expanded phylogeny of myxobacteria and evidence for cultivationof the ‘unculturables’

Ronald Garcia a,b, Klaus Gerth c, Marc Stadler d, Irineo J. Dogma Jr. e, Rolf Müller a,b,⇑a 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, Germanyb Department of Pharmaceutical Biotechnology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germanyc Microbial Drugs, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germanyd InterMed Discovery GmbH, Otto-Hahn Strasse 15, 4427 Dortmund, Germanye The Graduate School, University of Santo Tomas, 1015 España Blvd, Manila, Philippines

a r t i c l e i n f o a b s t r a c t

Article history:Received 28 May 2010Revised 10 August 2010Accepted 12 August 2010Available online 31 August 2010

Keywords:MyxobacteriaDelta-proteobacteria16S rDNAPhylogenyUnculturableSorangiineae

1055-7903/$ - see front matter � 2010 Elsevier Inc. Adoi:10.1016/j.ympev.2010.08.028

⇑ Corresponding author at: Department of Microbholtz-Institute for Pharmaceutical Research SaarlandInfection Research (HZI), Saarland University, CampGermany. Fax: +49 681 302 70202.

E-mail address: rom@mx.uni-saarland.de (R. Mülle

An expanded neighbour-joining tree of myxobacteria is presented based on the analysis of 16S rRNA genesequences of 101 strains (including types) representing 3 suborders, 6 families, 20 genera, 46 species, and12 other novel taxa. The distinctions amongst members of the three suborders (Sorangiineae, Cytobacte-rineae and Nannocystineae) are reaffirmed. The positions of anaerobic myxobacteria, novel groups (Pyxid-icoccus and several Cystobacter species) in Cystobacterineae, the marine genera (Plesiocystis, Haliangium,Enhygromyxa), and two additional novel taxa (‘Paraliomyxa miuraensis’, brackish-water isolate) weretogether revealed for the first time. Changes in the nomenclature of several isolates (Polyangium vitelli-num Pl vt1T, Polyangium thaxteri Pl t3, Polyangium cellulosum, NOSO-1, NOCB-2, NOCB-4) are also high-lighted. Suborders Sorangiineae and Nannocystineae hold great promise for novel strain discovery. InSorangiineae, the new family Phaselicystidaceae, with a monotypic genus, was added. Nine additionalnovel taxa were discovered in this suborder for which new genera or even families may be erected inthe near future. These taxa appear to represent the so-called viable but not culturable (VBNC) group ofmyxobacteria. Based on at least 4% phylogenetic distance, new clades were formed comprising of novelNannocystineae 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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1. Introduction

The myxobacteria are Gram-negative eubacteria famous fortheir production of unique secondary metabolites and complex cel-lular developmental cycles. They are believed to have evolvedalong with the purple bacteria in the delta branch of Proteobacteria(Kaiser, 1993; Shimkets and Woese, 1992) but therein are distinctby the formation of spore-bearing fruiting bodies, except in Anaer-omyxobacter and some marine myxobacteria (Iizuka et al., 2006a).Their developmental stages, from unicellular to aggregation byquorum sensing and then to ‘‘fructification” (fruiting body devel-opment), parallel only those of the protist cellular slime moulds(Acrasiomycetes) – a grand case of convergent evolution of prokary-otes and eukaryotes.

ll rights reserved.

ial Natural Products, Helm-(HIPS), Helmholtz Centre for

us C2 3, 66123 Saarbrücken,

r).

The taxonomy of myxobacteria is dependent primarily on mor-phology of vegetative cells, swarms, fruiting bodies, and myxosp-ores. Although such phenotypic characters are expressions of thegenotype, they are not stable and may change or be lost under arti-ficial growth conditions. For Chondromyces and Stigmatella, mor-phology-based identification remains largely valid because oftheir easily recognised stalked fruiting bodies with sporangioles.For most genera and species, however, identification and classifica-tion remains a daunting challenge, even to the expert eye.

Spröer et al. (1999) documented correlations between mor-phology and phylogeny of myxobacteria based on analysis of16S rDNAs of the then 26 recognised morphospecies and 54strains (38 Cystobacterineae, 5 Nannocystineae, and 11Sorangiineae). Many GenBank entries used in their study,however, were short and contained gaps. Since then, 16S rDNAsequences of cultured strains of halophilic (Iizuka et al.,2003a,b), halotolerant (Iizuka et al., 2006a), and anaerobic (Coateset al., 2002; Sanford et al., 2002) myxobacteria have becomeavailable. We have also discovered that the 16S DNAs of manyof our novel Sorangiineae are related to metagenomes of

R. Garcia et al. / Molecular Phylogenetics and Evolution 57 (2010) 878–887 879

‘‘unculturable” or viable but not culturable (VBNC) environmentalstrains. As will be seen later herein, the term VBNC only charac-terises living organisms that were hitherto not cultured, but theuse of novel sophisticated isolation techniques, selective culturemedia, and other methods may reveal in the future that mostof these bacteria can actually be cultured axenically under labora-tory conditions. VBNC may simply a reflection of the unknownphysiological and nutritional growth requirements of the organ-ism. It is, therefore, now appropriate to revise and complete the16S rDNA sequences of type strains, and to collate these withavailable sequences for newer taxa in order to appraise thepresent status of the phylogeny of myxobacteria.

Our study covers the available type and reference strains for all46 described cultured species, a number nearly double that of thestrains analysed previously (Spröer et al., 1999). The described spe-

Table 1Strains and their GenBank 16S rDNA accession numbers used in the phylogenetic tree.

Accession Strain name Ac

AF382400 Anaeromyxobacter dehalogenans 2CP-3 AFEU331406 Anaeromyxobacter dehalogenans DCP1-2D AJCP001359 Anaeromyxobacter dehalogenans 2CP-1T AJGU207872 Archangium gephyra DSM2261T EUAB218222 Archangium gephyra NBRC100087 AYAB303310 Brackish-water myxobacterium SYR-2 NI DAJ833647 Byssovorax cruenta By c2T = DSM14553T EUAJ233938 Chondromyces apiculatus Cm a14T = DSM14605T PN EUGU207874 Chondromyces crocatus Cm c5T = DSM14714T PN DFJ176773 Chondromyces crocatus KYC2712 DAJ233939 Chondromyces lanuginosus Sy t2T = DSM14631T PN EUFJ176774 Chondromyces lanuginosus KYC2904 DGU207875 Chondromyces pediculatus Cm p51T = DSM14607TPN CPAJ233942 Chondromyces robustus Cm c13T = DSM14608T AJAJ233941 Chondromyces robustus Cm a22 AJDQ768120 Corallococcus coralloides DSM2259T AJAJ811597 Corallococcus coralloides Cc c1242 = DSM52497 GAJ811598 Corallococcus exiguus Cc e167T = DSM14696T ABAJ233932 Corallococcus exiguus Cc e100 = DSM51889 EUDQ768107 Cystobacter armeniaca Cb a1T = DSM14710T AJDQ768108 Cystobacter badius Cb b2T = DSM14723T NGU207873 Cystobacter(Angiococcus) disciformis DSM52716T ABNR_025343 Cystobacter ferrugineus Cb fe18T = DSM14716T PN GAJ233900 Cystobacter ferrugineus Cb fe13 = DSM52759 GDQ768109 Cystobacter fuscus DSM2262T GAJ233897 Cystobacter fuscus Cb f6 = DSM52651 MEU262998 Cystobacter fuscus NM03 AJDQ768110 Cystobacter gracilis Cb g1T = DSM14753T GDQ768111 Cystobacter miniatus Cb a24T = DSM14712T FJDQ768113 Cystobacter minus Cb m2T = DSM14751T PN AFAJ233904 Cystobacter minus Cb m6 = DSM14772 RS AMDQ768115 Cystobacter velatus Cb v34T = DSM14718T AFDQ768114 Cystobacter violaceus Cb vi61T = DSM14727T AJAJ233905 Cystobacter violaceus Cb vi29 = DSM52806 EUAJ233906 Cystobacter violaceus Cb vi34 = DSM52808 EUNR_024807 Enhygromyxa salina SHK-1T = DSM15217T GAB097591 Enhygromyxa salina SMK-1-3 AJCP001804 Haliangium ochraceum DSM14365T AJNR_024781 Haliangium tepidum SMP-10T = DSM14436T AJAJ233949 Hyalangium minutum NOCB-2T = DSM14724T AJAJ233950 Hyalangium minutum NOCB-4 = DSM14725 DGU207876 Jahnella thaxteri Pl t4T = DSM14626T GAJ233943 Jahnella thaxteri Pl t3 = DSM14625 RS GGU249614 Jahnella thaxteri SBSr007 GAJ233944 Kofleria flava Pl vt1T = DSM14601T GAJ233907 Melittangium ‘alboraceum’ Me b7 = DSM52894 GAJ233908 Melittangium boletus Me b8T = DSM14713T PN GGU207877 (Melittangium lichenicola) ‘Corallococcus’ sp. DSM2275 GAM930269 Melittangium lichenicola ATCC25946T PN GAF482687 Myxobacterium KC NI GDQ768117 Myxococcus fulvus ATCC25199 T = DSM16525T M

Novel isolate (NI), proposed neotype (PN), reference strain (RS), outgroup (O). Quoted namfor a different or previous name of the strain. Melittangium lichenicola DSM2275 represe

cies are now placed in 20 genera and six families. Twelve otherstrains (nine in Sorangiineae, two in Nannocystineae, and one anaer-obic myxobacterium in Cystobacterineae) were also included for atotal of 101 cultured strains (Table 1). Aside from providing anupdated and significantly expanded phylogeny of the myxobacte-ria, it is also our objective to show that cultured strains exemplifiedby our nine novel Sorangiineae show high homology to VBNC andthat the description of these strains leads to a much a clearer dis-tinction between suborders Nannocystineae and Sorangiineae.Analysis of data from GenBank also revealed that many metage-nomic 16S rDNAs share significant homology with myxobacteriaalready known in culture. These data are also discussed to givean initial description of their possible phylogenetic status andthe likelihood that their source bacteria could be grown in thelaboratory in the future.

cession Strain name

466191 Myxococcus fulvus 125-1233918 Myxococcus fulvus Mx f421 = DSM52100233921 Myxococcus (Corallococcus) macrosporus Ccm8T = DSM14697T

262997 Myxococcus macrosporus Myxo9736072737 Myxococcus macrosporus strain 125-10-3

Q768118 Myxococcus stipitatus Mx s8T = DSM14675T PN271853 Myxococcus stipitatus KYC1101262652 Myxococcus stipitatus KYC1115

Q768119 Myxococcus virescens (flavescens) DSM2260T

Q768130 Myxococcus virescens DSM4946262649 Myxococcus virescens KYC1105

Q768116 Myxococcus xanthus ATCC25232T

000113 Myxococcus xanthus DK1622233945 ‘Nannocystis aggregans’ Na a1T = DSM14639T

233946 Nannocystis exedens Na e1T = DSM71T PN233947 Nannocystis exedens Na e571 = DSM53122

U207878 Nannocystis pusilla Na p29T = DSM14622T

252740 ‘Paraliomyxa miuraensis’ SMH-27-4 NI545827 Phaselicystis flava SBKo001T = DSM21295T

233948 Phaselicystis flava NOSO-1 = DSM53757 RSR_024795 Plesiocystis pacifica SIR-1T = DSM14875T

016469 Plesiocystis pacifica SHI-1U207879 Polyangium fumosum Pl fu5T = DSM14668T PNU207880 Polyangium sorediatum Pl s12T = DSM14670T PNU207881 Polyangium spumosum Pl sm5T = DSM14734T PN94280 Polyangium sp. PL4943233909 Pyxidicoccus fallax Py f5 = DSM14689 (A. disciformis An d1) RS

U249618 Pyxidicoccus fallax SBPx001457641 Sorangium cellulosum So ce1871T = DSM14627T

387629 Sorangium cellulosum So ce26746676 Sorangium cellulosum So ce56

467674 Sorangium cellulosum So9857316015 Sorangium cellulosum So ce90242519 Sorangium cellulosum KYC3025240498 Sorangium cellulosum (nigrum) So ce1654 = DSM14731 RS

U207882 Stigmatella aurantiaca DSM 17044T

233935 Stigmatella aurantiaca Sg a1233936 Stigmatella aurantiaca Sg a15970180 Stigmatella erecta DSM 16858T

233934 Stigmatella erecta Pd e19Q768129 Stigmatella hybrida Sg h20T = DSM14722T

U249608 Sorangiineae ‘Aetherobacter sp.’ SBSr001 NIU249609 Sorangiineae ‘Aetherobacter fasciculatus’ SBSr002 NIU249610 Sorangiineae ‘Aetherobacter rufus’ SBSr003 NIU249611 Sorangiineae ‘Aetherobacter sp.’ SBSr008 NIU249612 Sorangiineae SBSr004 NIU249613 Sorangiineae SBSr005 NIU249615 Sorangiineae SBSr006 NIU249616 Sorangiineae SBNa008 NIU249617 Sorangiineae SBCm007 NI34113 Desulfovibrio desulfuricans O

es represent the invalid or not formally accepted taxa. Names in parenthesis standnts a taxonomically misclassified strain.

880 R. Garcia et al. / Molecular Phylogenetics and Evolution 57 (2010) 878–887

2. Methods

2.1. Bacterial strains and cultivation

Most of the 22 myxobacterial strains used to generate 16S rDNAsequences came from our large collection at the Helmholtz Centrefor Infection Research (HZI) in Braunschweig, Germany, except Arch-angium gephyra DSM2261T, Cystobacter (Angiococcus) disciformisDSM52716T (=ATCC33172T), Melittangium lichenicola DSM2275T,and Stigmatella aurantiaca DSM17044T, which were purchased fromthe German Culture Collection (DSMZ), also in Braunschweig(Table 1). Novel Sorangiineae isolates are being maintained at theHZI-HIPS (MINS) in Saarbrücken, Germany. These organisms weregrown in buffered VY/2 agar (Garcia et al., 2009a) and MD1 broth(Shimkets et al., 2006), except Sorangiineae SBSr001-3 and SBSr008,which were cultivated on MD1G agar (0.35% Casitone, 0.05%CaCl2�2H2O, 0.2% MgSO4�7H2O, 0.35% glucose, 1.5% Bacto agar, pH7.0, adjusted using KOH) and its corresponding broth medium(without agar).

2.2. 16S rDNA amplification and phylogenetic tree construction

Myxobacterial strains, including novel Sorangiineae whose 16SrRNA sequences are unknown (or known but with gaps andunidentified bases), were prepared for repeated amplification andsequencing. Genomic DNA was obtained from actively growingcells scraped from agar surface and extracted using the manufac-turer’s protocol for Gram-negative bacteria in the ‘‘Qiagen Geno-mic DNA Purification Kit”. Amplification of the 16S rRNA genesusing a set of universal primers was as described previously (Gar-cia et al., 2009b). Only sequences of myxobacteria larger than1.4 Kb were chosen from GenBank entries; these were checkedfor their quality before inclusion in the alignment and final phylo-genetic tree reconstruction. The 22 strains sequenced now haveGenBank accession numbers GU207872–GU207882 andGU249608–GU249618 (Table 1).

The sequence of Desulfovibrio desulfuricans (GenBank accession:MR34113), a sulphate-reducing bacterium also in the delta branchof proteobacteria, was chosen as outgroup to root the phylogenetictree. Sequence alignments were performed using CLUSTAL W, ver-sion 2.0 (Larkin et al., 2007). Distance matrices between sequenceswere calculated using the Jukes–Cantor model (Jukes and Cantor,1969). From the distance matrices, a neighbour-joining tree wasconstructed (Saitou and Nei, 1987). The phylogenetic relationshipswere also confirmed using the maximum likelihood (PHYMLv2.4.5) program (Guindon and Gascuel, 2003). A bootstrap of1000 replicates was calculated (Felsenstein, 1985), and a consen-sus tree was built using the Geneious tree builder. All these pro-grams are packed in Geneious Pro 4.8.3 (Drummond et al., 2010).

2.3. Morphological observations of novel isolates

Colonies and fruiting bodies on agar plates were observed underan Olympus SH-ILLB stereoscopic microscope and photographedusing an Axiocam MRC (Carl Zeiss) camera. Fruiting bodies werealso analysed using bright field (Primo Star, Carl Zeiss) and phasecontrast (Axio Star plus, Carl Zeiss) microscopes.

3. Results and discussions

The phylogenetic tree by Spröer et al. (1999) was based on 54myxobacterial strains representing 21 valid species and nine gen-era in three suborders of myxobacteria. The three unclassifiedstrains in their study have already been named: NOSO-1 (neworganism of the Sorangiineae-type) as Phaselicystis flava in Phaseli-

cystidaceae (Garcia et al., 2009b), and NOCB-2 and NOCB-4 (neworganism of the Cystobacterineae-type) as Hyalangium minutum(Reichenbach, 2005). Several other strains that did not fit into theirphylogenetic tree were placed in new genera: for example, Angio-coccus disciformis An d1 to Pyxidicoccus fallax, Polyangium thaxteri Plt3 to Jahnella thaxteri, and Polyangium vitellinum Pl vt1T to Kofleriaflava (Reichenbach, 2005). Other invalid taxa (Spröer et al., 1999)were also validated as species (e.g., Chondromyces robustus, Corallo-coccus exiguus and Cystobacter violaceus) (Reichenbach, 2005). Sev-eral species were also added in Cystobacter, Stigmatella, andNannocystis, but ‘Nannocystis aggregans’ remains a subspecies ofN. exedens (Reichenbach, 2005). New genera were added, such asthe marine Haliangium, Plesiocystis, and Enhygromyxa in Nannocy-stineae (Fudou et al., 2002; Iizuka et al., 2003a,2003b), the cellulo-lytic Byssovorax in Polyangiaceae (Reichenbach et al., 2006), and theanaerobic Anaeromyxobacter in Cystobacterineae (Sanford et al.,2002). Twelve novel isolates have also been reported, namely theanaerobic ‘‘Myxobacterium KC” (Coates et al., 2002), two stillundescribed salt-tolerant isolates from Japan (Iizuka et al.,2006a; Ojika et al., 2008), and nine Sorangiineae from our collectionin Saarbrücken (Garcia et al., 2009a). The number of new isolates islikely to increase as the search for novel species continues. Explo-ration of neglected ecotopes has revealed novel isolates with pre-viously unknown chemo-physiological characteristics and as aresource for novel secondary metabolites (Garcia et al., 2009b).

The present phylogenetic tree includes nearly twice as manystrains (101) and more than twice the number of valid species(46) and genera (20) compared to Spröer et al. (1999) (Table 1).The robustness of N-J tree was supported by PHYML method whichboth produced almost the same topology (data not shown). With100% bootstrap support, it affirms the trifurcation of order Myxo-coccales into three suborders (Fig. 1) which differ from each otherby 18–25% in 16S rDNA sequence. As seen in the established andaccepted families (Kofleriaceae, Nannocystaceae, Phaselicystidaceae,and Myxococcaceae), a total of sixteen clusters or clades, most ofwhich are probably of family rank, are delineated in the subordersby at least 4% phylogenetic distance. Clusters I–V composed theNannocystineae, VI–XII in Sorangiineae, and XIII–XVI inCystobacterineae.

3.1. The Nannocystineae (Clusters I–V)

Nannocystis and Kofleria (‘‘Polyangium vitellinum Pl vt1T”) werethe only two known genera previously classified in this suborder(Spröer et al., 1999), each in its own family based on morphologyand size of vegetative cells (Reichenbach, 2005). Cells in Nannocyst-aceae are short, fat rods to almost cuboidal or oval, while those inKofleriaceae are long, cigar-shaped rods with blunt ends that aretypical for the Polyangiaceae. Several isolates recorded in the past10 years, including those of marine origin, belong to this suborder.Two major lineages with 99.7% bootstrap support were revealed inthe phylogenetic tree (Fig. 1). The first lineage includes Haliangiumand Kofleria, and the second is composed of Nannocystis and thehalophilic Enhygromyxa and Plesiocystis. Both lineages have 100%bootstrap support. The undescribed ‘Paraliomyxa miuraensis’ (Ojikaet al., 2008; Iizuka et al., 2006a) and the unclassified isolate SYR-2from brackish-water (GenBank accession: AB303310) in Japan arenested in the second lineage. Thus far, Nannocystineae is the onlysuborder that includes marine genera, and therefore is polyphy-letic. The divergence of the two ‘halophilic’ myxobacteria reflectstheir source habitat.

The moderately thermophilic clones designated as AT1-02, AT3-09, AT3-03, and SIBN-17 were phylogenetically affiliated withNannocystineae (Iizuka et al., 2006b). Clones AT1-02 and AT3-09formed a monophyletic cluster with brackish-water isolate SYR-2in clade V, while SIBN-17 and AT3-03 bifurcated to Nannocystis

Fig. 1. Neighbour-joining tree inferred from 16S rRNA gene sequences showing the positions of representative myxobacterial strains and unassigned isolates in the orderMyxococcales. The sequence of Desulfovibrio desulfuricans roots the tree. The numbers at branch points indicate the level of bootstrap support in percent based on 1000resamplings. Only values greater than 60 are shown. Bar, 0.05 substitutions per nucleotide position. Quoted names represent the invalid or not formally accepted taxa. Forother strains, it may mean taxonomically misclassified (M. lichenicola DSM2275). Name in parenthesis represents the previous taxonomic designation.

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882 R. Garcia et al. / Molecular Phylogenetics and Evolution 57 (2010) 878–887

clade III and Haliangium-Kofleria clades I–II, respectively. The psy-chrophilic myxobacteria discovered by Dawid et al. (1988) in soilsamples from the Antarctic exhibited morphological similaritieswith Nannocystis and Polyangium; however, their inaccessibilityfrom the open culture collection and absence of 16S rDNA se-quences make it impossible to determine their placement in thephylogenetic tree. Nannocystis NU-2 (Zhang et al., 2002), by its16S rDNA sequence (GenBank accession: AY030846), is a misclas-sified strain related to Cellvibrio of gamma proteobacteria. As men-tioned above, bacterial clones and strains only supported by shortand thus incomplete 16S rDNA sequences were not included in thephylogenetic tree.

3.2. I–II. Haliangium-Kofleria cluster

This is the only cluster with strains from both terrestrial (Kofle-ria) and marine (Haliangium) environments. Kofleria was formerlyclassified as Polyangium vitellinum Pl vt1T (Reichenbach, 2005;Spröer et al., 1999). It is monotypic, as well as the lone genus inKofleriaceae. The 4–5% difference in 16S rDNA between Kofleriaflava and Haliangium is suggestive for the latter as a separate family(‘‘Haliangiaceae”); this is supported by the similarity of Nannocystisexedens (type) to K. flava (79.5%) and to Haliangium ochraceum(type) (78.7%). Moreover, H. ochraceum differs in morphology andhas 95.3% identity in 16S rDNA to H. tepidum; this is lower thanthe 95.5% reported by Fudou et al. (2002). The two species also dif-fer from one another significantly in the required growth temper-ature and other physiological characteristics, which may justifytheir separation, at least at the genus level. Haliangium also shows84.3–85% similarity in 16S rDNA sequences to other halophilicmyxobacteria. An even closer affiliation (84.5–84.7%) exists be-tween undescribed halophilic ‘Paraliomyxa’ and SYR-2 from brack-ish-water. The significant difference in the 16S rDNA sequence andthe higher salt tolerance (6%) of Haliangium may reflect its inherentmarine origin.

3.3. III. Nannocystis cluster

The monophyletic cluster of Nannocystis was supported by 100%bootstrap value. At present, only N. exedens and N. pusilla are recog-nised in this genus, though the number of subspecies exceeds thatof species. These five subspecies of N. exedens were primarily dif-ferentiated by colour and shape of sporangioles (Reichenbach,2005).

This cluster is unique in Nannocystineae, or even in Myxococ-cales, due to the characteristic vegetative cells which are short rodsto almost cuboidal or oval. It shows branching with strain SMH-27-4, a suggested novel genus and species (‘Paraliomyxa miuraensis’)for soil myxobacterium isolated from the shore of the Miura Penin-sula in Kanagawa, Japan (Iizuka et al., 2006a). A 90.3% similaritywas found between N. pusilla and ‘P. miuraensis’. The bifurcationof Nannocystis with the other marine isolates is supported by100% bootstrap value, suggesting their divergence. Its affiliationis closer to the ‘halophilic’ Clusters IV and V (88.6–90.3%) than tothe Haliangium-Kofleria cluster (83.1–84.3%) (Fig. 1).

3.4. IV–V. ‘Halophilic’ cluster

The halophilic myxobacteria appear closely related to Nanno-cystis, as shown in tree topology and in the relationships amongstunclassified ‘halotolerant’ Nannocystineae. Strains SMH-27-4 andSYR-2 are 90% identical to their neighbour Nannocystis pusilla. In-deed, all strains in this cluster are related to each other by 91–96% similarity in 16S rDNA. Most closely related are Enhygromyxa,Plesiocystis, and the unidentified brackish-water isolate SYR-2 (95–

96%), while the most distantly related one is SMH-27-4 (‘Paral-iomyxa’) (91% identity).

This cluster is the largest in Nannocystineae to comprise purelyof ‘marine’ or salt-tolerant isolates. Included are SMH-27-4, SYR-2,Plesiocystis, and Enhygromyxa. Isolates in the latter two genera cantolerate up to 4% NaCl (Iizuka et al., 2003b), suggesting that theylikely evolved from a halotolerant ancestor. Since SMH-27-4 (Iizu-ka et al., 2006a) and SYR-2 strains clustered closely with Plesiocys-tis and Enhygromyxa, they may be assumed to tolerate almost thesame amount of sodium chloride concentration, or probably muchlower, as in the case of the brackish-water isolate. The higher per-centage (6%) salt tolerance by Haliangium in Cluster I (Fudou et al.,2002) and its divergence to Clusters IV and V suggests that it orig-inates from a truly halophilic organism.

3.5. The Sorangiineae (Clusters VI–XII)

The suborder bifurcates into two families, Polyangiaceae andPhaselicystidaceae (monotypic), which differ in 16S rDNA with100% bootstrap support. Polyangiaceae (Cluster VIII–XII) at presenthas at least five validly described genera, famous for their tree-likefruiting bodies, macromolecule degradation, and production ofbioactive secondary metabolites. Most of our novel isolates alsocluster in this family. Cluster VIII thus far is the only one in Sorang-iineae with members having sporangioles on stalks or slime cush-ions. Novel Sorangiineae SBCm007 also has stalked fruiting bodiesbut belongs to Cluster IX. Sorangiineae SBNa008 is another novelisolate and appears to represent a separate cluster (VI, SeeSection 3.16.1).

Isolates in this suborder are most difficult to isolate and purify,but the chances of their being novel are highest. Most of our newisolates that were characterised morphologically, chemo-physio-logically and genetically belong here. Finding novel thermophilesin Sorangiineae should not be surprising after the discovery of mod-erately thermophilic strains (Gerth and Müller, 2005). Iizuka et al.(2006b) considered the moderately thermophilic clones AT1-01and AT3-01 to branch in this suborder; however, our analysis re-vealed that both clones (GenBank accession: AB246771,AB246772) diverged from both Phaselicystidaceae and Polyangia-ceae in Sorangiineae, suggesting that they represent a truly novelgroup of VBNC.

3.6. VII. Phaselicystis cluster

Family Phaselicystidaceae was established for two soil isolateswith remarkable high production of arachidonic acid (Garciaet al., 2009b). The bifurcation of Cluster VII to Polyangiaceae showsthat it is a separate family. The long radial veins of the swarm stagein the monotypic genus Phaselicystis resemble those in the Cysto-bacterineae but are unknown in the Polyangiaceae.

3.7. VIII Chondromyces-Jahnella cluster

All five known culturable Chondromyces species form a phyloge-netically coherent cluster. Chondromyces apiculatus, C. pediculatus,C. lanuginosus and C. robustus are monophyletic (98.6–99.5%). Thetwo C. crocatus strains with 96.4–97.2% similarity to other Chondr-omyces appear to be divergent. Their fruiting bodies are phenotyp-ically complex on account of clusters of sporangioles supported byslime branches.

The genus Jahnella (‘Jahnia’) was described in the latest editionof Bergey’s Manual of Systematic Bacteriology based on Polyangiumthaxteri strains Pl t3 and Pl t4T (Reichenbach, 2005). The threestrains of J. thaxteri appear monophyletic with 93.4–96% bootstrapsupport. Their closest relatives in the phylogenetic tree are speciesof Chondromyces (95.5–97.1% similarity in 16S rDNA). Jahnella and

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Chondromyces unified together to bifurcate from the rest of thePolyangiaceae (Clusters IX–XII). Both genera exhibit orange swarmcolonies and have slime matrices to support fruiting bodies.

3.8. IX Polyangium cluster

The 16S rDNA sequences of three culturable species of Polyan-gium (P. spumosum, P. sorediatum, P. fumosum) are included in thephylogenetic analysis for the first time. These submitted sequencesin the GenBank belong to the proposed neotype strains (Reichen-bach, 2005) which are accessible at DSMZ (Table 1). Several morespecies have been described (Reichenbach, 2005) but, again, theabsence of type strains in the open collection hinders further ver-ification of their phylogenetic position. Only Polyangium sp. PL4943was included in previous phylogenetic analysis (Spröer et al.,1999). Based on its tree topology, strain PL4943 is closely relatedto P. spumosum. Not all strains morphologically described as Poly-angium belong to the suborder Sorangiineae, such as P. vitellinumstrain Pl vt1T, which now resides in Nannocystineae as K. flava.Other described Polyangium strains turned out to be novel taxa,as with P. thaxteri Pl t3 (=J. thaxteri) (Reichenbach, 2005).

The Polyangium cluster also includes unassigned isolates (seeSorangiineae SBSr004-006, Cluster IX, Section 3.16.3) representingnovel or previously described, but uncultivated or lost species ofPolyangium. The unassigned novel Sorangiineae SBCm007 appearsdivergent from other known Polyangium species. Though it hasthe swarming pattern similar to a Polyangium, this feature aloneis not sufficient for its classification; it is discussed in a later sec-tion (Sorangiineae SBCm007 Cluster IX).

3.9. X. Byssovorax cluster

The monotypic Byssovorax, only the second genus after Soran-gium known to degrade cellulose, is found in a cluster of its own.It was described earlier as branching with 95.7% similarity to thereference strain of Sorangium cellulosum as its closest relative(Reichenbach et al., 2006). The divergence of Byssovorax (ClusterX) from Sorangium became more striking in the present phyloge-netic tree after inclusion of novel Sorangiineae sequences. Byssovo-rax seems more related to novel Sorangiineae SBSr001-SBSr003,and SBSr008 (95.8–96.2%) than to the type strain of S. cellulosum(95.6%).

3.10. XII. Sorangium cluster

The seven strains included in the tree formed a monophyleticcluster. Swarming pattern and cellulose degradation are the mostremarkable distinguishable features. Separation of Sorangium fromPolyangium is justified by almost 5% difference in their 16S rDNAsequences and non-cellulolytic character of the latter. The distinctrelationships of Sorangium to Byssovorax as postulated by Reichen-bach et al. (2006) were reflected in the phylogenetic tree, as bothgroups of organisms formed distinct and well-supported cladesin the phylogenetic alignments. The 16S rDNA of S. cellulosumDSM14627T differs from B. cruenta DSM14553T by 4.4% and fromnovel Sorangiineae SBSr003 by 5.3%, thus supporting phylogeneticClusters X–XII for these strains.

3.11. The Cystobacterineae (Clusters XIII–XVI)

With the exception of Cluster XIII (Anaeromyxobacter), theCystobacterineae in the tree is divided into two main clades. Thefirst clade consists of Cystobacter, Archangium, and Melittangiumin the family Cystobacteraceae (Cluster XIV). The second cladebifurcates into Corallococcus, Pyxidicoccus, Myxococcus (Myxococca-ceae), Hyalangium, Stigmatella, and Cystobacter gracilis (Cluster XV).

Based on the tree topology, Cluster XV does not seem to be part ofthe Cystobacteraceae, but is rather more closely related to theMyxococcaceae (Cluster XVI). However, its bifurcation from theMyxococcaceae clade and significant differences in morphologicalcharacteristics such as myxospores and swarm patterns, suggestthat Cluster XV is uniquely different from Cluster XVI. Moreover,Cluster XV also shows branch divergence and morphological differ-ences from Cluster XIV. Members of Cluster XIV possess long, thin,needle-shaped A2-type cells, whereas those in Cluster XV resembleclosely the A3-type cells, which are shorter, moderately sized, andhave slightly blunted ends (Reichenbach, 2005). This distinction invegetative cell morphology of Clusters XIV and XV is mirrored inthe phylogenetic grouping of the strains based on 16S rDNA.

Wu et al. (2005) reported to have genetically detected 12groups of Cystobacterineae in a soil sample using specific primers.The 61 sequences that were cloned were claimed to representthe ‘‘unculturable” myxobacterial strains, but these sequences donot appear to be identical or highly similar to any of myxobacterial16S rDNA sequences. Surprisingly, BLASTn analysis of these se-quences shows homology to mostly eukaryotic organisms [e.g.,frog (AY803837), mosquito (AY803795), etc.]. In our experiencewith myxobacteria, the probability of finding new species in Cysto-bacterineae appears very low. However, novel strain discovery inthe suborder may depend on the ecological source of the sampleand new methods for isolation and cultivation.

3.12. XIII. Anaeromyxobacter cluster

Group XIII shows bifurcation from Cystobacterineae (ClustersXIV–XVI) with 100% bootstrap support. It includes only anaerobictaxa, but so far only Anaeromyxobacter dehalogenans is validly de-scribed (Sanford et al., 2002). All Anaeromyxobacter strains in thetree are 99.6% similar, suggesting that they are simply one homo-geneous species. Unidentified myxobacterium KC, reported asbranching with Stigmatella erecta (Coates et al., 2002), was discov-ered to be diverging from this cluster. Thus, strain KC and theAnaeromyxobacter constitute the anaerobic cluster of myxobacte-ria. These two appear to be different, as shown by their bifurcationin the tree with 100% bootstrap support. 89% identity was foundbetween type strains A. dehalogenans and Archangium gephyra, sug-gest that erection of a new family would eventually be justified.However, the definition and erection of new taxa is out of the scopeof this study and will be undertaken once additional morphologicaland physiological data on the respective strains and species be-come available.

A bacterial clone (PVB OTU 10B) from a hydrothermal vent inHawaii was shown earlier to branch with Chondromyces spp., Poly-angium sp., and Sorangium cellulosum in Sorangiineae (Moyer et al.,1995). Our analysis confirmed the bifurcation of this clone (Gen-Bank accession: U15117) with Sorangiineae, and it appears to bethe counterpart of Anaeromyxobacter in Cystobacterineae. This sug-gests that, given the right conditions for cultivation, a new taxo-nomic group representing the anaerobic Sorangiineae may beisolated in the future. This is likely, since myxobacteria are be-lieved to have evolved along with the sulphur- and sulphate-reducing eubacteria (Woese, 1987).

3.13. XIV. Archangium-Cystobacter-Melittangium cluster

3.13.1. Archangium clusterThe two strains represented in this cluster are 99.5% similar.

Based on tree topology, their closest neighbours appear to beCystobacter ferrugineus Cb fe13 (98.6%), C. minus Cb m6 (98.5%), C.violaceus Cb vi34 (98.5%), and C. disciformis DSM52716T (98%).Archangium and Cystobacter have identical vegetative cells, butthey differ in fruiting body morphology. A sporangiole wall encas-

884 R. Garcia et al. / Molecular Phylogenetics and Evolution 57 (2010) 878–887

ing the myxospores is absent in the former and present in the lat-ter. However, the difference in 16S rDNA between these genera isless than 2%, suggesting that they were closely related taxa that di-verged during evolution.

3.13.2. Cystobacter clusterThe current composition of the Cystobacter is polyphyletic with

members in group XIV and XV. The first group is composed of C.violaceus Cb vi29 and C. ferrugineus Cb fe13, which togetherbranched with the Archangium cluster. Cb vi29 is 97.8% similar toC. violaceus type strain, and Cb fe13 is 98% similar to the proposedtype of C. ferrugineus (Reichenbach, 2005). Neither strain is foundclustered with the type strain with which it was previously de-scribed as related (Spröer et al., 1999), indicating that Cb vi29and Cb fe13 are misclassified and perhaps represent novel taxa.The second group is composed of the neotype of Cystobacter(Angiococcus) disciformis ATCC33172T (=DSM52716T), C. violaceusCb vi34, and C. minus Cb m6. The designated neotype shows98.3%, 98.5%, and 98% identity with Cb vi34, Cb m6, and Archan-gium gephyra, respectively. Based on morphology, Brockman andMcCurdy (1989) transferred A. disciformis to Cystobacter, but phylo-genetic analysis shows that it appears bifurcated from the majorityof Cystobacter. If more strains are discovered for comparison, itmay become clearer that C. disciformis should be relegated backto its original genus, Angiococcus. Several described A. disciformisisolates appear to be Pyxidicoccus based on morphology (Dawid,2000; Reichenbach, 1984), and still others (e.g., strain An d4 andAn d6) seem to be related to Archangium (Spröer et al., 1999).

Type strains C. minus and C. violaceus cluster together with88.7% bootstrap support and 99.4% similarity in 16S rDNA se-quences; both show intense purple swarms in our study. The diver-gence of C. violaceus Cb vi34 and C. minus Cb m6 into a separatecluster has been already considered for generic transfer (Spröeret al., 1999). Both strains perhaps also have purple swarms,explaining their misidentification. Cystobacter miniatus representsthe third group which clusters with Melittangium ‘alboraceum’,showing 99.1% similarity together with M. boletus. It is also 97.6%similar to M. lichenicola ATCC25946, a proposed reference strain(McCurdy, 1971). We recommend further investigation of C. mini-atus, as it appears to be a species of Melittangium, based on highpercentage similarity in 16S rDNA sequence.

The fourth group covers the bulk of Cystobacter species, includ-ing C. ferrugineus, C. velatus, C. fuscus, and C. badius. These four spe-cies differ by less than 1% (0.1% between the latter two species) intheir 16S rDNA sequences and are therefore closely related. Thegroup also includes C. armeniaca and Melittangium lichenicolaATCC25946, which have 98.5–98.8% similarity to the four afore-mentioned Cystobacter species.

Cystobacter gracilis DSM14753T appears to constitute the fifthand last group in the genus. Based on topology, it does not belongto Cystobacter, but rather is an unexpected member of the Hyalan-gium and Stigmatella Cluster (XV). It is 97.5%, 96.3%, and 96.4% sim-ilar to Hyalangium minutum DSM14724T, Stigmatella aurantiaca, andC. fuscus, respectively. Moreover, C. gracilis type strain differs fromCystobacter in the morphology of the vegetative stage. This evidencesuggests that C. gracilis represents a novel genus of its own.

Our analysis showed that many Cystobacter strains did not matchwith their corresponding type strains, most likely due to their incor-rect morphological identification. Fruiting body characteristics varyin different media and are often lost after several transfers in thesame medium. In general, morphology-based characterisationalone is neither sufficient nor reliable for identification of this genus.

3.13.3. Melittangium clusterBased on topology, Melittangium falls between polyphyletic

branches of Cystobacter. The cluster includes the recently described

Cystobacter miniatus and C. armeniaca, which branch with M. ‘alb-oraceum’ Me b7 and M. lichenicola ATCC25946, respectively. Theproposed neotype strain of M. lichenicola (ATCC25946) by McCurdy(1971) was evidently divergent from M. ‘alboraceum’ and M. boletus(Lang and Spröer, 2008). The current type strain of M. lichenicola(DSM2275T = ATCC25944T) was found to reside in the Corallococcuscluster, suggesting a case of misclassification; the proposal for itsreplacement with the reference strain has recently been petitioned(Lang and Spröer, 2008).

3.14. XV. Hyalangium-Stigmatella cluster

Hyalangium was established based on two previously unas-signed isolates NOCB-2T and -4 (Reichenbach, 2005), which mor-phologically resembled Cystobacter (Spröer et al., 1999). Theunique phenotypic characteristic of its lone species, H. minutum,is the glassy to transparent appearance of the sporangioles (Rei-chenbach, 2005). The cluster bifurcates with and is 97.5% similarto its closest neighbour, Cystobacter gracilis DSM14753T. NOCB-2T

and NOCB-4 are distantly related to Stigmatella, with 96.5% identityto S. aurantiaca. Hyalangium undoubtedly represents a novel genusbased on its 16S rDNA sequence, unique branch in Cystobactera-ceae, and unusual morphology.

Stigmatella appears to be a homogeneous group, with 100%bootstrap support. All strains are matched with their correspond-ing types, indicating that the three species are distinct from eachother. Hyalangium minutum and Cystobacter gracilis appear to betheir immediate relatives. However, S. aurantiaca diverges in topol-ogy. Its complex tree-like fruiting body strikingly rivals that ofChondromyces in Sorangiineae. The genus, as typified by S. auranti-aca DSM17044T, shows 95.5% and 95.6% similarity to Cystobacterfuscus DSM2262T and Corallococcus coralloides DSM2259T, respec-tively. Cluster XV appears to represent a separate family, basedon at least 4% identity differences in 16S rDNA sequences andbranching patterns to Clusters XIV and XVI.

3.15. XVI. Corallococcus-Pyxidicoccus-Myxococcus cluster

3.15.1. Corallococcus clusterThe coherent clustering of Corallococcus is in agreement with

the findings of Spröer et al. (1999). The type strain of Corallococcuscoralloides, for example, is 97.3–98.1% identical to all Myxococcustype strains, including M. macrosporus (syn. Corallococcus macrosp-orus (Lang and Stackebrandt, 2009). The type strains of C. corallo-ides and C. exiguus show 99.9% 16S rDNA similarity, suggestingthat they represent only one species. The distinction between spe-cies in this genus hinges mainly on the size and colour of the fruit-ing body which, in our experience, may change depending on thegrowth conditions. For example, C. coralloides DSM2259T formstiny fruiting bodies on agar which could be mistaken for C. exiguus.This perhaps is also the case with C. exiguus Cc e100, whichbranches closely to C. coralloides DSM52497T. Melittangium licheni-cola DSM2275T appears to be a misclassified Corallococcus (seeSection 3.13.3).

3.15.2. Pyxidicoccus clusterPyxidicoccus reference Py f5 strain and strain SBPx001 from the

Philippines form a distinct cluster divergent from the Myxococcusclade in group XVI with 80.5% bootstrap support at the bifurcationnode. The cluster differs from Myxococcus by the walled sporangi-oles containing spherical myxospores. The lone species (P. fallax),previously referred to as Angiococcus disciformis (e.g., strain And1), was shown to branch with Myxococcus stipitatus Mx s33 andM. fulvus Mx f421 (Spröer et al., 1999). Our analysis confirms M. sti-pitatus (98.8%) and M. fulvus (99.3%) as it closest relatives.

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3.15.3. Myxococcus clusterThe clustering of Myxococcus strains with the type strains sug-

gests a homophyletic group. This was supported by the bootstrapvalues from 94.3% (M. fulvus) to 100% (M. macrosporus). Two groupswere formed based on topology. The first group is composed of M.stipitatus and M. fulvus, while M. virescens, M. xanthus, and M.macrosporus comprise the second group. Type strains M. stipitatusand M. fulvus are 99.4% similar; stalk and myxospore (1.2–1.6 lm) in both species are also morphologically closely similar.Together, they bifurcate to the genus Pyxidicoccus, which is sup-ported by differences in their myxospores size.

Both M. xanthus and M. virescens have yellow swarms andfruiting bodies, but their identification by pigmentation seemsto be unreliable (Spröer et al., 1999). Lang and Stackebrandt(2009) transferred Corallococcus macrosporus to Myxococcus.Strain 125-10-3 is nearly 100% identical to M. macrosporus. How-ever, the low homology (98%) of Myxo9736 to all Myxococcusspecies and its appearance in a separate branch from that ofMyxococcus macrosporus suggests that this strain is probably anovel taxon. Further chemotaxonomic, physiological, and phylo-genetic data should be made available to further clarify itsstatus.

Fig. 2. Colony morphology of novel myxobacterial isolates. (a) Swarm colony of Soranswarm of Sorangiineae SBSr006 on agar. (c) Clusters of tiny sporangioles produced byglobular sporangioles and scattered vegetative cells. (e) Sorangiineae SBSr008 bundles ofbright field (e) microscopes. Bars, (a) 15 mm, (b) 10 mm, (c) 100 lm, (d) 15 lm, (e) 45 l

3.16. The Novel clusters

3.16.1. VI. Sorangiineae SBNa008BLASTn showed that the myxobacterium strain SBNa008 is clo-

sely related to clones from uncultured bacteria (GenBank acces-sion: EU662572, EU104167, FJ479473, AM490752), with 95–96%similarity. The next closest similarities were found amongst typestrains of Byssovorax cruenta (95%), Phaselicystis flava (94%),Chondromyces lanuginosus KYC2904 (94%), and Sorangium cellulo-sum So ce56 (94%). When grown on buffered yeast agar, this novelisolate exhibits thin and soft swarm colonies similar to Nannocystis,but other growth stages differ significantly in morphology. Its long,slender, cigar-shaped vegetative cells are typical for Sorangiineae.No holes or deep agar excavation could be seen in the SBNa008 cul-ture, although the agar medium was sometimes depressed. In addi-tion, tiny and ovoid fruiting bodies, often arranged in clusters wereproduced on the agar (Fig. 2c). These features were remarkably dif-ferent from Nannocystis, although its 16S rDNA sequence is 78.3%,similar to that of the type strain of N. exedens. However, SBNa008does not cluster with Nannocystis, but surprisingly bifurcates withthe recently described Phaselicystis flava (94.4%) in Phaselicystida-ceae (Garcia et al., 2009b). Overall, SBNa008 represents a newly

giineae SBCm007 on filter paper showing pseudoplasmodial pattern. (b) Radiatingthe Sorangiineae SBNa008. (d) Slide-mount of Sorangiineae SBSr003 showing smallfruiting bodies. Pictures were taken under dissecting (a–c), phase-contrast (d), andm.

Fig. 3. Neighbour-joining tree generated from BLASTn showing homology of cultured novel Sorangiineae ‘Aetherobacter sp.’ SBSr008 to clones of ‘‘unculturable” bacteria.

886 R. Garcia et al. / Molecular Phylogenetics and Evolution 57 (2010) 878–887

discovered ‘unculturable’ myxobacterium within Sorangiineae, andwill be described in the future as a novel genus or perhaps family.

3.16.2. IX. Sorangiineae SBCm007Based on BLASTn searches using 16S rDNA sequences, strain

SBCm007 shows closest identity (95%) to a clone from the uncul-tured bacteria (GenBank accession: AF280858) and with S. cellulo-sum strains. It also appears that SBCm007 is divergent from otherstill unassigned novel strains (SBSr004, 005, 006) and to several de-scribed Polyangium species (Fig. 1). The bifurcation was supportedby a high bootstrap value (99.6%), indicating that SBCm007 is dif-ferent from the rest of the cluster. After Sorangium and Byssovorax,strain SBCm007 represents the third group of cellulose-degradingmyxobacteria discovered to date. Though it shows high 16S rDNAsequence similarity with S. cellulosum, it differs significantly in cel-lulose degradation pattern. Fig. 2a shows the initial swarming pat-tern of SBCm007 on filter paper. Topology shows clearly thebifurcation of the novel isolate with the type species Sorangiumcellulosum (95.3% similarity) and Byssovorax cruenta (95.2%).

SBCm007 also shows morphological affiliation to Polyangiumthrough its vegetative and myxospore stages, swarming pattern,and is 97.5% similar to P. fumosum Pl fu5T. Based on topology,SBCm007 appears to be a neighbour of Polyangium; however, theirbifurcation and 2.5% difference in 16S rDNA sequence support itsbid as a novel genus. Full descriptions of the species and genus willbe given in the near future.

3.16.3. IX. Sorangiineae SBSr004-006 clusterThese organisms branch closely with the type strains of Polyan-

gium. A BLASTn search also shows their high similarity to clonesfrom uncultured bacteria (96%) and with S. cellulosum strains(95%). Even higher similarity was found with Polyangium (96.4–97.7%), revealed for the first time only after 16S rDNA sequencingof the three proposed type strains (P. spumosum, P. fumosum, P.sorediatum) (Reichenbach, 2005). Swarms of the novel isolates nor-mally burrow deep within the agar to produce fan-shaped colonies(Fig. 2b), contrasting with the band-shaped appearance of the Poly-angium strains. In addition, swarms of both Polyangium and the no-vel isolates may be slimy when produced on surface of the agar;however, both never appear as radial veins. These novel strains ap-pear to be new species of Polyangium.

3.16.4. XI. Sorangiineae SBSr001-SBSr003 & SBSr008 clusterThis cluster lies in between the known genera of cellulose-

degrading myxobacteria, but appears to branch more closely withByssovorax than with Sorangium. All the strains seem to be coher-ent in this cluster with 100% bootstrap support. They do not de-grade cellulose, but instead exhibit bacteriolytic behaviour inregards to nutrition. Using a BLASTn search in the GenBank data-base, their best 16S rDNA sequence hit was found similar to clonesof uncultured bacteria (98%) and to the cellulose-degrading Bys-sovorax and Sorangium (96%) (e.g., SBSr008, Fig. 3). The four strainsare distinguishable via morphology of the growth stages and phys-ico-chemical characteristics, suggesting that they represent differ-ent species. Their growth morphologies appear to be different frommembers of Sorangiineae or even the order Myxococcales. Fig. 2dand 2e shows the fruiting bodies of Sorangiineae SBSr003 andSBSr008. The unique morphology is also supported by their iso-lated position in the phylogenetic tree, indicating the novelty ofthese isolates (Fig. 1) as a separate genus (‘‘Aetherobacter”).

4. Conclusions

Our genetic analysis has shown once again that myxobacteriaare a phylogenetically coherent group. Most of the strains usedin the phylogenetic tree matched with the type or proposed neo-type strains, except for members belonging to Cystobacter, Melit-tangium and Corallococcus, all in Cystobacterineae. The genusCystobacter holds the most number of misclassified isolates, whichperhaps represent more than three genera. In general, morphol-ogy-based characterisation alone is not conclusively reliable forthe classification of an isolate. Thus, it is highly recommended tocombine phenotypic, chemo-physiological, and genetic character-istics in order to identify a myxobacterial strain.

The replacement by neotype strains for some taxa in the lastdecades and their accessibility in culture collections guide theidentification of new strains. In addition, strains represented nowby Pyxidicoccus, Hyalangium, Kofleria, and Jahnella were properlyrenamed, reclassified, and their phylogenetic relationshipsclarified.

Many marine myxobacteria were also identified in the last dec-ade. A few of them still need to be given valid taxonomic status,but their phylogenetic positions in relation to recognised taxacould be inferred. Most striking was the discovery of a sizeable

R. Garcia et al. / Molecular Phylogenetics and Evolution 57 (2010) 878–887 887

number of new but still unnamed Sorangiineae strains which aremorphologically and phylogenetically novel. These were success-fully cultivated in vitro and were related to several ‘‘unculturable”or VBNC bacterial strains with 16S rRNA gene sequences inGenBank.

The proposed phylogenetic tree covers not only a diverse num-ber of myxobacterial isolates, but also integrates culturable typestrains and yet undescribed novel isolates. We hope that the treeserves as a key guide to the genetic- and morphology-based taxon-omy of myxobacteria, and also as an important tool for the discov-ery of interesting novel compounds from unexplored novel strains.

Acknowledgment

We are grateful to Ms. Janet Lei for proofreading of thismanuscript.

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