Complete genome sequence of Granulicella mallensis type strain MP5ACTX8T, an acidobacterium from tundra soil

S anda ds in Genomic Sciences (2013) 9:71-82 DOI:10.4056/sigs.4328031 The Genomic S anda ds Conso ium Comple e genome sequence o G anulicella mallensis ype s ain MP5ACTX8T, an acidobac e ium om und a soil Suman R. Rawa 1, Minna K. Männis ö2, Valen in S a o oy o 3, Lynne Goodwin4, Ma Nolan5 Lo en J. Hause 6, Mi iam Land6, Ka en Wals on Da enpo 4, Tanja Woyke5 and Max M. Häggblom1* 1 Depa men o Biochemis y and Mic obiology, Ru ge s, The S a e Uni e si y o New Je sey, New B unswick, New Je sey USA 2 Finnish Fo es Resea ch Ins i u e, Ro aniemi, Finland 3 Depa men o Cell Biology and Neu oscience, Ru ge s, The S a e Uni e si y o New Je sey, Pisca away, New Je sey, USA 4 Los Alamos Na ional Labo a o y, Bioscience Di ision, Los Alamos, New Mexico, USA 5 DOE Join Genome Ins i u e, Walnu C eek, Cali o nia, USA 6 Oak Ridge Na ional Labo a o y, Oak Ridge, Tennessee, USA *Co esponding au ho : Max M Häggblom (haggblom@sebs. u ge s.edu) Keywo ds: cold adap ed, acidophile, und a soil, Acidobac e ia G anulicella mallensis MP5ACTX8T is a no el species o he genus G anulicella in subdi ision 1o Acidobac e ia. G. mallensis is o ecological in e es being a membe o he dominan soil bac e ial communi y ac i e a low empe a u es and nu ien limi ing condi ions in A c ic alpine und a. G. mallensis is a cold-adap ed acidophile and a e sa ile he e o oph ha hyd olyzes a sui e o suga s and complex polysaccha ides. Genome analysis e ealed me abolic e sa ili y wi h genes in ol ed in me abolism and anspo o ca bohyd a es. These include gene mod- ules encoding he ca bohyd a e-ac i e enzyme (CAZyme) amily in ol ed in b eakdown, u ili- za ion and biosyn hesis o di e se s uc u al and s o age polysaccha ides including plan based ca bon polyme s. The genome o G anulicella mallensis MP5ACTX8T consis s o a single epli- con o 6,237,577 base pai s (bp) wi h 4,907 p o ein-coding genes and 53 RNA genes. In oduc ion S ain MP5ACTX8T (= ATCC BAA-1857T = DSM 23137T), is he ype s ain o he species G anulicella mallensis [1]. The genus G anulicella, in subdi ision 1 o Acidobac e ia, was i s de- sc ibed by Pank a o e al. in 2010 [2]. G anulicella mallensis (mal.len' sis. N. L. em. adj. mallensis; pe aining o i s isola ion om soil o Malla Na u e Rese e, Kilpisjä i, Finland; 69°01’N, 20°50’E) was desc ibed along wi h o he species o he genus G anulicella isola ed om und a soil [1] and is one o he wo wi h se- quenced genomes, ou o eigh alidly desc ibed G anulicella species. Acidobac e ia is one o he mos ubiqui ous bac e i- al phyla ound in di e se habi a s and is abundan in mos soil en i onmen s [3,4] including A c ic und a soils [5,6]. Acidobac e ia a e phylogene ically and physiologically di e se [7] ep esen ed by 26 phylogene ic subdi isions [8] o which only subdi isions 1, 3, 4, 8, and 10 a e de- ined by axonomically cha ac e ized ep esen a- i es. To da e, subdi ision 1 is comp ised o eigh gene a: Acidobac e ium [9], Te iglobus [10,11], Edaphobac e [12], G anulicella [1,2], Acidipila [13], Telma obac e [14], Acidicapsa [15] and B yocella [16]. Subdi ision 3, 4 and 10 include only one ge- nus each, namely B yobac e [17], Blas oca ella [18] and The mo omaculum [19], espec i ely, while subdi ision 8 includes h ee gene a; Holophaga [20], Geo h ix [21] and Acan hopleu ibac e [22]. Th ee species, ‘Candida us Ko ibac e e sa ilis’ [23], ‘Candida us Solibac e usi a us’ [23] and ‘Candida us Chlo acidobac e ium he mophilum’ [24] ha e been desc ibed as ‘Candida us’ axa. Acidobac e ia a e ela i ely di icul o cul i a e wi h slow g ow h G anulicella mallensis ype s ain MP5ACTX8T 72 S anda ds in Genomic Sciences a es and ypically equi e up o se e al weeks o de elop isible colonies on solid media. Ne e he- less, he phylogene ic di e si y, ubiqui y and abun- dance o his g oup sugges ha hey play im- po an ecological oles in soils. The abundance o Acidobac e ia has been ound o co ela e wi h soil pH [25,26] and ca bon [27,28], wi h subdi ision 1 Acidobac e ia being mos abundan in sligh ly acid- ic soils. Ou p e ious s udies ha e shown ha Acidobac e ia domina e in he acidic und a hea hs o no he n Finland [25,29-31]. Using selec i e iso- la ion echniques we ha e been able o isola e se - e al slow g owing and as idious s ains o Acidobac e ia [1,11]. On he basis o phylogene ic, pheno ypic and chemo axonomic da a, including 16S RNA, poB gene sequence simila i y and DNA– DNA hyb idiza ion, s ain MP5ACTX8T was classi- ied as a no el species o he genus G anulicella [1]. He e, we summa ize he physiological ea u es o- ge he wi h he comple e genome sequence, anno- a ion and da a analysis o G anulicella mallensis MP5ACTX8T (Table 1). Classi ica ion and ea u es Wi hin he genus G anulicella, eigh species a e de- sc ibed wi h alidly published names: G. mallensis MP5ACTX8T, G. und icola MP5ACTX9T, G. a c ica MP5ACTX2T and G. sapmiensis S6CTX5AT isola ed om A c ic und a soil [1] and G. paludicola OB1010T, G. pec ini o ans TPB6011T, G. osea TPO1014T and G. agg egans TPB6028T isola ed om sphagnum pea bogs [3]. S ain MP5ACTX8T showed 95.5 -96.1% 16S RNA gene sequence iden- i y o und a soil s ains, G. und icola MP5ACTX9T (95.5%), G. sapmiensis S6CTX5AT (96.2%) and G. a c ica MP5ACTX2T (96.1%) and 94.6 – 97.4% o G. osea TPO1014T (94.6%), G. agg egans TPB6028T (96.0%), G. pec ini o ans TPB6011T (96.1%), G. paludicola OB1010T (96.5%) and G. paludicola LCBR1 (97.4%). Phylogene ic analysis based on he 16S RNA gene o axonomically classi ied s ains o amily Acidobac e iaceae placed G. paludicola ype s ain OB1010 T as he closes axonomically classi ied ela i e o G. mallensis MP5ACTX8T (Fig- u e 1). Figu e 1. Phylogene ic ee highligh ing he posi ion o G. mallensis MP5ACTX8T (shown in bold) ela i e o he o h- e ype s ains wi hin SD1 Acidobac e ia. The maximum likelihood ee was in e ed om 1,361 aligned posi ions o he 16S RNA gene sequences and de i ed based on he Tamu a-Nei model using MEGA 5 [41]. Boo s ap al- ues >50 (exp essed as pe cen ages o 1,000 eplica es) a e shown a b anch poin s. Ba : 0.02 subs i u ions pe nu- cleo ide posi ion. The co esponding GenBank accession numbe s a e displayed in pa en heses. S ains whose ge- nomes ha e been sequenced, a e ma ked wi h an as e isk; G. mallensis MP5ACTX8T (CP003130), G. und icola MP5ACTX9T (CP002480), T. saanensis SP1PR4T (CP002467), T. oseus KBS63T (CP003379) and A. capsula um ATCC 51196T (CP001472). B yobac e agg ega us MPL3 (AM162405) in SD3 Acidobac e ia was used as an ou g oup. Rawa e al. h p://s anda dsingenomics.o g 73 Table 1. Classi ica ion and gene al ea u es o G. mallensis s ain MP5ACTX8T acco ding o he MIGS ecommenda- ions [32] MIGS ID P ope y Te m E idence codea Domain Bac e ia TAS [33] Phylum Acidobac e ia TAS [34,35] Class Acidobac e ia TAS [36,37] Classi ica ion O de Acidobac e iales TAS [36,38] Family Acidobac e iaceae TAS [34,39] Genus G anulicella TAS [1,2] Species G anulicella mallensis TAS [1] Type s ain: MP5ACTX8T (= ATCC BAA-1857T = DSM 23137T) G am s ain nega i e TAS [1] Cell shape od TAS [1] Mo ili y non-mo ile TAS [1] Spo ula ion no epo ed NAS Tempe a u e ange 4–28 °C TAS [1] Op imum empe a u e 24–27 °C TAS [1] pH ange 3.5–6.5 TAS [1] Op imum pH 5 TAS [1] Ca bon sou ce D-glucose, mal ose, D- uc ose, D-galac ose, lac ose, lac ulose, D-mannose, D- ibose, a inose, suc ose, e- halose, cellobiose, D-xylose, glucu ona e TAS [1] MIGS-6 Habi a e es ial TAS [1] MIGS-6.3 Salini y G ow h wi h up o 1.5% NaCl TAS [1] MIGS-22 Oxygen equi emen ae obic TAS [1] MIGS-15 Bio ic ela ionship ee-li ing TAS [1] MIGS-14 Pa hogenici y non-pa hogenic NAS MIGS-4 Geog aphic loca ion A c ic-alpine und a, Finland TAS [1] MIGS-5 Sample collec ion 2006 TAS [1] MIGS-4.1 La i ude 69°01’N, TAS [1] MIGS-4.2 Longi ude 20°50’E MIGS-4.4 Al i ude 700 m TAS [1] aE idence codes - IDA: In e ed om Di ec Assay; TAS: T aceable Au ho S a emen (i.e., a di ec epo exis s in he li e a u e); NAS: Non- aceable Au ho S a emen (i.e., no di ec ly obse ed o he li ing, isola ed sample, bu based on a gene ally accep ed p ope y o he species, o anecdo al e idence). These e idence codes a e om he Gene On ology p ojec [40]. G anulicella mallensis ype s ain MP5ACTX8T 74 S anda ds in Genomic Sciences Mo phology and physiology G. mallensis g ows on R2 medium (Di co) a pH 3.5–6.5 (op imum pH 5) and a +4 o +28 °C (op- imum 24–27 °C) [1]. On R2 aga , s ain MP5ACTX8T o ms opaque whi e mucoid colonies wi h a diame e o app oxima ely 1 mm. Cells a e G am-nega i e, non-mo ile, ae obic ods, app ox- ima ely 0.5–0.7 mm wide and 0.6–1.3 mm long. G ow h obse ed wi h up o 1.5% NaCl (w/ ) (Table 1). The cell-wall s uc u e in ul a hin sec- ions o elec on mic og aphs o cells o MP5ACTX8T is shown in Figu e 2. G. mallensis u ilizes D-glucose, mal ose, cellobiose, D- uc ose, D-galac ose, lac ose, lac ulose, D- mannose, D- ibose, a inose, suc ose, ehalose, D-xylose, N-ace yl-D-glucosamine, glucu ona e, glu ama e, melezi ose and salicin, bu does no u ilize D-a abinose, ace a e, o ma e, py u a e, mala e, manni ol, D- o L-alanine, D-glycine, L- leucine, L-o ni hine, gluconic acid, aspa a e, dulci ol, bu y a e, cap oa e, ale a e, lac a e, oxa- la e, p opiona e, uma a e, adoni ol, me hanol, e hanol, succina e, D-so bi ol o myoinosi ol, when g own using VL55 mine al medium wi h 100 mg yeas ex ac l-1. G. mallensis hyd olyzes aesculin, s a ch, pec in, lamina in and lichenan, bu no gela in, cellulose, xylan, sodium algina e, pullulan, chi osan o chi in on R2 medium. S ains show posi i e eac ion o acid and alkaline phos- pha ases, leucine a ylamidase, a-chymo ypsin, naph hol-AS-BI-phosphohyd olase, α- and β- galac osidases, α- and β-glucosidases, N-ace yl- β- glucosaminidase, β-glucu onidase, ypsin and aline a ylamidase, bu nega i e o α- ucosidase, α-mannosidase, es e ase (C4 and C8), lipase (C14) and cys ine a ylamidase. S ain MP5ACTX8T e- duces ni a e o ni i e. S ain MP5ACTX8T is e- sis an o he an ibio ics e y h omycin, chlo am- phenicol, neomycin, i ampicin, s ep omycin, gen- amicin, polymyxin B and penicillin, bu suscep i- ble o ampicillin, kanamycin, e acycline, lincomycin, no obiocin and baci acin [1]. Chemo axonomy The majo cellula a y acids in G. mallensis a e iso-C15:0 (45.3%), C16:1ω7c (28.7%), iso-C13:0 (8.3%) and C16:0 (8.9%). The cellula a y acid composi- ions o s ain MP5ACTX8T we e ela i ely simila o ha o o he G anulicella s ains wi h a y ac- ids iso-C15:0 and C16:1ω7c being mos abundan in all s ains. S ain MP5ACTX8T con ains MK-8 as he majo quinone. Genome sequencing and anno a ion Genome p ojec his o y G. mallensis s ain MP5ACTX8T was selec ed o sequencing in 2009 by he DOE Join Genome In- s i u e (JGI) communi y sequencing p og am. The Quali y D a (QD) assembly and anno a ion we e comple ed on Decembe 26, 2010. The comple e genome was made a ailable on Dec. 1, 2011. The genome p ojec is deposi ed in he Genomes On- Line Da abase (GOLD) [42] and he comple e ge- nome sequence o s ain MP5ACTX8T is deposi ed in GenBank (CP003130). Table 2 p esen s he p o- jec in o ma ion and i s associa ion wi h MIGS e sion 2.0 [32]. Figu e 2. Elec on mic og aph o G. mallensis MP5ACTX8T. G ow h condi ions and genomic DNA ex ac ion G. mallensis MP5ACTX8T was cul i a ed on R2 me- dium as p e iously desc ibed [1]. Genomic DNA (gDNA) o high sequencing quali y was isola ed using a modi ied CTAB me hod and e alua ed ac- co ding o he Quali y Con ol (QC) guidelines p o ided by he DOE Join Genome Ins i u e [43]. Rawa e al. h p://s anda dsingenomics.o g 75 Table 2. P ojec in o ma ion. MIGS ID P ope y Te m MIGS 31 Finishing quali y Finished MIGS-28 Lib a ies used Th ee lib a ies, an Illumina GAii sho gun lib a y (GSGY), a 454 Ti anium s anda d lib a y (GSXT, GWTA) and a pai ed end 454 (GSFP) lib a y MIGS 29 Sequencing pla o ms 454 Ti anium s anda d, 454 Pai ed End, Illumina MIGS 31.2 Fold co e age 18.5× (454), 213× (Illumina) MIGS 30 Assemble s Newble , VELVET, PHRAP MIGS 32 Gene calling me hod P odigaL, GenePRIMP Locus Tag AciX8 Genbank ID CP003130.1 GenBank Da e o Release Decembe 1, 2011 GOLD ID Gc02349 BIOPROJECT PRJNA49957, PRJNA47903 P ojec ele ance En i onmen al, Biogeochemical cycling o Ca bon, Bio echnological, GEBA Genome sequencing and assembly The inished genome o G. mallensis MP5ACTX8T (JGI ID 4088692) was gene a ed a he DOE Join genome Ins i u e (JGI) using a combina ion o Illumina [44] and 454 echnologies [45]. Fo his genome, an Illumina GAii sho gun lib a y which gene a ed 59,701,420 eads o aling 4537.3 Mb, a 454 Ti anium s anda d lib a y which gene a ed 136,708 eads and a pai ed end 454 lib a y wi h an a e age inse size o 10.3 kb which gene a ed 157,336 eads o aling 172.0 Mb o 454 da a, we e cons uc ed and sequenced. All gene al aspec s o lib a y cons uc ion and sequencing pe o med a he JGI can be ound a he JGI websi e [43]. The 454 Ti anium s anda d da a and he 454 pai ed end da a we e assembled wi h Newble , e sion 2.3. Illumina sequencing da a was assembled wi h Vel e , e sion 0.7.63 [46]. The 454 Newble con- sensus sh eds, he Illumina Vel e consensus sh eds and he ead pai s in he 454 pai ed end lib a y we e in eg a ed using pa allel ph ap, e - sion SPS - 4.24 (High Pe o mance So wa e, LLC) [47]. The so wa e Consed [48] was used in he inishing p ocess. The Ph ed/Ph ap/Consed so - wa e package [49] was used o sequence assem- bly and quali y assessmen in he subsequen in- ishing p ocess. Illumina da a was used o co ec po en ial base e o s and inc ease consensus quali y using he so wa e Polishe de eloped a JGI (Alla Lapidus, unpublished). Possible misassemblies we e co ec ed using gapResolu ion (Cli Han, un-published), Dup inishe [50] o sequencing cloned b idging PCR agmen s wi h sub-cloning. Gaps be ween con igs we e closed by edi ing in Consed, by PCR and by Bubble PCR (J-F Cheng, unpublished) p i- me walks. The inal assembly is based on 74.2 Mb o 454 da a which p o ides an a e age 18.5× co - e age and 1318.5 Mb o Illumina da a which p o- ides an a e age 213× co e age o he genome. G anulicella mallensis ype s ain MP5ACTX8T 76 S anda ds in Genomic Sciences Genome anno a ion Genes we e iden i ied using P odigal [51] as pa o he Oak Ridge Na ional Labo a o y genome an- no a ion pipeline, ollowed by a ound o manual cu a ion using he JGI GenePRIMP pipeline [52]. The p edic ed CDSs we e ansla ed and used o sea ch he Na ional Cen e o Bio echnology In- o ma ion (NCBI) non- edundan da abase, UniP o , TIGRFam, P am, PRIAM, KEGG, COGs [53,54], and In e P o. These da a sou ces we e combined o asse a p oduc desc ip ion o each p edic ed p o ein. Non-coding genes and miscel- laneous ea u es we e p edic ed using RNAscan- SE [55], RNAMMe [56], R am [57], TMHMM [58], and signalP [59]. Addi ional gene p edic ion analysis and unc ional anno a ion we e pe - o med wi hin he In eg a ed Mic obial Genomes Expe Re iew (IMG-ER) pla o m [60]. Genome p ope ies The genome consis s o one ci cula ch omosome o 6,211,694 bp in size wi h a GC con en o 57.8 mol% and consis s o 53 RNA genes (Figu e 3 and Table 3). O he 4,960 p edic ed genes, 4,907 a e p o ein-coding genes (CDSs) and 90 a e pseudogenes. O he o al CDSs, 70.5% ep esen COG unc ional ca ego ies and 16% consis o sig- nal pep ides. The dis ibu ion o genes in o COG unc ional ca ego ies is p esen ed in Figu e 3 and Table 4. Table 3. Genome s a is ics A ibu e Value % o To al Genome size (bp) 6,237,577 100 DNA coding egion(bp) 5,499,388 88.2 DNA G+C con en (bp) 3612173 57.9 DNA sca olds 1 100 To al genes 4,960 100 P o ein coding genes 4,907 98.9 RNA genes 53 1.3 Pseudo genes 90 1.8 Genes in in e nal clus e s 2,679 54 Genes wi h unc ion p edic ion 3,511 70.8 Genes assigned o COGs 3,496 70.5 Genes wi h P am domains 3,754 75.7 Genes wi h signal pep ides 797 16.1 Genes wi h ansmemb ane helices 1,291 26.0 CRISPR epea s 0 - The o al is based on ei he he size o he genome in base pai s o he p o ein coding genes in he anno a ed genome. Rawa e al. h p://s anda dsingenomics.o g 77 Figu e 3. Ci cula ep esen a ion o he ch omosome o G. mallensis MP5ACTX8T displaying ele an genome ea- u es. F om ou side o cen e ; Genes on o wa d s and (colo by COG ca ego ies), genes on e e se s and (colo by COG ca ego ies), RNA genes ( RNAs g een, RNAs ed, o he RNAs black), GC con en and GC skew. G anulicella mallensis ype s ain MP5ACTX8T 78 S anda ds in Genomic Sciences Table 4. Numbe o genes associa ed wi h gene al COG unc ional ca ego ies Code Value %age Desc ip ion J 167 4.32 T ansla ion, ibosomal s uc u e and biogenesis A 2 0.05 RNA p ocessing and modi ica ion K 332 8.58 T ansc ip ion L 156 4.03 Replica ion, ecombina ion and epai B 1 0.03 Ch oma in s uc u e and dynamics D 27 0.7 Cell cycle con ol, Cell di ision, ch omosome pa i ioning Y 0.0 0.0 Nuclea s uc u e V 76 1.96 De ense mechanisms T 139 3.59 Signal ansduc ion mechanisms M 322 8.32 Cell wall/memb ane biogenesis N 17 0.44 Cell mo ili y Z 0.0 0.0 Cy oskele on W 0.0 0.0 Ex acellula s uc u es U 79 2.04 In acellula a icking and sec e ion O 123 3.18 Pos ansla ional modi ica ion, p o ein u no e , chape ones C 193 4.99 Ene gy p oduc ion and con e sion G 355 9.18 Ca bohyd a e anspo and me abolism E 258 6.67 Amino acid anspo and me abolism F 76 1.96 Nucleo ide anspo and me abolism H 155 4.01 Coenzyme anspo and me abolism I 164 4.24 Lipid anspo and me abolism P 157 4.06 Ino ganic ion anspo and me abolism Q 125 3.23 Seconda y me aboli es biosyn hesis, anspo and ca abolism R 527 13.62 Gene al unc ion p edic ion only S 418 10.8 Func ion unknown - 1,464 29.52 No in COGs The o al is based on he o al numbe o p o ein coding genes in he genome. Rawa e al. h p://s anda dsingenomics.o g 79 Discussion G anulicella mallensis ype s ain MP5ACTX8T has he la ges genome size o 6.2 Mbp. among he h ee und a soil s ains o subdi ision 1 Acidobac e ia [28]. Genome analysis o G anulicella mallensis iden i ied a high abundance o genes assigned o COG unc ional ca ego ies o anspo and me abolism o ca bohyd a es (9.1%) and amino acids (6.7%) and in ol ed in cell en elope biogenesis (8.3%) and ansc ip ion (8.6%). Fu he genome analysis e ealed an abundance o gene modules encoding o unc- ional ac i i ies wi hin he ca bohyd a e-ac i e enzymes (CAZy) amily [61] in ol ed in b eak- down, u iliza ion and biosyn hesis o ca bohy- d a es. G. mallensis hyd olyzed complex ca bon polyme s, including CMC, pec in, lichenin, lamina in and s a ch, and u ilized suga s such as cellobiose, D-mannose, D-xylose, D- ehalose. This pa allels genome p edic ions o CDSs encoding o enzymes such as cellulases, pec inases, algi- na e lyases, ehalase and amylases. In addi ion, he G. mallensis genome con ained a clus e o genes in he neighbo hood o he cellulose syn- hase gene (bcsAB) which included cellulase (bscZ) (endoglucanase Y) o amily GH8, cellulose syn hase ope on p o ein (bcsC) and a cellulose syn hase ope on p o ein (yhjQ) in ol ed in cellu- lose biosyn hesis. De ailed compa a i e genome analysis o G. mallensis MP5ACTX8T wi h o he Acidobac e ia s ains o which inished genomes we e a ailable is epo ed in Rawa e al. [28]. The da a hus sugges s ha G. mallensis is in ol ed in hyd olysis, he u iliza ion o s o ed ca bohyd a es, and in he biosyn hesis o exopolysaccha ides om o ganic ma e and plan based polyme s in he soil. The e o e, we in e ha s ain G. mallensis may be cen al o ca bon cycling p ocesses in a c- ic and bo eal soil ecosys ems. Acknowledgemen s The wo k conduc ed by he US Depa men o Ene gy Join Genome Ins i u e is suppo ed by he O ice o Science o he US Depa men o Ene gy Unde Con ac No. DE-AC02-05CH11231. This wo k was unded in pa by he Academy o Finland and he New Je sey Ag icul u al Expe imen S a ion. Re e ences 1. Männis ö MK, Rawa S, S a o oy o V, Häggblom MM. G anulicella a c ica sp. no ., G anulicella mallensis sp. no ., G anulicella sapmiensis sp. no . and G anulicella und icola sp. no ., no el Acidobac e ia om und a soil o No he n Fin- land. In J Sys E ol Mic obiol 2012; 62:2097- 2106. PubMed h p://dx.doi.o g/10.1099/ijs.0.031864-0 2. Pank a o TA, Dedysh SN. G anulicella paludicola gen. no ., sp. no ., G anulicella pec ini o ans sp. no ., G anulicella agg egans sp. no . and G anulicella osea sp. no ., acidophilic, polyme deg ading acidobac e ia om Sphagnum pea bogs. In J Sys E ol Mic obiol 2010; 60:2951-2959. PubMed h p://dx.doi.o g/10.1099/ijs.0.021824-0 3. Janssen PH. Iden i ying he dominan soil bac e i- al axa in lib a ies o 16S RNA and 16S RNA genes. Appl En i on Mic obiol 2006; 72:1719- 1728. PubMed h p://dx.doi.o g/10.1128/AEM.72.3.1719- 1728.2006 4. Fie e N, B ad o d MA, Jackson RB. Towa d an ecological classi ica ion o soil bac e ia. Ecology 2007; 88:1354-1364. PubMed h p://dx.doi.o g/10.1890/05-1839 5. Campbell BJ, Polson SW, Hanson TE, Mack MC, Schuu EA. The e ec o nu ien deposi ion on bac e ial communi ies in A c ic und a soil. En i- on Mic obiol 2010; 12:1842-1854. PubMed h p://dx.doi.o g/10.1111/j.1462- 2920.2010.02189.x 6. Chu H, Fie e N, Laube CL, Capo aso JG, Knigh R, G ogan P. Soil bac e ial di e si y in he A c ic is no undamen ally di e en om ha ound in o he biomes. En i on Mic obiol 2010; 12:2998- 3006. PubMed h p://dx.doi.o g/10.1111/j.1462- 2920.2010.02277.x 7. Jones RT, Robeson MS, Laube CL, Hamady M, Knigh R, Fie e N. A comp ehensi e su ey o soil acidobac e ial di e si y using py osequencing and clone lib a y analyses. ISME J 2009; 3:442- 453. PubMed h p://dx.doi.o g/10.1038/ismej.2008.127 8. Ba ns SM, Cain EC, Somme ille L, Kuske CR. Acidobac e ia phylum sequences in u anium- con amina ed subsu ace sedimen s g ea ly ex- pand he known di e si y wi hin he phylum.