The Ecology of Acidobacteria

16 Pages·2016·2.88 MB·English

by  Eiko E. Kuramae

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REVIEW
published:31May2016
doi:10.3389/fmicb.2016.00744
The Ecology of Acidobacteria:
Moving beyond Genes and Genomes
AnnaM.Kielak1†,CristineC.Barreto2†,GeorgeA.Kowalchuk3,JohannesA.vanVeen1
andEikoE.Kuramae1*
1DepartmentofMicrobialEcology,TheNetherlandsInstituteofEcology–KoninklijkeNederlandseAkademievan
Wetenschappen,Wageningen,Netherlands,2GraduatePrograminGenomicSciencesandBiotechnology,Universidade
CatólicadeBrasília,Brasília,Brazil,3EcologyandBiodiversityGroup,UniversityofUtrecht,Utrecht,Netherlands
The phylum Acidobacteria is one of the most widespread and abundant on the planet,
yet remarkably our knowledge of the role of these diverse organisms in the functioning
of terrestrial ecosystems remains surprisingly rudimentary. This blatant knowledge gap
stems to a large degree from the difficulties associated with the cultivation of these
bacteria by classical means. Given the phylogenetic breadth of the Acidobacteria,
which is similar to the metabolically diverse Proteobacteria, it is clear that detailed
and functional descriptions of acidobacterial assemblages are necessary. Fortunately,
recent advances are providing a glimpse into the ecology of members of the phylum
Acidobacteria. These include novel cultivation and enrichment strategies, genomic
characterizationandanalysesofmetagenomicDNAfromenvironmentalsamples.Here,
Editedby:
RichBoden, we couple the data from these complementary approaches for a better understanding
UniversityofPlymouth,UK
oftheirroleintheenvironment,therebyprovidingsomeinitialinsightsintotheecologyof
Reviewedby:
this important phylum. All cultured acidobacterial type species are heterotrophic, and
StephanieA.Eichorst,
UniversityofVienna,Austria members of subdivisions 1, 3, and 4 appear to be more versatile in carbohydrate
HinsbyCadillo-Quiroz, utilization. Genomic and metagenomic data predict a number of ecologically relevant
ArizonaStateUniversity,USA
capabilities for some acidobacteria, including the ability to: use of nitrite as N source,
*Correspondence:
respond to soil macro-, micro nutrients and soil acidity, express multiple active
EikoE.Kuramae
[email protected] transporters, degrade gellan gum and produce exopolysaccharide (EPS). Although
†Theseauthorshavecontributed thesepredictedpropertiesalludetoacompetitivelifestyleinsoil,onlyveryfewofthese
equallytothiswork.
prediction shave been confirmed via physiological studies. The increased availability of
genomicandphysiologicalinformation,coupledtodistributiondatainfieldsurveysand
Specialtysection:
Thisarticlewassubmittedto experiments, should direct future progress in unraveling the ecology of this important
TerrestrialMicrobiology,
butstillenigmaticphylum.
asectionofthejournal
FrontiersinMicrobiology
Keywords:Acidobacteria,carbohydratemetabolism,transporters,nitrogenmetabolism,EPS,soilfactors
Received:08October2015
Accepted:03May2016
Published:31May2016 INTRODUCTION
Citation:
KielakAM,BarretoCC, AlthoughtheAcidobacteriawereonlyrecognizedasaphylumrelativelyrecently,theirabundance
KowalchukGA,vanVeenJA acrossarangeofecosystems,especiallysoils,hasdemandedresearchintotheirecology.16SrRNA
andKuramaeEE(2016)TheEcology
gene-based approaches as well as environmental shotgun metagenomic analyses have revealed
ofAcidobacteria:Movingbeyond
that the Acidobacteria represent a highly diverse phylum resident to a wide range of habitats
GenesandGenomes.
aroundtheglobe(Chowetal.,2002;Kuskeetal.,2002;Gremionetal.,2003;Quaiseretal.,2003;
Front.Microbiol.7:744.
doi:10.3389/fmicb.2016.00744 Fiereretal.,2005;Staffordetal.,2005;Janssen,2006;Sanguinetal.,2006;deCarceretal.,2007;
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Kielaketal. EcologyofAcidobacteria
Kimetal.,2007;Singhetal.,2007;DeAngelisetal.,2009;Jesus Acidobacteria phylum. Based on phylogenetic analysis of 16S
etal.,2009;Kielaketal.,2009;Navarreteetal.,2010,2013b;Zhang rRNA gene sequences, the Acidobacteria phylum raised from
etal.,2014).However,despitetheirhighabundanceanddiversity, the originally described four to six subdivisions (Kuske et al.,
we still have relatively little information regarding the actual 1997;Ludwigetal.,1997;Barnsetal.,1999,2007)toovereight
activitiesandecologyofmembersofthisphylum,ashortcoming subdivisions in 1998 (Hugenholtz et al., 1998) and in 2005
that can be attributed to a large extent to the difficulties in this number increased to 11 (Zimmermann et al., 2005) deeply
cultivatingthemajorityofacidobacteriaandtheirpoorcoverage branchingandstronglysupportedsubdivisions.Currentlythere
inbacterialculturecollections(Bryantetal.,2007;Leeetal.,2008; are26acceptedsubdivisions(Barnsetal.,2007)intheRibosomal
daRochaetal.,2009;Eichorstetal.,2011;Navarreteetal.,2013b). Database Project. The first recognized strain and species of the
However,environmentalsurveyshaveprovidedinsightintosome phylumAcidobacteriawasAcidobacteriumcapsulatumobtained
theenvironmentalfactorsthatmaydriveacidobacteriadynamics, from an acid mine drainage in Japan (Kishimoto and Tano,
such as pH and nutrients (Fierer et al., 2007; Jones et al., 2009; 1987; Kishimoto et al., 1991; Abed et al., 2002). Although the
Lauberetal.,2009;Navarreteetal.,2013b). second isolate belonging to this phylum was Holophaga foetida
In2009,thefirstsequencedgenomesofacidobacteriastrains first described in 1994, it was not initially recognized as related
became available, providing preliminary genetic insights into to Acidobacteria capsulatum. Instead, it was thought to belong
the potential physiology and environment functions of several to the phylum Proteobacteria (Liesack et al., 1994). A few years
members of this phylum (Ward et al., 2009). In these first later, a closely related bacterium named Geothrix fermentans
genomicstudies,fiveaspectsofphysiologicalreceivedparticular was isolated (Coates et al., 1999) and subsequently another
attention: (i) carbon usage, (ii) nitrogen assimilation, (iii) closely related bacterium Acanthopleuribacter pedis, the first
metabolism of iron, (iv) antimicrobials, and (v) abundance acidobacteria obtained from a marine sample, was described
of transporters. Besides genome sequencing of cultivated (Fukunaga et al., 2008). Since these isolates were very distantly
isolates, addition information regarding genomic properties of related to A. capsulatum, it was proposed that it should be
acidobacteriahasbeenderivedfrommetagenomicsstudies(Liles included in a new class named Holophagae. Acidobacteriia
etal.,2003;Quaiseretal.,2003,2008;Riazetal.,2008;Jonesetal., and Holophagae are the only classes currently included in the
2009; Kielak et al., 2010; Parsley et al., 2011; Faoro et al., 2012; mostrecenteditionoftheBergey’sManual(ThrashandCoates,
Navarreteetal.,2013b;Mendesetal.,2014). 2014).
In this review, we couple the complementary data coming Currently Acidobacteria phylum has 26 subdivisions based
from physiological, genomic and metagenomics studies to seek on the extremely broad diversity of acidobacterial populations
a better understanding of the role of Acidobacteria in the foundinuranium-contaminatedsoils(Barnsetal.,2007).Newly
environment, thereby providing some initial insights into the characterized acidobacteria from subdivision 1 may challenge
ecologyofthisimportantphylum.Weaimtonotonlygiveamore thistaxonomyinthenearfuture,sinceof16SrRNAgeneanalysis
completepictureofthecurrentknowledgeofAcidobacteria,but has consistently shown that the genera Acidobacteria,‘Acidipila’
also seek to provide a solid base for future experiments geared (Okamura et al., 2011), Telmatobacter (Pankratov et al., 2012),
toward gaining a better understanding of the ecological roles andAcidicapsa(Kulichevskayaetal.,2012)formagroupthatis
playedbymembersofthisphylum. distinctfromthegeneraGranulicella,Terriglobus,Bryocella,and
Edaphobacter(Eichorstetal.,2007;Kochetal.,2008;Pankratov
and Dedysh, 2010; Männistö et al., 2011, 2012; Rawat et al.,
HISTORY AND GENERAL INFORMATION
2012a,b;Baiketal.,2013;Whangetal.,2014).
ON THE PHYLUM Acidobacteria The vast majority of isolates cultivated to date are affiliated
withacidobacteriasubdivision1(ClassAcidobacteriia).Theyare
Theintroductionofmolecularbiologicalstrategiesintomicrobial all heterotrophic, most species are aerobic or microaerophilic
ecology over the past decades has yielded a new perspective on and some species (Telmatobacter bradus, Acidobacterium
the breadth and vastness of microbial diversity. The phylum capsulatum) are facultative anaerobic bacteria (Pankratov
of the Acidobacteria is one of the bacterial lineages that has et al., 2012). Members of subdivisions 3, 4, 8 (currently
profited most from the cultivation-independent interrogation Class Holophagae), 10, and 23 are heterotrophic as well.
of environmental samples. Indeed, in the past two decades, Thermotomaculum(subdivision10)andThermoanaerobaculum
this phylum has grown from being virtually unknown to being (subdivision23)arethermophilicanaerobicbacteria(Izumietal.,
recognized as one of the most abundant and diverse on Earth. 2012; Losey et al., 2013). Chloracidobacterium thermophilum
This phylum is particularly abundant in soil habitats that can is photoheterotrophic (Bryant et al., 2007; Tank and Bryant,
representupto52%fromthetotalbacterialcommunity(Dunbar 2015) and Pyrinomonas methylaliphatogenes can consume H
2
et al., 2002; Sait et al., 2002) and averaging approximately 20% (Greening et al., 2015), both from subdivision 4. Subdivision
of the microbial community across diverse soil environments 8 contains one aerobic (Acanthopleuribacter) and two strictly
(Janssen,2006). anaerobic isolates (Holophaga and Geothrix). There are reports
Although 16S rRNA gene sequences related to the of acidobacteria isolates belonging to subdivisions 2 and 6,
Acidobacteria were obtained as early as 1993 (Stackebrandt but they still do not have valid taxonomic names (Sait et al.,
et al., 1993) it was only in 1997 that they were associated 2002; George et al., 2011; Parsley et al., 2011). Subdivisions 1
with sequences belonging to cultured members of the current and 3 of the phylum Acidobacteria together with thermophilic
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Thermoanaerobacterspeciesarecapableofbiosynthesizingtotal acidophilicstrainsbelongingtosubdivision1(Saitetal.,2006).
fattyacidslipid(Damsteetal.,2011).Currently,thereatotalof This combination of strategies seems to enrich not only for
40speciesbelongingto22genera:elevengeneraofsubdivision1, Acidobacteria but for many other groups of slow-growing
twoofsubdivision3;fourofsubdivision4,threeofsubdivision bacteria. The association of a molecular technique such as
8, one of subdivision 10, and one of subdivision 23 (Figure 1). the high-throughput plate-wash PCR (Stevenson et al., 2004)
In addition, there are the genome sequences of Koribacter and or colony-PCR (de Castro et al., 2013), both using phylum-
Solibacter,butthereislittleinformationontheirphysiology. specific 16S rRNA gene primers has improved the screening
and identification of colonies belonging to the Acidobacteria
subgroup 1. Once Acidobacteria isolation under low nutrient
THE IMPACT OF NEW ISOLATION conditionsisachieved,strainscanoftenbetransferredtoricher
METHODS media (e.g., TSA and R2A) for more convenient propagation
(de Castro et al., 2013). Despite the importance of these recent
Changes in the traditional methods for culturing bacteria from advances in cultivation methods, further improvements are
soils have significantly improved the isolation of Acidobacteria clearly needed since only eight of a total of 26 subdivisions are
strains in recent years. These new strategies involve the use known to have representatives in culture. A large number of
of relatively low concentration of nutrients, non-traditional Acidobacteria isolates have been recovered from the Australian
sources of carbon or complex polysaccharides (Janssen et al., soilEllinbank(Janssenetal.,2002;Saitetal.,2002;Davisetal.,
2002; Sait et al., 2002; Pankratov et al., 2008; Eichorst et al., 2005). These studies were important during the development
2011), longer periods of incubation, the use of gellan gum as of new strategies for culturing soil bacteria, and two of
solidifying agent, (Janssen et al., 2002; Sait et al., 2002), non- these isolates, ‘Koribacter versatilis’ Ellin345 (CP000360) and
standardCO atmosphericconditionsofincubation,additionof ‘Solibacter usitatus’ Ellin6076 (CP000473), were used in the
2
quorum-signalingmolecules,catalaseorcations(Stevensonetal., first Acidobacteria genome investigations (Ward et al., 2009).
2004; George et al., 2011; Navarrete et al., 2013a), amendments However, many of these bacteria have not yet been fully
of inhibitors for undesired organisms, and amendment of characterized and still do not possess valid taxonomical names.
environmentalextractsingrowthmedia(Foeseletal.,2013). Further, micro-cultivation strategies combined with single-cell
It is suggested that raising the CO concentration may not sequencingshouldprovideaccesstonewacidobacterialgenomes,
2
only better mimic the CO concentrations typically found in and in turn this genomic information may help to inform
2
soils, but may also decrease medium pH, thereby benefiting future isolation efforts as cultivation is still required for most
certain members of the acidobacteria, especially moderate physiologicalcharacterizations.
FIGURE1|DendrogramshowingthegeneralcharacteristicsofAcidobacteriatypespecies,only.Thedendrogramwasobtainedusingnearly-full16S
rRNAgenesequencesobtainedandalignedusingtheRibosomalDatabaseProject.DendrogramwereobtainedwithMEGA7(Tamuraetal.,2011)usingthe
Neighbor-joiningmethod(SaitouandNei,1987);bootstrappingvalueswerebasedon1000repetitionsandareshownnexttothebranches(Felsenstein,1985).
Therewereatotalof1343positionsinthefinaldataset.1.Acidobacteriumcapsulatumwasoriginallydescribedasanaerobicbacteria,butlateritwasdemonstrated
aweakanaerobicgrowthbyfermentation(Pankratovetal.,2012).2.H.foetidaishomoacetogenandG.fermentansisfermentative.ND,notdetermined.Quote
marks(‘)indicatethatthisspeciesisdepositedinaculturecollection,butitsnamedoesnotretainitsvalidityandstandinginnomenclature.
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THE IMPACT OF ACIDOBACTERIA abletousechitinasacarbonsource(Foeseletal.,2013;Huber
GENOMES AND LINKS TO et al., 2014) (Figure 2). Most of the Acidobacteria subdivisions
1, 3, or 4 examined to date is unable to use carboxymethyl
PHYSIOLOGICAL STUDIES
cellulose, but there is evidence that Aridibacter kavangonensis
(subdivision 4) is able to utilize micro-crystalline cellulose
ThefirstcomparativegenomeanalysisbetweenofA.capsulatum
(Huber et al., 2014). Although it is still premature to draw
andtwobacteriaoriginatedfromtheEllincollection,‘S.usitatus’
generalconclusionsrelatedtothedegradationoftheseabundant
Ellin6076(subdivision1),and‘K.versatilis’Ellin345(subdivision
polysaccharides by Acidobacteria in nature, xylan degradation
3)providednumerousinsightsintothephysiologyofmembers
has been broadly demonstrated, which may play a role in plant
of the Acidobacteria (Ward et al., 2009; Challacombe et al.,
cellwalldegradation(Pankratovetal.,2008;Eichorstetal.,2011).
2011). Since then, the number of acidobacterial genomes being
Thediscrepanciesbetweengenomepredictionsandobserved
sequenced remains rather limited. Currently, there are 10
activities may stem from our ability to provide cultivation
published genomes of Acidobacteria available: five subdivision
conditions that lead to the expression of the target activities.
1 (Ward et al., 2009; Rawat et al., 2012a,b, 2013, 2014), one
Alternatively, current automatic genome annotation pipelines
subdivision3(Wardetal.,2009),twosubdivision4(Costasetal.,
may not successfully differentiate genes involved for instance
2012;Leeetal.,2015),andonesubdivision8–classHolophagae
in chitin and cellulose degradation from genes involved
(Anderson et al., 2012); 1 subdivision 23 (Stamps et al., 2014).
in the degradation of other glycosyl hydrolases, such as
Below, we summarize some of the major findings revealed via
xylan. Systematic studies on the degradation of cellulose by
thecurrentlyavailableacidobacterialgenomesequenceslinkedto
Acidobacteriagrownondifferentcultureconditionsmayhelpto
physiologicalstudies.
test the hypothesis of gene regulation by sugars present in the
media,forexample.Ontheotherhand,ithasbeenreportedthat
CARBOHYDRATE METABOLISM in bacteria many genes involved in cellulose degradation may
be involved in the infection of plant cells or in the synthesis of
Among all the physiological aspects revealed by genomics, bacterialcellulose(Koecketal.,2014).
carbohydrate metabolism has been studied most widely, which Enzymatic activities observed in Acidobacteria have usually
is not surprising considering that carbon usage is one of the been detected using commercial kits with chromogenic
physiological requirements for the description of new species substrates. Members of subdivision 1 possess a broader range
in taxonomic studies. At least one species of each of the eight of enzymes related to sugar usage than those from other
recognized genera of subdivision 1 is able to use D-glucose, D- subdivisions(Figure3;SupplementaryTableS1).Galactosidases
xylose, and lactose as carbon sources (Figure 2). The ability to are enzymes involved in the hydrolysis of galactose-containing
useglucoseandxylosemakessensegiventhefactthatcellulose sugars,whilebetagalactosidadesareinvolvedinthedegradation
orxylanareoftenthemajorcarbonsourcesintheculturemedia of lactose. Since all genera of Acidobacteria subdivision 1 are
mosttypicallyusedfortheisolationofAcidobacteria.Inaddition, able to use lactose, it is not surprising to find this enzyme
thesebacteriawereabletousemostofthetestedoligosaccharides, included in their enzymatic profile. Glucosidases are involved
althoughmaltoseandcellobiosewerenotabletosupportgrowth in the degradation of polysaccharides, especially cellulose
ofEdaphobacterspecies.Interestingly,themajorityofsubdivision and starch. Although starch is used by most Acidobacteria
1specieswereunabletousefucoseorsorbose,carbohydratesthat (Figure2),cellulosedegradationhasnotyetbeenunequivocally
areonlyminorcomponentsofplantcellwallsandratherscarce demonstratedformostAcidobacteria,asexplainedabove.
insoil(Lietal.,2013). Interestingly,β-glucosidasehassuccessfullybeenpurifiedand
Although several acidobacterial genomes have been shown characterized from A. capsulatum (Abed et al., 2002). This
to contain genes encoding for the degradation of different enzymewasinducedbythepresenceofcellobioseinthemedium,
polysaccharides (Figure 2), experimental data on the use of anditwasactiveonp-nitrophenyl-p-D-glucopyranoside(100%),
polysaccharides generally do not support genomic predictions. cellobiose(39%),andβ-gentiobiose(33%).Inasubsequentstudy,
At least 50% of the genera have members able to use starch, the gene xynA for a endo-β-1,4-xylanase from A. capsulatum
lamminarin, and xylan. In contrast, chitin usage has not yet (Kochetal.,2008)wasclonedandexpressedinEscherichiacoli
beendemonstratedforanymemberofAcidobacteriasubdivision (Dedyshetal.,2012).Thisenzymewasdemonstratedtobeactive
1. Similarly, cellulose was another substrate predicted to be on xylan and cellobiose (100% of relative activity), but has low
degraded by Acidobacteria genome annotation. However, only activityonCM-cellulose(5.4%)andnoactivityonfilterpaperof
Telmatobacter bradus (subdivision 1) has been demonstrated Avicel.
to be able to use crystalline cellulose (Pankratov et al., 2012) Janssen et al. (2002) were the pioneers to use gellan gum
and Edaphobacter cerasi (Yamada et al., 2014) is able to as solidifying agent in culture medium used for Acidobacteria
grow on CM-cellulose. Terracidiphilus gabretensis produces isolation. In contrast to agar, which is obtained from seaweed,
extracellular enzymes implicated in the degradation of plant- gellangumisasubstratethatisproduced(anddegraded)bysoil
derived biopolymers what was confirmed by genome analysis bacteria.AtleasttwospeciesofAcidobacteriahavedemonstrated
by the presence of enzymatic machinery required for organic ability to use gellan gum: Telmatobacter bradus and Bryocella
matterdecomposition(Garcia-Fraileetal.,2016).Incontrastto elongata. One known pathway for the degradation of gellan-
Acidobacteriafromsubdivision1,membersofsubdivision4are gum involves the action of gellan lyases, α-L-rhamnosidases,
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FIGURE2|UsageofcarbonsourcesbyAcidobacteriainculture-basedexperimentswithtypestrainspecies.Apositivescorewasrecordedifatleastone
specieswithinagenusisabletousearespectivesugar.(A)Acidobacteriasubdivision1.(B)Acidobacteriasubdivisions3and4.Usageofcarbonsourceobtained
fromoriginalreferencesthatdescribedeachofthetypespecies,inorderofpublication:Kishimotoetal.,1991;Liesacketal.,1994;Coatesetal.,1999;Eichorst
etal.,2007;Fukunagaetal.,2008;Kochetal.,2008;Kulichevskayaetal.,2010,2012,2014;PankratovandDedysh,2010;Männistöetal.,2011,2012;Okamura
etal.,2011;Dedyshetal.,2012;Izumietal.,2012;Pankratovetal.,2012;Baiketal.,2013;Foeseletal.,2013,2016;Loseyetal.,2013;Croweetal.,2014;Huber
etal.,2014;Whangetal.,2014;Yamadaetal.,2014;Pascualetal.,2015;TankandBryant,2015;Garcia-Fraileetal.,2016;Jiangetal.,2016;Lladoetal.,2016).
unsaturated glucuronyl hydrolases, and β-D-glucosidases (Baik genomes (Ward et al., 2009). Nitrate reduction has been
et al., 2013). Members of Acidobacteria subdivision 1 were investigated in almost all members of subdivision 1, with
reported to be able to use the monosaccharides rhamnose and the exception of Acidobacterium and Acidicapsa. Among all
glucose. Also, at least one β-D-glucosidase was characterized Granulicellaspecies,G.mallensiswasreportedtoperformnitrate
from A. capsulatum, which may be involved in gellan gum reduction (Männistö et al., 2012). A. rosea and B. elongata are
degradation. However, the in silico comparison of 10 available alsoabletoreducenitratetonitrite.Amongothersubdivisions,
genomes, offered no evidence of gellan lyase (EC 4.2.2.25) only Geothrix fermentans subdivision 8 was shown to be able
genes for gellan lyase usage. Moreover, Naumoff and Dedysh to reduce nitrate. This organism is an iron reducer that can
(2012) reported that the presence of α-rhamnosidases is not use nitrate as an alternative electron acceptor. All of these
a phylogenetically determined trait, but that this function was Acidobacteria were able to use yeast extract that, in addition to
obtained by lateral gene transfer from Bacteroidetes and in the ammonium, may be a preferred nitrogen source (Coates et al.,
caseofHolophagafoetidafromafungus.Theinvestigationofthe 1999). The presence of the nirA gene, which encodes nitrate
enzymaticpathwayforgellangumdegradationmaymeritfurther reductase,alsoappearstobelimitedtosubdivision1,suggesting
investigation,sincethisisabacterialpolysaccharide.Therefore, thatmembersofthissubdivisionmayreducenitratetonitriteby
inadditiontothepossiblemetabolismofpolysaccharidesderived theassimilatorypathway,whichisfurtherreducedtoammonia
fromplants,theusageofgellangumsuggestsaninteractionwith and assimilated into glutamate. Nevertheless, the direct uptake
othersoilbacteria(Dedyshetal.,2012). of ammonium seems likely as all genomes described to date
appear to contain genes for the ammonia transporter channel
(Amt) family (TC 1.A.11). Nitric oxide reductase genes (norB
NITROGEN METABOLISM butnotnorC)wereidentifiedin‘Koribacterversatilis,’‘Solibacter
usitatus’ and Geothrix fermentans genomes. Genes encoding
Nitrite reduction was observed in all three genomes reported dinitrogenase, a heterotetramer of the proteins NifD and NifK
in 2009, and nitrate reduction in two of the initially analyzed (genesnifDandnifK,respectively)anddinitrogenasereductase,
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FIGURE3|Enzymesencodinggenesofpolysaccharidedegradation(EC.3.2-)indifferentAcidobacteriasubdivisions(GP)genomes.Thecomparisons
weredoneusingIMG:theintegratedmicrobialgenomesdatabaseandcomparativeanalysissystem.
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FIGURE4|Familiesoftransporters(TC:3.A)indifferentAcidobacteriasubdivisions(GP)genomes.ThecomparisonsweredoneusingIMG:theintegrated
microbialgenomesdatabaseandcomparativeanalysissystem.
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a homodimer of the protein NifH (gene nifH), were found et al., 2012b) to 9.18 % in Granulicella mallensis type strain
only in the genome of H. foetida. Ammonia monooxygenase MP5ACTX8T (Rawat et al., 2013). An overview of transporter
(amo)andnitrous-oxidereductase(nosZ)geneswerenotfound families in 10 acidobacterial genomes is provided in Figure 4.
in any of the available genomes. Contrary to the previous The majority of transporters found in acidobacterial genomes
report (Ward et al., 2009), homologs of nitrate reductases narB belongtotheDrug/Metabolitetransportersuperfamily.Thehigh
and narG were not found in available genome sequences via numberofdifferenttransportsystemsfacilitatestheacquisition
in silico genome comparison, and physiological testing would ofabroadrangeofsubstratecategories,includingaminoacids,
therefore be required to suggest this function in Acidobacteria. peptides, siderophores, cation, or anions. The presence of a
In summary, there is no clear evidence for the involvement of broadsubstraterangeoftransportersfornutrientuptakesuggests
AcidobacteriainkeyN-cycleprocessessuchasnitrogenfixation, an advantage of Acidobacteria in complex environments and
nitrification,ordenitrification. adaptation to oligotrophic conditions, such as nutrient-limited
soilconditions(Figure4).
Although iron metabolism and iron transporters were
EXOPOLYSACCHARIDES discussed in genome sequence exploration studies, these
characteristics have not been unequivocally demonstrated
Exopolysaccharide (EPS) production has frequently been in culture-based studies. The only direct indication is the
reportedinculturedAcidobacteriaspecies(Eichorstetal.,2007; observation of iron accumulation in B. elongata (Dedysh
PankratovandDedysh,2010;Whangetal.,2014).Initialgenomic et al., 2012). Based on genome content, we speculate that
analyses revealed that at least one Acidobacteria encodes genes the representatives of subdivisions 4, 8 and B. aggregatus
involvedintheEPSbiosynthesis,specificallyfortheproduction may also be able to uptake ferric iron, and genes encoding
of bacterial cellulose, genes involved in the cellulose synthesis transport systems involved in translocation across the outer
are encoded on genomes belonging to subdivision 1 (exception and cytoplasmic membranes, i.e., cobalamin/Fe3+-siderophore
‘K. versatilis’ Ellin345). However, it is not known if this is a uptake transporters and Fe3+ hydroxamate transporters, have
general characteristic of the phylum Acidobacteria. It has been beenidentifiedinthesegenomes.Genomicanalysesalsosuggest
suggested that EPS-producing bacteria may be able to survive that Acidobacteria may release siderophores to scavenge iron
for long periods in soil due to the protection provided by their fromsoilmineralsbyformationofFe3+ complexesthatcanbe
EPS. The dominance of Acidobacteria in acidic environments taken up by those transporters or use siderophores from other
and its resistance to pollutants like uranium (Ellis et al., 2003; microorganisms.
Gremionetal.,2003;Barnsetal.,2007),petroleumcompounds
(Abed et al., 2002), linear alkylbenzene sulfonate (Sanchez-
ECOLOGICAL INFERENCES DERIVED
Peinado et al., 2010) and p-nitrophenol (Paul et al., 2006) may
therefore be related to the ability to produce large amounts FROM METAGENOMIC APPROACHES
ofEPS.
ThefunctionsofEPSinsoilarenumerous.Itmaybeinvolved Large genome fragments recovered by metagenomics may
in the formation of the soil matrix, may serve as a water and contain intact metabolic pathways for mining ecologically
nutrition trap, and may be involved in bacterial adhesion that relevant genome fragments from the environment. The first
can facilitate soil aggregate formation (Eichorst et al., 2007, acidobacterial metagenomic insert was described by Liles et al.
2011; Pankratov and Dedysh, 2010). Based upon the presence (2003). From a bacterial artificial chromosome (BAC) library,
of cellulose synthesis genes and a large number of novel high- 12 (out of 24,400) clones were identified as containing
molecular-weightproteinswithexcretionpathwaymotifs,ithas acidobacterial16SrRNAsequences(nineclonesfromsubdivision
been postulated that many Acidobacteria have the potential to 6,twofromsubdivision4,andonefromsubdivision5),andone
form biofilms, resist desiccation and facilitate soil aggregate cloneaffiliatedwithsubdivision5wasselectedforfullsequencing.
formation. However, to date, there are still no physiological Up to date there is no representative isolate available for this
studies demonstrating actual acidobacterial EPS production or subdivision5.Theannotationof20ORFsrevealedgenesinvolved
demonstrationofitsecologicalrole. incellcycling,celldivision,folicacidbiosynthesis,DNArepair,
and an ABC transporter. In addition, a novel 1,4-butanediol
diacrylateesterasegenewasfoundwith40%sequenceidentityto
TRANSPORTERS an esterase from Brevibacterium linens. This enzyme is known
tocatalyzetheconversionofinsolublebutanedioldiacrylatetoa
Acidobacteria have a large proportion of genes encoding for hydrolyzedsolubleformfortheuseasacarbonsource,suggesting
transporters (Challacombe et al., 2011). The comparison of that the bacterium containing this fragment may possess this
three acidobacterial genomes (two Acidobacterium capsulatum capability.
subdivision1andoneEllin6076subdivision3)showedabout6% Anothersixacidobacterialgenomicfragments(fouroutofsix
ofthetotalcodingsequencesaretransporters(Wardetal.,2009). relatedtosubdivision6)wererecoveredfromasandyecosystem
The Carbohydrate transport and metabolism category given by (Quaiseretal.,2003).Interestingly,twooftherecoveredclones
cluster of orthologous groups (COG) classification can range affiliated with subdivision 6 contained regions of homology
from8.6%inTerriglobussaanensistypestrainSP1PR4T(Rawat encodingatyrosyl-tRNAsynthetase,ametal-dependingprotease,
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FIGURE5|TheAcidobacteriasubdivisionsphylogenetictree.Thephylogenetictreeisbasedon220sequencesof26differentsubdivisions(GPs)of
AcidobacteriafromSilvadatabase(http://www.arb-silva.de/)classifiedbyRDPclassifier.ThesequenceswerealignedinClustalX12andtheselectionofconserved
blocksfrommultiplealignmentwascarriedoutbyGblocks(TalaveraandCastresana,2007)forphylogeneticanalysis.Thephylogenetictreewasbasedon
Neighbor-Joiningclusteringalgorithmwith1000bootstrap.Circlesinthebranchesofthetreerepresentbootstrapsupportmorethan75%.OutgroupisCastenholzii
roseiflexus.
as well as eight or nine purine biosynthesis proteins. In a generevealedthatnineoutof20ORFswererelatedtosequences
subsequent examination of fosmid libraries from deep sea derived from members of Acidobacteria. Similarly, genes
sediments (Quaiser et al., 2008), recovered this same syntenic involved in polyketide synthesis pathways were identified from
region in eight out of 11 acidobacterial genome fragments afosmidlibraryinclonedinsertscontaininggenessignificantly
affiliated with subdivision 6. In a metagenomic study of similar to genes from ‘S. usitatus’ (Parsley et al., 2011). Primers
Acidobacteriainaformeragriculturalsoil,anadditionalfourout targeting the mtaD homolog (encoding protein involved in
of 17 fosmids (from a library of 28,800 clones) were recovered myxothiazol biosynthesis) identified in a metagenomic library
with the same genomic region (Kielak et al., 2010). Thus, it werealsousedtoscreenacidobacterialisolates.Infouroutofsix
appearsthatalargepercentageofthesubdivision6Acidobacteria isolates examined (belonging to subdivisions 3, 4, and 6) mtaD
members present in both terrestrial and marine environments, homologous sequences were identified, suggesting widespread
contain this conserved genomic region adjacent to their rRNA distributionofPKSpathwaysamongAcidobacteria(Parsleyetal.,
operons. However, the ecological and evolutionary significance 2011). Genes involved in PKS biosynthesis were also identified
ofthisstrikingpatternremainsunknown. in sequenced acidobacterial genomes (Ward et al., 2009). The
Inastudydesignedtorecovergenesencodingthesynthesisof only report of antibacterial metabolites in relation to genomic
N-acylhomoserinelactones(NAHL),Riazetal.(2008)identified potentialwasdescribedbyCraigetal.(2009),whoisolatedand
a qlcA gene with a lactonase activity for the degradation of characterized metabolites derived from acidobacterial genome
NAHLs. Sequencing of the genomic fragment containing this fragmentshostedbyRalstoniametallidurans.Thesecompounds
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showed inhibitory activity against E. coli, Bacillus subtilis, and nutrient cycling and plant growth after drastic disturbance
Staphylococcus aureus. However, further analysis revealed that (Huangetal.,2015).
thenovelmetabolitesreportedbytheseauthorsappearedtoarise A number of studies have compared acidobacterial
from a mixed biosynthetic pathway involving both the type III distribution and diversity in relation to proximity to plant
polyketidesynthaseencodedbyacidobacterialgenomefragments roots or plant exudates. Numerous studies based on 16S rRNA
and endogenous R. metalliduransenzymes. Multiple reports on sequences have shown a higher proportion and diversity of
PKS pathways identified in Acidobacteria suggest widespread Acidobacteriainthebulksoilascomparedtointherhizosphere
distribution of such pathways across this phylum, suggesting a (Marilley and Aragno, 1999; Sanguin et al., 2006; Fierer et al.,
roleinthepersistence,resistanceandabundanceofthesebacteria 2007; Singh et al., 2007; Kielak et al., 2008). Other studies
in soil ecosystems. However, without the characterization of have shown Acidobacteria abundant in red pepper (Capsicum
the polyketide products, the production of antimicrobials by annuumL.)rhizosphere(Jungetal.,2015).Additionally,itwas
Acidobacteriaremainsspeculative. shownbymeansofshotgunmetagenomicsthatAcidobacteriais
A moderately thermostable lipase (optimum temperature overrepresentedinthesoybeanrhizosphereascomparedtothe
between50and60◦C)fromamemberofAcidobacteriaphylum bulksoil(Mendesetal.,2014).
was also described by metagenomic approach from forest In several cases, Acidobacteria have appeared to tolerate
soil (Faoro et al., 2012). Interestingly, phylogenetic analysis variouspollutantsuchasPCBsandpetroleumcompounds,linear
revealed that the lipase-encoding gene was of fungal origin alkylbenzene sulfonate, p-nitrophenol, (Abed et al., 2002; Paul
and was acquired via horizontal gene transfer. In total, large- et al., 2006; Sanchez-Peinado et al., 2010) and heavy metals
insert metagenomics analyses have served to recover numerous (Ellis et al., 2003; Gremion et al., 2003; Barns et al., 2007)
acidobacterialgenomicregions,buttheactualecologicalinsights leadingtospeculationthatAcidobacteriamaybeinvolvedinthe
offeredfromsuchfragmenteddatasetsremainlimited. degradationofcertainpollutants.However,althoughtherelative
abundanceofAcidobacteriahasoftenbeencorrelatedtospecific
pollutants, no data, up to date have been reported that support
actualactivitiesrelatedtopollutantdegradation.Suchpollutants
ENVIRONMENTAL SURVEYS THAT
appear to have little effect on acidobacterial diversity levels.
CORRELATE Acidobacteria
Forexample,uranium-contaminatedsoilpossessedanextremely
DISTRIBUTION WITH ENVIRONMENTAL
broaddiversityofacidobacterialpopulations,andthesesoilswere
FACTORS OR CONSTRAINTS actuallythebasisfortheexpansionofacidobacterialsubdivisions
to26(Barnsetal.,2007).
Given the high diversity within the Acidobacteria phylum, as With the broader characterization of subdivisions and
well as within particular subdivisions (Figure 5), it is expected increasing depth of coverage it has now become possible to
that they also represent a wide range of physiological traits, break down analyses to the subdivision level, which can be
as observed for other highly abundant and diverse bacterial farmoreinformative.Theavailablestudiesprovidedistribution
phyla, such as the Proteobacteria. However, most of the studies patterns of different acidobacterial subdivisions across different
up to date focus on Acidobacteria at phylum level leading environmentalgradientssuchaspH,nutrients,andcarbon.
to gross generalizations that may not mirror the ecological EspeciallystrikingisthepredominanceofAcidobacteriainlow
traits representative of lower taxonomic levels. Nevertheless, pH conditions, in particular members from subdivision 1 (Sait
some general trends have been discerned from such broad- et al., 2006). On the other hand, Barns et al. (1999) suggested
level analyses. In the most expansive study conducted to date, thatsomeacidobacterialsubdivisionshadanaversiontolowpH
pyrosequencingof16SrRNAgenefragmentwasusedtoexamine conditions in soil and other case, subdivision 6 can be either
the biotic or abiotic factors that most influence the abundance, positivelyornegativelycorrelatedwithsoilpH(Chanetal.,2006;
diversity and composition of soil acidobacterial communities Mukherjeeetal.,2014).Theabundanceofsubdivisions1,2,3,12,
in different types of soils (88 types; Jones et al., 2009). Fierer 13,15wasnegativelycorrelatedwithsoilpH,yetsubdivisions4,
et al. (2007) studies have shown, based upon 16S rRNA gene 6,7,10,11,11,16,17,18,22,25showedapositivecorrelation.
sequence distributions across 71 soils differing in geochemical Similarly, terminal restriction length polymorphism (T-RFLP)
characteristics,thattheabundanceofAcidobacteriawasgenerally and cultivation strategies detected a significant decrease of
higher in soils with very low resource availability (low C Acidobacteriafromsubdivisions1,2,and3atsoilpHhigherthan
mineralization rate) and that the proportions of Acidobacteria 5.5 (Männistö et al., 2007). This trend appears also to hold for
were higher in C-poor bulk soils in comparison to the cold-adaptedpopulationsofAcidobacteria(LipsonandSchmidt,
rhizosphere. However, this position has been challenged by 2004; Männistö et al., 2007). Similar trends have been found in
Jones et al. (2009) and Navarrete et al. (2013b) who found other environments as well, and Acidobacteria from acid mine
a positive correlation between acidobacterial abundance and drainagesystemsseemtobeevenbetteradaptedtomoreacidic
organic carbon availability. At the phylum level, many studies conditions(pH2–3)thanAcidobacteriafromsoilenvironments
have shown that Acidobacteria is sensitive to inorganic and (Kleinsteuber et al., 2008). Furthermore, it has been observed
organic nutrients inputs (Cederlund et al., 2014; Koyama et al., that the phylogenetic diversity of acidobacterial communities
2014; Pan et al., 2014; Navarrete et al., 2015) and Acidobacteria becomes increasingly constrained as soil pH deviates from
seemed to have a role in recovering soils as beneficial to soil neutrality (Jones and Martin, 2006). A possible explanation
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