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Mi , crob 1 ial lnteractions in Soi 1 Jan Dirk van Elsa s, Lin g
Mi , crob 1 ial lnteractions in Soi 1 Jan Dirk van Elsa s, Lin g

Mi ,crob 1ial lnteractions

in Soi 1

Jan Dirk van Elsa s, Ling Tam, Roger D . Fin /ay;

Ken Killham 1 and Jack T. Trevors

CONTENTS

7. i

Introduction

........ .... ... .. ..

.

... ....... . . ......... ... . .

>

... ......

~

.. ............... .. ....... .. ........... . ........ . .. .

..

178

  • 7.2 Ecological Categmies of M.ic robial Interactio:os in Soil

.... ...............

  • 7.3 M'icrobia! As eJt1blages, Island ' and MicrobiaJ

Interactioru. ... ......

...

7.3. 1

Tne Ishmd Coneept of Soil ao d lmpiications for

't 80

t 82

7.3.2 Microbial A embl ages a nd Gene Expression ......... ........ ...... 184
7.3.2
Microbial A
embl ages a nd Gene Expression
......... ........ ......
184
  • 7.4 Molecular Mec'hani sn1s Underlying Microbial lnteractioUB

. ........ ..... .

7.4.J

Molecular Sen.sing ar1d Sig:nali ng

........

.......,

.... . .....

,.... .. ............

  • 7.4.2 Quorum Sertíling-

Tile Paradigm of Signaling betwoon

185

I 85

Mi , crob 1 ial lnteractions in Soi 1 Jan Dirk van Elsa s, Lin g
 
  • 7.4.3 U e af and. Be trn.yal \vith QS mSoil

191

7.4.4

Altemative Punctions fo r AHL

193

7.4 .5

Environmen.tal Se,osing Me,cl1ani ms iu Fllllgi

193

7.5

T)rpes of Mi crobial lntet'áctions io So il

197

7.5 . 1 Mctabol i c Ir1teracti:ons in Soil

197

7.5 .2

7.5."

Antagonisti.c InterJetiort in Soil

.............................................

200

Pred atory Jnterttctio n in Soi1-8de1Jovibrio and

 

Myxobt

_.

lCteric1

?

"

.

........

,

,.

..

202·

Bacterial I nteraction

witi1 Fungí

....

203

 

5 .5

Fu11gaJ Intentctio r1s witb Bac teria,

 

......

2fl5

7 .6

Coneludirig Re marks ·······~·········8······~··························.o!,

 

206

Referen.ce

 

,

201·

1 1 7

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M icrobíal l otera ctions in SoH

1 6 1

Ne ulrali.fm can be c b.a:rac tetized as the lack of interactio:n (s) between

mi cro bial population . For ex.tllllple , microbial populati o:ns may be spa.ciall y

di s tru1t (occ ur 011 diffcr:ent 'islands," see below ) ar population.'i may ocrur in

very low nu111ber

that do

.no t

contact o:r sense o t her po pulatio11( ) . The

rnicrobial proces e

rr1ay oot overlap or affect o·ne aaotber, ~o thc o.rganisms

rnay be fu.nctio11ally

eparate. En viron1nenta1 coi1di tion

(e .g . nutrient limí-

tation, low te mperatures o r the pre ' ence of toxic oompounds) that do no t allow

rrücrobi~ll g rowth a nd ce ll di vision f avo r a ne utral intemctio:.o.

Com111emalism i . 11 unidU: ectionaI i riteractioo bet\veen rr1icroorg:aoisa1 in whí c h one microb.ia.1 population benefits fr om ano ther oue whi le the latter is

not affected (33). For exarnple , one rni c ro bial popul.a.ti on may produce growtb

fac tors-

such as vi ta n11ns and/or amino acids-

t hat o.re

u ¡ed by

the other

mi crob ial p<rpuJation. to tlle sol e beilefit of the l atrer .

Mi 1tualism is an internction i 11 whi c h the tnutual benefits fro ·m ttm partnership ( uch a

in teractin g orgacis.ms receive

in gymhios-is, sytl8r gism or

sy1itl'ophy [ero ' - fe edi .n g]). Mtttua1 S)tmbi os i., c an be a · o~~uloo uec·tosym-

bio i s,"

in

whicl1 the symbi ont occ ur

o n the

ex te m a l

wface of the host .

IDramples include

internctions of, for in~"'tance, nitrogen-fixJng rhizobia with

pl~Ln·cs \vbich donate bound nitroge11 n.nd re.ceive b ound carboo in rerurn;

..

See C h.apter 8 for a.furth e r ex te n io n of th is i sue . Anothe:r irnpo rt ant category

of muruali tic int.emction

are the my oorrhizal . ymbios.es be tween. plan es ru1d

fu.ngi . described in Chapter 5 . Syntroph y is a form of metabolic coll aboi-aíion .

An essen.tiat ineta bolite m.ay be produced by o ri.e mi croorg-.miSll'l whlch etmnot

be prod.uc.ed b)' ano th er ooo. Synergi m is a facultative interaction. in wh.icb

both mi c robial population.

nre

c:il1 c apable of growfu and

n irviv al

iJ1 th.e

absence of the othe:r. For example, on.e populatio n ma y ·produ ce a m etabolic

compound tha,t tbe other popu] ntion cao furthe r metabol ize to a compou:nd t'.Wlt

both popula.tio ns can utili ze .

Parasitisni!Pred<filo n are pro cesses in whic b one organi .m. gain

an

ad vantage at tb e expense of anotber one (pa.rasitism) , or con,, wnes the t1ther

one {preda tio o), obviou ly to the detriment of tbe la tter. Por int.anoe~ the pred.ator organi in .mJiy e nguJf. a t tack o r dige.~t the prey organisn1, sucb a o u.tline d i n Chap ter 6 fo r soi1 protozo a. Thi , can resuJt in a cyc lic internction.

in which the prey is overtaken b y me pre-dator~ resulting in a d.ecline ~o:f the

pre y d ensi ry . whlch

in nirn i nduce:

a ·ub. eque.nt deeline of the predator

p o pi1laticltt As the prey po puJ.atio o. i ncreases again as a r esn l t of the retluced predatory pressure, the predator po pulation will incr~ttse and rhe cycJe reµea t . Exam ples of paras iti sm/pre<iation in oil inc lude bacteria th at ai'e dige.st ed

by soi l protozo:n ( ee ·Cbapter 6) or by other bacteria (see Sectioo

7.

.5

3)

.. .

fun gi

th at are degraded by other fu n. an d organi s ms like Rhi soplty diw11 and

Phy rridi u1rt th.ar can paras itize alg-ae.

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Microbial tnt'eract io:ns in Soil

185

o.x.ygeu, com.p:ared to cells in lower, ofte11 oxygen- depJeted layers . 'Ihu.s 1 ever1

cel ls of l'b.e same species can oocur in different physiologicaJ

tates over veey

sma ll ,clistan:ees witbin n. microbial asse.n1blage i n. soi l. This cancept is mghly relevant for our consielerotion of inter:icti\ 1 e p:r~ and. prod'llction of · econdary metabolites , i ncluding certa ín anribioci.cs. Moreover, the disposal <>f yroducts of cellttlar metabolism oommonly varies ,baween dilferent Jayem .of

a biofilm. In. suinm-ary , a ma tu.re microbial biofilm moay con~ of varlous

layers , whic h are l inked by channels. Conditions will vaey 'between ccll la}re:r ·

at di:fferent depth s and \.vil.l tberefore drive c1ifferentia1 ge.ne expres,s.ion. Por

instnnce, genes for the i~1lation of ftagelJ.ac"{frlven motility. c.eLtuJru· e>Slno-

1a:rity, oxygen linútation and bigb cell density (&ee SecOOD: 7~4.2} ru:e aro.ong

t11or·e ti1at are differentially expressed

..

Hor.nogeireous mi crobla:l amernbl.age

will tbu . sho\v ciear tI:atification, and &ucb s t:ratífteation may even be n1ore

pror1ounced. :in J1eterogenooW! on~ . The latter ty pe of biatilm has been poorl y

tudied to date, but s tructure-function rela.tionSh:ips ha.ve be~n describ.ed in

biofil.rru in. edime11ts coroposed of s.ulfate 'reducer an.d methanog:ens.~ as well

a · in uitrifying 0011sartia containing mttlti.species bacteria.

Cel l- to--cell in:teraeti(}Th,q within bíofilms ( uel1 as signaling) play i.mpommt

roles in the differentitltion proce sses of tire individual cells, and su,eb inter-

actjon ' wilI coortlintlte group behavior. Cell -to-cell cootintmieation in bacteria

occurs thro ugh secre:t:ed. (diffusibte) c lienúcal compounds., as will be di c ussed ío Section 7.4 .2. The regulation of a r a n ge of bact:e.rial f unction:s is related

to ce11-to~celJ commuoieation, and ofteo s ucb regulati.oo. oco.Cür& u1 ca.ses w ben

higher ceil cotl'centrati.ons 'provid.e an eoologica'I advant.age i11 t.h.e natura l envirorunent. Diffusible sign a! molecules bave a direct role in ac.ti vating cell

growt11 ill biofilms and the ab-ility of cell populations to respon:d to changes ro nutrie11t co11cerJtmtions f5) . Parallel forms o f sigo.aling tak~ p l a.ce in. fu.agi and

are disc·WiSed in Section 7.4~5.

7. 4 MOLECULAR MECHANISMS UNDERlVING MICR081Al

INTERACTIONS

7.4,. 1 MO LECULA R S ENSI NC ANO S1GNAL ING

Key features of tl1e genotnes of i11icroorganism

iu 001nplex .b:abitats like soi\

are the p:resence of a large nwnbe:r of di verse oo.nscrry mecbanmms tha:t emible

the e organisms to m.orutar tite co11díti ons prevailing m their SUn 'OWdi_ngs

(e .g . tbe con ce.ntration of a range of aompoonds s.uch. as PO-h divers~ sm.Trces

of C an.d N. temp.e.rnture an.ci pH). Microorgani sms in ~'tlil bave mus evolved

p ecific genetj c . y tems t o s ense their bi otic and ab i.atic envirooments and

respond to pc:rceived s.ignals . The e systems~ the so-c.allet.l tw·o-eompooent

sensor/response {regulatory) systern a ll m\' an. a.dequate ;rei poru;e to the

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Microb ia l ln tera c tions in Soi l

189

\Vítltin the n1icrobial as

n co mmurrit y

re pon

embl11ge t.o tbe QS n10lecules can be charru

..

'1erized as

e.

The

detec t íon

of lhe accu1nulated

.i.gnali n g

iuole-eules by a specifi c c.eJJula:r receptor, th e AHL receptor protein. elicits

a sign.ali ng ca ·ca.el e an<i activa.tes ge ne ex pre sion. The exib'tence o f complex

.regu lator y nerv orks .in th.e ce lJ tbat are associ a ted with QS mggests tlult ~e

sy "tem.s, in creating pos iti ve feedback loop , may be utjlized fot the l'llpjd

amplificatio n of exogcr1ous

ignals (7) . Qu o rum

ensing tl1us reli e

proteins, an AHL

ynthase ancl an AHL receptor protein [7] .

c)·n two

Th e abíli.ty to pro du ce QS signal ing rn olecute bru; bee11 demon strated foc meinbers of th e a.-, f3- and y-subcla.s ses of the P.roieobact erla [7], an.c:l the igJl.al respon e mechanism J1a. been o bs.erved in over 30 species. A.') snnwn

in Figtire

den sitie

..

7. 1, Grnm -posi ti ve bacte ri a a.re al so responsive to cell papulation

Th ey

oc-rete ptoces ed peJJti de

ignali ng molecule

usually b)! a

dedicated K f P - b inding cassette ex p orter pro tein (AB C) [8] . Tbis sigruillng

U:b-stru.cture i · a pb o ph oryla ti on/de p.hospl1orylation tw<rcomponent c~cade

.of varyi ng co.mp lex ity and regularory factor s . In b:rief,

ecr eted peptid e a.u to-

i nd.ucer increase in. co11c.entn1tio11 as a func ti on of cel l popul~ú:ion dens ity .

A ".en.sor prorein. sensor kinase, detect.~ t:he peptide signru

and inten1cts

\vitt1 these. i 11irJa.ti ng a series of poos phorylation events that cttlmjnate in th:e

pho pho r yfa.tio11 of a cog11n:te respon se regu lator 1)roteir1. Th.e phosp~1oryJ ..

atio n prucesi

ac f,ivates thi s respo n e regu l ator, all owi n g .it to bit:td to DNA

a nd a lter the tr1lns.<:ri.ption o f QS -co·ntroll e d ge ne ( . ). Wha t ph enotypes are C\Jn:trolled by QS ? Bacteri a use QS comm1.micatio'.o

to regul~1te a very diverse ar rny of p .hysiol ogica l. activitie

\VÍthio. m icrobini

populati.o ns. Phe no'types th at ttre a

oc iat e.c1 ~rith A.HL p1'0d1tctinn an.d sen'Siog

inc lude biolu1n inesce nce , pro(l~1ction of virul ence f~tetor co nj u gative tra nsfer of T i pla mid · i n Agrobactl~riutn ttlt nefaciens, antibiotic produc"tio·n,

starvatio n resJ>ou :e ( Rliizobiurtr. legu.t1.7i.tto-sarun1 , Vibr.io · pp.).motilit y and

biofilm f ormati or1 (7 ,8] . Onl y o rne of tl1ese p1oces es are r.elevant fur ooil, ruttl Ta.ble 7.2 li sts th e phe11otypes rnost t1elevan t fo,r this llab i t at. lmp ortantly maoy

AHL -regulated gen es are in vol ed in rl1e ecological .inrera.cti ons ·of bacteria

with their bioti.c or a·biotic environ me nt. suc h as in the case of tb e productioo

of aotibiotics and c bitirutses . bio'fi!1n fo rn1ati on,

rruionary phase response~

m otil ity an{1 lig11t p rodu crjon . Spcci ti ca:l ly. QS often directs the inte1'tl.ction s

be twee n bacter ia and e ukaryotic 11osts (e .g. patl1ogooe: i ). Per or p nism, rr1ore

than one :Phen otype may be controlled by QS . For insranc.e. Stnorhlmbit1ni

t1ze liloti l1a ºl' t<) 5% of itS genes be longirrg tO differ.e:n:t re gulcms u:nd:er

QS control.

'Wh at i the eco1og:icaJ s ignific:ance of QS in oiJ ? By regulatin:g gioup

proce s

..

es

uc h

a

:ymb iosi , virul e nce. oompete nce fo r transformu1ion,,

coujugation , an tibiotic pro,d:ucti on, 1notilil) 1 sporu.l.arion and 'bicr.til:m fo:r:mation

[35) ; QS ~eems to p rovicl e a meeh;1ni m i.n ooil by \Vhi c h bacteria orch.estrnte

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Microbíal lnteractions in Soif

193

to bacterial AHLs . Fo.r example , tb:e expres ion

of over 100 plant genes

was fo un d to be u;preguJated at leasl fo urfold ( 16). Hence, plant rooo 4<listen ..

to bacrerial co mmunica tioo, a.nd in tun)

phys iological response incl udin g

tre

·

S\Vitc h o-n u r.ange of

aJ1d defe11se (i od.uc e,d

pecific

y te111ic

re is t.anc.e--:lSR) response . See al . o Chapter 20 .

7.4~4 A tTERN,ATJVE FuNcrtoNs FOR AH ILs

Very recer1tly, it Wtls reported that the canoriical QS autoi.nducet of t:he AHL

type al o pass.es additional f'U.nctions . Spec ifically. some AHLs were found to

act Iike a ntibiotics, inh ib iting the g;rowtb of . ensitive organimns. In addition. a

ideropbore- like action (~equestering of iro n} was found a a no:ther potential

m.ecl1arti m of action . He 11ce. ir

i

possible thal AHú.

are .actuaJ1y muJti.-

purpose molecules t hat can perfo:m1 differe.nt ecol ogical roles i'o accordan.ce

\\l:Í.th tbe need of the producing o rg.anJ " .OJ. in jrs local environment. T ties-e roles

are likely linked to lhe ac tivicy of tite org11nis:m in it:s nabitat.

7. 4. 5

ENV JRONMENTAL SiNStNG M ECHANISMS IN f UNGI

Fungí occur botb a unicel lu.Jar and 01ulticelltU.ar filamento us forros and also need to peroeive environmeotal cue rutd regulate their responses appro- priate ly. Clearly. the problems faced by a multicel lular filamenrous tn:ycellutn

are

not exactly the same as

tbo e

fared

by unicellular organis:ms such a

bacteria and yeasts , but

011le ir1r,ere ting parallel

exlst. These lirie dis-cussed,

below w1d. refe rred to Jn Table 7.3.

Fungal mycelia are reg,ulatecl b;,r · ophisticated c bemosensory mechani . m

whlch play importanr. rol es in the interaction" wit11 o.ther organ.Lmu:J . Por

instan ce , \\' it.h

pla11t ho ts,

eücilors and

inbibito:rs a re important; \ ith

co1npetiton, antibiotics inftuence tl1e interaction.s; arld in tungal I?athoge11

mycotoxin s are involved . Addit:ionJillly. there are " in -hoo eº sig.o.aling mecha:u-

i sm , invol ving pheromonei

which faci lítate the intern.cti.on of ca:mpatjble

gametes and de, relopmen.tal ho·rm.ones wb.ich regulate tbe formation or

,m.aint1::n111ice of di:fferen tiated .m.ul'tice IJ.ular struct:ures. B.amples of th.ese are

given belo\.v. A f11rtber broad category of in-bou se ignals c.on sist of tm array

of endogenous c ue s that bave collecti\~ely be.en t~rm.ed aritoregrúu:tors [ló].

T11ese signal s convey in.fonnation on envir:onm,e ntal oonditions o r the status of

c.ell within a fu:ngal colon.y o:r mycelium ~u1d are transmitted as extracell ular

met.abolites. A ut oregulatory s igoal s ens11re coordinated fun cticm and are

involved in ger111i.11atio n, morphogene.~i , asexual and sexua l development

and.in dimorphi sm of ·pec'ies exi ting both ,ru¡ sio.gle cells í:.tnd myceu iL J\ s yet"

we stil l have mther limited knowledge of th~ m-0lecular mec l1anisms of

reg·ulati.on and o:f the aerual

ignal mola.'11le. involved . Ma-ny siudies ha.ve

bee o cou.ducte.d \Vith tnode l specie , whicb. are not alwny s typ.icaJ

oil fu ngL

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Microb ial lnteractiorrs in Soil

197

e.o enabie the colo nization of fresli~ nutri.en.t rich substta.tes. Duri ng tbis

process and o ther. ' , progrnmmed or environntenta.lly induoed c-ell deam may

oocltr. Cel.l d.entb can occLrr through autopllftgy 1 apAptO$is or .nur:os.ls. The

fir$1: two prooease~ are programmed and genetically re.gulated. wher-eas the third i en virnomei1tal1y indu:eed. ProgramJtled cdl duatli allows for the ren)OVal of un Wáilted ce ll ", n1akir1g w.ay fo r cellular remod.eli:ng and

differen.ti.ation [20] .

  • 7.5 TYPES OF MICROBIAI. INTERACTIONS IN SO IL

Gi ven the fact that life in sml is ooncen.ttate.cl wi thin micro1patial ~a rtcts.:Ot

b.ot spots, ch.e ecological and evolutionary need for mi.craorgllllisms to lnteract

with oti1er organism~ í

Iikely ro be greaL As d1scus~ed. d.epending on th.e

microhabit.at type , a multitude of interactions between. or.ganiStllS that 'hare

tbe ame microbabitat is :po ·sib.le L1~2l,22]. Here we di eu ss relev ant aspeen! of tbe ecology .of micrQorgaa_i . ms invol ve d in selected:

Metabolic in.leractions in ·l

Ant.ugon istic ínteractio-ns in uOil

Pred.atory interac tions in

oil

Internction

witb. fru1gi

I11terac tio1:}S witb ba.cteria

  • 7.5.1 M ETABOLl:C I NTERA.CTlONS IN SOl l

Mic-robial rr1et:aboJjc acti vity is the key determinam of tbe s·tn.tcture aud

compooition of a microbial co mmunity formir1g an a s embtage. So-me

tnicrobial processes ate can·ied o ut by juS"t 011e patficul-ar gro:up of miao-

o:rgatris'fns~ resulting in a largely hcrmogen.oous assembla w:b~rea other

..

,get

processes c annot be performed by single microbial g:rou11Js. The la.tter processes are thus dependent oo a fun ctio.o.· drlv-en microbial ab

..

~mblage

\vbich eonslsts of n1ore tllan o n:e species, ~ming a b.etero~eneous assem-

blage. MJcroorgani ms in soíl can. in t.erac t metaboli.cally in: ditfereo:t ways . Two o:r more miaoorganisn:ts can oantribute different e1.ements of a comu1on me taboJ.ic patblva·y . resu lti,, g in the net synthesi.s or degf'adation o.f speci.tic

compoonds , to the beneftt of all patrl ci pants in tb:i

metabollt (syntrophic)

network. Nitrlflcatw n , the couvers ion of ummonia to nitrate via nitrlte iJ:1

differe11r steps (see Cl1ap tet· 9 for furtber d.etails) is on:e example of sucb

cooperatioo. This process need

the cnmbin ed a.ctlon of OOJn'lOnia-oxiditing

( e.g . Nitroson1o n.r;;s spp .) and nitrir.e-oxidiz iog (e .g. Ni trob m:ter spp .) bac teria. ldeally , bo.th bacterial spec i·e.s are pre s.en.t in tl1e urne physical l ocatio:n and are

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Microbial lnteractions in Soil

201

f un gi

m ay be assoc i a te d

with defen se

o f territory , s ince

th e

release of

enzyme s

to

d eg rade

polymer s

represents an

i n vestmen t of r eso urces.

Competi t io n with o th er o rga ni s m s fo r b reakdown products c an first be

prevented by tight feedback regul ation o f depolymerizing enzymes a nd

th e

u e of wall-bound enzy m e fo r the final stage of polymer breakdown,

che

m os t easily u sed monomers a re th is less ava iJabl e to co mpetin g microorgan - is ms . Another second ary defen se of territory mechanis m is the produ ctio n of a ntibi otics o r othe r s uppress ive metabolite s [26]. As further outJi n ed in C ha pter 8 a nd C hapte r 18, clea r evi d e nce for the ecological role o f a ntib i os is in so il co1nes from s tudie s o n th e biological co ntro l of plant pathoge n s. F or in s tance, Pse11do111onas fluorescens Fl 13 is ab le, by the produ c tion of 2,4-diacety l phlorog lucin o l (DAPG), to con trol th e patato soft ro t pathogen Envinia carotovo ra ss p . atrosept i ca as a res ult of its ca paci t y to produce DAPG . Evidence for the ro l e of DAPG pro du ction was ob tain ed by co ntrols wilh mutants in which DAPG produccion was ina c tivated [27]. Sorne hi g her orga ni s m ma y even u e th e antibiotic power o f bac teria to th e ir own a d vantage . One reveali ng rece nt fi nd ing was the fact that specific ants u