Competition and evolutionary opportunity: from birds to bacteria

A new study in Evol­u­tion Let­ters uses exper­i­ment­al evol­u­tion to demon­strate how spe­cies inter­ac­tions shape abi­ot­ic adapt­a­tion, and provides rare insight into the under­ly­ing genet­ics. Lead author James P.J. Hall tells us more.

On the Galapa­gos island of Daphne Major lives the medi­um ground finch Geo­sp­iza fortis. This small bird eats seeds, large and small, with indi­vidu­als with lar­ger beaks able to crack open lar­ger seeds. In 1982, a new com­pet­it­or arrived on the island: big-beaked G. mag­nirostris, which out­com­peted G. fortis for the lar­ger, harder to crack seeds. In response, G. fortis spe­cial­ised to eat smal­ler seeds, evolving smal­ler beaks to do so.

A sim­il­ar story comes from islands off the coast of Flor­ida, where the small liz­ard Anolis car­olin­en­sis lives in trees, occupy­ing hab­it­ats from the ground to the can­opy. Intro­duc­tion of A. sagrei, a related spe­cies, dis­placed A. car­olin­en­sis to high­er perches in the tree. As any­body who has climbed trees will tell you, the high­er you climb, the more unstable and nar­row become the branches. Adapt­ing to their new envir­on­ment, A. car­olin­en­sis evolved lar­ger, stick­i­er toe­p­ads, help­ing them to cling on in their more pre­cari­ous habitat.

In each of these cases, inter­act­ing with a com­pet­it­or altered the rela­tion­ship that a spe­cies has with its envir­on­ment (its food, or its hab­it­at), gen­er­at­ing select­ive pres­sure and res­ult­ing in evol­u­tion­ary change. Indeed, one of the fas­cin­at­ing things about evol­u­tion is that sim­il­ar pat­terns occur in very dif­fer­ent spe­cies liv­ing in very dif­fer­ent envir­on­ments. In the Brock­hurst Lab at the Uni­ver­sity of Shef­field, we invest­ig­ate evol­u­tion in bac­teria as a way of under­stand­ing gen­er­al evol­u­tion­ary pro­cesses. Bac­teria are excel­lent study organ­isms as they’re rel­at­ively easy and cheap to grow, and they evolve quickly. Mul­tiple inde­pend­ent pop­u­la­tions are allowed to evolve in the lab, allow­ing us to invest­ig­ate the repeat­ab­il­ity of evol­u­tion, and how out­comes vary under dif­fer­ent exper­i­ment­al con­di­tions. These exper­i­ment­al pop­u­la­tions can be frozen — allow­ing us to hold ances­tral pop­u­la­tions in stas­is while their des­cend­ants evolve — and then thawed, allow­ing evolved and ances­tral bac­teria to com­pete dir­ectly against one anoth­er. This exper­i­ment­al evol­u­tion approach allows us to under­stand the drivers of evol­u­tion in con­trolled set­tings. We’re par­tic­u­larly inter­ested in under­stand­ing inter­ac­tions between spe­cies: between spe­cies of bac­teria, and between bac­teria and ele­ments such as plas­mids and phage.

In one of these evol­u­tion exper­i­ments, we cul­tured Pseudo­mo­nas fluor­es­cens bac­teria in soil micro­cosms with or without Pseudo­mo­nas putida com­pet­it­ors for ~440 gen­er­a­tions (read a pre­vi­ous blog post about this exper­i­ment here). Both of these bac­teria are nat­ur­al inhab­it­ants of soil, which nor­mally hosts huge, diverse pop­u­la­tions of microbes. As part of this exper­i­ment we meas­ured the fit­ness of the evolved P. fluor­es­cens. As expec­ted, all the tested pop­u­la­tions had increased in fit­ness rel­at­ive to their ancest­ors, due to adapt­a­tion to the exper­i­ment­al cul­tur­ing regime. How­ever, those which had evolved along­side P. putida did not gain as much fit­ness, when tested without P. putida, as those which had evolved alone. As with the finches and the liz­ards, the pres­ence of com­pet­it­ors had affected the evol­u­tion­ary oppor­tun­it­ies avail­able to our bacteria.

actP2
Spe­cies inter­ac­tions affect the evol­u­tion of nutri­ent acquis­i­tion, both for Galapa­gos finches and for soil bac­teria. Fig­ure by Ellie Harrison.

One of the major advant­ages of study­ing evol­u­tion in bac­teria is that sequen­cing and ana­lys­ing gen­omes is usu­ally much easi­er and cheap­er than the equi­val­ent in euk­a­ryotes. These ‘evolve and resequence’ stud­ies can be very power­ful at reveal­ing the genet­ic basis of adapt­a­tion. By sequen­cing our lab-evolved lines and com­par­ing them with the ances­tral gen­omes we can identi­fy mutated loci, and most inter­est­ingly, par­al­lel muta­tions: inde­pend­ent muta­tions in the same gene occur­ring in dif­fer­ent pop­u­la­tions. Par­al­lel muta­tions are a strong sign of adapt­a­tion, and where par­al­lel muta­tions occur repeatedly in the same treat­ment (but not in the oth­er) they indic­ate spe­cif­ic adapt­a­tion to those par­tic­u­lar con­di­tions. And that is what we saw. Only one gene clearly stood out: the acet­ate trans­port­er actP. P. fluor­es­cens grown alone almost always had muta­tions in actP, where­as this muta­tion was nev­er found in pop­u­la­tions co-cul­tured with P. putida. To invest­ig­ate these mutants, we grew evolved clones with wild-type actP, or clones with the dis­rup­ted actP, in soil micro­cosms either with or without P. putida com­pet­it­ors. The actP mutants grew faster than the wild-type, but this effect was absent when P. putida was present. We had there­fore iden­ti­fied a gene which, when dis­rup­ted, enhanced growth in the soil envir­on­ment. In the pres­ence of a com­pet­it­or, how­ever, there was no benefit.

ActP’s known activ­it­ies — nutri­ent acquis­i­tion and tox­in sens­it­iv­ity — make intu­it­ive sense in the con­text of between-spe­cies inter­ac­tions. Com­pet­it­ors change the loc­al envir­on­ment by alter­ing nutri­ent avail­ab­il­ity and neut­ral­ising com­mon tox­ins, which is likely to have implic­a­tions for the costs and bene­fits of main­tain­ing a func­tion­ing ActP. We also iden­ti­fied two cases where a broken trans­port­er from the same fam­ily as ActP was react­iv­ated by muta­tions revert­ing a pre­ma­ture stop codon. Both of these were in clones which had evolved along­side P. putida, hint­ing at a gen­er­ally import­ant role of nutri­ent trans­port­ers in spe­cies inter­ac­tions. While for the liz­ards and the finches com­pet­i­tion res­ul­ted in the evol­u­tion of spe­cial­ism, it seems that for our soil-dwell­ing bac­teria the pres­ence of a com­pet­it­or selec­ted indi­vidu­als that had a broad­er range of eco­lo­gic­al functions.

Our work provides a rare glimpse of genet­ics under­ly­ing the evol­u­tion of spe­cies inter­ac­tions. Future exper­i­ments aim to get to the bot­tom of ActP’s role in adapt­a­tion, and its costs and bene­fits in inter­ac­tions with spe­cies oth­er than P. putida. It would also be inter­est­ing to see how read­ily actP mutants revert when single-spe­cies-evolved P. fluor­es­cens is intro­duced to P. putida, and to invest­ig­ate the func­tion of the re-activ­ated trans­port­er. From finches to liz­ards to soil bac­teria, spe­cies inter­ac­tions play a key role in evol­u­tion, and evol­u­tion exper­i­ments offer a power­ful oppor­tun­ity to explore their effects.

James P. J. Hall (@jpjhall) is a postdoc­tor­al research assist­ant at the Uni­ver­sity of Shef­field, Depart­ment of Anim­al & Plant Sci­ences. The ori­gin­al study is freely avail­able to read and down­load from Evol­u­tion Let­ters here.