Mi­cro­bial Com­mu­nity Ecol­ogy

by Roberto

Many present-day mi­cro­bial ecol­ogy stud­ies in­volve some sort of se­quenc­ing ef­fort to de­termine which mi­crobes are present in a sam­ple. Al­most in­vari­ably, such analy­ses of mi­crobial com­mu­ni­ties in­volve de­ter­min­ing the rel­a­tive abun­dance of the dif­fer­ent types of mi­crobes present – from phyla to strains, de­pend­ing on the study. The fig­ure shows an ex­ample of such an analy­sis; I sus­pect most STC read­ers are quite fa­mil­iar with these co­lorful bar graphs. (This one I se­lected ran­domly, thus the lack of any fur­ther de­scrip­tion; just en­joy view­ing if you will.)

Fig. 1. Typ­i­cal col­or­ful bar graph show­ing mi­cro­bial com­munity com­po­si­tion in dif­fer­ent sam­ples. Source

It seems that dur­ing the last three decades, every con­ceiv­able ecosys­tem of Earth and its in­hab­i­tants has been thus ex­plored. In a few in­stances, re­search is be­gin­ning to make in­roads in un­der­stand­ing the func­tional sig­nif­i­cance of the com­po­si­tion of some commu­nities. But for the most part, much of the in­for­ma­tion ob­tained only an­swers the ques­tion of who is there. There's pre­cious lit­tle in terms of un­der­stand­ing how come a com­mu­nity has its par­tic­u­lar com­po­si­tion; we still do not know much about the mech­a­nis­tic de­tails un­der­ly­ing mi­cro­bial com­mu­nity ecol­ogy. In con­trast, we know much – some­times in ex­ceed­ingly fine de­tail – about how some mi­crobes, when an­a­lyzed in pure cul­ture, func­tion. How can we bridge this large gap in un­der­stand­ing? What will it take to un­der­stand (at least some) mi­cro­bial com­munities the way we un­der­stand some model mi­crobes? In a re­cent Jour­nal of Bac­te­ri­ol­ogy ed­i­to­r­ial, en­ti­tled "We have a com­mu­nity prob­lem,"  George O'Toole points us in the di­rec­tion of model syn­thetic mi­cro­bial com­mu­ni­ties as a way for­ward. I could not agree more. I strongly be­lieve that if sev­eral re­search groups rally be­hind a few model syn­thetic com­mu­ni­ties it is likely that fun­da­men­tal and maybe even uni­ver­sal prin­ci­ples will emerge.

I also be­lieve that as in­ves­ti­ga­tors dive deeply into the study of a few model mi­cro­bial com­munities, they should be guided by a gen­eral the­ory of what dri­ves the co-ex­is­tence of dif­fer­ent mi­cro­bial types. Naively, one might think that for a given mi­crobe to be main­tained in a com­mu­nity at a char­ac­ter­is­tic abun­dance, it must be due to its hav­ing some se­lec­tive ad­van­tages that al­low it to be there and reach those num­bers. But it clearly can­not be that sim­ple; there are so many in­ter­ac­tions to con­sider even in sim­pli­fied com­mu­ni­ties! If fact, the mech­a­nis­tic un­der­stand­ing of com­mu­nity ecol­ogy can at first sight ap­pear mind-bog­g­ling and un­at­tain­able.

Fig. 2. The The­ory of Com­mu­nity Ecol­ogy. Se­lec­tion, drift, spe­ci­a­tion, and dis­per­sal in­ter­act to de­ter­mine com­mu­nity dy­nam­ics across spa­tial scales. The de­lin­eation of dis­crete spa­tial scales is ar­bi­trary. Source

But does com­mu­nity ecol­ogy nec­es­sar­ily have to be seen from the lens of re­mark­able and thus im­pen­e­tra­ble com­plex­ity? I say no. I came to rec­og­nize the pos­si­bil­ity of sim­pli­fi­ca­tion af­ter read­ing the 2010 es­say by Mark Vel­lend "Con­cep­tual Syn­the­sis in Com­mu­nity Eco­lo­gy."  The au­thor pro­poses that, de­spite all the com­plex in­ter­ac­tions, the pat­terns of com­munity com­po­si­tion are dri­ven by only four classes of processes: se­lec­tion, drift, spe­ci­a­tion and dis­per­sal. (Given that we still de­bate what is a mi­cro­bial species, think of the word spe­ci­a­tion here as di­ver­si­fi­ca­tion or vari­a­tion.) How el­e­gant a the­ory, re­duc­ing ap­par­ent chaos to the in­ter­play of four processes. In the author's words: "Se­lec­tion rep­re­sents de­ter­min­is­tic fit­ness dif­fer­ences among species, drift rep­re­sents sto­chas­tic changes in species abun­dance, spe­ci­a­tion cre­ates new species, and dis­per­sal is the move­ment of or­gan­isms across space."  More­over, this frame­work al­lows "for the ar­tic­u­la­tion of a very gen­eral the­ory of com­mu­nity dy­nam­ics: species are added to com­mu­ni­ties via spe­ci­a­tion and dis­per­sal, and the rel­a­tive abun­dances of these species are then shaped by drift and se­lec­tion, as well as on­go­ing dis­per­sal, to drive com­mu­nity dy­nam­ics."  I am all for start­ing from sim­ple prin­ci­ples. And I am par­tic­u­larly at­tracted to this the­ory be­cause it ap­plies across spa­tial scales. Maybe this sim­ple con­cep­tual syn­the­sis will guide fu­ture de­tailed stud­ies of a few model mi­cro­bial com­mu­ni­ties around the world. I, for one, would be thrilled to see that hap­pen.

 

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