A Mi­crobe By Any Other Name Would Smell As Sweet…

by Mark O. Mar­tin

It has long been known that the sense of smell can evoke the rich­est mem­o­ries. Oliver Wen­dell Holmes wrote: Mem­o­ries, imag­i­na­tion, old sen­ti­ments, and as­so­ci­a­tions are more read­ily reached through the sense of smell than through any other chan­nel. How does this re­late to mi­cro­bi­ol­ogy? One of the most com­mon com­plaints from stu­dents new to a mi­cro­bi­ol­ogy lab is that "bac­te­ria smell bad." (I usu­ally re­mind them to in­clude the ar­chaea in their eu­kary­ocen­tric judg­men­tal­ism.) But odors—sweet or not—are due to volatile chem­i­cals and can be a form of in­for­ma­tion, re­veal­ing meta­bolic char­ac­ter­is­tics and con­vey­ing sub­tle sig­nals be­tween dif­fer­ent or­gan­isms.

Source

Pseudomonas aerug­i­nosa can fa­mously gen­er­ate a 'grape juice' smell in in­fected burn pa­tients. Anaer­obes are par­tic­u­larly pun­gent due to their re­liance on sulfhydryl com­pounds to main­tain re­dox bal­ance. (Closer to home, Gram neg­a­tive anaer­obes are of­ten re­spon­si­ble for 'morn­ing breath'. Many of the pleas­ant aro­mas of fer­mented foods can be traced to the pro­duc­tion of volatile mol­e­cules by mi­cro­bial ac­tion. Cer­tain cyanobac­te­ria and actin­o­mycetes syn­the­size geosmin, a volatile chem­i­cal that is rem­i­nis­cent of pot­ting soil. (Nor­man Pace has been known to wax lyri­cal here, call­ing geosmin "the breath of the mi­cro­bial world.") Even the dis­tinc­tive aroma of the seashore is due in large part to mi­cro­bial ac­tiv­ity. In fact, the trea­sured ocean fra­grance is due to none other than di­methyl sul­fide, an odor oth­er­wise as­so­ci­ated with hu­man di­ges­tion. In my own ex­pe­ri­ence, I once found a con­t­a­m­i­nant dur­ing a course I was teaching—a flat, yel­low colony grow­ing on stan­dard nu­tri­ent agar—that smelled very much like a spe­cific brand of tor­tilla chips. Which sug­gests the ques­tion of why tor­tilla chips smell like, well, tor­tilla chips. Some ques­tions are bet­ter left un­ex­am­ined.

Geosmin. Source

The pos­si­bil­ity of mi­cro­bially-me­di­ated ol­fac­tory com­mu­ni­ca­tion may go still far­ther. It's in­trigu­ing that re­cent ev­i­dence points to an­i­mal-as­so­ci­ated mi­cro­bial com­mu­ni­ties pro­duc­ing odor­ants that al­low dif­fer­ent kin groups of hye­nas to rec­og­nize one an­other in the wild.

Volatiles stream­ing from a 'hot' com­post pile. Source

There was even an ASM ses­sion at the Gen­eral Meet­ing in Philadel­phia two years ago, chaired by Mel Rosen­berg, on the sub­ject of odors and mi­cro­bi­ol­ogy. Top­ics ranged from the role of spe­cific mi­cro­biota in pro­duc­ing bad breath, to sub­du­ing the gen­er­a­tion of methane in the hu­man gas­troin­testi­nal tract via pre­bi­otics, to re­duc­ing the ol­fac­tory im­pact of swine sewage ponds. But I sus­pect that the is­sue of odor is more sub­tle and wide­spread (and mi­cro­bi­o­log­i­cally in­ter­est­ing) than a sim­ple in­ven­tory of those un­pleas­ant to us, and the ses­sion at­ten­dees clearly agreed with that sen­ti­ment. I would re­mind the reader of Ju­lian Davies' con­cept of the 'par­vome', the uni­verse of small mol­e­cules that act as sig­nals be­tween mi­crobes. Why not volatile chem­i­cals, uti­liz­ing a mi­cro­bial equiv­a­lent of ol­fac­tion? Could prokary­otes have a sense of, well, smell? Surely they do, as wit­nessed by their abil­ity to rec­og­nize volatile sig­nals. There is some ev­i­dence for such sig­nal­ing be­tween mi­crobes and plant roots in the soil and for its in­volv­ment in colony for­ma­tion among some mi­crobes.

Davies re­minded me re­cently that the great Joshua Leder­berg once wrote that bac­te­ria were com­mu­ni­cat­ing all the time; we sim­ply didn't know the fre­quency! Maybe the 'fre­quen­cies' are chem­i­cal, the mes­sages volatile and aro­matic, and we are but 'deaf' eaves­drop­pers hold­ing our metaphor­i­cal noses in a world much richer and more in­for­ma­tion-packed than we might ex­pect.

Mark is as­so­ciate pro­fes­sor in the De­part­ment of Bi­ol­ogy, Uni­ver­sity of Puget Sound, an As­so­ciate Blog­ger for STC, and a pas­sion­ate ad­vo­cate for the Small Things.