The Way Up and The Way Down

by Elio

I ad­mit to not hav­ing paid much at­ten­tion to the mech­a­nisms that plants and an­i­mals use to stand up straight, or, in the case of plants, also to de­scend into the soil. Yet, on re­flec­tion, the skill in de­tect­ing the ef­fect of grav­ity, now called grav­it­ro­pism, the older term be­ing ge­ot­ro­pism, is es­sen­tial for life. Per­haps my ne­glect is due to this topic not be­ing much of a mi­cro­bial con­cern (al­though, in fact, what isn't?). How­ever, as we will see, some mi­crobes do know the way up and the way down.

Fig­ure 1. Pleu­ro­tus dry­i­nus on a tree. Source

Fungi and Peo­ple

I will post here pieces that oth­ers have writ­ten on the sub­ject (more to rec­og­nize their ex­per­tise than to re­veal my lazi­ness). This from an ar­ti­cle called "Which way is up? Mush­rooms Grav­it­ro­pism" by my friend Britt Bun­yard in a fab­u­lous mag­a­zine called Fungi, regard­ing mush­rooms and hu­mans, he says: "Monzer (1996, 1995) more re­cently pro­posed a …. sim­ple ex­pla­na­tion for how grav­i­ta­tional sens­ing is ac­com­plished in fungi. And that it's very sim­i­lar to the sys­tem of otolith or­gans (tech­ni­cally the utri­cle and sac­cule) of hu­mans. Within all of us, deep in­side our in­ner ear, there are or­gans that con­tain a liq­uid filled with tiny stone-like par­ti­cles called otoliths or oto­co­nia (they re­ally are stony, es­sen­tially made of lime­stone and a pro­tein) that rub against tiny hairs that line the in­side of the otolith or­gan. Most of the time, the par­ti­cles are uni­formly set­tled telling us which way is down. If you are spun around or shaken like a snow globe, the par­ti­cles move all about giv­ing you a feel­ing of dis­ori­en­ta­tion, even dizzi­ness.

Fig­ure 2. An Amanita sub­al­li­acea mush­room reposi­tion­ing af­ter be­ing placed hor­i­zon­tally overnight. Source: Britt Bun­yard.

Now for more: "And this, Monzer has con­cluded, is sim­i­lar to how fun­gal cells sense grav­ity. Within hy­phal cells, nu­clei act as fun­gal otoliths; their sed­i­men­ta­tion within the cells in re­sponse to the di­rec­tion of the grav­i­ta­tional forces tells the fun­gal cells which way is up. The nu­clei are en­meshed in pro­teina­ceous actin fil­a­ments that make up the cell's in­ter­nal "skele­ton" (the cy­toskele­ton). As these nu­clei set­tle, they tug on actin fil­a­ments, which in turn tug on the cell walls at their points of at­tach­ment. This ten­sion trig­gers cel­lu­lar changes in re­sponse to grav­ity, and on the side of the cell feel­ing gravity's force, mi­crovesi­cles be­gin to fill and ex­pand, vac­uoles ex­pand, and the en­tire process causes the ex­pan­sion of hy­phal cells. The net re­sult is that the mush­room stem bends away from the grav­i­ta­tional sen­sa­tion." See here for a fine piece by Phil Pin­zone on grav­it­ro­pism in the tree-grow­ing mush­room Flam­mulina ve­lu­tipes.

Plants

How about plants? The Wikipedia says: "Grav­it­ro­pism (also known as ge­ot­ro­pism) is a turn­ing or growth move­ment by a plant or fun­gus in re­sponse to grav­ity. It is a gen­eral fea­ture of all higher and many lower plants as well as other or­gan­isms. Charles Dar­win was one of the first to sci­en­tif­i­cally doc­u­ment that roots show pos­i­tive grav­it­ro­pism and stems show neg­a­tive grav­it­ro­pism. That is, roots grow in the di­rec­tion of grav­i­ta­tional pull (i.e., down­ward) and stems grow in the op­po­site di­rec­tion (i.e., up­wards). This be­hav­ior can be eas­ily demon­strated with any pot­ted plant. When laid onto its side, the grow­ing parts of the stem be­gin to dis­play neg­a­tive grav­it­ro­pism, grow­ing (bi­ol­o­gists say, turn­ing; see tro­pism) up­wards."

How do plants man­age these tricks? Con­sider the be­hav­ior of the roots. At the tip of the roots is a sub­set of cells that con­tain spe­cial or­ganelles called amy­lo­plasts (more about them later) that are in­volved in per­ceiv­ing grav­ity. These amy­lo­plasts are denser than the cy­to­plasm and thus grav­ity makes them fall down to the bot­tom of the cells. These struc­tures, called sta­toliths, are en­cir­cled by a web of actin, which is thought to ac­ti­vate car­ri­ers of the plant growth hor­mones, the aux­ins. The changed lo­cal con­cen­tra­tion of auxin leads to dif­fer­en­tial growth of root tis­sues, which leads to the turn­ing of the root. Sta­toliths are also found in the shoots of plants, where they are in­volved in their turn­ing up­ward, in the di­rec­tion op­po­site that of the grav­ity stim­u­lus. Thus, roots and shoots, dis­sim­i­lar though they are, use a com­mon mech­a­nism to sense grav­ity. See here for a re­view and here for a nice blog piece on this topic.

Fig­ure 3. Wino­grad­sky col­umn used at the Ecosys­tems Cen­ter, Ma­rine Bi­o­log­i­cal Lab­o­ra­tory at Woods Hole. By Joseph Vallino. Source

Now about the amy­lo­plasts. The Wikipedia says: "Amy­lo­plasts are non-pig­mented or­ganelles found in some plant cells. They are re­spon­si­ble for the syn­the­sis and stor­age of starch gran­ules. Amy­lo­plasts also con­vert this starch back into sugar when the plant needs en­ergy. Large num­bers of amy­lo­plasts can be found in fruit and in un­der­ground stor­age tis­sues of some plants, such as in potato tu­bers. Amy­lo­plasts and chloro­plasts are closely re­lated, and amy­lo­plasts can turn into chloro­plasts; this is for in­stance ob­served when potato tu­bers are ex­posed to light and turn green." No­tice that the amy­lo­plasts likely orig­i­nated by the en­dosym­bio­sis of a bac­terium, thus we are back in the mi­cro­bial world.

Bac­te­ria

Cer­tain bac­te­ria and ar­chaea also know which way is up, but, best I can tell, none use grav­it­ro­pism for this pur­pose (the huge Achro­matium bac­te­ria prob­a­bly be­ing the no­table ex­cep­tion; there are al­ways ex­cep­tions in bi­ol­ogy). This is not sur­pris­ing, given that the small di­men­sions of most mi­cro­bial cells do not al­low for sig­nif­i­cant dif­fer­ences in the force of grav­ity be­tween the two ends of a rod-shaped bac­terium. Rather, many mi­crobes sense chem­i­cal cues in the en­vi­ron­ment such as gra­di­ents in the con­cen­tra­tion of oxy­gen, sul­fides, and any of a large va­ri­ety of other sub­strates. Pho­to­taxis, (pos­i­tive and neg­a­tive – pho­to­pho­bia) also hap­pen, and so do re­ac­tions to tem­per­a­ture gra­di­ents, toxic chem­i­cals, and un­told other fac­tors. These re­sponses of­ten re­sult in the lay­er­ing of a given species in a wa­ter col­umn or in soils. Clear ex­am­ples in the lab are Wino­grad­sky columns (dis­cussed here).

Fig­ure 4. Thio­ploca mats on the con­ti­nen­tal shelf off the coast of Chile sway­ing more or less up­right in the cur­rent. Source

Among the most in­tri­cate ex­am­ples of lay­er­ing are sul­fide-ox­i­diz­ing bac­te­ria that ob­tain their en­ergy from ox­i­diz­ing sul­fides and use ni­trate as the elec­tron ac­cep­tor. In the shal­low wa­ters off the coast of Chile, such bac­te­ria, in the genus Thio­ploca, make up gi­gan­tic mats. To quote from this blog, "sul­fides are abun­dant in the sed­i­ment, ni­trates in the wa­ter col­umn. How to bring the two to­gether? Thio­plo­cas solve the prob­lem by mak­ing tubu­lar sheaths that stick out from the ocean's sed­i­ment. These sheaths can be as long as 15 cm. In­side them, fil­a­ments of the or­gan­isms glide up and down, gath­er­ing sul­fides be­low and ni­trate above. Thio­plo­cas chemo­tax to­wards ni­trate. They ab­sorb it and trans­port it down­wards, to where the sul­fide is abun­dant, at speeds of about one cen­time­ter per hour. In other words, thio­plo­cas take an el­e­va­tor to work." The topic of grav­it­ro­pism in bac­te­ria had an early his­tor­i­cal mishap. It took the great Mar­t­i­nus Bei­jer­inck to sort it out.

Fig­ure 5. Bun­dle of Thio­ploca arau­cae ex­tend­ing out of their sheath. The ap­pear­ance of a braid is seen where the fil­a­ments cross over one an­other, hence the name Thio­ploca, 'sul­fur braid.' Source

Among other ex­am­ples of how bac­te­ria travel along ver­ti­cal axes, the most ex­cit­ing per­haps are the mag­ne­to­tac­tic bac­te­ria. Again, the Wikipedia says: "To per­form this task, these bac­te­ria have or­ganelles called mag­ne­to­somes that con­tain mag­netic crys­tals. The bi­o­log­i­cal phe­nom­e­non of mi­croor­gan­isms tend­ing to move in re­sponse to the environment's mag­netic char­ac­ter­is­tics is known as mag­ne­to­taxis (al­though this term is mis­lead­ing in that every other ap­pli­ca­tion of the term taxis in­volves a stim­u­lus-re­sponse mech­a­nism). In con­trast to the mag­ne­tore­cep­tion of an­i­mals, the bac­te­ria con­tain fixed mag­nets that force the bac­te­ria into align­ment – even dead cells align, just like a com­pass nee­dle The align­ment is be­lieved to aid these or­gan­isms in reach­ing re­gions of op­ti­mal oxy­gen con­cen­tra­tion."

In Con­clu­sion

So here you have it, when it comes to grav­it­ro­pism, an­i­mals, plants, and mush­rooms all tell which way is up or down us­ing tiny weights: small peb­bles, or­ganelles, and nu­clei, re­spec­tively. Bac­te­ria, when fac­ing up-and-down re­lated chal­lenges, use ex­ter­nal sig­nals other than grav­ity, mainly by sens­ing chem­i­cal gra­di­ents, mag­net­ism, and light. Chaque'un a son goût, but in Bi­ol­ogy each taste works per­fectly well to re­spond to a par­tic­u­lar en­vi­ron­men­tal trial. Vive la Vie!