«de­scende, au­dax vi­a­tor...»

Pic­tures Con­sid­ered #27

by Christoph

In 2008, a team of 20 sci­en­tists lead by Dy­lan Chi­vian pub­­lished their find­ing of a motile, spore-form­ing, strictly anaer­o­bic, au­totrophic bac­terium of the Fir­mi­cutes fa­mi­ly in frac­ture wa­ter (60°C, pH 9.3) col­lected at a depth of 2.8 km in the Mpo­neng gold mine (Fig. 1). This mine is lo­cated south-west of Jo­han­nes­burg, South Africa within the Wit­wa­ter­srand basin (150 x 300 km), and cur­rently the deep­est mine in the world (op­er­at­ing depths range from 2.4 km to more than 3.9 km). "Find­ing" is the ap­pro­pri­ate term here since the au­thors did not ac­tu­ally iso­late Desul­forudis au­daxvi­a­tor, as they named it, by grow­ing it in the lab. In­stead, they fil­ter-col­lected its cells (3.3 x 10⁴ cells/ml) from a co­pi­ous 5,600 liters of frac­tion wa­ter and se­quenced the ob­tained DNA, a scanty 40 µg of high-mo­le­cu­lar weight DNA. Much to their sur­prise – and to their de­light, prob­a­bly – they found >99.9% of the se­quence reads be­long­ing to one sin­gle species, whose genome they as­sem­bled com­pletely with­out hav­ing to re­sort to (te­dious) metage­nomic bin­ning. They had not only found the (so far) deep­est soil-dwelling bac­terium but also a unique 'one-species' ecosys­tem. Their fil­te­ring tech­nique did not catch sub-mi­crom­e­ter bac­te­ria or phages, though.

Fig­ure 1. Scan­ning elec­tron mi­cro­graphs were taken of mi­croscopy sam­ple #1 from bore­hole MP104 lo­cated 2.8 km be­low land sur­face (main page), and of a sam­ple from a dif­fer­ent mine, 648 me­ters down in bore­hole D8A (here), where D. au­daxvi­a­tor is also the predomi­nant or­gan­ism. Only one mor­pho­type was ob­served at both lo­ca­tions. The tiny glob­u­lar ob­jects seen in the mi­cro­graph (here) are pre­sum­ably sili­cates, which have been found to pre­cip­i­tate upon cool­ing af­ter sam­ple col­lec­tion. Source

As if these 'records' were not enough, yet an­other sur­prise was wait­ing for Chi­vian and col­la­bo­ra­tors. Iso­topic analy­ses of traces of no­ble gases in the frac­ture wa­ter at the Mpo­neng mine sam­ple site sug­gested that the fluid that houses D. au­daxvi­a­tor last mixed with wa­ter from over­ly­ing aqui­fers at least ~3−4 Ma (=mil­lion years) ago. This earned D. au­daxvi­a­tor the du­bi­ous moniker of "the loneli­est bac­terium" but shows that liv­ing in con­sor­tia is not the only suc­cess­ful evo­lu­tion­ary path for bac­te­ria, even in the long run. Desul­forudis is not a her­mit species, con­fined within the Mpo­neng mine, as its ri­bo­type was also pre­dom­i­nant in sam­ples (>1.5 km depth) from 4 other lo­cations in the Wit­wa­ter­srand basin. But not only that! One re­port lo­cal­ized D. au­daxvi­a­tor ­– or a very close rel­a­tive – in Out­okumpu, Fin­land, again in a depth of ~1.5 km, and one yet un­con­fir­med study claims to have found it in bore­holes 900 m deep near Death Val­ley, CA. Thus, De­sul­fo­ru­dis seems to get around a lot. I can't sup­press the no­tion that plate tec­ton­ics ap­par­ently acts much like a gi­ant Dri­gal­ski spat­ula – a ven­er­a­ble tool from 20th cen­tury mi­cro­bi­ol­ogy lab – that in­oc­u­lates the Earth's crust all over and thor­oughly, that is, deeply, with what­ever soil mi­cro­or­ga­nisms come in its ways.

But back to the pic­ture. Note that the slim, elon­gated D. au­daxvi­a­tor cell shown in Fig. 1 (0,3 x 4.8 µm) has a sur­face-to-vol­ume ra­tio that is roughly twice that of a spher­i­cal cell of the same vol­ume (some­what lower if the cell shown were shortly be­fore di­vid­ing). A high sur­face-to-vol­ume ra­tio is crit­i­cal for opr op­ti­miz­ing the flux of nutrients/waste prod­ucts into and out of the cell, and clearly an ad­van­tage when thriv­ing in a nu­tri­ent-poor en­vi­ron­ment; the Al­phapro­teobac­terium Pelagi­bacter ubique em­ploys the same 'trick' in the open ocean.

Fig­ure 2. Model of the sin­gle-species ecosys­tem at sam­ple site MP104. D. au­daxvi­a­tor's ma­chi­ne­ry is shown in a car­toon rep­re­sen­ta­tion, in­clu­ding path­ways for sul­fate re­duc­tion, ni­tro­gen fix­a­tion, and car­bon fix­a­tion. Sig­nal trans­duc­tion pro­teins are re­ported in­clud­ing the num­ber found in paren­the­ses, with MCP in­di­cat­ing methyl-ac­cept­ing chemo­taxis pro­teins; HPK, his­ti­dine pro­tein ki­nases; and RR, re­sponse reg­u­la­tors. Trans­porters in­clude ap­prox­i­mate sub­strates. Also shown are the ra­di­olyt­i­cally gen­er­ated sources of en­ergy and nu­tri­ents for the ecosys­tem. Source

The 2.35 Mb genome of D. au­daxvi­a­tor codes for 2,157 pro­teins (and 45 tR­NAs, and 6 rRNAs), roughly 1,000 ge­nes more than found in two other self-sus­tain­ing bac­terial species, Prochloro­coc­cus mar­i­nus (~1.6 Mb) and Pelag­ibac­ter ubique (~1.3 Mb). There are no signs for stream­lin­ing in the D. au­daxvi­a­tor genome and its size well within the range of other genomes from the Clos­tri­diales branch, mostly soil-dwelling anaer­obes, of the Fir­mi­cutes phy­lum. Taken every­thing to­gether, the ge­no­mic analy­ses re­vealed the pres­ence of com­plete path­ways for amino acid syn­the­sis – all 21, that is, in­clud­ing se­leno­cys­teine – , for sugar me­tab­o­lism, for ni­tro­gen and phos­pho­rus up­take, and for fla­gella and en­dospore for­ma­tion. Sure enough, also prophage rem­nants are present in the genome, as are CRISPR/Cas se­quences and trans­posons. And, fi­nally, ex­tra copies of an ar­chaea-type sul­fate adeny­lyl­trans­ferase and of a H⁺-translo­cat­ing py­ro­phos­phatase point to hor­i­zon­tal gene trans­fer (HGT) from Ar­chaea in the past. Every­thing is there, as if pur­po­se­ly com­piled for a com­pre­hen­sive (imag­i­nary) text­book "The Bac­te­r­ial Genome; Chap­ter IV. Anaer­obes".

By com­bin­ing geo­chem­i­cal data from the sam­ple site with their ge­nomic analy­ses, Chi­vian and col­lab­o­ra­tors ten­ta­tively re­con­structed the com­plete en­ergy me­tab­o­lism of D. au­daxvi­a­tor: "En­ergy and ma­te­r­ial for the ecosys­tem comes from the ra­di­olytic pro­duc­tion of H₂ and re­ac­tive H₂O₂, which in turn re­acts with H₂S to pro­duce SO₄^2‒ or with pyrite (FeS₂) to pro­duce SO₄^2‒ and Fe(OH)₃ as de­tailed by Lin et al., and shown ex­per­i­men­tally by Left­i­cariu et al. (Fig. 2). The H⁺ pro­duced by the cell and re­leased by ox­i­da­tion re­ac­tions dis­solves cal­cite (CaCO₃) re­leas­ing Ca²⁺ and bi­car­bon­ate (HCO₃^‒). The Ca²⁺ in turn may ex­change with NH₄⁺ in chlo­rite min­eral. The HCO₃^‒ can ei­ther be taken up by the pu­ta­tive Na⁺/HCO₃^‒ sym­porter or it may be ra­di­olyt­i­cally re­duced to for­mate (HCO₂^‒). All three forms of in­or­ganic car­bon may be uti­lized by the Acetyl-CoA car­bon fix­a­tion path­way, as well as CO. The H₂S pro­duced by the SO₄^2‒ re­duc­tion path­way can dif­fuse out of the cell and, in ad­di­tion to re­act­ing with H₂O₂ to re­plen­ish SO₄^2‒, can re­act with the Fe(OH)₃ to re­gen­er­ate SO₄^2‒ and re­lease PO₄^3‒. The Fe²⁺ re­leased by this last re­ac­tion can com­bine with H₂S to pre­cip­i­tate FeS or FeS₂". In ad­di­tion to the well known pho­totrophic, chemotrophic, and elec­tro­trophic – think of She­wanella grow­ing on elec­trodes – lifestyles we have now also: a ra­diotrophic lifestyle. Note that 'ra­diotro­phy' is not con­fined to prokary­otes, ra­diotrophic fungi have al­ready been con­sid­ered here in this blog. In con­clu­sion, mi­cro­bial phys­i­ol­ogy has a new 'drawer', an­other cat­e­gory to char­ac­ter­ize the en­ergy me­tab­o­lism of a crea­ture.

You may won­der about the name given to this re­mark­able bac­terium. The genus name, 'De­sul­fo­ru­dis',  re­flects – in the cus­tom­ary Latin – the lifestyle ("re­duc­ing sul­fur com­pounds") of the rod-shaped cells (rudda (old norse) = rod). The species name 'au­daxvi­a­tor' is a ref­er­ence to the 19^th cen­tury French au­thor Jules Verne and his fa­mous novel 'Voy­age au cen­tre de la Terre'. In this novel, the pro­tag­o­nists has­ten to de­scend to the cen­ter of the Earth af­ter hav­ing de­ci­phered a me­dieval runic in­scrip­tion de­scrib­ing a fea­si­ble route. One half-sen­tence of this in­scrip­tion reads: "...de­scende, au­dax vi­a­tor, et ter­restre cen­trum at­tinges" (de­scend, bold trav­eller, ... and you will at­tain the cen­tre of the earth). You see, also mi­cro­bi­ol­o­gists are ap­par­ently some­times, umh, ro­mantic... . Less ro­man­tic is the no­tion that one would prob­a­bly have to grow D. au­daxvi­a­tor in the iso­tope lab, with ura­nium in the medium to pro­vide ra­di­ol­y­sis. This, how­ever, hasn't been done so far, and for­mally its name stands as "Can­di­da­tus Desul­forudis au­daxvi­a­tor" MP104C, there­fore.

Note. Desul­forudis au­daxvi­a­tor made its first ap­pear­ance in STC in a blog post by Elio back in 2008.

 

Ref­er­ences

Chi­vian D, Brodie EL, Alm EJ, Cul­ley DE, De­hal PS, De­San­tis TZ, Gihring TM, Lapidus A, Lin LH, Lowry SR, Moser DP, Richard­son PM, Southam G, Wanger G, Pratt LM, An­der­sen GL, Hazen TC, Brock­man FJ, Arkin AP, On­stott TC. 2008. En­vi­ron­men­tal ge­nomics re­veals a sin­gle-species ecosys­tem deep within Earth. Sci­ence, 322, 275 − 278. PMID 18845759

Moser DP. 2012. Deep Mi­cro­bial Ecosys­tems in the U.S. Great Basin: A Sec­ond Home for Desul­forudis au­daxvi­a­tor? Ab­stract B41F-08 pre­sented at 2012 Fall Meet­ing, AGU, San Fran­cisco, CA