Re­sus­ci­tated: 100-Mil­lion-Year-Old Seafloor Sed­i­ment Bac­te­ria

This ar­ti­cle is reprinted by kind per­mis­sion of the au­thor from Sci­en­tific Amer­i­can.

by Jen­nifer Frazer

In 2010, Japan­ese sci­en­tists from the In­te­grated Ocean Drilling Program's Ex­pe­di­tion 329 sailed in­to the South Pa­cific Gyre with a gi­ant drill and a big ques­tion.

The gyre is a ma­rine desert more bar­ren than all but the aridest places on Earth. Ocean cur­rents swirl around it, but within the gyre, the wa­ter stills and life strug­gles be­cause few nu­tri­ents en­ter. Near the cen­ter is both the Oceanic Pole of In­ac­ces­si­bil­ity (made fa­mous by H.P. Lo­vecraft as the home of the be-ten­ta­cled Cthulhu) and the South Pa­cific garbage patch. At times the clos­est peo­ple are as­tro­nauts pass­ing above on the In­ter­na­tional Space Sta­tion.

The seafloor-drilling ship Joides Res­o­lu­tion. Cre­dit: Ar­ito Sak­aguchi & IODP/TAMU Wiki­me­dia

The sea here is so miserly that it takes one mil­lion years for a me­ter of "ma­rine snow" – corpses, poo and dust – to ac­cu­mu­late on the bot­tom. The tale of all that time can to­tal as lit­tle as 10 cen­time­ters. It is the least pro­duc­tive patch of wa­ter on the planet.

Through nearly 6,000 me­ters of this sea­wa­ter the IODP team low­ered a drill. The straw­like bit plunged into pelagic clay and cal­care­ous nanofos­sil ooze at three sites on the bot­tom.

By the time the cores of sed­i­ment were raised to the sur­face, the tubes con­tained up to 100 mil­lion years of Earth his­tory. What the team wanted to know was how long and in what state mi­crobes trapped in this mi­lieu could sur­vive in an al­most-com­pletely raided oceanic re­frig­er­a­tor. They were in for a sur­prise.

Their re­sults, pub­lished in Na­ture Com­mu­ni­ca­tions in July, re­vealed that the sed­i­ments con­tained bac­te­r­ial cells, which they ex­pected (not many, though: just 100 to 3,000 per cu­bic cen­time­ter). But when given food, most of them quickly re­vived, which the sci­en­tists did not ex­pect.

a Scat­ter plots of mi­cro­bial growth charac­ter­istics cal­culated from bio­mass (bio­mass-based spe­cific growth rate, µ_B [day⁻¹]), car­bon and ni­trogen sub­strate (sub­­s­trate-based bio­mass ge­ne­ration rates, ^Cµ_S [day⁻¹] for car­bon and ^Nµ_S [day⁻¹] for ni­tro­gen, re­spec­tively. n = 76 samp­les were an­a­lyzed for the calcu­lation of µ_B, n = 4298 and n = 6028 cells were an­a­lyzed for the calcu­lation of ^Cµ_S and ^Nµ_S, re­spec­tively [of total­ly 6253 cells an­a­lyzed, non-zero val­ues of ^Cµ_S and ^Nµ_S were used for this plot]). b Re­la­tion­ship of com­mu­nity com­po­si­tion to ad­di­tion of sub­strates along the time of in­cu­ba­tion. The com­munity com­po­si­tions at "In­cu­ba­tion time 0" show the com­po­si­tions be­fore in­cu­ba­tion. c Non-met­ric mul­tidimensional scal­ing (NMDS) or­di­na­tion plot based on Bray–Curtis dissimi­larities of com­mu­nity com­po­si­tions at dif­fer­ent in­cu­ba­tion con­di­tions and time points (stress = 0.209). Ar­rows rep­re­sent en­vi­ron­men­tal vari­ables that were sig­nif­i­cantly (p < 0.005, permu­tations = 10000) re­lated to the or­di­na­tion. n = 76 sam­ples (one for In­cu­ba­tion time 0 and three for in­cu­ba­tion sam­pling points [days 21, 68, and 557] per sub­strate for each sed­i­ment sam­ple). Source

The mi­crobes got straight to work do­ing what bac­te­ria do, and within 68 days of in­cu­ba­tion had in­creased their num­bers up to 10,000-fold. They dou­bled about every five days (E. coli bac­te­ria in the lab dou­ble in around 20 min­utes). Their prog­eny con­tained spe­cially la­beled iso­topes of car­bon and ni­tro­gen that made the sci­en­tists sure that the mi­crobes were eat­ing what they had been of­fered.

It's worth paus­ing to con­sider the mean­ing of these re­sults. In this ex­per­i­ment, cells awoke and mul­ti­plied that set­tled to the bot­tom when pterosaurs and ple­siosaurs drifted over­head. Four ge­o­logic pe­ri­ods had ground by, but these mi­crobes, pro­tected from ra­di­a­tion and cos­mic rays by a thick coat of ocean and sed­i­ment, qui­etly per­sisted. And now, when of­fered a bite, they awoke and car­ried on as if noth­ing un­usual had hap­pened.

In a sense, it hadn't. If you think it feels like 100 mil­lion years since the pan­demic be­gan, think about the condi­tions (and en­ter­tain­ment op­tions) of these poor mi­crobes. It was a re­ally long 100 mil­lion years down there. The toll of all that time was not zero, though. The old­est cells mul­ti­plied about half as fast as their spryer brethren that had "only" been there a few mil­lion years.

Con­sider now that 70 per­cent of Earth's sur­face is cov­ered by ma­rine sed­i­ment, whose mi­cro­bial res­i­dents rep­re­sent some­where be­tween a tenth and a half of all mi­cro­bial bio­mass on Earth. There's a whole lot of se­nior cit­i­zen mi­crobes down there.

Some­what sur­pris­ingly, the ma­jor­ity of the cells were, like us, forms that breathe oxy­gen. In fact, the sed­i­ment they were pulled from is full of oxy­gen. Clearly, lack of "air" is not the prob­lem for the life in gyre sed­i­ments. It's the lack of food.

Con­tribut­ing to the prob­lem is the den­sity of the sed­i­ment, which ap­proaches some­thing like flour­less choco­late cake: the pore size is an es­ti­mated 0.02 mi­crom­e­ters. Given that a typ­i­cal bac­terium is a few mi­crom­e­ters across, you can see the prob­lems in­her­ent to mi­grat­ing in search of food, or even hop­ing some blun­ders into you. Once you end up in South Pa­cific Gyre seafloor se­diment, you are trapped – un­less res­cued by an ocean drilling pro­gram.

More sur­prises lay in store when the sci­en­tists checked the iden­ti­ties of the cells by prob­ing their DNA; there was a lack of spore-form­ing bac­te­ria. Some bac­te­ria make re­sis­tant struc­tures called en­dospores that are for­ti­fied and meta­bol­i­cally in­ac­tive, seem­ingly formed to al­low bac­te­ria to en­dure harsh con­di­tions. Yet these bac­te­ria were rel­a­tively ab­sent. Spores were not how these su­per­an­nu­ated bac­te­ria had sur­vived.

Even more sur­pris­ing, dis­cov­ered in one sam­ple was a thriv­ing pop­u­la­tion of light-har­vest­ing bac­teria called Chroococ­cid­iop­sis, cyanobac­te­ria with a rep­u­ta­tion for sur­vival so for­mi­da­ble that they are be­ing con­sid­ered for ter­raform­ing Mars (and fea­tured here in STC). In ad­di­tion to be­ing able to live un­der translu­cent rocks in dry, cold, salty and ra­di­a­tion-drenched places, they have the un­usu­al abil­ity to cap­i­tal­ize on red light, pos­si­bly a re­sult of their pre­ferred dim con­di­tions. How these pho­to­syn­thetic mi­crobes man­aged to re­pro­duce in the dark af­ter 13 mil­lion years be­neath the seafloor re­mains a mys­tery.

Putting it all to­gether – the tight quar­ters, the lack of spores and the rapid re­an­i­ma­tion – these sci­en­tists think it's likely that the ma­jor­ity of the bac­te­ria in this im­pov­er­ished sed­i­ment have been alive but idling these 100 mil­lion years.

A few years ago, I wrote about bac­te­ria (here in STC) that may have been res­ur­rected from coal from the Pa­le­o­zoic. Now we have re­ports of bac­te­ria from the Cre­ta­ceous seafloor sed­i­ment wak­ing ap­par­ently non­plussed. Back then I spec­u­lated that un­der cer­tain highly con­strained but pos­sibly abun­dant con­di­tions, bac­te­ria may be ef­fec­tively im­mor­tal. Now it seems even more likely we may be sit­ting atop a planet that's full of liv­ing fos­sils that are lit­er­ally that – both fos­sils and alive.

The di­nosaur peo­ple (and to be fair, who among us aren't di­nosaur peo­ple?) have their mu­se­ums filled with bones and teeth and tracks. The plant peo­ple have their pet­ri­fied forests and fos­sil fronds. But the mi­crobe peo­ple have some­thing even bet­ter: our di­nosaurs aren't dead.

 

Jen­nifer Frazer is a AAAS Sci­ence Jour­nal­ism Award-win­ning sci­ence writer. She has de­grees in bi­ol­ogy, plant pa­tho­lo­gy/my­co­lo­gy, and sci­ence writ­ing, and has spent many happy hours study­ing life in si­tu.