In­side Earth, Mi­crobes Ap­proach Im­mor­tal­ity

Mostly dead is slightly alive
 

This ar­ti­cle is reprinted by kind per­mis­sion of the au­thor from her Sci­en­tific Amer­i­can blog, The Art­ful Ameba.

by Jen­nifer Frazer

Last De­cem­ber, the Deep Car­bon Ob­ser­va­tory an­nounced an as­tound­ing fact: the mass of the mi­crobes liv­ing be­neath Earth's sur­face amounts to 15 to 23 bil­lion tons of car­bon, a sum some 245 to 385 times greater than the car­bon mass of all hu­mans. That's amaz­ing. It wasn't so long ago we weren't even sure life at depth was pos­si­ble.

But buried in the press re­lease was a de­tail I found much more sur­pris­ing and in­ter­est­ing than the mass of sub­ter­ranean life: its age.

Back in the late 1920s, a sci­en­tist named Charles Lip­man, a pro­fes­sor at the Uni­ver­sity of Califor­nia, Berke­ley, be­gan to sus­pect there were bac­te­ria in rocks. Not fos­sil bac­te­ria. Alive bac­te­ria.

He had been con­tem­plat­ing the fact that bac­te­ria in his lab­o­ra­tory could be re­an­i­mated af­ter 40 years in dry soil in sealed bot­tles. If they could sur­vive four decades, was there re­ally any limit?

Coal seemed like a rock ripe for test­ing, made as it is from swamp muck. He be­gan crush­ing lumps of coal to see if he could get any­thing to grow from the dust. He did.

Fig­ures 1+2. Forty-eight-hour cul­ture iso­lated from Penn­syl­va­nia coal, heated in oven at 160° to 170°C for fif­teen hours and crushed. Fig­ures are in all cases mag­ni­fied 1129 di­am­e­ters. Fig. 2 Same cul­ture three months old. Source

When placed in so­lu­tions of coal dust and ster­ile wa­ter, in two to three weeks he be­gan to see what looked like bac­te­ria. When placed in so­lu­tions en­riched with bac­te­ria chow called pep­tone, it took as lit­tle as five hours.

In­trigu­ingly, he found that a re­hy­dra­tion pe­riod of at least a few days in liq­uid was es­sen­tial for re­vivification. If the crushed coal was wet­ted but im­me­di­ately placed on food-in­fused gelatin-like agar in a Petri dish, noth­ing grew.

He had, of course, in­cluded con­trols and taken pre­cau­tions to en­sure no con­t­a­m­i­nants caused the growth. His dra­con­ian clean­ing and ster­il­iza­tion pro­ce­dure for the pre-crushed lumps in­volved scrub­bing, soak­ing, bak­ing, and/or pres­sur­iz­ing the lumps of coal for hours or days prior to pul­ve­ri­zation. In fact, he found that heat­ing the sam­ple for hours at 160°C never man­aged to kill the bac­te­ria in­side the coal. If any­thing, it only seemed to en­cour­age them. The longer they were baked – up to an in­cred­i­ble 50 hours – the bet­ter they seemed to grow when the coal was subse­quently crushed (If his re­sults were gen­uine, they may not be al­to­gether sur­pris­ing given both the con­di­tions that cre­ate coal and the ef­fects of heat shock pro­teins).

Lip­man did not be­lieve that the bac­te­ria he coaxed from coal were alive in the sense that the bac­teria in your gut are alive. Rather, he be­lieved that dur­ing the process of form­ing coal, the bac­te­ria had dried up and en­tered sus­pended an­i­ma­tion.

"...[T]he mi­croor­gan­isms found in coal are ac­tu­ally sur­vivors, im­pris­oned in the coal at the time it was formed, from ma­te­r­ial which orig­i­nally was prob­a­bly very rich in mi­croor­gan­isms since it was peat-like in na­ture," he wrote in the Jour­nal of Bac­te­ri­ol­ogy.

"It is my view that here and there scat­tered through the masses of the coal mea­sures an occa­­sio­nal spore or some sim­i­larly re­sis­tant rest­ing stage of a mi­croor­gan­ism has sur­vived the viciss­itu­des of time and cir­cum­stance and re­tained its liv­ing char­ac­ter, its power to de­velop into a vegeta­tive form, and its power to mul­ti­ply when con­di­tions are ren­dered pro­pi­tious for it."

Fig­ures 3+4. Forty-eight-hour cul­ture iso­lated from Penn­syl­va­nia coal, heated ten hour in oven at 160 to 170°C and crushed, Af­ter stay­ing in the un­crushed con­di­tion for thirty-nine days in coal ex­tract pep­tone medium, with­out show­ing growth. Fig. 4 Same cul­ture three months old (also on front­page). Source

This dessi­cated con­di­tion we now call an­hy­dro­bio­sis, and it is in such a state that or­gan­isms like wa­ter bears can with­stand the vac­uum of space and bom­bard­ment with ra­di­a­tion.

Lipman's coal came from Wales and Penn­syl­va­nia, where some was ex­tracted from a depth of 1,800 feet. Penn­syl­va­nia coal in­spired the name of an en­tire ge­o­logic sub­pe­riod – the Pennsyl­van­ian.

It is at least 300 mil­lion years old.

The year was 1931. His col­leagues prob­a­bly thought he was nuts. But from where we sit in 2019, it's look­ing in­creas­ingly likely that Lip­man was not nuts. The world's old­est liv­ing in­di­vid­u­als may not be gnarled bristle­cone pines or shim­mer­ing as­pen clones, but tiny mi­crobes locked in rock miles be­neath the sur­face whose goal is to not to grow or re­pro­duce, but sim­ply to cheat death.

A grow­ing num­ber of pa­pers pub­lished in the last decade in­di­cate that bac­te­ria liv­ing – many of them in a hy­drated, ac­tive state – in sed­i­ments, in rocks, and in pock­ets and fis­sures buried deep un­der­ground are old be­yond be­lief.

For in­stance, in the early 2000s, sci­en­tists re­vealed that the rate at which mi­crobes in aquifers and sed­i­ments were breath­ing was vastly slower than that of mi­crobes at the sur­face. The bio­mass turnover rates – the time in which it takes to re­place the mol­e­cules in a cell – were mea­sured on the or­der of hun­dreds to thou­sands of years.

"We do not know whether the mi­crobes of these sub­sur­face en­vi­ron­ments re­pro­duce at these slow rates of bio­mass turnover," wrote Fred­er­ick Col­well and Steven D'Hondt in a re­view called Na­ture and Ex­tent of the Deep Bios­phere in 2013, "or live with­out di­vid­ing for mil­lions to tens of mil­lions of years."

A 2017 pa­per in PNAS found low den­si­ties of bac­te­ria (al­though "low" is still 50–2,000 cells per cu­bic cen­time­ter) in 5 to 30 mil­lion-year-old coal and shale beds lo­cated  two kilo­me­ters be­neath the floor of the Pa­cific Ocean off the coast of Japan.

They were still ac­tively, if ex­tremely slowly, liv­ing. Their gen­er­a­tion times ranged from months to over 100 years. But this es­ti­mate was likely low, the au­thors con­ceded. The gen­er­a­tion time of E. coli in the lab: 15 to 20 min­utes.

A 2018 study pub­lished in Geo­bi­ol­ogy of mi­crobes liv­ing in deep ma­rine sed­i­ments in the South Pa­cific Gyre con­cluded that the fit­ness in such sed­i­ments is not about grow­ing but merely sur­vi­ving. Such mi­crobes' only food source is what­ever hap­pened to be buried with them, the au­thors con­cluded. The amount of car­bon they con­sume for main­te­nance and re­pair each year is just 2% of the cell's own car­bon con­tent.

"Just the fact that in­tact mi­cro­bial cells are found in this an­cient habi­tat has re­mark­able im­plica­tions con­cern­ing the re­silience of these or­gan­isms," the au­thors wrote.

In their com­puter mod­els run­ning multi-mil­lion year sim­u­la­tions, af­ter four mil­lion years, all cells had ceased growth. They were merely putting what­ever re­sources they could scrounge into keep­ing the old jalopy run­ning, like the des­per­ate sur­vivors in a Mad Max film.

How long can that zero-sum game go on? Will they even­tu­ally starve? Will they meta­mor­phose in­to the dessi­cated, sus­pended state that Charles Lip­man claimed to dis­cover in Penn­syl­va­nia coal? Or does that re­quire the spe­cial con­di­tions of coal­i­fi­ca­tion?

Ev­i­dence is also ac­cu­mu­lat­ing that such nu­tri­ent-de­prived, su­per­an­nu­ated bac­te­ria are not "mi­cro­bial zom­bies". On the con­trary, nu­mer­ous stud­ies have found that when deep sub­sur­face mi­crobes are placed in more mod­er­ate en­vi­ron­ments, they quickly re­vive.

Taken to­gether, these find­ings aren't as lu­di­crous as they may seem when you also con­sider that mi­crobes buried deep be­neath Earth's sur­face are pro­tected from cos­mic ra­di­a­tion – a fre­quent killer of the preter­nat­u­rally aged – by thick over­bur­dens of wa­ter, sed­i­ment, and/or rock (Muons, the form in which cos­mic ra­di­a­tion reaches Earth's sur­face, can only pen­e­trate tens of me­ters into rock). Such ra­di­a­tion steadily mu­tates the DNA of or­gan­isms liv­ing on Earth's sur­face.

Pansper­mia hy­pothe­ses that life seeded the uni­verse by hitch­hik­ing in­side as­ter­oids have al­ways seemed very tin-foil hat to me. But these find­ings, to­gether with the re­cent re­al­iza­tion that life may have ap­peared on Earth al­most as soon as it was pos­si­ble, force me to at least re­con­sider. Al­though space is vast, life is in­sis­tent.

To sum up, Earth's crust ap­pears to be sim­ply lousy with idling, an­cient bac­te­ria parked in power-save mode, ready at nearly a moment's no­tice to throw the gearshift into drive. But what a life! Eons spent en­tombed in a dark, air­less, silent ma­trix, barely eat­ing, barely breath­ing, barely mov­ing, barely liv­ing. But not dead. Not dead.

If Charles Lip­man was right, there are also bac­te­r­ial cells in­side our planet that be­gan life 50 mil­lion years be­fore di­nosaurs evolved that could be­gin di­vid­ing again to­mor­row. That... is breath­tak­ing.

But like the grail knight in In­di­ana Jones and the Last Cru­sade, for these mag­i­cal ef­fects to oc­cur, bac­teria must re­main locked within a sub­ter­ranean prison. For that is the bound­ary, and the price, of vir­tual im­mor­tal­ity.

 

Ref­er­ences

Bradley, James A., Jan P. Amend, and Dou­glas E. LaRowe. "Sur­vival of the fewest: Mi­cro­bial dor­man­cy and main­te­nance in ma­rine sed­i­ments through deep time." Geo­bi­ol­ogy (2018).

Col­well, Fred­er­ick S., and Steven D'Hondt. "Na­ture and ex­tent of the deep bios­phere." Re­views in Min­er­al­ogy and Geo­chem­istry 75, no. 1 (2013): 547–574. (Open Acess PDF)

Lip­man, Chas B. "Liv­ing mi­croör­gan­isms in an­cient rocks." Jour­nal of Bac­te­ri­ol­ogy 22, no. 3 (1931): 183. (Open Ac­cess PDF)

Trem­bath-Re­ichert, Eliz­a­beth, Yuki Mo­rono, Akira Ijiri, Tat­suhiko Hoshino, Kather­ine S. Daw­son, Fu­mio In­a­gaki, and Vic­to­ria J. Or­phan. "Methyl-com­pound use and slow growth char­ac­ter­ize mi­crobial life in 2‑km-deep sub­seafloor coal and shale beds." Pro­ceed­ings of the Na­tional Acad­emy of Sci­ences (2017): 201707525.

 

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.