Putting Life on Earth in Per­spec­tive

by Roberto

Last week I was very for­tu­nate. I had the op­por­tu­nity to fo­cus my atten­tion on putting life on Earth in perspec­tive. It was a wel­come respite consid­ering these try­ing times. Al­most one year ago, thanks to Nas­sos Ty­pas, I re­ceived an invit­ation to speak on micro­bial di­ver­sity at the Eu­ro­pean Mol­e­c­u­lar Bi­ol­ogy Lab­oratory (EMBL) in Heidel­berg. The oc­ca­sion was to be their 21st Sci­ence and So­ci­ety Con­fer­ence en­ti­tled "Our house is burn­ing: sci­en­tific and so­ci­etal re­sponses to mass ex­tinc­tion." The con­ference should have been last week but, of course, there was no trip to Heidel­berg. In­stead, it went vir­tual. But it still pro­vided me with a wonder­ful oppor­tunity for think­ing. Let me share some of those thoughts with you.

By us­ing the phrase "our house is burn­ing" the or­ga­niz­ers man­aged to con­vey the sense of hor­ror of watch­ing our prop­erty de­stroyed by fire. It is im­possible to not be shaken by that men­tal im­age. Since the house be­ing re­ferred to is planet Earth, the feel­ings that emerge be­come ever more shock­ing. To al­le­vi­ate this shock, I found it ex­tremely use­ful to put diff­erent life forms in per­spec­tive in terms of their rel­a­tive sizes, num­bers and their time of res­i­dence on the planet.

Fig. 1. Earth as seen from the EPIC im­ager on the DSC­OVR on March 29, 2017. Credit NASA. Source

This is an im­age of our house, mag­nificent planet Earth, in what I con­sider one of its most stun­ning perspec­tives, a por­trait from space. The very fact that such im­ages can be cap­tured speaks vol­umes as to what hu­mans can accom­plish. And human­ity's never-end­ing search for mean­ing is epit­o­mized by our de­sire to ex­plore, even send­ing crafts out to space, leav­ing Earth far be­hind, a "mote of dust sus­pended in a sun­beam," Carl Sagan's Pale Blue Dot. But hu­mans also caused many of the prob­lems that the planet now faces, global warm­ing and mas­sive loss of bio­diversity prime among them. How does an or­gan­ism, whose di­men­sion is about one me­ter, have such devastat­ing ef­fects on a planet whose dia­meter is 10⁷ times larger? These days that's not too hard to imag­ine, we are all aware that an en­tity 10^-7 the size of a hu­man eas­ily wreaks havoc on its host. Wel­come to the Anthropo­cene, the epoch in the nat­ural his­tory of Earth charac­terized by no­tice­able hu­man im­pact on eco­systems and ge­ol­ogy. Lest you think – as some pro­po­nents do – that the Anthropo­cene started with the Trin­ity test, I re­mind you that the ex­tinc­tion of South Amer­i­can mega­fauna some 12,000 years ago co­in­cided with the ar­rival of Homo sapi­ens.

The con­fer­ence overview state­ment started by putting the cur­rent loss of bio­diversity in the con­text of Earth's his­tory: "There have been five mass extinc­tions in Earth's his­tory, but are we al­ready in the midst of a sixth? At least one mil­lion an­i­mal and plant species are cur­rently threat­ened with ex­tinc­tion, many within decades – a rate unprece­dented in hu­man his­tory." But what about the mi­crobes? Did they suf­fer great de­clines in the prior five mass extinc­tions? Are mi­crobes de­clin­ing in the midst of a sixth? (Do these sound like Tal­mu­dic Ques­tions?)

To me the mi­crobes are the most foun­da­tional of all life forms. Though largely in­visible as in­dividuals, they play and have al­ways played key roles in the function­ing of all eco­systems. So much so, that I do not think of this planet as 'our' house, rather it is the mi­crobes' house. Homo sapi­ens only re­cently step­ped in as a guest and, mind you, thus far we have been far from an ideal guest. We can only hope that this im­proves in the near fu­ture.

What have been the dy­nam­ics of mi­cro­bial pop­u­la­tions along Earth's his­tory? Answer­ing this ques­tion is not an easy task. Over the long run, the mi­cro­bial fos­sil record is poor com­pared to that of plants and an­i­mals. Plus, assess­ment of cur­rent over­all changes is made dif­fi­cult due to the gargan­tuan micro­bial cell pop­u­la­tion and diver­sity. There are some 10³⁰ cells and up­wards of 10¹² species (though the very con­cept of species is de­bat­able, as we dis­cussed here be­fore).

Let's first have a look at the so-called "Big Five" mass extinc­tion events. The first hap­pened 440 mil­lion years ago, the fifth, 65 mil­lion years ago. From the fos­sil record, the per­cent of species lost range from 75−95%. The causes were usu­ally planet­ary cool­ing and volcan­ism. The fifth one also in­volved the Dec­can Traps and the now fa­mous as­ter­oid col­li­sion that cre­ated the Chicx­u­lub crater, and fa­mously led to the demise of the dino­saurs, among oth­ers. When it comes to mi­crobes, there's no di­rect ev­i­dence for their demise dur­ing these five pe­ri­ods. How­ever, through in­di­rect ap­proaches, inves­tigators have spec­ulated both ways. In 1998 Dykhuizen ar­gued that bac­te­ria intrinsic­ally have very low extinc­tion rates and very high spe­ci­a­tion rates. These at­trib­utes would ren­der them resis­tant to mass extinc­tion. In con­trast, in 2007 Wein­bauer and Rassoul­zadegan spec­ulated that when­ever an an­i­mal or plant species be­comes ex­tinct, many of the host-as­so­ci­ated mi­cro­bial species fol­low along. But would this have led to mass extinc­tions? A more re­cent (2018) pa­per by Louca et al. at­tempts to an­swer that ques­tion. The au­thors dev­eloped meth­ods to an­a­lyze the phylo­genies of nearly half-mil­lion bac­te­r­ial lin­eages and deter­mined the frac­tion of ex­tant bac­te­r­ial diver­sity miss­ing from the phylo­genies. From their re­sults they con­clude: "Most bac­te­r­ial lin­eages ever to have inhab­ited this planet are esti­mated to be ex­tinct. Our find­ings dis­prove the no­tion that bac­te­ria are un­likely to go ex­tinct, and pro­vide a valu­able pers­pective on the evolu­tionary his­tory of a do­main of life with a sparse and cryp­tic fos­sil record." Impor­tantly, while they ar­gue for bac­te­r­ial extinc­tions, they con­clude that their "find­ings sug­gest that, dur­ing the past bil­lion years, global bac­terial spe­ci­a­tion and ex­tinc­tion rates were not sub­stantially af­fected dur­ing the mass extinc­tion events seen in eu­kary­otic fos­sil records."

Fig. 2. Time­line of life on Earth. Source: Roberto Kolter

Let's now put those mass extinc­tions of plants and ani­mals in the pers­pective of the en­tire nat­ural his­tory of the planet. Look­ing at my rough time­line sev­eral fea­tures stand out. First, Homo sapi­ens just re­cently en­tered the scene. Sec­ond, the five mass extinc­tion events I've dis­cussed are rel­atively re­cent be­cause, af­ter all, plants and an­i­mals were not around for the vast ma­jor­ity of Earth's his­tory. Third, there were only mi­crobes for the first three bil­lion years of evol­ution.

By the time plants and an­i­mals first evolved, the pla­net was re­plete with mi­crobes. And they had been respon­sible for one of the most remark­able changes in the planet's his­tory: The Great Oxygen­ation Event (GOE). Not long af­ter the first mi­crobes ap­peared, some evolved photo­synthesis, the cap­acity to har­ness the en­ergy from light to con­vert CO₂ into sug­ars. A by-prod­uct of the re­ac­tion was the prod­uction of highly reac­tive oxy­gen gas. Ini­tially, most of the oxy­gen re­acted with iron in sea­water to form iron ox­ides on the ocean bot­tom, giv­ing rise to what we now know as "banded iron form­ations." But even­tually oxy­gen be­gan to ac­cumulate. This poi­son­ing of the atmo­sphere with such a re­ac­tive mol­e­cule must have led to the great­est mass extinc­tion of all time, but it took sev­eral hun­dred mil­lion years to un­fold. That gave time for life on the planet to adapt. Two key evol­utionary steps re­lated to the pres­ence of oxy­gen occur­red as a conse­quence of the GOE that changed our planet for­ever. First, bac­teria evolved the capa­city to dump elec­trons onto oxy­gen and thus gen­er­ate en­ergy much ef­fi­ciently. For the first time there were aer­o­bic respir­ers. Subseq­uently, an ar­chaeon some­where be­came en­tangled and even­tually fused with one of these aer­obes and gave rise to LECA, the last eu­karyote com­mon an­ces­tor. The rest is… well, nat­ural his­tory.

To end, let's fast for­ward to the present, to the midst of the "sixth extinc­tion" and in­quire whether mi­crobes are suf­fering the same fate as so many of the plants and an­i­mals. To ad­dress this, I will side­step the is­sue of extinc­tion. This I do for two rea­sons. The im­mensity of micro­bial bio­diversity and the dif­ficulty in defin­ing a species makes it al­most fu­tile to deter­mine if spe­cific lin­eages have be­come ex­tinct "for­ever." More impor­tantly, as Ce­bal­los et al. have ar­gued, fo­cus­ing on species extinc­tions "leads to a com­mon mis­impression that Earth's biota is not im­me­diately threat­ened, just slowly enter­ing an epi­sode of ma­jor bio­diversity loss." It is far bet­ter to deter­mine if pop­ulation sizes and ranges are af­fected. For plants and an­i­mals, the ev­i­dence is stun­ning. In their words: "Dwin­dling pop­ulation sizes and range shrink­ages amount to a mas­sive anthropo­­genic ero­sion of bio­diversity and of the eco­system ser­vices es­sen­tial to civil­ization. This 'bio­logical annihil­ation' under­lines the serious­ness for human­ity of Earth's on­going sixth mass extinc­tion event. Sadly, sim­i­lar bio­logical annihil­ation is ob­served among mi­crobes. Here are just a cou­ple of ex­am­ples: Global phyto­plankton has de­clined dramat­ically over the past cen­tury and the divers­ity of the in­testi­nal micro­biota of "western­­ized" hu­mans is about half that found in prev­iously un­contacted Amerindi­ans. Is the sit­u­a­tion bleak be­yond re­pair? I don't think so, but then I con­sider my­self an op­ti­mist. I be­lieve if micro­bial eco­systems are al­lowed to re­cover, they will. It's just that hu­mans need to take dra­matic ac­tions. We need to con­tinue to pur­sue ag­gressive ac­tions as com­munities, as coun­tries, as a world, even when some lead­ers in­sist on turn­ing a blind eye to the cata­strophe. And as an in­di­vid­ual I'll con­tinue with lessons that have been ham­mered home by the pan­demic: drive less, fly less and eat less meat.