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Microbes may help fossilize ancient embryos

Nov. 24, 2008
Courtesy Indiana University
and World Science staff

Bac­te­ri­al de­cay was once viewed as the mor­tal en­e­my of fos­sil­iz­a­tion. But new re­search sug­gests re­sil­ient col­o­nies of bac­te­ria, called bio­films, may have ac­tu­ally helped pre­serve the fos­sil rec­ord’s most vul­ner­a­ble stuff: an­i­mal em­bryos and soft tis­sues.

This early-stage em­bry­o is pro­tected by a fer­ti­li­za­tion en­ve­lope, seen here as a white line en­cir­cling the em­bry­o cells. (Cred­it: E.C. Raff and R.A. Raff)


Sci­en­tists have found that bac­te­ria can in­vade dy­ing em­bry­o cells and form densely packed bio­films in those those cells. These com­pletely re­place the cell struc­ture and gen­er­ate a rep­li­ca of the em­bry­o, say the re­search­ers, who call this forma­t­ion of bac­te­ria fill­ing the shape of an em­bry­o a “pseu­do­morph.” 

The in­ves­ti­ga­tors, led by In­di­ana Uni­ver­s­ity Bloom­ing­ton bi­ol­o­gists Ru­dolf and Eliz­a­beth Raff, re­port their find­ings in this week’s early on­line is­sue of the re­search jour­nal Pro­ceed­ings of the Na­tional Acad­e­my of Sci­ences.

“The bac­te­ria con­sume and re­place all the cy­to­plasm in the cells, gen­er­at­ing a lit­tle sculp­ture of the em­bryo,” said Eliz­a­beth Raff, the re­port’s lead au­thor. 

But “cer­tain con­di­tions must be met if the bac­te­ria are go­ing to aid the pre­serva­t­ion pro­cess.” For one, she ex­plained, the em­bry­o must have died in a low-oxygen en­vi­ron­ment, such as the bot­tom of a deep ocean or bur­ied in lake­side mud. Ox­y­gen would make em­bryos self-destruct as di­ges­tive en­zymes break free and wreak hav­oc.

Then, “bac­te­ria able to sur­vive in low-oxygen con­di­tions must then in­fest the cells of the dy­ing em­bry­o,” Raff said. The bac­te­ria form bio­films, crowd­ed as­sem­blies of bac­te­ri­al cells held to­geth­er by sticky fibers made of pro­teins and sug­ars. As the bio­films fill the em­bry­o cells, the ti­ny bac­te­ria in­sin­u­ate them­selves be­tween and among the struc­tures with­in the cells, form­ing a faith­ful rep­re­senta­t­ion of the cel­l’s in­nards.

High-resolution im­ag­ing of a trove of half-a-billion-year-old em­bry­o fos­sils from Chi­na, of­fered ev­i­dence that bac­te­ria may have been in­volved in the pres­er­va­tion, re­search­ers say. (Cred­it: F.R. Turn­er, E.C. Raff, and R.A. Raff)


Last, the bac­te­ria must leave a per­ma­nent rec­ord, she added: in the case of fi­nely pre­served fos­sil em­bryos, the bac­te­ria likely ex­crete ti­ny crys­tals of cal­ci­um phos­phate which even­tu­ally re­place the bac­te­ri­al sculp­tures. These crys­tals would pro­vide the sup­port for em­bryo and soft tis­sue fos­sil­iz­a­tion.

High res­o­lu­tion im­ag­ing of a trove of half-bil­lion-year-old an­i­mal em­bry­o fos­sils from Dou­shan­tuo, Chi­na, of­fered sci­en­tists tan­ta­liz­ing ev­i­dence that bac­te­ria may have been in­volved in the pre­serva­t­ion of the del­i­cate cells, she said.

The Raffs stud­ied early-stage em­bryos of two Aus­tral­ian sea ur­chin spe­cies, He­lio­ci­daris ery­thro­gram­ma and He­lio­ci­daris tu­ber­cu­lata. Ex­pe­ri­men­tal re­sults with mod­ern em­bryos were com­pared to the high res­o­lu­tion im­ages of fos­sil em­bryos pre­pared by col­leagues.

Al­though it’s im­pos­si­ble to know wheth­er bac­te­ria aided the pre­serva­t­ion of the em­bryo fos­sils from Dou­shan­tuo and else­where, the Raffs ar­gue the ev­i­dence they gath­ered strongly fa­vors the view that bac­te­ria are a fun­da­men­tal force in fos­sil forma­t­ion, as rap­id bi­o­log­i­cal pro­cesses must be availa­ble to con­vert del­i­cate cells in­to a sta­ble form and trig­ger their min­er­al­iz­a­tion.

“This work is im­por­tant be­cause it helps us un­der­stand fos­sil­iz­a­tion as a bi­o­log­i­cal as well as ge­o­log­i­cal pro­cess,” Eliz­a­beth Raff said. “It gives us a win­dow on­to the ev­o­lu­tion of the em­bryos of the earth’s first an­i­mals.”


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Bacterial decay was once viewed as the mortal enemy of fossilization. But new research suggests resilient colonies of bacteria, called biofilms, may have actually helped preserve the fossil record’s most vulnerable stuff: animal embryos and soft tissues. Scientists have found that bacteria can invade dying embryo cells and form densely packed biofilms in those those cells. These completely replace the cell structure and generate a replica of the embryo, say the researchers, who call this formation of bacteria filling out the shape of an embryo a “pseudomorph.” The investigators, led by Indiana University Bloomington biologists Rudolf and Elizabeth Raff, report their findings in this week’s early online issue of the research journal Proceedings of the National Academy of Sciences. “The bacteria consume and replace all the cytoplasm in the cells, generating a little sculpture of the embryo,” said Elizabeth Raff, the report’s lead author. But “certain conditions must be met if the bacteria are going to aid the preservation process.” For one, she explained, the embryo must have died in a low-oxygen environment, such as the bottom of a deep ocean or buried in lakeside mud. Oxygen would make embryos self-destruct as digestive enzymes break free and wreak havoc. Then, “bacteria able to survive in low-oxygen conditions must then infest the cells of the dying embryo,” Raff said. The bacteria form biofilms, crowded assemblies of bacterial cells held together by sticky fibers made of proteins and sugars. As the biofilms fill the embryo cells, the tiny bacteria insinuate themselves between and among the structures within the cells, forming a faithful representation of the cell’s innards. Last, the bacteria must leave a permanent record. In the case of finely preserved fossil embryos, the bacteria likely excrete tiny crystals of calcium phosphate which eventually replace the bacterial sculptures. These crystals, Raff said, provide the support for embryo and soft tissue fossilization. High resolution imaging of a trove of half-a-billion-year-old animal embryo fossils from Doushantuo, China, offered scientists tantalizing evidence that bacteria may have been involved in the preservation of the delicate cells, Raff said. The Raffs studied early-stage embryos of two Australian sea urchin species, Heliocidaris erythrogramma and Heliocidaris tuberculata. The experimental results with modern embryos were compared to the high resolution images of fossil embryos prepared by colleagues from China, England, Sweden, and Switzerland. Although it is impossible to know whether bacteria aided the preservation of 550-million-year-old embryo fossils from Doushantuo and elsewhere, the Raffs argue the evidence they gathered strongly favors the view that bacteria are a fundamental force in fossil formation, as rapid biological processes must be available to convert highly delicate cells into a stable form and trigger mineralization. “This work is important because it helps us understand fossilization as a biological as well as geological process,” Elizabeth Raff said. “It gives us a window onto the evolution of the embryos of the earth’s first animals.”