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In 1859, Charles Dar­win included a novel tree of life in his trail­blaz­ing book on the the­ory of evo­lu­tion, On the Ori­gin of Species. Now, sci­en­tists from Rut­gers University-​New Brunswick and their inter­na­tional col­lab­o­ra­tors want to reshape Darwin’s tree.

A new era in sci­ence has emerged with­out a clear path to por­tray­ing the impacts of microbes across the tree of life. What’s needed is an inter­dis­ci­pli­nary approach to clas­si­fy­ing life that incor­po­rates the count­less species that depend on each other for health and sur­vival, such as the diverse bac­te­ria that coex­ist with humans, corals, algae and plants, accord­ing to the researchers, whose paper is pub­lished online on 7 June in the jour­nal Trends in Ecol­ogy and Evo­lu­tion.

Debashish Bhat­tacharya, co-​author, Depart­ment of Ecol­ogy, Evo­lu­tion and Nat­ural Resources and Depart­ment of Bio­chem­istry and Micro­bi­ol­ogy, Rut­gers Uni­ver­sity, New Brunswick, New Jer­sey, USA.

“The goal is to trans­form a two-​dimensional tree into one that is multi-​dimensional and includes bio­log­i­cal inter­ac­tions among species,” Bhat­tacharya added.

A tree of life has branches show­ing how diverse forms of life, such as bac­te­ria, plants and ani­mals, evolved and are related to each other. Much of the Earth’s bio­di­ver­sity con­sists of microbes, such as bac­te­ria, viruses and fungi, and they often inter­act with plants, ani­mals and other hosts in ben­e­fi­cial or harm­ful ways. Forms of life that are linked phys­i­cally and evolve together (i.e. are co-​dependent) are called sym­bio­mes, the paper says.

Exam­ples of sym­bio­mes: (A) Switch­grass root hair growth pro­mo­tion in the pres­ence of the dark sep­tate endo­phyte (DSE) fun­gus, cidome­la­nia pani­ci­cola. Warm sea­son C4 grasses such as switch­grass rely on their sym­biome to per­sist in stress­ful envi­ron­ments such as the Pine Bar­rens of New Jer­sey, USA. (B) Sym­bio­sis between the water fern Azolla and the cyanobac­terium Anabaena that involves ver­ti­cal inher­i­tance of the cyanobac­terium via the mega-​spore appa­ra­tus of the water fern. This is a trans­verse sec­tion of the megas­pore appa­ra­tus that shows the megas­pore (m), the floats (f), and the cyanobac­te­ria (c; red region at the top of the megas­pore appa­ra­tus). © Exam­ples of the oblig­ate lichen sym­bio­sis. Top two rows show exam­ples of lichen species present in the south­ern Appalachian Moun­tains. The lower row shows light micro­graphs of dif­fer­ent types of algal asso­ci­a­tions (indi­cated with arrows, from L to R: Tre­bouxia, Trentepohlia, Nos­toc) in lichen thalli.
Credit: (A) Images pre­pared by E. Walsh, Rut­gers Uni­ver­sity. (B) Image pre­pared by H. Schnei­der. © Images by E.A. Tripp and J.C. Lende­mer. | No usage restrictions

The authors pro­pose a new tree of life frame­work that incor­po­rates sym­bio­mes. It’s called SYM­PHY, short for sym­biome phy­lo­ge­net­ics. The idea is to use sophis­ti­cated com­pu­ta­tional meth­ods to paint a much broader, more inclu­sive pic­ture of the evo­lu­tion of organ­isms and ecosys­tems. Today’s tree of life fails to recog­nise and include sym­bio­mes. Instead, it largely focuses on indi­vid­ual species and lin­eages, as if they are inde­pen­dent of other branches of the tree of life, the paper says.

The authors believe that an enhanced tree of life will have broad and likely trans­for­ma­tive impacts on many areas of sci­ence, tech­nol­ogy and soci­ety. These include new approaches to deal­ing with envi­ron­men­tal issues, such as inva­sive species, alter­na­tive fuels and sus­tain­able agri­cul­ture; new ways of design­ing and engi­neer­ing machin­ery and instru­ments; enlight­ened under­stand­ing of human health prob­lems; and new approaches to drug discovery.

“By con­nect­ing organ­isms to their micro­bial part­ners, we can start detect­ing pat­terns of which species asso­ciate under spe­cific eco­log­i­cal con­di­tions,” Bhat­tacharya said. “For exam­ple, if the same microbe is asso­ci­ated with the roots of very dif­fer­ent plants that all share the same kind of habi­tat (nutrient-​poor and high in salt, for exam­ple), then we have poten­tially iden­ti­fied a novel lin­eage that con­fers salt and stress tol­er­ance and could be used to inoc­u­late crop plants to pro­vide this valu­able trait.”

In gen­eral, any ques­tion that would ben­e­fit from the knowl­edge of species asso­ci­a­tions in sym­bio­mes could be addressed using SYM­PHY, he said.

“We’d actu­ally have trees inter­act­ing with trees, and that sort of net­work allows you to show con­nec­tions across mul­ti­ple dif­fer­ent organ­isms and then por­tray the strength of the inter­ac­tions between species,” he said.

The sci­en­tists are call­ing for the U.S. National Sci­ence Foun­da­tion, National Nat­ural Sci­ence Foun­da­tion of China and other fund­ing agen­cies to sup­port a work­ing group of diverse researchers who would pro­pose plans to cre­ate the new SYM­PHY system.

“What we wish to clearly stress is that we are not engaged in Darwin-​bashing. We con­sider Dar­win a hero of sci­ence,” Bhat­tacharya said. “New tech­nolo­gies have brought rad­i­cal new insights into the com­plex world of micro­bial inter­ac­tions that require a fresh look at how we clas­sify life forms, beyond clas­si­cal two-​dimensional trees.”

We should also aim to unify sys­tem­at­ics (meth­ods of clas­si­fy­ing life) research under the SYM­PHY umbrella so that depart­ments with dif­fer­ent spe­cial­ties, such as zool­ogy, botany, micro­bi­ol­ogy and ento­mol­ogy, work together to por­tray how biotic inter­ac­tions impact species evo­lu­tion, ecol­ogy and organ­is­mal biol­ogy in general.

(Source: Rut­gers news release, 07.06.2017)