Meet the Microbes That Breathe Nitrate Instead of Oxygen – And They’re Everywhere

Scientists have discovered a remarkable new form of symbiosis — a bacterium that lives inside a single-celled organism (a ciliate) and provides it with energy. Unlike mitochondria, which use oxygen, this microbe powers its host by breathing nitrate.

Initially found in a freshwater lake, researchers set out to determine how widespread these microbes are. To their surprise, they uncovered them in diverse environments worldwide, from lakes and groundwater to even wastewater. This discovery challenges our understanding of microbial partnerships and reveals how these tiny organisms play a hidden yet significant role in global ecosystems.

A New Symbiotic Discovery

In 2021, scientists at the Max Planck Institute for Marine Microbiology in Bremen, Germany, made a remarkable discovery: a unique bacterium that lives inside a ciliate — a single-celled eukaryote — and provides it with energy. This symbiotic relationship is similar to the role mitochondria play in cells, but with one major difference: instead of using oxygen, this endosymbiont generates energy by respiring nitrate.

To better understand the distribution and diversity of these unusual microbes, the researchers in Bremen expanded their study. Now the re­search­ers from Bre­men set out to learn more about the en­vir­on­mental dis­tri­bu­tion and di­versity of these pe­cu­liar sym­bionts. “After our ini­tial dis­cov­ery of this sym­biont in a fresh­wa­ter lake, we wondered how com­mon these or­gan­isms are in nature,” explains Jana Milucka from the Max Planck In­sti­tute for Mar­ine Mi­cro­bi­o­logy. “Are they ex­tremely rare and there­fore eluded de­tec­tion so long? Or do they ex­ist else­where and if so, what are their meta­bolic ca­pa­cit­ies?”

A Global Inhabitant

To find answers, the scientists searched massive public sequencing databases containing genetic data from a wide range of environmental samples. Their findings were surprising: these symbionts appeared in about 1,000 different datasets. “We were sur­prised how ubi­quit­ous they are. We could find them on every in­hab­ited con­tin­ent,” says Milucka. “Moreover, we learned that they can live not only in lakes and other fresh­wa­ter hab­it­ats but also in ground­wa­ter and even wastewa­ter.”

Meet the Family: New Members Do New Tricks

The sci­ent­ists dis­covered not only the ori­ginal sym­biont in these data­sets, but also some new close re­l­at­ives. “We ended up identi­fy­ing four new spe­cies, two of which ac­tu­ally con­sti­tuted a new genus. Be­cause this new genus of sym­bionts likely has a sim­ilar role as the ori­gin­ally dis­covered Azoamicus (name mean­ing “ni­tro­gen friend”), we named the new genus Azoso­cius (“ni­tro­gen as­so­ci­ate”), ex­plains first-au­thor Daan Speth. “Lucky for us, one of the new Azoso­cius spe­cies was re­trieved not too far from Bre­men, from a ground­wa­ter sample in Hainich, Ger­many.”

Evolving Capabilities: A Surprising Oxygen Connection

Now the sci­ent­ists wanted to dig deeper into the life of these new spe­cies. Thanks to a col­lab­or­a­tion with Kirsten Küsel and Will Over­holt from the Friedrich Schiller Uni­versity in Jena, Ger­many, who ini­tially col­lec­ted the Hainich samples, they were able to ac­cess the sampling site and look into meta­tran­scrip­tomic data, i.e. data de­scrib­ing the gene ex­pres­sion in the sample and in­dic­at­ing mi­cro­bial activ­ity.

“Here, we were in for an­other sur­prise – these res­pir­at­ory sym­bionts can do new tricks,” Speth con­tin­ues. Un­like the ori­ginal sym­biont spe­cies, which can only per­form an­aer­obic res­pir­a­tion (i.e. de­ni­tri­fic­a­tion), all new sym­biont spe­cies ac­tu­ally en­code a ter­minal ox­i­dase – an en­zyme that en­ables them to also respire oxy­gen in ad­di­tion to ni­tro­gen. “This can ex­plain why we find these sym­bionts also in en­vir­on­ments that are fully or par­tially oxic.”

Evolutionary and Ecological Implications

These res­ults, now presen­ted in the journal Nature Communications, an­swer the sci­ent­ists’ open ques­tions re­gard­ing the sym­biont’s biogeo­graphy. “Thanks to the dis­cov­ery of these new spe­cies, we can now also start think­ing more about their evol­u­tion,” Milucka looks ahead. “We can hope­fully un­der­stand bet­ter how these be­ne­fi­cial sym­bi­oses be­gin and how they evolve over time.”

Moreover, there is an eco­lo­gical as­pect to this re­search: “By per­form­ing de­ni­tri­fic­a­tion, this sym­bi­osis im­pacts the ni­tro­gen cycle of their re­spect­ive hab­itat and has the po­ten­tial to re­move nu­tri­ents, such as ni­tro­gen ox­ides, as well as pro­duce green­house gases, such as ni­trous ox­ide,” adds Speth.

Marvels of Microbial Symbiosis

And last but not least, there is the simple ap­pre­ci­ation of the in­triguing world of mi­crobes. “This or­gan­ism is a mar­vel of nature,” Milucka en­thuses. “Prot­ists are cap­able of such as­ton­ish­ing meta­bolic in­nov­a­tions, of­ten be­cause they so read­ily jump into re­la­tion­ships with proka­ryotes. To me, this is just fas­cin­at­ing. When it comes to un­der­stand­ing the evol­u­tion of eu­k­a­ryotes, these or­gan­isms are an im­port­ant piece of the puzzle.”

Reference: “Genetic potential for aerobic respiration and denitrification in globally distributed respiratory endosymbionts” by Daan R. Speth, Linus M. Zeller, Jon S. Graf, Will A. Overholt, Kirsten Küsel and Jana Milucka, 8 November 2024, Nature Communications.
DOI: 10.1038/s41467-024-54047-x

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