Phylogenomic Evidence for the Origin of Obligate Anaerobic Anammox Bacteria Around the Great Oxidation Event

Abstract

The anaerobic ammonium oxidation (anammox) bacteria can transform ammonium and nitrite to dinitrogen gas, and this obligate anaerobic process accounts for up to half of the global nitrogen loss in surface environments. Yet its origin and evolution, which may give important insights into the biogeochemistry of early Earth, remains enigmatic. Here, we performed comprehensive phylogenomic and molecular clock analysis of anammox bacteria within the phylum Planctomycetes. After accommodating the uncertainties and factors influencing time estimates, which includes implementing both a traditional cyanobacteria-based and a recently developed mitochondria-based molecular dating approach, we estimated a consistent origin of anammox bacteria at early Proterozoic and most likely around the so-called Great Oxidation Event (GOE; 2.32 to 2.5 billion years ago [Ga]) which fundamentally changed global biogeochemical cycles. We further showed that during the origin of anammox bacteria, genes involved in oxidative stress adaptation, bioenergetics and anammox granules formation were recruited, which might have contributed to their survival on an increasingly oxic Earth. Our findings suggest the rising levels of atmospheric oxygen, which made nitrite increasingly available, was a potential driving force for the emergence of anammox bacteria. This is one of the first studies that link the GOE to the evolution of obligate anaerobic bacteria.

Nitrite accumulation and anammox bacterial niche partitioning in Arctic Mid-Ocean Ridge sediments

“…Bathyanammoxibiaceae is also consistent with the recent phylogenomic and molecular clock analysis of anammox bacteria [78]. In this work, anammox bacteria on Earth were inferred to emerge around the Great Oxidation Event [78], before which ammonium was the dominant oceanic nitrogen species [1]. Ca.…”

Salinity Tolerance and Osmoadaptation Strategies in Four Genera of Anammox Bacteria: Brocadia, Jettenia, Kuenenia, and Scalindua

“…Brocadia” appeared. This evolutionary phylogenetic tree is consistent with the 16S rRNA gene-based tree (Figure ). “ Ca .…”

“…Scalindua" probably emerged in marine environments in the early Proterozoic and most likely around the so-called Great Oxidation Event (GOE; 2.32−2.5 Ga). 76 In the early Proterozoic, oxygen (O 2 ) concentration in the atmosphere just started increasing gradually due to the emergence of oxygenic cyanobacteria, and hence nitrite (NO 2 − ) was produced by aerobic ammonium oxidation. This evolutionary history of anammox bacteria may be consistent with the salt tolerance of the different genera of anammox bacteria obtained in this study: ″Ca.…”

Dating ammonia-oxidizing bacteria with abundant eukaryotic fossils

“…the posterior age estimates(Dos Reis et al 2018;Liao et al 2022); ii) using gene sets without verticality examination results in bias in posterior age estimation, as shown in the present study Yang et al (2021). argued thatRen et al (2019) adopted a strict clock rate model, but in realityRen et al (2019) employed an independent rate clock model (see the source code:…”

“…These eukaryotic fossils provide many more time boundaries, particularly the maxima, for dating analyses (Wang and Luo 2023;Clark and Donoghue 2017). With the incorporation of two eukaryotic fossils each with a maximum constraint, Liao et al (2022) estimated the origin of anaerobic ammonia oxidation (anammox) bacteria (AnAOB) at ~2.3 Ga.…”