Illuminating the ecology and evolution of ammonia-oxidizing archaea in freshwater ecosystem

Like Comment
Read the paper

Ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread across a great variety of ecosystems and play a significant role in global nitrogen and carbon cycling. Since the first reports of the non-extremely archaea from marine water column [1, 2], there are increasingly advancements in our understanding of the ecology and evolution of the Thaumarchaeota partially owing to the development of sequencing technology. However, owing to historical reasons, the habitat of the archaea is mainly restricted to marine and soil environments, which is supported by the uneven number of the single-marker genes (i.e. ammonia monooxygenase subunits A (amoA)) in different habitats [3]. Freshwater Thaumarchaeota are paid less attention when compared to their marine and soil relatives. Considering that freshwater ecosystem plays an important role in mediating global climate changes, it is greatly necessary to explore the ecology and evolution of Thaumarchaeota across freshwater ecosystem.

Our study reconstructed 17 high-quality thaumarchaeotal MAGs from Lake Lugu with a maximum depth 95 m and the published metagenome datasets of two rivers (Yangtze River and Amazon Rivers). After integrating additional MAGs available in public databases, freshwater Thaumarchaeota are mainly partitioned into three clades, which are closely related to the genera Nitrosoarchaeum, Nitrosopumilus and Nitrosotenuis. We also observed a contrasting water-depth pattern for the abundance of Thaumarchaeota in deep lakes based on metagenomic and amplicon sequencing data. Specifically, the Nitrosopumilus-like clade dominates the shallow layers and the Nitrosoarchaeum-like clade increases toward deep waters. Although vertical separation has been reported previously [4], here we revealed different divergence pattern, and provided metabolic potential underlying the niche different based on the reconstructed genome sequence. The abundance patterns are consistently observed in two deep lakes, Lake Fuxian and Lake Baikal, both of which are geographically more than 3000 km apart. These results indicate that a very long time of niche separation of the two clades of freshwater Thaumarchaeota in deep lakes since their divergence from their last common ancestor.

Although phylogenetic structure shows a complex historical evolution of freshwater Thaumarchaeota within the phylum, the inference of evolutionary history for the family Nitrosopumilaceae (based on GTDB taxonomy [5]) could be enabled based on the clear separation by phylogenetic relatedness and habitat. The phylogenetic clustering patterns support at least one freshwater-to-marine and two marine-to-freshwater transitions within the family. And the former freshwater-to-marine transition agrees with the colonization events from terrestrial to marine enivironments as previously proposed [6, 7], and further provide a highly resolution for the possible evolutionary path. The inference of the latter two marine-to-freshwater transitions provides clear insights into the complex evolutionary history of freshwater Thaumarchaeota, like the direct colonization from terrestrial (soil) habitats and from recolonization of marine ancestors. Comparative genomics and ancestral genomic analyses suggested their occurrences of transition events were accompanied by horizontal transfer of the genes involved in nutrition regulation, osmoregulation and cell motility during their colonization to freshwater habitats.

Beside the three main clades freshwater Thaumarchaeota discussed in our manuscript, there are freshwater genomes scattered in the phylogenetically distant clades, where no freshwater Thumarchaeota are reported yet. For example, a MAG from a deep lake is assigned to Nitrosotalea, an acidophilic clade exclusively consisting of soil Thaum and the other freshwater MAG in non-AOA group, a paraphyletic group consisting of the species from hot spring, marine and vents. Further study of the ecology and evolution of these ‘novel’ freshwater Thaumarchaeota are temporarily hindered by the availability of genome sequence. The occurrence of these diverse freshwater thaumarchaeotal genomes suggests the huge genomic diversity of freshwater habitats are needed to explore in future studies. The AOA related to the genus Nitrososphaeria are found in rivers ecosystem (like Thames River [8]) during the revision of our manuscript. However, no genomes of Nitrospsphaeria-associated genomes are recovered from all 79 samples (including water column and sediment) from two great rivers in our study. The results, on one hand, could be explained by a possibility that these archaea initially thrived on soil environment near river bank are transported and colonized the river sediment due to regular erosion of river banks. The hypothesis should be proved or refuted by future studies that compare the similarity of AOA population in the rivers and the near terrestrial habitats. On the other side, these results confirm the enormous genomic diversity of freshwater Thaumarchaeota.

Our study is now a first step in closing an important knowledge gap about freshwater Thaumarchaeota. The elucidation of genomic diversity of freshwater Thaumarchaeota would provide complementary insights to the current understanding of the archaea regarding biogeography and evolutionary history. However, more spatially and temporally monitor analyses of the archaea in freshwater habitats are needed to investigate their distribution, ecology and evolution.

Further information on our research can be found here:




  1. DeLong, E.F., Archaea in coastal marine environments. Proceedings of the National Academy of Sciences, 1992. 89(12): p. 5685–5689.
  2. Fuhrman, J.A., K. McCallum, and A.A. Davis, Novel major archaebacterial group from marine plankton. Nature, 1992. 356(6365): p. 148-149.
  3. Alves, R.J.E., et al., Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes. Nature Communications, 2018. 9(1): p. 1517.
  4. Auguet, J.-C., et al., Vertical segregation and phylogenetic characterization of ammonia-oxidizing Archaea in a deep oligotrophic lake. The ISME Journal, 2012. 6(9): p. 1786-1797.
  5. Rinke, C., et al., A standardized archaeal taxonomy for the Genome Taxonomy Database. Nature Microbiology, 2021. 6(7): p. 946-959.
  6. Ren, M., et al., Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution. The ISME Journal, 2019. 13(9): p. 2150-2161.
  7. Yang, Y., et al., The evolution pathway of ammonia-oxidizing archaea shaped by major geological events. Molecular Biology and Evolution, 2021. 38(9): p. 3637-3648.
  8. Sheridan, P.O., et al., Gene duplication drives genome expansion in a major lineage of Thaumarchaeota. Nature Communications, 2020. 11(1): p. 5494.

Minglei Ren

Researcher, Nanjing Institute of Geography and Limnology, CAS