Genomes of Thaumarchaeota from deep sea sediments reveal specific adaptations of three independently evolved lineages

Abstract

Marine sediments represent a vast habitat for complex microbiomes. Among these, ammonia oxidizing archaea (AOA) of the phylum Thaumarchaeota are one of the most common, yet little explored, inhabitants, which seem extraordinarily well adapted to the harsh conditions of the subsurface biosphere. We present 11 metagenome-assembled genomes of the most abundant AOA clades from sediment cores obtained from the Atlantic Mid-Ocean ridge flanks and Pacific abyssal plains. Their phylogenomic placement reveals three independently evolved clades within the order Nitrosopumilales, of which no cultured representative is known yet. In addition to the gene sets for ammonia oxidation and carbon fixation known from other AOA, all genomes encode an extended capacity for the conversion of fermentation products that can be channeled into the central carbon metabolism, as well as uptake of amino acids probably for protein maintenance or as an ammonia source. Two lineages encode an additional (V-type) ATPase and a large repertoire of DNA repair systems that may allow to overcome the challenges of high hydrostatic pressure. We suggest that the adaptive radiation of AOA into marine sediments occurred more than once in evolution and resulted in three distinct lineages with particular adaptations to this extremely energy-limiting and high-pressure environment.

Nitrite accumulation and the associated anammox bacteria niche partitioning in marine sediments

“…To better understand the relative importance of anammox bacteria for ammonium consumption in GC04, we examined, in addition to anammox bacteria themselves, the distribution (i.e., both the relative and absolute abundances) of aerobic ammonia-oxidizing archaea (AOA) and bacteria (AOB) in this core using the two microbial quantitative methods described above. Consistent with their requirement of oxygen [58,59], both AOA (affiliated with the class Nitrosopumilales of the phylum Thaumarchaeota [60,61]) and AOB are mainly detected in the upper 10 cm sediments of the oxic zone (Fig. 2B and 2C).…”

Genome-Resolved Metagenomic Insights into Massive Seasonal Ammonia-Oxidizing Archaea Blooms in San Francisco Bay

“…MAGs generated in this study are in bold. Genes are clustered based on whether they are conserved or variable in AOA based on the work of Ren et al ( 75 ) and Kerou et al ( 108 ). Genes are further grouped by general function, labeled at the top of the plot.…”

High Abundance of Thaumarchaeota Found in Deep Metamorphic Subsurface in Eastern China

“…Cluster 1 mainly included the sequences from the South African gold mines, with relatively long phylogenetic distances. Cluster 2 contained the majority of sequences from the Deccan Traps [ 26 ] and all non-AOA sequences were obtained from previous publications [ 3 , 51 ], which suggested that the Deccan Traps Thaumarchaeota may be anaerobes or facultative aerobes. Cluster 3 mainly consisted of the sequences from the rocks and biofilm from the CCSD drilling.…”