Depth-related distribution of a key gene of the tetraether lipid biosynthetic pathway in marine Thaumarchaeota

The distribution of isoprenoid glycerol dialkyl glycerol tetraethers (GDGT) lipids synthesized by Thaumarchaeota has been shown to be temperature-dependent in world oceans. Depth-related differences in the ammonia monooxygenase (amoA) of Thaumarchaeota have led to the classification of 'shallow' and 'deep water' clusters, potentially affecting GDGT distributions. Here, we investigate if this classification is also reflected in a key gene of the thaumarchaeotal lipid biosynthetic pathway coding for geranylgeranylglyceryl phosphate (GGGP) synthase. We investigated metagenomic databases, suspended particulate matter and surface sediment of the Arabian Sea oxygen minimum zone. These revealed significant differences in amoA and GGGP synthase between 'shallow' and 'deep water' Thaumarchaeota. Intriguingly, amoA and GGGP synthase sequences of benthic Thaumarchaeota clustered with the 'shallow water' rather than with 'deep water' Thaumarchaeota. This suggests that pressure and temperature are unlikely factors that drive the differentiation, and suggests an important role of ammonia concentration that is higher in benthic and 'shallow water' niches. Analysis of the relative abundance of GDGTs in the Arabian Sea and in globally distributed surface sediments showed differences in GDGT distributions from subsurface to deep waters that may be explained by differences in the GGGP synthase, suggesting a genetic control on GDGT distributions.