Metabolic potential of fatty acid oxidation and anaerobic respiration by abundant members of Thaumarchaeota and Thermoplasmata in deep anoxic peat

Abstract

To probe the metabolic potential of abundant Archaea in boreal peats, we reconstructed two nearcomplete archaeal genomes, affiliated with Thaumarchaeota group 1.1c (bin Fn1, 8% abundance), which was a genomically unrepresented group, and Thermoplasmata (bin Bg1, 26% abundance), from metagenomic data acquired from deep anoxic peat layers. Each of the near-complete genomes encodes the potential to degrade long-chain fatty acids (LCFA) via β-oxidation. Fn1 has the potential to oxidize LCFA either by syntrophic interaction with methanogens or by coupling oxidation with anaerobic respiration using fumarate as a terminal electron acceptor (TEA). Fn1 is the first Thaumarchaeota genome without an identifiable carbon fixation pathway, indicating that this mesophilic phylum encompasses more diverse metabolisms than previously thought. Furthermore, we report genetic evidence suggestive of sulfite and/or organosulfonate reduction by Thermoplasmata Bg1. In deep peat, inorganic TEAs are often depleted to extremely low levels, yet the anaerobic respiration predicted for two abundant archaeal members suggests organic electron acceptors such as fumarate and organosulfonate (enriched in humic substances) may be important for respiration and C mineralization in peatlands.

Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical spongeIanthella basta

“…Interestingly, many members of the Aigarchaeota, a sister group to the Thaumarchaeota (Guy and Ettema, ), also encode the full livFGHMK operon, and a single cell aigarchaeal‐like genome from cold marine sediments encodes additional extracellular proteases, di‐ or tripeptide transporters and aminotransferases (Lloyd et al ., ). It is therefore tempting to speculate that the thaumarchaeal ancestor was a mixotroph or even strict heterotroph (as also indicated by genomic and experimental data that deep branching clade I1c and d members in the Thaumarchaeota lack genes required for ammonia oxidation; Beam et al ., ; Lin et al ., ; Weber et al ., ), and that sponge Thaumarchaeota along with a few other members of this clade retained the capability to use amino acids due to specialized environmental conditions. Future experiments would need to demonstrate uptake of amino acids by Ca .…”

Contribution of ammonia oxidation to chemoautotrophy in Antarctic coastal waters

“…Assuming Redfield stoichiometry for labile organic matter (Redfield et al , 1963) and that ammonium release is linked to complete oxidation of that organic matter, 6.6 mol of C must be mineralized per mole of ammonium regenerated. For each mole of Thaumarchaeota biomass C produced, ~27 mol of ammonia are oxidized by Thaumarchaeota; thus, 178 mol of labile organic C must be oxidized to support chemoautotrophic production of 1 mol of Thaumarchaeota C, unless AOA are mixotrophic or heterotrophic (Spang et al , 2012; Qin et al , 2014; Lin et al , 2015) or they are able to access other forms of reduced nitrogen (e.g., organic nitrogen in urea or other small molecules) more directly. Note that chemoautotrophy fueled by AO is not ‘new production', sensu Eppley and Peterson (1979), even though carbon is being fixed: since AO depends on a source of reduced N supplied by organic matter mineralization, at an ecosystem level it is part of a net oxidative process (Smith and Hollibaugh, 1989).…”

Plant Community and Nitrogen Deposition as Drivers of Alpha and Beta Diversities of Prokaryotes in Reconstructed Oil Sand Soils and Natural Boreal Forest Soils

“…However, the soil Crenarchaeotic group only comprised 9% of the Thaumarchaeota sequences in the natural soils. All known members of the soil Crenarchaeotic group are autotrophic ammonia-oxidizing archaea (AOA) (46,47). Nicol et al demonstrated that the abundance of the bacterial amoA gene (one of the genes responsible for ammonia oxidation) declined under acidic conditions, while the archaeal amoA gene abundance increased in acidic conditions, demonstrating the potential importance of archaea (and especially of Thermoarchaeota) for N cycling in acidic soils (48).…”