Aerobic heterotrophy and RuBisCO-mediated CO₂metabolism in marineThaumarchaeota

Abstract

1Thaumarchaeota constitute an abundant and ubiquitous phylum of Archaea that play critical 2 roles in the global nitrogen and carbon cycles. Most well-characterized members of the phylum 3 are chemolithoautotrophic ammonia-oxidizing archaea (AOA), which comprise up to 5 and 20 % 4 of the total single-celled life in soil and marine systems, respectively. Using two high-quality 5 metagenome-assembled genomes (MAGs), here we describe a divergent marine thaumarchaeal 6 clade that is devoid of the ammonia-oxidation machinery and the AOA-specific carbon-fixation 7 pathway. Phylogenomic analyses placed these genomes within the uncultivated and largely 8 understudied marine pSL12-like thaumarchaeal clade. The predominant mode of nutrient 9 acquisition appears to be aerobic heterotrophy, evidenced by the presence of respiratory 10 complexes and various organic carbon degradation pathways. Unexpectedly, both genomes 11 encoded a form III RuBisCO. Genomic composition of the MAGs is consistent with the role of 12RuBisCO in nucleotide salvage, as has been proposed previously for archaea harboring the form 13 III variant. Metabolic reconstructions revealed a complete nonoxidative pentose phosphate 14 pathway (PPP) and gluconeogenesis, which can cyclize the RuBisCO-mediated carbon metabolic 15 pathway. We conclude that these genomes represent a hitherto unrecognized evolutionary link 16 between predominantly anaerobic basal thaumarchaeal lineages and mesophilic marine AOA, 17 with important implications for diversification within the phylum Thaumarchaeota. 18

Heterotrophic Thaumarchaea with Small Genomes Are Widespread in the Dark Ocean

“…The presence of a large-subunit RuBisCO homolog (rbcL) in the HMT genomes is a notable feature of this group. We identified this gene in 4 of 5 HMT MAGs (missing only in HMT_AABW); it is also present in the ASW8 MAG, as previously reported (24). A phylogenetic analysis of the HMT RuBisCO homologs placed it with other form III-a members of this protein family, albeit with long branches that demonstrate it is divergent from any previously identified homolog (Fig.…”

“…However, AMPase, a key enzyme of the AMP salvage pathway responsible for generating R15P, could not be identified in the HMT genomes. This was also reported for the ASW8 MAG (24), where those authors suggested that R15P is generated from phosphoribosyl pyrophosphate by a Nudix hydrolase. Homologs for all genes in this proposed pathway cyclization are present in the HMT genomes (Fig.…”

“…S1 in the supplemental material). The reference genome UBA57, which was previously assembled from a Mid-Cayman Rise metagenome as part of a large-scale genomes-from-metagenomes workflow (23), also fell within the HMT group, as did the ASW8 MAG, which was recently assembled from a Monterey Bay metagenome (24) (Table 1 and Fig. S1).…”

“…These results suggest that HMT are globally distributed but comprise a relatively small fraction of the thaumarchaeal population in the dark ocean compared to AOA. A recent study identified the presence of the ASW8 MAG genome in Monterey Bay (depths of 5 to 500 m) and reported that it represented abundances of Ͻ0.5% of the total thaumarchaeal population (24), further suggesting that this group comprises a relatively small fraction of total archaea in shallow waters.…”