Heterotrophic Thaumarchaea with Small Genomes Are Widespread in the Dark Ocean
ABSTRACT The Thaumarchaeota is a diverse archaeal phylum comprising numerous lineages that play key roles in global biogeochemical cycling, particularly in the ocean. To date, all genomically characterized marine thaumarchaea are reported to be chemolithoautotrophic ammonia oxidizers. In this study,...
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2020-06-01
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| Series: | mSystems |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/mSystems.00415-20 |
| _version_ | 1818347224268013568 |
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| author | Frank O. Aylward Alyson E. Santoro |
| author_facet | Frank O. Aylward Alyson E. Santoro |
| author_sort | Frank O. Aylward |
| collection | DOAJ |
| description | ABSTRACT The Thaumarchaeota is a diverse archaeal phylum comprising numerous lineages that play key roles in global biogeochemical cycling, particularly in the ocean. To date, all genomically characterized marine thaumarchaea are reported to be chemolithoautotrophic ammonia oxidizers. In this study, we report a group of putatively heterotrophic marine thaumarchaea (HMT) with small genome sizes that is globally abundant in the mesopelagic, apparently lacking the ability to oxidize ammonia. We assembled five HMT genomes from metagenomic data and show that they form a deeply branching sister lineage to the ammonia-oxidizing archaea (AOA). We identify this group in metagenomes from mesopelagic waters in all major ocean basins, with abundances reaching up to 6% of that of AOA. Surprisingly, we predict the HMT have small genomes of ∼1 Mbp, and our ancestral state reconstruction indicates this lineage has undergone substantial genome reduction compared to other related archaea. The genomic repertoire of HMT indicates a versatile metabolism for aerobic chemoorganoheterotrophy that includes a divergent form III-a RuBisCO, a 2M respiratory complex I that has been hypothesized to increase energetic efficiency, and a three-subunit heme-copper oxidase complex IV that is absent from AOA. We also identify 21 pyrroloquinoline quinone (PQQ)-dependent dehydrogenases that are predicted to supply reducing equivalents to the electron transport chain and are among the most highly expressed HMT genes, suggesting these enzymes play an important role in the physiology of this group. Our results suggest that heterotrophic members of the Thaumarchaeota are widespread in the ocean and potentially play key roles in global chemical transformations. IMPORTANCE It has been known for many years that marine Thaumarchaeota are abundant constituents of dark ocean microbial communities, where their ability to couple ammonia oxidation and carbon fixation plays a critical role in nutrient dynamics. In this study, we describe an abundant group of putatively heterotrophic marine Thaumarchaeota (HMT) in the ocean with physiology distinct from those of their ammonia-oxidizing relatives. HMT lack the ability to oxidize ammonia and fix carbon via the 3-hydroxypropionate/4-hydroxybutyrate pathway but instead encode a form III-a RuBisCO and diverse PQQ-dependent dehydrogenases that are likely used to conserve energy in the dark ocean. Our work expands the scope of known diversity of Thaumarchaeota in the ocean and provides important insight into a widespread marine lineage. |
| first_indexed | 2024-12-13T17:30:46Z |
| format | Article |
| id | doaj.art-8c921349eaf64a87a4e7a0e516b18324 |
| institution | Directory Open Access Journal |
| issn | 2379-5077 |
| language | English |
| last_indexed | 2024-12-13T17:30:46Z |
| publishDate | 2020-06-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mSystems |
| spelling | doaj.art-8c921349eaf64a87a4e7a0e516b183242022-12-21T23:37:04ZengAmerican Society for MicrobiologymSystems2379-50772020-06-015310.1128/mSystems.00415-20Heterotrophic Thaumarchaea with Small Genomes Are Widespread in the Dark OceanFrank O. Aylward0Alyson E. Santoro1Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USADepartment of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California, USAABSTRACT The Thaumarchaeota is a diverse archaeal phylum comprising numerous lineages that play key roles in global biogeochemical cycling, particularly in the ocean. To date, all genomically characterized marine thaumarchaea are reported to be chemolithoautotrophic ammonia oxidizers. In this study, we report a group of putatively heterotrophic marine thaumarchaea (HMT) with small genome sizes that is globally abundant in the mesopelagic, apparently lacking the ability to oxidize ammonia. We assembled five HMT genomes from metagenomic data and show that they form a deeply branching sister lineage to the ammonia-oxidizing archaea (AOA). We identify this group in metagenomes from mesopelagic waters in all major ocean basins, with abundances reaching up to 6% of that of AOA. Surprisingly, we predict the HMT have small genomes of ∼1 Mbp, and our ancestral state reconstruction indicates this lineage has undergone substantial genome reduction compared to other related archaea. The genomic repertoire of HMT indicates a versatile metabolism for aerobic chemoorganoheterotrophy that includes a divergent form III-a RuBisCO, a 2M respiratory complex I that has been hypothesized to increase energetic efficiency, and a three-subunit heme-copper oxidase complex IV that is absent from AOA. We also identify 21 pyrroloquinoline quinone (PQQ)-dependent dehydrogenases that are predicted to supply reducing equivalents to the electron transport chain and are among the most highly expressed HMT genes, suggesting these enzymes play an important role in the physiology of this group. Our results suggest that heterotrophic members of the Thaumarchaeota are widespread in the ocean and potentially play key roles in global chemical transformations. IMPORTANCE It has been known for many years that marine Thaumarchaeota are abundant constituents of dark ocean microbial communities, where their ability to couple ammonia oxidation and carbon fixation plays a critical role in nutrient dynamics. In this study, we describe an abundant group of putatively heterotrophic marine Thaumarchaeota (HMT) in the ocean with physiology distinct from those of their ammonia-oxidizing relatives. HMT lack the ability to oxidize ammonia and fix carbon via the 3-hydroxypropionate/4-hydroxybutyrate pathway but instead encode a form III-a RuBisCO and diverse PQQ-dependent dehydrogenases that are likely used to conserve energy in the dark ocean. Our work expands the scope of known diversity of Thaumarchaeota in the ocean and provides important insight into a widespread marine lineage.https://journals.asm.org/doi/10.1128/mSystems.00415-20Thaumarchaeotamarine archaeaTACKPQQ-dehydrogenaseRuBisCO |
| spellingShingle | Frank O. Aylward Alyson E. Santoro Heterotrophic Thaumarchaea with Small Genomes Are Widespread in the Dark Ocean mSystems Thaumarchaeota marine archaea TACK PQQ-dehydrogenase RuBisCO |
| title | Heterotrophic Thaumarchaea with Small Genomes Are Widespread in the Dark Ocean |
| title_full | Heterotrophic Thaumarchaea with Small Genomes Are Widespread in the Dark Ocean |
| title_fullStr | Heterotrophic Thaumarchaea with Small Genomes Are Widespread in the Dark Ocean |
| title_full_unstemmed | Heterotrophic Thaumarchaea with Small Genomes Are Widespread in the Dark Ocean |
| title_short | Heterotrophic Thaumarchaea with Small Genomes Are Widespread in the Dark Ocean |
| title_sort | heterotrophic thaumarchaea with small genomes are widespread in the dark ocean |
| topic | Thaumarchaeota marine archaea TACK PQQ-dehydrogenase RuBisCO |
| url | https://journals.asm.org/doi/10.1128/mSystems.00415-20 |
| work_keys_str_mv | AT frankoaylward heterotrophicthaumarchaeawithsmallgenomesarewidespreadinthedarkocean AT alysonesantoro heterotrophicthaumarchaeawithsmallgenomesarewidespreadinthedarkocean |