Nitrosopumilus maritimus gen. nov., sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., four marine ammonia-oxidizing archaea of the phylum Thaumarchaeota

Qin, Wei; Heal, Katherine R.; Ramdasi, Rasika; Kobelt, Julia N.; Martens‐Habbena, Willm; Bertagnolli, Anthony D.; Amin, Shady A.; Walker, Christopher B.; Urakawa, Hidetoshi; Könneke, Martin; Devol, Allan H.; Moffett, James W.; Armbrust, E. Virginia; Jensen, Grant J.; Ingalls, Anitra E.; Stahl, David A.

doi:10.1099/ijsem.0.002416

Cited by 172 publications

(131 citation statements)

References 81 publications

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“…Sediment samples collected from the SCTLD epidemic zone had significantly higher relative abundances of the family Nitrosopumilaceae compared to both endemic and vulnerable zones (Figure 3C). Nitrosopumilaceae consist of a group of ammonia-oxidizing archaea (Qin et al, 2017) commonly found in marine environments (Gajigan et al, 2018;He et al, 2018) and are positively correlated with high levels of nitrite and nitrate (Gajigan et al, 2018). Nitrosopumilaceae is likely not directly responsible for SCTLD, but this group of archaea may signify environmental conditions that promote the prevalence of SCTLD, or could be a secondary response to disease occurrence in the reef.…”

Section: Potential Microbial Signatures Associated With Sctld Outbreamentioning

confidence: 99%

Rhodobacterales and Rhizobiales Are Associated With Stony Coral Tissue Loss Disease and Its Suspected Sources of Transmission

et al. 2020

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In 2014, Stony Coral Tissue Loss Disease (SCTLD) was first detected off the coast of Miami, FL, United States, and continues to persist and spread along the Florida Reef Tractr (FRT) and into the Caribbean. SCTLD can have up to a 61% prevalence in reefs and has affected at least 23 species of scleractinian corals. This has contributed to the regional near-extinction of at least one coral species, Dendrogyra cylindrus. Initial studies of SCTLD indicate microbial community shifts and cessation of lesion progression in response to antibiotics on some colonies. However, the etiology and abiotic sources of SCTLD transmission are unknown. To characterize SCTLD microbial signatures, we collected tissue samples from four affected coral species: Stephanocoenia intersepta, Diploria labyrinthiformis, Dichocoenia stokesii, and Meandrina meandrites. Tissue samples were from apparently healthy (AH) corals, and unaffected tissue (DU) and lesion tissue (DL) on diseased corals. Samples were collected in June 2018 from three zones: (1) vulnerable (ahead of the SCTLD disease boundary in the Lower Florida Keys), (2) endemic (post-outbreak in the Upper Florida Keys), and (3) epidemic (SCTLD was active and prevalent in the Middle Florida Keys). From each zone, sediment and water samples were also collected to identify whether they may serve as potential sources of transmission for SCTLD-associated microbes. We used 16S rRNA gene amplicon highthroughput sequencing methods to characterize the microbiomes of the coral, water, and sediment samples. We identified a relatively higher abundance of the bacteria orders Rhodobacterales and Rhizobiales in DL tissue compared to AH and DU tissue. Also, our results showed relatively higher abundances of Rhodobacterales in water from the endemic and epidemic zones compared to the vulnerable zone. Rhodobacterales and Rhizobiales identified at higher relative abundances in DL samples were also detected in sediment samples, but not in water samples. Our data indicate that Rhodobacterales and Rhizobiales may play a role in SCTLD and that sediment may be a source of transmission for Rhodobacterales and Rhizobiales associated with SCTLD lesions.

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Section: Potential Microbial Signatures Associated With Sctld Outbreamentioning

confidence: 99%

Rhodobacterales and Rhizobiales Are Associated With Stony Coral Tissue Loss Disease and Its Suspected Sources of Transmission

et al. 2020

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“…Relatively little is known about the biogeochemical cycling of DON compared to that of dissolved inorganic nitrogen (predominately ammonium, nitrite, and nitrate). Recent reports show that some cultivated Thaumarchaeota can grow by oxidizing the N in urea (Tourna et al ; Bayer et al ; Qin et al ; Carini et al ) or cyanate (Palatinszky et al ), that Thaumarchaeota in the coastal Arctic Ocean can assimilate significant amounts of urea‐N into DNA (Connelly et al ), and that thaumarchaeal ureC genes are present in many ocean basins (Yakimov et al ; Alonso‐Sáez et al ; Smith et al ; Tolar et al ). These observations suggest that some organic N compounds can be oxidized by nitrifiers, verified by recent measurements of the contribution of urea‐derived N to nitrification in several Thaumarchaeota‐dominated nitrifier communities (Tolar et al ).…”

mentioning

confidence: 99%

Microbial oxidation of nitrogen supplied as selected organic nitrogen compounds in the South Atlantic Bight

Damashek

Tolar

Liu

et al. 2018

Limnology & Oceanography

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Dissolved organic nitrogen (DON) can account for a large fraction of the dissolved nitrogen (N) pool in the ocean, but the cycling of marine DON is poorly understood. Recent discoveries that urea-and cyanate-N can be oxidized by some strains of Thaumarchaeota suggest that these abundant microbes may be able to access and oxidize a fraction of the DON pool. However, measurements of the oxidation of N supplied as DON compounds are scarce. Here, we compare oxidation rates of N supplied as a variety of DON compounds in samples from Georgia coastal waters, where nitrifier communities are numerically dominated by Thaumarchaeota. Our data indicate that polyamine-N is particularly amenable to oxidation compared to the other DON compounds tested. Oxidation of N supplied as putrescine (1,4-diaminobutane) was generally higher than that of N supplied as glutamate, arginine, or urea, and was consistently 5-10% of the ammonia oxidation rate. Our data also suggest that the oxidation rate of polyamine-N may increase as the length of the carbon skeleton increases. Oxidation of N supplied as putrescine, urea, and glutamate were all highest near the coast and lower further offshore, consistent with patterns of ammonia oxidation in these waters. Though it is unclear whether oxidation of polyamine-N reflects direct oxidation by Thaumarchaeota or combines remineralization and subsequent ammonia oxidation, more rapid oxidation of N from putrescine compared to amino acids or urea suggests that polyamine-N may contribute significantly to nitrification in the ocean.

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“…Pairwise relative phylogenetic distances between each genome were subjected to hierarchical clustering using single linkage Pearson correlation and taxonomic levels corresponding to class, order and family were defined as Pearson’s distances of less than 0.34, 0.13 and 0.015, respectively. These cut-off distances were chosen by comparison to existing thaumarchaeotal taxonomy 5-7, 55-63 . The taxonomic levels for genus and species levels were defined with AAI thresholds higher than 70% and 95%, respectively 64, 65 .…”

Section: Methodsmentioning

confidence: 99%

“…Ammonia oxidation is limited to a small number of microbial phyla but is one of the most important microbial metabolisms on the planet as it implements an essential and rate-limiting step in the nitrogen cycle, the conversion of ammonia to nitrite (via hydroxylamine). Within Thaumarchaeota, ammonia oxidising archaea (AOA) are ubiquitous and abundant in mesophilic soils and oceans, and are classically placed in four order-level phylogenetic lineages 1 : the Nitrososphaerales 4 , Nitrosopumilales 5 , Candidatus Nitrosotaleales 6 and Candidatus Nitrosocaldales 7 .…”

Section: Introductionmentioning

confidence: 99%

Gene duplication drives genome expansion in Thaumarchaeota

Sheridan

Raguideau

Quince

et al. 2020

Preprint

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13Ammonia-oxidising archaea of the phylum Thaumarchaeota are keystone species in global 14 nitrogen cycling. However, only three of the six known families of the terrestrially ubiquitous 15 order Nitrososphaerales possess representative genomes. Here we provide genomes for the 16 three remaining families and examine the impact of gene duplication, loss and transfer events 17 across the entire phylum. Much of the genomic divergence in this phylum is driven by gene 18 duplication and loss, but we also detected early lateral gene transfer that introduced 19 considerable proteome novelty. In particular, we identified two large gene transfer events into 20 Nitrososphaerales. The fate of gene families originating on these branches was highly lineage-21 specific, being lost in some descendant lineages, but undergoing extensive duplication in 22 others, suggesting niche-specific roles within soil and sediment environments. Overall, our 23 results suggest that lateral gene transfer followed by gene duplication drives Nitrososphaerales 24 evolution, highlighting a previously under-appreciated mechanism of genome expansion in 25 archaea. 26 27 73 provided a well-supported thaumarchaeotal phylogenomic tree (Figure 1), with most nodes 74 with UF bootstrap values > 95 % and SH-aLRT values > 95 %. This phylogenomic tree was 75 the best supported tree after comparison of several phylogenomic reconstruction 76 5methodologies (Supplementary Information: Extended phylogenomics). The tree is broadly 77 similar to previously published work 11 with some exceptions, mainly relating to poorly-78 supported basal branches in both trees (Supplementary Information: Extended phylogenomics). 79Previous classifications of Thaumarchaeota have been based on phylogenetic analyses of 80 the ammonia monooxygenase (amoA) gene, but this gene is not present in all members of the 81 phylum. We therefore suggest a phylum-wide thaumarchaeotal classification based on our 82 phylogenomic analysis that maintains maximum consistency with previous work while 83 incorporating the early-diverging lineages that lack amoA 2, 17, 18 (Table S2). Our genome dataset 84 of Thaumarchaeota represent a diverse phylum comprising 8 classes, 10 orders, 28 families, 31 85 genus and 103 species. While the classically used thaumarchaeotal nomenclature is congruent 86 with the taxonomic stratification, a few exceptions were observed. For example, the order 87 Nitrosopumilales encompasses Candidatus Nitrosotalea and Cenarchaeum, which were 88 previously suggested to represent orders of their own, and Nitrososphaerales contains a 89 minimum of 8 genera, with Ca. Nitrososphaera gargensis and Nitrososphaera viennensis and 90Ca. Nitrososphaera evergladensis belonging to different genera. 91 We also used the Genome Taxonomy Database Toolkit (GTDB-Tk) to evaluate the 92 genomic diversity of our 12 new MAGs. While one of these genomes (TH1173) is a close 93 relative of a published genome, MY3, the range of relative evolutionary divergence (RED) 19 94 values for the other 11 MA...

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Nitrosopumilus maritimus gen. nov., sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., four marine ammonia-oxidizing archaea of the phylum Thaumarchaeota

Abstract: Nitrosopumilus maritimus gen. nov., sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., four marine ammonia-oxidizing archaea of the phylum Thaumarchaeota

Cited by 172 publications

References 81 publications

Rhodobacterales and Rhizobiales Are Associated With Stony Coral Tissue Loss Disease and Its Suspected Sources of Transmission

Rhodobacterales and Rhizobiales Are Associated With Stony Coral Tissue Loss Disease and Its Suspected Sources of Transmission

Microbial oxidation of nitrogen supplied as selected organic nitrogen compounds in the South Atlantic Bight

Gene duplication drives genome expansion in Thaumarchaeota

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