Light and temperature control the seasonal distribution of thaumarchaeota in the South Atlantic bight

Liu, Qian; Tolar, Bradley B.; Ross, Meredith; Cheek, J. B.; Sweeney, C. M.; Wallsgrove, Natalie J.; Popp, Brian N.; Hollibaugh, James T.

doi:10.1038/s41396-018-0066-4

Cited by 39 publications

(66 citation statements)

References 76 publications

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“…Samples were collected from four regions (inshore, mid‐shelf, shelf‐break, and oceanic) of the SAB off the Georgia (U.S.A.) coast (Fig. ; Supporting Information Table S1), with terminology modified from Liu et al () as follows. “Inshore” stations were within the barrier island complex.…”

Section: Methodsmentioning

confidence: 99%

“…Thaumarchaeota populations in deeper outer shelf and shelf‐break waters are primarily from the marine clades “Water Column A” (WCA) and “Water Column B” (WCB), considered shallow‐ and deep‐water ecotypes, respectively (Francis et al ; Beman et al ). There is less seasonal variability at these offshore locations (Liu et al ).…”

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confidence: 97%

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confidence: 99%

“…Previous work in the South Atlantic Bight (SAB) demonstrated a correlation between Thaumarchaeota abundance and ammonia oxidation rates, with highest rates at inshore stations and a subsurface maxima near the shelf‐break (Tolar et al ; Liu et al ). Ammonia‐oxidizing communities in the SAB are composed predominantly of Thaumarchaeota, but with important geographic differences in phylogenetic identity (Liu et al ). Thaumarchaeal populations in inshore waters around Sapelo Island are similar to the strain Nitrosopumilus maritimus SCM1 (16S, 99.4–99.6%; amoA , 91.2–98.8% nucleotide identity) and display a strong seasonal cycle of abundance, increasing > 3 orders of magnitude in the summer to dominate the ammonia‐oxidizing microbial population (Hollibaugh et al , ; Whitby et al ; Liu et al ).…”

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confidence: 99%

“…Ammonia‐oxidizing communities in the SAB are composed predominantly of Thaumarchaeota, but with important geographic differences in phylogenetic identity (Liu et al ). Thaumarchaeal populations in inshore waters around Sapelo Island are similar to the strain Nitrosopumilus maritimus SCM1 (16S, 99.4–99.6%; amoA , 91.2–98.8% nucleotide identity) and display a strong seasonal cycle of abundance, increasing > 3 orders of magnitude in the summer to dominate the ammonia‐oxidizing microbial population (Hollibaugh et al , ; Whitby et al ; Liu et al ). Thaumarchaeota populations in shallow nearshore waters over the continental shelf show high diversity, including Nitrosopumilus ‐like, Nitrosoarchaeum ‐like, and group 1.1b Archaea (Liu et al ).…”

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confidence: 99%

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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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Section: Methodsmentioning

confidence: 99%

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confidence: 97%

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confidence: 99%

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confidence: 99%

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confidence: 99%

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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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Candidatus Nitrosopelagicus

Santoro¹,

Bayer²,

Elling³

et al. 2021

Bergey's Manual of Systematics of Archaea and Bacteria

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Ni.tro.so.pe.la'gi.cus. N.L. masc. adj. nitrosus nitrous; L. masc. adj. pelagicus of the open sea; N.L. masc. n. Nitrosopelagicus a nitrite producer of the open sea. Thermoproteota / Nitrososphaeria / Nitrososphaerales / Nitrosopumilaceae / Candidatus Nitrosopelagicus The genus Candidatus Nitrosopelagicus is composed of marine ammonia‐oxidizing archaea, almost all of which are uncultivated. They are found in shallow waters (<200 m depth) of the oligotrophic tropical, subtropical, and temperate open oceans. A single species has been described, Candidatus Nitrosopelagicus brevis, which couples growth with the oxidation of ammonia to nitrite. One described strain ( Ca . N. brevis U25) is capable of hydrolyzing urea to supply the ammonia required for growth. Cells are obligately aerobic, small, and nonmotile rods. They grow free‐living, not associated with surfaces. No growth enhancement has been observed in the presence of organic carbon compounds; a reduction in the lag phase of growth has been observed with addition of α‐ketoacids, potentially serving as radical oxygen scavengers. Organisms are mesophilic and obligately marine. Lipid composition distinguishes Ca . Nitrosopelagicus from Nitrosopumilus using glycerol dibiphytanyl glycerol tetraether (GDGT) distributions, with lower amounts of GDGT‐2 and higher amounts of GDGT‐0 and GDGT‐1 found in Ca . Nitrosopelagicus. Abundance of Ca . Nitrospelagicus‐like organisms is correlated with nitrification rates, suggesting that these organisms are the dominant ammonia oxidizers in epipelagic and upper mesopelagic environments of the low‐ and mid‐latitude open oceans. DNA G + C content (mol%) : 33.1. Type species : Candidatus Nitrosopelagicus brevis Santoro et al. 2015.

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Time series assessment of Thaumarchaeota ecotypes in Monterey Bay reveals the importance of water column position in predicting distribution–environment relationships

Tolar

Reji

Smith

et al. 2020

Limnology & Oceanography

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Nitrification plays a key role in marine ecosystems where Thaumarchaeota are thought to be responsible for most of the ammonia oxidation in the water column. Over a 2‐yr, near‐monthly time series at two sites in Monterey Bay we observed repeatable seasonal and depth‐based patterns of Thaumarchaeota ecotype abundance that highlighted a clear delineation between populations in shallow euphotic (< 50 m) vs. deeper mesopelagic (60–500 m) depths. Euphotic depths show greater seasonality and influence from light, while mesopelagic waters have trends based on water mass and other covarying features with depth. Three major ecotypes were recovered: a Nitrosopumilus‐like (NP) group, a Nitrosopelagicus‐like ecotype containing “shallow” water column A (WCA) members, and an ecotype affiliated with the “deep” water column B (WCB) Thaumarchaeota. These ecotypes show a strong depth distribution, with WCB dominant at ≥ 200 m depth and WCA most abundant in surface (5–100 m) waters. The NP ecotype was found throughout the water column with the highest abundance in summer, and was the only ecotype showing a correlation with measured nitrification rates. We also found three abundant taxa related to Nitrospina—the major nitrite‐oxidizing bacteria in the ocean; these showed clear connections to each of the three Thaumarchaeota ecotypes, suggesting a specific relationship between both steps of nitrification. Our results support the importance of ecotype‐based analysis of Thaumarchaeota and show that their abundance and distribution are controlled based on their water column position, with a distinct shift at 50 m between euphotic and mesopelagic depths.

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Light and temperature control the seasonal distribution of thaumarchaeota in the South Atlantic bight

Cited by 39 publications

References 76 publications

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

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

Candidatus Nitrosopelagicus

Time series assessment of Thaumarchaeota ecotypes in Monterey Bay reveals the importance of water column position in predicting distribution–environment relationships

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