Diverse Thaumarchaeota Dominate Subsurface Ammonia-oxidizing Communities in Semi-arid Floodplains in the Western United States

Cardarelli, E.; Bargar, John R.; Francis, Christopher A.

doi:10.1007/s00248-020-01534-5

Cited by 18 publications

(19 citation statements)

References 89 publications

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“…Although many Nitrospira can be found in lowoxygen (and possibly anoxic) habitats (e.g., Daims et al, 2001), they typically lack a fully anaerobic metabolism (Bock et al, 1995;Ehrich et al, 1995;Koch et al, 2014), so their presence and increased abundance plausibly indicates oxygen intrusion and a reversion from fully anaerobic conditions. Similarly, Thaumarchaeota -the primary ammonia-oxidizing group in this system (Cardarelli et al, 2020) catalyzing the critical step preceding nitrite oxidation during nitrification -having rapidly decreased in abundance post-flood in the four deepest soil layers (July 7; Supplementary Figure S7), recovered in abundance in late summer alongside the observed increase in Nitrospira sp. This suggests a return to nitrifying conditions in late summer, but further activity measurements would be needed to confirm this.…”

Section: Microbial Community Dynamicsmentioning

confidence: 94%

Stability of Floodplain Subsurface Microbial Communities Through Seasonal Hydrological and Geochemical Cycles

et al. 2020

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Riparian floodplains represent an interaction zone between the terrestrial subsurface and rivers, where regional groundwater flows, infiltration, and evapotranspiration drive mixing of water and import/export of nutrients and contaminants. These dynamics create seasonally transient redox conditions that drive biogeochemical transformations, which strongly modify groundwater quality. Microbial responses to changing hydrological conditions are perhaps the critical step connecting hydrology to geochemical transformations and groundwater quality, yet are not well understood. We aimed to address this knowledge gap by monitoring seasonal transitions at the United States Department of Energy legacy uranium ore processing site in Riverton, WY, through spring-summer-fall hydrological transitions. Our goal was to characterize the microbial community throughout the soil profile, down to the saturated aquifer, and observe its response to wet-dry transitions across a full season and compare to changes in geochemistry and hydrology. Next-generation sequencing was employed to identify biogeochemically relevant microbial taxa based on the 16S rRNA gene; we found a broad diversity of microbial clades including taxa involved in sulfur and metal cycling, as well as nitrification. These data were paired with measurements of soil moisture, major nutrients and cations, and trace elements. Overall microbial community composition was dependent on soil depth or type, with seasonal effects only observed in the topsoil or subsurface aquifer. This finding indicates that microbial communities in the transiently reduced center of the soil profile at the Riverton, WY site are remarkably stable, despite moisture and redox inversions. In addition, these communities likely impact the communities in surrounding soil horizons through export of metabolites and solutes as the water table rises and falls throughout the season.

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Section: Microbial Community Dynamicsmentioning

confidence: 94%

Stability of Floodplain Subsurface Microbial Communities Through Seasonal Hydrological and Geochemical Cycles

et al. 2020

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“…Interestingly, Thaumarchaeota sequences were mainly affiliated with the Nitrosoarchaeum genus, as was only recently described with the novel species Nitrosoarchaeum koreense from agricultural soils [51,52]. To date, few reports are available on the detection of Nitrosoarchaeum sequences, including those related to N. limnium, and they refer to floodplains [51,53]. Among Euryarchaeota, the moderate occurrence of sequences related to extremely halophilic Halobacterium species suggests that the analyzed coffee compost experienced a large salinity phase.…”

Section: Metagenomic Analysis: 16s Rrna Gene Amplicon Sequencingmentioning

confidence: 95%

Prokaryotic Diversity of the Composting Thermophilic Phase: The Case of Ground Coffee Compost

et al. 2021

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Waste biomass coming from a local coffee company, which supplied burnt ground coffee after an incorrect roasting process, was employed as a starting material in the composting plant of the Experimental Station of the University of Naples Federico II at Castel Volturno (CE). The direct molecular characterization of compost using 13C-NMR spectra, which was acquired through cross-polarization magic-angle spinning, showed a hydrophobicity index of 2.7% and an alkyl/hydroxyalkyl index of 0.7%. Compost samples that were collected during the early “active thermophilic phase” (when the composting temperature was 63 °C) were analyzed for the prokaryotic community composition and activities. Two complementary approaches, i.e., genomic and predictive metabolic analysis of the 16S rRNA V3–V4 amplicon and culture-dependent analysis, were combined to identify the main microbial factors that characterized the composting process. The whole microbial community was dominated by Firmicutes. The predictive analysis of the metabolic functionality of the community highlighted the potential degradation of peptidoglycan and the ability of metal chelation, with both functions being extremely useful for the revitalization and fertilization of agricultural soils. Finally, three biotechnologically relevant Firmicutes members, i.e., Geobacillus thermodenitrificans subsp. calidus, Aeribacillus pallidus, and Ureibacillus terrenus (strains CAF1, CAF2, and CAF5, respectively) were isolated from the “active thermophilic phase” of the coffee composting. All strains were thermophiles growing at the optimal temperature of 60 °C. Our findings contribute to the current knowledge on thermophilic composting microbiology and valorize burnt ground coffee as waste material with biotechnological potentialities.

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“…As such, the majority of studies on the AOA community have focused on topsoil where O 2 is readily available to these microorganisms [ 8 , 9 ]. Constrained by O 2 availability, AOA communities only reach a depth of a little more than 2 m in floodplain sediments [ 2 ], while in the semi-arid floodplains of the western United States, AOA have been recovered from a depth of more than 10 m [ 10 ]. These studies observed great variations in the AOA community over depth [ 2 , 10 ].…”

Section: Introductionmentioning

confidence: 99%

“…Constrained by O 2 availability, AOA communities only reach a depth of a little more than 2 m in floodplain sediments [ 2 ], while in the semi-arid floodplains of the western United States, AOA have been recovered from a depth of more than 10 m [ 10 ]. These studies observed great variations in the AOA community over depth [ 2 , 10 ]. Beyond the parameter of O 2 , cultivation-based and cultivation-independent studies have extended the habitat of AOA from mesophilic environments to thermophilic environments, i.e., terrestrial hot springs [ 11 , 12 , 13 , 14 , 15 , 16 , 17 ].…”

Section: Introductionmentioning

confidence: 99%

High Abundance of Thaumarchaeota Found in Deep Metamorphic Subsurface in Eastern China

et al. 2022

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Members of the Thaumarchaeota phylum play a key role in nitrogen cycling and are prevalent in a variety of environments including soil, sediment, and seawater. However, few studies have shown the presence of Thaumarchaeota in the terrestrial deep subsurface. Using high-throughput 16S rRNA gene sequencing, this study presents evidence for the high relative abundance of Thaumarchaeota in a biofilm sample collected from the well of Chinese Continental Scientific Drilling at a depth of 2000 m. Phylogenetic analysis showed a close relationship of these thaumarchaeotal sequences with known ammonia-oxidizing archaea (AOA) isolates, suggesting the presence of AOA in the deep metamorphic environment of eastern China which is believed to be oxic. Based on fluid geochemistry and FAProTax functional prediction, a pathway of nitrogen cycling is proposed. Firstly, heterotrophic nitrogen fixation is executed by diazotrophic bacteria coupled with methane oxidation. Then, ammonia is oxidized to nitrite by AOA, and nitrite is further oxidized to nitrate by bacteria within the phylum Nitrospirae. Denitrification and anaerobic ammonia oxidation occur slowly, leading to nitrate accumulation in the subsurface. With respect to biogeochemistry, the reaction between downward diffusing O2 and upward diffusing CH4 potentially fuels the ecosystem with a high relative abundance of Thaumarchaeota.

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Diverse Thaumarchaeota Dominate Subsurface Ammonia-oxidizing Communities in Semi-arid Floodplains in the Western United States

Cited by 18 publications

References 89 publications

Stability of Floodplain Subsurface Microbial Communities Through Seasonal Hydrological and Geochemical Cycles

Stability of Floodplain Subsurface Microbial Communities Through Seasonal Hydrological and Geochemical Cycles

Prokaryotic Diversity of the Composting Thermophilic Phase: The Case of Ground Coffee Compost

High Abundance of Thaumarchaeota Found in Deep Metamorphic Subsurface in Eastern China

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