Competition for Ammonia Influences the Structure of Chemotrophic Communities in Geothermal Springs

Abstract

Source waters sampled from Perpetual Spouter hot spring (pH 7.03, 86.4°C), Yellowstone National Park, WY, have low concentrations of total ammonia, nitrite, and nitrate, suggesting nitrogen (N) limitation and/or tight coupling of N cycling processes. Dominant small-subunit rRNA sequences in Perpetual Spouter source sediments are closely affiliated with the ammonia-oxidizing archaeon "Candidatus Nitrosocaldus yellowstonii" and the putatively nitrogen-fixing (diazotrophic) bacterium Thermocrinis albus, respectively, suggesting that these populations may interact at the level of the bioavailable N pool, specifically, ammonia. This hypothesis was evaluated by using a combination of geochemical, physiological, and transcriptomic analyses of sediment microcosms. Amendment of microcosms with allylthiourea, an inhibitor of ammonia oxidation, decreased rates of acetylene reduction (a proxy for N 2 fixation) and nitrite production (a proxy for ammonia oxidation) and decreased transcript levels of structural genes involved in both nitrogen fixation (nifH) and ammonia oxidation (amoA). In contrast, amendment of microcosms with ammonia stimulated nitrite production and increased amoA transcript levels while it suppressed rates of acetylene reduction and decreased nifH transcript levels. Sequencing of amplified nifH and amoA transcripts from native sediments, as well as microcosms, at 2 and 4 h postamendment, indicates that the dominant and responsive populations involved in ammonia oxidation and N 2 fixation are closely affiliated with Ca. Nitrosocaldus yellowstonii and T. albus, respectively. Collectively, these results suggest that ammonia-oxidizing archaea, such as Ca. Nitrosocaldus yellowstonii, have an apparent affinity for ammonia that is higher than that of the diazotrophs present in this ecosystem. Depletion of the bioavailable N pool through the activity of ammonia-oxidizing archaea likely represents a strong selective pressure for the inclusion of organisms capable of nitrogen fixation in geothermal communities. These observations help to explain the strong pattern in the codistribution of ammonia-oxidizing archaea and diazotrophs in circumneutral-to-alkaline geothermal springs.

Greater temporal changes of sediment microbial community than its waterborne counterpart in Tengchong hot springs, Yunnan Province, China

“…Overall, these results confirmed that time-course changes of microbial species were associated with the changing environmental conditions49. These results are consistent with previous studies in hot springs that microbial community structure and diversity in hot springs were significantly affected by physicochemical parameters such as pH, temperature and water/sediments chemistry3491019355051525354.…”

Illumina sequencing‐based analysis of sediment bacteria community in different trophic status freshwater lakes

“…The high content of NO x − ‐N in region A‐3 in fall directly controls the abundance of bacteria in the taxa of Oxalobacteraceae , Pseudomonadaceae , Flavobacteriaceae , and Bacillales (Figure ) because those bacteria are involved in the transformation of NO x ‐N (Gaspar, Ferreira, Gonzalez, da Clara, & Santana, ; Choi, Lee, & Cha, ; Jung et al., ; Dodsworth, Hungate, & Hedlund, ). In summer, the average value of NH 4 + ‐N in pore water (2.4 mg L −1 ) is higher than other three seasons (Figure ), and the higher concentration of NH 4 + ‐N in pore water promotes the growth of Nitrospirales (Figure ) because the metabolism of this bacteria needs the input of NH 4 + ‐N (Hamilton et al., ), higher abundances of Nitrospirales contributed to the higher NH 4 + ‐N transformation efficiencies (Zhong et al., ). The content of TOM is more than 45 g kg −1 in winter and less than 20 g kg −1 in other three seasons (Figure ), the increase of TOM in winter directly influence the abundance of Cloacibacterium (Figure ), because these bacteria participate in organic matter degradation, and TOM provide nutrient for the growth of Cloacibacterium (Bauer et al., ).…”

Geochemistry and microbial community composition across a range of acid mine drainage impact and implications for the Neoarchean‐Paleoproterozoic transition

“…Water, biofilms, sediment, and contextual samples (soil, leaf litter, and coal) were collected as described previously [ Havig , ; Havig et al , ; Hamilton et al , ]. In short, at the time of water sampling, pH, conductivity, dissolved oxygen (DO), and temperature were measured using an Extech Instruments DO700 meter (Extech Instruments Corporation, Nashua, NH, USA).…”