Nitrogen Isotope Fractionation During Archaeal Ammonia Oxidation: Coupled Estimates From Measurements of Residual Ammonium and Accumulated Nitrite

The naturally occurring nitrogen (N) isotopes,N-15 and(14)N, exhibit different reaction rates during many microbial N transformation processes, which results in N isotope fractionation. Such isotope effects are critical parameters for interpreting natural stable isotope abundances as proxies for biological process rates in the environment across scales. The kinetic isotope effect of ammonia oxidation (AO) to nitrite (NO2-), performed by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), is generally ascribed to the enzyme ammonia monooxygenase (AMO), which catalyzes the first step in this process. However, the kinetic isotope effect of AMO, or epsilon(AMO), has been typically determined based on isotope kinetics during product formation (cumulative product, NO2-) alone, which may have overestimated epsilon(AMO)due to possible accumulation of chemical intermediates and alternative sinks of ammonia/ammonium (NH3/NH4+). Here, we analyzed(15)N isotope fractionation during archaeal ammonia oxidation based on both isotopic changes in residual substrate (RS, NH4+) and cumulative product (CP, NO2-) pools in pure cultures of the soil strainNitrososphaera viennensisEN76 and in highly enriched cultures of the marine strainNitrosopumilus adriaticusNF5, under non-limiting substrate conditions. We obtained epsilon(AMO)values of 31.9-33.1 parts per thousand for both strains based on RS (delta(NH4+)-N-15) and showed that estimates based on CP (delta(NO2-)-N-15) give larger isotope fractionation factors by 6-8 parts per thousand. Complementary analyses showed that, at the end of the growth period, microbial biomass was(15)N-enriched (10.1 parts per thousand), whereas nitrous oxide (N2O) was highly(15)N depleted (-38.1 parts per thousand) relative to the initial substrate. Although we did not determine the isotope effect of NH(4)(+)assimilation (biomass formation) and N2O production by AOA, our results nevertheless show that the discrepancy between epsilon(AMO)estimates based on RS and CP might have derived from the incorporation of(15)N-enriched residual NH(4)(+)after AMO reaction into microbial biomass and that N2O production did not affect isotope fractionation estimates significantly

Inhibitory Effects of C₂ to C₁₀ 1-Alkynes on Ammonia Oxidation in Two Nitrososphaera Species

A previous study showed that ammonia oxidation by the Thaumarchaeota Nitrosopumilus maritimus (group 1.1a) was resistant to concentrations of the C₈ 1-alkyne, octyne, which completely inhibits activity by ammonia-oxidizing bacteria. In this study, the inhibitory effects of octyne and other C₂ to C₁₀ 1-alkynes were evaluated on the nitrite production activity of two pure culture isolates from Thaumarchaeota group 1.1b, Nitrososphaera viennensis strain EN76 and Nitrososphaera gargensis. Both N. viennensis and N. gargensis were insensitive to concentrations of octyne that cause complete and irreversible inactivation of nitrite production by ammonia-oxidizing bacteria. However, octyne concentrations (≥20 μM) that did not inhibit N. maritimus partially inhibited nitrite production in N. viennensis and N. gargensis in a manner that did not show the characteristics of irreversible inactivation. In contrast to previous studies with an ammonia-oxidizing bacterium, Nitrosomonas europaea, octyne inhibition of N. viennensis was: (i) fully and immediately reversible, (ii) not competitive with NH₄⁺, and (iii) without effect on the competitive interaction between NH₄⁺ and acetylene. Both N. viennensis and N. gargensis demonstrated the same overall trend in regard to 1-alkyne inhibition as previously observed for N. maritimus, being highly sensitive to ≤C₅ alkynes and more resistant to longer-chain length alkynes. Reproducible differences were observed among N. maritimus, N. viennensis, and N. gargensis in regard to the extent of their resistance/sensitivity to C₆ and C₇ 1-alkynes, which may indicate differences in the ammonia monooxygenase binding and catalytic site(s) among the Thaumarchaeota

Схиигумен Сергий как маргинальная языковая личность в пространстве религиозно-политической коммуникации

SummaryThaumarchaeota are globally distributed and abundantmicroorganisms occurring in diverse habitats and thusrepresent a major source of archaeal lipids. The scopeof lipids as taxonomic markers in microbial ecologicalstudies is limited by the scarcity of comparative dataon the membrane lipid composition of cultivated representatives,including the phylum Thaumarchaeota.Here, we comprehensively describe the core and intactpolar lipid (IPL) inventory of ten ammonia-oxidisingthaumarchaeal cultures representing all four characterizedphylogenetic clades. IPLs of these thaumarchaealstrains are generally similar and consist of membranespanning,glycerol dibiphytanyl glycerol tetraetherswith monoglycosyl, diglycosyl, phosphohexose andhexose-phosphohexose headgroups. However, the relativeabundances of these IPLs and their core lipidcompositions differ systematically between the phylogeneticsubgroups, indicating high potential forchemotaxonomic distinction of thaumarchaeal clades.Comparative lipidomic analyses of 19 euryarchaeal andcrenarchaeal strains suggested that the lipid methoxyarchaeol is synthesized exclusively by Thaumarchaeotaand may thus represent a diagnostic lipidbiomarker for this phylum. The unprecedented diversityof the thaumarchaeal lipidome with 118 differentlipids suggests that membrane lipid composition andadaptation mechanisms in Thaumarchaeota are morecomplex than previously thought and include uniquelipids with as yet unresolved properties

Differential depth distribution of microbial function and putative symbionts through sediment- hosted aquifers in the deep terrestrial subsurface

An enormous diversity of previously unknown bacteria and archaea has been discovered recently, yet their functional capacities and distributions in the terrestrial subsurface remain uncertain. Here, we continually sampled a CO2-driven geyser (Colorado Plateau, Utah, USA) over its 5-day eruption cycle to test the hypothesis that stratified, sandstone-hosted aquifers sampled over three phases of the eruption cycle have microbial communities that differ both in membership and function. Genome-resolved metagenomics, single-cell genomics and geochemical analyses confirmed this hypothesis and linked microorganisms to groundwater compositions from different depths. Autotrophic Candidatus "Altiarchaeum sp." and phylogenetically deep-branching nanoarchaea dominate the deepest groundwater. A nanoarchaeon with limited metabolic capacity is inferred to be a potential symbiont of the Ca. "Altiarchaeum". Candidate Phyla Radiation bacteria are also present in the deepest groundwater and they are relatively abundant in water from intermediate depths. During the recovery phase of the geyser, microaerophilic Fe-and S-oxidizers have high in situ genome replication rates. Autotrophic Sulfurimonas sustained by aerobic sulfide oxidation and with the capacity for N-2 fixation dominate the shallow aquifer. Overall, 104 different phylum-level lineages are present in water from these subsurface environments, with uncultivated archaea and bacteria partitioned to the deeper subsurface

The consequences of niche and physiological differentiation of archaeal and bacterial ammonia oxidisers for nitrous oxide emissions

The authors are members of the Nitrous Oxide Research Alliance (NORA), a Marie Skłodowska-Curie ITN and research project under the EU's seventh framework program (FP7). GN is funded by the AXA Research Fund and CGR by a Royal Society University Research Fellowship (UF150571) and a Natural Environment Research Council (NERC) Standard Grant (NE/K016342/1). The authors would like to thank Dr Robin Walker and the SRUC Craibstone Estate (Aberdeen) for access to the agricultural plots, Dr Alex Douglas for statistical advice and Philipp Schleusner for assisting microcosm construction and sampling.Peer reviewedPublisher PD

Isotopic techniques to measure N2O, N2 and their sources

GHG emissions are usually the result of several simultaneous processes. Furthermore, some gases such as N2 are very difficult to quantify and require special techniques. Therefore, in this chapter, the focus is on stable isotope methods. Both natural abundance techniques and enrichment techniques are used. Especially in the last decade, a number of methodological advances have been made. Thus, this chapter provides an overview and description of a number of current state-of-theart techniques, especially techniques using the stable isotope 15N. Basic principles and recent advances of the 15N gas flux method are presented to quantify N2 fluxes, but also the latest isotopologue and isotopomer methods to identify pathways for N2O production. The second part of the chapter is devoted to 15N tracing techniques, the theoretical background and recent methodological advances. A range of different methods is presented from analytical to numerical tools to identify and quantify pathway-specific N2O emissions. While this chapter is chiefly concerned with gaseous N emissions, a lot of the techniques can also be applied to other gases such as methane (CH4), as outlined in Sect. 5.3

The responses of an anaerobic microorganism, Yersinia intermedia MASE-LG-1 to individual and combined simulated Martian stresses

The limits of life of aerobic microorganisms are well understood, but the responses of anaerobic microorganisms to individual and combined extreme stressors are less well known. Motivated by an interest in understanding the survivability of anaerobic microorganisms under Martian conditions, we investigated the responses of a new isolate, Yersinia intermedia MASE-LG-1 to individual and combined stresses associated with the Martian surface. This organism belongs to an adaptable and persistent genus of anaerobic microorganisms found in many environments worldwide. The effects of desiccation, low pressure, ionizing radiation, varying temperature, osmotic pressure, and oxidizing chemical compounds were investigated. The strain showed a high tolerance to desiccation, with a decline of survivability by four orders of magnitude during a storage time of 85 days. Exposure to X-rays resulted in dose-dependent inactivation for exposure up to 600 Gy while applied doses above 750 Gy led to complete inactivation. The effects of the combination of desiccation and irradiation were additive and the survivability was influenced by the order in which they were imposed. Ionizing irradiation and subsequent desiccation was more deleterious than vice versa. By contrast, the presence of perchlorates was not found to significantly affect the survival of the Yersinia strain after ionizing radiation. These data show that the organism has the capacity to survive and grow in physical and chemical stresses, imposed individually or in combination that are associated with Martian environment. Eventually it lost its viability showing that many of the most adaptable anaerobic organisms on Earth would be killed on Mars today