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  • Graeme Nicol
Graeme Nicol

Graeme Nicol
Ecole Centrale de Lyon | ECL · Laboratoire AMPERE (Génie Electrique, Electromagnétique, Automatique, Micro-Biologie Environnementale et Applications)

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279
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Publications

Publications (279)
Article
Small genes (<150 nucleotides) have been systematically overlooked in phage genomes. We employ a large-scale comparative genomics approach to predict >40,000 small-gene families in ∼2.3 million phage genome contigs. We find that small genes in phage genomes are approximately 3-fold more prevalent than in host prokaryotic genomes. Our approach enric...
Article
Full-text available
The influence of biotic and abiotic factors on viral communities across environmental gradients in soil is relatively unknown. While soil pH strongly influences microbial community structure, it is unclear whether there is a similar influence on soil viruses. In this study, prokaryotic and viral communities were characterized in soils from a long-t...
Article
Full-text available
The impact of DMPP (3,4-dimethylpyrazole phosphate), applied at two doses (low: recommended for agronomic use; high: > 100 × the recommended), on the function, diversity, and dynamics of target microorganisms (ammonia-oxidizing microorganisms, AOM), functionally associated microorganisms (nitrite-oxidizing bacteria (NOB) and denitrifiers), and tota...
Preprint
Full-text available
Viruses shape microbial community structures, impacting metabolic pathways and influencing biogeochemical cycles. Despite their importance, the influence of biotic and abiotic factors on viral community structures across environmental gradients in soil is relatively unknown compared to their prokaryotic hosts. While soil pH strongly influences micr...
Article
Crop harvest followed by a fallow period can act as a disturbance on soil microbial communities. Cropping systems intended to improve alpha-diversity of communities may also confer increased compositional stability during succeeding growing seasons. Over a single growing season in a long-term (18 year) agricultural field experiment incorporating co...
Article
The concentration of atmospheric methane (CH 4 ) continues to increase with microbial communities controlling soil–atmosphere fluxes. While there is substantial knowledge of the diversity and function of prokaryotes regulating CH 4 production and consumption, their active interactions with viruses in soil have not been identified. Metagenomic seque...
Article
Full-text available
Human activities have massively increased the amount of reactive nitrogen in the biosphere, which is leading to increased nitrogen (N) inputs in terrestrial ecosystems. The retention of N is a crucial ecosystem function of both managed and natural ecosystems, and there is a long history of experimental, observational, and conceptual studies identif...
Article
Full-text available
Nitrification, the oxidation of ammonia to nitrate, is an essential process in the biogeochemical nitrogen cycle. The first step of nitrification, ammonia oxidation, is performed by three, often co-occurring guilds of chemolithoautotrophs: ammonia-oxidizing bacteria (AOB), archaea (AOA), and complete ammonia oxidizers (comammox). Substrate kinetics...
Article
Full-text available
It has been estimated that up to 90% of human exposure to cadmium is through food, and that cadmium within rice grains can be a major contributor to that dietary source. In this study genome wide association mapping was conducted on the Bengal and Assam Aus Panel (BAAP) of rice to identify quantitative trait loci and candidate genes for lowering gr...
Article
Functional, physiological traits are the underlying drivers of niche differentiation. A common framework related to niches occupied by terrestrial prokaryotes is based on copiotrophy or oligotrophy, where resource investment is primarily in either rapid growth or stress tolerance, respectively. A quantitative trait-based approach sought relationshi...
Article
Potential rate assays are used in soil microbial ecology to determine the rates of a functional process in environmental samples under a defined set of conditions. While they can be used appropriately to provide mechanistic insights, potential rates are also often used to estimate the abundance of specific taxonomic groups and their in situ activit...
Preprint
Full-text available
Nitrification, the oxidation of ammonia to nitrate, is an essential process in the biogeochemical nitrogen cycle. The first step of nitrification, ammonia oxidation, is performed by three, often co-occurring guilds of chemolithoautotrophs: ammonia-oxidizing bacteria (AOB), archaea (AOA), and complete ammonia oxidizers (comammox). Substrate kinetics...
Preprint
Full-text available
The concentration of atmospheric methane continues to increase with microbial communities controlling soil-atmosphere fluxes. While there is substantial knowledge of the diversity and function of organisms regulating methane production and consumption, the frequency and impact of interactions with viruses on their activity in soil is unknown. Metag...
Article
Full-text available
Nitrification inhibitors (NIs) applied to soil reduce nitrogen fertilizer losses from agro-ecosystems. NIs that are currently registered for use in agriculture appear to selectively inhibit ammonia-oxidizing bacteria (AOB), while their impact on other nitrifiers is limited or unknown. Ethoxyquin (EQ), a fruit preservative shown to inhibit ammonia-o...
Article
Nitrification is the microbial conversion of reduced forms of nitrogen (N) to nitrate (NO3-), and in fertilized soils it can lead to substantial N losses via NO3- leaching or nitrous oxide (N2O) production. To limit such problems, synthetic nitrification inhibitors have been applied but their performance differs between soils. In recent years, ther...
Article
Full-text available
Investigation of niche specialisation in microbial communities is important in assessing consequences of environmental change for ecosystem processes. Ammonia oxidising bacteria (AOB) and archaea (AOA) present a convenient model for studying niche specialisation. They coexist in most soils and effects of soil characteristics on their relative abund...
Preprint
Full-text available
Potential rate assays are used in soil microbial ecology to determine the maximum rate of a functional process in environmental samples. They assume that all contributing organisms in a community are active at a maximum rate under one set of optimal incubation conditions. Potential rates are then often compared to the abundance of specific taxonomi...
Preprint
Full-text available
Nitrification inhibitors (NIs) reduce nitrogen fertilizer losses from agricultural ecosystems. Currently available NIs appear to selectively inhibit ammonia-oxidizing bacteria (AOB), while their impact on other groups of nitrifiers is limited. Ethoxyquin (EQ), a preservative shown to inhibit ammonia-oxidizers (AO) in soil, is rapidly transformed to...
Preprint
Full-text available
Resistance is the capacity for a community to remain unchanged, and resilience the capacity to return to an original state, in response to disturbance. Increasing species richness may increase both dynamics. In a long-term agricultural field experiment incorporating conventional (CON), integrated (INT), conservation (CA) and organic (ORG) cropping...
Article
Full-text available
“ Candidatus Nitrosocosmicus franklandus” C13 is an ammonia-oxidizing archaeon (AOA) isolated from soil. Its complete genome is 2.84 Mb and possesses predicted AOA metabolic pathways for energy generation and carbon dioxide fixation but no typical surface layer (S-layer) proteins, only one ammonium transporter, and divergent A-type ATP synthase gen...
Article
Oxidation of ammonia to nitrite by bacteria and archaea is responsible for global emissions of nitrous oxide directly and indirectly through provision of nitrite and, after further oxidation, nitrate to denitrifiers. Their contributions to increasing N2O emissions are greatest in terrestrial environments, due to the dramatic and continuing increase...
Article
Pesticide toxicity on soil microorganisms is an emerging issue in pesticide risk assessment, dictated by the pivotal role of soil microorganisms in ecosystem services. However, the focus has traditionally been on parent compounds, while transformation products (TPs) are largely overlooked. We tested the hypothesis that TPs can be major contributors...
Chapter
The global nitrogen cycle is initiated by the fixation of atmospheric N2, by either natural or chemical processes, to bioavailable ammonium (NH4⁺). Nitrification is the oxidative process that transforms this ammonium to nitrate, via a nitrite intermediate. Nitrification is performed solely by microorganisms: ammonia‐oxidising bacteria and archaea o...
Article
Although soil nitrification has been studied intensively, with an effort to elucidate the relative contributions of both ammonia-oxidizing archaea (AOA) and bacteria (AOB), their relative contributions to N2O production remain unclear. Understanding the temperature- and depth-dependent activities of AOA and AOB, as well as production of N2O, is of...
Article
Full-text available
High and low rates of ammonium supply are believed to favour ammonia-oxidising bacteria (AOB) and archaea (AOA), respectively. Although their contrasting affinities for ammonium are suggested to account for these differences, the influence of ammonia concentration on AOA and AOB has not been tested under environmental conditions. In addition, while...
Article
Nitrification, as a crucial step in nitrogen cycling and plant nutrition, is a biologically mediated process responsible for enormous losses of nitrogen fertilizer and a contributor to environmental pollution. The recent progress in our understanding of nitrification and nitrifiers, specifically in acidic soils, is discussed and reviewed. At one ti...
Data
Fig. S1. Differential coverage plot comparing a metagenome obtained from native fen soil and a metagenome obtained from the heavy fractions of the same soil after SIP. Only scaffolds larger than 10 knt are shown. Scaffolds binned to Ca. N. bavarica SbT1 are marked by black borders. Scaffolds with no reads mapped from untreated or SIP metagenomes ar...
Article
Full-text available
Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about mi...
Article
Full-text available
Obligate acidophilic members of the thaumarchaeotal genus Candidatus Nitrosotalea play an important role in nitrification in acidic soils, but their evolutionary and physiological adaptations to acidic environments are still poorly understood, with only a single member of this genus (Ca. N. devanaterra) having its genome sequenced. In this study, w...
Article
Coastal areas worldwide are challenged by climate change-associated increases in sea level and storm surge quantities that potentially lead to more frequent flooding of soil ecosystems. Currently, little is known of the effects of inundation events on microorganisms controlling nitrification in these ecosystems. The goal of this study was to invest...
Article
Full-text available
Ammonia oxidising bacteria (AOB) are thought to emit more nitrous oxide (N2O) than ammonia oxidising archaea (AOA), due to their higher N2O yield under oxic conditions and denitrification in response to oxygen (O2) limitation. We determined the kinetics of growth and turnover of nitric oxide (NO) and N2O at low cell densities of Nitrosomonas europa...
Poster
For over 100 years, aerobic nitrification was thought to be a separated two-step process, with ammonia oxidised to nitrite by ammonia oxidisers (AO), which was subsequently oxidised to nitrate by nitrite oxidising bacteria (NOB), including members of the Nitrospira and Nitrobacter genera in soil. This dogma was recently challenged by the discovery...
Article
Thaumarchaeota are globally distributed and abundant microorganisms occurring in diverse habitats and thus represent a major source of archaeal lipids. The scope of lipids as taxonomic markers in microbial ecological studies is limited by the scarcity of comparative data on the membrane lipid composition of cultivated representatives, including the...
Article
Full-text available
Thaumarchaeota are globally distributed and abundant microorganisms occurring in diverse habitats and thus represent a major source of archaeal lipids. The scope of lipids as taxonomic markers in microbial ecological studies is limited by the scarcity of comparative data on the membrane lipid composition of cultivated representatives, including the...
Article
Ammonia oxidising archaea (AOA) are an abundant and ubiquitously distributed group of soil microorganisms and contribute significantly to nitrogen cycling processes. Soil pH has been identified as a major driver of AOA diversification, but other environmental factors may also be important. The aim of this study was to determine whether soil pH also...
Article
The ability of some archaea to contribute to nitrogen cycling processes has been known for many decades (albeit some of these organisms were not initially recognised as archaea). These included both assimilatory (e.g. fixation of atmospheric nitrogen) and dissimilatory (e.g. denitrification) processes. However, these reactions were associated with...
Chapter
Ni.tro.so.ta.le.a'les. N.L. fem. n. Ca. Nitrosotalea type genus of the family; -ales ending to denote order; N.L. pl. n. Ca. Nitrosotaleales the Ca. Nitrosotalea order. Thaumarchaeota / Nitrososphaeria / Candidatus Nitrosotaleales
Chapter
Ni.tro.so.ta.le.a.ce'ae. N.L. fem. n. Nitrosotalea type genus of the family; -aceae ending to denote family; N.L. fem. pl. n. Nitrosotaleaceae the Nitrosotalea family. Thaumarchaeota / Nitrososphaeria / Candidatus Nitrosotaleales / Candidatus Nitrosotaleaceae
Chapter
Ni.tro.so.ta'le.a. N.L. adj. nitrosus, full of natron; here intended to mean nitrous; L. fem. n. talea, a slender staff, rod, stick; N.L. fem. n. Nitrosotalea a nitrite-forming slender rod. Thaumarchaeota / Nitrososphaeria / Candidatus Nitrosotaleales / Candidatus Nitrosotaleaceae / Candidatus Nitrosotalea Since the late nineteenth century, aerobic...
Article
Full-text available
Nitrogen fertilization and returning straw to paddy soil are important factors that regulate CH4 production. To evaluate the effect of rice straw and/or nitrate amendment on methanogens, a paddy soil was anaerobically incubated for 40 days. The results indicated that while straw addition increased CH4 production and the abundances of mcrA genes and...
Article
Full-text available
Studies of the distribution of ammonia oxidising archaea (AOA) and bacteria (AOB) suggest distinct ecological niches characterised by ammonia concentration and pH, arising through differences in substrate affinity and ammonia tolerance. AOA form five distinct phylogenetic clades, one of which, the ‘Nitrososphaera sister cluster’, has no cultivated...
Article
Nitrogen fertilisation of agricultural soil contributes significantly to emissions of the potent greenhouse gas nitrous oxide (N2O), which is generated during denitrification and, in oxic soils mainly by, ammonia oxidisers. Although laboratory cultures of ammonia oxidising bacteria (AOB) and archaea (AOA) produce N2O, their relative activities in s...
Article
Full-text available
Ammonia oxidation is the first and rate-limiting step in nitrification and is dominated by two distinct groups of microorganisms in soil: ammonia-oxidising archaea (AOA) and bacteria (AOB). AOA are often more abundant than AOB, and dominate activity in acid soils. The mechanism of ammonia oxidation in acidic conditions has been a long-standing para...
Article
Full-text available
Thaumarchaeota form a ubiquitously distributed archaeal phylum, comprising both the ammonia-oxidising archaea (AOA) and other archaeal groups in which ammonia oxidation has not been demonstrated (including Group 1.1c and Group 1.3). The ecology of AOA in terrestrial environments has been extensively studied using either a functional gene, encoding...
Article
Full-text available
In this study, we investigated the impact of soil pH on the diversity and abundance of archaeal ammonia oxidizers in 27 different forest soils across Germany. DNA was extracted from topsoil samples, the amoA gene, encoding ammonia monooxygenase, was amplified; and the amplicons were sequenced using a 454-based pyrosequencing approach. As expected,...
Data
Effects of addition of 100 μM TCA cycle intermediates on cell abundance (a) and yield normalised against production (b).
Data
Maximum-likelihood phylogenetic analysis of inferred AmoA amino acid sequences translated from amoA gene sequences of Nitrosotalea devanaterra Nd1 and Nitrosotalea sp.
Data
AOA cultures reported in literature. Table S2. Capacity of organic compounds to restore growth in the pure culture of Nitrosotalea devanaterra. Table S3. Properties of the examined organic acids.
Article
Full-text available
Autotrophic ammonia oxidation is performed by two distinct groups of microorganisms: ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB). Although AOA outnumber their bacterial counterparts in many soils, at times by several orders of magnitude, relatively little is known of their physiology due to the lack of cultivated isolates....
Data
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
Data
##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
Article
Soil pH is an important determinant of microbial community composition and diversity, yet few studies have characterized the specific effects of pH on individual bacterial taxa within bacterial communities, both abundant and rare. We collected composite soil samples over two years from an experimentally maintained pH gradient ranging from 4.5 to 7....
Article
Full-text available
The soil archaeon Nitrosotalea devanaterra is a representative of an abundant ammonia oxidising archaeal lineage. The effects of three nitrification inhibitors (allylthiourea (ATU), dicyandiamide (DCD) and nitrapyrin) on growth in both soil and liquid culture were compared. DCD and nitrapyrin inhibited nitrification at similar concentrations to bac...
Data
Full-text available
Soil physicochemical properties and microbial communities are highly heterogeneous and vary widely over spatial scales, necessitating careful consideration of sampling strategies to provide representative and reproducible soil samples across field sites. To achieve this, the study aimed to establish appropriate sampling methodology and to determine...
Article
The factors driving the abundance and community composition of soil microbial communities provide fundamental knowledge on the maintenance of biodiversity and the ecosystem services they underpin. Several studies have suggested that microbial communities are spatially organized, including functional groups and much of the observed variation is expl...
Article
Both bacterial and archaeal ammonia oxidizers (AOB and AOA) are abundant in most soils, but their relative contributions to soil nitrification under different conditions are still debated. This study investigates the influence of long-term zinc (Zn) stress on the ammonia oxidizer community and determines the role of AOB and AOA in Zn tolerant nitri...