Publications by authors named "Gubry-Rangin C"

Biological nitrification inhibition (BNI) refers to the plant-mediated process in which nitrification is inhibited through rhizospheric release of diverse metabolites. While it has been assumed that interactive effects of these metabolites shape rhizosphere processes, including BNI, there is scant evidence supporting this claim. Hence, it was a primary objective to assess the interactive effects of selected metabolites, including caffeic acid (CA), vanillic acid (VA), vanillin (VAN), syringic acid (SA), and phenylalanine (PHE), applied as single and combined compounds, against pure cultures of various ammonia-oxidising bacteria (AOB, Nitrosomonas europaea, Nitrosospira multiformis, Nitrosospira tenuis, Nitrosospira briensis) and archaea (AOA, Nitrososphaera viennensis), as well as soil nitrification.

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The soil microbiome determines the fate of plant-fixed carbon. The shifts in soil properties caused by land use change leads to modifications in microbiome function, resulting in either loss or gain of soil organic carbon (SOC). Soil pH is the primary factor regulating microbiome characteristics leading to distinct pathways of microbial carbon cycling, but the underlying mechanisms remain understudied.

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  • Two new strains of ammonia-oxidising archaea were isolated from acidic soils in the UK and China, showing over 99% genetic similarity but distinct physiological features.
  • Both strains, Nd1 and Nd2, are non-motile chemolithotrophs that oxidize ammonia to gain energy, but cannot use urea as an ammonia source.
  • The strains were classified into a new genus, with Nd1 and Nd2 designated as type strains for new species, alongside the proposal of a new family and order.
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  • Biological Nitrification Inhibition (BNI) is a process where plants release metabolites to hinder nitrifying microbes, and intermediate wheatgrass (Kernza®) exhibits potential BNI traits yet to be fully explored.
  • Researchers tested the presence of BNI metabolites in Kernza® compared to annual winter wheat using advanced analyses and bioassays with ammonia-oxidizing bacteria (AOB) and archaea (AOA).
  • The study found that Kernza® not only contained significant BNI metabolites that inhibited AOB and AOA growth but also that ammonia enrichment triggered further release of inhibitory phenolic compounds, showcasing its effectiveness in suppressing soil nitrification.
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Nitrification is the dominant process for nitrous oxide (NO) production under aerobic conditions, but the relative contribution of the autotrophic nitrifiers (the ammonia-oxidising archaea (AOA), the ammonia-oxidising bacteria (AOB) and the comammox) to this process is still unclear in some soil types. This is particularly the case in paddy soils under different fertilization regimes. We investigated active nitrifiers and their contribution to nitrification and NO production in a range of unfertilized and fertilized paddy soils, using CO-DNA based stable isotope probing (SIP) technique combined with a series of specific nitrification inhibitors, including acetylene (CH), 3, 4-dimethylpyrazole phosphate (DMPP) and 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO).

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Ecological theory predicts that organismal distribution and abundance depend on the ability to adapt to environmental change. It also predicts that eukaryotic specialists and generalists will dominate in extreme environments or following environmental change, respectively. This theory has attracted little attention in prokaryotes, especially in archaea, which drive major global biogeochemical cycles.

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Biogeographical reconstructions of the Indo-Australian Archipelago (IAA) have suggested a recent spread across the Sunda and Sahul shelves of lineages with diverse origins, which appears to be congruent with a geological history of recent tectonic uplift in the region. However, this scenario is challenged by new geological evidence suggesting that the Sunda shelf was never submerged prior to the Pliocene, casting doubt on the interpretation of recent uplift and the correspondence of evidence from biogeography and geology. A mismatch between geological and biogeographical data may occur if analyses ignore the dynamics of extinct lineages, because this may add uncertainty to the timing and origin of clades in biogeographical reconstructions.

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  • Phylogenetic reconciliation is a method used to study how gene trees evolve in relation to species trees, helping to explain changes through events like gene duplications and losses.
  • This approach is beneficial for understanding genome evolution, aiding in tasks such as inferring ancestral gene content and analyzing metabolic evolution across microbial lineages.
  • There are many opportunities to expand this method in microbiology, including improving models for realism, scalability, and integrating ecological factors to enhance our understanding of microbial diversity.
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Microplastics (MiPs) can potentially influence soil structural stability, with impacts likely dependent on their chemistry, concentration, size, and degradation in soil. This study used high-energy moisture characteristics (HEMC; water retention at matric suctions from 0 to 50 hPa) to quantify the effects of these MiP properties on soil structure stabiltiy. The HEMCs of soil samples contaminated with polypropylene (PP) or polyethylene (PE) were measured and modelled.

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  • The study investigates the relationship between ammonia oxidation processes and nitrous oxide emissions in agricultural soils, identifying key nitrifying bacteria and their responses to soil conditions and treatments.
  • Results show that nitrous oxide emissions increase with soil pH but decrease with soil organic carbon in alkaline soils, and nitrification inhibitor nitrapyrin effectively reduces emissions by inhibiting specific ammonia-oxidizing bacteria.
  • The findings highlight the importance of understanding bacterial communities, particularly AOB Nitrosospira cluster 3a.2 (D11), in managing nitrous oxide emissions from agricultural practices, providing insights for potential mitigation strategies.
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Knowledge of deeply-rooted non-ammonia oxidising Thaumarchaeota lineages from terrestrial environments is scarce, despite their abundance in acidic soils. Here, 15 new deeply-rooted thaumarchaeotal genomes were assembled from acidic topsoils (0-15 cm) and subsoils (30-60 cm), corresponding to two genera of terrestrially prevalent Gagatemarchaeaceae (previously known as thaumarchaeotal Group I.1c) and to a novel genus of heterotrophic terrestrial Thaumarchaeota.

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  • Understanding the origins of biodiversity and what drives certain clades to diversify more than others is crucial in evolutionary biology.
  • Sophisticated models like state-dependent speciation and extinction (SSE) help assess the relationship between diversity rates and trait evolution, but they are sensitive to the quality of empirical data used.
  • This study highlights how issues like sampling fraction and biases heavily influence SSE model outcomes, showing that lower completeness can lead to inaccurate estimates and increased false positives, suggesting a cautious approach to estimating sampling efforts is preferable.
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The relative contribution of speciation and extinction into current diversity is certainly unknown, but mathematical frameworks that use genetic information have been developed to provide estimates of these processes. To that end, it is necessary to reconstruct molecular phylogenetic trees which summarize ancestor-descendant relationships as well as the timing of evolutionary events (i.e.

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Interpreting phylogenetic trees requires a root, which provides the direction of evolution and polarizes ancestor-descendant relationships. But inferring the root using genetic data is difficult, particularly in cases where the closest available outgroup is only distantly related, which are common for microbes. In this chapter, we present a workflow for estimating rooted species trees and the evolutionary history of the gene families that evolve within them using probabilistic gene tree-species tree reconciliation.

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The Terrestrial Miscellaneous Euryarchaeota Group has been identified in various environments, and the single genome investigated thus far suggests that these archaea are anaerobic sulfite reducers. We assemble 35 new genomes from this group that, based on genome analysis, appear to possess aerobic and facultative anaerobic lifestyles and may oxidise rather than reduce sulfite. We propose naming this order (representing 16 genera) "Lutacidiplasmatales" due to their occurrence in various acidic environments and placement within the phylum Thermoplasmatota.

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  • Acute environmental changes lead to quick shifts in microbial communities, while ongoing disturbances tend to stabilize these communities into new, alternative states.
  • Research involving pristine and hydrocarbon-contaminated sediments shows that acute perturbations significantly alter community structure, while chronically polluted sediments maintain their original structure due to a historical legacy.
  • Despite these variations, both community types demonstrate functional resilience, effectively degrading hydrocarbons, indicating that the history of pollution affects how communities respond to environmental changes.
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  • Grazing in grassland soils leads to a significant reduction in methane uptake and an increase in nitrous oxide emissions, impacting overall greenhouse gas dynamics.
  • A 14-month study showed that grazing negatively affects both methane oxidation and nitrification processes, reducing the diversity of active microorganisms involved in these functions.
  • The findings enhance our understanding of the interactions between methane- and ammonia-oxidizing microbes, which can improve predictions regarding greenhouse gas emissions in grazed ecosystems.
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  • Ammonia oxidising archaea (AOA) play a crucial role in nitrification in acidic agricultural soils, with two main phylogenetic groups, Nitrososphaerales and Candidatus Nitrosotaleaceae, identified as dominant in these environments.
  • The study examined how varying fertilisation practices over 20 years affected the composition and activity of AOA in low pH soils, using high-throughput sequencing of the ammonia monooxygenase gene (amoA) and measuring nitrification rates.
  • Findings showed that long-term fertilisation significantly influences AOA community structure and activity, especially favoring Nitrososphaerales, while revealing that different fertilisation histories contribute to the diversity and stability of AOA
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  • Ammonia-oxidising archaea from the Thaumarchaeota phylum are crucial for the nitrogen cycle, yet their evolutionary mechanisms into various ecosystems are not well understood.
  • Researchers analyzed multiple thaumarchaeotal genomes, including 12 new ones from the Nitrososphaerales group, focusing on lateral gene transfer (LGT), gene duplication, and loss.
  • Findings indicate that gene duplication, particularly after LGT, is significant for genome expansion and may lead to niche specialization, especially in soil and sediment environments.
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Investigation of niche specialization in microbial communities is important in assessing consequences of environmental change for ecosystem processes. Ammonia oxidizing bacteria (AOB) and archaea (AOA) present a convenient model for studying niche specialization. They coexist in most soils and effects of soil characteristics on their relative abundances have been studied extensively.

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  • The conversion of tropical forests to oil palm plantations in Southeast Asia causes soil acidification due to intensive nitrogen use, affecting ammonia-oxidizing microorganisms that play a key role in nitrification.
  • Experimental studies show that forest soils, with neutral pH, have higher nitrification rates compared to acidic oil palm soils, and that acidification reduces ammonia oxidizer activity in forests but can be restored by liming in oil palm soils.
  • This research highlights the varying sensitivity of ammonia-oxidizing bacteria (AOB) and archaea (AOA) to pH changes, indicates AOB may serve as bioindicators for nitrification responses, and suggests that anthropogenic activities compromise the stability of nitrogen cycling processes in these ecosystems.
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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 N O emissions are greatest in terrestrial environments, due to the dramatic and continuing increases in use of ammonia-based fertilizers, which have been driven by requirement for increased food production, but which also provide a source of energy for ammonia oxidizers (AO), leading to an imbalance in the terrestrial nitrogen cycle. Direct N O production by AO results from several metabolic processes, sometimes combined with abiotic reactions.

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  • "Nitrosocosmicus franklandus" C13 is an ammonia-oxidizing archaeon isolated from soil, known for its role in the nitrogen cycle.
  • Its complete genome measures 2.84 Mb and includes metabolic pathways that allow it to generate energy and fix carbon dioxide.
  • Notably, it lacks typical surface layer proteins, has only one ammonium transporter, and possesses divergent A-type ATP synthase genes.
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Background: Characterisation of microbial communities increasingly involves use of high throughput sequencing methods (e.g. MiSeq Illumina) that amplify relatively short sequences of 16S rRNA or functional genes, the latter including ammonia monooxygenase subunit A (amoA), a key functional gene for ammonia oxidising bacteria (AOB) and archaea (AOA).

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