Differential sensitivity of ammonia oxidising archaea and bacteria to matric and osmotic potential

MOB was supported by a University of Aberdeen Elphinstone Scholarship and by TETFund through Adekunle Ajasin University Akungba (AAUA) Nigeria. CGR was funded by a Royal Society University Research Fellowship (UF150571) and CT by the Natural Environment Research Council (NERC, NE/L006286/1) and AXA Chair in Ecosystem Engineering and Microbial Ecology.Peer reviewedPostprin

Functional Diversification of Fungal Glutathione Transferases from the Ure2p Class

The glutathione-S-transferase (GST) proteins represent an extended family involved in detoxification processes. They are divided into various classes with high diversity in various organisms. The Ure2p class is especially expanded in saprophytic fungi compared to other fungi. This class is subdivided into two subclasses named Ure2pA and Ure2pB, which have rapidly diversified among fungal phyla. We have focused our analysis on Basidiomycetes and used Phanerochaete chrysosporium as a model to correlate the sequence diversity with the functional diversity of these glutathione transferases. The results show that among the nine isoforms found in P. chrysosporium, two belonging to Ure2pA subclass are exclusively expressed at the transcriptional level in presence of polycyclic aromatic compounds. Moreover, we have highlighted differential catalytic activities and substrate specificities between Ure2pA and Ure2pB isoforms. This diversity of sequence and function suggests that fungal Ure2p sequences have evolved rapidly in response to environmental constraints

Isolation of ‘Candidatus Nitrosocosmicus franklandus’, a novel ureolytic soil archaeal ammonia oxidiser with tolerance to high ammonia concentration

Acknowledgements The authors would like to thank Mr Kevin Mackenzie and Mrs Gillian Milne (University of Aberdeen) for technical support with scanning electron microscopy, and Dr Robin Walker for access to the Woodlands Field experimental plots at the SRUC,Craibstone Estate, Aberdeen. Funding This work was financially supported by Natural Environmental Research Council (standard grants NE/I027835/1 and NE/L006286/1 and fellowship NE/J019151/1), EC Marie Curie ITN NORA, Grant Agreement No. 316472, the AXA Research Fund and the Centre for Genome Enabled Biology and Medicine, University of Aberdeen.Peer reviewedPublisher PD

Microglia maintain structural integrity during fetal brain morphogenesis

Microglia (MG), the brain-resident macrophages, play major roles in health and disease via a diversity of cellular states. While embryonic MG display a large heterogeneity of cellular distribution and transcriptomic states, their functions remain poorly characterized. Here, we uncovered a role for MG in the maintenance of structural integrity at two fetal cortical boundaries. At these boundaries between structures that grow in distinct directions, embryonic MG accumulate, display a state resembling post-natal axon-tract-associated microglia (ATM) and prevent the progression of microcavities into large cavitary lesions, in part via a mechanism involving the ATM-factor Spp1. MG and Spp1 furthermore contribute to the rapid repair of lesions, collectively highlighting protective functions that preserve the fetal brain from physiological morphogenetic stress and injury. Our study thus highlights key major roles for embryonic MG and Spp1 in maintaining structural integrity during morphogenesis, with major implications for our understanding of MG functions and brain development.</p

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

Influence des Interactions bactéries-champignons sur la dissipation des HAP dans la rhizosphère

The dissipation of Polycyclic Aromatic Hydrocarbons (PAHs), very common and persistant pollutants in soils from industrial wastelands, involve the action of bacterial and fungal microorganisms. However their respective contribution, and the influence of the microbial and plant-microbe interactions on in situ PAH dissipation, are poorly known and fungal communities were scarcely studied in such environments. This work aimed to study the fate of PAHs in rhizosphere under the influence of microorganisms and their interactions and to estimate the fungal diversity in contaminated soils. The dynamic of fungal communities was monitored in situ for 5 years, by real-time PCR and Temporal Temperature Gradient Electrophoresis (TTGE) in an aged PAH-polluted soil and in the same soil treated by thermal desorption. The results showed that plants had a positive effect on fungal abundance and diversity and were the main driver of fungal community structure, dominated by Ascomycetes. Besides, bacterial and fungal strains were isolated from this soil and screened for their ability to dissipate PAHs in vitro. Among them, the bacteria Arthrobacter oxydans Pyr2MsHM11 and the fungus Fusarium solani MM1 were chosen as model strains to study their individual and simultaneous effect on PAH dissipation in different experimental conditions, from liquid cultures to planted soil microcosms with a complex microflora. It was found that interactions between microorganisms, notably competition, had a crucial influence on their growth and on the expression of their PAH dissipation potentialLa dissipation des Hydrocarbures Aromatiques Polycycliques (HAP), polluants persistants majoritaires des sols de friches industrielles, implique l'action de microorganismes bactériens et fongiques. Cependant, leur contribution relative à la dissipation in situ, en fonction des interactions entre ces microorganismes ou avec les plantes et les polluants, est mal connue et les communautés fongiques ont été très peu étudiées dans de tels environnements. L'objectif de cette thèse était de préciser l'écodynamique des HAP dans la rhizosphère sous l'effet des microorganismes et de leurs interactions et d'évaluer la diversité fongique dans des sols contaminés. La dynamique des communautés fongiques a été étudiée in situ pendant 5 années, par PCR en temps réel et Temporal Temperature Gradient Electrophoresis (TTGE), dans un sol historiquement contaminé en présence ou non de plantes et dans le même sol ayant subi un traitement de remédiation par désorption thermique. Les plantes avaient un effet positif sur l'abondance et la diversité des champignons et étaient le facteur déterminant la structure des communautés fongiques, dominées par les Ascomycètes. D'autre part, des souches bactériennes et fongiques ont été isolées de ce sol et testées pour leur capacité à dégrader les HAP in vitro. Parmi celles-ci, la bactérie Arthrobacter oxydans Pyr2MsHM11 et le champignon Fusarium solani MM1 ont été choisies comme souches modèles pour étudier leur action individuelle ou conjointe sur la dissipation de trois HAP, dans différentes conditions, des plus simples (cultures liquides) aux plus complexes (microcosmes de sol planté en présence d'une microflore). Les résultats ont montré l'importance fondamentale des interactions entre microorganismes, notamment des phénomènes de compétition, pour la croissance des souches modèles et pour l'expression de leurs potentiels de dissipation des HA

Influence of bacterial-fungal interactions on PAH dissipation in the rhizosphere

La dissipation des Hydrocarbures Aromatiques Polycycliques (HAP), polluants persistants majoritaires des sols de friches industrielles, implique l'action de microorganismes bactériens et fongiques. Cependant, leur contribution relative à la dissipation in situ, en fonction des interactions entre ces microorganismes ou avec les plantes et les polluants, est mal connue et les communautés fongiques ont été très peu étudiées dans de tels environnements. L'objectif de cette thèse était de préciser l'écodynamique des HAP dans la rhizosphère sous l'effet des microorganismes et de leurs interactions et d'évaluer la diversité fongique dans des sols contaminés. La dynamique des communautés fongiques a été étudiée in situ pendant 5 années, par PCR en temps réel et Temporal Temperature Gradient Electrophoresis (TTGE), dans un sol historiquement contaminé en présence ou non de plantes et dans le même sol ayant subi un traitement de remédiation par désorption thermique. Les plantes avaient un effet positif sur l'abondance et la diversité des champignons et étaient le facteur déterminant la structure des communautés fongiques, dominées par les Ascomycètes. D'autre part, des souches bactériennes et fongiques ont été isolées de ce sol et testées pour leur capacité à dégrader les HAP in vitro. Parmi celles-ci, la bactérie Arthrobacter oxydans Pyr2MsHM11 et le champignon Fusarium solani MM1 ont été choisies comme souches modèles pour étudier leur action individuelle ou conjointe sur la dissipation de trois HAP, dans différentes conditions, des plus simples (cultures liquides) aux plus complexes (microcosmes de sol planté en présence d'une microflore). Les résultats ont montré l'importance fondamentale des interactions entre microorganismes, notamment des phénomènes de compétition, pour la croissance des souches modèles et pour l'expression de leurs potentiels de dissipation des HAPThe dissipation of Polycyclic Aromatic Hydrocarbons (PAHs), very common and persistant pollutants in soils from industrial wastelands, involve the action of bacterial and fungal microorganisms. However their respective contribution, and the influence of the microbial and plant-microbe interactions on in situ PAH dissipation, are poorly known and fungal communities were scarcely studied in such environments. This work aimed to study the fate of PAHs in rhizosphere under the influence of microorganisms and their interactions and to estimate the fungal diversity in contaminated soils. The dynamic of fungal communities was monitored in situ for 5 years, by real-time PCR and Temporal Temperature Gradient Electrophoresis (TTGE) in an aged PAH-polluted soil and in the same soil treated by thermal desorption. The results showed that plants had a positive effect on fungal abundance and diversity and were the main driver of fungal community structure, dominated by Ascomycetes. Besides, bacterial and fungal strains were isolated from this soil and screened for their ability to dissipate PAHs in vitro. Among them, the bacteria Arthrobacter oxydans Pyr2MsHM11 and the fungus Fusarium solani MM1 were chosen as model strains to study their individual and simultaneous effect on PAH dissipation in different experimental conditions, from liquid cultures to planted soil microcosms with a complex microflora. It was found that interactions between microorganisms, notably competition, had a crucial influence on their growth and on the expression of their PAH dissipation potentia

Differential response of non-adapted ammonia oxidising archaea and bacteria to drying rewetting stress

We would like to acknowledge funding of the European Commission's FP7 programme, EU-project ‘EcoFINDERS’ No. 264465. The authors also wish to thank Dr Franciska De Vries and Professor Richard Bardgett, University of Manchester and Prof Paul Hallett, University of Aberdeen, for their valuable comments and advice.Peer reviewedPostprin

Influence des Interactions bactéries-champignons sur la dissipation des HAP dans la rhizosphère

La dissipation des Hydrocarbures Aromatiques Polycycliques (HAP), polluants persistants majoritaires des sols de friches industrielles, implique l'action de microorganismes bactériens et fongiques. Cependant, leur contribution relative à la dissipation in situ, en fonction des interactions entre ces microorganismes ou avec les plantes et les polluants, est mal connue et les communautés fongiques ont été très peu étudiées dans de tels environnements. L'objectif de cette thèse était de préciser l'écodynamique des HAP dans la rhizosphère sous l'effet des microorganismes et de leurs interactions et d'évaluer la diversité fongique dans des sols contaminés. La dynamique des communautés fongiques a été étudiée in situ pendant 5 années, par PCR en temps réel et Temporal Temperature Gradient Electrophoresis (TTGE), dans un sol historiquement contaminé en présence ou non de plantes et dans le même sol ayant subi un traitement de remédiation par désorption thermique. Les plantes avaient un effet positif sur l'abondance et la diversité des champignons et étaient le facteur déterminant la structure des communautés fongiques, dominées par les Ascomycètes. D'autre part, des souches bactériennes et fongiques ont été isolées de ce sol et testées pour leur capacité à dégrader les HAP in vitro. Parmi celles-ci, la bactérie Arthrobacter oxydans Pyr2MsHM11 et le champignon Fusarium solani MM1 ont été choisies comme souches modèles pour étudier leur action individuelle ou conjointe sur la dissipation de trois HAP, dans différentes conditions, des plus simples (cultures liquides) aux plus complexes (microcosmes de sol planté en présence d'une microflore). Les résultats ont montré l'importance fondamentale des interactions entre microorganismes, notamment des phénomènes de compétition, pour la croissance des souches modèles et pour l'expression de leurs potentiels de dissipation des HAPThe dissipation of Polycyclic Aromatic Hydrocarbons (PAHs), very common and persistant pollutants in soils from industrial wastelands, involve the action of bacterial and fungal microorganisms. However their respective contribution, and the influence of the microbial and plant-microbe interactions on in situ PAH dissipation, are poorly known and fungal communities were scarcely studied in such environments. This work aimed to study the fate of PAHs in rhizosphere under the influence of microorganisms and their interactions and to estimate the fungal diversity in contaminated soils. The dynamic of fungal communities was monitored in situ for 5 years, by real-time PCR and Temporal Temperature Gradient Electrophoresis (TTGE) in an aged PAH-polluted soil and in the same soil treated by thermal desorption. The results showed that plants had a positive effect on fungal abundance and diversity and were the main driver of fungal community structure, dominated by Ascomycetes. Besides, bacterial and fungal strains were isolated from this soil and screened for their ability to dissipate PAHs in vitro. Among them, the bacteria Arthrobacter oxydans Pyr2MsHM11 and the fungus Fusarium solani MM1 were chosen as model strains to study their individual and simultaneous effect on PAH dissipation in different experimental conditions, from liquid cultures to planted soil microcosms with a complex microflora. It was found that interactions between microorganisms, notably competition, had a crucial influence on their growth and on the expression of their PAH dissipation potentialMETZ-SCD (574632105) / SudocNANCY1-Bib. numérique (543959902) / SudocNANCY2-Bibliotheque electronique (543959901) / SudocNANCY-INPL-Bib. électronique (545479901) / SudocSudocFranceF

Inoculation of PAH-degrading strains of Fusarium solani and Arthrobacter oxydans in rhizospheric sand and soil microcosms: microbial interactions and PAH dissipation

International audienceVery little is known about the influence of bacterial-fungal ecological interactions on polycyclic aromatic hydrocarbon (PAH) dissipation in soils. Fusarium solani MM1 and Arthrobacter oxydans MsHM11 can dissipate PAHs in vitro. We investigated their interactions and their effect on the dissipation of three PAHs-phenanthrene (PHE), pyrene (PYR) and dibenz(a,h)anthracene (DBA)-in planted microcosms, in sterile sand or non-sterile soil. In sterile sand microcosms planted with alfalfa, the two microbes survived and grew, without any significant effect of co-inoculation. Co-inoculation led to the dissipation of 46 % of PHE after 21 days. In soil microcosms, whether planted with alfalfa or not, both strains persisted throughout the 46 days of the experiment, without any effect of co-inoculation or of alfalfa, as assessed by real-time PCR targeting taxon-level indicators, i.e. Actinobacteria 16S rDNA and the intergenic transcribed spacer specific to the genus Fusarium. The microbial community was analyzed by temporal temperature gradient electrophoresis and real-time PCR targeting bacterial and fungal rDNA and PAH-ring hydroxylating dioxygenase genes. These communities were modified by PAH pollution, which selected PAH-degrading bacteria, by the presence of alfalfa and, concerning the bacterial community, by inoculation. PHE and PYR concentrations significantly decreased (91 and 46 %, respectively) whatever the treatment, but DBA concentration significantly decreased (30 %) in planted and co-inoculated microcosms only