Nitrogen storage and remobilization by trees : ecophysiological relevance in a changing world

Peer reviewedPreprin

Metaxa : a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets

Peer reviewedPostprin

Tidying up international nucleotide sequence databases

Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi

Chemical formation of hybrid di-nitrogen calls fungal codenitrification into question

Removal of excess nitrogen (N) can best be achieved through denitrification processes that transform N in water and terrestrial ecosystems to di-nitrogen (N-2) gas. The greenhouse gas nitrous oxide (N2O) is considered an intermediate or end-product in denitrification pathways. Both abiotic and biotic denitrification processes use a single N source to form N2O. However, N-2 can be formed from two distinct N sources (known as hybrid N-2) through biologically mediated processes of anammox and codenitrification. We questioned if hybrid N-2 produced during fungal incubation at neutral pH could be attributed to abiotic nitrosation and if N2O was consumed during N-2 formation. Experiments with gas chromatography indicated N-2 was formed in the presence of live and dead fungi and in the absence of fungi, while N2O steadily increased. We used isotope pairing techniques and confirmed abiotic production of hybrid N-2 under both anoxic and 20% O-2 atmosphere conditions. Our findings question the assumptions that (1) N2O is an intermediate required for N-2 formation, (2) production of N-2 and N2O requires anaerobiosis, and (3) hybrid N-2 is evidence of codenitrification and/ or anammox. The N cycle framework should include abiotic production of N-2

Tidying Up International Nucleotide Sequence Databases: Ecological, Geographical and Sequence Quality Annotation of ITS Sequences of Mycorrhizal Fungi

Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi

COMPARAISON DE LA REMOBILISATION SAISONNIERE DE L'AZOTE PAR VACCINIUM MYRTILLUS (CADUQUE) ET V. VITIS-IDAEA (SEMPERVIRENTE)

CLERMONT FD-BCIU Sci.et Tech. (630142101) / SudocSudocFranceF

Ecology of ericoid mycorrhizal fungi: what insight have we gained with molecular tools and what’s missing?

International audienc

Translocation of Nitrogen in the Xylem of Field-Grown Cherry and Poplar Trees during Remobilization

Studies of small trees growing in pots have established that individual amino acids or amides are translocated in the xylem sap of a range of tree species following bud burst, as a consequence of N remobilization from storage. This paper reports the first study of N translocation in the xylem of large deciduous, field-grown trees during N remobilization in the spring. 15N fertilizer was applied to the soil around ten year old Prunus avium and Populus trichocharpa var. Hastata (Dode) x Populus balsamifera var. Michauxii (Henry) Farewell trees before bud burst and used to label N taken up by the roots. Recovery of unlabelled N in xylem sap and leaves was used to demonstrate that P. avium remobilizes N in both glutamine (glu) and asparagine (asn). Sap concentration of both rose sharply after bud burst, peaking 14 days after bud burst for gln, and remaining high for some 45 days for asn. No 15N enrichment of either amide was found until 21 days after bud burst. In the Populus trees nearly all the N was translocated in the sap as gln, the concentration of which peaked and then declined again before the amide was enriched with 15N, 40 days after bud burst. Sampling the xylem sap of clonal P. avium trees at different positions within the crown was used to assess if the position of sampling affected the amino acid and amide composition of the sap. Sap was sampled during remobilization (when the concentration of gln was maximal), at the end of remobilisation and at the end of the experiment (68 days after bud burst). While the date of sampling had a highly significant effect upon sap composition, the effect of position of sampling was found to be marginal. The results are discussed in relation to the N translocation in adult trees and the possibility of measuring N remobilization by calculating the flux of N translocation in the xylem.JRC.H.2-Climate chang

New insights into the mycorrhizal Rhizoscyphus ericae aggregate : spatial structure and co-colonization of ectomycorrhizal and ericoid roots

Fungi in the Rhizoscyphus ericae aggregate have been recovered from the roots of co-occurring ericaceous shrubs and ectomycorrhizal trees. However, to date, there is no evidence that the same individual genotypes colonize both hosts, and no information on the extent of the mycelial networks that might form. Using spatially explicit core sampling, we isolated fungi from neighbouring Pinus sylvestris (ectomycorrhizal) and Vaccinium vitis-idaea (ericoid mycorrhizal) roots and applied intersimple sequence repeat (ISSR) typing to assess the occurrence and extent of shared genets. Most isolates were identified as Meliniomyces variabilis, and isolates with identical ISSR profiles were obtained from neighbouring ericoid and ectomycorrhizal roots on a number of occasions. However, genet sizes were small (< 13 cm), and several genets were found in a single soil core. Genetic relatedness was independent of spatial separation at the scales investigated (<43 m) and M. variabilis populations from sites 20 km apart were genetically indistinguishable.We conclude that individual genets of M. variabilis can simultaneously colonize Scots pine and Vaccinium roots, but there is no evidence for the formation of large mycelial networks. Our data also suggest significant genotypic overlap between widely separated populations of this ubiquitous root-associated fungus