Community profiling and gene expression of fungal assimilatory nitrate reductases in agricultural soil

Abstract

Although fungi contribute significantly to the microbial biomass in terrestrial ecosystems, little is known about their contribution to biogeochemical nitrogen cycles. Agricultural soils usually contain comparably high amounts of inorganic nitrogen, mainly in the form of nitrate. Many studies focused on bacterial and archaeal turnover of nitrate by nitrification, denitrification and assimilation, whereas the fungal role remained largely neglected. To enable research on the fungal contribution to the biogeochemical nitrogen cycle tools for monitoring the presence and expression of fungal assimilatory nitrate reductase genes were developed. To the ∼100 currently available fungal full-length gene sequences, another 109 partial sequences were added by amplification from individual culture isolates, representing all major orders occurring in agricultural soils. The extended database led to the discovery of new horizontal gene transfer events within the fungal kingdom. The newly developed PCR primers were used to study gene pools and gene expression of fungal nitrate reductases in agricultural soils. The availability of the extended database allowed affiliation of many sequences to known species, genera or families. Energy supply by a carbon source seems to be the major regulator of nitrate reductase gene expression for fungi in agricultural soils, which is in good agreement with the high energy demand of complete reduction of nitrate to ammonium.

Novel P450nor Gene Detection Assay Used To Characterize the Prevalence and Diversity of Soil Fungal Denitrifiers

“…To date, only a limited number of studies have relied on molecular methods to detect, identify, and/or characterize fungal denitrifiers (13,27,28,29,35,36). The study by Long et al (36) (4,17,37), most strains isolated in the present study were not able to reduce NO 3 Ϫ to N 2 O, with the exception of Fusarium strains (data not shown).…”

Soil Fungal Cellobiohydrolase I Gene ( cbhI ) Composition and Expression in a Loblolly Pine Plantation under Conditions of Elevated Atmospheric CO 2 and Nitrogen Fertilization

“…4). Such disconnects between dominant members of DNA profiles and expression profiles have been noted in the past for bacteria (e.g., see references 17, 19, 30, and 40) and have recently been noted for fungal laccase genes (24), nitrate reductase genes (13), and cellobiohydrolase genes (3). Collectively, our results, combined with those of others, indicate that "rare" taxa in DNA-based libraries may have some of the most abundant gene transcripts and may be making substantial contributions to cellulose degradation, but the link between transcript numbers and relative contribution to activity remains to be explicitly demonstrated.…”

Mineral nitrogen forms alter 14C-glucose mineralisation and nitrogen transformations in litter and soil from two sugarcane fields

“…Energy supply by carbohydrates (e.g. glucose) acts as primary signal to turn on NO 3 À reductase gene expression, allowing NO 3 À acquisition by fungi for incorporation into biomass (Gorfer et al, 2011). Similarly, in some prokaryotes, transcription of NO 3 À assimilation genes is activated at a high C/N ratio or N depletion (Luque-Almagro et al, 2011).…”