Nitrate assimilation in Candida nitratophila and other yeasts

Comparative metabarcoding and biodiversity of gut-associated fungal assemblages of Dendroctonus species (Curculionidae: Scolytinae)

The genus Dendroctonus is a Holarctic taxon composed of 21 nominal species; some of these species are well known in the world as disturbance agents of forest ecosystems. Under the bark of the host tree, these insects are involved in complex and dynamic associations with phoretic ectosymbiotic and endosymbiotic communities. Unlike filamentous fungi and bacteria, the ecological role of yeasts in the bark beetle holobiont is poorly understood, though yeasts were the first group to be recorded as microbial symbionts of these beetles. Our aim was characterize and compare the gut fungal assemblages associated to 14 species of Dendroctonus using the internal transcribed spacer 2 (ITS2) region. A total of 615,542 sequences were recovered yielding 248 fungal amplicon sequence variants (ASVs). The fungal diversity was represented by 4 phyla, 16 classes, 34 orders, 54 families, and 71 genera with different relative abundances among Dendroctonus species. The α-diversity consisted of 32 genera of yeasts and 39 genera of filamentous fungi. An analysis of β-diversity indicated differences in the composition of the gut fungal assemblages among bark beetle species, with differences in species and phylogenetic diversity. A common core mycobiome was recognized at the genus level, integrated mainly by Candida present in all bark beetles, Nakazawaea, Cladosporium, Ogataea, and Yamadazyma. The bipartite networks confirmed that these fungal genera showed a strong association between beetle species and dominant fungi, which are key to maintaining the structure and stability of the fungal community. The functional variation in the trophic structure was identified among libraries and species, with pathotroph-saprotroph-symbiotroph represented at the highest frequency, followed by saprotroph-symbiotroph, and saprotroph only. The overall network suggested that yeast and fungal ASVs in the gut of these beetles showed positive and negative associations among them. This study outlines a mycobiome associated with Dendroctonus nutrition and provides a starting point for future in vitro and omics approaches addressing potential ecological functions and interactions among fungal assemblages and beetle hosts.

Expanding the Knowledge on the Skillful Yeast Cyberlindnera jadinii

Cyberlindnera jadinii is widely used as a source of single-cell protein and is known for its ability to synthesize a great variety of valuable compounds for the food and pharmaceutical industries. Its capacity to produce compounds such as food additives, supplements, and organic acids, among other fine chemicals, has turned it into an attractive microorganism in the biotechnology field. In this review, we performed a robust phylogenetic analysis using the core proteome of C. jadinii and other fungal species, from Asco- to Basidiomycota, to elucidate the evolutionary roots of this species. In addition, we report the evolution of this species nomenclature over-time and the existence of a teleomorph (C. jadinii) and anamorph state (Candida utilis) and summarize the current nomenclature of most common strains. Finally, we highlight relevant traits of its physiology, the solute membrane transporters so far characterized, as well as the molecular tools currently available for its genomic manipulation. The emerging applications of this yeast reinforce its potential in the white biotechnology sector. Nonetheless, it is necessary to expand the knowledge on its metabolism, regulatory networks, and transport mechanisms, as well as to develop more robust genetic manipulation systems and synthetic biology tools to promote the full exploitation of C. jadinii.

Identification and characterization of the nitrate assimilation genes in the isolate of Streptomyces griseorubens JSD-1

Background

Streptomyces griseorubens JSD-1 is a novel actinomycete isolated from soil that can utilize nitrate as its sole nitrogen source for growth and these nitrate assimilation genes active in this biotransformation are expected to be crucial. However, little is known about its genomic or genetic background related to nitrogen metabolism in this isolate. Thus, this study concentrates on identification and characterization of genes involved in nitrate assimilation.

Results

To investigate the molecular mechanism of nitrate metabolism, genome sequencing was performed by Illumina Miseq platform. Then the draft genome of a single linear chromosome with 8,463,223 bp and an average G+C content of 72.42% was obtained, which has been deposited at GenBank under the accession number JJMG00000000. Sequences of nitrate assimilation proteins such as nitrate reductase (EC 1.7.99.4), nitrite reductase (EC 1.7.1.4), glutamine synthetase (EC 6.3.1.2), glutamate synthase (EC 1.4.1.13) and glutamate dehydrogenase (EC 1.4.1.2) were acquired. All proteins were predicted to be intracellular enzymes and their sequences were highly identical to those from their similar species owing to the conservative character. Putative 3D structures of these proteins were also modeled based on the templates with the most identities in the PDB database. Through KEGG annotated map, these proteins proved to be located on the key positions of nitrogen metabolic signaling pathway. Finally, quantitative RT-PCR indicated that expression responses of all genes were up-regulated generally and significantly when stimulated with nitrate.

Conclusion

In this manuscript, we describe the genome features of an isolate of S. griseorubens JSD-1 following with identification and characterization of these nitrate assimilation proteins such as nitrate reductase, nitrite reductase, glutamine synthetase, glutamate synthase and glutamate dehydrogenase accounts for the ability to utilize nitrate as its sole nitrogen source for growth through cellular localization, multiple sequence alignment, putative 3D modeling and quantitative RT-PCR. In summary, our findings provide the genomic and genetic background of utilizing nitrate of this strain.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-014-0174-4) contains supplementary material, which is available to authorized users.

Yeast diversity associated with invasive Dendroctonus valens killing Pinus tabuliformis in China using culturing and molecular methods

Bark beetle-associated yeasts are much less studied than filamentous fungi, yet they are also considered to play important roles in beetle nutrition, detoxification, and chemical communication. The red turpentine beetle, Dendroctonus valens, an invasive bark beetle introduced from North America, became one of the most destructive pests in China, having killed more than 10 million Pinus tabuliformis as well as other pine species. No investigation of yeasts associated with this bark beetle in its invaded ranges has been conducted so far. The aim of this study was to assess the diversity of yeast communities in different microhabitats and during different developmental stages of Den. valens in China using culturing and denaturing gradient gel electrophoresis (DGGE) approaches and to compare the yeast flora between China and the USA. The yeast identity was confirmed by sequencing the D1/D2 domain of LSU ribosomal DNA (rDNA). In total, 21 species (13 ascomycetes and eight basidiomycetes) were detected by culturing method, and 12 species (11 ascomycetes and one basidiomycetes) were detected by molecular methods from China. The most frequent five species in China were Candida piceae (Ogataea clade), Cyberlindnera americana, Candida oregonensis (Metschnikowia clade), Candida nitratophila (Ogataea clade) and an undescribed Saccharomycopsis sp., detected by both methods. Seven species were exclusively detected by DGGE. Ca. oregonensis (Metschnikowia clade) was the most frequently detected species by DGGE method. Eight species (all were ascomycetes) from the USA were isolated; seven of those were also found in China. We found significant differences in yeast total abundance as well as community composition between different developmental stages and significant differences between the surface and the gut. The frass yeast community was more similar to that of Den. valens surface or larvae than to the community of the gut or adults. Possible functions of the yeast associates are discussed.

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

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.

Functional properties and differential mode of regulation of the nitrate transporter from a plant symbiotic ascomycete

Nitrogen assimilation by plant symbiotic fungi plays a central role in the mutualistic interaction established by these organisms, as well as in nitrogen flux in a variety of soils. In the present study, we report on the functional properties, structural organization and distinctive mode of regulation of TbNrt2 (Tuber borchii NRT2 family transporter), the nitrate transporter of the mycorrhizal ascomycete T. borchii. As revealed by experiments conducted in a nitrate-uptake-defective mutant of the yeast Hansenula polymorpha, TbNrt2 is a high-affinity transporter (K(m)=4.7 microM nitrate) that is bispecific for nitrate and nitrite. It is expressed in free-living mycelia and in mycorrhizae, where it preferentially accumulates in the plasma membrane of root-contacting hyphae. The TbNrt2 mRNA, which is transcribed from a single-copy gene clustered with the nitrate reductase gene in the T. borchii genome, was specifically up-regulated following transfer of mycelia to nitrate- (or nitrite)-containing medium. However, at variance with the strict nitrate-dependent induction commonly observed in other organisms, TbNrt2 was also up-regulated (at both the mRNA and the protein level) following transfer to a nitrogen-free medium. This unusual mode of regulation differs from that of the adjacent nitrate reductase gene, which was expressed at basal levels under nitrogen deprivation conditions and required nitrate for induction. The functional and expression properties, described in the present study, delineate TbNrt2 as a versatile transporter that may be especially suited to cope with the fluctuating (and often low) mineral nitrogen concentrations found in most natural, especially forest, soils.

Differential NO3 - dependent patterns of NO3 - uptake in Pinus pinaster, Rhizopogon roseolus and their ectomycorrhizal association

•  A different NO₃ ^- dependent pattern of NO₃ ^- uptake at low [NO₃ ^- ] (0-0.1 mM) is shown in Pinus pinaster and in the ectomycorrhizal fungus Rhizopogon roseolus. In ectomycorrhizal symbiosis, the fungal pattern is pre-eminent. •  Net NO₃ ^- uptake rates were deduced in plant and fungus from solution depletion measurements. Net NO₃ ^- fluxes were estimated at the surface of mycorrhizal and nonmycorrhizal short roots, using NO₃ ^- selective microelectrodes. •  In NO₃ ^- starved seedlings, maximum NO₃ ^- uptake rates were reached after 3 d of incubation in 0.05 mM NO₃ ^- . In R. roseolus mycelia, NO₃ ^- uptake rates did not change after withdrawing NO₃ ^- for up to 7 d, or after adding NO₃ ^- for 3 d. Net NO₃ ^- fluxes in nonmycorrhizal short roots were increased twofold by a 3-d exposure to NO₃ ^- whereas in ectomycorrhiza they were similar irrespective of the NO₃ ^- pretreatment, but always higher than the fluxes measured in nonmycorrhizal roots. •  Ectomycorrhiza have a greater capacity to use NO₃ ^- than nonmycorrhizal short roots, whatever the NO₃ ^- concentration in the solution. This may give mycorrhizal plants a greater ability to use fluctuating concentrations of NO₃ ^- in the soil solution.

Ammonium assimilation by the nitrate-utilizing yeast, Candida nitratophila

Ammonium-nitrogen was assimilated rapidly by nitrogen-replete cultures of the nitrate-utilizing yeast, Candida nitratophila as long as a suitable source of carbon was available. These cultures contained high activities of an NADPH-dependent glutamate dehydrogenase with a relatively high affinity for ammonium (K_m = 0.27 mM) and high glutamine synthetase activity. Both enzyme activities were apparently derepressed when glutamine-grown cultures were starved of nitrogen or transferred to nitrate medium. Nitrogen-deficient cultures also contained NADH-dependent glutamate synthase activity that was inhibited by azaserine in vitro. Ammonium assimilation in vivo, was inhibited by methionine sulphoximine whilst addition of azaserine resulted in an accumulation of intracellular glutamine and an inhibition of glutamate production. Our results suggest that, in C. nitratophila, there is a potential for ammonium assimilation via both the glutamate dehydrogenase pathway and the glutamine synthetase/glutamate synthase pathway with the latter pathway predominating in nitrogen-deficient cells.

Changes in intracellular amino acids and glutamine : glutamate during N-deprivation and feeding in Candida nitratophila

In the yeast, Candida nitratophila Shifrine et Phaff, the intracellular concentrations of α-amino acids decreased rapidly during N-deprivation, with the ratio of glutamine: glutamate (Gln: Glu) falling from 07 in NH₄ ⁺ -grown cells, or 0.5 in NO₃ ^- -grown cells, to 0.1 after 1 h. Addition of NH₄ ⁺ to N-deprived cultures resulted in rapid increases in glutamate, glutamine and alanine with Gln: Glu exceeding 1.5 within 30 min. Recovery of other amino acids, such as arginine, was much slower. Addition of NO³ , resulted in a less rapid increase in the concentration of some intracellular amino acids, including glutamate and glutamine, while levels of arginine continued to fall for 30 min after addition of this N-source. Gln: Glu was slow to rise in NO₃ ^- pulsed cells. Addition of NH₄ ⁺ to cells growing on NO^3- produced little change over the following 2 h other than decreases in arginine and histidine. Carbon deprivation resulted in a rapid decrease in levels of glutamate, glutamine and alanine, but not of aspartate (which this yeast is unable to use as a sole C-source for growth) or arginine. Gln: Glu increased during C-deprivation but fell within 10 min to normal levels on addition of glucose. It is concluded that, in C. nitratophila, Gln:Glu values correlate well with C-N status.

The role of yeasts in oral cancer by means of endogenous nitrosation

Oral leukoplakias, particularly non-homogeneous types, are often invaded by yeasts, with Candida albicans being the dominant species. The more advanced precancerous leukoplakia lesions yield more rarely occurring biotypes of C. albicans, suggesting a causal role for these biotypes in the malignant transformation. N-nitroso-benzylmethylamine (NBMA) is a compound able to induce carcinoma of the esophagus and the oral cavity in the rat. The catalytic potential of yeasts, isolated from leukoplakia lesions and from normal mucosa, to produce NBMA from the precursors N-benzyl-methylamine and nitrite was assessed at pH 6.8. The yeast strains differed in nitrosation potential, ranking from 0 to 1.2 micrograms NBMA/10(6) cells. C. albicans strains of the more rarely occurring biotypes showed the highest nitrosation potential, whereas C. tropicalis, C. parapsilosis, and Torulopsis glabrata were ranked lower. Strains with high nitrosation potential were generally isolated from lesions with more advanced precancerous changes. Thus, further evidence is provided supporting the hypothesis that yeasts play a causal role in oral cancer by means of endogenous nitrosamine production.