Impact of soil chemistry, nutrient supplements, and fungicides on the health and yield of field-grown processing tomatoes NN Maharaj, EM Miyao, RM Davis, S Uroz, JHJ Leveau. European Journal of Plant Pathology, 1-1

Abstract

We report the results of a 3-year study in which we collected and analyzed soil and yield data from experimental plots in six commercial processing tomato fields in Yolo and Solano counties in California. Our objective was to assess the effect of soil chemistry and soil-delivered nutrients and fungicides on tomato plant health and fruit yield at harvest. Marketable yield, leaf necrosis, and fruit loss due to sunburn differed significantly between individual fields, with averages ranging from 81.2–138.5 Mg ha⁻¹, 32–72% leaf necrosis and 1.9 to 8.8% sunburnt fruit, respectively. Higher-yielding fields showed significantly lower levels of leaf necrosis and sunburn damage and a positive correlation with pre-plant soil parameters such as potassium concentration and cation exchange capacity (CEC). Interestingly, soil amendments of composted poultry manure or other nutrient supplements in low-CEC fields, but not high-CEC fields, resulted in higher fruit yield and less leaf necrosis. While all fields showed symptoms typical of Verticillium wilt and some fields showed symptoms of Fusarium wilt, Fusarium crown and root rot, corky root, and root knot nematode, none of our soil amendments, including chemical and biological fungicides, significantly or consistently reduced incidence or severity of these diseases. We discuss our findings in the context of premature vine decline of tomato, an emerging phenomenon in production fields in the Sacramento Valley, which is characterized by the loss of plant vigor and canopy cover at the onset of fruit ripening and for which causative agent(s) and management options in California remain elusive.

Trametes versicolor Glutathione Transferase Xi 3, a dual Cys‐GST with catalytic specificities of both Xi and Omega classes M Schwartz, T Perrot, A Deroy, T Roret, M Morel‐Rouhier, G Mulliert, … FEBS letters

Abstract

Multi-omic analyses of extensively decayed Pinus contorta reveal expression of diverse array of lignocellulose degrading enzymes C Hori, J Gaskell, D Cullen, G Sabat, PE Stewart, K Lail, Y Peng, K Barry, … Applied and environmental microbiology, AEM. 01133-18

ABSTRACT

Fungi play a key role cycling nutrients in forest ecosystems but the mechanisms remain uncertain. To clarify the enzymatic processes involved in wood decomposition, metatranscriptomics and metaproteomics of extensively decayed lodgepole pine were examined by RNAseq and LC-MS/MS, respectively. Following de novo metatranscriptome assembly, 52,011 contigs were searched for functional domains and homology to database entries. Contigs similar to to basidiomycete transcripts dominated and many of these were most closely related to ligninolytic white rot fungi or cellulolytic brown rot fungi. A diverse array of carbohydrate active enzymes (CAzymes) representing a total of 132 families or subfamilies were identified. Among these were 672 glycoside hydrolases including highly expressed cellulases or hemicellulases. The CAzymes also included 162 genes encoding redox enzymes classified within Auxiliary Activity (AA) families. Eighteen of these were manganese peroxidases, key components of ligninolytic white rot fungi. Expression of other redox enzymes supported the working of hydroquinone reduction cycles capable of generating reactive hydroxyl radical. The latter has been implicated as a diffusible oxidant responsible for cellulose depolymerization by brown rot fungi. Thus, enzyme diversity and the coexistence of brown and white rot fungi suggest complex interactions of fungal species and degradative strategies during the decay of logdepole pine.

Tree genotype and seasonal effects on soil properties and biogeochemical functioning in Mediterranean pine forests. L Pérez‐Izquierdo, L Saint‐André, P Santenoise… – European Journal of Soil Science

Summary

Draft Genome Sequence of Tuber borchii Vittad., a Whitish Edible Truffle C Murat, A Kuo, KW Barry, A Clum, RB Dockter, L Fauchery, M Iotti, … Genome Announcements 6 (25), e00537-18

Oak genome reveals facets of long lifespan C Plomion, JM Aury, J Amselem, T Leroy, F Murat, S Duplessis, S Faye, …Nature Plants, 1

Abstract

Conserved functions of Arabidopsis mitochondrial late-acting maturation factors in the trafficking of iron‑sulfur clusters MA Uzarska, J Przybyla-Toscano, F Spangar, F Zannini, R Lill, …Biochimica et Biophysica Acta (BBA)-Molecular Cell Research

Abstract

Numerous proteins require iron‑sulfur (Fe-S) clusters as cofactors for their function. Their biogenesis is a multi-step process occurring in the cytosol and mitochondria of all eukaryotes and additionally in plastids of photosynthetic eukaryotes. A basic model of Fe-S protein maturation in mitochondria has been obtained based on studies achieved in mammals and yeast, yet some molecular details, especially of the late steps, still require investigation. In particular, the late-acting biogenesis factors in plant mitochondria are poorly understood. In this study, we expressed the factors belonging to NFU, BOLA, SUFA/ISCA and IBA57 families in the respective yeast mutant strains. Expression of the Arabidopsis mitochondrial orthologs was usually sufficient to rescue the growth defects observed on specific media and/or to restore the abundance or activity of the defective Fe-S or lipoic acid-dependent enzymes. These data demonstrate that the plant mitochondrial counterparts, including duplicated isoforms, likely retained their ancestral functions. In contrast, the SUFA1 and IBA57.2 plastidial isoforms cannot rescue the lysine and glutamate auxotrophies of the respective isa1-isa2Δ and iba57Δ strains or of the isa1-isa2-iba57Δ triple mutant when expressed in combination. This suggests a specialization of the yeast mitochondrial and plant plastidial factors in these late steps of Fe-S protein biogenesis, possibly reflecting substrate-specific interactions in these different compartments.

Purification of Fungal High Molecular Weight Genomic DNA from Environmental Samples. L Fauchery, S Uroz, M Buée, A Kohler. Fungal Genomics, 21-35

Abstract

Sequencing of a high number of fungal genomes has become possible due to the development of next generation sequencing techniques (NGS). The most recent developments aim to sequence single-molecule long-reads in order to improve genome assemblies, but consequently needs higher quality (minimum >20 kbp) DNA as starting material. However, environmental-derived samples from soil, wood, or litter often contain phenolic compounds, pigments, and other molecules that can be inhibitors for reactions during sequencing library construction. In this chapter, we propose an optimized protocol allowing the preparation of high quality and long fragment DNA from different samples (mycelium, fruiting body, soil) compatible with the current sequencing requirements.

Molecular recognition of wood polyphenols by phase II detoxification enzymes of the white rot Trametes versicolor M Schwartz, T Perrot, E Aubert, S Dumarçay, F Favier, P Gérardin, …Scientific Reports 8 (1), 8472

Abstract

Ericoid mycorrhizal fungi and their genomes: another side to the mycorrhizal symbiosis? S Perotto, S Daghino, E Martino. The New phytologist.

Summary

The genome of an organism bears the signature of its lifestyle, and organisms with similar life strategies are expected to share common genomic traits. Indeed, ectomycorrhizal and arbuscular mycorrhizal fungi share some genomic traits, such as the expansion of gene families encoding taxon‐specific small secreted proteins, which are candidate effectors in the symbiosis, and a very small repertoire of plant cell wall‐degrading enzymes. A large gene family coding for candidate effectors was also revealed in ascomycetous ericoid mycorrhizal (ERM) fungi, but these fungal genomes are characterised by a very high number of genes encoding degradative enzymes, mainly acting on plant cell wall components. We suggest that the genomic signature of ERM fungi mirrors a versatile life strategy, which allows them to occupy several ecological niches.