Gnomoniopsis smithogilvyi causes chestnut canker symptoms in Castanea sativa shoots in Switzerland.

A screening of Castanea sativa scions for grafting for the presence of endophytes showed that the opportunistic fungal pathogen Gnomoniopsis smithogilvyi was the most abundant member of the endophytic flora. This fungus is known as a pathogen affecting chestnut fruits in Italy and Australia. Here, we present evidence that it causes cankers very similar to the ones due to Cryphonectria parasitica infection on twigs and scions of chestnut trees. We found natural infections of G. smithogilvyi in healthy grafted plants as well as in scions from chestnut trees. The identity of the fungus isolated from asymptomatic tissues was verified by applying Koch's postulates and corroborated by DNA sequencing of four different gene regions. In contrast to C. parasitica that appears on the bark as yellow to orange pycnidia, stromata and slimy twisted tendrils, G. smithogilvyi forms orange to red and black pycnidia, gray stromata and cream-colored to beige slimy twisted tendrils on the bark. These Swiss strains are closely related to G. smithogilvyi strains from Australia and from New Zealand, Gnomoniopsis sp. and Gnomoniopsis castanea from New Zealand, Italy, France and Switzerland. While the strains from Ticino are genetically very close to G. smithogilvyi and G. castanea from Italy, the differences between the strains from Ticino and Geneva suggest two different origins. The present study supports the hypothesis that a single species named G. smithogilvyi, which is known to be the agent of chestnut rot, also causes wood cankers on chestnut.

Green fluorescent protein (GFP) as a reporter gene for the plant pathogenic oomycete Phytophthora ramorum.

Transgenic Phytophthora ramorum strains that produce green fluorescent protein (GFP) constitutively were obtained after stable DNA integration using a polyethylene glycol and CaCl2-based transformation protocol. Green fluorescent protein production was studied in developing colonies and in different propagules of the pathogen to evaluate its use in molecular and physiological studies. About 12% of the GFP transformants produced GFP to a level detectable by a confocal laser scanning microscope. Green fluorescent protein could be visualized in structures with vital protoplasm, such as hyphal tips and germinating cysts. In infection studies with Rhododendron, one of the GFP expressing strains showed aggressiveness equal to that of the corresponding non-labelled isolate. Thus, GFP could be used as a reporter gene in P. ramorum. Limitations of the technology are discussed.

Evolution of the cutinase gene family: evidence for lateral gene transfer of a candidate Phytophthora virulence factor.

Lateral gene transfer (LGT) can facilitate the acquisition of new functions in recipient lineages, which may enable them to colonize new environments. Several recent publications have shown that gene transfer between prokaryotes and eukaryotes occurs with appreciable frequency. Here we present a study of interdomain gene transfer of cutinases -- well documented virulence factors in fungi -- between eukaryotic plant pathogens Phytophthora species and prokaryotic bacterial lineages. Two putative cutinase genes were cloned from Phytophthora brassicae and Northern blotting experiments showed that these genes are expressed early during the infection of the host Arabidopsis thaliana and induced during cyst germination of the pathogen. Analysis of the gene organisation of this gene family in Phytophthora ramorum and P. sojae showed three and ten copies in tight succession within a region of 5 and 25 kb, respectively, probably indicating a recent expansion in Phytophthora lineages by gene duplications. Bioinformatic analyses identified orthologues only in three genera of Actinobacteria, and in two distantly related eukaryotic groups: oomycetes and fungi. Together with phylogenetic analyses this limited distribution of the gene in the tree of life strongly support a scenario where cutinase genes originated after the origin of land plants in a microbial lineage living in proximity of plants and subsequently were transferred between distantly related plant-degrading microbes. More precisely, a cutinase gene was likely acquired by an ancestor of P. brassicae, P. sojae, P. infestans and P. ramorum, possibly from an actinobacterial source, suggesting that gene transfer might be an important mechanism in the evolution of their virulence. These findings could indeed provide an interesting model system to study acquisition of virulence factors in these important plant pathogens.

Intraspecific and within-isolate sequence variation in the ITS rRNA gene region of Pythium mercuriale sp. nov. (Pythiaceae).

Sixteen Pythium isolates from diverse hosts and locations, which showed similarities in their morphology and sequences of the internal transcribed spacer (ITS) region of their rRNA gene, were investigated. As opposed to the generally accepted view, within single isolates ITS sequence variations were consistently found mostly as part of a tract of identical bases (A-T) within ITS1, and of GT or GTTT repeats within the ITS2 sequence. Thirty-one different ITS sequences obtained from 39 cloned ITS products from the 16 isolates showed high sequence and length polymorphisms within and between isolates. However, in a phylogenetic analysis, they formed a cluster distinct from those of other Pythium species. Additional sequencing of two nuclear genes (elongation factor 1 alpha and beta-tubulin) and one mitochondrial gene (nadh1) revealed high levels of heterozygosity as well as polymorphism within and between isolates, with some isolates possessing two or more alleles for each of the nuclear genes. In contrast to the observed variation in the ITS and other gene areas, all isolates were phenotypically similar. Pythium mercuriale sp. nov. (Pythiaceae) is characterized by forming thin-walled chlamydospores, subglobose to obovoid, papillate sporangia proliferating internally and smooth-walled oogonia surrounded by multiple antheridia. Maximum likelihood phylogenetic analyses based on both ITS and beta-tubulin sequence data place P. mercuriale in a clade between Pythium and Phytophthora.

Multi-loci sequence typing (MLST) for two lacto-acid bacteria (LAB) species: Pediococcus parvulus and P. damnosus.

The control of wine microbial population during and beyond fermentation is of huge importance for wine quality. Lactic acid bacteria (LAB) in wine are responsible for malolactic fermentation (MLF) which can be desired in some cases and undesirable in others. Some LAB do not perform MLF and their uncontrolled growth could contribute to severe wine spoilage such as undesired flavours. Their identification and detection is considered crucial for numerous biotechnological applications in food fermentations, where, through acidification and secretion of bacteriocins, they contribute to reduce food spoilage and growth of pathogenic microorganisms. LAB have traditionally been classified using morphological or biochemical features. Primary isolation, biochemical identification and phenotypic analysis are laborious, time consuming and inaccurate and often lead to misidentification within some genera such as Pediococcus. Molecular identification based on suitable marker genes could be an attractive alternative to conventional morphological and biochemical methods. We assessed here the applicability of four housekeeping genes recA, rplB, pyrG and leuS in combination with the mle gene in multi-loci sequence typing (MLST) of Pediococcus parvulus and Pediococcus damnosus. Sequencing and comparative analysis of sequence data were performed on 19 strains collected during wine fermentation. A combination of these five marker genes allowed for a clear differentiation of the strains analysed, indicating their applicability in molecular typing. Analysis of the observed nucleotide polymorphisms allowed designing highly discriminative primers for a multi-loci sequence typing (MLST) method that proved successful in detecting a particular isolate or sequence type of P. parvulus when using either conventional PCR or Real Time PCR.

Pythium recalcitrans sp. nov. revealed by multigene phylogenetic analysis.

A new species of Pythium collected from grapevine roots (Vitis vinifera) in South Africa and roots of common beet (Beta vulgaris) in Majorca, Spain, is described. The phylogenetic position of the new species was investigated by multigene sequence analyses of the internal transcribed spacers (ITS1 and ITS2) of the rDNA region, as well as three other nuclear and three mitochondrial coding genes. Maximum likelihood phylogenetic analyses based on ITS rDNA and concatenated beta-tubulin and cytrochrome c oxidase II alignment place Pythium recalcitrans together with P. sylvaticum and P. intermedium. Pythium recalcitrans sp. nov. is morphologically almost indistinguishable from other Pythium species that only form hyphal swellings in culture. However its species status is justified by the distinctiveness of the DNA sequences in all the genes examined. In culture P. recalcitrans exhibits fast radial growth, abundant spherical to subglobose hyphal swellings but produces no zoosporangia. Sexual structures are not seen in agar media but form in autoclaved grass blades floated on water. Multiple antheridia (1-7) are encountered with most of them diclinous and crook-necked. Oospores are thin-walled and either aplerotic or plerotic. P. recalcitrans was pathogenic to seedlings of Beta vulgaris and Solanum lycopersicum.

Metagenomes and Metatranscriptomes of Activated Sludge from a Sewage Plant, with or without Aerobic Granule Enrichment.

We report here the metagenomes and metatranscriptomes of activated sludge bioreactors, enriched or not enriched with aerobic granules, at an initial state and after 1 month of incubation. Data showed that the added granular biomass expressed higher levels of expression of genes involved in ammonia elimination.

Metatranscriptomic and metagenomic description of the bacterial nitrogen metabolism in waste water wet oxidation effluents.

Anaerobic digestion is a common method for reducing the amount of sludge solids in used waters and enabling biogas production. The wet oxidation process (WOX) improves anaerobic digestion by converting carbon into methane through oxidation of organic compounds. WOX produces effluents rich in ammonia, which must be removed to maintain the activity of methanogens. Ammonia removal from WOX could be biologically operated by aerobic granules. To this end, granulation experiments were conducted in 2 bioreactors containing an activated sludge (AS). For the first time, the dynamics of the microbial community structure and the expression levels of 7 enzymes of the nitrogen metabolism in such active microbial communities were followed in regard to time by metagenomics and metatranscriptomics. It was shown that bacterial communities adapt to the wet oxidation effluent by increasing the expression level of the nitrogen metabolism, suggesting that these biological activities could be a less costly alternative for the elimination of ammonia, resulting in a reduction of the use of chemicals and energy consumption in sewage plants. This study reached a strong sequencing depth (from 4.4 to 7.6 Gb) and enlightened a yet unknown diversity of the microorganisms involved in the nitrogen pathway. Moreover, this approach revealed the abundance and expression levels of specialised enzymes involved in nitrification, denitrification, ammonification, dissimilatory nitrate reduction to ammonium (DNRA) and nitrogen fixation processes in AS.

Metagenome-Assembled Genome Sequence of Rhodopseudomonas palustris Strain ELI 1980, Commercialized as a Biostimulant.

We report here the draft genome sequence of strain ELI 1980 of Rhodopseudomonas palustris, commercialized as a biostimulant for agriculture. The genome was reconstructed from the metagenome of a commercial product containing this strain as its major component.

Pythium sterilum sp. nov. isolated from Poland, Spain and France: its morphology and molecular phylogenetic position.

In a survey of Phytophthora species associated with forest decline in Spain, Poland and France, we found three Pythium isolates, which have been characterized with internal transcribed spacer rRNA gene sequences and with classical morphological descriptors for Pythium spp. These isolates showed unique internal transcribed spacer sequences, different enough from those of any described species to justify new species status. These three distinct isolates failed to produce any sex organs with an entirely asexual reproduction and were found to represent a new species for which the name Pythium sterilum is proposed. This paper describes and illustrates the morphology of P. sterilum and presents its taxonomic position and relationships with other, related Pythium species belonging to clade K.

Phytophthora polonica, a new species isolated from declining Alnus glutinosa stands in Poland.

In a survey of Phytophthora associated with alder decline in Poland, several isolates of a homothallic Phytophthora sp., which could not be assigned to other taxa including Phytophthora alni subspecies, were consistently recovered from rhizosphere soil samples. Their morphology and pathogenicity, as well as sequence data for three nuclear regions (internal transcribed spacer rDNA, elongation factor-1alpha and beta-tubulin) and a coding mitochondrial DNA region (nadh1), were examined. The new Phytophthora species is characterized by the moderate to slow growth rate of its colony in carrot agar at 20 degrees C, high optimal (c. 30 degrees C) and maximum (c. 38 degrees C) growth temperatures, formation of catenulate, often lateral, hyphal swellings, large chlamydospores in agar media and in soil extract, persistent, ovoid to ellipsoid nonpapillate sporangia and large oogonia with paragynous and sometimes amphigynous antheridia. Phytophthora polonica was slightly pathogenic to alder twigs and not pathogenic to trunks of several tree species. In a phylogenetic analysis using either Bayesian inference or maximum likelihood methods, P. polonica falls in clade 8 'sensu Kroon et al. (2004)' of Phytophthora.

A new species of Pythium with ornamented oogonia: morphology, taxonomy, internal transcribed spacer region of its ribosomal RNA, and its comparison with related species.

Pythium spiculum sp. nov. was isolated from soil samples taken in a vineyard in the Burgundian region of France and from different locations in Spain and Portugal. The oomycete has spiny oogonia and does not sporulate readily. It resembles Pythium mamillatum Meurs, but has its own distinguishing characteristics. It also exhibits sickle-shaped as well as spherical appressoria which at times are associated with sex organs like those found in Pythium abappressorium Paulitz and Pythium contiguanum Paul. Sequencing of the internal transcribed spacer region of its nuclear ribosomal DNA and a close look at its morphological characters have now enabled us to describe it as a new species. The internal transcribed spacer region of its rRNA gene sequence is comprised of 945 bases. This oomycete is closely related to the members that form ornamented or spiny oogonia like Pythiummamillatum, Pythium spinosum and Pythium irregulare but also with those producing smooth-walled oogonia like Pythium paroecandrum, Pythium sylvaticum and Pythium cylindrosporum. Taxonomic description of this new species, its comparison with related oomycetes, the sequence of the internal transcribed spacer region of its rRNA gene and the phylogenetic tree, are given here.

Whole-Genome Sequence of Bradyrhizobium elkanii Strain UASWS1015, a Highly Ammonia-Tolerant Nitrifying Bacterium.

Bradyrhizobium elkanii UASWS1015 was isolated from a sewage plant in Switzerland. Its genome indicates that it is fully equipped for ammonia assimilation and aromatic compound degradation, and it displays a large type IV secretion system, which characterizes plant-associated microbes. Totally deprived of toxins, it could be considered for agricultural and environmental uses.

Whole-Genome Sequence of Enteractinococcus helveticum sp. nov. Strain UASWS1574 Isolated from Industrial Used Waters.

We report here the whole-genome shotgun sequences of the strain UASWS1574 of the undescribed Enteractinococcus helveticum sp. nov., isolated from used water. This is the first genome registered for the whole genus.

Whole-Genome Sequence of Pseudomonas xanthomarina Strain UASWS0955, a Potential Biological Agent for Agricultural and Environmental Uses.

We report here the whole-genome shotgun sequence of the strain UASWS0955 of the species Pseudomonas xanthomarina, isolated from sewage sludge. This genome was obtained with an Illumina MiniSeq and is the second genome registered for this species, which is considered as a promising resource for agriculture and bioremediation of contaminated soils.

Whole-Genome Sequence of Mesorhizobium hungaricum sp. nov. Strain UASWS1009, a Potential Resource for Agricultural and Environmental Uses.

We report here the whole-genome shotgun sequences of the strain UASWS1009 of the species Mesorhizobium hungaricum sp. nov., which are different from any other known Mesorhizobium species. This is the first genome registered for this new species, which could be considered as a potential resource for agriculture and environmental uses.

Whole-Genome Sequence of Bradyrhizobium elkanii Strain UASWS1016, a Potential Symbiotic Biofertilizer for Agriculture.

Bradyrhizobium elkanii UASWS1016 has been isolated from a wet oxidation sewage plant in Italy. Fully equipped for ammonia assimilation, heavy metal resistances, and aromatic compounds degradation, it carries a large type IV secretion system, specific of plant-associated microbes. Deprived of toxins, it could be considered for agricultural and environmental uses.

Whole-Genome Sequence of Pseudomonas graminis Strain UASWS1507, a Potential Biological Control Agent and Biofertilizer Isolated in Switzerland.

We report here the whole-genome shotgun sequence of the strain UASWS1507 of the species Pseudomonas graminis, isolated in Switzerland from an apple tree. This is the first genome registered for this species, which is considered as a potential and valuable resource of biological control agents and biofertilizers for agriculture.

Whole-Genome Sequences of Seven Strains of Bacillus cereus Isolated from Foodstuff or Poisoning Incidents.

We present here the whole shotgun genome sequences of seven strains of Bacillus cereus isolated from foodstuff samples or food poisoning incidents.

Whole-Genome Sequence of Pseudomonas putida Strain UASWS0946, a Highly Ammonia-Tolerant Nitrifying Bacterium Isolated from Sewage Sludge Aerobic Granules.

We report here the genome of Pseudomonas putida strain UASWS0946, a highly ammonia-tolerant nitrifying strain isolated from sewage sludge aerobic granules, which displays adequate genetic equipment for soil depollution, sludge treatment, and biological fertilization in agriculture.