3-Chloro-5-trifluoromethylpyridine-2-carboxylic acid, a Metabolite of the Fungicide Fluopyram, Causes Growth Disorder in Vitis vinifera.

The aim of this study was to investigate the effect of 3-chloro-5-trifluoromethylpyridine-2-carboxylic acid (PCA), a metabolite of the fungicide fluopyram, on grapevine. During spring and summer 2015, grapevine growth disorders were observed in several countries in Europe. An unprecedented herbicide-like damage was diagnosed on leaves and flowers, causing significant loss of harvest. This study proposes PCA as the causing agent of the observed growth disorders. PCA was shown to cause leaf epinasty, impaired berry development that leads to crop loss, and root growth anomalies in Vitis vinifera similar to auxin herbicides in a dose-dependent manner. Using both field trials and greenhouse experiments, the present study provides first evidence for a link between the application of fluopyram in vineyards 2014, the formation of PCA, and the emergence of growth anomalies in 2015. Our data could be useful to optimize dosage, application time point, and other conditions for an application of fluopyram without phytotoxic effects.

Droplets deposition pattern from a prototype of a fixed spraying system in a sloping vineyard.

In Italy high-quality vines are sometimes grown in small fields with slope steeper than 5-10%, where an air-blast sprayer is impractical so spray-gun application of pesticides is used, a technique that is very costly and labour intensive, and that causes high pesticide exposure of the operators. A possible alternative is the use of a fixed spraying system, and the first researches are in progress in Italy. A fixed spraying system prototype was built in a vineyard at Laimburg Research Centre with an upper line with micro-sprinkler and a lower line with cooler-type nozzles, and a trial was performed with the aim of measuring the deposition pattern of droplets on the row and between rows with water sensitive papers, also in comparison with a precise low-drift air-blast sprayer. Results show that with the fixed spraying system the treated crop row accounts for 38-44% of total deposition, that about 85-88% of sprayed solution falls on the sprayed row and on the closest right and left adjacent inter-rows, and that at 4 m from the spraying line the spray drift was <0.1%. This highlights that a fixed spraying system has the potential to apply plant protection products without generating drift problems, with a field performance similar to a low-drift sprayer, becoming an opportunity for vineyards on very steep slopes.

Dietary yeast affects preference and performance in Drosophila suzukii.

Yeasts play an important role in nutrition physiology and host attraction of many Drosophila species, and associations with various yeast species are documented for several drosophilid flies. The pest Drosophila suzukii (Matsumura) has a predominant association with the yeast Hanseniaspora uvarum. However, research has not been conducted on the nutritional physiology of the yeasts associated with D. suzukii (spotted wing drosophila). Therefore, in this study, we determined whether dietary yeast was nutritionally relevant and whether yeast species closely associated with D. suzukii positively affected life-history traits. Our results confirm a crucial role of dietary yeast in the larval development and survival of D. suzukii. Furthermore, we found specific effects of the closely associated yeast species H. uvarum and Candida sp. on larval survival. Observations of the egg-laying behaviour of D. suzukii on cherry fruits artificially colonised with different yeast species revealed that the number of eggs laid increased on fruits colonised with Candida sp. and Saccharomyces cerevisiae.

Forward genetic in planta screen for identification of plant-protective traits of Sphingomonas sp. strain Fr1 against Pseudomonas syringae DC3000.

Sphingomonas sp. strain Fr1 has recently been shown to protect Arabidopsis thaliana against the bacterial leaf pathogen Pseudomonas syringae DC3000. Here, we describe a forward genetic in planta screen to identify genes in Sphingomonas sp. Fr1 necessary for this effect. About 5,000 Sphingomonas sp. Fr1 mini-Tn5 mutants were assayed for a defect in plant protection against a luxCDABE-tagged P. syringae DC3000 derivative in a space-saving 24-well plate system. The bioluminescence of the pathogen was used as the indicator of pathogen proliferation and allowed for the identification of Sphingomonas sp. Fr1 mutants that had lost the ability to restrict pathogen growth before disease symptoms were visible. Potential candidates were validated using the same miniaturized experimental system. Of these mutants, 10 were confirmed as plant protection defective yet colonization competent. The mutants were subsequently evaluated in a previously described standard microbox system, and plants showed enhanced disease phenotypes after pathogen infection relative to those inoculated with the parental strain as a control. However, the disease severities were lower than those observed for control plants that were grown axenically prior to pathogen challenge, which suggests that several traits may contribute to plant protection. Transposon insertion sites of validated mutants with defects in plant protection were determined and mapped to 7 distinct genomic regions. In conclusion, the established screening protocol allowed us to identify mutations that affect plant protection, and it opens the possibility to uncover traits important for in planta microbe-microbe interactions.

Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice.

The above- and below-ground parts of rice plants create specific habitats for various microorganisms. In this study, we characterized the phyllosphere and rhizosphere microbiota of rice cultivars using a metaproteogenomic approach to get insight into the physiology of the bacteria and archaea that live in association with rice. The metaproteomic datasets gave rise to a total of about 4600 identified proteins and indicated the presence of one-carbon conversion processes in the rhizosphere as well as in the phyllosphere. Proteins involved in methanogenesis and methanotrophy were found in the rhizosphere, whereas methanol-based methylotrophy linked to the genus Methylobacterium dominated within the protein repertoire of the phyllosphere microbiota. Further, physiological traits of differential importance in phyllosphere versus rhizosphere bacteria included transport processes and stress responses, which were more conspicuous in the phyllosphere samples. In contrast, dinitrogenase reductase was exclusively identified in the rhizosphere, despite the presence of nifH genes also in diverse phyllosphere bacteria.

Protection of Arabidopsis thaliana against leaf-pathogenic Pseudomonas syringae by Sphingomonas strains in a controlled model system.

Diverse bacterial taxa live in association with plants without causing deleterious effects. Previous analyses of phyllosphere communities revealed the predominance of few bacterial genera on healthy dicotyl plants, provoking the question of whether these commensals play a particular role in plant protection. Here, we tested two of them, Methylobacterium and Sphingomonas, with respect to their ability to diminish disease symptom formation and the proliferation of the foliar plant pathogen Pseudomonas syringae pv. tomato DC3000 on Arabidopsis thaliana. Plants were grown under gnotobiotic conditions in the absence or presence of the potential antagonists and then challenged with the pathogen. No effect of Methylobacterium strains on disease development was observed. However, members of the genus Sphingomonas showed a striking plant-protective effect by suppressing disease symptoms and diminishing pathogen growth. A survey of different Sphingomonas strains revealed that most plant isolates protected A. thaliana plants from developing severe disease symptoms. This was not true for Sphingomonas strains isolated from air, dust, or water, even when they reached cell densities in the phyllosphere comparable to those of the plant isolates. This suggests that plant protection is common among plant-colonizing Sphingomonas spp. but is not a general trait conserved within the genus Sphingomonas. The carbon source profiling of representative isolates revealed differences between protecting and nonprotecting strains, suggesting that substrate competition plays a role in plant protection by Sphingomonas. However, other mechanisms cannot be excluded at this time. In conclusion, the ability to protect plants as shown here in a model system may be an unexplored, common trait of indigenous Sphingomonas spp. and may be of relevance under natural conditions.

Community proteogenomics reveals insights into the physiology of phyllosphere bacteria.

Aerial plant surfaces represent the largest biological interface on Earth and provide essential services as sites of carbon dioxide fixation, molecular oxygen release, and primary biomass production. Rather than existing as axenic organisms, plants are colonized by microorganisms that affect both their health and growth. To gain insight into the physiology of phyllosphere bacteria under in situ conditions, we performed a culture-independent analysis of the microbiota associated with leaves of soybean, clover, and Arabidopsis thaliana plants using a metaproteogenomic approach. We found a high consistency of the communities on the 3 different plant species, both with respect to the predominant community members (including the alphaproteobacterial genera Sphingomonas and Methylo bacterium) and with respect to their proteomes. Observed known proteins of Methylobacterium were to a large extent related to the ability of these bacteria to use methanol as a source of carbon and energy. A remarkably high expression of various TonB-dependent receptors was observed for Sphingomonas. Because these outer membrane proteins are involved in transport processes of various carbohydrates, a particularly large substrate utilization pattern for Sphingomonads can be assumed to occur in the phyllosphere. These adaptations at the genus level can be expected to contribute to the success and coexistence of these 2 taxa on plant leaves. We anticipate that our results will form the basis for the identification of unique traits of phyllosphere bacteria, and for uncovering previously unrecorded mechanisms of bacteria-plant and bacteria-bacteria relationships.

Identification of anammox bacteria in a full-scale deammonification plant making use of anaerobic ammonia oxidation.

The existence of anaerobic ammonia-oxidizing (anammox) bacteria was postulated in the late 1970s. Approximately 20 years later, these lithotrophic members of the nitrogen cycle were identified as deep-branching members of the planctomycetes. Recently, full-scale implementation of biological deammonification was successfully achieved in the DEMON reactor at the wastewater treatment plant in Strass, Austria. The sludge of this reactor contains red granules and brownish flocs that can be physically separated. The two fractions yielded different banding patterns in denaturing gradient gel electrophoresis of PCR products obtained with primer sets targeting the 16S rRNA genes of planctomycetes. Comparative analysis of partial sequences of almost full-length 16S rRNA gene clones obtained from the granules and flocs confirms the differences in the community composition of the two fractions. The sequences retrieved from the red granules were 93% similar to those of Candidatus Brocadia anammoxidans, a bacterium known to catalyze the anaerobic ammonia oxidation.

Microbial community related to volatile organic compound (VOC) emission in household biowaste.

Malodorous emissions and potentially pathogenic microorganisms which develop during domestic organic waste collection are not only a nuisance but may also pose health risks. The aim of the present study was to determine whether the presence of specific microorganisms in biowastes is directly related to the composition of the emitted volatile organic compounds (VOCs). The succession of microbial communities during 16 days of storage in organic waste collection bins was studied by denaturing gradient gel electrophoresis (DGGE) of amplified 16S ribosomal DNA in parallel with a classical cultivation and isolation approach. Approximately 60 different bacterial species and 20 different fungal species were isolated. Additionally, some bacterial species were identified through sequencing of excised DGGE bands. Proton transfer reaction mass spectrometry (PTR-MS) was used to detect VOCs over the sampling periods, and co-inertia analyses of VOC concentrations with DGGE band intensities were conducted. Positive correlations, indicating production of the respective VOC or enhancement of microbial growth, and negative correlations, indicating the use of, or microbial inhibition by the respective compound, were found for the different VOCs. Measurement of the VOC emission pattern from a pure culture of Lactococcus lactis confirmed the positive correlations for the protonated masses 89 (tentatively identified as butyric acid), 63 (tentatively identified as dimethylsulfide), 69 (likely isoprene) and 73 (likely butanone).