Brassica cover crops can reduce nematode pests

The possibility of controlling soil-borne pest nematodes by using Brassica species plants as cover crops in the inter-row space of vineyards followed by biomass incorporation and so called biofumigation was investigated in the CORE Organic Cofund project BIOVINE

Almighty Cover Crops

Fungal pathogens are able to produce inoculum (spores) on plant debris present on the soil surface of vineyards. These spores can then reach plant surfaces and cause severe grapevine infections when environmental conditions are favourable. The capacity of plant diversity to increase the resistance of crops towards pests and invasive species is very well-known. For instance, Brassica spp. have been already investigated for their capacity to effectively suppress soil-borne inoculum of some causal agents of Black-foot disease in grapevines in vineyard soils. It may also have positive effect on the some dagger nematodes. Cover crops also stimulate the development of microbial communities such as arbuscular mycorrhizal fungi. Many management strategies have been developed against these important grapevine pathogens, but the effects of soil cover vegetation or organic mulching against spore dispersal, acting as a barrier, have been scarcely explored. Thus, in the BIOVINE project (www.biovine.eu) specific experiments were planned in order to verify the possibility of using cover crops: i) to control some relevant pathogens producing inoculum (spores) on plant debris present on the soil surface of vineyards; ii) to determine the presence of causal agents of Petri disease of grapevines on the roots of cover crops; iii) to promote mykorrhizal communities associated with grapevine roots; iv) to control arthropod pests (repellent of arthropods or attracting beneficials); v) to investigate Brassica plants effect on the soil-borne pest nematode Xiphinema index

The use of advanced technologies for integrated management of root-knot nematodes (Meloidogyne spp., Nematoda: Meloidogynidae)

Tropske vrste ogorčic koreninskih šišk (RKN) so izredno polifagni škodljivci v kmetijstvu, kjer povzročajo velike izgube pridelka. Nekatere vrste, kot so Meloidogyne ethiopica, M. inornata in M. luci (MEG), je zaradi visoke sorodnosti težavno razlikovati. Sekvencirali smo 7 izolatov ogorčic iz skupine MEG ter po zlaganju zaporedij genomov določili filogenetsko umestitev v rod. Zloženi genom ogorčice M. luci SI-Smartno V13 je s 327 kontigi, N50 dolžini kontigov 1,7 Mb in končni dolžini zloženega zaporedja 209,2 Mb, trenutno najpopolnejši javno dostopen genom RKN. Filogenetska analiza je pokazala na umestitev vseh izolatov iz skupine MEG v enoten monofiletski klad, vrsta M. luci se je bistveno razlikovala od vrst M. ethiopica in M. inornata. Preizkušali smo uporabnost hiperspektralnega slikanja za zgodnje razločevanje biotskega stresa (napad RKN) od abiotskega stresa (suša) pri rastlinah paradižnika. Z analizo hiperspektralnih posnetkov v območju spektra 400-2500 nm je bilo mogoče razlikovati med dobro zalitimi ter sušnimi rastlinami s 100 % natančnostjo, z 90-100 % natančnostjo pa je bilo mogoče razlikovati med zdravimi in napadenimi rastlinami. Ovrednotili smo nematicidno aktivnost in analizirali genoma bakterij Bacillus firmus I-1582 in Bacillus sp. ZZV12-4809, v katerih smo našli številne potencialne dejavnike virulence. V lončnih poskusih in na mikroparcelah je sev I-1582 zmanjšal število ogorčic M. luci za 51-53 % v primerjavi s kontrolo. Bakterije I-1582 so delovale nematicidno ter spodbudile rast rastlin, kar smo pokazali z meritvami morfologije rastlin, relativne vsebnosti klorofila, vsebnostjo elementov in analizo hiperspektralnih posnetkov. Z analizo hiperspektralnih posnetkov z nadzorovano klasifikacijo smo uspešno razlikovali med rastlinami tretiranimi z B. firmus in rastlinami brez bakterij – v lončnem poskusu smo dosegli 97,4 % uspešnost, na mikroparcelah pa 96,3 %.Tropical root-knot nematodes (RKN) are extremely polyphagous pests causing large yield losses in agriculture. Some species, such as Meloidogyne ethiopica, M. inornata and M. luci (MEG) are highly related and difficult to distinguish. We sequenced 7 RKN isolates from the MEG group and following the genome assembly, determined their phylogenetic position within the genus. The genome assembly of M. luci SI-Smartno V13 is currently the most complete publicly available RKN genome, having 327 contigs, N50 contig size of 1.7 Mb, and final assembly size of 209.2 Mb. Phylogenetic analysis showed the positioning of all MEG-group isolates within a single monophyletic clade, and the species M. luci differed significantly from the species M. ethiopica and M. inornata. We tested the applicability of hyperspectral imaging for the early differentiation of biotic stress (RKN infestation) from abiotic stress (drought) in tomato plants. Using hyperspectral image analysis in the 400-2500 nm spectral range, it was possible to distinguish well-watered from water deficient plants with 100 % accuracyand nematode-infested from healthy plants with 90-100 % accuracy. We also evaluated nematicidal activity and analysed the genomes of Bacillus firmus I-1582 and Bacillus sp. ZZV12-4809 and found multiple putative virulence factors. In the pot experiments as well as in the microplots, the strain I-1582 reduced M. luci infestation rates by 51-53 % compared to untreated control. I-1582 showed nematicidal and plant-growth promoting effects, as indicated by plant morphology measurements, relative chlorophyll content, leaf nutrient composition, and hyperspectral image analysis. Utilising supervised classification for hyperspectral image analysis, we successfully discriminated between B. firmus-treated and untreated plants – in the pot experiment we achieved 97.4 % and in the microplot experiment 96.3 % classification success

The use of advanced technologies for integrated management of root-knot nematodes (Meloidogyne spp., Nematoda: Meloidogynidae)

Tropske vrste ogorčic koreninskih šišk (RKN) so izredno polifagni škodljivci v kmetijstvu, kjer povzročajo velike izgube pridelka. Nekatere vrste, kot so Meloidogyne ethiopica, M. inornata in M. luci (MEG), je zaradi visoke sorodnosti težavno razlikovati. Sekvencirali smo 7 izolatov ogorčic iz skupine MEG ter po zlaganju zaporedij genomov določili filogenetsko umestitev v rod. Zloženi genom ogorčice M. luci SI-Smartno V13 je s 327 kontigi, N50 dolžini kontigov 1,7 Mb in končni dolžini zloženega zaporedja 209,2 Mb, trenutno najpopolnejši javno dostopen genom RKN. Filogenetska analiza je pokazala na umestitev vseh izolatov iz skupine MEG v enoten monofiletski klad, vrsta M. luci se je bistveno razlikovala od vrst M. ethiopica in M. inornata. Preizkušali smo uporabnost hiperspektralnega slikanja za zgodnje razločevanje biotskega stresa (napad RKN) od abiotskega stresa (suša) pri rastlinah paradižnika. Z analizo hiperspektralnih posnetkov v območju spektra 400-2500 nm je bilo mogoče razlikovati med dobro zalitimi ter sušnimi rastlinami s 100 % natančnostjo, z 90-100 % natančnostjo pa je bilo mogoče razlikovati med zdravimi in napadenimi rastlinami. Ovrednotili smo nematicidno aktivnost in analizirali genoma bakterij Bacillus firmus I-1582 in Bacillus sp. ZZV12-4809, v katerih smo našli številne potencialne dejavnike virulence. V lončnih poskusih in na mikroparcelah je sev I-1582 zmanjšal število ogorčic M. luci za 51-53 % v primerjavi s kontrolo. Bakterije I-1582 so delovale nematicidno ter spodbudile rast rastlin, kar smo pokazali z meritvami morfologije rastlin, relativne vsebnosti klorofila, vsebnostjo elementov in analizo hiperspektralnih posnetkov. Z analizo hiperspektralnih posnetkov z nadzorovano klasifikacijo smo uspešno razlikovali med rastlinami tretiranimi z B. firmus in rastlinami brez bakterij – v lončnem poskusu smo dosegli 97,4 % uspešnost, na mikroparcelah pa 96,3 %.Tropical root-knot nematodes (RKN) are extremely polyphagous pests causing large yield losses in agriculture. Some species, such as Meloidogyne ethiopica, M. inornata and M. luci (MEG) are highly related and difficult to distinguish. We sequenced 7 RKN isolates from the MEG group and following the genome assembly, determined their phylogenetic position within the genus. The genome assembly of M. luci SI-Smartno V13 is currently the most complete publicly available RKN genome, having 327 contigs, N50 contig size of 1.7 Mb, and final assembly size of 209.2 Mb. Phylogenetic analysis showed the positioning of all MEG-group isolates within a single monophyletic clade, and the species M. luci differed significantly from the species M. ethiopica and M. inornata. We tested the applicability of hyperspectral imaging for the early differentiation of biotic stress (RKN infestation) from abiotic stress (drought) in tomato plants. Using hyperspectral image analysis in the 400-2500 nm spectral range, it was possible to distinguish well-watered from water deficient plants with 100 % accuracyand nematode-infested from healthy plants with 90-100 % accuracy. We also evaluated nematicidal activity and analysed the genomes of Bacillus firmus I-1582 and Bacillus sp. ZZV12-4809 and found multiple putative virulence factors. In the pot experiments as well as in the microplots, the strain I-1582 reduced M. luci infestation rates by 51-53 % compared to untreated control. I-1582 showed nematicidal and plant-growth promoting effects, as indicated by plant morphology measurements, relative chlorophyll content, leaf nutrient composition, and hyperspectral image analysis. Utilising supervised classification for hyperspectral image analysis, we successfully discriminated between B. firmus-treated and untreated plants – in the pot experiment we achieved 97.4 % and in the microplot experiment 96.3 % classification success

Discrimination between abiotic and biotic drought stress in tomatoes using hyperspectral imaging

Crop plants are subjected to various biotic and abiotic stresses. Both root-knot nematodes (biotic stress) and water deficiency (abiotic stress) lead to similar drought symptoms in the plant canopy. In this work, hyperspectral imaging was used for early detection of nematode infestation and water deficiency (drought) stress in tomato plants. Hyperspectral data in the range from 400 to 2500 nm of plants subjected to different watering regimes and nematode infestation levels were analysed by partial least squares – discriminant analysis (PLS-DA) and partial least squares – support vector machine (PLS-SVM) classification. PLS-SVM classification achieved up to 100% accuracy differentiating between well-watered and water-deficient plants, and between 90 and 100% when identifying nematode-infested plants. Grouping the data according to the time of imaging increased the accuracy of classification. Shortwave infrared spectral regions associated with the OH and CH stretches were most relevant for the identification of nematode infested plants and severity of infestation. This study demonstrates the capability of hyperspectral imaging to identify and discriminate between biotic and abiotic plant stresses

From Genome to Field—Observation of the Multimodal Nematicidal and Plant Growth-Promoting Effects of Bacillus firmus I-1582 on Tomatoes Using Hyperspectral Remote Sensing

Root-knot nematodes are considered the most important group of plant-parasitic nematodes due to their wide range of plant hosts and subsequent role in yield losses in agricultural production systems. Chemical nematicides are the primary control method, but ecotoxicity issues with some compounds has led to their phasing-out and consequential development of new control strategies, including biological control. We evaluated the nematicidal activity of Bacillus firmus I-1582 in pot and microplot experiments against Meloidogyne luci. I-1582 reduced nematode counts by 51% and 53% compared to the untreated control in pot and microplot experiments, respectively. I-1582 presence in the rhizosphere had concurrent nematicidal and plant growth-promoting effects, measured using plant morphology, relative chlorophyll content, elemental composition and hyperspectral imaging. Hyperspectral imaging in the 400–2500 nm spectral range and supervised classification using partial least squares support vector machines successfully differentiated B. firmus-treated and untreated plants, with 97.4% and 96.3% accuracy in pot and microplot experiments, respectively. Visible and shortwave infrared spectral regions associated with chlorophyll, N–H and C–N stretches in proteins were most relevant for treatment discrimination. This study shows the ability of hyperspectral imaging to rapidly assess the success of biological measures for pest control

Early Detection of Wireworm (Coleoptera: Elateridae) Infestation and Drought Stress in Maize Using Hyperspectral Imaging

The objective of our research was to test hyperspectral imaging as a method for early detection and discrimination of biotic and abiotic stress in maize. We investigated the individual and combined effects of wireworm feeding and drought stress on leaf spectral responses and on various morphological and physiological traits of maize plants, selecting two hybrids with different tolerance to drought. Physiological parameters were determined at three time points (14, 21 and 28 days after adding wireworms and changing watering regime), along with hyperspectral imaging. Most of the differences in physiological characteristics between treatments were detected on day 21, when drought was the main cause of the negative physiological outcome, while the presence of wireworms only caused lower relative chlorophyll content, resulting in lower combined stress damage in some treatments. The morphological data showed greater wireworm damage to hybrid ZP341 and a greater negative effect of combined stress on hybrid FuturiXX. Hyperspectral imaging detected pest infestation and drought stress before they were detected by classical methods, with the highest overall accuracy on day 14 (84.7%) and the lowest on day 28 (67%). It can therefore be used as a method for early detection of wireworm infestation and/or drought in maize