Soil suppressiveness and functional diversity of the soil microflora in organic farming systems

Arable fields of 10 organic farms from different locations within the Netherlands were sampled in four subsequent years. The soil samples were analysed for disease suppressiveness against Rhizoctonia solani, Streptomyces scabies and Verticillium dahliae. Furthermore, a variety of microbial characteristics and chemical and physical soil properties were assessed. All these characteristics and different environmental factors were correlated by multivariate analyses. Significant differences in soil suppressiveness were found for all three diseases. Suppressiveness against Rhizoctonia was more or less consistent between the sampled fields in 2004 and 2005. This suppressiveness correlated with higher numbers of Lysobacter and Pseudomonas antagonists, as well as fungal diversity in DGGE patterns. Furthermore, results of 2006 showed that one year of grass-clover clearly stimulated Rhizoctonia suppression. Also Streptomyces soil suppressiveness was consistent between 2004 and 2005, but it concerned other soils than the ones which were suppressive against Rhizoctonia. Streptomyces suppression correlated with higher numbers of antagonists in general, Streptomyces and the fungal/bacterial biomass ratio, but with a lower organic matter content and respiration. Soil suppressiveness against Verticillium was not consistent between the years and therefore probably not related to soil factors

Disease suppression in cress and sugar beet seedlings with frass of the Black Soldier Fly (Hermetia illucens)

This report describes two bioassays for testing disease suppression by BSF frass in an agricultural soil with two crops: sugar beet (Beta vulgaris) and cress (Lepidium sativum). In the bioassay with beet, soil was infected with the plant-pathogenic fungus Rhizoctonia solani while in the bioassay with cress, soil was non-infected or infected with the plant-pathogenic fungus Pythium ultimum. Both concentrations of the BSF frass (7.5 and 15 g/kg soil) proved to be useful as soil application, leading to good plant emergence and growth of sugar beet and cress plants. The highest concentration of BSF frass (15 g/kg soil, both as total product) had a large fertilizer effect. In experiments with cress without addition of Pythium (i.e. with only natural soil infections), disease suppression with BSF frass was found. In all tests, keratin was added as a positive control treatment, which had a higher disease suppression effect than BSF frass but comparable fertilizer effects

Characterization of the microbial community involved in the suppression of <i>Pythium aphanidermatum</i> in cucumber grown on rockwool

The root pathogen Pythium aphanidermatum induced lower levels of disease in cucumber (Cucumis sativus) plants on unsterilized, re-used rockwool slabs than on heat-sterilized, re-used rcckwool. Several recolonization treatments of the sterilized rockwool enhanced the suppressiveness of the rockwool. Microbial community structures in the different rockwool treatments were investigated by plate counts on selective media. Disease suppressiveness in the different rockwool treatments showed the highest correlation with the culturable number of filamentous actinomycetes in both experiments (r = 0.79 and 0.94), whereas the numbers of Trichoderma spp. correlated with suppression only in the first experiment (0.86). The numbers of total culturable bacteria, fluorescent pseudomonads, Bacillus spores, and fungi all showed lower correlations with disease suppressiveness. The filamentous actinomycetes enumerated with the plate counts were mainly Streptomyces spp., of which 10% were antagonistic toward P. aphanidermatum in dual culture. The composition of the bacterial and actinomycete populations was studied with polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE). Multivariate analyses of these patterns with canonical correspondence analysis showed significant correlations between the microbial composition and the disease suppressiveness. However, none of the bands in PCR-DGGE patterns occurred exclusively in the treatments that had enhanced disease suppressiveness. Bands extracted from the actinomycete-specific DGGE gels showed closest similarity with members of several actinomycete genera, i.e., Streptomyces, Mycobacterium, Microbacterium, Rhodococcus, Curtobacterium, and Tsukamurella. The possible mechanism of disease suppressiveness in used rockwool slabs, based on the results obtained with culture-dependent and culture-independent detection methods, is discussed

Indigenous Populations of Three Closely Related Lysobacter spp. in Agricultural Soils Using Real-Time PCR

Previous research had shown that three closely related species of Lysobacter, i.e., Lysobacter antibioticus, Lysobacter capsici, and Lysobacter gummosus, were present in different Rhizoctonia-suppressive soils. However, the population dynamics of these three Lysobacter spp. in different habitats remains unknown. Therefore, a specific primer–probe combination was designed for the combined quantification of these three Lysobacter spp. using TaqMan. Strains of the three target species were efficiently detected with TaqMan, whereas related non-target strains of Lysobacter enzymogenes and Xanthomonas campestris were not or only weakly amplified. Indigenous Lysobacter populations were analyzed in soils of 10 organic farms in the Netherlands during three subsequent years with TaqMan. These soils differed in soil characteristics and crop rotation. Additionally, Lysobacter populations in rhizosphere and bulk soil of different crops on one of these farms were studied. In acid sandy soils low Lysobacter populations were present, whereas pH neutral clay soils contained high populations (respectively, <4.0–5.87 and 6.22–6.95 log gene copy numbers g−1 soil). Clay content, pH and C/N ratio, but not organic matter content in soil, correlated with higher Lysobacter populations. Unexpectedly, different crops did not significantly influence population size of the three Lysobacter spp. and their populations were barely higher in rhizosphere than in bulk soil

Using Verticillium albo-atrum WCS850 to control Dutch elm disease

Approximately 100 years after the first introduction of Dutch elm disease (DED) in Europe, an effective commercial biocontrol product is available to protect susceptible elm trees against DED transmission by beetles. Injection of trees with conidiospores of the fungus Verticilium albo-atrum isolate WCS850, product name DutchTrig®, reduces infection to less than 0.2% of treated trees. This biocontrol agent, its mode of action, application, efficacy and limitations in controlling DED are described in this chapter

Twenty-four years of Dutch Trig^® application to control Dutch elm disease

Since 1992 elm trees have been treated with a biological control product Dutch Trig® to protect them from infection by Ophiostoma novo-ulmi causing Dutch elm disease (DED). The active ingredient of the biocontrol product consists of the fungus Verticillium albo-atrum strain WCS850. A conidiospore suspension of this fungus is injected into the vascular system of elm trees at a height of 1.3 m. This biocontrol product prevents healthy elm trees from fungal infection transmitted by elm bark beetles. Dutch Trig®, however, does not protect already infected trees or trees connected with diseased trees via root grafts. Since 2010, only 0.1 % of the injected elms became infected with DED through beetle transmission and an additional 0.4 % of the treated elms were infected through root contact in the Netherlands. Regression analysis considering all injected elm trees in the Netherlands since 1992 indicated that DED infection through beetle transmission had significantly decreased during the 24 years application of Dutch Trig®. In 2015, approximately 28,300 trees in five countries (Netherlands, USA, Germany, Canada and Sweden) were treated with Dutch Trig® to protect valuable susceptible elm trees, mainly in urban environments.</p

Bodemgezondheidproef 2017-2020 : langjarig onderzoek naar het effect van verschillende maatregelen en teeltsystemen op het bodemmicrobioom en ziektewering

In een lang termijn veldproef sinds 2006, zijn in 2018 10 verschillende bodemmaatregelen uitgevoerd in zowel een gangbaar als een biologisch landbouwsysteem. De maatregelen waren zwarte braak (CTR), teelt van gras/klaver (GRK), teelt van Tagetes patula (TAG), teelt van een groenbemestermengsel (MIX), compost (CMP), chitine (CHI), haarmeel (HRM), anaerobe grondontsmetting (ASD), grondontsmetting (ONT: NGO of CAL) en een combinatie van anaerobe grondontsmetting, haarmeel en compost (AHC). Vervolgens werden of verschillende tijdstippen in 2018, 2019 en 2020 een aantal microbiologische en bodembiologische parameters gemeten. In 2018 is het bodemmicrobioom geanalyseerd, i.e. de samenstelling van de bacteriële en schimmelgemeenschap in de bodem. In vergelijking met de controle was de diversiteit van beide groepen verlaagd in de diverse ontsmettingsbehandelingen. Ook verschilde de samenstelling van de microbiële gemeenschappen duidelijk tussen de ontsmettingsbehandelingen en de overige behandelingen. Wel was de DNA concentratie van zowel schimmels als bacteriën vaak hoger in met name de anaerobe grond ontsmetting (ASD) en de combi (AHC) behandeling. Het biologische en gangbare landbouwsysteem verschilden weinig van elkaar.In zowel 2018 als 2019 zijn biotoetsen uitgevoerd om de weerbaarheid van de grond tegen Rhizoctoniasolani en Pythium ultimum te meten. Voor R. solani was de ziekteincidentie in alle behandelingen hoog en er is dus nauwelijks weerbaarheid gemeten. Voor P. ultimum daarentegen was de weerbaarheid in beide jaren duidelijk hoger in de AHC behandeling dan in de andere behandelingen.In 2020 is het microbioom middels PLFA analyse onderzocht in de CTR, CMP en AHC behandelingen. Hierbij waren veel parameters, zoals de microbiële biomassa, het aantal bacteriën en schimmels en mycorrhiza verhoogd in het biologische landbouwsysteem vergeleken met het gangbare systeem. De meeste parameters waren het hoogst in de combi behandelingen, wat duidt op hogere biomassa en activiteit van het microbioom.De schimmel en bacterie biomassa werd tegelijkertijd ook met klassieke microscopische methoden in kaart gebracht. Deze toonden geen correlatie met de PLFA metingen en er waren geen significanteverschillen tussen de landbouwsystemen en behandelingen.HWC (heet-water extraheerbare koolstof) is in 2019 gemeten in alle behandelingen, met significant hogere waardes in de combi behandeling en de anaerobe grond ontsmetting. Dit komt overeen met de hogere microbiële biomassa en hogere concentratie van schimmel- en bacterie DNA. Ook de MIX, CMPen CHI behandelingen bevatten meer HWC dan de controle. In 2020 waren zowel HWC als PMN(potentieel mineraliseerbare stikstof) het hoogst in de AHC behandeling.In 2020 is in de controle, compost en combi behandelingen bodemrespiratie gemeten en het vermogen van de microbiële gemeenschap om verschillende organische stoffen te mineraliseren (i.e. Microresp).Respiratie was verhoogd in de AHC behandeling. Voor de Microresp analyse is geen duidelijk patroon van verschillen tussen de behandelingen waargenomen.Alle metingen tonen een sterk effect van de combinatie behandeling op het bodemmicrobioom, wat een van de meest ingrijpende behandelingen voorstelde. De meeste veranderingen waren positief, zoals verhoogde weerbaarheid tegen P. ultimum en een verhoogde microbiële biomassa en activiteit. Maar ook andere behandelingen, zoals compost en anaerobe grondontsmetting lieten effecten zien op het microbioom. De verschillen tussen het biologische en gangbare landbouwsysteem waren doorgaans minder groot