Bodemmicrobiologie als indicator voor bodemkwaliteit?

De Rusch-test is een relatief goedkope en eenvoudige microbiologische test die werd ontwikkeld door dokter en wetenschapper Hans Peter Rusch uit Duitsland, maar tot hiertoe weinig toepassing gekend heeft. De doelstelling van dit project was na te gaan of de Rusch-test kan dienen als indicator voor een goede bodemkwaliteit en of deze eenvoudige test, voor de teler interessante info kan opleveren in verband met de gevolgde of te volgen teeltpraktijk. Hiervoor werd in het eerste luik van het project, op verschillende biologische percelen in Vlaanderen, gedurende twee jaren, de bodemmicrobiologie door middel van drie verschillende methodes bepaald (Rusch, PLFA en DGGE). Naast het analyseren van de bodemmicrobiologie, werden tijdens het eerste jaar ook een aantal chemische indicatoren voor de bodemkwaliteit bepaald. Vervolgens werden een aantal kennisuitwisselingsmomenten georganiseerd over deze verschillende methodes en over de relaties tussen het microbieel leven in de bodem en het bodembeheer in de praktijk

Biochar-amended potting medium reduces the susceptibility of rice to root-knot nematode infections

Background: Biochar is a solid coproduct of biomass pyrolysis, and soil amended with biochar has been shown to enhance the productivity of various crops and induce systemic plant resistance to fungal pathogens. The aim of this study was to explore the ability of wood biochar to induce resistance to the root-knot nematode (RKN) Meloidogyne graminicola in rice (Oryza sativa cv. Nipponbare) and examine its histochemical and molecular impact on plant defense mechanisms. Results: A 1.2 % concentration of biochar added to the potting medium of rice was found to be the most effective at reducing nematode development in rice roots, whereas direct toxic effects of biochar exudates on nematode viability, infectivity or development were not observed. The increased plant resistance was associated with biochar-primed H2O2 accumulation as well as with the transcriptional enhancement of genes involved in the ethylene (ET) signaling pathway. The increased susceptibility of the Ein2b-RNAi line, which is deficient in ET signaling, further confirmed that biochar-induced priming acts at least partly through ET signaling. Conclusion: These results suggest that biochar amendments protect rice plants challenged by nematodes. This priming effect partially depends on the ET signaling pathway and enhanced H2O2 accumulation

Stuurbaar bodemleven? Effect van lignine-rijke gewasresten op Verticillium

In de biologische glastuinbouw is een goede bodemgezondheid van cruciaal belang. Het streven is om een systeem te ontwikkelen met meer veerkracht en een betere bodemweerbaarheid. In dit onderzoek wordt het bodemleven gevoed met lignine-rijke gewasresten. Het doel is om de natuurlijk voorkomende witrotschimmels te stimuleren die lignine omzetten, en daarmee ook de overlevingsstructuren (microsclerotiën) van plant-pathogene Verticillium schimmels af te breken. Houtige gewassen bevatten het meeste lignine, gevolgd door grassen en granen. Ook gewasresten van broccoli en boon bevatten relatief veel lignine. In een laboratorium proef is grond van twee bedrijven met een natuurlijke besmetting met Verticillium dahliae gemengd met 7 lignine-rijke gewasresten. De twee gronden reageerden verschillend. Op locatie Schalkwijk (rivierklei) hadden maïsstengels, broccoli, rietstengels en Japanse haver (Avena strigosa av. astrigosa) een significant effect op de hoeveelheid levensvatbare microsclerotiën in de bodem. In 4 weken is in de variant met 10% (m/m) maïsstengels de hoeveelheid Verticillium met 69% afgenomen ten opzichte van de controle. Op locatie Tinte (zeeklei) hadden alleen rietblad en rietstengel een significant effect. Door toevoeging van rietblad (10% m/m) neemt de hoeveelheid Verticillium met 66% af. Op locatie Tinte is er een significante relatie tussen de hoeveelheid toegevoegde lignine en de afname van het aantal microsclerotiën van Verticillium. Voor locatie Schalkwijk is dit verband niet gevonden, hier spelen mogelijk andere mechanismen een rol. In de potproef is 1, 2 en 10% (m/m) riet en 2% tarwestro ingewerkt in van nature met Verticillium besmette grond. Na 12 weken zijn in de variant met 2% riet 75% minder microsclerotiën van Verticillium aanwezig dan in de controle, maar deze afname is niet significant. Resultaten van real-time PCR analyse laten echter wel een significante afname van de hoeveelheid Verticillium zien, in de varianten waar 1% en 10% riet is ondergewerkt. Bij toenemende percentages riet, neemt ook de immobilisatie van stikstof significant toe. Stro veroorzaakt meer immobilisatie dan riet. In de praktijkproef is 2% (m/m) riet ondergewerkt. Na 3 weken is er op het perceel paprika geplant. Na in totaal 12 weken is de afname van de hoeveelheid Verticillium bepaald. Uitplaten laat een lichte stijging zien van de hoeveelheid Verticillium in de controle, terwijl in de behandeling met 2% riet de hoeveelheid Verticillium afneemt. Deze verschillen zijn echter niet significant. Bij de real-time PCR analyse zien we een significant effect van het bemonsteringstijdstip. In december is er meer DNA van Verticillium in de bodem dan in maart. Dit is echter ook in de controle het geval. Er is dus geen significant effect meetbaar van het toevoegen van de gewasresten aan de bodem. In alle experimenten is veel meer Verticillium tricorpus aanwezig dan Verticillium dahliae. V. dahliae kan al in zeer kleine hoeveelheden gewasschade aanbrengen. De rol van V. tricorpus is onduidelijk. DNA sequencing van een isolaat van V. tricorpus op het betreffende glastuinbouw bedrijf laat zien dat deze soort geclassificeerd kan worden als Verticillium isaacii. Het is noodzakelijk een goed beeld te krijgen van de aanwezige Verticillium soorten en hun pathogeniciteit voordat nieuwe bestrijdingsmethoden van Verticillium verder ontwikkeld worden

Quantification of extracellular proteases and chitinases from marine bacteria

A total of 92 marine bacteria belonging to Pseudomonas, Pseudoalteromonas, Psychrobacter, and Shewanella were first screened for their proteolytic activity. In total, four Pseudomonas strains belonging to Ps. fluorescens, Ps. fragi, Ps. gessardii, and Ps. marginalis; 14 Pseudoalteromonas strains belonging to Psa. arctica, Psa. carrageenovora, Psa. elyakovii, Psa. issachenkonii, Psa. rubra, Psa. translucida, and Psa. tunicata; and two Shewanella strains belonging to S. baltica and S. putrefaciens were identified to have a weak to high proteolytic activity (from 478 to 4445 mU/mg trypsin equivalent) against skim milk casein as protein source. Further chitinolytic activity screening based on these 20 proteolytic strains using colloidal chitin yielded five positive strains which were tested against three different chitin substrates in order to determine the various types of chitinases. Among the strains that can produce both proteases and chitinases, Psa. rubra DSM 6842T expressed not only the highest proteolytic activity (2558 mU/mg trypsin equivalent) but also the highest activity of exochitinases, specifically, β-N-acetylglucosaminidase (6.33 mU/107 cfu) as well. We anticipate that this strain can be innovatively applied to the valorization of marine crustaceans side streams

Tapping into the maize root microbiome to identify bacteria that promote growth under chilling conditions

Background When maize (Zea mays L.) is grown in the Northern hemisphere, its development is heavily arrested by chilling temperatures, especially at the juvenile phase. As some endophytes are beneficial for plants under stress conditions, we analyzed the impact of chilling temperatures on the root microbiome and examined whether microbiome-based analysis might help to identify bacterial strains that could promote growth under these temperatures. Results We investigated how the maize root microbiome composition changed by means of 16S rRNA gene amplicon sequencing when maize was grown at chilling temperatures in comparison to ambient temperatures by repeatedly cultivating maize in field soil. We identified 12 abundant and enriched bacterial families that colonize maize roots, consisting of bacteria recruited from the soil, whereas seed-derived endophytes were lowly represented. Chilling temperatures modified the root microbiome composition only slightly, but significantly. An enrichment of several chilling-responsive families was detected, of which the Comamonadaceae and the Pseudomonadaceae were the most abundant in the root endosphere of maize grown under chilling conditions, whereas only three were strongly depleted, among which the Streptomycetaceae. Additionally, a collection of bacterial strains isolated from maize roots was established and a selection was screened for growth-promoting effects on juvenile maize grown under chilling temperatures. Two promising strains that promoted maize growth under chilling conditions were identified that belonged to the root endophytic bacterial families, from which the relative abundance remained unchanged by variations in the growth temperature. Conclusions Our analyses indicate that chilling temperatures affect the bacterial community composition within the maize root endosphere. We further identified two bacterial strains that boost maize growth under chilling conditions. Their identity revealed that analyzing the chilling-responsive families did not help for their identification. As both strains belong to root endosphere enriched families, visualizing and comparing the bacterial diversity in these communities might still help to identify new PGPR strains. Additionally, a strain does not necessarely need to belong to a high abundant family in the root endosphere to provoke a growth-promoting effect in chilling conditions

Chemically versus thermally processed brown shrimp shells or Chinese mitten crab as a source of chitin, nutrients or salts and as microbial stimulant in soilless strawberry cultivation

Brown shrimp (Crangon crangon) shells and Chinese mitten crab (Efiocheir sinensis) were chemically demineralized and deproteinized (denoted as M1 to M4 for the shrimp shells and MS to M7 for the Chinese mitten crab), and shrimp shells were torrefied at 200 to 300 degrees C (denoted as R200, R255, R300), and were compared with a commercially available chitin source (denoted as reference chitin). Based on their chemical characteristics, a selection of chitin sources was tested for their N mineralization capacity. The N release was high for the chemically treated shrimp shells and Chinese mitten crab, but not for the Dandled shrimp shells with or without acid treatment, indicating that treatment at 200 et or higher resulted in low N availability. Interaction with nutrients was tested in a leaching experiment with limed peat for three thermally and two chemically processed shrimp shells and the reference chitin source. The K concentrations in the leachate for the chemically treated shrimp shells and the reference chitin were lower than for limed peat during fertigation. Irreversible K retention was observed for one source of chemically treated shrimp shells, and the reference chitin. The thermally treated shrimp shells had a significantly higher net release of P. Na and CI than the treatment without chitin source. Three shrimp shell based materials (M4, R200 and 8300) and the reference chitin were tested in a greenhouse trial with strawberry at a dose of 2 g/L limed peat. A very positive and significant effect on Borryris cinerea disease suppression in the leaves was found for the reference chitin, M4 and R200 compared to the unamended control. The disease suppression of the 3 chitin sources was linked with an increase of the microbial biomass in the limed peat with 24% to 28% due to chitin decomposition and a 9-44% higher N uptake in the plants

Grow - store - steam - re-peat : reuse of spent growing media for circular cultivation of Chrysanthemum

Substantially extending the life span of peat- and perlite-based growing media is a measure to increase the sustainability of soilless cultivation. The extraction of peat from pristine peatlands threatens these sensitive ecosystems and carbon sinks, meanwhile resulting in increased emissions of greenhouse gasses. Each batch of peat that is reused, results in a clear reduction in CO2 emissions and a lower impact on the climate. After using growing media for one cultivation, we aim at reusing the spent material as growing medium for another crop. Spent peat and perlite-based growing media from strawberry and cucumber cultivation were upcycled after steam treatment. We tested the effectiveness of steaming to reduce phytosanitary risks. The hygienisation efficiency of the steam treatment was confirmed: plant pathogenic fungi, larvae of vine weevils and weed seeds added or already present before the process were killed by the steam treatment. As the upcycled spent growing medium already contained high nutrient levels, the fertilizer application in the reused growing medium should be reduced, especially for P and K. Five indicators for assessing stability of the materials were used: CO2 flux measurements, oxygen uptake rate (OUR), biodegradation potential, mineral N content and risk for N immobilization. The spent growing media had a low decomposition rate and the release of nutrients in a leaching experiment was lower than for a fertilized peat-based growing medium, being a reference blend for open field cultivated Chrysanthemum. N mineralisation and P uptake were tested in an incubation and pot trial, respectively, and the upcycled spent growing medium was found to be an important source of plant-available K and P. Steam treatment did not severely affect the microbial biomass and diversity of the spent growing media. Blending the steam-treated spent media with other materials or inoculating by a commercially available biocontrol fungus also had a limited effect, indicating that newly introduced microorganisms do not easily establish in steamed-treated spent growing media (SSGM). Acidification of the SSGM was achieved by a low dose of elemental S. The steam-treated growing medium was tested for growing Chrysanthemum cuttings and plantlets. Spent growing media were not able to supply sufficient mineral N, but the stored amounts of P and K in the media were sufficiently plant available for optimal crop growth

Daring to be differential : metabarcoding analysis of soil and plant-related microbial communities using amplicon sequence variants and operational taxonomical units

Background: Microorganisms are not only indispensable to ecosystem functioning, they are also keystones for emerging technologies. In the last 15 years, the number of studies on environmental microbial communities has increased exponentially due to advances in sequencing technologies, but the large amount of data generated remains difficult to analyze and interpret. Recently, metabarcoding analysis has shifted from clustering reads using Operational Taxonomical Units (OTUs) to Amplicon Sequence Variants (ASVs). Differences between these methods can seriously affect the biological interpretation of metabarcoding data, especially in ecosystems with high microbial diversity, as the methods are benchmarked based on low diversity datasets. Results: In this work we have thoroughly examined the differences in community diversity, structure, and complexity between the OTU and ASV methods. We have examined culture-based mock and simulated datasets as well as soil- and plant-associated bacterial and fungal environmental communities. Four key findings were revealed. First, analysis of microbial datasets at family level guaranteed both consistency and adequate coverage when using either method. Second, the performance of both methods used are related to community diversity and sample sequencing depth. Third, differences in the method used affected sample diversity and number of detected differentially abundant families upon treatment; this may lead researchers to draw different biological conclusions. Fourth, the observed differences can mostly be attributed to low abundant (relative abundance < 0.1%) families, thus extra care is recommended when studying rare species using metabarcoding. The ASV method used outperformed the adopted OTU method concerning community diversity, especially for fungus-related sequences, but only when the sequencing depth was sufficient to capture the community complexity. Conclusions: Investigation of metabarcoding data should be done with care. Correct biological interpretation depends on several factors, including in-depth sequencing of the samples, choice of the most appropriate filtering strategy for the specific research goal, and use of family level for data clustering