Thematic Session 7 - Microbiome Research

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Thematic Session 7

Microbiome Research

Wednesday 10 February 2021 | 10:00-12:00 hrs


LINK TO ZOOM MEETING: Will Follow soon.


10:00 – 10:05 Introduction by the chair - Esther van der Ent (PhD candidate @ Naturalis Biodiversity Center)
10:05 – 10:20 KEYNOTE LECTURE | Generalist soil microbiome members as important drivers of plant-soil feedbacks?
Rutger Wilschut @ Ecology Group, University of Konstanz

Plant-soil feedbacks are soil-microbiome-mediated plant-plant interactions. Specialist antagonists are thought to determine the negative plant-soil feedbacks that many species experience, but generalist antagonists may also contribute. Here, we tested that specialists may particularly drive negative feedbacks of slow-growing, well-defended perennials, while generalists mainly drive plant-soil feedbacks of fast-growing, poorly-defended annuals. We examined feedback responses of 18 annuals and perennials in all conspecific and heterospecific soils, and show that annuals experienced more negative feedbacks than perennials. Surprisingly, species feedback responses did not depend on conditioning species identity, suggesting that plant-soil feedbacks in this experiment were primarily driven by generalist antagonists.
10:20 – 10:30 Soil microbial diversity and community composition during conversion from conventional to organic agriculture
Sophie van Rijssel @ Terrestrial Ecology, Netherlands Institute of Ecology

A transition to sustainable agricultural management may have large implications for soil biodiversity and functioning. Here, we sequenced bacterial, archaeal, and fungal communities in paired organic and conventional fields on marine clay and sand using a chronosequence that covered 25 years of conversion to organic management. We found that fungal diversity increased and community composition changed with time since conversion in organic, but also in paired conventional fields. Yet, shifts in microbial diversity and community composition were related to soil abiotic conditions, such as soil organic matter content. We conclude that environmental conditions play a more important role driving microbial community composition than time since conversion to organic management.
10:30 – 10:40 The soil microbiome responding to drought and chitin disturbances: The size of the change matters!
Lisa Joos @ Plant Sciences Unit, Institute for Agricultural and Fisheries Research (ILVO)

Soil microorganisms are known to be sensitive to disturbances happening in their surroundings, and those microbial shifts can represent the state of the soil health. In this study, we want to understand the link between soil health and microorganisms to select potential bio-indicators. Therefore, the response of the soil bacterial and fungal communities were studied upon negative (drought) and positive (chitin application) disturbances, by metabarcoding (relative changes) and PLFA analysis (absolute biomass). Community changes (occurrence) and the disturbance impact on the community (the size of the change) were considered as potential bio-indicators for soil health.
10:40 – 10:50 Context dependency of using beneficial microbes for improving plant growth and defense
Haymanti Saha @ Terrestrial Ecology, Netherlands Institute of Ecology

Beneficial microbes are known to improve plant growth and/or defense during their symbiotic associations via induced systemic resistance (ISR). However, such microbes do not always conform to their expected functionality. Alteration in abiotic factors affect not just plants but also microbe associated with plants. To test this context dependency, the current study assesses the effect different soil phosphorous level on the association between Solanum lycopersicum (cv. Moneymaker) wildtype and phytochromeB1B2 mutant line (mimicking shaded plants) with arbuscular mycorrhizae (Rhizoglomus irregulare). Results show interaction effect of soil P and tomato line on the beneficial effects of arbuscular mycorrhizae.
10:50 – 11:10 Joint coffee / tea break and time to socialise within your breakout room
11:10 – 11:20 Aphid endosymbionts in greenhouses and nature
Helena Donner @ Laboratory of Genetics & Laboratory of Entomology, Wageningen University

Aphids can carry primary and secondary endosymbionts. Aphid secondary endosymbionts can confer many different traits to the aphids, such as protection against fungi, parasitoid wasps and heat stress. Given the large effects they could have on community dynamics and also on biocontrol of aphids using parasitoid wasps, little is known about their occurrence in field populations and greenhouses in the Netherlands. Our findings show that secondary endosymbionts occur in many aphid species in the Netherlands and they also occur in strawberry greenhouses.
11:20 – 11:30 Convergent gut microbiota as a signature of non-adaptive speciation
Thomas Blankers @ Evolutionary and Population Biology, University of Amsterdam

Gut microbiomes in invertebrates may be both transient, environmentally acquired, as well as adaptive. In either case, it may be expected that the microbiome offers a window into the ecology of its host, differentiated from the microbiomes of hosts that are differentially adapted ecologically. We can therefore explore the potential for cryptic ecological differentiation in species radiations. Here we show that for the rapidly speciating, ecologically cryptic swordtail crickets of Hawaii, the gut microbiome varies among sampling locations, but not among sympatrically occurring species, confirming the hypothesis that these crickets have speciated in the absence of ecological differentiation.
11:30 – 11:40 Nanopore sequencing for fast microbiome analysis
Mariska Madelon Beekman @ Laboratory of Genetics & Laboratory of Entomology, Wageningen University

"In microbial ecology, species identification is commonly done through sequencing of the 16S rRNA gene. Illumina is the most frequently used platform for this. A big downside to Illumina is that most labs have to outsource the sequencing, resulting in delays between sampling and microbiome identification, potentially causing community compositions to have already changed significantly by the time the results become clear. Here we will discuss the use of the MinION (Oxford Nanopore Technologies), a portable device that allows for real-time sequencing of DNA, for fast bacterial identification and microbiome analysis.
11:40 – 11:55 General discussion and wrap up of the session