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Methods to Assess Microbial Communities

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Microbial communities, comprising bacteria, archaea, and eukaryotic microorganisms, inhabit diverse ecosystems and play crucial roles in environmental and biological processes. Their diversity is defined by three main parameters: species richness (the number of distinct species), species abundance (the relative quantity of each species), and species evenness (how uniformly individual species are distributed in various locations). These factors together shape the structure and ecological balance...

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Empirical, Metagenomic, and Computational Techniques Illuminate the Mechanisms by which Fungicides Compromise Bee Health

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Seed quantity affects the fungal community composition detected using metabarcoding.

Funda Oskay¹, Anna Maria Vettraino², H Tuğba Doğmuş³

¹Faculty of Forestry, Çankırı Karatekin University, 18200, Çankırı, Turkey.

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|February 24, 2022

Summary

Increasing sample size and PCR replicates in high-throughput sequencing (HTS) of tree seeds improves detection of fungal diversity and potential plant pathogens. This is crucial for effective pest risk assessment in forest trade.

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Published on: May 5, 2023

Area of Science:

Plant pathology
Mycology
Molecular biology

Background:

Pest introductions via trade in tree seeds pose significant risks.
Current diagnostic protocols for forest tree seeds may be inadequate.
High-throughput sequencing (HTS) offers advanced tools for pest and pathogen screening.

Purpose of the Study:

To investigate the impact of sample size on fungal community diversity detection in Pinus sylvestris seeds using HTS.
To assess the correlation between sample size, taxonomic/functional diversity, and pathogen detection.
To optimize HTS protocols for screening tree seeds for harmful organisms.

Main Methods:

Analysis of fungal communities in Pinus sylvestris seeds using HTS.
Varying sample sizes from 100 to 1000 seeds.
Assessment of fungal alpha and beta diversity.
Evaluation of taxonomic and functional diversity in relation to sample size.
Impact of PCR replicates on pathogen detection.

Main Results:

Fungal alpha diversity increased with larger sample sizes.
Beta-diversity analyses revealed significant differences in mycobiota between samples.
Taxonomic and functional diversity did not correlate with sample size.
Increased PCR replicates led to higher detection of plant pathogens.

Conclusions:

Increasing sample size is essential for comprehensive fungal diversity detection in tree seeds.
Higher PCR replication enhances the detection of potentially harmful plant pathogens.
Optimized HTS protocols with larger sample sizes and replicates are critical for effective seed pest screening.