Recent studies using NGS technology to look at microbial communities have shown that above and belowground plant tissues, as well as surrounding rhizospheric soils are host to a diverse community of prokaryotic and eukaryotic microorganisms. In order to better understand the relative roles of environmental filtering, competition and niche differentiation in determining community structure and function, we must first accurately identify organisms and their spatial patterns within these systems. However, the spatial heterogeneity of microbial communities is often assumed, or disregarded in favor of more cost-efficient sampling strategies. This oversite can lead to misrepresentation of true microbial community structure and function and subsequently obscure downstream ecological interpretations. Unfortunately, there’s no current consensus for an ideal sampling strategy for environmental microbial communities, and few studies address the potential spatial heterogeneity of these systems.
In this study, we investigated the microbial communities in leaves and roots associated with showy milkweed (Asclepias speciosa). We employed two common but different sampling strategies in both roots and leaves of 20 plants. Microbial groups analyzed included bacteria, arbuscular mycorrhizal fungi (AMF), and endophytic fungi. Additionally, we extracted microbial DNA from entire plant tissues to determine how sub-sampling can underrepresent true microbial diversity within hosts.
Results/Conclusions
The two sampling methods tested 1.) Homogenizing and subsampling based on tissue volume and 2.) homogenizing and subsampling based on tissue surface area, resulted in differences in both microbial community richness as well as composition. We saw high variability in sampling strategy performance depending on tissue type (roots/leaves) and microbial groups being sampled (endophytic fungi, AMF and bacteria). AMF showed the most consistent community structure across methods, with a 57% overlap in species detected using both sampling strategies. Fungal endophytes in roots had only 42% species overlap between sampling strategies and bacteria in roots had 33%. Fungal endophytes in leaves showed the greatest spatial heterogeneity, with only 11% of fungal species being picked up in both sampling strategies. Comparing subsamples to whole plant tissues, we also demonstrate that current sub-sampling strategies may be insufficient in characterizing true biodiversity within these systems. Based on Procrustes analyses and mantel tests, these differences in community structure resulted in significantly different downstream ecological interpretations for all microbial groups.