Influence of Plant Host and Organ, Management Strategy, and Spore Traits on Microbiome Composition

Abstract

Microbiomes from maize and soybean were characterized in a long-term three-crop rotation research site, under four different land management strategies, to begin unraveling the effects of common farming practices on microbial communities. The fungal and bacterial communities of leaves, stems, and roots in host species were characterized across the growing season using amplicon sequencing and compared with the results of a similar study on wheat. Communities differed across hosts, and among plant growth stages and organs, and these effects were most pronounced in the bacterial communities of the wheat and maize phyllosphere. Roots consistently showed the highest number of bacterial OTUs compared to above-ground organs, whereas the alpha diversity of fungi was similar between above- and below-ground organs. Network analyses identified putatively influential members of the microbial communities of the three host plant species. The fungal taxa specific to roots, stems, or leaves were examined to determine if the specificity reflected their life histories based on previous studies. The analysis suggests that fungal spore traits are drivers of organ specificity in the fungal community. Identification of influential taxa in the microbial community and understanding how community structure of specific crop organs is formed, will provide a critical resource for manipulations of microbial communities. The ability to predict how organ specific communities are influenced by spore traits will enhance our ability to introduce them sustainably.

Non-target impacts of fungicide disturbance on phyllosphere yeasts in different crop species and management systems

“…A higher proportion of fOTUs altered by fungicide application in the no-till management system showed improved resilience within the study period, which may be explained by the differences in microbial communities present in the phyllosphere of each management before fungicide applications, as has been demonstrated previously at the KBS LTER site (Longley et al, 2020;Gdanetz & Trail, 2017). A previous study from the KBS LTER site has demonstrated that aerially dispersed yeasts are enriched in the phyllosphere but also found in lower abundance in belowground plant organs (Gdanetz et al, 2021).…”

“…CC-BY-NC-ND 4.0 International license available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is madeThe copyright holder for this preprint this version posted September 21, 2021. ; https://doi.org/10.1101/2021…”

Non-target impacts of fungicide disturbance on phyllosphere yeasts in conventional and no-till management

“…Sampling and DNA extractions were performed as described previously [37,42]. In addition, amplicon sequencing library preparation, bioinformatic sequence processing, and preprocessing before statistical analyses were performed as previously described [37,43,44].…”

Under Attack: Fungal Landscape of Spring Barley From Seedling Emergence to Harvest During a Severe Puccinia Hordei Epidemic

“…Temporal development of fungal communities in root and shoot tissue has not yet been reported in detail yet although several studies show clear differences in roots vs shoots communities at certain growth stages of crop development [11,26]. The type of habitat in leaves, stems and heads determines community structures, and fungal members that have specialized habitat preferences depending on growth habits [42], for instance, Epicoccum and Alternaria evolved to colonize certain tissues [43].…”