Kristi Gdanetz | Search bioRxiv

bioRxiv2020

The phytobiomes of a three-crop rotation: Influence of land management, host, and plant organ on microbial diversity

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.

microbiology↗

bioRxiv2020

Activity throughout the lichen phylogeny indicates a focus on regulation of specialized metabolites

Lichens are complex multi-microorganismal communities that have evolved the ability to share their thalli with a variety of microorganisms. As such, the lichenized fungus becomes a scaffold for a variety of microbes and occasionally insects. Lichens are known to produce a plethora of unique specialized (secondary) compounds that demonstrate biological activities, including antibacterial, antifungal, antiviral, and antioxidant, that may provide protection from harmful microbes. The longevity of lichens and their robustness, despite a close association with diverse microbes, provides an interesting study system to view the role of specialized metabolites in managing a microbial community. The objective of this study was to identify the effects lichens may have on basic functions of fungi in and on the lichens. We tested chemical extracts from lichen species across the phylogenetic tree for their effects on sporulation, hyphal growth and specialized metabolite production, using two well-studied mycotoxigenic fungi (Aspergillus parasiticus (aflatoxin) and Fusarium graminearum (trichothecenes) whose functions are easily observed in culture. By far the most prevalent activity among the 67 lichens we tested were effects on accumulation of fungal specialized metabolites, which appeared in 92% of the lichen species analyzed across the phylogeny, although the lichen extracts were also active against fungal sporulation (31%) and growth (12%). The consistent presence of this regulatory activity for specialized metabolism indicates this is an important aspect of lichen integrity. Interestingly, inhibition of accumulation of products of the aflatoxin biosynthetic pathway was the predominant activity, whereas increased accumulation versus decreased accumulation of the production of trichothecenes were about equal. This suggests multiple mechanisms for addressing fungal processes. We performed microbiome analysis of four lichen species and identified oomycetes as members of the microbiomes. Although a small sample size was used for comparing microbiomes, the lichen species exhibiting lower effects on the test fungi had a higher number of OTUs. Members of the lichen community may manipulate specialized metabolism of the essential and transient fungal members and thus attenuate negative interactions with the incumbent fungi or, alternatively, may support the production of compounds by beneficial fungal partners. The ability to control the microbiome by specialized metabolites as opposed to controlling by reducing sporulation of growth, can be effective, discerning, and energetically thrifty, allowing the microbiome members to be controlled without being invasive. Elucidating the role of specialized metabolites in the mechanisms underlying lichen assembly and function has important implications for understanding not only lichen community assembly but for revealing the fundamental processes in microbiota in general.

microbiology↗