Temporal and spatial changes in phyllosphere microbiome of acacia trees growing in arid environments

Abstract

Background: The evolutionary relationships and interactions between plants and their microbiomes are of high importance to the survival of plants in extreme conditions. Changes in the plant’s microbiome can affect plant development, growth and health. Along the arid Arava, southern Israel, acacia trees (Acacia raddiana and Acacia tortilis) are considered keystone species. In this study, we investigated the ecological effects of plant species, microclimate (different areas within the tree canopy) and seasonality on the epiphytic and endophytic microbiomes associated with these two tree species. One hundred and thirty nine leaf samples were collected throughout the year and their microbial communities were assessed using 16S rDNA gene amplified with five different primers (targeting different gene regions) and sequenced (150 bp paired-end) on an Illumina MiSeq sequencing platform.Results: Epiphytic bacterial diversity estimates (Shannon-Wiener, Chao1, Simpson and observed number of OTUs), were found to be nearly double compared to endophyte counterparts, in addition epi- and endophyte communities were significantly different from each other. Interestingly, the epiphytic bacterial diversity was similar in the two acacia species but the canopy sides and sample months exhibited different diversity, while the endophytic bacterial communities were different in the two acacia species but similar throughout the year. Abiotic factors, such as air temperature and precipitation, were shown to significantly affect both epi- and endophytes communities. Bacterial community compositions showed that Firmicutes dominate Acacia raddiana and Proteobacteria dominate Acacia tortilis; these bacterial communities only consisted of a small number of bacterial families mainly Bacillaceae and Comamonadaceae in the endophyte for A. raddiana and A. tortilis, respectively, and Geodematophilaceae and Micrococcaceae for epiphyte bacterial communities. Interestingly, about 60% of the obtained bacterial classification were unclassified below family level. Conclusions: These results shed light on the unique desert phyllosphere microbiome highlighting the importance of multiple genotypic and abiotic factors in shaping the epiphytic and endophytic microbial communities. This study also shows that only a few bacterial families dominate both epi- and endophytes, highlighting the importance of climate change (precipitation, air temperature and humidity) in affecting arid land ecosystems where acacia trees are considered keystone species.

On the origin of feces: Fungal diversity, distribution, and conservation implications from feces of small mammals

“…Our study began with the simple idea of using readily available fecal samples from small mammals, collected routinely by the Natural History Museum of Utah, to investigate fungal diversity by applying techniques generally used to investigate microbial communities. Metabarcoding of environmental samples has become a popular technique to interrogate organismal communities that would otherwise be difficult to study (Al Ashhab et al, 2021; Andújar et al, 2015; Compson et al, 2020; Dieleman et al, 2015; Kesanakurti et al, 2011; McGee et al, 2019). Here we used the same strategy to target fungal communities in small mammal feces from 138 specimens and were able to identify 4650 ASVs in 531 genera of fungi.…”

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

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