Type II Photosynthetic Reaction Center Genes of Avocado (Persea americana Mill.) Bark Microbial Communities are Dominated by Aerobic Anoxygenic Alphaproteobacteria

Abstract

The tree bark environment is an important microbial habitat distributed worldwide on thrillions of trees. However, the microbial communities of tree bark are largely unknown, with most studies on plant aerial surfaces focused on the leaves. Recently, we presented a metagenomic study of bark microbial communities from avocado. In these communities, oxygenic and anoxygenic photosynthesis genes were very abundant, especially when compared to rhizospheric soil from the same trees. In this work, Evolutionary Placement Algorithm analysis was performed on metagenomic reads orthologous to the PufLM gene cluster, encoding for the bacterial type II photosynthetic reaction center. These photosynthetic genes were found affiliated to different groups of bacteria, mostly aerobic anoxygenic photosynthetic Alphaproteobacteria, including Sphingomonas, Methylobacterium and several Rhodospirillales. These results suggest that anoxygenic photosynthesis in avocado bark microbial communities functions primarily as additional energy source for heterotrophic growth. Together with our previous results, showing a large abundance of cyanobacteria in these communities, a picture emerges of the tree holobiont, where light penetrating the trees canopies and reaching the inner stems, including the trunk, is probably utilized by cyanobacteria for oxygenic photosynthesis, and the far-red light aids the growth of aerobic anoxygenic photosynthetic bacteria.

Interpreting phylogenetic placements for taxonomic assignment of environmental DNA

“…Many of the colpodean OTUs analyzed here had multiple likely placement locations on the reference tree. These alternative placements were not considered in most published phylogenetic placement studies using EPA‐ng (Aguirre‐von‐Wobeser, 2021; Bass et al, 2018; Fuchsman et al, 2022; Gottschling et al, 2021; Iniesto et al, 2021; Metz et al, 2021; Schoenle et al, 2020). Here, for the first time, we showcased together the features of the program GAPPA tool that can take multiple likely placements when performing taxonomic assignments into account.…”

Comparison of phylogenetic placements to pairwise alignments for taxonomic assignment of ciliate OTUs

“…Many of the colpodean OTUs analysed here had multiple likely placement locations on the reference tree. These alternative placements were not considered in most published phylogenetic placement studies using EPA-ng, (Aguirre-von-Wobeser, 2021; Bass et al, 2018; Fuchsman et al, 2022; Gottschling et al, 2021; Iniesto et al, 2021; Metz et al, 2021; Schoenle et al, 2020). Here, for the first time, we showcased together the features of the program GAPPA tool that can take multiple likely placements when performing taxonomic assignments into account.…”