Functional metagenomics of bark microbial communities from avocado trees (Persea americana Mill.) reveals potential for bacterial primary productivity

Abstract

Bark microbial communities are poorly understood, and information on the metabolic capacities of their inhabitants is lacking. Bark microbial communities share part of their taxonomic composition with soil, but the functional differences and similarities are unknown. By comparing bark microbial communities of avocado trees (Persea americana, Mill.) with rhizospheric soil, functional processes relevant to the bark environment were identified. DNA from bark and soil communities was extracted from the same trees, and shotgun metagenomics sequencing was performed using nextSeq technology. Genes were identified by BLAST methods, and functional annotation was performed with KEGG databases as a reference. Bacterial oxygenic and anoxygenic photosynthesis genes were highly abundant in bark as compared to soil. Furthermore, increased presence of nitrogenase genes suggests a potential for nitrogen fixation. Genes for methanol utilization were abundant in bark, but no evidence of methane utilization potential was observed. Bark microbial communities have the genetic information for potential primary productivity, which might contribute to microbial growth independent of plant-derived carbon substrates.

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

“…Recently, a bark metagenomic study was conducted on bark from avocado trees, revealing highly diverse microbial communities dominated by bacteria, with the presence of archaea, fungi, algae and other eukaryotic groups [8]. Functional analysis of these communities revealed the presence of many oxygenic and anoxygenic photosynthetic genes, which were absent from rhizospheric soil from the same trees [9]. The presence of these genes in avocado bark suggests active phototrophic communities.…”

“…In this work, the diversity and phylogenetic affiliation of anoxygenic photosynthetic bacteria utilizing type II reaction centers in avocado bark microbial communities is explored. EPA analysis was performed on the avocado bark metagenomic dataset presented previously [8,9] of the PufLM gene cluster, encoding for a type II photosynthetic reaction center. A dominance of aerobic anoxygenic photosynthetic bacteria was clearly observed among PufLM-carrying bacteria of the avocado bark environment.…”

Accumulator, Transporter, Substrate, and Reactor: Multidimensional Perspectives and Approaches to the Study of Bark

“…Materials also leach from bark surfaces, moving through the bark into external solution that drains to the surface during storms. Growing on and within bark surfaces, epiphytic plants (e.g., mosses, ferns, and bromeliads) intercept, retain, and leach substances (Mendieta-Leiva et al, 2020), while bark-dwelling microorganisms and fauna produce, transform, and decompose materials (Aguirre-von-Wobeser, 2020). Exchanges between epiphytic communities and their substrates create additional pathways for material cycling within and below canopies.…”

Type II photosynthetic reaction center genes of avocado (Persea americanaMill.) bark microbial communities are dominated by aerobic anoxygenic Alphaproteobacteria

“…Recently, a bark metagenomic study was conducted on bark from avocado trees, revealing highly diverse microbial communities dominated by bacteria, with the presence of archaea, fungi, algae and other eukaryotic groups [8]. Functional analysis of these communities revealed the presence of many oxygenic and anoxygenic photosynthetic genes, which were absent from rhizospheric soil from the same trees [9]. The presence of these genes in avocado bark suggests active phototrophic communities.…”

“…In this work, the diversity and phylogenetic affiliation of anoxygenic photosynthetic bacteria utilizing type II reaction centers in avocado bark microbial communities is explored. EPA analysis was performed on the avocado bark metagenomic dataset presented previously [8,9] of the PufLM gene cluster, encoding for a type II photosynthetic reaction center. A dominance of aerobic anoxygenic photosynthetic bacteria was clearly observed among PufLM-carrying bacteria of the avocado bark environment.…”