Systems-level Proteomics of Two Ubiquitous Leaf Commensals Reveals Complementary Adaptive Traits for Phyllosphere Colonization

Abstract

Plants are colonized by a diverse community of microorganisms, the plant microbiota, exhibiting a defined and conserved taxonomic structure. Niche separation based on spatial segregation and complementary adaptation strategies likely forms the basis for coexistence of the various microorganisms in the plant environment. To gain insights into organism-specific adaptations on a molecular level, we selected two exemplary community members of the core leaf microbiota and profiled their proteomes upon Arabidopsis phyllosphere colonization. The highly quantitative mass spectrometric technique SWATH MS was used and allowed for the analysis of over two thousand proteins spanning more than three orders of magnitude in abundance for each of the model strains. The data suggest that Sphingomonas melonis utilizes amino acids and hydrocarbon compounds during colonization of leaves whereas Methylobacterium extorquens relies on methanol metabolism in addition to oxalate metabolism, aerobic anoxygenic photosynthesis and alkanesulfonate utilization. Comparative genomic analyses indicates that utilization of oxalate and alkanesulfonates is widespread among leaf microbiota members whereas, aerobic anoxygenic photosynthesis is almost exclusively found in Methylobacteria. Despite the apparent niche separation between these two strains we also found a relatively small subset of proteins to be coregulated, indicating common mechanisms, underlying successful leaf colonization. Overall, our results reveal for two ubiquitous phyllosphere commensals speciesspecific adaptations to the host environment and provide evidence for niche separation within the plant microbiota. Molecular & Cellular Proteomics 15: 10.1074/mcp.M116.058164, 3256-3269, 2016.

Drivers of phyllosphere microbial functional diversity in a neotropical forest

“…Core functional microbiomes in host-associated systems have also been reported for other hosts. Our study supports findings of an important role for the metabolism of carbohydrates and amino acids in bacterial survival in the phyllosphere [18, 46, 47] that is consistent with the abundance of these compounds in leaf leachates and photosynthates. The main mechanism of energy acquisition from these compounds appeared to be the TCA (citric acid) cycle, as reported in experimental studies of bacterial colonization of the phyllosphere [47].…”

“…Our study supports findings of an important role for the metabolism of carbohydrates and amino acids in bacterial survival in the phyllosphere [18, 46, 47] that is consistent with the abundance of these compounds in leaf leachates and photosynthates. The main mechanism of energy acquisition from these compounds appeared to be the TCA (citric acid) cycle, as reported in experimental studies of bacterial colonization of the phyllosphere [47]. Membrane transporters were also reported to be an important component of the epiphytic microbe functional repertoire, maximising the ability to monopolize otherwise limiting resources [48].…”

The Generation of a Comprehensive Spectral Library for the Analysis of the Guinea Pig Proteome by SWATH‐MS

“…Interpretation of SWATH spectra, however, requires reference to a spectral library of peptide sequence matching (including established m / z and LC retention time co‐ordinates), itself oft‐obtained from the outcomes of multiple DDA runs. Spectral libraries of notable depth are available for only a few species (or specialized cells/tissues)—including human, mouse, a few microbiota, drosophila and tomato, zebrafish, and yeast—that, at present, limits the breadth of uptake of SWATH.…”

In planta bacterial multi-omics analysis illuminates regulatory principles underlying plant-pathogen interactions

“…Although transcriptome analysis is a useful and widely used approach to elucidate cellular function, it has been well established that mRNA expression does not always reflect protein expression, and thus it becomes clear that a better understanding of cellular behavior requires direct interrogation of protein expression (4,5). A previous study showed that proteome 45 analysis of leaf commensal bacteria can reveal metabolic changes in bacteria residing on the leaf surface (6). However, the capacity of proteomics to describe plant-associated bacteria remains limited (7).…”