Community proteogenomics reveals insights into the physiology of phyllosphere bacteria.
Aerial plant surfaces represent the largest biological interface on Earth and provide essential services as sites of carbon dioxide fixation, molecular oxygen release, and primary biomass production. Rather than existing as axenic organisms, plants are colonized by microorganisms that affect both their health and growth. To gain insight into the physiology of phyllosphere bacteria under in situ conditions, we performed a culture-independent analysis of the microbiota associated with leaves of soybean, clover, and Arabidopsis thaliana plants using a metaproteogenomic approach. We found a high consistency of the communities on the 3 different plant species, both with respect to the predominant community members (including the alphaproteobacterial genera Sphingomonas and Methylo bacterium) and with respect to their proteomes. Observed known proteins of Methylobacterium were to a large extent related to the ability of these bacteria to use methanol as a source of carbon and energy. A remarkably high expression of various TonB-dependent receptors was observed for Sphingomonas. Because these outer membrane proteins are involved in transport processes of various carbohydrates, a particularly large substrate utilization pattern for Sphingomonads can be assumed to occur in the phyllosphere. These adaptations at the genus level can be expected to contribute to the success and coexistence of these 2 taxa on plant leaves. We anticipate that our results will form the basis for the identification of unique traits of phyllosphere bacteria, and for uncovering previously unrecorded mechanisms of bacteria-plant and bacteria-bacteria relationships.
Delmotte
Nathanaël
N
Institute of Microbiology, Eidgenössische Technische Hochschule Zurich, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland.
Knief
Claudia
C
Chaffron
Samuel
S
Innerebner
Gerd
G
Roschitzki
Bernd
B
Schlapbach
Ralph
R
von Mering
Christian
C
Vorholt
Julia A
JA
D001419:Bacteria / Q000145:classification / Q000235:genetics* / Q000378:metabolism*; D018407:Bacterial Physiological Phenomena; D001426:Bacterial Proteins / Q000032:analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D017753:Ecosystem; D004591:Electrophoresis, Polyacrylamide Gel; D023281:Genomics / Q000379:methods*; D008969:Molecular Sequence Data; D010802:Phylogeny; D010944:Plants / Q000382:microbiology*; D040901:Proteomics / Q000379:methods*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D021241:Spectrometry, Mass, Electrospray Ionization
D001426:Bacterial Proteins; D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S