title: Bacterial diversity and composition in the fluid of pitcher plants of the genus Nepenthes.
abstract: Pitchers are modified leaves used by carnivorous plants for trapping prey. Their fluids contain digestive enzymes from the plant and they harbor abundant microbes. In this study, the diversity of bacterial communities was assessed in Nepenthes pitcher fluids and the composition of the bacterial community was compared to that in other environments, including the phyllosphere of Arabidopsis, animal guts and another pitcher plant, Sarracenia. Diversity was measured by 454 pyrosequencing of 16S rRNA gene amplicons. A total of 232,823 sequences were obtained after chimera and singleton removal that clustered into 3260 distinct operational taxonomic units (OTUs) (3% dissimilarity), which were taxonomically distributed over 17 phyla, 25 classes, 45 orders, 100 families, and 195 genera. Pyrosequencing and fluorescence in situ hybridization yielded similar estimates of community composition. Most pitchers contained high proportions of unique OTUs, and only 22 OTUs (<0.6%) were shared by ≥14/16 samples, suggesting a unique bacterial assemblage in each pitcher at the OTU level. Diversity analysis at the class level revealed that the bacterial communities of both opened and unopened pitchers were most similar to that of Sarracenia and to that in the phyllosphere. Therefore, the bacterial community in pitchers may be formed by environmental filtering and/or by phyllosphere bacteria.
authors.affiliation: Institute of Evolutionary Biology and Environmental Studies and Institute of Plant Biology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
authors.forename: Yayoi
authors.initials: Y
authors.lastname: Takeuchi
authors.affiliation: Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
authors.forename: Samuel
authors.initials: S
authors.lastname: Chaffron
authors.affiliation: Limnological Station, Institute of Plant Biology, University of Zurich, Seestrasse 187, 8802 Kilchberg, Switzerland.
authors.forename: Michaela M
authors.initials: MM
authors.lastname: Salcher
authors.affiliation: Institute of Evolutionary Biology and Environmental Studies and Institute of Plant Biology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
authors.forename: Rie
authors.initials: R
authors.lastname: Shimizu-Inatsugi
authors.affiliation: Institute of Evolutionary Biology and Environmental Studies and Institute of Plant Biology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
authors.forename: Masaki J
authors.initials: MJ
authors.lastname: Kobayashi
authors.affiliation: Botanical Research Centre Semenggoh, Km 20 Borneo Height Road, 93250 Kuching, Sarawak, Malaysia.
authors.forename: Bibian
authors.initials: B
authors.lastname: Diway
authors.affiliation: Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
authors.forename: Christian
authors.initials: C
authors.lastname: von Mering
authors.affiliation: Limnological Station, Institute of Plant Biology, University of Zurich, Seestrasse 187, 8802 Kilchberg, Switzerland.
authors.forename: Jakob
authors.initials: J
authors.lastname: Pernthaler
authors.affiliation: Institute of Evolutionary Biology and Environmental Studies and Institute of Plant Biology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland. Electronic address: kentaro.shimizu@ieu.uzh.ch.
authors.forename: Kentaro K
authors.initials: KK
authors.lastname: Shimizu
mesh_terms: D000818:Animals; D017360:Arabidopsis / Q000382:microbiology; D001419:Bacteria / Q000145:classification* / Q000235:genetics*; D044822:Biodiversity; D016000:Cluster Analysis; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D041981:Gastrointestinal Tract / Q000382:microbiology; D017404:In Situ Hybridization, Fluorescence; D019684:Magnoliopsida / Q000382:microbiology*; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S
keywords: Alphaproteobacteria; Borneo; CARD–FISH; Gammaproteobacteria; NMDS; Pyrosequencing