Diverse microbial communities hosted by the model carnivorous pitcher plant Sarracenia purpurea: analysis of both bacterial and eukaryotic composition across distinct host plant populations

Abstract

BackgroundThe pitcher plant Sarracenia purpurea supplements nutrient acquisition through carnivory, capturing insect prey which are digested by a food web community of eukaryotes and bacteria. While the food web invertebrates are well studied, and some recent studies have characterized bacteria, detailed genetic analysis of eukaryotic diversity is lacking. This study aimed to compare eukaryotic and bacterial composition and diversity of pitcher communities within and between populations of host plants in nearby but distinct wetland habitats, and to characterize microbial functions across populations and in comparison with another freshwater community.MethodsPitcher fluid was sampled from the two wetlands, Cedarburg and Sapa Bogs, community DNA was extracted, and 16S and 18S rRNA amplicons were sequenced and data processed for community-level comparisons.Results and ConclusionsBacterial diversity in the small pitcher volume rivaled that of larger aquatic communities. Between pitcher plant populations, several bacterial families (Kiloniellaceae, Acetobacteraceae, Xanthobacteraceae, Sanguibacteraceae, Oligoflexaceae, Nitrosomonadaceae, Chromatiaceae, Saprospiraceae) were significantly higher in one population. However, although predicted pitcher bacterial functions were distinct from other freshwater communities, especially for some amino acid metabolism, functions were similar across all the pitchers in the two populations. This suggests some functional redundancy among bacterial taxa, and that functions converge to achieve similar food web processes. The sequencing identified a previously under-appreciated high diversity of ciliates, Acari mites, fungi and flagellates in pitcher communities; the most abundant sequences from eukaryotic taxa were Oligohymenophorea ciliates, millipedes and Ichthyosporea flagellates. Two thirds of taxa were identified as food web inhabitants and less than one third as prey organisms. Although eukaryotic composition was not significantly different between populations, there were different species of core taxonomic groups present in different pitchers—these differences may be driven by wetland habitats providing different populations to colonize new pitchers. Eukaryotic composition was more variable than bacterial composition, and there was a poor relationship between bacterial and eukaryotic composition within individual pitchers, suggesting that colonization by eukaryotes may be more stochastic than for bacteria, and bacterial recruitment to pitchers may involve factors other than prey capture and colonization by eukaryotic food web inhabitants.

Exploring Microbiome Functional Dynamics through Space and Time with Trait-Based Theory

“…As a test case to examine successional trajectories within the Y-A-S framework, we followed microbial communities over 2 months in 10 individual S. purpurea pitchers from the Cedarburg Bog ( 47 ). On days 3, 7, 14, 28, and 62 after the leaves had opened into their characteristic pitcher shape, 3 ml of natural pitcher water was collected from each of the 10 pitchers using a sterile syringe and tubing ( 43 ), and community DNA was extracted for sequencing ( 47 ). 16S rRNA V3_4 sequence data were processed with QIIME2 version 2020.2 and used for PICRUSt2 analysis ( 34 ) to generate predictions of microbiome functions.…”

Bacterial Recruitment to Carnivorous Pitcher Plant Communities: Identifying Sources Influencing Plant Microbiome Composition and Function

“…The eukaryotic and bacterial food web members play different roles in shredding and digesting the prey, releasing nutrients for host plant uptake. The presence of eukaryotic taxa in the food web can vary between habitats ( Gray, 2012 ; Grothjan and Young, 2019 ) and can depend on the presence of different predator taxa ( Gebühr et al, 2006 ; Paisie et al, 2014 ). The larger invertebrate organisms in these food webs have been well documented ( Trzcinski et al, 2005 ; Gotelli and Ellison, 2006 ; Hoekman, 2007 ; Baiser et al, 2013 ) and more recently comprehensive eukaryotic diversity has been examined with DNA sequencing ( TerHorst, 2011 ; Satler et al, 2016 ; Grothjan and Young, 2019 ).…”

Selective Bacterial Community Enrichment between the Pitcher Plants Sarracenia minor and Sarracenia flava

“…Previous Sarracenia pitcher plant microbiome studies have focused on a range of temporal ( 5 – 8 ) and geographic ( 7 , 9 – 11 ) questions. To date, only one study ( 12 ) has investigated whether Sarracenia microbiomes are more impacted by plant-specific features (such as biochemical secretions or attracted prey) or geographic location (including environmental factors and their impact on prey pools).…”