The Carnivorous Pale Pitcher Plant Harbors Diverse, Distinct, and Time-Dependent Bacterial Communities

Abstract

The ability of American carnivorous pitcher plants (Sarracenia) to digest insect prey is facilitated by microbial associations. Knowledge of the details surrounding this interaction has been limited by our capability to characterize bacterial diversity in this system. To describe microbial diversity within and between pitchers of one species, Sarracenia alata, and to explore how these communities change over time as pitchers accumulate and digest insect prey, we collected and analyzed environmental sequence tag (454 pyrosequencing) and genomic fingerprint (automated ribosomal intergenic spacer analysis and terminal restriction fragment length polymorphism) data. Microbial richness associated with pitcher plant fluid is high; more than 1,000 unique phylogroups were identified across at least seven phyla and 50 families. We documented an increase in bacterial diversity and abundance with time and observed repeated changes in bacterial community composition. Pitchers from different plants harbored significantly more similar bacterial communities at a given time point than communities coming from the same genetic host over time. The microbial communities in pitcher plant fluid also differ significantly from those present in the surrounding soil. These findings indicate that the bacteria associated with pitcher plant leaves are far from random assemblages and represent an important step toward understanding this unique plant-microbe interaction.

Succession in the aquatic Sarracenia purpurea community: deterministic or driven by contingency?

“…A similar result was found when 454 sequencing was using to identify the seasonal change in bacterial composition inside the leaves of the co-gener, S. alata (Koopman et al 2010). A similar, but weaker, pattern was also found for similarities based on abundance data for the culturable bacteria collected from the 20 pitchers in 2007.…”

“…While culturable bacteria densities decreased and species richness remained constant through time, both total protozoan densities and richness increased as succession progressed (Table 1) to compare the similarity in the successional pattern between a larger subset of bacteria than that of just the culturable bacteria, which are only 1 % of the bacterial diversity. When cloning is used instead of highthroughput sequencing (e.g., Koopman et al 2010;Koopman and Carstens 2011), a much smaller sampling of diversity occurs. Therefore, this study is not claiming to capture the entire bacterial diversity in this system.…”

“…No species are present in the community before the leaf opens (Peterson et al 2008) and each habitat island within a bog has access to the same regional pool. The species that colonize each habitat island are predominately microorganisms with short generation times and insect larvae, making this system ideal for following successional patterns through hundreds to thousands of generations and across multiple habitat islands (e.g., Koopman et al 2010 for the co-gener S. alata, Miller and terHorst 2012). Larger scale systems contain longer-lived organisms, limiting the long-term datasets needed to determine whether a community has a successional endpoint.…”

Reproducibility and quantitation of amplicon sequencing-based detection

“…At present, the 454 pyrosequencing technology has been widely used to reveal microbial diversity and ecology in different natural environments, such as the deep sea (Sogin et al, 2006;Huber et al, 2007), extreme hydrogeological conditions (Edwards et al, 2006) and soil (Leininger et al, 2006;Roesch et al, 2007). In addition, multiplexed high-throughput pyrosequencing of individual genes (for example, 16S rRNA) by tagging or bar coding with short nucleotides (also called pyrotag sequencing ) Parameswaran et al, 2007;Roesch et al, 2007;Hamady et al, 2008) has been developed to process many samples simultaneously and has been widely used in microbial community studies (Youssef et al, 2009;Cheung et al, 2010;Chun et al, 2010;He et al, 2010a, b;Koopman et al, 2010;Schutte et al, 2010;Teixeira et al, 2010;Uroz et al, 2010). A similar strategy has also been used for sequencing functional genes (Iwai et al, 2010).…”

Diversity and heritability of the maize rhizosphere microbiome under field conditions

“…Microbes in both the phyllosphere and rhizosphere can be endophytic, epiphytic, or closely associated. Examples of close microbial associates in the phyllosphere include those inhabiting the fluid in pitcher plants (1), and close microbial associates in the rhizosphere include those not touching roots, but heavily influenced by root exudates in the nearby soil (2). The host plant often relies on the microbiome to provide it with critical nutrients, as minerals present in the soil may be in forms inaccessible to plants (2).…”