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. 2022 Sep 16:10:e13958.
doi: 10.7717/peerj.13958. eCollection 2022.

Assembling microbial communities: a genomic analysis of a natural experiment in neotropical bamboo internodes

Sonia Ahluwalia  1   2 , Iris Holmes  1   3 , Rudolf von May  1   4 , Daniel L Rabosky  1 , Alison R Davis Rabosky  1
Affiliations

Assembling microbial communities: a genomic analysis of a natural experiment in neotropical bamboo internodes

Sonia Ahluwalia et al. PeerJ. .

Abstract

Microbes participate in ecological communities, much like multicellular organisms. However, microbial communities lack the centuries of observation and theory describing and predicting ecological processes available for multicellular organisms. Here, we examine early bacterial community assembly in the water-filled internodes of Amazonian bamboos from the genus Guadua. Bamboo stands form distinct habitat patches within the lowland Amazonian rainforest and provide habitat for a suite of vertebrate and invertebrate species. Guadua bamboos develop sealed, water-filled internodes as they grow. Internodes are presumed sterile or near sterile while closed, but most are eventually opened to the environment by animals, after which they are colonized by microbes. We find that microbial community diversity increases sharply over the first few days of environmental exposure, and taxonomic identity of the microbes changes through this time period as is predicted for early community assembly in macroscopic communities. Microbial community taxonomic turnover is consistent at the bacteria phylum level, but at the level of Operational Taxonomic Units (OTUs), internode communities become increasingly differentiated through time. We argue that these tropical bamboos form an ideal study system for microbial community ecology due to their near-sterile condition prior to opening, relatively consistent environment after opening, and functionally limitless possibilities for replicates. Given the possible importance of opened internode habitats as locations of transmission for both pathogenic and beneficial microbes among animals, understanding the microbial dynamics of the internode habitat is a key conservation concern for the insect and amphibian species that use this microhabitat.

Keywords: Amazon; Bamboo; Microbial community-assembly; Succession.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Figure 1
Figure 1. Guadua weberbaurei characteristics and associated animals.
(A) cross-section of a closed internode partially filled with water (the phytotelmata), (B) a representation of the experimental opening and sampling of bamboo water, (C) the frog Ranitomeya sirensis, which lays its eggs in bamboo internodes, (D) weevil feeding on bamboo sap. A and B illustrated by Karin von May, photo credit for C to Rudolf von May, photo credit for D to Marcos Ríos.
Figure 2
Figure 2. Species composition and community diversity through time.
(A) abundance of the top four most common bacteria taxa in each sampling day. Triangles represent mean abundances across bamboos, small circles are single bamboo measures. (B) Measures of Shannon diversity of the bacteria community of each bamboo on each sampling day.
Figure 3
Figure 3. Community progression through time.
(A) OTUs of the four most abundant bacteria taxa (represented by x-shaped points) cluster in different regions of the NMDS space, (B) centroids of the communities (circular points) for each sample cluster according to day, and (C) pairwise distances between bamboo samples within sampling days become larger over time.
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