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

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 (ie, containing small loads of endosphere-associated microbes) 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 ..., Sample Collection
We collected our samples at Los Amigos Biological Station in southern Peru starting on 30 November 2016. Los Amigos is located in lowland tropical rain forest adjacent to the Madre de Dios river, an Amazon river tributary. We collected water samples from eight bamboo stalks of the species Guadua weberbaueri that were distributed across two plots in upland terra firme forest (Figure 1A). We sampled four stalks from each plot. We determined the following eligibility for internode sampling: the internode must be 1 to 2 meters above the ground, contain water, and be closed. We opened the walls of bamboo internodes using a bleach-sterilized blade to cut a 20 – 40 mm notch horizontally near the top of the node, above the water level. Then we pulled back a section of the internode’s external skin using the edge of the blade (Figure 1B). We chose this method because it mimics the actions of foraging brown capuchin monkeys (Davidson et al. 2006; Jacobs and von May 2012).
At the..., , # Assembling microbial communities: a genomic analysis of a natural experiment in neotropical bamboo internodes

[https://doi.org/10.5061/dryad.4qrfj6qd1](https://doi.org/10.5061/dryad.4qrfj6qd1)

## Description of the data and file structure

This repository contains two data files and an R script that calls them. The data files are 16S rRNA metabarcode data that has been processed through the Mothur pipeline. The R script performs all analyses and generates all figures from the paper.

### Files and variables

#### File: fin.opti\_mcc.shared

**Description:** a sample x OTU matrix from samples from water in experimentally opened bamboo internodes. The OTUs are from 16S rRNA metabarcode data that has been processed through the Mothur pipeline.

#### File: fin.opti\_mcc.0.03.cons.taxonomy

**Description:** Taxonomic identification of OTUs in the sample x OTU matrix

#### File: bamboo\_code.R

**Description:**  The R script performs all analyses and generates all figures from the paper...