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...微生物与多细胞生物类似，同样参与生态群落的构建。然而，针对多细胞生物的生态过程描述与预测已拥有数百年的观测与理论研究积累，微生物群落却缺乏此类研究基础。本研究聚焦于亚马逊瓜多竹属（Guadua）植物充满水的节间空腔内早期细菌群落的组装过程。竹林在亚马逊低地雨林中形成独特的生境斑块，为多种脊椎动物与无脊椎动物提供栖息场所。瓜多竹在生长过程中会形成密封且充满水的节间空腔，未开放的节间空腔被认为是无菌或近乎无菌的（即仅携带少量内生相关微生物），但多数节间最终会被动物破坏并与外界环境连通，随后被微生物定植。我们发现，在暴露于环境的最初数天内，微生物群落多样性会急剧上升，且微生物的分类学特征也会随此过程发生变化…… 【样本采集】 样本采集工作于2016年11月30日启动，地点位于秘鲁南部的洛斯阿莫斯生物站（Los Amigos Biological Station）。该站地处毗邻马德雷德迪奥斯河（亚马逊河支流）的低地热带雨林中。我们在两块高地旱地森林样地中，采集了8株韦氏瓜多竹（Guadua weberbaueri）的积水样本，每个样地采集4株竹秆（图1A）。节间采样需满足以下条件：节间距地面高度为1至2米、内部存有积水且处于密封状态。我们使用经漂白粉灭菌的手术刀，在节间顶部水位以上位置水平切出一个20至40毫米的切口以打开竹秆节间壁层，随后用刀刃挑起节间的部分外部表皮（图1B）。该采样方法的设计灵感来源于觅食的棕卷尾猴的行为（Davidson等，2006；Jacobs与von May，2012）。 # 组装微生物群落：新热带区竹秆节间自然实验的基因组分析 [https://doi.org/10.5061/dryad.4qrfj6qd1] ## 数据与文件结构说明 本数据集仓库包含两份数据文件与一份调用它们的R脚本。数据文件为经Mothur流程处理后的16S rRNA宏条形码（metabarcode）测序数据。该R脚本可复现论文中的全部分析流程并生成所有图表。 ### 文件与变量说明 #### 文件：fin.opti_mcc.shared **描述**：该文件为实验打开的竹秆节间积水样本的样本×操作分类单元（OTU, Operational Taxonomic Unit）矩阵，其OTU信息来自经Mothur流程处理的16S rRNA宏条形码测序数据。 #### 文件：fin.opti_mcc.0.03.cons.taxonomy **描述**：该文件包含样本×OTU矩阵中所有OTU的分类学鉴定结果。 #### 文件：bamboo_code.R **描述**：该R脚本可复现论文中的全部分析流程并生成所有图表。