Describing macroecological patterns in microbes: Approaches for comparative analyses of operational taxonomic unit read number distribution with a case study of global oceanic bacteria. Issue 4 (26th February 2020)

• Record Type: Journal Article
• Authors: Nakadai, Ryosuke; Okazaki, Yusuke; Matsuoka, Shunsuke
• Is Part Of: Environmental DNA. Volume 2:Issue 4(2020:Oct.)
• Page Start: 535
• Page End: 543
• Publication Date: 2020-02-26
• Subjects: skewness -- species abundance distribution -- Weibull distribution -- Whittaker plot; DNA -- Periodicals; Biology -- Periodicals; Microbial ecology -- Periodicals; Biology; DNA; Microbial ecology; Electronic journals; Periodicals; 572.86
• DOI: 10.1002/edn3.78
• Languages: English
• ISSNs: 2637-4943

Abstract

Abstract: Describing the variation in commonness and rarity in a community is a fundamental method of evaluating biodiversity. Such patterns have been studied in the context of species abundance distributions (SADs) among macroscopic organisms in numerous communities. Recently, models for analyzing variation in local SAD shapes along environmental gradients have been constructed. The recent development of high‐throughput sequencing enables evaluation of commonness and rarity in local communities of microbes using operational taxonomic unit (OTU) read number distributions (ORDs), which are conceptually similar to SADs. However, few studies have explored the variation in local microbial ORD shapes along environmental gradients. Therefore, the similarities and differences between SADs and ORDs are unclear, clouding any universal rules of global biodiversity patterns. We investigated the similarities and differences in ORD shapes versus SADs, and how well environmental variables explain the variation in ORDs along latitudinal and depth gradients. Herein, we integrate ORDs into recent comparative analysis methods for SAD shape using datasets generated on the Tara Oceans expedition. About 56% of the variance in skewness of ORDs among global oceanic bacterial communities was explained with this method. Moreover, we confirmed that the parameter combination constraints of Weibull distributions were shared by ORDs of bacterial communities and SADs of tree communities, suggesting common long‐term limitation processes such as adaptation and community persistence acting on current abundance variation. On the other hand, skewness was significantly greater for bacterial communities than tree communities, and many ecological predictions did not apply to bacterial communities, suggesting differences in the community assembly rules for microbes and macroscopic organisms. Approaches based on ORDs provide opportunities to quantify macroecological patterns of microbes under the same framework as macroscopic organisms. Abstract : We integrated concepts and methods from recent comparative analyses of species abundance distribution (SAD) into the relationship between operational taxonomic units (OTUs) and the read number for each OTU obtained from high‐throughput sequencing (referred to as the OTU read number distribution, ORD). Our results clearly showed similarities and differences between ORDs and SADs through comparison between bacteria communities and tree communities.