AB 24:9-15 (2015)  -  DOI: https://doi.org/10.3354/ab00629

Unreliable quantitation of species abundance based on high-throughput sequencing data of zooplankton communities

Changsen Sun1, Yan Zhao2, Haitao Li3, Yanhong Dong3, Hugh J. MacIsaac4, Aibin Zhan2,*

1School of Life Science, Taizhou University, 1139 Shifu Avenue, Taizhou, Zhejiang 318000, PR China
2Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, PR China
3South China Sea Environmental Monitoring Center, State Oceanic Administration, 155 Xingang Road West, Guangzhou, Guangdong 510300, PR China
4Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset Avenue, Windsor, Ontario N9B 3P4, Canada
*‑Corresponding author:

ABSTRACT: High-throughput sequencing (HTS) is rapidly becoming a popular and robust tool to characterize biodiversity of complex communities, especially for those dominated by microscopic species such as zooplankton. The popular use of HTS-based methods has prompted a possible method of inferring relative species abundance from sequencing data. However, these methods remain largely untested in many communities as to whether sequence data can reliably quantify relative species abundance. Here we tested the relationship between species abundance and sequence abundance in zooplankton using 2 methods: (1) spiking known amounts of indicator species into existing zooplankton communities, and (2) comparing results obtained from parallel replicates for the same natural zooplankton communities. Although we detected a general trend that low-abundance species usually corresponded to low-abundance sequence reads, further statistical analyses revealed that sequencing data could not reliably quantify relative species abundance, even for the same indicator species spiked into different zooplankton communities. The distribution of sequence reads statistically varied even between parallel replicates of the same natural zooplankton communities. Our study reveals that sequence abundance may generally qualitatively reflect species abundance as the general trend between these 2 variables exists; however, extra caution is required when using HTS-based approaches to make quantitative inferences regarding zooplankton communities.

KEY WORDS: Biodiversity · Biomass · High-throughput sequencing · HTS · Small subunit ribosomal DNA · SSU 18S rDNA · Species abundance · Zooplankton

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Cite this article as: Sun C, Zhao Y, Li H, Dong Y, MacIsaac HJ, Zhan A (2015) Unreliable quantitation of species abundance based on high-throughput sequencing data of zooplankton communities. Aquat Biol 24:9-15. https://doi.org/10.3354/ab00629

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