Diversity, community structure, and quantity of eukaryotic phytoplankton revealed using 18S rRNA and plastid 16S rRNA genes and pigment markers: a case study of the Pearl River Estuary.
Shumin Xu, Guihao Li, Cui He, Yi Huang, Dan Yu, Huiwen Deng, Zhuyin Tong, Yichong Wang, Christine Dupuy, Bangqin Huang, Zhuo Shen, Jie Xu, Jun Gong
{"title":"Diversity, community structure, and quantity of eukaryotic phytoplankton revealed using 18S rRNA and plastid 16S rRNA genes and pigment markers: a case study of the Pearl River Estuary.","authors":"Shumin Xu, Guihao Li, Cui He, Yi Huang, Dan Yu, Huiwen Deng, Zhuyin Tong, Yichong Wang, Christine Dupuy, Bangqin Huang, Zhuo Shen, Jie Xu, Jun Gong","doi":"10.1007/s42995-023-00186-x","DOIUrl":null,"url":null,"abstract":"<p><p>Understanding consistencies and discrepancies in characterizing diversity and quantity of phytoplankton is essential for better modeling ecosystem change. In this study, eukaryotic phytoplankton in the Pearl River Estuary, South China Sea were investigated using nuclear 18S rRNA and plastid 16S or 23S rRNA genes and pigment analysis. It was found that 18S abundance poorly explained the variations in total chlorophyll <i>a</i> (Chl-<i>a</i>). However, the ratios of log-transformed 18S abundance to Chl-<i>a</i> in the major phytoplankton groups were generally environment dependent, suggesting that the ratio has potential as an indicator of the physiological state of phytoplankton. The richness of 18S-based operational taxonomic units was positively correlated with the richness of 16S-based amplicon sequence variants of the whole phytoplankton community, but insignificant or weak for individual phytoplankton groups. Overall, the 18S based, rather than the 16S based, community structure had a greater similarity to pigment-based estimations. Relative to the pigment data, the proportion of haptophytes in the 18S dataset, and diatoms and cryptophytes in the 16S dataset, were underestimated. This study highlights that 18S metabarcoding tends to reflect biomass-based community organization of eukaryotic phytoplankton. Because there were lower copy numbers of plastid 16S than 18S per genome, metabarcoding of 16S probably approximates cell abundance-based community organization. Changes in biomass organization of the pigment-based community were sensitive to environmental changes. Taken together, multiple methodologies are recommended to be applied to more accurately profile the diversity and community composition of phytoplankton in natural ecosystems.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s42995-023-00186-x.</p>","PeriodicalId":53218,"journal":{"name":"Marine Life Science & Technology","volume":"5 3","pages":"415-430"},"PeriodicalIF":5.8000,"publicationDate":"2023-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10449762/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Marine Life Science & Technology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1007/s42995-023-00186-x","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2023/8/1 0:00:00","PubModel":"eCollection","JCR":"Q1","JCRName":"MARINE & FRESHWATER BIOLOGY","Score":null,"Total":0}
引用次数: 0
Abstract
Understanding consistencies and discrepancies in characterizing diversity and quantity of phytoplankton is essential for better modeling ecosystem change. In this study, eukaryotic phytoplankton in the Pearl River Estuary, South China Sea were investigated using nuclear 18S rRNA and plastid 16S or 23S rRNA genes and pigment analysis. It was found that 18S abundance poorly explained the variations in total chlorophyll a (Chl-a). However, the ratios of log-transformed 18S abundance to Chl-a in the major phytoplankton groups were generally environment dependent, suggesting that the ratio has potential as an indicator of the physiological state of phytoplankton. The richness of 18S-based operational taxonomic units was positively correlated with the richness of 16S-based amplicon sequence variants of the whole phytoplankton community, but insignificant or weak for individual phytoplankton groups. Overall, the 18S based, rather than the 16S based, community structure had a greater similarity to pigment-based estimations. Relative to the pigment data, the proportion of haptophytes in the 18S dataset, and diatoms and cryptophytes in the 16S dataset, were underestimated. This study highlights that 18S metabarcoding tends to reflect biomass-based community organization of eukaryotic phytoplankton. Because there were lower copy numbers of plastid 16S than 18S per genome, metabarcoding of 16S probably approximates cell abundance-based community organization. Changes in biomass organization of the pigment-based community were sensitive to environmental changes. Taken together, multiple methodologies are recommended to be applied to more accurately profile the diversity and community composition of phytoplankton in natural ecosystems.
Supplementary information: The online version contains supplementary material available at 10.1007/s42995-023-00186-x.
期刊介绍：
Marine Life Science & Technology (MLST), established in 2019, is dedicated to publishing original research papers that unveil new discoveries and theories spanning a wide spectrum of life sciences and technologies. This includes fundamental biology, fisheries science and technology, medicinal bioresources, food science, biotechnology, ecology, and environmental biology, with a particular focus on marine habitats.
The journal is committed to nurturing synergistic interactions among these diverse disciplines, striving to advance multidisciplinary approaches within the scientific field. It caters to a readership comprising biological scientists, aquaculture researchers, marine technologists, biological oceanographers, and ecologists.
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号
