Determining diversity of benthic diatoms in the tidal flat using the environmental metabarcoding

Abstract

Benthic diatoms are most dominant group in tidal flats and play major roles in maintaining ecosystem functions. In order to study the diversity and dynamics of benthic diatom communities, it should be available for identification and classification of species. The diatoms are traditionally identified and classified on the basis of morphological characteristics, however it usually takes a lot of time and effort to master. Therefore, it is necessary to establish a classification system based on a genetic approach because overcoming the limitations of morphological identification still remains a great challenge. To investigate the temporal variation in diversity and distribution of benthic diatoms, a total of 80 samples were collected at Guenso Bay, West Coast of Korea, from May 2009 to May 2015 and sequenced using the Miseq platform with novel rbcL gene. We obtained 1,362,742 reads with a length of 431 bp. The reads that pre-clustered in 99% similarity by K-Nearest Neighbor (k-NN) algorithm were divided 454 OTUs. Among them, the 31 OTUs comprising more than 1% frequency were used for the analysis and these were represented two classes, seven orders, 12 families, 15 genera and 52 clades (including 12 unknown clades). Monthly variations in relative abundance of OTUs comprising more than 1% frequency ranged from 34.0 to 48.2%. Navicula was the most abundant genus, followed by Amphora, Nitzschia, Gyrosigma, Entomoneis etc.fication of species. The diatoms are traditionally identified and classified on the basis of morphological characteristics, however it usually takes a lot of time and effort to master. Therefore, it is necessary to establish a classification system based on a genetic approach because overcoming the limitations of morphological identification still remains a great challenge. To investigate the temporal variation in diversity and distribution of benthic diatoms, a total of 80 samples were collected at Guenso Bay, West Coast of Korea, from May 2009 to May 2015 and sequenced using the Miseq platform with novel rbcL gene. We obtained 1,362,742 reads with a length of 431 bp. The reads that pre-clustered in 99% similarity by K-Nearest Neighbor (k-NN) algorithm were divided 454 OTUs. Among them, the 31 OTUs comprising more than 1% frequency were used for the analysis and these were represented two classes, seven orders, 12 families, 15 genera and 52 clades (including 12 unknown clades). Monthly variations in relative abundance of OTUs comprising more than 1% frequency ranged from 34.0 to 48.2%. Navicula was the most abundant genus, followed by Amphora, Nitzschia, Gyrosigma, Entomoneis etc.