Illumina MiSeq Analysis and Comparison of Freshwater Microalgal Communities on Ulleungdo and Dokdo Islands

	Seonginbong	Dongdo	Seodo
Total reads	580 853	534 141	469 920
Validated reads	290 919	289 610	275 387
Mean read length (bp)	408.1	416.7	412.54
Maximum read length (bp)	418	418	408
Number of OTUs¹	834	203	182
Chao1²	834	203.75	182
Shannon³	6.722	2.038	5.118
Simpson⁴	0.9655	0.5569	0.9174
Goods Coverage⁵	1	0.9999	1

11 OTUs: Operational taxonomic units

22 Chao1: Species richness estimation

33 Shannon: Shannon diversity index (> 0, higher is more diverse)

44 Simpson: Simpson diversity index (0–1, 1 = most simple)

55 Goods Coverage: 1 – (number of singleton OTUs/number of sequences); 1 = 100% coverage

Rarefaction curves for operational taxonomic units (OTUs) from the Seonginbong, Dongdo, and Seodo samples. (a) Shannon, (b) Simpson, and (c) Chao1 indexes. (d) UPGMA tree based on the community structures of Seonginbong, Dongdo, and Seodo. Seonginbong (red line), Dongdo (blue line), and Seodo (orange line).

Table II

Number of eukaryotic microalgal taxa observed in the Seonginbong, Dongdo, and Seodo samples.

	Seonginbong		Dongdo		Seodo
	c¹	uc²	c¹	uc²	c¹	uc²
Phylum	165 646	125 273	30 911	258 699	164 678	110 709
Class	128 160	162 759	23 011	266 599	144 662	130 725
Order	99 964	190 955	22 791	266 819	123 329	152 058
Family	96 751	194 168	22 751	266 859	120 206	155 181
Genus	92 628	198 291	22 707	266 903	110 674	164 713
Species	84 154	206 765	17 930	271 680	97 541	177 846

11 Number of sequencing reads with a scientific name for the taxon (classified, c)

27 Number of sequencing reads either unclassified into a sublevel or classified as an unknown name for the taxon (unclassified, uc)

Taxonomic composition of the eukaryotic microbial phyla on Seonginbong, Dongdo, and Seodo.

Taxonomic composition of the microalgal classes on Seonginbong, Dongdo, and Seodo.

Table III

Relative abundance of eukaryotic microalgal families in the Seonginbong, Dongdo, and Seodo samples.

Taxonomy				Seonginbong		Dongdo		Seodo
Phylum	Class	Order	Family	%¹	Fr²	%¹	Fr²	%¹	Fr²
Bacillariophyta	Bacillariophyceae	–	–	0.00	0	0.00	0	21.62	59 531
Bacillariophyta	Bacillariophyceae	–	Achnanthaceae	0.00	0	0.00	0	1.54	4 239
Bacillariophyta	Bacillariophyceae	–	Bacillariaceae	0.15	423	0.00	0	3.26	8 974
Bacillariophyta	Bacillariophyceae	Naviculales	Amphipleuraceae	0.00	0	0.00	0	0.23	645
Bacillariophyta	Bacillariophyceae	Naviculales	Diadesmidaceae	0.00	0	0.00	7	2.38	6 551
Bacillariophyta	Bacillariophyceae	Naviculales	Naviculaceae	0.00	0	0.00	0	0.29	802
Bacillariophyta	Bacillariophyceae	Naviculales	Pinnulariaceae	0.09	256	0.00	0	0.00	0
Bacillariophyta	Bacillariophyceae	Naviculales	Sellaphoraceae	0.00	0	0.00	0	3.12	8 579
Bacillariophyta	Bacillariophyceae	Naviculales	Stauroneidaceae	1.16	3 379	0.00	0	0.00	0
Bacillariophyta	Bacillariophyceae	Thalassiophysales	Catenulaceae	0.00	0	0.00	0	0.12	329
Bacillariophyta	Coscinodiscophyceae	Melosirales	Stephanopyxidaceae	0.00	0	0.00	0	3.14	8 660
Bacillariophyta	Coscinodiscophyceae	Paraliales	–	0.00	0	0.00	0	0.13	354
Chlorophyta	–	–	–	0.00	0	0.02	65	0.00	0
Chlorophyta	–	Chlorodendrales	–	0.00	0	0.01	21	0.00	0
Chlorophyta	Chlorophyceae	–	–	0.03	91	0.00	13	0.62	1 708
Chlorophyta	Chlorophyceae	Chlamydomonadales	–	2.53	7 368	0.09	271	0.00	0
Chlorophyta	Chlorophyceae	Chlamydomonadales	Characiochloridaceae	0.34	1 002	0.00	0	0.00	0
Chlorophyta	Chlorophyceae	Chlamydomonadales	Chlamydomonadaceae	0.38	1 096	0.02	48	0.00	0
Chlorophyta	Chlorophyceae	Chlamydomonadales	Chlorococcaceae	1.53	4 437	18.46	53 463	0.00	0
Chlorophyta	Chlorophyceae	Chlorosarcinales	–	1.29	3 761	0.00	0	0.00	0
Chlorophyta	Chlorophyceae	Sphaeropleales	–	3.47	10 096	0.00	2	0.00	0
Chlorophyta	Chlorophyceae	Sphaeropleales	Scenedesmaceae	0.08	243	0.00	0	0.22	597
Chlorophyta	Trebouxiophyceae	–	–	0.56	1 624	0.00	0	0.12	329
Chlorophyta	Trebouxiophyceae	–	Coccomyxaceae	0.01	23	0.00	0	0.00	0
Chlorophyta	Trebouxiophyceae	Chlorellales	–	0.00	0	0.00	7	0.00	0
Chlorophyta	Trebouxiophyceae	Chlorellales	Chlorellaceae	0.58	1 689	64.91	187 999	0.06	162
Chlorophyta	Trebouxiophyceae	Ctenocladales	Ctenocladaceae	0.21	604	0.00	0	0.00	0
Chlorophyta	Trebouxiophyceae	Microthamniales	–	0.11	323	0.02	48	0.00	0
Chlorophyta	Ulvophyceae	Ulotrichales	–	0.55	1 605	0.00	0	0.00	0
Chlorophyta	Ulvophyceae	Ulvales	–	0.00	0	0.00	0	0.05	136

1 The microalgal families detected in at least one of the three samples are shown. Unclassified taxonomic names (phylum, class, order, and family) are replaced with a dash (–)

21 Relative abundance

32 Frequency of microalgae detected at each sampling site

Molecular phylogenetic analysis using a maximum likelihood (ML) tree. The boundary between phyla is marked with a yellow box, and the boundaries between classes are marked with purple boxes. Five classes are displayed about the species names in the phylogenetic tree. The dominant species in each sample is marked with a colored box (Seonginbong: red; Dongdo: blue; Seodo: green). The class of each group is presented at the edge (Bacillariophyceae; red, Coscinodiscophyceae; yellow, Chlorophyceae; blue, Trebouxiophyceae; green and Ulvophyceae; purple).

Table IV

Relative abundance of eukaryotic microalgal genera in the Seonginbong, Dongdo, and Seodo samples.

Taxonomy					Seonginbong		Dor	gdo	Seodo
Phylum	Class	Order	Family	Genus	%¹	Fr²	%¹	Fr²	%¹	Fr²
Bacillariophyta	Bacillariophyceae	–	–	–	0.00	0	0.00	0	0.86	2 363
Bacillariophyta	Bacillariophyceae	–	–	Achnanthidium	0.00	0	0.00	0	20.76	57 168
Bacillariophyta	Bacillariophyceae	–	Achnanthaceae	Achnanthes	0.00	0	0.00	0	1.54	4 239
Bacillariophyta	Bacillariophyceae	–	Bacillariaceae	Hantzschia	0.15	423	0.00	0	0.00	0
Bacillariophyta	Bacillariophyceae	–	Bacillariaceae	Nitzschia	0.00	0	0.00	0	3.26	8 974
Bacillariophyta	Bacillariophyceae	Naviculales	Amphipleuraceae	-	0.00	0	0.00	0	0.23	645
Bacillariophyta	Bacillariophyceae	Naviculales	Diadesmidaceae	Diadesmis	0.00	0	0.00	0	2.15	5 922
Bacillariophyta	Bacillariophyceae	Naviculales	Diadesmidaceae	Luticola	0.00	0	0.00	7	0.23	629
Bacillariophyta	Bacillariophyceae	Naviculales	Naviculaceae	Navicula	0.00	0	0.00	0	0.29	802
Bacillariophyta	Bacillariophyceae	Naviculales	Pinnulariaceae	Pinnularia	0.09	256	0.00	0	0.00	0
Bacillariophyta	Bacillariophyceae	Naviculales	Sellaphoraceae	Sellaphora	0.00	0	0.00	0	3.12	8 579
Bacillariophyta	Bacillariophyceae	Naviculales	Stauroneidaceae	Stauroneis	1.16	3 379	0.00	0	0.00	0
Bacillariophyta	Bacillariophyceae	Thalassiophysales	Catenulaceae	Amphora	0.00	0	0.00	0	0.12	329
Bacillariophyta	Coscinodiscophyceae	Melosirales	Stephanopyxidaceae	Stephanopyxis	0.00	0	0.00	0	3.14	8 660
Bacillariophyta	Coscinodiscophyceae	Paraliales	–	Paralia	0.00	0	0.00	0	0.13	354
Chlorophyta	–	–	–	-	0.00	0	0.02	65	0.00	0
Chlorophyta	–	Chlorodendrales	–	-	0.00	0	0.01	21	0.00	0
Chlorophyta	Chlorophyceae	–	–	-	0.03	91	0.00	13	0.62	1708
Chlorophyta	Chlorophyceae	Chlamydomonadales	–	-	1.48	4 308	0.09	249	0.00	0
Chlorophyta	Chlorophyceae	Chlamydomonadales	–	Actinochloris	0.00	0	0.01	22	0.00	0
Chlorophyta	Chlorophyceae	Chlamydomonadales	–	Ettlia	0.62	1 793	0.00	0	0.00	0
Chlorophyta	Chlorophyceae	Chlamydomonadales	–	Spongiochloris	0.44	1 267	0.00	0	0.00	0
Chlorophyta	Chlorophyceae	Chlamydomonadales	Characiochloridaceae	Characiochloris	0.34	1002	0.00	0	0.00	0
Chlorophyta	Chlorophyceae	Chlamydomonadales	Chlamydomonadaceae	-	0.02	50	0.00	0	0.00	0
Chlorophyta	Chlorophyceae	Chlamydomonadales	Chlamydomonadaceae	Chlamydomonas	0.35	1026	0.00	0	0.00	0
Chlorophyta	Chlorophyceae	Chlamydomonadales	Chlamydomonadaceae	Chloromonas	0.01	20	0.02	48	0.00	0
Chlorophyta	Chlorophyceae	Chlamydomonadales	Chlorococcaceae	Chlorococcum	1.53	4 437	18.46	53 463	0.00	0
Chlorophyta	Chlorophyceae	Chlorosarcinales	–	Chlorosarcinopsis	1.29	3 761	0.00	0	0.00	0
Chlorophyta	Chlorophyceae	Sphaeropleales	–	-	1.47	4 271	0.00	2	0.00	0
Chlorophyta	Chlorophyceae	Sphaeropleales	–	Bracteacoccus	1.89	5 490	0.00	0	0.00	0
Chlorophyta	Chlorophyceae	Sphaeropleales	–	Dictyochloris	0.12	335	0.00	0	0.00	0
Chlorophyta	Chlorophyceae	Sphaeropleales	Scenedesmaceae	Coelastrella	0.02	64	0.00	0	0.22	597
Chlorophyta	Chlorophyceae	Sphaeropleales	Scenedesmaceae	Desmodesmus	0.06	179	0.00	0	0.00	0
Chlorophyta	Treb ouxiophyceae	–	–	-	0.04	102	0.00	0	0.00	0
Chlorophyta	Treb ouxiophyceae	–	–	Myrmecia	0.51	1487	0.00	0	0.12	329
Chlorophyta	Treb ouxiophyceae	–	–	Watanabea	0.01	35	0.00	0	0.00	0
Chlorophyta	Treb ouxiophyceae	–	Coccomyxaceae	Coccomyxa	0.01	23	0.00	0	0.00	0
Chlorophyta	Treb ouxiophyceae	Chlorellales	–	-	0.00	0	0.00	7	0.00	0
Chlorophyta	Treb ouxiophyceae	Chlorellales	Chlorellaceae	-	0.06	182	63.78	184 700	0.06	162
Chlorophyta	Treb ouxiophyceae	Chlorellales	Chlorellaceae	Auxenochlorella	0.34	999	0.00	2	0.00	0
Chlorophyta	Treb ouxiophyceae	Chlorellales	Chlorellaceae	Chlorella	0.04	102	0.00	0	0.00	0
Chlorophyta	Treb ouxiophyceae	Chlorellales	Chlorellaceae	Heveochlorella	0.00	0	0.00	12	0.00	0
Chlorophyta	Treb ouxiophyceae	Chlorellales	Chlorellaceae	Lobosphaera	0.00	14	0.00	0	0.00	0
Chlorophyta	Treb ouxiophyceae	Chlorellales	Chlorellaceae	Pseudochlorella	0.13	392	1.13	3 285	0.00	0
Chlorophyta	Treb ouxiophyceae	Ctenocladales	Ctenocladaceae	Leptosira	0.21	604	0.00	0	0.00	0
Chlorophyta	Treb ouxiophyceae	Microthamniales	–	-	0.09	272	0.00	0	0.00	0
Chlorophyta	Treb ouxiophyceae	Microthamniales	–	Dictyochlompsis	0.02	51	0.00	0	0.00	0
Chlorophyta	Treb ouxiophyceae	Microthamniales	–	Stichococcus	0.00	0	0.02	48	0.00	0
Chlorophyta	Ulvophyceae	Ulotrichales	–	-	0.55	1605	0.00	0	0.00	0
Chlorophyta	Ulvophyceae	Ulvales	–	-	0.00	0	0.00	0	0.05	136

1 The microalgal genera detected in at least one of the three samples are shown. Unclassified taxonomic names (phylum, class, order, family, and genus) are replaced with a dash (–)

21 Relative abundance

32 Frequency of microalgae detected at each sampling site

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Articles in this issue

DOI: https://doi.org/10.33073/pjm-2019-053 | Journal eISSN: 2544-4646 | Journal ISSN: 1733-1331

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Language: English

Page range: 527 - 539

Submitted on: Jul 25, 2019

Accepted on: Oct 30, 2019

Published on: Dec 5, 2019

Published by: Polish Society of Microbiologists

In partnership with: Paradigm Publishing Services

Publication frequency: 4 issues per year

Keywords:

amplicon sequencing,

Dokdo Island,

microalgal community,

MiSeq system,

Ulleungdo Island

Related subjects:

Life sciences,

Microbiology and virology

© 2019 HYUN-SIK YUN, YOUNG-SAENG KIM, HO-SUNG YOON, published by Polish Society of Microbiologists
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

Volume 68 (2019): Issue 4 (January 2019)

Illumina MiSeq Analysis and Comparison of Freshwater Microalgal Communities on Ulleungdo and Dokdo Islands

Figures & Tables

Table I

Fig. 1.

Table II

Fig. 2.

Fig. 3.

Table III

Fig. 4.

Table IV

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