First Gut Content Analysis of 4th Instar Midge Larvae (Diptera: Chronomidae) In Large-Scale Weirs Using a DNA Meta-Barcoding Approach
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Area and Field Sampling
2.2. DNA Extraction of Gut Contents and Metagenomic Sequencing
2.3. Data Collection and Statistical Analysis
3. Results
3.1. Meta-Barcoding and Taxonomic Assignment of Operational Taxonomic Unit (OTU)
3.2. Ecological Traits Based on Selectivity Index (E’) and Water Quality
4. Discussion
4.1. Prey Preference of Chironomidae Larvae
4.2. Efficiency of Meta-Barcoding for Analysis of Chironomidae Larvae Gut Contents
4.3. Potential Indicator of the Surrounding Environment
Author Contributions
Funding
Conflicts of Interest
Appendix A
Sample ID | Sampling Depth (m) | Sampling Date (Month) | Sampling Sites |
---|---|---|---|
SJ-A | 0.5 | July | Sejong Weir |
SJ-B | 1 | June | Sejong Weir |
JS-D | 0.5 | July | Juksan Weir |
JS-E | 0.5 | July | Juksan Weir |
GG-A | 0.5 | June | Gangjeong-Goryeong Weir |
GG-D | 0.5 | June | Gangjeong-Goryeong Weir |
DS-B | 0.5 | June | Dalseong Weir |
DS-E | 0.5 | June | Dalseong Weir |
Step | Details |
---|---|
Washing | Remove impurities from the larva surface |
Weight measurement | Weigh with an electronic balance (SHIMADZU, Kyoto, Japan) |
Total length measurement | Observe the larva using a dissecting microscope (LEICA LED2000, Wetzlar, Germany), and measure its length |
Identification of larva stage | 1st, 2nd, 3rd, 4th of instar larva |
Dissection | Grab the head of the larva and cut the tissue of the torso with a scalpel |
DNA extraction | Samples of micro-tubes were extracted DNA by DNeasy Blood & Tissue Kit (Cat. No. 69504, Qiagen, Düsseldorf, Germany) |
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Order | Family | Genus + Species | SJ.A. | SJ.B. | JS.D. | JS.E. | GG.A. | GG.D. | DS.B. | DS.E. | Total | % | Identity | Query | Access ID |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Ochromonadales | Ochromonadaceae | Poterioochromonas malhamensis | 11 | 415 | 197 | 1,240 | 303 | 48 | 207 | 78 | 2499 | 0.6 | 99 | 100 | MH536661.1 |
Fragilariales | Fragilariaceae | Synedra berolinensis | 577 | 1088 | 81 | 120 | 5 | 4 | 5 | 1880 | 0.5 | 99 | 100 | EF491890.1 | |
Chlamydomonadales | Volvocaceae | Pleodorina starrii | 2196 | 1 | 1 | 2198 | 0.5 | 99 | 99 | LC086359.1 | |||||
Chlorellales | Chlorellaceae | Micractinium sp. | 174 | 318 | 140 | 983 | 1256 | 1 | 129 | 3,001 | 0.7 | 99 | 100 | MF959935.1 | |
Oocystaceae | Oocystis sp. | 4 | 1652 | 1,656 | 0.4 | 98 | 97 | LC472542.1 | |||||||
Thalassiosirales | Stephanodiscaceae | Cyclotella meneghiniana | 755 | 1720 | 1 | 22 | 4 | 671 | 3,173 | 0.8 | 99 | 100 | AB430591.1 | ||
Naviculales | Naviculaceae | Eolimna minima | 96 | 63 | 316 | 1026 | 210 | 1,711 | 0.4 | 99 | 100 | AJ243063.2 | |||
Navicula sp. | 1 | 1146 | 1,147 | 0.3 | 99 | 100 | FN398345.1 | ||||||||
Oedogoniales | Oedogonium howardii | 4885 | 4,885 | 1.2 | 99 | 100 | EF616486.1 | ||||||||
Sphaeropleales | Scenedesmaceae | Desmodesmus armatus | 2416 | 3675 | 1951 | 1,837 | 623 | 63 | 4 | 7110 | 17,679 | 4.4 | 99 | 100 | MK541798.1 |
Tetradesmus dimorphus | 644 | 290 | 690 | 1 | 165 | 38 | 2 | 7539 | 9,369 | 2.3 | 99 | 100 | MN238814.1 | ||
Desmodesmus sp. | 386 | 1417 | 339 | 8 | 26 | 3 | 3132 | 5,311 | 1.3 | 99 | 100 | MF326555.1 | |||
Hydrodictyaceae | Pseudopediastrum sp. | 6 | 2 | 781 | 1 | 5555 | 1 | 5069 | 11,415 | 2.8 | 99 | 100 | KT883909.1 | ||
Biddulphiales | Biddulphiaceae | Biddulphia tridens | 226 | 2 | 1 | 6 | 5152 | 5,387 | 1.3 | 96 | 100 | JX401228.1 | |||
Bacillariales | Bacillariaceae | Nitzschia palea | 171 | 72 | 646 | 219 | 1,108 | 0.3 | 98 | 100 | KU948218.1 | ||||
Colpodida | Colpodidae | Bresslaua vorax | 1 | 2 | 16,835 | 1 | 16,839 | 4.2 | 98 | 100 | AF060453.1 | ||||
Hymenostomatida | Tetrahymenidae | Tetrahymena sp. | 30,932 | 29 | 1 | 6 | 21 | 30,989 | 7.7 | 96 | 97 | KX759198.1 | |||
Diptera | Chironomidae | Dicrotendipes fumidus | 388 | 77,195 | 1 | 11 | 19 | 77,614 | 19.2 | 98 | 95 | AY821866.1 | |||
Cypriniformes | Cyprinidae | Hemibarbus labeo | 6 | 114 | 2,165 | 216 | 186 | 109 | 846 | 108 | 3,750 | 0.9 | 98 | 100 | MH843153.1 |
Dorylaimida | Actinolaimidae | Paractinolaimus sp. | 79,807 | 79,807 | 19.7 | 96 | 99 | KM067902.1 | |||||||
Harpellales | Legeriomycetaceae | Smittium cf. | 2845 | 2,845 | 0.7 | 96 | 99 | JQ302895.1 | |||||||
Number of sequences | 36,794 | 86,402 | 8542 | 4716 | 31,533 | 80,102 | 3913 | 32,261 | 284,263 | ||||||
Number of OTUs | 17 | 15 | 11 | 10 | 16 | 9 | 9 | 17 | 21 |
Taxa | Relative Abundance of Prey | Selectivity Index (E’) | |
---|---|---|---|
Gut Contents (Ri) | In the Water (Pi) | ||
Cyclotella meneghiniana | 8.85 | 73.53 | −0.79 |
Desmodesmus armatus | 49.32 | 3.98 | 0.85 |
Eolimna minima | 4.77 | 0.53 | 0.80 |
Navicula sp. | 3.20 | 1.38 | 0.40 |
Nitzschia palea | 3.09 | 10.61 | −0.55 |
Oocystis sp. | 4.62 | 7.16 | −0.22 |
Tetradesmus dimorphus | 26.14 | 2.81 | 0.81 |
Study Sites | Temp.(°C) | Cond.(µS/cm) | DO (mg/L) | pH | NTU | TN | TP | TOC | DOC | Chl-a |
---|---|---|---|---|---|---|---|---|---|---|
SJ-A | 24.6 | 321 | 5.01 | 8.27 | 23.70 | 2.813 | 0.081 | 3.2 | 2.1 | 31.0 |
SJ-B | 20.7 | 287 | 4.50 | 7.60 | 23.00 | 2.434 | 0.142 | 3.8 | 2 | 5.2 |
JS-D | 25.7 | 249 | 4.23 | 7.93 | 23.80 | 6.984 | 0.116 | 4.7 | 4.5 | 11.4 |
JS-E | 26.0 | 246 | 4.25 | 8.03 | 25.12 | 4.106 | 0.106 | 5.0 | 4.5 | 23.0 |
GG-A | 18.6 | 380 | 6.57 | 8.74 | 17.40 | 4.589 | 0.068 | 2.8 | 2.7 | 35.3 |
GG-D | 27.4 | 496 | 3.93 | 8.66 | 3.49 | 2.150 | 0.045 | 3.5 | 3 | 2.9 |
DS-B | 23.3 | 427 | 5.51 | 8.45 | 5.24 | 2.129 | 0.052 | 3.0 | 3 | 4.9 |
DS-E | 24.4 | 402 | 8.04 | 9.34 | 9.18 | 3.574 | 0.067 | 3.0 | 3 | 11.0 |
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Jo, H.; Choi, B.; Park, K.; Kim, W.-S.; Kwak, I.-S. First Gut Content Analysis of 4th Instar Midge Larvae (Diptera: Chronomidae) In Large-Scale Weirs Using a DNA Meta-Barcoding Approach. Int. J. Environ. Res. Public Health 2020, 17, 2856. https://doi.org/10.3390/ijerph17082856
Jo H, Choi B, Park K, Kim W-S, Kwak I-S. First Gut Content Analysis of 4th Instar Midge Larvae (Diptera: Chronomidae) In Large-Scale Weirs Using a DNA Meta-Barcoding Approach. International Journal of Environmental Research and Public Health. 2020; 17(8):2856. https://doi.org/10.3390/ijerph17082856
Chicago/Turabian StyleJo, Hyunbin, Bohyung Choi, Kiyun Park, Won-Seok Kim, and Ihn-Sil Kwak. 2020. "First Gut Content Analysis of 4th Instar Midge Larvae (Diptera: Chronomidae) In Large-Scale Weirs Using a DNA Meta-Barcoding Approach" International Journal of Environmental Research and Public Health 17, no. 8: 2856. https://doi.org/10.3390/ijerph17082856