General Information
- Experiment ID
- OEX011312
- Experiment Name
- OEX_xiafei_2101091650
- Experiment Type
- Metagenomic
- Description
- Protists in aquaculture ponds are key components associated with primary productivity, nutrient cycling, and fish healthy. However, the protist metacommunity diversity, as well as the ecological and environmental factors that structure protist metacommunity in aquaculture ponds remain poorly understood. This study examined protist metacommunities in water and sediment of larval, small juvenile and large juvenile grass carp ponds. The results indicated sediment resuspension became stronger with the increased fish size, which led to high levels of total suspended solids and nitrogen but low levels of phosphate, chlorophyll a and transparency in water. Moreover, sediment resuspension subsequently increased the alpha diversity indexes (i.e., OTU number, Shannon index and Simpson index) of protist communities in water and sediment. Meanwhile, sediment resuspension increased the relative abundance of heterotrophic Ciliophora and Cercozoa, but decreased the relative abundance of autotrophic Chlorophyta, Stramenopiles X, and Ochrophyta. Besides, some mixotrophic and heterotrophic protists showed competitive advantages in the turbidity water, which led to the increase of negative interactions in the protist co-occurrence networks. Based on the null model, sediment resuspension strengthened homogeneous selection (deterministic process) and weakened dispersal limitation (stochastic process) processes of protist community assembly. Indeed, protist community dissimilarity within each local community and each habitat (water or sediment) both decreased while the community dissimilarity between habitats increased with the increase of fish size. Therefore, sediment resuspension did not enhance the dispersal path between water and sediment, but decreased the dispersal limitation within sediment and water coupled with the strengthening of environmental selection. These results indicated that grass carp could restructure the protist metacommunity in aquaculture ponds through bottom up way of sediment resuspension. This study advances our understanding of the relationship between fish and protist metacommunity assembly in aquaculture systems.
- Protocol
- Extraction and purification of protist community DNA from filtered water and sediment were carried out using the PowerWater DNA Isolation Kit and PowerSoil DNA Isolation Kit (MO BIO laboratories, Carlsbad, USA), respectively. For sediments, we combined the freeze-grind DNA extraction method with the MoBio PowerSoil kit as described in http://www.ou.edu/ieg/tools/protocols. The quantity and quality of DNA were determined using a NanoDrop Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA). The V4 region of the eukaryotic small-subunit 18S rRNA gene was amplified using the universal primer pair TAReuk454FWD1 (5′-CCAGCA(G/C)C(C/T)GCGGTAATTCC-3′) and TAReukREV3 (5′-ACTTTCGTTCTTGAT(C/T)(A/G)A-3′) (Stoeck et al., 2010). The PCR program was composed of an initial denaturation step at 95 °C for 5 min; 30 cycles of 94 °C for 30 s, 47 °C for 45 s and 72 °C for 1 min; and a final 5-min extension at 72 °C (Yang et al., 2018). The PCR product of each sample was purified with equal quantity and sequenced on the Illumina HiSeq2500 platform (Illumina, Inc., San Diego, CA, USA) using a paired-end (2 × 250 bp) approach.
Experiment information
- Attributes
-
library_layout Paired mate_pair n/a insertion_size n/a number_of_reads_sequenced n/a library_name n/a library_selection PCR library_strategy AMPLICON platform Illumina HiSeq 2500 - Project
-
1
Project ID Project name Create Date OEP001497 protist in aquaculture ponds 2021-01-09 - Samples
-
96
Sample ID Sample Name Organism Tissue Create Date OES065193 L1W aquatic metagenome N/A 2021-01-14 OES065194 L11W aquatic metagenome N/A 2021-01-14 OES065195 L12W aquatic metagenome N/A 2021-01-14 OES065196 L13W aquatic metagenome N/A 2021-01-14 OES065197 L2W aquatic metagenome N/A 2021-01-14 OES065198 L21W aquatic metagenome N/A 2021-01-14 OES065199 L22W aquatic metagenome N/A 2021-01-14 OES065200 L23W aquatic metagenome N/A 2021-01-14 OES065201 L3W aquatic metagenome N/A 2021-01-14 OES065202 L31W aquatic metagenome N/A 2021-01-14 OES065203 L32W aquatic metagenome N/A 2021-01-14 OES065204 L33W aquatic metagenome N/A 2021-01-14 OES065205 J1W aquatic metagenome N/A 2021-01-14 OES065206 J11W aquatic metagenome N/A 2021-01-14 OES065207 J12W aquatic metagenome N/A 2021-01-14 OES065208 J13W aquatic metagenome N/A 2021-01-14 OES065209 J2W aquatic metagenome N/A 2021-01-14 OES065210 J21W aquatic metagenome N/A 2021-01-14 OES065211 J22W aquatic metagenome N/A 2021-01-14 OES065212 J23W aquatic metagenome N/A 2021-01-14 OES065213 J3W aquatic metagenome N/A 2021-01-14 OES065214 J31W aquatic metagenome N/A 2021-01-14 OES065215 J32W aquatic metagenome N/A 2021-01-14 OES065216 J33W aquatic metagenome N/A 2021-01-14 OES065217 M1W aquatic metagenome N/A 2021-01-14 OES065218 M11W aquatic metagenome N/A 2021-01-14 OES065219 M12W aquatic metagenome N/A 2021-01-14 OES065220 M13W aquatic metagenome N/A 2021-01-14 OES065221 M2W aquatic metagenome N/A 2021-01-14 OES065222 M21W aquatic metagenome N/A 2021-01-14 OES065223 M22W aquatic metagenome N/A 2021-01-14 OES065224 M23W aquatic metagenome N/A 2021-01-14 OES065225 M3W aquatic metagenome N/A 2021-01-14 OES065226 M31W aquatic metagenome N/A 2021-01-14 OES065227 M32W aquatic metagenome N/A 2021-01-14 OES065228 M33W aquatic metagenome N/A 2021-01-14 OES065229 A1W aquatic metagenome N/A 2021-01-14 OES065230 A11W aquatic metagenome N/A 2021-01-14 OES065231 A12W aquatic metagenome N/A 2021-01-14 OES065232 A13W aquatic metagenome N/A 2021-01-14 OES065233 A2W aquatic metagenome N/A 2021-01-14 OES065234 A21W aquatic metagenome N/A 2021-01-14 OES065235 A22W aquatic metagenome N/A 2021-01-14 OES065236 A23W aquatic metagenome N/A 2021-01-14 OES065237 A3W aquatic metagenome N/A 2021-01-14 OES065238 A31W aquatic metagenome N/A 2021-01-14 OES065239 A32W aquatic metagenome N/A 2021-01-14 OES065240 A33W aquatic metagenome N/A 2021-01-14 OES065241 L1S aquatic metagenome N/A 2021-01-14 OES065242 L11S aquatic metagenome N/A 2021-01-14 OES065243 L12S aquatic metagenome N/A 2021-01-14 OES065244 L13S aquatic metagenome N/A 2021-01-14 OES065245 L2S aquatic metagenome N/A 2021-01-14 OES065246 L21S aquatic metagenome N/A 2021-01-14 OES065247 L22S aquatic metagenome N/A 2021-01-14 OES065248 L23S aquatic metagenome N/A 2021-01-14 OES065249 L3S aquatic metagenome N/A 2021-01-14 OES065250 L31S aquatic metagenome N/A 2021-01-14 OES065251 L32S aquatic metagenome N/A 2021-01-14 OES065252 L33S aquatic metagenome N/A 2021-01-14 OES065253 J1S aquatic metagenome N/A 2021-01-14 OES065254 J11S aquatic metagenome N/A 2021-01-14 OES065255 J12S aquatic metagenome N/A 2021-01-14 OES065256 J13S aquatic metagenome N/A 2021-01-14 OES065257 J2S aquatic metagenome N/A 2021-01-14 OES065258 J21S aquatic metagenome N/A 2021-01-14 OES065259 J22S aquatic metagenome N/A 2021-01-14 OES065260 J23S aquatic metagenome N/A 2021-01-14 OES065261 J3S aquatic metagenome N/A 2021-01-14 OES065262 J31S aquatic metagenome N/A 2021-01-14 OES065263 J32S aquatic metagenome N/A 2021-01-14 OES065264 J33S aquatic metagenome N/A 2021-01-14 OES065265 M1S aquatic metagenome N/A 2021-01-14 OES065266 M11S aquatic metagenome N/A 2021-01-14 OES065267 M12S aquatic metagenome N/A 2021-01-14 OES065268 M13S aquatic metagenome N/A 2021-01-14 OES065269 M2S aquatic metagenome N/A 2021-01-14 OES065270 M21S aquatic metagenome N/A 2021-01-14 OES065271 M22S aquatic metagenome N/A 2021-01-14 OES065272 M23S aquatic metagenome N/A 2021-01-14 OES065273 M3S aquatic metagenome N/A 2021-01-14 OES065274 M31S aquatic metagenome N/A 2021-01-14 OES065275 M32S aquatic metagenome N/A 2021-01-14 OES065276 M33S aquatic metagenome N/A 2021-01-14 OES065277 A1S aquatic metagenome N/A 2021-01-14 OES065278 A11S aquatic metagenome N/A 2021-01-14 OES065279 A12S aquatic metagenome N/A 2021-01-14 OES065280 A13S aquatic metagenome N/A 2021-01-14 OES065281 A2S aquatic metagenome N/A 2021-01-14 OES065282 A21S aquatic metagenome N/A 2021-01-14 OES065283 A22S aquatic metagenome N/A 2021-01-14 OES065284 A23S aquatic metagenome N/A 2021-01-14 OES065285 A3S aquatic metagenome N/A 2021-01-14 OES065286 A31S aquatic metagenome N/A 2021-01-14 OES065287 A32S aquatic metagenome N/A 2021-01-14 OES065288 A33S aquatic metagenome N/A 2021-01-14 - Runs
-
96
Run ID Run Name Sample Data Num Create Date OER099151 L1W_run L1W 2 2021-01-14 OER099152 L11W_run L11W 2 2021-01-14 OER099153 L12W_run L12W 2 2021-01-14 OER099154 L13W_run L13W 2 2021-01-14 OER099155 L2W_run L2W 2 2021-01-14 OER099156 L21W_run L21W 2 2021-01-14 OER099157 L22W_run L22W 2 2021-01-14 OER099158 L23W_run L23W 2 2021-01-14 OER099159 L3W_run L3W 2 2021-01-14 OER099160 L31W_run L31W 2 2021-01-14 OER099161 L32W_run L32W 2 2021-01-14 OER099162 L33W_run L33W 2 2021-01-14 OER099163 J1W_run J1W 2 2021-01-14 OER099164 J11W_run J11W 2 2021-01-14 OER099165 J12W_run J12W 2 2021-01-14 OER099166 J13W_run J13W 2 2021-01-14 OER099167 J2W J2W 2 2021-01-14 OER099168 J21W J21W 2 2021-01-14 OER099169 J22W J22W 2 2021-01-14 OER099170 J23W J23W 2 2021-01-14 OER099171 J3W J3W 2 2021-01-14 OER099172 J31W J31W 2 2021-01-14 OER099173 J32W J32W 2 2021-01-14 OER099174 J33W J33W 2 2021-01-14 OER099175 M1W M1W 2 2021-01-14 OER099176 M11W M11W 2 2021-01-14 OER099177 M12W M12W 2 2021-01-14 OER099178 M13W M13W 2 2021-01-14 OER099179 M2W M2W 2 2021-01-14 OER099180 M21W M21W 2 2021-01-14 OER099181 M22W M22W 2 2021-01-14 OER099182 M23W M23W 2 2021-01-14 OER099183 M3W M3W 2 2021-01-14 OER099184 M31W M31W 2 2021-01-14 OER099185 M32W M32W 2 2021-01-14 OER099186 M33W M33W 2 2021-01-14 OER099187 A1W A1W 2 2021-01-14 OER099188 A11W A11W 2 2021-01-14 OER099189 A12W A12W 2 2021-01-14 OER099190 A13W A13W 2 2021-01-14 OER099191 A2W A2W 2 2021-01-14 OER099192 A21W A21W 2 2021-01-14 OER099193 A22W A22W 2 2021-01-14 OER099194 A23W A23W 2 2021-01-14 OER099195 A3W A3W 2 2021-01-14 OER099196 A31W A31W 2 2021-01-14 OER099197 A32W A32W 2 2021-01-14 OER099198 A33W A33W 2 2021-01-14 OER099199 L1S L1S 2 2021-01-14 OER099200 L11S L11S 2 2021-01-14 OER099201 L12S L12S 2 2021-01-14 OER099202 L13S L13S 2 2021-01-14 OER099203 L2S L2S 2 2021-01-14 OER099204 L21S L21S 2 2021-01-14 OER099205 L22S L22S 2 2021-01-14 OER099206 L23S L23S 2 2021-01-14 OER099207 L3S L3S 2 2021-01-14 OER099208 L31S L31S 2 2021-01-14 OER099209 L32S L32S 2 2021-01-14 OER099210 L33S L33S 2 2021-01-14 OER099211 J1S J1S 2 2021-01-14 OER099212 J11S J11S 2 2021-01-14 OER099213 J12S J12S 2 2021-01-14 OER099214 J13S J13S 2 2021-01-14 OER099215 J2S J2S 2 2021-01-14 OER099216 J21S J21S 2 2021-01-14 OER099217 J22S J22S 2 2021-01-14 OER099218 J23S J23S 2 2021-01-14 OER099219 J3S J3S 2 2021-01-14 OER099220 J31S J31S 2 2021-01-14 OER099221 J32S J32S 2 2021-01-14 OER099222 J33S J33S 2 2021-01-14 OER099223 M1S M1S 2 2021-01-14 OER099224 M11S M11S 2 2021-01-14 OER099225 M12S M12S 2 2021-01-14 OER099226 M13S M13S 2 2021-01-14 OER099227 M2S M2S 2 2021-01-14 OER099228 M21S M21S 2 2021-01-14 OER099229 M22S M22S 2 2021-01-14 OER099230 M23S M23S 2 2021-01-14 OER099231 M3S M3S 2 2021-01-14 OER099232 M31S M31S 2 2021-01-14 OER099233 M32S M32S 2 2021-01-14 OER099234 M33S M33S 2 2021-01-14 OER099235 A1S A1S 2 2021-01-14 OER099236 A11S A11S 2 2021-01-14 OER099237 A12S A12S 2 2021-01-14 OER099238 A13S A13S 2 2021-01-14 OER099239 A2S A2S 2 2021-01-14 OER099240 A21S A21S 2 2021-01-14 OER099241 A22S A22S 2 2021-01-14 OER099242 A23S A23S 2 2021-01-14 OER099243 A3S A3S 2 2021-01-14 OER099244 A31S A31S 2 2021-01-14 OER099245 A32S A32S 2 2021-01-14 OER099246 A33S A33S 2 2021-01-14
Author Information
- Create Date
- 2021-01-09
- Last Modified
- 2021-03-01
- Submission
- xiafei zheng
- Sun Yat-sen university