DNA Enrichment Methods for Microbial Symbionts in Marine Bivalves
High-throughput sequencing is a powerful tool used for bivalve symbiosis research, but the largest barrier is the contamination of host DNA. In this work, we assessed the host DNA reduction efficiency, microbial community structure, and microbial diversity of four different sample pre-treatment and...
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MDPI AG
2022-02-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/10/2/393 |
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| author | Qiqi Li Yu Chen Si Zhang Yuanjiao Lyu Yiyang Zou Jie Li |
| author_facet | Qiqi Li Yu Chen Si Zhang Yuanjiao Lyu Yiyang Zou Jie Li |
| author_sort | Qiqi Li |
| collection | DOAJ |
| description | High-throughput sequencing is a powerful tool used for bivalve symbiosis research, but the largest barrier is the contamination of host DNA. In this work, we assessed the host DNA reduction efficiency, microbial community structure, and microbial diversity of four different sample pre-treatment and DNA extraction methods employed in bivalve gill tissue samples. Metagenomic sequencing showed the average proportions of reads belonging to microorganisms retrieved using PowerSoil DNA extraction kit, pre-treatment with differential centrifugation, pre-treatment with filtration, and HostZERO Microbial DNA kit samples were 2.3 ± 0.6%, 2.5 ± 0.2%, 4.7 ± 1.6%, and 42.6 ± 6.8%, respectively. The microbial DNA was effectively enriched with HostZERO Microbial DNA kit. The microbial communities revealed by amplicon sequencing of the 16S rRNA gene showed the taxonomic biases by using four different pre-treatment and DNA extraction methods. The species diversities of DNA samples extracted with the PowerSoil DNA extraction kit were similar, while lower than DNA samples extracted with HostZERO Microbial DNA kit. The results of this study emphasized the bias of these common methods in bivalve symbionts research and will be helpful to choose a fit-for-purpose microbial enrichment strategy in future research on bivalves or other microbe–invertebrate symbioses. |
| first_indexed | 2024-03-09T21:24:08Z |
| format | Article |
| id | doaj.art-dbfbac58a30b42d6b7d7f77fc8ecf8d4 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-09T21:24:08Z |
| publishDate | 2022-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-dbfbac58a30b42d6b7d7f77fc8ecf8d42023-11-23T21:15:27ZengMDPI AGMicroorganisms2076-26072022-02-0110239310.3390/microorganisms10020393DNA Enrichment Methods for Microbial Symbionts in Marine BivalvesQiqi Li0Yu Chen1Si Zhang2Yuanjiao Lyu3Yiyang Zou4Jie Li5CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, ChinaSouthern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, ChinaCAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, ChinaCAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, ChinaCAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, ChinaCAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, ChinaHigh-throughput sequencing is a powerful tool used for bivalve symbiosis research, but the largest barrier is the contamination of host DNA. In this work, we assessed the host DNA reduction efficiency, microbial community structure, and microbial diversity of four different sample pre-treatment and DNA extraction methods employed in bivalve gill tissue samples. Metagenomic sequencing showed the average proportions of reads belonging to microorganisms retrieved using PowerSoil DNA extraction kit, pre-treatment with differential centrifugation, pre-treatment with filtration, and HostZERO Microbial DNA kit samples were 2.3 ± 0.6%, 2.5 ± 0.2%, 4.7 ± 1.6%, and 42.6 ± 6.8%, respectively. The microbial DNA was effectively enriched with HostZERO Microbial DNA kit. The microbial communities revealed by amplicon sequencing of the 16S rRNA gene showed the taxonomic biases by using four different pre-treatment and DNA extraction methods. The species diversities of DNA samples extracted with the PowerSoil DNA extraction kit were similar, while lower than DNA samples extracted with HostZERO Microbial DNA kit. The results of this study emphasized the bias of these common methods in bivalve symbionts research and will be helpful to choose a fit-for-purpose microbial enrichment strategy in future research on bivalves or other microbe–invertebrate symbioses.https://www.mdpi.com/2076-2607/10/2/393bivalvesmicrobial DNA enrichmentmicrobial abundancemicrobial composition |
| spellingShingle | Qiqi Li Yu Chen Si Zhang Yuanjiao Lyu Yiyang Zou Jie Li DNA Enrichment Methods for Microbial Symbionts in Marine Bivalves Microorganisms bivalves microbial DNA enrichment microbial abundance microbial composition |
| title | DNA Enrichment Methods for Microbial Symbionts in Marine Bivalves |
| title_full | DNA Enrichment Methods for Microbial Symbionts in Marine Bivalves |
| title_fullStr | DNA Enrichment Methods for Microbial Symbionts in Marine Bivalves |
| title_full_unstemmed | DNA Enrichment Methods for Microbial Symbionts in Marine Bivalves |
| title_short | DNA Enrichment Methods for Microbial Symbionts in Marine Bivalves |
| title_sort | dna enrichment methods for microbial symbionts in marine bivalves |
| topic | bivalves microbial DNA enrichment microbial abundance microbial composition |
| url | https://www.mdpi.com/2076-2607/10/2/393 |
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