Comparison of the diversity of cultured and total bacterial communities in marine sediment using culture-dependent and sequencing methods
Despite recent great advances in microbial culture, most microbes have not yet been cultured, and the impact of medium composition on the isolation of microbes from natural systems has not been elucidated. To optimize media for culturing marine microbes, microbial communities in three sediment sampl...
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2020-10-01
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| Online Access: | https://peerj.com/articles/10060.pdf |
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doaj-122bb563d5b746faada200edbf8b3c792020-11-25T04:02:02ZengPeerJ Inc.PeerJ2167-83592020-10-018e1006010.7717/peerj.10060Comparison of the diversity of cultured and total bacterial communities in marine sediment using culture-dependent and sequencing methodsMeng Wang0Samina Noor1Ran Huan2Congling Liu3JiaYi Li4Qingxin Shi5Yan-Jiao Zhang6Cuiling Wu7Hailun He8School of Life Science, Central South University, Changsha, ChinaSchool of Life Science, Central South University, Changsha, ChinaSchool of Life Science, Central South University, Changsha, ChinaSchool of Life Science, Central South University, Changsha, ChinaSchool of Life Science, Central South University, Changsha, ChinaSchool of Life Science, Central South University, Changsha, ChinaQingdao Agricultural University, Qingdao, ChinaChangzhi Medical College, Changzhi, ChinaSchool of Life Science, Central South University, Changsha, ChinaDespite recent great advances in microbial culture, most microbes have not yet been cultured, and the impact of medium composition on the isolation of microbes from natural systems has not been elucidated. To optimize media for culturing marine microbes, microbial communities in three sediment samples were described using high-throughput sequencing (HTS) and culture-dependent techniques. HTS revealed communities dominated by Gammaproteobacteria, and culture-based methods revealed communities dominated by Actinobacteria. Among the total operational taxonomic units (OTUs) from the HTS dataset, 6% were recovered in the culture collection. Four potentially novel bacterial strains belonging to Oceaniovalibus, Psychrobacter and Salegentibacter were isolated. The combination of media cultured more taxa than any single medium. Nutrient-rich and single-carbon/nitrogen-source media supported the growth of relatively few taxa, and the quality of nitrogen strongly influenced the types of bacteria isolated.https://peerj.com/articles/10060.pdfMarine sedimentCulturable microbial diversityMicrobial diversityMedia componentsPhysiochemical parameters |
| collection |
DOAJ |
| language |
English |
| format |
Article |
| sources |
DOAJ |
| author |
Meng Wang Samina Noor Ran Huan Congling Liu JiaYi Li Qingxin Shi Yan-Jiao Zhang Cuiling Wu Hailun He |
| spellingShingle |
Meng Wang Samina Noor Ran Huan Congling Liu JiaYi Li Qingxin Shi Yan-Jiao Zhang Cuiling Wu Hailun He Comparison of the diversity of cultured and total bacterial communities in marine sediment using culture-dependent and sequencing methods PeerJ Marine sediment Culturable microbial diversity Microbial diversity Media components Physiochemical parameters |
| author_facet |
Meng Wang Samina Noor Ran Huan Congling Liu JiaYi Li Qingxin Shi Yan-Jiao Zhang Cuiling Wu Hailun He |
| author_sort |
Meng Wang |
| title |
Comparison of the diversity of cultured and total bacterial communities in marine sediment using culture-dependent and sequencing methods |
| title_short |
Comparison of the diversity of cultured and total bacterial communities in marine sediment using culture-dependent and sequencing methods |
| title_full |
Comparison of the diversity of cultured and total bacterial communities in marine sediment using culture-dependent and sequencing methods |
| title_fullStr |
Comparison of the diversity of cultured and total bacterial communities in marine sediment using culture-dependent and sequencing methods |
| title_full_unstemmed |
Comparison of the diversity of cultured and total bacterial communities in marine sediment using culture-dependent and sequencing methods |
| title_sort |
comparison of the diversity of cultured and total bacterial communities in marine sediment using culture-dependent and sequencing methods |
| publisher |
PeerJ Inc. |
| series |
PeerJ |
| issn |
2167-8359 |
| publishDate |
2020-10-01 |
| description |
Despite recent great advances in microbial culture, most microbes have not yet been cultured, and the impact of medium composition on the isolation of microbes from natural systems has not been elucidated. To optimize media for culturing marine microbes, microbial communities in three sediment samples were described using high-throughput sequencing (HTS) and culture-dependent techniques. HTS revealed communities dominated by Gammaproteobacteria, and culture-based methods revealed communities dominated by Actinobacteria. Among the total operational taxonomic units (OTUs) from the HTS dataset, 6% were recovered in the culture collection. Four potentially novel bacterial strains belonging to Oceaniovalibus, Psychrobacter and Salegentibacter were isolated. The combination of media cultured more taxa than any single medium. Nutrient-rich and single-carbon/nitrogen-source media supported the growth of relatively few taxa, and the quality of nitrogen strongly influenced the types of bacteria isolated. |
| topic |
Marine sediment Culturable microbial diversity Microbial diversity Media components Physiochemical parameters |
| url |
https://peerj.com/articles/10060.pdf |
| work_keys_str_mv |
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