Comparison of the diversity of cultured and total bacterial communities in marine sediment using culture-dependent and sequencing methods

• Published in: PeerJ (San Francisco, CA) Vol. 8; p. e10060
• Main Authors: Wang, Meng, Noor, Samina, Huan, Ran, Liu, Congling, Li, JiaYi, Shi, Qingxin, Zhang, Yan-Jiao, Wu, Cuiling, He, Hailun
• Format: Journal Article
• Language: English
• Published: San Diego PeerJ. Ltd 21.10.2020; PeerJ, Inc; PeerJ Inc
• Subjects: Analysis; Bacteria; Biotechnology; Carbon; Cluster analysis; Culturable microbial diversity; Deoxyribonucleic acid; Discriminant analysis; DNA; Marine Biology; Marine sediment; Media components; Methods; Microbial diversity; Microbiology; Molecular Biology; Multiculturalism; Next-generation sequencing; Nitrogen; Physiochemical parameters; Seawater; Sediments; Sediments (Geology); South China Sea; China; Japan
• ISSN: 2167-8359; 2167-8359
• DOI: 10.7717/peerj.10060

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.