Unraveling the unseen players in the ocean: A field guide to water chemistry and marine microbiology

TitleUnraveling the unseen players in the ocean: A field guide to water chemistry and marine microbiology
Publication TypeJournal Article
Year of Publication2014
AuthorsHaas AF, Knowles B., Lim Y.W, Somera T.M, Kelly LW, Hatay M., Rohwer F
JournalJove-Journal of Visualized Experiments
Date Published2014/11
Type of ArticleArticle
ISBN Number1940-087X
Accession NumberWOS:000349311400063
Keywordsbacterioplankton; coral; DAPI; deep; dissolved organic carbon; dissolved organic-carbon; doc; Environmental Sciences; Issue 93; marine environment; metagenomics; microbial metagenomics; nitrogen; nutrient limitation; nutrients; Organic matter; particulate; sea; SYBR; viral; virioplankton; viruses
Abstract

Here we introduce a series of thoroughly tested and well standardized research protocols adapted for use in remote marine environments. The sampling protocols include the assessment of resources available to the microbial community (dissolved organic carbon, particulate organic matter, inorganic nutrients), and a comprehensive description of the viral and bacterial communities (via direct viral and microbial counts, enumeration of autofluorescent microbes, and construction of viral and microbial metagenomes). We use a combination of methods, which represent a dispersed field of scientific disciplines comprising already established protocols and some of the most recent techniques developed. Especially metagenomic sequencing techniques used for viral and bacterial community characterization, have been established only in recent years, and are thus still subjected to constant improvement. This has led to a variety of sampling and sample processing procedures currently in use. The set of methods presented here provides an up to date approach to collect and process environmental samples. Parameters addressed with these protocols yield the minimum on information essential to characterize and understand the underlying mechanisms of viral and microbial community dynamics. It gives easy to follow guidelines to conduct comprehensive surveys and discusses critical steps and potential caveats pertinent to each technique.

DOI10.3791/52131
Student Publication: 
No
Research Topics: 
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