title: Unraveling the unseen players in the ocean - a field guide to water chemistry and marine microbiology.
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.
authors.affiliation: Department of Biology, San Diego State University; Andreas.florian.haas@gmail.com.
authors.forename: Andreas Florian
authors.initials: AF
authors.lastname: Haas
authors.affiliation: Department of Biology, San Diego State University.
authors.forename: Ben
authors.initials: B
authors.lastname: Knowles
authors.affiliation: Department of Biology, San Diego State University; ywlim.s@gmail.com.
authors.forename: Yan Wei
authors.initials: YW
authors.lastname: Lim
authors.affiliation: Scripps Institution of Oceanography, University of California San Diego.
authors.forename: Tracey
authors.initials: T
authors.lastname: McDole Somera
authors.affiliation: Department of Biology, San Diego State University.
authors.forename: Linda Wegley
authors.initials: LW
authors.lastname: Kelly
authors.affiliation: Department of Biology, San Diego State University.
authors.forename: Mark
authors.initials: M
authors.lastname: Hatay
authors.affiliation: Department of Biology, San Diego State University.
authors.forename: Forest
authors.initials: F
authors.lastname: Rohwer
mesh_terms: D001419:Bacteria / Q000235:genetics; D017753:Ecosystem; D054892:Metagenome; D056186:Metagenomics / Q000379:methods*; D009792:Oceans and Seas; D012623:Seawater / Q000737:chemistry* / Q000382:microbiology*; D014780:Viruses / Q000235:genetics; D014871:Water Microbiology