Isolates as models to study bacterial ecophysiology and biogeochemistry

TitleIsolates as models to study bacterial ecophysiology and biogeochemistry
Publication TypeJournal Article
Year of Publication2018
AuthorsHagstrom A., Azam F, Berg C., Zweifel U.L
JournalAquatic Microbial Ecology
Volume80
Pagination15-27
Date Published2018/01
Type of ArticleArticle
ISBN Number0948-3055
Accession NumberWOS:000414556400002
Keywordsbacteria; bacterioplankton communities; culture; dissolved organic-matter; growth-characteristics; large fraction; marine-bacteria; microbial; microscale nutrient patches; oligotrophic bacteria; pan-genome; physiology; ribosomal-rna; seawater cultures
Abstract

Here, we examine the use of bacterial isolates growing in artificial media or seawater as a means to investigate bacterial activity in the upper ocean. The discovery of a major role of bacteria in the ocean's carbon cycle owes greatly to the development of culture-independent assemblage-level approaches; however, this should not detract from the recognition of model isolates as representing the environmental microbiome. A long-established tool for culturing bacteria, in medicine and general microbiology, has been agar plates. In addition, a great variety of liquid substrates including seawater have been used to successfully identify and cultivate important bacteria such as Pelagibacter ubique. Yet, the discrepancy between microscopic counts and plate counts, the great plate count anomaly, has led to a biased perception of the limited relevance of isolated bacteria. Linking isolates to whole-genome sequencing, phylogenetic analysis and computational modeling will result in culturable model bacteria from different habitats. Our main message is that bacterial ecophysiology, particularly growth rates in seawater, and functionalities inferred through the identity, abundance and expression of specific genes could be mechanistically linked if more work is done to isolate, culture and study bacteria in pure cultures. When we rally behind a strategy aimed at culturing targeted phenotypes, we are not saying that culture independent studies of bacteria in the sea are not informative. We are suggesting that culturebased studies can help integrate the ecological and genomic views.

DOI10.3354/ame01838
Short TitleAquat. Microb. Ecol.
Student Publication: 
No
sharknado