Isolates as models to study bacterial ecophysiology and biogeochemistry

Abstract

AME Aquatic Microbial Ecology Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials AME 80:15-27 (2017) - DOI: https://doi.org/10.3354/ame01838 AME Special 6: 'SAME 14: progress and perspectives in aquatic microbial ecology' AS WE SEE IT Isolates as models to study bacterial ecophysiology and biogeochemistry Åke Hagström1,*, Farooq Azam2, Carlo Berg1, Ulla Li Zweifel3 1Department of Biology and Environmental Science, Linnaeus University, 391 82 Kalmar, Sweden 2Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093-0202, USA 3Swedish Institute for the Marine Environment, Gothenburg University, Box 260, 405 30 Göteborg, Sweden *Corresponding author: ake.hagstrom@lnu.se 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 culture-based studies can help integrate the ecological and genomic views. KEY WORDS: Bacteria · Culture · Physiology Full text in pdf format Supplementary material PreviousNextCite this article as: Hagström Å, Azam F, Berg C, Zweifel UL (2017) Isolates as models to study bacterial ecophysiology and biogeochemistry. Aquat Microb Ecol 80:15-27. https://doi.org/10.3354/ame01838 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in AME Vol. 80, No. 1. Online publication date: August 11, 2017 Print ISSN: 0948-3055; Online ISSN: 1616-1564 Copyright © 2017 Inter-Research.