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Isolates as models to study bacterial ecophysiology and biogeochemistry
Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
Univ Calif San Diego, USA.
Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.ORCID iD: 0000-0001-7815-1077
University of Gothenburg.
2018 (English)In: Aquatic Microbial Ecology, ISSN 0948-3055, E-ISSN 1616-1564, Vol. 80, no 1, p. 15-27Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2018. Vol. 80, no 1, p. 15-27
Keywords [en]
Bacteria, Culture, Physiology
National Category
Microbiology Ecology
Research subject
Ecology, Microbiology
Identifiers
URN: urn:nbn:se:lnu:diva-69666DOI: 10.3354/ame01838ISI: 000414556400002OAI: oai:DiVA.org:lnu-69666DiVA, id: diva2:1172612
Available from: 2018-01-10 Created: 2018-01-10 Last updated: 2018-01-10Bibliographically approved

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Hagström, ÅkeBerg, Carlo

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