The Culturing Crisis: Why Aquatic Microbiology Needs More than Sequences

Abstract Microbial communities are essential components of aquatic ecosystems, yet a stark contrast persists between the vast diversity revealed by environmental sequencing and the limited taxa recoverable by culturing. This disparity has contributed to a shift toward sequencing due to its cost‐effectiveness and broad applicability to ecological questions. Despite this, culturing remains essential for understanding microbial physiology and function. Here, we compare published culturing efforts between freshwater and marine ecosystems, focusing on select phytoplankton representatives, and present a case study of a successful culture collection. We highlight the critical need to sequence the genome of isolates to build reference repositories for aquatic science. We conclude with a call to action for expanded, standardized culture collections that bridge the gap between sequencing discovery and functional understanding.

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Publication Details

Journal
Limnology and Oceanography Bulletin
Published
2026-11-05
DOI
https://doi.org/10.1002/lob.70074
Primary Topic
Microbial Community Ecology and Physiology
Type
article
Field-Weighted Citation Impact
0.00
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article

The Culturing Crisis: Why Aquatic Microbiology Needs More than Sequences

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Limnology and Oceanography Bulletin
Microbial Community Ecology and Physiology
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The Culturing Crisis: Why Aquatic Microbiology Needs More than Sequences

Anika Happe, Arianna I. Krinos, Emily N. Hallett, Ewaldo Leitão, Brittany N. Zepernick, Heather L. Wander, Andrian Gajigan
article en

Abstract

Abstract Microbial communities are essential components of aquatic ecosystems, yet a stark contrast persists between the vast diversity revealed by environmental sequencing and the limited taxa recoverable by culturing. This disparity has contributed to a shift toward sequencing due to its cost‐effectiveness and broad applicability to ecological questions. Despite this, culturing remains essential for understanding microbial physiology and function. Here, we compare published culturing efforts between freshwater and marine ecosystems, focusing on select phytoplankton representatives, and present a case study of a successful culture collection. We highlight the critical need to sequence the genome of isolates to build reference repositories for aquatic science. We conclude with a call to action for expanded, standardized culture collections that bridge the gap between sequencing discovery and functional understanding.

Limnology and Oceanography Bulletin
University of Hawaiʻi at Mānoa (US), Carl von Ossietzky Universität Oldenburg (DE), University of North Carolina Wilmington (US), Université du Québec à Montréal (CA), Duke University (US), Cornell University (US), Brown University (US), University of the Philippines Diliman (PH)
Openalex Percentile: Top 18%
Microbial Community Ecology and Physiology
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