sparse-growth-curve: a Computational Pipeline for Parsing Cellular Growth Curves with Low Temporal Resolution

Cheng, Chuankai; Thrash, J. Cameron

doi:10.1128/mra.00296-21

Cited by 11 publications

(10 citation statements)

References 12 publications

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“…Cell concentrations were enumerated using a Guava EasyCyte 5HT flow cytometer (Millipore, Massachusetts, USA) with previously reported settings [19,31]. Growth rates were calculated using sparse-growth-curve [58].…”

Section: Growth Experimentsmentioning

confidence: 99%

Ecophysiology and genomics of the brackish water adapted SAR11 subclade IIIa

et al. 2023

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The Order Pelagibacterales (SAR11) is the most abundant group of heterotrophic bacterioplankton in global oceans and comprises multiple subclades with unique spatiotemporal distributions. Subclade IIIa is the primary SAR11 group in brackish waters and shares a common ancestor with the dominant freshwater IIIb (LD12) subclade. Despite its dominance in brackish environments, subclade IIIa lacks systematic genomic or ecological studies. Here, we combine closed genomes from new IIIa isolates, new IIIa MAGS from San Francisco Bay (SFB), and 460 highly complete publicly available SAR11 genomes for the most comprehensive pangenomic study of subclade IIIa to date. Subclade IIIa represents a taxonomic family containing three genera (denoted as subgroups IIIa.1, IIIa.2, and IIIa.3) that had distinct ecological distributions related to salinity. The expansion of taxon selection within subclade IIIa also established previously noted metabolic differentiation in subclade IIIa compared to other SAR11 subclades such as glycine/serine prototrophy, mosaic glyoxylate shunt presence, and polyhydroxyalkanoate synthesis potential. Our analysis further shows metabolic flexibility among subgroups within IIIa. Additionally, we find that subclade IIIa.3 bridges the marine and freshwater clades based on its potential for compatible solute transport, iron utilization, and bicarbonate management potential. Pure culture experimentation validated differential salinity ranges in IIIa.1 and IIIa.3 and provided detailed IIIa cell size and volume data. This study is an important step forward for understanding the genomic, ecological, and physiological differentiation of subclade IIIa and the overall evolutionary history of SAR11.

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Section: Growth Experimentsmentioning

confidence: 99%

Ecophysiology and genomics of the brackish water adapted SAR11 subclade IIIa

et al. 2023

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“…Strain purity and identity were verified at the end of experiments using PCR of the 16S rRNA gene as previously reported ( 10 ). Growth rates for all experiments were calculated with the sparse-growth-curve script ( https://github.com/thrash-lab/sparse-growth-curve ) ( 113 ).…”

Section: Methodsmentioning

confidence: 99%

Ecophysiology of the Cosmopolitan OM252 Bacterioplankton ( Gammaproteobacteria )

et al. 2021

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“…GTDB-tk placed the LSUCC0859 genome within the Flavobacteriaceae , with the nearest neighbor being the metagenome-assembled genome (MAG) “MAG-120531 sp000173115” (average nucleotide identity, 78.71%). The organism had a mean growth rate of 2.4 doublings day −1 (calculated as described in reference 12 ) at room temperature in MWH3 medium ( Fig. 1 ).…”

Section: Announcementmentioning

confidence: 99%

“… Growth curves (left) and calculated growth rates (right) for LSUCC0859 growing at room temperature on MWH3 medium. Output is from sparse-growth-curve ( 12 ). …”

Section: Announcementmentioning

confidence: 99%