Growth of a common planktonic diatom quantified using solid medium culturing

The ability to grow on solid culture medium is a pre-requisite for a successful microbial genetic model organism. Skeletonema marinoi, a bloom-forming, planktonic marine microalga, is widely used in ecological, evolutionary and population genetics studies. We have tested and confirmed the ability of this common organism to grow on solid culture medium (agar) under experimentally manipulated conditions. We established a protocol for quantifying growth characteristics - length of lag phase, growth rate, maximum biomass yield - on agar medium. The procedure was tested under experimental treatments and the resulting growth changes correlated with those observed in standard liquid culture. The ability to grow on solid medium broadens the use of S. marinoi as a molecular model, where agar is routinely used for various purposes (growth, selection, storage); and the possibility to quantify colony growth opens the way for high throughput, automated, or semi-automated phenotyping solutions

PRECOG: a tool for automated extraction and visualization of fitness components in microbial growth phenomics.

BACKGROUND: Phenomics is a field in functional genomics that records variation in organismal phenotypes in the genetic, epigenetic or environmental context at a massive scale. For microbes, the key phenotype is the growth in population size because it contains information that is directly linked to fitness. Due to technical innovations and extensive automation our capacity to record complex and dynamic microbial growth data is rapidly outpacing our capacity to dissect and visualize this data and extract the fitness components it contains, hampering progress in all fields of microbiology. RESULTS: To automate visualization, analysis and exploration of complex and highly resolved microbial growth data as well as standardized extraction of the fitness components it contains, we developed the software PRECOG (PREsentation and Characterization Of Growth-data). PRECOG allows the user to quality control, interact with and evaluate microbial growth data with ease, speed and accuracy, also in cases of non-standard growth dynamics. Quality indices filter high- from low-quality growth experiments, reducing false positives. The pre-processing filters in PRECOG are computationally inexpensive and yet functionally comparable to more complex neural network procedures. We provide examples where data calibration, project design and feature extraction methodologies have a clear impact on the estimated growth traits, emphasising the need for proper standardization in data analysis. CONCLUSIONS: PRECOG is a tool that streamlines growth data pre-processing, phenotypic trait extraction, visualization, distribution and the creation of vast and informative phenomics databases

Cross‐contamination risks in sediment‐based resurrection studies of phytoplankton

Abstract Resurrection studies can answer some fundamental questions in aquatic ecology and evolutionary biology. For phytoplankton resting stages, longevity of thousands to millions of years has recently been reported. However, contamination during sediment sampling could distort these estimates, and this risk has not been systematically evaluated. Here we used 4.5 μm diameter microspheres to quantify contamination while reviving the resting stages of seven abundant estuarine diatom and cyanobacterial taxa. We observed a sharp decline in resting stages abundance from 106 (g wet sediment)−1 at the surface to < 0.8 (g wet sediment)−1 at 12.5 cm depth. Added microspheres (~ 4.5 × 107 cm−2) were translocated even deeper down the sediment and could well explain the vertical distributions and abundances of revived cells. Without this control, we could have claimed to have revived seven multi‐decades to centennial‐old taxa. Our findings suggest that improved contamination controls are needed for sediment core sampling of rare cells, microfossils, or DNA molecules

Cross-contamination risks in sediment-based resurrection studies of phytoplankton

Resurrection studies can answer some fundamental questions in aquatic ecology and evolutionary biology. For phytoplankton resting stages, longevity of thousands to millions of years has recently been reported. However, contamination during sediment sampling could distort these estimates, and this risk has not been systematically evaluated. Here we used 4.5 μm diameter microspheres to quantify contamination while reviving the resting stages of seven abundant estuarine diatom and cyanobacterial taxa. We observed a sharp decline in resting stages abundance from 106 (g wet sediment)−1 at the surface to < 0.8 (g wet sediment)−1 at 12.5 cm depth. Added microspheres (~ 4.5 × 107 cm−2) were translocated even deeper down the sediment and could well explain the vertical distributions and abundances of revived cells. Without this control, we could have claimed to have revived seven multi-decades to centennial-old taxa. Our findings suggest that improved contamination controls are needed for sediment core sampling of rare cells, microfossils, or DNA molecules

High single-cell diversity in carbon and nitrogen assimilations by a chain-forming diatom across a century

Summary Almost a century ago Redfield discovered a relatively constant ratio between carbon, nitrogen and phosphorus in particulate organic matter and nitrogen and phosphorus of dissolved nutrients in seawater. Since then, the riverine export of nitrogen to the ocean has increased 20 fold. High abundance of resting stages in sediment layers dated more than a century back indicate that the common planktonic diatom Skeletonema marinoi has endured this eutrophication. We germinated unique genotypes from resting stages originating from isotope-dated sediment layers (15 and 80 years old) in a eutrophied fjord. Using secondary ion mass spectrometry (SIMS) combined with stable isotopic tracers, we show that the cell-specific carbon and nitrogen assimilation rates vary by an order of magnitude on a single-cell level but are significantly correlated during the exponential growth phase, resulting in constant assimilation quota in cells with identical genotypes. The assimilation quota varies largely between different clones independent of age. We hypothesize that the success of S. marinoi in coastal waters may be explained by its high diversity of nutrient demand not only at a clone-specific level but also at the single-cell level, whereby the population can sustain and adapt to dynamic nutrient conditions in the environment

Concerted Evolution of Life Stage Performances Signals Recent Selection on Yeast Nitrogen Use

acceptedVersio

Additional file 1: Table S1. of PRECOG: a tool for automated extraction and visualization of fitness components in microbial growth phenomics

Feature comparison of the different PRECOG platforms. (DOCX 17 kb