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

Dataset: Kontamineringsrisker vid sediment-baserat återupplivande av växtplankton

The data contains sediment core measurements from two locations in the Baltic Sea. The aim of the study was to determine if the age of phytoplankton resting stages could be determined based on their vertical position or if contamination from surface population was a major confounding factor. To this end, the concentration of seven abundant species of diatoms and cyanobacteria were enumerated using the Most Probable Number (MPN) approach. Sediment sections were dated using standard radiometric methods, and surface sediment contamination was quantified using 4.5 μm microsphere tracers. Furthermore, ex-situ longevity was monitored over four years and decreased substantially withing this timeframe. In the cores, microspheres (>2×10^-6 fractions) were translocated from the sediment surface and could well explain the vertical distributions and abundances of viable cells (between ~106 to <0.8 g sediment^-1). Our conclusion was therefore that there are substantial contamination risks, and that age determination of resting stages using only radiometric age determination of bulk sediment is flawed without additional contamination controls. The study design consisted of two field expeditions (2017 and 2020) where six to ten, 50 cm cores were collected. Cores were inspected for signs of damage and preservation of laminated patterns, and the best cores were selected for further analysis. Selected cores were section onboard for bulk radiometric dating (210Pb and 137Cs) and Total Organic Carbon (TOC) and Nitrogen (TN) profiles. MPN enumeration of diatom and cyanobacterial resting stages was performed on cores transported intact to Gothenburg, which were processed within two to six months (reported as initial concentration). Survival ex-situ was monitored from 2017 to 2021 in surface samples stored under dark, cold (4C), and anoxic conditions, in 20-40 mL of sediment in 50 mL non-transparent Falcon tubes. To assess the validity of the radiometric age determination of diatoms from 2017, we quantified contamination during the 2020 sampling. Non-toxic, yellow-green fluorescing polystyrene microspheres (Thermo Scientific™ Fluoro-Max) were used to track surface sediment contamination in three VG20 cores. Microspheres were injected into the water headspace of three replicate cores (in Gothenburg) and allowed to settle onto the surface before sectioning. The translocation of microsphere from the sediment surface could then be traced in tandem with enumeration of resting stages. See file Metadata_Andersson2022.docx for a detailed description of files and data.Datasetet innehåller geologiska och biologiska observationer från två svenska Östersjö-fjärdar. Det innehåller isotopiska dateringsdata och andra standardiserade geologiska parametrar, samt kvantifiering av vertikaldistributionen av vilostadier av växtplankton, främst kiselalger och cyanobakterier. Utöver detta kvantifierades kontaminering mellan sedimentdjupen med hjälp av fluorescerande 4,5 μm mikroplastkulor. Läs filen Metadata_Andersson2022.docx för detaljerad information om filer och datainsamling

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