Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
  • BCO-DMO Processing Description
• Data Files
• Supplemental Files
• Related Publications
• Parameters
• Instruments
• Project Information
• Funding

This data set summarises the chemotactic response of the model heterotrophic bacteria Psuedoalteromonas haloplanktis towards phage-infected cyanobacteria Synechococcus cells/exudates respectively. Phage treatments are fully described in: https://doi.org/10.1038/s43705-022-00169-6.

Experimental Culture Details:

Pseudoalteromonas haloplanktis (ATCC 700530) from −80°C stock were grown in 2216 media for 24 hours at room temperature without agitation. The overnight culture was then centrifuged (1500 RCF for 5 min), and 4 ml of culture was washed twice and resuspended in 0.5 ml of ASW.

Artificial seawater (ASW) was prepared following the NCMA ESAW Medium recipe, which was adapted from Harrison et al.and modified by Berges, and filtered through a 0.2um filter immediately prior to use.

Axenic Synechococcus WH8102 (CCMP 490 2370) were grown in SN media, prepared with ASW, in sterile 40 ml polystyrene culture flasks at 22°C on a 14 h : 10 h light-dark cycle at 50 µmol photons m−2 s −1 . Culture growth was tracked using a SpectraMax ID3 plate reader (Molecular Devices) and cell counts were measured using a CytoFLEX flow cytometer (Beckman Coulter).

Microfluidic Device Details: 

A simple three-inlet gradient generation microfluidic device was used to produce the chemical gradients.  Microfluidic devices were made using standard soft lithography techniques. Polydimethylsiloxane (Dow Corning SYLGARD 184) channels were cast on photoresist (Microchem) moulds fabricated via photolithography and plasma bonded to standard glass slides. Gradient generation channels were designed with three inlets (width 0.5mm) carrying the chemostimulus solution, cell suspension and ASW media, respectively. Prior to use, the chambers were pretreated with a 0.5% BSA solution to mitigate cell adhesion. The three solutions were flow stratified for a minimum of 2min using a syringe pump (Harvard Apparatus), whereby flow rates were adjusted to maintain a 4:1:4 ratio of the stream widths. Upon halting the flow, a monotonic chemotaxis profile was established through diffusion. A chemostimulus gradient develops in the channel via diffusion, and the chemotactic response of the cell population was observed over time. Imaging was performed with phase-contrast microscopy (4×; Zeiss AxioObserver) at 1 fps over the course of ~10 min using a CMOS camera (Grasshopper S, Teledyne FLIR). An example of the gradient generator used can be found in:  https://doi.org/10.7554/eLife.85348

Experiment Details:

Six microfluidic experiments were conducted each on different days: three with phage infection and three control, uninfected experiments. Both uninfected and phage-infected experiments were performed identically, with the substitution of phage addition for an equivalent volume of SN media in the uninfected experiments. All infection experiments were performed within a week using the same phage stock, with the infectious phage titer of the stock determined to be 1.4x10^8 pfu/ml via plaque assay method with Synechococcus WH8102 as the host. One day prior to experiments, exponential phase Synechococcus cultures were diluted with fresh SN media to a cell concentration of 7-9x10^5 cells/ml. 

This data set summarises the chemotactic response of a model marine bacteria (Pseudoalteromonas haloplanktis  ATCC 700530) to filtered exudates of the cyanobacteria Synechococcus sp WH8102. Two filtrate sets were collected, each spanning 6 time points (named T1 -> T6), with the initial assays split into 4 biological replicates (named A, B, C, and D). The two treatments were:

1) A control treatment (named "Control", or shortened to "C")

2) A phage-infected treatment (named "Phage", or shortened to "P"), where host Synechococcus were infected with the T-4 like Myovirus S-SSM5, with data collected over the pre-lysis cycle.

These treatments are fully described in: https://doi.org/10.1038/s43705-022-00169-6. The filtrates were kept frozen at -80C in 1ml aliquots, and only thawed to room temperature immediately prior to experimental use.

For two time points (T1 = 2 hpi, T6 = 12 hpi; hpi: hours post-infection), two sets of chemotaxis assays were collected: Phage vs ASW, Control vs ASW.  Each set comprised of three physical replicates, repeated with two biological replicates corresponding to filtrate samples A and B. The chemotactic preference of P. haloplanktis was measured by analyzing the cell distribution over time and comparing the cell populations on opposite sides of the channel.

Flow Cytometry Data Details

This data is captured in Supplemental File fcm.countdata_synwh8102_s-ssm5.csv.

Flow cytometry data quantifying Synechococcus cell concentrations and S-SSM5 cyanophage particle concentrations in each biological replicate culture. Samples were collected from cultures, fixed in 0.5% glutaraldehyde, and flash frozen in LN2 before being stored at -80°C. Samples were thawed on ice prior to being quantified.

The Sample Name column indicates the time at which samples were collected (e.g., 1hpi = 1-hour post-infection). Samples named ‘SN’, ‘SW’, or ‘TE Blank’ correspond to blanks (negative controls) performed with SN media, 0.2μm filtered natural seawater, and TE buffer. The Sample Type column indicates whether Synechococcus cells or S-SSM5 cyanophage were quantified. Synechococcus were detected by chlorophyll-a autofluorescence using a 488nm laser with emission detected using a 690/50nm filter. A violet laser (405nm) was used to detect side scatter of particles (405/10nm emission filter). Cyanophages were stained with SYBR Green I which was also excited using a 488nm laser with emission detected using a 525/40nm filter. Size of particles was determined using the same violet side scatter parameters as above. The condition and replicate number are both indicated in the Treatment column.

Raw counts are given in the Count column with blank subtracted counts shown in the Blank Adjusted Count column. The acquisition time, volume of sample run, and the calculated concentration of either Synechococcus or cyanophage are given in the following columns, respectively. ‘NA’ indicates that data were not acquired for those specific samples. Particle concentrations were determined by calculating the number of gated particles per volume of sample analyzed, then accounting for the sample dilution.

The flow cytometry data support the chemotaxis experiments by providing data to show that uninfected Synechococcus cultures maintained their cell concentrations over the course of each experiment and that no cyanophage were detected in these cultures. Similarly, cyanophage-infected Synechococcus cultures displayed cell loss characteristic of viral lysis and increases in cyanophage concentration which combined are indicative of a productive infection. These data support that the observed directional motility biases (or lack thereof) in chemotaxis of V. alginolyticus were indeed in response to either uninfected and cyanophage-infected Synechococcus.

Data processing step summary:

1. Locate particles using a bandpass filter/peak finding algorithm (available: https://site.physics.georgetown.edu/matlab/)
2. Bin particles according to x-position to examine distribution across the field of view

All data were processed using custom MATLAB scripts (version 2021b). These MATLAB scripts are captured in the Supplemental File, Filtrate_Chemotaxis_Analysis.zip. 

Spaces in column names have been replaced with underscores ("_").

All chemotaxis data values have been rounded to maximum precision (14).

Time values have been rounded to a precision of 4.

NSF Award Abstract:
Drifting photosynthetic microbes in surface ocean waters carry out nearly half of global carbon (C) fixation, both supporting the marine food web and reducing atmospheric carbon dioxide (CO2) levels. The fate of C in ocean ecosystems is controlled by myriad individual interactions within a highly interconnected planktonic food web, the sheer complexity of which has hindered predictive understanding of global C cycling. Chemical cues govern microbial interactions, and during infection, marine viruses manipulate the metabolism of phytoplankton and bacteria, facilitating the release of dissolved organic matter from infected cells. This research aims to determine how viral metabolic reprogramming of and organic matter release from intact, infected phytoplankton influences microbial interactions and C cycling. The interdisciplinary, collaborative nature of the project will enable direct training of two postdoctoral researchers, one graduate student, and undergraduate students in viral ecology, microfluidics, and metabolomics. An educational outreach program that engages middle school students in hands-on, high speed imaging of microbes will be expanded, and the project will culminate in a three-day workshop to advance the application of microfluidic devices and mass spectrometry analyses in microbial ecology.

The overarching hypothesis behind this research is that viral infection alters the chemical landscape of intact, infected picophytoplankton cells, attracting neighboring chemotactic bacteria and protistan zooplankton, and altering C flux pathways. To test this idea, a series of linked multi-scale laboratory-based experiments will be run to 1) Characterize the response of diverse model marine microbes to dissolved organic matter (DOM) released from intact, virus-infected picophytoplankton using microfluidics-based chemotaxis assays, 2) Identify key viral-derived DOM compounds eliciting chemotactic responses using stable isotope labeling, metabolomics analyses, and chemotaxis assays, and 3) Quantify micron-scale cross-trophic encounter dynamics and evaluate their impact on bulk-scale C cycling using liter-scale measurements of C dynamics linked to high spatiotemporal resolution live imaging of microbial food webs. The ultimate goal of the project is to develop a mechanistic understanding of the role of intact, virus-infected cells in oceanic C cycling.