Table of Contents

• Dataset Description
  • Methods & Sampling
  • Data Processing Description
• Data Files
• Parameters
• Instruments
• Deployments
• Project Information
• Funding

Standard oceanographic measurements collected from CTD casts during 5 cruises in Delaware and Chesapeake Bays, representing coastal marine ecosystems.  Measurements included nutrients, chlorophyll and light attenuation, bacterial and viral production.

This is a new version with both new data and updated older data.  March 31, 2016

DMO notes:

changed ND to nd
,, to ,nd,
space between degree_decimal minutes to no space
change nutrient names to chemical symbols
added toplevel to put all three cruises in the same object
got rid of extra lines in ACTII
fixed bad lat/lon points in each cruise with PI input

The water samples were collected with a Seabird 911+ CTD.

Nutrient concentrations were measured by standard wet chemical methods using a SEAL Analytical AA3 Continuous Segmented Flow Analyzer.

Samples for chlorophyll a concentrations were collected by filtering 100 ml of water through Whatman GF/F filters and stored at -20 ^oC until analysis. To estimate concentrations, the filters were placed into 90% acetone and 40% dimethyl sulfoxide (DMSO) and then the fluorescence in the extract was measured with a Turner Designs 10-AU fluorometer.

The attenuation coefficient was estimated by measuring photosynthetically active radiance with a Biospherical PNF-210 radiometer over a depth profile. In nearly all cases, the downcast and upcast profiles of radiance were indistinguishable and all data were used. When differences between the down and upcasts were apparent, only the downcast data were used.

Nutrient concentrations were not processed except for converting raw spectrometric or fluorometric readings to concentrations.

Radiance values at very shallow or very deep depths were excluded from the analysis to calculate the attenuation coefficient when these values were clearly not along the ln (radiance) vs. depth line.

Bacterial Production: Assumes average C per cell = 15 fg and 0.125 nmol-C/pmol of leucine.

Description from NSF award abstract:
Prokaryotic organisms in marine systems are highly diverse and carry out many types of metabolic processes important in biogeochemical cycles. However, the contribution of individual bacterial taxa to biochemical processes is not well understood. Similarly, previous studies have had limited success in understanding the regulation of bacterial communities by looking at correlations between abundance of individual taxa and environmental factors. Estimates of growth rates will help understand both problems. The contribution of specific bacterial taxa to biogeochemical cycles is likely to scale with growth rate as well as abundance, and these rates are also likely to be more sensitive to environment fluctuations than abundance.

This project will examine the following questions and hypotheses about a fundamental property of organisms, growth rates: 1) what is the relationship between growth rate and abundance of specific bacterial taxa in controlled experiments? Do 16S rRNA:rDNA ratios or other growth-regulated transcript:gene ratios reflect real differences in growth rates? The PIs hypothesize that growth responsive transcript:gene ratios will correlate with growth rates independent of metabolic strategy and phylogeny, even though ratios and absolute rates will vary among bacterial species or within a taxa growing under different conditions. This hypothesis will be explored in environmentally relevant isolated bacteria whose genomes have been sequenced as well as in individual taxa in natural communities, whose genomes will be sequenced via a single cell approach. 2) What is the relationship between growth rate and abundance in situ? How are variations in the environment reflected in bacterial growth rates? The PIs hypothesize that growth rates, estimated by either 16S rRNA:rDNA ratios or by other growth responsive transcript:gene ratios, will be better correlated to environmental factors than abundance alone. Variation in growth rates within and between taxa will correlate with changes in the environment, especially with light and nutrients. The project will test this hypothesis by analyzing three well-­studied diverse marine ecosystems: a coastal Microbial Observatory site which has been sampled since 2006, and the Delaware and Chesapeake Bays.

To investigate the questions and hypotheses outlined above, the PIs will use a combination of single cell genomics, high throughput sequencing, and QPCR approaches to examine levels of 16S rRNA and other growth-regulated transcripts as well as their corresponding genes under various nutrient conditions and different in situ temporal and spatial scales. High throughput sequencing avoids amplification and cloning artifacts and is cost effective. Growth-­responsive transcript:gene ratios, microbial abundance, and biogeochemical properties will be examined over hourly, daily, weekly and monthly time scales to investigate the influence of environmental factors on growth rates of individual bacterial taxa and to explore bottom-­up control of microbial communities.

The results from this project will do much to alter our perception of microbial processes in the oceans and estuaries by providing answers to long-­standing questions about relationships between activity and standing stocks of bacterial populations. It will begin to link quantitative rate measurements of specific bacterial taxa to the extensive genomic data now becoming available.