Global Cycles 2021

information and code for course projects for the biogeochemical cycles class at the LMU for 2021

The project will consist of:

• 8-10 page report featuring primary analysis about a nutrient/element of choice (at least one, or combinations for rarer ones) from the GEOTRACES database
• can be either journal article format (Intro-Methods-Results-Discussion) or report format (Intro-Sections-Conclusion)
• for journal article format, include an abstract, introduction, brief methods, results/description of observations, discussion, figures (roughly 1-2 pages of combined figures) and references
• for report format, include an abstract, introduction, then 2-4 relevant sections with headings, and conclusions, figures (roughly 1-2 pages of combined figures) and references
• can be a global overview, or detailed about a location of interest; this can be determined after beginning to look at the data
• for figures, number the figures, include captions after the figure, and refer to them in the text by number ("As shown in Figure 1...")
• embed all of the images/figures into the document, around the context that you are talking about them (as in, do not put them all at the end)
• export it as a PDF from word/whatever program you are typing in and send it as a single file with your name in the filename

The following items can be used by all for comparison:

CTDPRS_T_VALUE_SENSOR_dbar       CTDTMP_T_VALUE_SENSOR_deg.C
CTDSAL_D_CONC_SENSOR_pss.78      SALINITY_D_CONC_BOTTLE
OXYGEN_D_CONC_BOTTLE_umol.kg     CTDOXY_D_CONC_SENSOR_umol.kg
PHOSPHATE_D_CONC_BOTTLE_umol.kg  SILICATE_D_CONC_BOTTLE_umol.kg
NITRATE_D_CONC_BOTTLE_umol.kg    NITRITE_D_CONC_BOTTLE_umol.kg
PH_TOT_BOTTLE                    TALK_D_CONC_BOTTLE_umol
DIC_D_CONC_BOTTLE_umol

Using the GEOTRACES database

We will make use of recently collected data from the GEOTRACES database (part of SCOR), which collects data on marine trace metal concentrations from around the world. The cruise tracks can be viewed here.

The basic dataset we will be using for the course consists of ~90k samples. CTD data are available for most samples, while the trace metals in the set have around 1k to 10k samples. These data were minimally processed for use in R, only by changing some symbols to allow smooth importing. The raw data can be downloaded at the webODV website if necessary.

Some publications and reviews have already been generated using the GEOTRACES datasets.

We are not restricted to GEOTRACES. Other datasets would be allowed for comparisons, such as the NOAA World Ocean Database dataset (better for longer timeseries studies), or the Integrated Ocean Drilling Program datasets.

Setting up R

For the analysis portion, we will be using the programming/statistics language R.

It is probably best to use a development environment like RStudio. R-base (files of the programming language) must be installed on your system first. If you have used R before, and have a preferred working environment, you can of course use that instead.

RStudio can be downloaded here (get the Desktop version), and Rbase can be downloaded here, for MacOS, Windows, or Linux.

For an overview tutorial about RStudio and R, first watch this tutorial about using RStudio.

For more details about statistics in R, see learning statistics with R, and another good place to start would be Chapter 3 of that book (free as a pdf). IF YOU HAVE NEVER USED R OR ANY OTHER PROGRAMMING LANGUAGE, PLEASE READ CHAPTER 3, AND FOLLOW ALONG WITH RSTUDIO. Note: this is Chapter 3: Getting started with R NOT Section III Working with data.

We will make frequent use of two supplemental packages: dplyr for data management/organization, and ggplot for mapping/plotting. These can be installed from the Tools -> Install Packages... menus in RStudio. The usage of those two packages differs substantially from standard R, and it may seem like it is almost another language.

Analysis of GEOTRACES in R

The basic dataset can be downloaded here. This includes sample metadata, nutrients, trace metals, radionuclides, and dissolved rare earth elements.

We will be starting with the sort of analyses in this tutorial.

Intro or Discussion

For the discussion about the nutrient or metal, consider trying to answer some of the following questions:

• is it evenly distributed around the world? do some ocean basins have more or less?
• is it constant with depth? does it have a conservative, nutrient, or scavenged profile? see review by Bruland 2003
• do organisms use this substance, say for enzymes? which enzymes, and which biological processes? check KEGG or Uniprot DB
• are there natural sources, say from volcanoes or rivers? how much does this contribute?
• are there human sources, say from industrial processes? which ones? what do they make? is that region well known for that industry? does this industry cause other problems?

Other links for the class

• video of carbon cycle https://www.youtube.com/watch?v=dwVsD9CiokY