what is biodiversity?

Biodiversity is a term scientists use to describe the abundance and variety of life on planet Earth. By studying biodiversity, we can understand how species have evolved over millions of years, how species interact, and their function in ecosystems as a whole. It can be a challenge to measure biodiversity; large or commercially important species are often well documented, but rare or microscopic organisms are much more difficult to sample. Additionally, large disturbances like a major storm or volcanic eruption, can disrupt biodiversity, which recovers over time, if it can recover at all.

Marine phytoplankton are a group of diverse and vital organisms within marine ecosystems. Like land plants, they use energy from the sun and nutrients to make food for themselves and other organisms, releasing oxygen. In fact, marine phytoplankton are responsible for about half of the oxygen production on Earth. They are also vitally important within marine food webs and in chemical cycling in marine environments. Not all phytoplankton perform the same function, however. Some are large and some are small, some have different appetites for different types of nutrients, and some are a better source of food for larger animals than others.

Studying the diversity of phytoplankton can tell us a lot about what is going on in marine environments. Traditionally, this has been done with light microscopes, where scientists look at a sample and visually identify cells. In the upcoming segments, we will learn about new methods to characterize the phytoplankton community, including imaging flowcytobot and machine learning technology, and metabarcoding and metatranscriptomics, both of which were used by scientists at Texas A&M University to document changes in the phytoplankton community along the Texas Coast after Hurricane Harvey in 2017.

Computers have expanded the capability of scientists to work with huge amounts of data. For scientists studying phytoplankton communities at Texas A&M University, the imaging flowcytobot and machine learning have allowed for continuous cataloguing of the phytoplankton community at a temporal resolution that would be impossible for humans.

The supermarket often uses a labeling barcoding system to identify their items quickly and easily. Scientists studying biodiversity can do something similar with DNA. In DNA barcoding, a short fragment of DNA at a specific site is amplified using a universal primer and then sequenced to identify what species it comes from.

Barcoding begins with identifying a segment of DNA that is conserved within species, but also variable enough to distinguish among species. A useful barcode should also include a conserved region with little variability among the sequences between species for the purpose of designing universal primers. A primer is essentially a small piece of DNA that matches a specific site and initiates the process of copying DNA. Applying this approach to one species is called barcoding; when applied to a large community like phytoplankton it is called DNA metabarcoding. For metabarcoding, one such useful region is the V4 region of the larger 18S ribosomal RNA gene.

Following Hurricane Harvey, scientists from Texas A&M University conducted a research cruise tracking the impact of the storm on the marine ecosystem along the Texas Coast. One of the goals of this cruise was to characterize the phytoplankton community using DNA metabarcoding methods. To do this, scientists collected and filtered water samples to extract environmental, or eDNA. eDNA can then be amplified and sequenced using primers. Sequencing produces a large number of sequences, which scientists then compare with a database of sequences to identify which sequences correspond to which taxonomic group. Not only can scientists see which species were present, but also in what relative proportion, as a larger number of sequences belonging to a specific organism typically indicates a larger number of that individual present.

IFCB image analysis and DNA metabarcoding can tell us about the species composition of marine ecosystems, but how can we find out what these species are doing? To answer this, scientists at Texas A&M University use metatranscriptomics. Metatranscriptomics is similar to metabarcoding, but instead of DNA, RNA is sequenced. RNA is a chain of nucleotides that translates the genes coded for by DNA into the proteins that play a role in metabolism. So metatranscriptomics gives us an idea of the diversity of the active genes in an environment.

Once the RNA sequences are assembled, scientists try to assign them to a function and to a species. From this, scientists can understand which genes are being expressed, and the role of a given species in that ecosystem. This information can also provide information about how these organisms tackle hostile or changing conditions. For example, predation or changes in temperature, salinity, or nutrient abundance. This information helps scientists to predict how ecosystems will respond to future disturbances or shifts in marine environments.

To determine the function of a gene, sequences are compared with reference gene sequences with known functions. If the unknown sequence matches a known sequence in the database, the function of the unknown gene can be inferred. The type of genes and associated species found in a specific environment is a proxy of the state of the marine environment. By comparing the responses of the species to natural disturbances, we can understand how species respond physiologically to protect themselves in hostile conditions. The abundance of a particular set of genes indicates which genes are required for survival during specific conditions.

How do you track changes in a community of organisms that can’t be seen with the naked eye? Luckily, oceanographers at Texas A&M University have the right tools. After Hurricane Harvey, the marine environment along the Texas coast was massively altered. This presented an opportunity for oceanographers to study the response and recovery of marine phytoplankton, which are integral to the function of marine ecosystems. To do this, they used imaging, DNA metabarcoding, and metatranscriptomics methods to characterize the phytoplankton community shift during a one-week period following Hurricane Harvey.