Hunting for halophiles at the South Bay Saltworks

Hello! My name is Melissa Hopkins. I just finished my first quarter as an undergraduate researcher in the Bowman Lab. The project I am working on involves the diversity of halophiles from the South Bay Saltworks lakes in San Diego. The South Bay Saltworks is an active solar salt harvesting facility that is part of the San Diego Bay National Wildlife Refuge. The goal of this project is to use 16S/18S community structure to identify microbial taxa that are currently poorly represented in existing genomes. We want to contribute to halophile genomes to learn more about halophiles, and this helps us decide which new genomes to sequence.

Aharan Oren’s open access review Microbial life at high concentrations” phylogenetic and metabolic diversityexplains the different classes and orders that contain halophiles, as well as the similarities of strategies used by these halophiles. Here, he uses the definition of halophiles as microbes that are able to tolerate 100 g/L salt but grow optimally at 50 g/L salt (seawater contains 35 g/L salt). Extreme halophiles (including the haloarchaea) are defined as growing best at salt concentrations of 2.5-5.2 M, and moderate halophiles as growing optimally at salt concentrations of 1.5-4.0 M. This assumes that the salt is sodium chloride however, different salts such as magnesium chloride can present additional challenges to life.

Halophiles are able to survive these high salt concentration environments in two different ways: pumping salt ions into their cells from the surrounding environment, or synthesizing organic solutes to match the concentration of their surrounding environment. Synthesizing organic solutes is more energetically expensive because it requires energy to make the high concentration of organic solutes needed, thus keeping salt ions out of the cytoplasm. But, this strategy is actually found widely across halophiles species. Pumping specific salt ions into their cells that don’t interfere with biological processes is less energetically expensive, but requires proteins in the cell to be specially adapted to high salt conditions. Because of this that strategy is not seen as often across the different species of halophiles. Different families and orders of halophiles use variations of these strategies to survive. There have been some new halophile species, such as Salinbacter, that are outliers, as in they use a different survival strategy then other halophiles they are related to. Sequencing many more halophile genomes will give us new information on how these adaptive strategies across different halophiles.

For this project, Jeff, Natalia and I spent the day sampling lakes from South Bay Saltworks on October 6. Out goal was to sample from 3 different points in each of several lakes of different salt concentrations, and to sample as many lakes as possible.

We started out at the lower salinity lakes to see how the equipment would function and get used to the sampling process. At each point, we took unfiltered samples using a peristaltic pump for respiration tests, bacterial abundance, measurements of photosynthetic efficiency and chlorophyll concentration, turbidity, and salinity.

We then placed a GF/F filter on the housing of the pump to collect a coarsely filtered sample for ion composition analysis, FDOM, and dissolved inorganic nutrients. Finally, we placed a 0.2 micron filter on the housing to collect bacteria, archaea, and phytoplankton for DNA analysis.

In all, we sampled 7 lakes: one low salt concentration lake, one medium salt concentration lake, 2 high salt concentration lakes, and 3 magnesium chloride lakes. Unfortunately, due to time constraints and the high viscosity of the magnesium chloride lakes (its like trying to filter maple syrup), we were only to sample from 1 point for each of the magnesium chloride lakes.

Natalia and I setting up for sampling on one of the lower salinity lakes.  You can see the large piles of harvested salt in the background.

One of the magnesium chloride lakes we sampled. Due to the high salt concentration and extremely high attraction between water and magnesium chloride these lakes have an oily texture and high viscosity, making them difficult to sample.

One of the saltier sodium chloride lakes that we sampled from.  The pink color comes from pigments in the different microorganisms that we’re studying.

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