... He then raised his saliva moistened finger to gauge the wind characteristics (as I’m sure you’ve seen in movies) and confidently declared, "spring is coming." In this case, it was not White Walkers we were anticipating. No. It was the unchecked proliferation of algae, AKA an algal bloom, along our California coast and the uncertainty of its impact. Would it be large in magnitude, extending from Santa Cruz to Santa Monica, or local? Would it be short-lived or last for weeks on end? The number one question on everyone’s mind was would the algae be toxic and pose a serious threat to human health and the local economy?
Algae are the foundations of the oceanic food webs simply because everything* in the ocean is solar powered. Photosynthetic organisms use energy from the sun to convert inorganic carbon in the air, CO2, into organic ‘body parts’ that can then be consumed by larger, non-photosynthetic organisms. The oceanic food chain, starting from photosynthetic organisms like algae, leads up to higher trophic levels like fish and eventually humans with many intermediate steps along the way (viruses - parasites - heterotrophic protists - copepods- etc.). The more algae there are, the more material there is for consumption. Therefore algal blooms are like an annual all-you-can-eat buffet that can sustain commercial fisheries or even shut them down in the case of algal blooms involving species that produce harmful toxins.
Simplified marine food chain starts with primary producers, photosynthetic organisms and works itself up the chain to larger and larger organisms. The whole chain breaks down if we remove any link, especially the primary producers, which supply the entire system.
Local algal populations can consist of hundreds of distinct species with unique nutritional and energy requirements. These requirements are conferred by their distinct distinct physical characteristics (morphotypes) as well as physiological attributes. This is somewhat intuitive if you think about the many varieties of plants. Consider trees, shrubs, ferns, mosses, vines, cacti, flowering plants, plants that eat insects, etc, and the diversity within each of these categories. Algal diversity also abounds beyond our current conception both physically and physiologically. Some algae contain tails for swimming (Akashiwo, Karenia) while others are made of glass shells and control buoyancy by other means (diatoms). Some are tiny (Pelagomonas, Ostreococcus) and some are large (diatoms). Some wear armor plating (Emiliania, Lingulodinium) while others are naked (Dunaliella, Chlamydomonas, Volvox).
Flavors of algae: Shown are just a few common genera of algae with their own evolutionary history, skills, preferences, requirements, tolerances, and metabolic capacities.
Just as racing sports have several racers, and only room for three on the winners podium, algal blooms, when they occur, usually consist of only a few dominant species that have somehow outcompeted the other hundreds for nutrients, sunlight, and/or other resources. The others may have better luck next spring. We know there will be a bloom and when, but what if we could predict the winner?
The best descriptions of algal populations that we have are generalizations regarding nutrient concentrations and the preferences of dinoflagellate and diatom species. Dinoflagellates and diatoms are two very different groups of organisms that contain algal species that typically dominate blooms on the California coast. Dinoflagellate algae can swim and sometimes eat small prey, and as I mentioned before, diatoms are large, made of glass -literally, and cannot swim. Both groups contain toxic species, although they are relatively few with an infamous reputation such as Alexandrium (dino) and Pseudonitzschia (diatom). Dinoflagellates typically prefer summer conditions when the nutrients are low, and the water warm and calm, whereas diatoms prefer the high nutrient with high turbidity keeping them at the surface.
Characteristics of two notorious algae on the California coast. Alexandrium and Pseudonitzschia are two genera of algae that have the ability to produce toxins. Pseudonitzschia, being the diatom has a large size, which probably gives it an advantage in high-nutrient, spring conditions, whereas the mobile and small Alexandrium most likely dominates in the calm, low nutrient summer waters. Despite its size, its can pack a punch. Saxitoxins can be extremely deadly.
The ability to produce toxins is widespread, and most theories about the evolutionary purpose of toxins revolve around competition for survival. Toxic algae may simply taste worse to predators than non-toxic algae, making them like the black jelly bean among other better tasting colors. Toxins may also be employed as a form of chemical warfare against other algae once secreted into the water. But no theory has been established building a case for attack on humans and global domination. We are likely just occasionally caught in the trophic crossfire between a diverse community of microbes competing for space and survival in an environment with scarce resources. A good review on the evolution of chemical warfare in bacteria has been written by Elisa T. Granato (Granato 2019), and a possible example of a long standing war between Streptomyces (bacteria) and Aspergillus (fungi) was described by Zeinab G. Khalil (Khalil 2018). Regardless of the reason, many evoloutionarily distinct species have the ability to concoct their own unique chemical toxin and release once antagonized.
I would like to understand how the environment determines which species dominates during spring blooms to better predict the occurrence of algal blooms that can have a negative impact (harmful algal blooms) and which anthropogenic practices (such as dumping, fertilizer runoff, etc.) can be modified to mitigate this impact on the Souther California Coast. In a nutshell, I will be comparing the physical and chemical conditions of a body of water to the resulting microbial community composition. To characterize the physical and chemical seawater characteristics, I will measure nutrient (nitrogen and phosphorous) concentrations, along with a suite of other chemical and physical characteristics at a location in the Santa Monica Bay -salinity, temperature, dissolved oxygen, and chlorophyll a. The microbes are the sexier component of the project -‘who’ is present, ‘what’ they are doing, and ‘how’ they are interacting.
To determine the community of things we cannot see with our naked eyes, ie microbes, I could use a microscope. However, taking a census of an entire community would not be feasible without an army of experts. There’s also the problem of size and resolution. Some species are so tiny that confidently identifying distinguishing features is impossible without more expensive equipment and time consuming prep. Which leaves us back at the issue of scope -this cannot be done for an entire community of critters.
Instead of microscopy based identification, DNA and RNA extracted from all of the organisms present in the community can be used as a barcode for species identification and its relative abundance in the community. I’ve leaned toward using RNA over DNA because it is more of a representation of the living, active community. DNA is so stable, that it can it can be captured from dead cells or even freely floating in the water. RNA on the other hand requires effort and a lot of energy for a cell to produce in a process called ‘transcription.’ Therefore, the presence of an organism’s RNA implies that it was alive and able to transcribe it at the time it was collected.
My study site, The Santa Monica Bay (Santa Monica Pier)
Santa Monica Pier
I collected and analyzed microbial communities from the Santa Monica Bay during two different spring blooms in the spring of 2018 and 2019 for 15 and 22 consecutive days, respectively. An overview of how I went from sea water to characterizing microbial community structure went as follows: 1. I collected 20L of water from a designated spot. In this case I am describing communities in the Santa Monica Bay. 2. I next used a vacuum to pull the sea water through a filter with specific pore size (0.7µm). This enabled things smaller than this size to pass through, such as most bacteria and viruses while capturing the larger things on the filter such as protists. 3. I then used special detergents to extract DNA and RNA from the cells that were captured on the filter. Once extracted, the unique sequences of each piece of DNA and RNA were decoded (sequenced) at an outside facility, and (4) finally used to determine the individual species present and the overall community structure in terms of relative proportions of species.
From seawater to microbial community structure. Water is collected and (1) passed through a special filter while things larger than the pore size of 0.7µm, ie most protists, are captured onto it. (2) DNA and RNA are extracted sequenced, and (3) the differences are interpreted and designated as distinct variants (‘operational taxonomic units (OTUs) or amplicon sequence variants (ASVs)) using computer algorithms and later given species names by running those sequences through a database containing similar sequences and the names of the organisms from which the sequence originated. (4) finally, the ASVs or OTUs are tallied to give an overall picture of the relative proportion of each species in the community and facilitate more rigorous statistical analyses.
To determine the species present and those dominating during a spring bloom, we used 18S rRNA V4 amplicon sequencing of RNA extracted from the cells of the free-living community of unicellular eukaryotes, AKA protists. The 18S rRNA V4 amplicon is basically a barcode containing four letters, A-T-C-G, in sequences unique to every species. For example, the 18S rRNA V4 sequence for species A might be “ATCCGTACTG”, while species B is “ATCCGTAGTG”. Now imagine these sequences of letters are written in invisible ink. “Sequencing” the rRNA means using a fancy machine to decode the otherwise invisible sequences. So, sequencing all of the 18S rRNA from the protistan community in a body of water allows me to take a census and ask questions like “who is there?” and “how abundant are they relative to others in the community?” Because me and my group did this every day for an extended period, we can investigate the dynamic changes in chemical and biological factors that occur within the community. For example, the increase in Nitrogen concentrations due to upwelling, followed by its rapid decrease that is simultaneous with a spike in chlorophyll a concentrations would represent a cascade of events that led up to a bloom of an unknown alga. The alga remain unknown until we view the 18S rRNA sequence information…
The chain reaction: Cascade of events from wind driven upwelling of Nitrogen and phosphorus and the rapid proliferation of algae as a result (chlorophyll a concentration).
Daily dynamics in the diatom and dinoflagellate communities according to 18S rRNA sequencing. Only a few of several species proliferate by outcompeting the others for limited nutrients (Nitrogen and Phosphorous).
In using these tools and methods to characterize the daily changes in community structure, I have produced a bunch of data that can be used to produce information starting with pictures and statistical analyses that have meaningful conclusions. I hope that the information that I produce will translate to knowledge that can simply spark interest and appreciation for how nature works in the general public as well as influence policy decisions such as those that help mitigate our role in the promotion of harmful algal blooms.
