Showing posts with label Marine. Show all posts
Showing posts with label Marine. Show all posts

Sunday, November 11, 2018

Florida’s coastal nightmare

*This is a guest post by Katherine Datuin- student in my 'Causes & Consequences of Biodiversity' course. 

Imagine going on vacation to beautiful, warm Florida just to find entire beaches strewn with the rotting remains of hundreds of fish, sea turtles and manatees. This is unfortunately not a nightmare, but a current reality for the residents of southwestern Florida, and it has been this way for almost a year now. What causing all this? This little guy. 

Figure 1. Kareina brevis living cell. Photo modified from Florida Fish & Wildlife Conservation Commission.
These events were brought to my attention through a recent article published by Vox news highlighting the consequences of such large and long-lasting harmful algal blooms, specifically the “Red Tide” in southwestern Florida (Resnick B. 2018). Kareina brevis, the algal species responsible, has been in bloom since November of last year. According to the article, this event constitutes the longest “Red Tide” algal bloom in history. Regularly, blooms occur seasonally, lasting only from a few weeks to a couple months. The length of bloom in combination with the species responsible is catastrophic for the surrounding environment. This species of algae produces a suite of neurotoxins known as brevetoxins (Gebhard et al. 2015). Exposure to these toxins within marine environments has resulted in massive fish kills and increased mortality in loggerhead turtle, and marine mammal populations (Walsh C. et al. 2010).

Figure 2. Kemp's ridley sea turtle on Sanibel Island. Photo modified from Andrew West/The News-Press via USA TODAY
Then why is all this so scary? It is because such Red Tide of this nature have never been recorded. This situation is novel, and therefore its overall effect on the underlying ecosystem is unknown. What is known is that mortality rates are increasing. More and more animals are dying as a result of this bloom, but the significance of the losses is still unknown. Will the affected species recover following this event? Will species be lost? Is the length of this bloom unique or will future blooms also be so long? What factors contributed to or enabled such a long-lasting bloom?   

It is equally important to consider the impacts such events will have on us humans. Human health can be directly or indirectly effected by these toxins through toxic aerosols and consumption of contaminated shellfish respectively. Studies have shown that an increased incidence of both respiratory and digestive illnesses can be found in relation to Red Tide presence, especially in those aged 55 or older (Hoagland P. et al. 2014). According to the United States Census Bureau, from estimates in 2017, about 20% of Florida’s population is 65 years of age or older. This means a high percentage of the population is at risk of suffering either respiratory or digestive illnesses due to this bloom. As well as its effects on human health, the Red Tide greatly impacts Florida’s fishing and tourism industries.

Figure 3. Red Tide devastation in Florida. Photo modified from Ben Depp Via National Geographic.
What can we do to prevent these blooms?
Although the specific conditions which enabled this bloom are unknown, many studies have hypothesized which factors likely contributed to this increase in length and frequency. The article states that human activity and climate change are likely the two factors with greatest influence. This is probably because like all other algal species, K. brevis requires sufficient macro-nutrient to enable blooms (Hoagland P. et al. 2014). Increased agricultural practices, water runoff and changes to atmospheric depositions could all contribute to a surplus of nutrients entering the water system and thus becoming available for these algae (Hoagland P. et al. 2014).  To mitigate the impacts of Red Tides, it is important to educate the local communities about how their actions effect their environment. For example, improving the public understanding of how fertilizer use can lead to greater blooms and how blooms effect charismatic species like turtles and dolphins. The public should also be informed of the ways in which Red Tides directly affect their communities from damage to fisheries and tourism to public health concerns.

The effects of the Florida Red Tide can be felt among all trophic levels in the surrounding marine and terrestrial environments. The causes and consequences of this specific event are still unknown and will likely be the subject of rigorous future studies. We should look to determine how we can prevent or minimize the length and severity of these blooms in order to protect the marine environment, the fisheries and tourism industries, and finally our own health.

Gebhard, E., Levin M., Bogomolni A., Guise S.D., “Immunomodulatory effects of brevetoxin (PbTx-3) upon in vitro exposure in bottlenose dolphins (Tursiops truncates)” Harmful Algae. 44(2015): 52-62.

Hoagland P., Jin D., Beet A., Kirkpatrick B., Reich A., Ullmann S., Fleming L.E., Kirkpatrick G. “The human health effects of Florida Red Tide (FRT) blooms: expanded analysis”. Environment International. 68 (2014) 144-153.

Resnick, B. Why Florida’s red tide is killing fish, manatees, and turtles. Vox news. October 8th, 2018.

Walsh C.J., Leggett S.R., Carter B.J., Colle C. “Effects of brevetoxin exposure on the immune system of loggerhead sea turtles”. Aquatic toxicology. 97(2010): 293-303.

Wednesday, April 4, 2018

Life in Plastic Ain’t so Fantastic

Guest post by Louis Vassos, MEnvSci Candidate in the Professional Masters of Environmental Science program at the University of Toronto-Scarborough

Much like the Buggles’ 1980 debut album, our material preferences are well within the age of plastic. Thanks to its light weight, durability, inertness, and low manufacturing costs, our use of plastics has increased dramatically since the mid-20th century. From bottles and toys to car parts and electronics, there is seemingly no application beyond its reach. Despite its uses and benefits, it has come under increasing scrutiny by environmentalists in recent years. In this regard, we tend to think of larger-scale and more visible environmental impacts, such as accumulation in landfills and petrochemical use in manufacturing. There has also been a significant amount of research on plastic in marine environments, usually focused on larger debris known as macroplastics. Over the past decade, however, there has been increasing concern about a new type of plastic debris in our oceans. Though its presence was first highlighted in the 1970s, we are only just beginning to realize the impact of fragments known as microplastics. As their name would suggest, they are small pieces of plastic, typically measuring less than 5mm in diameter and sorted into two distinct classifications.

Primary microplastics are manufactured to be microscopically sized and are typically used in air blasting as a paint and rust remover, as well as in personal care products as an exfoliating scrubber. This latter use has risen sharply in cosmetics and facial cleansers since the 1980s, with plastic “microbeads” replacing natural materials such as pumice and ground almonds. Regardless of application they usually enter water bodies through drainage systems, and are easily able to pass through filtration systems at sewage treatment plants due to their small size.

Microbeads in toothpaste. Retrieved from:

Secondary microplastics arise from the breakdown of larger pieces of plastic debris on both land and in water. Larger debris will typically enter marine ecosystems directly or indirectly through careless waste disposal, often being transported through river systems. Sources of transfer include coastal tourism, extreme weather events, fishing, other marine industries, and accidental spillage during transportation. Over time, a culmination of processes such as exposure to UV radiation can reduce the debris’ structural integrity, causing brittleness, cracking, and yellowing. This in turn can lead to fragmentation through abrasion and waves, and fragments will gradually become smaller over time before reaching microplastic size (Cole et al, 2011).

As Eriksen et al (2014) have estimated, there is a minimum of 5.25 trillion plastic particles weighing 268,940 tons in the world’s oceans. Microplastics account for 92.4% of this mass, and their reach has been substantial. Because of their buoyancy and durability, they have the ability to travel long distances without degrading for years. Denser plastics (such as PVC) will sink and have the potential to reach coastal sediment (Andray, 2011). Other marine microplastics will end up trapped in ocean current systems known as gyres, the most famous grouping of which is the “Great Pacific Garbage Patch” in the North Pacific Gyre. Despite what the name would suggest, it is not an island-like mass of floating debris, but is more akin to an extensive “soup” of debris difficult to see with the naked eye. At a density of 334,271 pieces/km2, microplastic mass in the area was found to be 6 times that of plankton (Moore et al, 2001). 
Potential microplastic transport pathways (From Wright et al, 2013)

Densities such as this increase potential microplastic ingestion by various marine organisms, especially filter feeders, plankton, and suspension feeders. These species may mistake debris for prey based on size or colour, or passively ingest them without being selective (Wright et al, 2013). In Farrell and Nelson’s (2013) study of mussel-eating crabs, they found that it is possible for microplastics to be transferred to individuals at a higher trophic level. The large surface area to volume ratio of microplastics makes them susceptible to water-borne pollutant contamination, and can cause toxic plastic additives such as BPA and PCB to leach into the water. This debris can also act as a dispersal vector for microbial communities, including potentially pathogenic species (Jiang et al, 2018). While the ingested debris can accumulate within individuals and be transferred up the food chain, the exact effects of this are not entirely known at this point in time (Avio et al, 2017). A recent study by Lei et al (2018), however, found that microplastics can cause oxidative stress and intestinal damage in zebrafish and nematodes, and that their toxicity is closely dependent on particle size.
Intestinal damage in zebrafish caused by exposure to 1.0 mg L-1 of different microplastic types and sizes. Photograph A shows control (top), survival (middle), and dead after exposure (bottom) zebrafish (From Jiang et al, 2018)
Fluorescent microspheres on a crab’s gill lamella transferred from ingesting mussels, each measuring 5 micrometres in diameter (From Farrell and Nelson, 2013)

          What does the future hold for microplastics? Because their effects on both marine life and humans is relatively unknown, it is important to try and prevent them from entering and accumulating within marine environments. Properly dispose of larger plastic items to prevent them from entering waterways and breaking down into secondary microplastics, and be conscious about the presence of primary microplastics in other products. Make informed decisions when buying cosmetics, and choose ones that use natural exfoliating materials. Microbead bans have already begun to be enacted in several countries, including the UK, US, Canada and New Zealand (Pfeifer, 2018). There is also the potential for future studies on topics such as the health effects of microplastic ingestion and leached additives, debris behavior within the water column, and new standardized techniques for detection and sampling (Cole et al, 2011). It is hard to say what will happen next, but the removal of these 5.25 trillion particles from our oceans will prove to be a very difficult challenge without the development of novel extraction methods.


Anadrady, A.L. 2011. Microplastics in the marine environment. Marine Pollution Bulletin 62:1596 – 1605
Avio, C.G., S. Gorbi, and F. Regoli. 2017. Plastics and microplastics in oceans: from emerging pollutants to emerged threat. Environmental Research 128: 2 – 11
Cole, M., P. Lindeque, C. Halsband, and T.S. Galloway. 2011. Microplastics as contaminants in the marine environment: a review. Marine Pollution Bulletin 62:2588 – 2597
Eriksen, M., L.C.M. Lebreton, H.S. Carson, M. Thiel, C.J. Moore, J.C. Borerro. F. Galgani, P.G. Ryan, and J. Reisser. 2014. Plastic pollution in the world’s oceans: more than 5 trillion plastic pieces weighing over 250,000 tons afloat at sea. PLOS One
Farrell, P., and K. Nelson. 2013. Trophic level transfer of microplastic: Mytilus edulis (L.) to Carcinus maenas (L.). Environmental Pollution 177:1 – 3
Jiang, P., S. Zhao, L. Zhu, and L. Daoji. 2018. Microplastic-associated bacterial assemblages in the intertidal zone of the Yangtze Estuary. Science of the Total Environment 624:48 – 54
Lei, L., S. Wu, S. Lu, M. Liu, Y. Song, Z. Fu, H Shi, K. Raley-Susman, and D. He. 2018. Microplastic particles cause intestinal damage and other adverse effects in zebrafish Danio rerio and nematode Caenorhabditis elegans. Science of the Total Environment 619:1 – 8
Moore, C.J., S.L. Moore, M.K. Leecaster, and S.B. Weisberg. 2001. A comparison of plastic and plankton in the North Pacific Central Gyre. Marine Pollution Bulletin 42:1297 – 1300
Pfeifer, H. 2018. The UK now has one of the world’s toughest microbead bans. CNN. Retrieved from:
Wright, S.L., R.C. Thompson, and T.S. Galloway. 2013. The physical impacts of microplastics on marine organisms: a review. Environmental Pollution 178:483 – 492

Thursday, January 7, 2010

Double or nothing

As I finished my undergrad career and started thinking about graduate school, I was totally infatuated with the chromosomal speciation of treefrogs in the genus Hyla. Hyla versicolor and H. chrysoscelis, the 'gray treefrogs', have similar geographic distributions and look almost identical - except that one is a tetraploid version of the other. The increase in genome size is associated with a slight increase in cell size, which has trickle-down effects into physiology, the sound of their call, and other ecological factors, and of course they are reproductively isolated. As it turns out, Margaret Ptacek and colleagues were unraveling this mystery at the genetic level just as I was learning of it, and while I was disappointed not to be able to explore this for my graduate work, Margaret made up for it by paying for all the drinks when I visited Clemson a few years back.

So it was with considerable interest that I stumbled across one of the first tables of contents of the new year, in BMC Evolutionary Biology. Two co-occurring populations of the diatom Ditylum brightwellii, it turns out, differ in genome size. In this case, the belief is that there is a single taxonomic species harboring a very recent genome duplication polymorphism (which are likely cryptic species). Of course, a species by any other name... well, that's the problem isn't it? In the world of diatoms, according to Koester and colleagues, the 'barcode' standard is to use the 18S rDNA gene sequences and silica cell wall morphology in diagnosing species. However, already armed with evidence that two substantially distinct populations could be identified with the more rapidly-evolving ITS gene region, these researchers explored how differences in reproductive rates and size distributions might be associated with genome size.

See, diatoms are the petri dishes of the natural world. In order to reproduce, each side of the interlocking silica case separates and generates a new nested case. One of the offspring of this fission will be the same size as the parental individual, the other will be slightly smaller - the smaller of the two original cell walls, with an even smaller one nested within. At least that is how I understand it. Over time, these clonal lineages reduce substantially in size, and cell size is eventually limited by genome size; sexual reproduction then allows them to regain a larger cell size and the process repeats. So, the life history of this species requires an interesting interaction among the genome (which places a lower bound on cell size, and a lower bound on reproductive rate) and the population.

In Ditylum, Koester et al. were able to show that there are not only two very distinct genetic lineages, but that the one that is regionally localized to Puget Sound appears to have been generated through genome duplication. That is, there is a cosmopolitan species, and an offshoot lineage that was formed through some form of genome duplication, with concomitant changes in cell size, rates of population growth, and reproductive isolation. Koester et al. conclude that these lineages are cryptic species, and that this form of isolation may be common in marine diatoms.

More generally, this shows another way in which our understanding of biodiversity is changing rapidly thanks to molecular diversity analysis. The latest term to be coined by John Avise, biodiversity genetics, reflects the fact that we must now consider all of the new ways in which this technology can accelerate the rate of discovery in our natural world. Taxonomists trained in the morphology and phenotypic diversity of life are few; certainly too few to keep up with growing scientific collections, and the bottleneck in describing species can be a difficult one for management and conservation. The '18S or bust' approach in diatoms may be one standard that will change as more studies like this one, out of Armbrust's lab at Washington, illuminate how dynamic biological diversity can be.

Sunday, November 22, 2009

Something fishy

Of the many victories wrought by DNA barcoding - the ability to place an unknown sample in a phylogenetic, and often taxonomic, context using short fragments of DNA sequence data - some of the most useful applications for management have come from the sea. One of the best citation-to-data ratios in this regard belongs to a 2004 study by Peter Marko. This project extended naturally from Marko's molecular ecology course: students purchased samples of "red snapper" from various fish markets, and sequence data from the mitochondrial cytochrome b gene region showed that most of these specimens were not, in fact, Lutjanus campechinus - they were often understudied and probably rare relatives, or in some cases not snapper at all. The conservation implications from this study were huge, and a number of papers have followed suit, looking at a variety of similar systems. If you aren't interested in adding to your list of papers to read, check out the short film based on work done in Steve Palumbi's lab that documents their work to identify shark fins.

In a paper by Lowenstein et al., published last week in PLoS ONE, the focus was on sushi, specifically tuna. The common labeling errors were caught again: there were mismatches between what restaurants called the fish, and what was actually being offered. In some cases, very phylo-distant species are being sold as "tuna", and these species can actually make consumers ill. The story is an interesting one of how fraud develops in samples of organisms that can no longer be visually tied to the species they came from, and the difficulties in protecting consumers from fraud under current regulations. Obviously, the perils of overfishing are becoming quite clear and interested readers should carry their Monterey Bay Aquarium seafood guides or similar (there's even an iPhone app for that!) with them before ordering at restaurants.

A particularly interesting advance in this study was taking the barcoding approach beyond the visual appeal of tree-building and similarity with databased sequence data. One concern about barcoding has been that even when a new clade appears in a phylogeny, taxonomy cannot be updated without some sort of diagnostic characters. It is uncommon for new species (especially of animals) to be described based on DNA sequence data alone, but it is nevertheless the norm to define the character states that uniquely define a species from its relatives. In Lowenstein et al.'s paper, they identified 14 diagnostic DNA substitutions that could be used to uniquely identify all species of Thunnus and suggested that focusing on particular characters within the "barcode gene" (mitochondrial cytochrome oxidase I) will also be necessary for new technologies to accelerate in-the-field identification.

This latter step is of interest for anybody interested in cryptic species, or identifications when other reference material is not available. I hassled one of my former Ph.D. students endlessly as she revised her dissertation because we had been comfortably using a phylogenetic tree to assign unknown individuals to one of three cryptic taxa (in the isopod genus Idotea), but prior to publication we knew that diagnostic characters would be necessary for subsequent work to be readily comparable. And, since the undergraduate evolution lab at the University of Georgia repeats Marko's work on red snapper every few years (the local Kroger now knows not to advertise their special on "red snapper from Indonesia"), perhaps the lab can be extended by having the students generate these characters for the genus Lutjanus as well. I don't seem to have any problem convincing students to do their homework when it involves going out for sushi.

Monday, October 26, 2009

Conscientious conservation?

A colleague once said at a bar that she didn't believe in "conservation genetics". I'm not quite sure which aspect she was disputing, but one certain conflict is between gearing research toward conservation, while watching chemicals and consumables go into the waste stream. Most of the reactions in my lab are done using pipet tips and tubes made of virgin polypropylene. Nobody wants to recycle this stuff - even though 99% of the chemicals we use are fairly meek reagents like ethanol, water, nucleotides, and barnacle DNA, there's just no way to guarantee the waste stream coming from a building that does molecular research (e.g. you'd probably balk if that plastic got melted down and used for toys). Researchers have enough problems with reactions going wrong to also worry about whether their supplies are contaminated with the products of reactions past. Still, we have to constantly consider how we can minimize waste in the lab.

Lab Waste from Eva Amsen on Vimeo.

As a marine biologist, I'm also very conscious where all this plastic eventually ends up. I'm entertaining ideas for tip and tube recycling, though it is barely worth the effort for a single lab to do so: my lab probably consumes about 10kg of virgin polypropylene a year, into the trash. Super bummer. But that recycling effort could be balanced out if I just got my entire lab (including me) to stop drinking so much soda! Better would be to find institutional solutions, and we're a long way off on that.

Of course a lab is more than plastic. There are chemicals - which we've chosen to avoid some of the nastier ones, like ethidium bromide (using Ames-tested GelRed instead), isotopes (fluorescent-labeled primers), but still must use a little bit of polyacrylamide and a few other things in very small quantities that you wouldn't want to put in a smoothie. There are heating and cooling costs, which we can't do a lot about in our grumpy 1980's-era building at the University of Georgia (we'll assume that under budget constraints physical plant is doing what they can in that regard, though we did install some motion sensors on lights in the auxiliary rooms).

And then, there are all the gizmos. For the holidays I got a fun gift: a Kill-A-Watt. As procrastination during grant writing, I decided not only to check the energy consumption of things at home, but things in the lab. I don't know whether I believe paying to balance carbon emissions works (though at $3/month, I do it anyway), but it is interesting to know what the footprint of a lab like mine is. To make a long story short, it's mostly about the computers. Each computer in my lab used around 5kWh/day - up to $150 in annual energy bills, and actually the only things that compete with computers are my big chromatography fridge and my ultracold freezers (the -80° will use around 6000kWh/year!). Anyway, by unplugging some things that weren't being effectively used - one of the refrigerators, some water baths, an incubator, 2 of the computers - and ensuring that the rest were using the most appropriate power-saving settings - I cut the kWh consumption of my lab (only counting plug-in stuff) by over 10%.

The question is, how does this energy usage affect the science? One could argue that my research program hasn't expanded to fill the resources I had available, or that I can only cut back to the detriment of productivity. Only time will tell! We may have to devise a metric for productivity per kWh - but right now if I calculate my Hirsch index per kWh, it is not the thrilling kind of number I want to run to the administration with. I better get back to work.

Friday, September 25, 2009

Global warming and shifts in food web strucutre

ResearchBlogging.orgPredicting the effects of global warming on biological systems is of critical importance for informing proactive policy decisions. Most research so far has been on trying to predict shifts in species distributions and changes in interactions within local habitats. But what many of these studies assume is that the basic biological processes and requirements of the individual species will not change -that is their biology is fixed and they simply need to find the place that best suits them. Not so, say Mary O'Connor and colleagues, in a just-released study in PLoS Biology.

O'Connor and colleagues experimentally warmed marine microcosms and tested two alternative hypotheses on food web structure: 1) that productivity increases with warming; and 2) warming increases metabolic rates, thus changing consumer-autotroph (i.e., primary producers) interactions. What they found was that warming indeed altered consumer-autotroph interactions. Warming increased base metabolic rates of consumers, as well as primary production, and the net effect was that food webs shifted towards increasing consumer control (i.e., top-down control).

What this research means is that global warming may alter food web interactions by increasing resource needs of organisms as their metabolic rates increase. This may increase the stress on communities and change diversity patterns as increased needs may shift competitive hierarchies or affect autotroph's ability to withstand consumer effects.

O'Connor, M., Piehler, M., Leech, D., Anton, A., & Bruno, J. (2009). Warming and Resource Availability Shift Food Web Structure and Metabolism PLoS Biology, 7 (8) DOI: 10.1371/journal.pbio.1000178

Sunday, March 1, 2009

Phytoplankton motility and morphology might influence red tides

ResearchBlogging.orgThin layers, intense congregations of phytoplankton that can extend horizontally for kilometers, can be either a boon or a bust to marine food webs. On the one hand, these layers can stimulate the food web from the bottom up by providing elevated concentrations of marine snow (e.g., protozoa and organic detritus), bacteria, and plankton. On the other hand, because many of the phytoplankton species found in thin layers can be toxic, these layers can disrupt grazing, cause zooplankton and fish die-offs, and seed algal blooms at the ocean’s surface that can generate red tides. Understanding the processes driving the formation of thin layers is crucial for predicting their occurrence and ecological impact.

Although thin layer formation was previously thought to be solely influenced by abiotic forces, a recent paper in Science by William M. Durham and colleagues suggests that plankton’s swimming and shape play a role. Many phytoplankton species swim upward against gravity. When the water is calm, they swim up in a straight path. But add ocean currents to the equation, and the plankton start to encounter vertical shear where layers of faster- and slower- moving water meet. These shear forces can cause the plankton to tumble and spin instead of swimming straight up. The tumbling plankton become trapped in these regions of high shear, accumulating in a thin layer. The strength of the shear forces interacts with the morphology of the plankton to determine which species get trapped. For instance, bottom heavy species require higher shear to knock them off their straight path. Durham et al.’s findings suggest that vertical shear and cell morphology could be important predictors of red tides.

W. M. Durham, J. O. Kessler, R. Stocker (2009). Disruption of Vertical Motility by Shear Triggers Formation of Thin Phytoplankton Layers Science, 323 (5917), 1067-1070 DOI: 10.1126/science.1167334