A Tale of Plankton and Sewage

Welcome back for another update! Our urban kelp survey is now 100% live. Thanks to you all we BLEW through our first round of images (seriously, over 8000 images in exactly one month!!!) , and we are now ready to start classifying kelp!

Today we’ll briefly talk about our choice for our California site, Los Angeles. 

Image Description: Satellite image of Los Angeles
Image Source: Google Earth, accessed 6/12/2020

LA is currently the largest in our study, at least in terms of population/density. It saw its biggest population boom in the early to mid 1900s as both the entertainment and war industries grew. Unfortunately for us, we don’t have satellite data from this time. While we are missing the major population growth spike, Los Angeles continues to be a major metropolitan hub – it is the 2nd most populated city in the United States, and one of the largest worldwide!

The kelp forests in California have a patchy (ha ha…) history that is often closely linked to human activities – If you ask a phycologist about it, you’ll almost certainly hear about the Point Loma and Palos Verdes kelp forests. These two coastal kelp beds are located near San Diego and Los Angeles, respectively, and are infamous for sustaining massive kelp loss in the first half of the 1900s. This was due to a variety of factors, some natural and some human, but it seems that urban sewage discharge was the straw that broke the kelp forests back.

In the case of Point Loma, a broken sewage pipe discharged almost 200 million gallons of sewage into the kelp forest, leading to quick and major kelp loss. Luckily the area quickly recovered after the pipe was repaired – one advantage of kelp’s fast and furious life style is that it can quickly repopulate a large area if environmental conditions are restored! Palos Verdes has had a longer road to recovery, although recent restoration efforts have been successful in recovering many acres of kelp forest.

Discharge from sewer systems is bad for kelp in several ways.  The discharge tends to be full of sediments (solid material suspended in the water). This can prevent growing kelp from getting sufficient light or can even completely bury small individuals.  Another negative impact associated with these outfalls is nutrient pollution. In some cases, chemicals like ammonia can spike to toxic levels, causing immediate damage.

 In other cases, elevated nutrient levels can simply “fertilize” the water. Your first reaction might be to think that this would be good for the kelp, and maybe in a vacuum it would be, but nature isn’t that simple. In this case, the complication comes from phytoplankton, which can compete with kelp for light by forming floating algal mats that block light and shade the seafloor.

Kelp grows quickly, but not as quickly as phytoplankton. When water nutrient levels are elevated (a condition called eutrophication), plankton growth can ramp up into what is called a plankton bloom. That’s a lot of words to say that these algal blooms can have major effects on the ecosystem. This picture might “clear” things up (ecological puns never get old…).  These thick green algal blooms are more characteristic of fresh water, but I think this does a good job of illustrating how severe these can be.

Image description: Body of water that is overgrown with a thick algal mat. A researcher is collecting a water sample
Image source: Tim Otten, Oregon State University

The immediate, kelp-relevant effect is a reduction in light at the sea floor.  The longer term effects can include reduced oxygen levels in the water, creating uninhabitable “dead zones. This low-oxygen condition is called hypoxia and is a result of rotting phytoplankton. The typical life cycle of a bloom goes something like this:

  1. Eutrophication event (discharge or runoff causes elevated nutrient levels in the water)
  2. Algal bloom (opportunistic plankton grow exponentially given high nutrient levels)
  3. Overgrowth (algal population exceeds available nutrients; growth eventually stops as nutrients are depleted) – Light levels beneath the water’s surface reduced
  4. Decomposition (algal bloom dies and decomposes. Bacteria associated with decomposition consume oxygen, creating a dead zone) – Hypoxic conditions form, many animals die or leave

Kelps are potentially affected by almost every step of this process. They are shaded out by the initial bloom and then potentially buried in detritus as the plankton decomposes. Many of the animals found in kelp forests are vulnerable to the dead zones caused by algal blooms. Loss of these kelp forest residents can further destabilize the ecosystem.

While the stories of Point Loma and Palos Verdes unfortunately played out mostly outside of Floating Forest’s time window, they serve as clear reminders that human activities can seriously affect kelp forests. Things like sewage discharge and eutrophication are global issues; California may be a high profile example, but is far from the only one. As we continue to explore the effects of urbanization, we will be sure to include as many local factors (such as sewage treatment outfall points) as possible to best understand each of our sites.

Kelp and the Big City

If you’ve read through our “about section” or seen our blog in the past, you’ll know that kelp is threatened by climate change. This is perhaps the main reason why we are so interested in kelp in the first place, and so far Floating Forests has allowed us to build some of the most complete kelp forest datasets around. Soon we will be adding a new set of images to the project, this time examining a few key, high-risk locations with a fine-toothed comb. We’re interested in how coastal construction or development might impact kelp forests – it’s time to take our kelp research to the city! We will be taking a close look at kelp forests in California, Chile, Argentina, Australia, and New Zealand.

While global climate change is extremely important, there is great value in examining smaller scales as well.  In fact, studies such as this one have shown that kelp forests are strongly affected by local conditions! As you might expect, changes to these local environmental conditions can have significant effects on the local wildlife.

We call changes that affect the environment “drivers”. For example, a construction project could “drive” environmental change by releasing sand and dirt (which are collectively referred to as “sediments”) into the water. When two different drivers interact and affect each other, we refer to them as “synergistic”.  Occasionally they can create especially favorable conditions, but often one exacerbates the negative effects of the other, so we call these “synergistic stressors”.

One way to think about this is to say that one driver can amplify the effects of another. For example: a marine ecosystem might be able to handle a 2° Celsius increase in average temperature without collapsing. Separately, it also might be able to handle the effects of a large construction project. However, the effects of both at the same time could prove catastrophic: organisms already stressed by warming might not be able to cope with disturbances caused by the construction, and most importantly, things might get bad much more quickly than we might expect.

Because an emoji is worth a thousand words:

This example is one of the many that play out across an ever-developing world. One consistent trend over the last several decades has been a large increase in coastal population. To say this more plainly – more people than ever before live near the coast. As coastal cities grow, constant expansion is needed in order to keep up with the population. This conversion of land from natural to urban terrain is known as “urbanization” and brings with it a host of environmental impacts – some of which are potentially harmful for kelp forests.

By digging into the satellite record, we can get an idea of how kelp forests in urban areas have changed over the last few decades in response to this trend of development. What’s really exciting about this opportunity is that with the power of citizen science we can cover a lot of ground: we want to compare cities across the globe in order to build a better understanding of how kelp in different places is affected by human activities. We expect there to be many interesting differences between these locations – it would probably be more surprising to learn that kelp in Australia was acting exactly like kelp in Chile!

Stay tuned as we prep for the launch of this exciting phase of Floating Forests – details about our study sites and more about the connections between urbanization and kelp coming soon!

Kelp On The Edge!

With the Falklands classifications wrapping up, it’s time to move on to our next phase of global kelp mapping – kelp on the edge! Giant kelp is a cold water species – warm nutrient poor water is a definite no. Their range extends towards the equator wherever they are found until they hit a wall of warm water. There they shall stop, and no further.

But what about when that wall – that range edge – starts heating up? That’s when you’ve got…

We’ve witnessed a variety of other kelps die back when things got to hot, and our own Jorge Assis has shown some projected major range shifts of kelps in the future.

With the data from Floating Forests, one question we want to ask is, how have kelps on the edge been faring? Over the past 35 years, have we seen kelps on warm water range edges dwindling? Have any of those populations blinked out? Have the ranges of giant kelp actually been on the move?

The great thing about this project is the simplicity of the question. Rather than circling kelp beds (although we’ll get there), we want to begin just by looking at range edges of giant kelp around the planet and the area up to 500km away and ask you just to note, do you see any kelp? Yes or no? That’s it!

We’re also putting kelp on the edge into the Zooniverse app where you can swipe right for kelp! click here for the iPhone app or here for android!

The first set of images is up – from Baja California using Landsat 7 and 8. L4 and L5 imagery will come in the next few days, and more of Baja and then New Zealand next week.

So what are you waiting for! Pull out your phones and get swiping! (or click here.

Also… the music we can’t get out of our heads

There’s somethin’ wrong with the kelp today
I don’t know what it is
Something’s you’ll see with our eyes

We’re classifyin’ things in a different way
With swipe fast left or right
The data will surprise

Kelp’s livin’ on the edge!

Zoom is coming!

Hey, all! You have asked us multiple times for a zoom interface. We have some reasons not to use a zoom tool – tradeoffs with speed, variability in accuracy between classifiers, etc. – but are intrigued and want to put our intuition to the test. If it’s better, we’ll switch to it full time, most likely! If the tradeoff isn’t worth it, we’ll know, and we’ll probably have an interesting paper come out of it.

But – we want to hear from you! In addition to the zoom interface itself (basically, the classify interface + a pan and zoom tool), are there questions you think we should be asking you after you complete a zoom classification that could yield new and interesting insights? Let us know over here!

Kelp, Seasons, and the Falkland Islands

I’ve been playing around with some of the incoming classifications and thought I’d share this little map as a preview of what is possible with the data created by all of you! Click the map to launch an interactive map of the Falkland Islands! Use the menu in the top right to toggle each season on/off, and try zooming in to see individual patches!

The green patches represent the aggregates of everyone’s classifications – what you are looking at here is all of our data from the Falkland Islands.  All years are lumped together for now as there are still some gaps in the time series (we’re almost there, just 16% to go!). In other words, these patches represent maximum patch size for each season.  Another technical note: these polygons are based off a 6 user consensus, our current candidate for best accuracy. 

Giant kelp growth patterns are often dominated by seasonal processes such as storms. This can lead to an annual ebb and flow in which kelp patches grow rapidly throughout the spring and summer before dying back (or getting wiped out) in the winter.

We can see this pattern in our data too! Note how the annual minimum kelp extent occurs in the austral winter (June, July, and August), with growth beginning in the austral spring (September, October, November) and increasing throughout the summer.

One great thing about Floating Forests is that I am constantly amazed with how much we can learn even with a quick look at the data. Check out the waypoint marked “Tyssen Patch”. This is actually an undersea shoal (note the color difference on the basemap), and notice how much kelp is there!  Here is the google maps link if you want to prove it to yourself – definitely #sokelpy!

Once we get the time series data online I am very interested to see how persistent this patch has been over the years. Stay tuned!

Floating Forests and Google Maps

Often when citizen scientists view an image, they want context. Where is this? Am I really seeing kelp, or is this sand or mudflats? Fortunately, we have you covered. In the video below, I show you how you can view the metadata about each individual image, including how to view the area pictures in Google Maps. Now, the map on Google Maps isn’t going to be from the same time as the Landsat image, so, there may or may not be kelp in the same places. But you can at least get a better high resolution view of the area to make decisions about your classifications if you want it.

Does Citizen Science Consensus Alter Time Series?

One question that has come up a few times with our consensus classifications is, does the level really matter when it comes to looking at change in kelp forests over the long-term?

While our data isn’t quite up to looking at large-scale timeseries yet (we’re still digging through a few thorny methodological issues), I grabbed the complete dataset we have for the Landsat scene around Los Angeles from work Isaac is doing and decided to take a look. Note, this is totally raw and I haven’t done any quality control checking on it, but the lessons are so clear I wanted to share them with you, our citizen scientists.

After aggregating to quarterly data and then selecting the scene that had the highest kelp abundance for that quarter (i.e., probably the fewest clouds obscuring the view), we can see a few things. First, yeah, 1 classifier along is never good.

Screen Shot 2018-02-02 at 1.38.03 PM

Note, I haven’t transformed the data to area covered, instead we’re just going with number of pixels (1 pixel = 30 x 30m). But, wow, we need consensus!

But what if we impose a more conservative filter? Say, a 4-10 user agreement threshold? What does that show us?

Screen Shot 2018-02-02 at 1.38.34 PM

What I find remarkable about this image is that while we see the effect of decreases in detection when more and more citizen scientists have to agree on a pixel, the trends remain the same. This means that while we will try to chose the best threshold that will give us the closest true estimate of kelp area, that there will be multiple intermediate thresholds that give us the same qualitative results to any future attempts at asking questions of this data set.

This is a huge relief. It means that, as long as we stay within a window where we are comfortable with consensus values, this data set is going to be able to tell us a lot about kelp around the world. It means that citizen science with consensus classifications is robust to even some of the choices we’re going to have to make as we move forward with this data.

It means you all have done some amazing work here! And we can be incredibly confident in how it will help us learn more about the future of our world’s Floating Forests!

Lining Up Consensus

In working on a recent submission for a renewal grant to the NASA Citizen Science program, I whipped up a quick script that takes the data posted and overlays it with the actual image. I really like the results, so here’s one. Feel free to grab the script, data, and play along at home!

consensus_classification

Coastlines of Floating Forests

Some of you have noted in earlier posts of this preliminary dataset that some classifications show up on land – particularly at low thresholds. This is likely due to some images being served up that, shouldn’t have been (we’ve fixed this in the new pipeline), and the zeal of some classifiers. Regardless, we can crop out those areas, as we know that there’s no real kelp there. But do to it, we need some very very good maps of the coastline. Fortunately, there’s a solution!

The Global Self-consistent, Hierarchical, High-resolution Geography Database is an incredible resource, with some coastline data files that are remarkable in their detail. The data is also, of course, huge. So, for anyone playing along at home, we’ve subsetting it down to a few files for you delectation. These are all in the common ESRI Shapefile format, but if folks want them otherwise, we’re happy to provide. Here’s what we’ve created for you. Click on the names of the areas below to download the zip files.

First, California

Then, Tasmania

And last, the absolutely stunning Falkland Islands

When we used them for coastal cropping, they worked great – we’ll show some timeseries with cropped data next week!

Red areas are in the ocean, blue is on land.

Kelpy Consensus

At Floating Forests, we get confronted with two issues a lot. First, how good is the data? A lot of scientists are still skeptical of citizen science (wrongly!) Second, many citizen scientists worry that they need to achieve a level of accuracy that would require near-pixel levels of zooming. We approach both of these issues with consensus classification – namely, that every image is seen by 15 people as soon as it’s noted that it has kelp in it. We can then build up a picture of kelp forests where, for each pixel, we note how many users select it as, indeed having kelp. You can read an initial entry about this here.

So, how does this pan out in the data I posted a few days back? Let’s explore, and I’ll link to code in our github repo for any who want to play along at home if you’re using R – I’d love to see things generated in other platforms!

The data is a series of spatial polygons, each one representing one level of consensus. After loading the data we can look at a single subject to see what consensus does.

I love this, as you can see both at the 1 threshold at least one person was super generous in selecting kelp. However, at the 10 threshold (unclear why we’re maxing at 10 here – likely nothing was higher!) super picky classifiers end up conflicting with each other so it looks like there’s no kelp here.

How does this play out over the entire coast? Let’s take a look with some animations. First, the big kahuna – the whole coast! Here are all of the classifications from 2008-2012 overlapping (I’ll cover timeseries another time).

I love this, because you can really see how crazy things are at a single user, but then they tamp down very fast. You can also see, given that we have the whole coastline, how, well, coastal kelp is! Relative to the entire state, the polygons are not very large. It’s a bit hard to see.

Let’s look at the coastline north of San Francisco Bay, from Tomales to roughly Point Arena.

Definitely clearer. You can also see we accidentally served up some lake photos, and folk probably circled plankton blooms. Oops! Now the question becomes, what is the right upper threshold? Time (and some ongoing analysis which is suggesting somewhere between 6-8) will tell!

If you have ideas for other visualizations you want to see, queries for the data that you want us to make, or more, let us know in the comments! If you want to see some other visualizations we’ve been whipping up, see here!