PlanktonPlanet

innovative citizen sailing oceanography

Just discovered this, after reading the Tara Expedition news periodical while visiting Tara in Miami! This is a very interesting Citizen Science project inspired from the Tara Expeditions. The idea is to “recruit” the help of volunteer sailors across the world and have them collect plankton using a very simple method of sample preservation. The sample is then sent to a lab for DNA barcoding to look at the different species present in the sample. A very elegant way to do oceanography.

 

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go visit:  www.planktonplanet.org

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Happy anniversary Plankton Portal 2.0!

Blog post by Jean-Olivier Irisson

A year ago, we announced Plankton Portal 2.0, which featured a more streamlined design, a simpler tagging interface, and most importantly, a whole new dataset. Since then, this new data from the Mediterranean Sea has spurred a lot of interest and plenty of new questions. Participants on the site were surprised by the difference in size of everyone’s favourite jellies, the Solmarisidae (Solmaris rhodoloma in California, Solmissus albescens in the Med), which are much larger! Siphonophores also seem more abundant there. And the Mediterraean data came with brand new categories of organisms to mark: nice and cute medusa ephyrae (i.e. baby jellies), elegant Pteropods and the elusive fish larvae.
In total, as of last Sunday, 368,361 organisms were marked, on 50,519 distinct images. Through time, the classifications were marked by two peaks in activity: a huge one when the new version was announced through a mailing to the Zooniverse community (thanks everyone!) and another one when we pushed for 1,000,000 classifications in total, to celebrate Jessica’s PhD defense. When we zoom in, we see activity fluctuating around 1000 and now 500 classifications per day. This is still great (but coming back to 1000 would be even better! 😉 ).
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The top 11 contributors, all authors of over 5000 classifications each, are displayed below. If you made this top 11, we owe you special thanks (and probably a beer too). We hope you will stay interested and involved in this project. If you did not, you should really not be disappointed because all other volunteers still collectively account for 60% of the classifications; so you matter very much! Hopefully all of you will be happy to see some of the outcome of your work below.
who

 

Time for a bit of science! The most common classification was… nothing, empty, zero, zlich, zip… Well, you get the idea. Indeed, when we film the sea, we most often see nothing (nothing living at least). Even though we pre-selected potentially interesting frames for Plankton Portal (the ones having some kind of large object in them), about a third of your classifications did not contain any organism we were interested in. In real life, the proportion of dead detritus vs. living organisms is more around 95% vs. 5%, so our pre-filtering still avoided you a lot of blank frames! In terms of organisms, the 10 most abundant are shown in the figure below.

what

 

Doliolids, Copepods, and Radiolarian colonies dominate the rest. We immediately noticed, when we shot the images, that Doliolids were particularly abundant. Those organisms are very effective filtering machines and they may therefore have an impact on the density of smaller organisms, in particular unicellular algae. The relative abundance of Copepods and Radiolarian colonies is to be interpreted carefully: Radiolarian colonies can be large and span several frames (therefore increasing the total count) and Copepods are likely under-estimated because we mostly see the larger ones with ISIIS, and they are not the dominant ones in the Mediterranean. Still, it echoes nicely a recent Nature paper by Tristan Biard (a contributor to PlanktonPortal’s talk, under the username Collodaria), which showed that Rhizaria (a large taxonomic group to which Radiolarians belong) can be equivalent in biomass to Copepods, who were previously thought to largely dominate the plankton. These findings were also based on in situ images, because these fragile Rhizaria cannot be collected with nets.

 

Finally, the images in the Mediterranean were collected along transects (i.e. straight lines) perpendicular to the shore. We were interested in how organisms were distributed along a gradient between coastal and open ocean conditions. In the plots below, the coast is on the left, the open ocean on the right and the vertical direction is depth (top: surface; bottom: 100 m depth). So you basically see a “slice” of water along which ISIIS undulated. The size of the dots is proportional to the number of classifications recorded. You can immediately notice that Doliolids (first plot) are concentrated near the surface, and fish larvae (second plot) even more so! This is a surprising finding for fish larvae, which sometimes ended up in concentrations of over 10  individuals per cubic meter, a number much higher than what was previously observed elsewhere, with conventional plankton nets.
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Radiolarian colonies, on the opposite, tend to be concentrated in mid water (see figure below). Within this messy picture, some structure seems to emerge. Indeed, the white lines on top of the plot are contours of the concentration of Chlorophyll A in the water (i.e. of the amount of unicellular algae). If you look carefully, you will see that those lines are moving up, towards the surface, as we travel offshore (from left to right on the plot). This is actually well known in this region. What is interesting is that the radiolarians seem so follow the same pattern, and that higher concentrations of colonies sit on top of this high Chlorophyll region. Something is definitely going on between these two!
distrib_radiolarian_colonies_w_icon
That’s it for now — thanks again to everyone for this wonderful year of activity! We apologise for not being as active as we would like to be on Talk. To that end, we thank the active moderators who take over this important responsibility. And finally, we thank Zooniverse for the great opportunity and community they created. Now, on to next year!

1 million classifications!

Last week, Jean-Olivier and Zuzana organized a push to one million (1,000,000) classifications here at Plankton Portal in honor of my defending my PhD on Friday, October 30, 2015.

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Title slide for Jessica’s defense seminar

The PhD defense at the University of Miami essentially consists of a 1-hour public seminar on my dissertation research, which I had conducted over the last five+ years, and then a multi-hour private question-and-answer session with my  committee. In my case, my committee consisted of my advisor, Dr. Robert K. Cowen, and four other professors, Drs. Su Sponaugle, Gary Hitchcock, Rob Condon, and Jean-Olivier Irission. At the end of the private session, if the work and the answers to the questions were deemed satisfactory, then the student passes and essentially is this granted a doctorate.

So I have two happy news: 1) My PhD defense was successful – all went well! and 2) We did it! Plankton Portal reached one million classifications by the time I defended!

PP_1million

The above photo shows Professor Cowen, me (Jessica), and Cedric Guigand with ISIIS (the instrument that collects all the cool images in Plankton Portal!) on board the R/V Walton Smith on a cruise in the Florida Keys this past summer. We had taken it in anticipation of a Plankton Portal classification milestone; little did I know that it would be in conjunction with my PhD milestone!

In my PhD, I looked at gelatinous zooplankton (jellies) in marine ecosystems from three contexts: in aggregations at fronts (that’s the California current dataset on Plankton Portal!), as predators of other plankton in driving vertical migrations, and as contributors to the global carbon cycle. For the first two parts (“chapters”), I focused on small jellies, and studied them using ISIIS, and for the last chapter, I conducted a modeling study on all jellies (medusas, comb jellies, and salps/pelagic tunicates) over the global oceans. It’s been a really educational process for me, learning about jellies, imaging systems, modeling, and overall, how to do science. I’ve been able to publish one of my dissertation chapters already, and look forward to publishing the rest over the next six months. Grad school has also been a really fun opportunity for me to get out in the field (on five research cruises), go to conferences all around the world (Japan, Spain, Hawaii), help run citizen science projects like Plankton Portal, and just overall meet some incredible people who do fascinating work. It’s been a total privilege, one that I haven’t taken lightly. And I look forward with anticipation to the journey to come. Onwards and upwards!

Announcing Plankton Portal 2.0!

There is a new dataset on PlanktonPortal!

In summer 2013, a group from the original science team behind PlanktonPortal (Bob Cowen, Cédric Guigand, and Jessica Luo) teamed up with French colleagues (Jean-Olivier Irisson, Robin Faillettaz and other members of the Laboratoire d’Océanographie de Villefranche) through a Partner University Fund-sponsored project. We roamed the Mediterranean sea, equipped with ISIIS, the instrument which takes the images seen on PlanktonPortal, and a collection of other sensors. Our aim was to understand how physical discontinuities in the ocean (such as the strong coastal current along the French Riviera) influence the plankton. These discontinuities often create conditions in which plankton thrives and this has important consequences down the rest of the food chain.

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Bob, and Jean-Olivier (in the background), ready to load ISIIS on the Tethys II oceanographic ship in Nice’s harbour

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Cédric setting his baby up with the crew of the NO Tethys II

After a rocky start (see our project blog), we eventually managed to get almost five full days of sampling. Five days; it seems short. And ISIIS was actually acquiring data of scientific interest during only 93 h within those five days. That is 3.8 full days, which seems even shorter. But that amounts to about 17.5TB of data (terabytes, as in 1024 gigabytes). In terms of images, that represents 19 trillion pixels, which could be divided into 34 million PlanktonPortal frames. So, clearly, we need your help!

We actually spent much of the last two years processing the images and classifying organisms in a small fraction of them, to be able to filter out most frames with no organisms using computer algorithms. Now we are ready. Ready with a few hundred thousands frames from the last two days of the cruise that no one has seen before and in which you can help us identify plankton.

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ISIIS in font of a Mediterranean sunset

Tree Map update and budding siphonophores

Thanks everyone for your phenomenal response to the treemap that I posted for the 300,000 classifications post. It’s really neat to be able to see how different users have classified more, or less over time. Of course, if you are one of the top classifiers, it’s fun to see your name up there!

At the suggestion of Lee Henderson, MD (wow! cool to see people from all professions and walks of life on Plankton Portal), I made an updated treemap with classifications from the past month. If there’s interest in periodic updates in this manner, let me know in the comments and I can post one of these up every couple weeks. But I don’t want to make it too much of a competition. Actually, it probably is a giant competition. So compete away!

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Top 10 classifiers from the past month:
1. yshish
2. AnnaThema
3. phf13
4. Siiw
5. aplincoln
6. scopedriver
7. RachaelB
8. kredman
9. isadora paradijsvogel
10. ssushi

Thanks everyone!

 

On another note, our star moderator yshish emailed me today with a few questions about some cool siphonophores she found on PP. (side note: yshish has the BEST image collections on Talk. I regularly will be able to find specific images or taxa that I’m looking for by going through her collections.) Anyway, check out this series of images:


http://talk.planktonportal.org/#/subjects/APK00064cn 51d1bee33ae74008a405a4db

http://talk.planktonportal.org/#/subjects/APK0003nz4 51d1be363ae74008a4033c72 http://talk.planktonportal.org/#/subjects/APK0003xhv 51d1be3f3ae74008a40382ff

You might remember that we featured the top image in a previous Fantastic Finds Friday (FFF) post. Now we bring it back because of the other two images that were found (the last one found 1 hr ago). These images found three months apart might be the same organism but in neighboring frames. We can’t tell right away, but once we go back into the raw data, we will be able to pull out the locations and times of these three images to check.

Now, the interesting question posed here is — is this siphonophore budding? Are these siphonophores asexually reproducing as we imaged it? And the answer — yes! absolutely! (I addressed this question earlier in a Talk post but now’s the time to feature it in the blogs!) All the little round bells that you see on the tentacles are small siphonophores developing from the gonozooids (reproductive ‘organs’) that will eventually be released and form free-swimming “eudoxids.” When they are released, these eudoxids will develop and then be capable of sexual reproduction. Weird, right? But wait, there’s more.

These eudoxids then develop little reproductive organs along its stem. Instead of eudoxids functionally male or female, they actually develop male and female reproductive parts – eggs and sperm – alternating between the two, sometimes regularly, sometimes irregularly. That way, they can ensure that the eggs are fertilized and can develop into larvae, then post-larvae, then adults.

The open ocean is a vast place, and animals have developed vastly different strategies for how to ensure the continuation of their species, whether it is in spawning aggregations (e.g. Grouper fish spawning in the Caribbean – and larvaceans also apparently form spawning aggregations) or being hermaphroditic (like Ctenophores and some fish), and being able to asexually bud and reproduce sexually. These siphonophores have adopted the strategy of being both hermaphroditic AND able to reproduce sexually and asexually.

This is the best diagram I’ve found to describe the life history of a Calycophoran siphonophore (all of the ‘rocketship’ and ‘two-cup’ siphonophores). This one is from C. Carre and D. Carre (1991).

siphonophore_lifehistory1

300,000! THANK YOU!

Whoa! We reached 300,000 classifications today! I saw the classification number creep up there earlier this week but didn’t get a chance to write a blog post about pushing the classifications up to 300,000. But YOU DID IT!

Who are the folks who made 300,000 classifications? To explain this we made a treemap to show the number of classifications that each person has made. We borrowed this idea from Margaret Kosmala of Snapshot Serengeti and Philip Brohan of Old Weather, who have created similar graphics for their projects.

In this graphic, each box represents one user, except for the users who were not logged in (those were all grouped together). We have over 2600 registered users on this site! And the size of the box reflects the number of classifications. Can you find yourself in this graphic?Usertreemap

What you’ll see here is that unlike some other projects (e.g. Snapshot Serengeti), our top 2-3 classifiers have done many more classifications than all the non-logged-in users combined! It’s interesting to us — because while Plankton might not have a very broad appeal to the general public, there are some people — YOU — who love this project so much that they dedicate a lot of time to it. You help carry this project along, and in the process, you become our ambassadors to your schools, communities, and cities. It’s quite amazing.

To that end, I’d like to thank our top 10 citizen scientists:

1. yshish *
2. elizabeth *
3. Siiw *
4. CindyLou
5. phf13
6. lynb
7. charcinders
8. VBear
9. mlmuniz
10. starburst42

Our next 10 top classifiers are: Ingolme, Valraukar, Jurel, KarenLK, cnorvalk, lekape, scopedriver, SandersClan, Rebecca_W, and localwormguy. Those whose names are marked with an asterisk (*) also help moderate the discussion boards – give a round of applause to them!

For our top classifiers and everyone who has participated in Plankton Portal, we thank you! Our friendly mascot, Solmaris, is offering free hugs:

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We hope that you all have enjoyed your time on this site – we have certainly enjoyed interacting with all of you on the discussion boards! It’s been very fun getting people all around the world involved in this project. Here’s to 300,000 more!

 

P.S. Also a huge congratulations to Zooniverse for being awarded a $1.8 million Google Global Impacts Award!

From the citizen scientists: #FFF

This week, we asked one of our top volunteers, Zuzana, a very lovely lady from the Czech Republic, to pick her favorite images for a special Fantastic Finds Friday (FFF) post. She went way above and beyond — did research on her own, wrote up information and background — and we are very pleased to present to you this week’s #FFF post.


Hello everyone. My name is Zuzana, also known as the user Yshish. I was asked by Jessica of the scientist team to put together my favorite pictures from this amazing Plankton Portal and write a short FFF post about them. So here they are:

*The first of my most favorite finds for the last week is definitely this beauty – Aegina citrea.

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[http://talk.planktonportal.org/#/subjects/APK0006f6z]

This image of Aegina citrea was captured at a depth of 43.42 m and at temperature of 13.55°C.

Aegina citrea

Aegina is one of the jellyfish belonging to the Narcomedusae Order, like its more familiar relative Solmaris.

Members of this order do not normally have a polyp stage. The medusa has a dome-shaped bell with thin sides. The tentacles are attached above the lobed margin of the bell with a gastric pouch typically found above each. There are no bulbs on the tentacles and no radial canals. Narcomedusa are mostly inhabitants of the open ocean and deep waters.

A. citrea is a very rare species in the Plankton Portal images but if you were lucky to get an image with it, mark it as a 4tentacles medusa and start a discussion with using #Aegina tag.

An additional note: Narcomedusa ‘babies’ are very interesting, and act as parasites on other jellies after exiting the mother! Check out this link:

CreatureCast – Narcomedusae from Casey Dunn.

* The second find I chose for this post is my favorite species: ‘Thalasso’ – Thalassocalyce inconstans.

ysh_thalasso

This is a compilation of three separate Plankton Portal images. The Thalasso on the top right was caught while feeding! You can see him opening his ‘mouth’ widely to catch something tasty in the water!

Thalassocalyce inconstans, which we have nicknamed ‘thalasso’ on the Portal, belongs to the phylum Ctenophora – the comb jellies. The Order Thalassocalycida contains only one known species first described in 1978 [Madin and Harbison 1978]. They are closely related to the other ctenophore Orders such as Lobata, Cydippida and Cestidae.

They have an extremely fragile body that can reach 15 cm in width and is shortened in the oral-aboral direction. Thalassocalyce have short comb-rows on the surface furthest from the mouth, originating from near the aboral pole. They capture prey by movements of the bell as you can see in the pictures.

To me they look like an opened umbrella with a beautiful distinct linear drawing engraved on it. Their look is simply beautiful!

Also I can’t forget to mention that I’m fascinated by their bioluminescent abilities. The wavelength of the emitted light from Thalassocalyce is 491 nm (SHD Haddock & JF Case 1999).

* The third fantastic find is this beautiful ‘Corncob Sipho’ – Physonect siphonophore – Forskalia genus.

51d1bdbb3ae74008a401f2ed[http://talk.planktonportal.org/#/subjects/APK00029a8]

Physonect siphonophore

The Siphonophores are an order of the Hydrozoa, a class of marine invertebrates belonging to the phylum Cnidaria which include coral and ‘jellyfish.’ Although a siphonophore appears to be a single organism, each specimen is actually a colony composed of many individual animals. Most colonies are long, thin, transparent organisms that float in the open ocean.

All of the zooids of a physonect colony are arranged on a long stem. This stem has a gas filled float known as a pneumatophore at one end. That’s the funny ‘nose’ we are used to seeing and are typical of the Physonectae family of siphonophores.

Just behind the pneumatophore are the nectophores. These are powerful medusae specialized for moving the colony through the water. They contract in coordination, propelling the entire colony forward, backwards, and in turns. The region of the colony containing the nectophores is called the nectosome.

Just behind the nectosome is the siphosome, which has all of the remaining zooids of the colony. These include feeding polyps capture food with their single, long tentacle, providing nourishment for the entire colony. [http://www.siphonophores.org/SiphPlan.php]
Siphonophores catch prey by putting out their long tentacles and waiting for something to bump into them.

Here is a nice schematic of a physonect siphonophore which could help you understand these awesome creatures:

Physonect siphonophore diagram – Casey Dunn

* My fourth pick is another Siphonophore, this fascinating ‘Thimble Rocket-ship’ – one of the Sphaeronectes genera captured here in a stunning feeding display.

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[http://talk.planktonportal.org/#/subjects/APK0005o03]

You can see that he’s able to cover all the space around himself with his branching tail. It looks almost like a spiderweb to me. In this position he’s waiting for other plankton swimming around to catch and eat.

As I mentioned above, Sphaeronectes is a genus of the Siphonophorae order.

Most siphonophores capture their prey by trapping it with special side branches (termed tentilla) which originate from the tentacle of each gastrozooid. During feeding, the tentilla and the tentacles are extended into the water to form a large transparent net. The prey is first ensnared by the terminal filament and its entangling cnidae (stinging cells). The terminal filament then contracts, bringing the prey into the cnidoband, which contains many stinging cells. (Mackie and Marx 1988; Mackie 1999). [Siphonophora (Cnidaria: Hydrozoa) of Canadian Pacific Waters. Gillian M. Mapstone,Mary N. Arai]

* My final favorite find is this fish – probably a Clupeid (Herring)

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[http://talk.planktonportal.org/#/subjects/APK0004ajk]

Clupeidae is the family of the herrings, shads, sardines, hilsa and menhadens. It includes many of the most important food fishes in the world. Clupeids typically feed on plankton, and range from 2 to 75 centimetres in length. After hatching, the larvae are planktonic and live among other plankton until they metamorphose and grow into adults. The adults typically live in large shoals in the coastal oceans.

The larvae are 5 to 6 millimetres long at hatching and have a small yolk sac for nourishment that is absorbed by the time the larva reaches 10 millimetres. Only the eyes are well pigmented while it is a larva. The rest of the body is nearly transparent, virtually invisible under water and in natural lighting conditions.

The larvae are very slender and can easily be distinguished from all other young fish of their range by the location of the vent, which lies close to the base of the tail and is an opening for excretion of eggs and sperm. But distinguishing clupeids from other types of larval fish at this stage requires expertise and close examination. ISIIS images are of a high enough resolution to allow experts to determine the taxa of larval fish captured in the data!


I hope the article wasn’t too boring for you and that you have enjoyed reading it as much as I’ve enjoyed writing it. And do not forget, if you think you’ve found something really neat on the Portal use hashtag #FFF in the discussion boards. I can’t wait to see what else will be found next! Big thanks to Ben Grassian for the consultations!

-Zuzana

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Plankton Portal “en Français” (in french) coming soon!

plankton french

Artwork by Jean-Olivier Irisson

Great news! We are working on translating Plankton Portal in French with our
French Collaborators: Fabrice Not from the Station Biologique de Roscoff and Jean-Olivier Irisson from the Observatoire Océanologique and Station Zoologique de Villefranche-sur-mer. “The idea is also to get some interest from French schools to develop a curriculum around Plankton Portal” Dr. Irisson explains.  Stay Tuned.