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Macrofauna? Meiofauna?

Macrofaunal montage by Brian Paavo

Polychaetes are major movers and shakers in the world ocean from above the high tide line to the deepest trenches, but they're not alone down there!  Animals (fauna) living on (epifauna) or in (infauna) the seafloor are benthic ('bottom living').  If they are large enough to be collected on a sieve with 0.3 mm wide holes or larger, they are often called macrofauna.  Smaller animals, usually living between individual grains of sand, are often called meiofauna.


Every phylum of animal is represented somewhere in the benthos, but macrofauna samples are usually dominated by annelids, arthropods, molluscs, and echinoderms.  Although this is kind of an arbitrary way to divide up the animals living on the seafloor it turns out that the basic physics (and biology) of being small or large means that the animals have to deal with very different selective pressures so they have evolved to respond to conditions in often very different ways. Meiofauna samples are often dominated by nematodes, arthropods, annelids, and a whole bunch of really wacky animals including tardigrades (water-bears), mud-dragons (kinorhynchs), and many more!


In my toy box

Worm Gear! Get it?Toys!  My garage and lab is full of them and I want more!  It's a fact, playing with toys stimulates your brain.  My favourite toys also happen to be tools for benthic research.  In the wise words of Adam Savage 'The difference between science and screwing around is writing it down.'  Some research tools are as basic as a kitchen collander and turkey baster, which means you can do benthic research in your classroom or local beach, while others are high-end pieces of specialised equipment with frickin' laser beams. 


The Essentials: Buckets, Sieves, and Forceps

Some of the first animals described by Carl Linnaeus, creator of the binomial system of biological nomenclature, in the 18th century were polychaetes.  I find it amazing that here in the 21st century we can still walk into the intertidal zone or scrape up a fish net and  find new benthic species using the same basic tools.  A bucket to hold water in and slosh back and forth, a sieve (or series of them) to help separate the animals from the sand, and fine-tipped forceps to gently pick up critters and put them in small dishes where it is easier to observe them.  For the large animals, that's all that's required, but add a magnifying glass or a simple microscope and anyone can find animals they've never seen before in sand from a beach, inlet, estuary, river, or lake.

Endecott Sieves


The carefully regulated and certified Endecott sieves are the gold-standard among worm folk and I have several myself, but cheap and effective options exist from plastic sieves or bolting cloth right down to homemade window screens and kitchen collanders.  Most soft sediments are made up grains of different sizes.  You can put sediments through a nested series of sieves to find out how much of each size it contains, their grainsize distribution.  Knowing that can help scientists estimate what kind of conditions the benthic animals live in, especially water motion (hydrodynamics).  Some animals can only tolerate to live in areas with certain kinds of grains present.  Pectinarids, commonly known as ice-cream cone worms, make their tubes by sticking sand grains together like bricks.  They can't make their homes if they don't have the right kind of sand grains around!


ForcepsA selection of forceps from blunt to needle-fine are needed for carefully picking and manipulating animals.  If you have to dissect a worm, sharp scalpels or the very fine scissors surgeons use for eye surgery are useful.  Some of the most useful worm tools aren't pricey though.  Insect pins (size '0', '00', and  '000') tick into the end of a chopstick are incredibly handy.  Microangela taught me how to use (washed) eyelashes glued onto the ends of sticks to move REALLY small animals around for scanning electron microscopy (SEM)!


Ponar Grab

Ponar GrabThere are many different ways to grab sediments from the seafloor. One way is to SCUBA dive down and grab them myself. I have fun with projects where I get to do that, but we can only dive to shallow depths (about 30 m) and it is very time consuming and expensive. Most of the time we collect sediments from a boat.  There are dozens of kinds of grabs (or dredges) out there. The kind of grab I use on a project depends upon the size of the boat I have, the size of the sample I need, how deep the water is, how soft the seafloor is, and whether or not it's OK for the sample to be disturbed when I get it.


One of my grabs is a standard ponar grab.  The jaws are held open by a pin that usually pops open when it is deployed to the seafloor.  The jaws close when we haul it back to the boat.  We use a winch to haul it because it can weigh up to 30 kg when it's full of mud and water.   It's still hard work, but we try to make a game of it and compete for the best number of successful grabs.



AirliftSometimes animals live deep down in the sediment (infauna) or they're too 'rare' (only a few per square metre on the seafloor) to be collected by grabs.  Then I go hunting for them!  Sometimes I pick a spot randomly or according to pre-defined rules and sometimesI look for specific burrows or other signs.  Then I use an airlift to quickly suck up the sand through a pipe higher up and pass it through a sieve while still underwater.  I made an airlift to suck Otago, New Zealand Mantis Shrimpmantis shrimp out of their burrows.  It's called an airlift because the energy creating the suction comes from air.  I stream a lot of little bubbles (like an aquarium airstone) into the bottom of the pipe from a SCUBA cylinder.  Because the bubble-filled water in the pipe is less dense than the seawater around it, the seawater pushes into the bottom of the pipe taking sand, animals, and sometimes your fingers along with it.   


Sonar (single-beam and sidescan)

Usually when I want to study a place, an animal, a community, or a process I want to take a look at it first!  That seems natural right?  Terrestrial, land-based, scientists can usually just visit the site, walk or drive around it and get a lot of information through their eyes.  Where are the ridges, valleys, burrows, where does the sun shine brightest or longest, where does the wind most often blow from, where are good places for different animals and plants to live, etc.  They're lucky!  Most of the time we can't see very far underwater, usually a few 10s of metres at most and sometimes much less than that.  So we use the same trick dolphins (and some other animals too!) use.  We project sound into the water through a transducer and then gather information about the habitat from analysis of the sound that bounces back to us.


For my projects I usually use two kinds of sonar.  Whenever I"m on the water in a boat I use Single-beam sonar to find out how deep the water is. By mapping each depth reading with a GPS, and then subtracting the tide and waves from my data, I gradually build up a map of the seafloor.  When you're in a room with lots of hard surfaces (like a gym) and your clap your hands, you hear sharp echoes.  When you clap your hands in a room with soft surfaces (like a movie theatre) you hear very soft echoes.  In the same way my sonar changes the returning sound into a graph on the screen and I can see if the echoes indicate that I'm over hard, rocky bottoms, or soft-muddy or sandy ones.  Multibeam sonar systems, usually on larger research ships, use a lot of individual sonar units to map a wide area at once. I don't have one of these in my garage...yet.


Sidescan imageSometimes I use sonar like a searchlight, twisting it around to look at different angles from the boat.  My favourite kind of sonar has two transducers in a little-torpedo shaped container, called a fish, that I tow very near the seafloor.  It's called sidescan sonar because it 'looks' sideways.  Low frequency sidescan sonar (around 100 kHz) is useful for images over a big area (100s of m), but with very poor resolution.  Low frequency sonar is good for studying big underwater canyons and such.  High-frequency sonar can only look at small areas of the seafloor (10s of m), but with very good detail. When I analyse the echoes and shadows and put them together using my GPS positions, I can make a rough map of the seafloor!  In some ways the sonar picture is better than a camera picture, because I can examine the echoes and see what the seafloor and objects are made of.  Sometimes you can even 'see' through soft layers of mud and look at what's underneath.


Triops and other Underwater Cameras

Burrows in sandy environmentWhile sonar helps me look at big areas of habitat at once, I often have to look at the bottom carefully with underwater video systems I've built towed or dropped from a boat.  When I see something important I snap a higher-resolution picture with one of the on-board digital cameras.  If a picture is worth a thousand words imagine how useful 500 pictures is!  I look at hundreds of pictures of a site and write down information about whether it's sandy, muddy, or rocky.  I look at what kinds of animals I see, or what kinds of burrows there are which lets me know what's living in the sand. In the picture at left, the white scale bar is 100 mm long, the bright red dot is one part of a laser beam system to help me measure things in the pictures.  I then condense all of my notes into a map on a geographic information system (GIS), a map-making application.  Sometimes I  record videos as I swim along identifying and counting fish, algae, corals, or other large invertebrates. 


QuadratPhotoquadrats are frames that hold cameras steady and flat over seabed of a known area.  That makes it easier to count algae, seagrass, animals, burrows, etc.  Worms and most other benthic animals are too small to be seen in photos, but the photos provide useful information about their habitat.  When I collect macrofauna or meiofauna using corers, I often take photos with a quadrat as well.  It's easy when walking in the intertidal zone, but it can be tricky managing it all underwater while diving!



SPIScan ImageWhen I'm trying to understand how animals live IN the sediment it's often not enough to see the surface of the seabed.  I need to peak under the covers and look into the macrofaunal burrows.  In the late 1970s two scientists called Rhoades and Germano took some of the first pictures of slices into the seabed.  Their equipment is very useful, but it also tends to be very big and expensive so I had to invent my kind of sediment profile imager (SPI).  I wrote a Wikipedia article about it here.  A SPI device slices into the seafloor and takes a sideways picture so we can see the water, the surface of the seabed, the burrows animals make, and sometimes animals, bacterial colonies, fungi, and other organisms themselves.



Simon at Dissecting MicroscopeI LOVE microscopes!  And there are so many kinds!  I have binocular dissecting microscopes which are useful for picking animals out of sand, assembling small circuit boards, and watching live animals move around.  I also have a binocular compound microscope.  I have to put animals onto a slide or a VERY small dish (a depression slide) in order to see them using a compound microscope, but with it I can magnify animals about 100x (though usually 5, 10, 20, or 40x is enough) and see details all the way down to the cellular level.  It's called a compound microscope because it has several lenses, each magnifying the image from the one in front of it. 



BioTally SetupCounting thousands of the animals for each project can take a lot of time if you have to pick up a pencil or look up at a computer screen and type on a keyboard.  To help myself and other scientists we combined a very cool computer gaming pad which allows you to make your own keyboard, with some new software.  The software allows you to choose animals from a database with names, pictures, scientific papers, and biological relationships and assign them to each key.  Clicking on of the keys each time you find that animals makes counting go faster and since data are automatically entered into a database, there are no additional places to make typing mistakes and exporting the data to statistics programmes is much faster and easier.  This isn't the most complex toy in my toy box, but it is one of my very favourites as it lets me spend more of my time on the fun parts of the science. 


ROV - Remotely Operated Vehicle

Oh I wish!  I used to have a couple of these in my toy box, and I've played with several others, but sadly I don't have one of my own...yet.  It has never been cheaper or easier to build one of your own either.  My favourite observation-class mini-ROV is produced by VideoRay.  They're tough, portable, and have enough power and good design to handle themselves and their umbilical cords in realistic coastal conditions.  Most larger ROV systems are built to specific requirements for their science mission or the size of the support vessel they are launched from.  Small, inexpensive cameras, and simple, open-source electronic packages like Arduino means that people can make ROVs small enough for their swimming pools and fish tanks!   The most expensive part is often the umbilical cord providing electricity and communications with the people on the ship.  It can cost $1000s for even a short ROV cable (50m) and most science ROVs have tethers a kilometre or more long!



On my bookshelf

A lot!  My dream home is pretty much a hobbit-hole with wall-to-wall bookshelves attached to a greenhouse on the ocean, but these are just a few of my wormy favourites that I use regularly from serious research to bedtime stories.

Gary Larson Book Cover"There's a Hair in my Dirt!" by Gary Larson, Forward by E.O. Wilson


I love the Lorax and all things Seussy, but this is far-and-away my favourite bedtime story for anyone aged 4-122.  We are shown the dangers of anthropomorphising animals and animal behaviours as told by a family of oligochaetes sitting down to dinner while appreciating the real mysteries of the forest.  This treat is a feat of educational self-contradiction that only Gary Larson can pull off and I think every organismal biologist, ecologist, teacher, parent, or guy-who-wants-to-be-liked-at-late-night-parties should have on his shelf.   Thank you to the fabulous Kjristi for giving me this awesome book.  I've read it to hundreds of people and I've not yet found one who didn't laugh and learn something at the same time.


Polychaetes by Rouse and Pleijel "Polychaetes" by Greg Rouse and Fredrik Pleijel


When it arrived at my door and I eagerly tore open the packaging my girlfriend asked "Is that really an entire book just about worms?"  Oh yeah.  It is still the first book my students, employees, and I reach for when we want an overview for a particular family of polychaetes.  Besides being an excellent reference, Greg and Fred included a bunch of their beautiful and informative worm photos (wormguys and wormladies eagerly await their calendar produced once every three years).  Every university library and marine field station should have a copy.


Polychaetes and Allies: A Southern Synthesis Book Cover"Polychaetes and Allies: A Southern Synthesis" by Beesley, Ross, and Glasby


When we put morphology and genetics together we learn a lot about polychaete evolution and their relationships with other animals long thought to represent very different groups.  Are sipunculans really polychaetes? What are oligochaetes?  What about spoonworms (echiurans)?  The Southern Synthesis, besides having a most bitchin' Aussie worm shot on the cover, is an immensely useful volume about annelids and kin in general while proving especially helpful for Australia and New Zealand.  Also a must have for any marine research library.


Book cover of Polychaetes of the Santa Maria Basin "Taxonomic Atlas of the Santa Maria Basin and Western Santa Barbara Channel (4 parts)" by Blake and Hilbig (eds) 


With a mundanely informative title and unassuming soft-bindings this set of books is an excellent example of a working atlas which is hugely useful for US West coast workers, but also concentrates taxonomic information valuable to the rest of the globe in the same way that Day did for South Africa.  Speaking of the West Coast, hats off to many of the contributors working together in the impressively collegial and practical SCAMIT organisation!


Book Cover NZ Coastal Marine Invertebrates "New Zealand Coastal Marine Invertebrates" by Steven de C. Cook (ed)


We waited, and waited, and waited, but when this book hit the shelves was it worth the wait.  The first of two volumes, this is the first appreciably expansive compilation of critters you might see in the coastal benthos of New Zealand. 


Book Cover NZ Inventory of Biodiversity"New Zealand Biodiversity Inventory" (Volume 1) by Dennis P. Gordon


Dennis worked hard and long to put together this amazing set of books.  One might reasonably expect an inventory to be a dry collection of lists which are useful, but as appetising as Weet-bix without milk.  This book is anything but.  A marvelously concise, well-researched, and attractively illustrated synthesis of each group worthy of inclusion in a book of their own leads each chapter.  These books are always within reach when I'm at my microscope or writing a report. (And I'm not saying that just because I'm included in Volume 2!)


 Polychaetes CDROM cover"Polychaetes: an Interactive Identification Guide (CD-ROM)"


It's starting to show its age and it wasn't perfect to begin with, but that doesn't detract from the fact that this CD should probably be your first acquisition when you are faced with a polychaete you haven't seen before or are training new polychaete folks.  The guide uses the DELTA database system to help workers examine specimens with the characters they can observe much more easily than a fixed dichotomous key can.  Though it varies from family to family, a high standard of informative character state illustrations is a major accomplishment.  Except for that one time I watched 'Ferris Buehler's Day Off' I don't think I've removed this CD from one of my lab computers since 2004. 


Worms Game CoverWorms, the computer game  (All Volumes)  by Team17


The fine folks at TEAM17 have produced an addictive series of computer games where one team of worms attempts to destroy the other with a variety of wacky weapons. I highly recommend trying one of the early games before graduating to 'Worms 3D' or later. Games can be played solo or head-to-head over LAN.  I've found 'Worms: World Party' a marvelous way to relax after dealing with Prionospio all day, and have reached the rank of Superstar in deathmatch much to the detriment of some manuscripts.


Book Cover Ecology of Marine Sediments "Ecology of Marine Sediments" by Gray & Elliot


An excellent introduction to thinking about the seafloor the way it really works, synthetically.  This book treats subjects from basic sampling methodologies to management strategies. 


Book Cover Primer of EcologyBook Cover Primer Ecological Statistics "A Primer of Ecological Statistics" and "A Primer of Ecology" by Gotelli & Ellison


Need a reminder about stats while you're writing that report?  Teaching an ecology lab?  Handy, understandable, concise books that treat some of the main concepts and procedures of ecology.