I am on a ship 950 miles away from the nearest landmass. Here, in the middle of the equatorial Pacific Ocean, our team sends a remotely-operated vehicle 2.5 miles down to the flat abyssal plain. As deep-sea biologists, we get to see some pretty AH-MAZING sights and this time is no exception: an anemone-like animal with 8-foot tentacles that billow across the seafloor. This creature, Relicanthus sp., is so different from other anemones it was recently moved to a new order.

As incredible as seeing this tentacled beast was, I couldn’t help but feel a tinge of sadness. It’s difficult for a marine biologist working in an area that may be forever changed within the next two decades. As the demand for metals increases, humans are seeking resources in ever more remote places and the next frontier of mining will likely take place in the deep ocean.

So what are countries after 3 miles deep in the central Pacific Ocean? Potato-sized lumps of metallic ore laden with cobalt, copper, nickel and other rare metals known as polymetallic nodules. The Clarion-Clipperton Zone has the most valuable beds of these nodules that sit like cobbles on a street and form at a rate of a few millimeters per million years. As the Clarion-Clipperton Zone is in international waters, it falls under the mandate of the International Seabed Authority (ISA). So far, there have been 15 mining exploration areas allocated, each up to 75,000 km² or roughly the size of Panama.

Let’s be honest, nodule mining is going to do some damage. Nodules will be removed resulting in local extinctions of the many animals (corals, sponges, bryozoans, polychaetes, nematodes etc.) that call these nodules home and leaving no possibility for their re-establishment in the future. Machines, similar to combine harvesters, will disturb and compact large swathes of sediment, kicking up sediment plumes, which will travel for kilometers before depositing elsewhere. Further entombment of the seafloor will occur when tailings are discharged into the water column. Not to mention other possible impacts that include light and noise pollution from machinery, and major changes to the geochemistry of the sediment, food webs and carbon sequestration pathways. The cumulative impacts of these operations aren’t yet understood but will likely be long-standing and ocean-wide.

Despite this looming threat, the Clarion-Clipperton Zone is critically underexplored. We know little of what species live there. It is mandatory that contractors undertake baseline studies of the biology living at the seafloor before EIAs and mining can begin. The ABYSSLINE Project, which I work on, is doing just that in the easternmost claim area leased to UK Seabed Resources Ltd (UKSRL). My research is trying to find out what megafauna (the awesome charismatic animals over 2 cm in size) live in the UKSRL claim, how abundant and diverse they are, and what ranges they occupy, not only within the claim but also across the entire Clarion-Clipperton Zone. Over the last two years, ABYSSLINE scientists have spent over two months out in the middle of the Pacific Ocean sampling the seafloor with a menagerie of oceanographic equipment (plankton pumps, fish traps, a remotely-operated vehicle, an autonomous underwater vehicles, sleds, corers etc.).

Preliminary results show that the UKSRL claim area is rich not only in metals but also in life. The seabed, at a first glance, appeared to not have much living there. Taking a closer look, we realized that there were small animals everywhere: tiny white corals, pink and purple sea cucumbers, bright red shrimp and strange unicellular animals that create sedimented homes the size of your fist. On our first expedition, we sampled an area the size of Hong Kong (30 x 30 km) and found 170 tentative species of megafauna and that’s likely an underestimate! These levels of biodiversity are the highest in the Clarion-Clipperton Zone and are comparable to many other abyssal regions worldwide. We also collected 12 megafauna species and half of those were new to science, including some of the most commonly seen, reiterating how little we know of the abyssal life in this region.

The post Megafauna and Minerals on the Pacific Abyss first appeared on Deep Sea News.

The Notorious B.I.G., Mase, and Puff Daddy understand. Increase one variable in a system and another variable rises en suite. For the B.I.G. this was money and problems. It’s like the more money we come across. The more problems we see. In the biological realm, increasing the food available increases the number of species. More food, more species.

In the case of B.I.G., Mase, and Puff how more money becomes more problems is clear. The trio “rock” and “sell out in the stores” which leads to more money. Bag a money much longer than yours. This leads to more purchases. Gotta call me on the yacht. The success and belongings are coveted by others who try to bring the trio down in an effort to elevate themselves. Know you’d rather see me die than to see me fly. But scientists are much less clear about how mo’ food leads to mo’ species. Scientists have erected dozens of hypotheses to explain this rather simple pattern.   Enter a deep-sea experiment that I dedicated 10 years of my life to.

Mo’ individuals, mo’ species hypothesis

Wright posed the more individuals hypothesis. The basic ideas is that low food supports smaller populations of species; any species is likely to be represented by just a few individuals. This makes these species more susceptible to being wiped out locally by a catastrophic event like a storm or predator. If in low food environments species are often going locally extinct, exacerbated by their low population numbers, then these environments are likely possess far less species overall. Wright’s hypothesis is ultimately a no food, mo’ problems, no species hypothesis.

Nothing-special hypothesis

Tilman, in one of the most influential papers in ecology, proposed the resource-ratio hypothesis. To simplify his elegant idea, few species are biologically equipped to deal with any resource at low availability. Mo’ food, mo’ species that can occur. Tilman actually proposed that species in resource-limited areas were just subsets of those living in high-resource areas. This is because any species can benefit with a little mo’ food, but conversely not every species can live with a little less. Tillman took these ideas a step further and actually predicted that at very high food availability the number of species should decrease because another resource would become limiting, i.e. high food habitats are not some beautiful utopia where everything, e.g. habitat space or other nutrients, is abundant.

The diva species/unique and special snowflake hypothesis

Of course this is not the real name of the hypothesis (none of the headings are). Several ecologists have converged on the idea that mo’ food allows for more specialized species. These diva species are very particular in their food type requirements. At low overall food availability, these specific food types are rare and cannot support a diva species. To restate, mo’ food allows species to be specialized. No food and species need to be generalists and take what they can get.

Mo’ food, mo’ prey hypothesis

Another ideas is that mo’ food allows for mo’ prey. This in turns supports mo’ types of predators, thereby increasing diversity. A more sophisticated variant of this is that mo’ complex food webs, containing mo’ species, can occur at higher food availabilities.

Mo’ food, mo’ giants and miniatures

This is a hypothesis of my own creation. Basically, there is “right” size for a given animal to be. This optimal size reflects a balancing of constraints. For example, too big and a species requires too much food. Too small and species does not have enough fat reserves to weather starvation. This suggests that areas with little food would only possess species of this intermediate and optimal size. Mo’ food and these caloric constraints are released and and species can get away with not being an optimal size. Thus both large- and small-sized species are allowed increasing diversity

Tourist hypothesis

Chase proposed another hypothesis that is fundamental to the mo’ food, mo’ species pattern; this pattern can only exist when low and high food habitats are isolated. If migration by adults or larvae can occur from high food to low food, diversity will be artificially elevated in low-food habitats. These tourist species from high-food areas cannot sustain themselves in low-food areas without consistent visits of individuals from these high food areas. Cut the flow of tourists and the diversity of low-food habitats diminishes.

Wood fall, the experiment

Scientists have published lots of creative studies testing aspects of these ideas. However, studies are rare that experimentally alter the food supply to a habitat and observe what happens. It’s not obvious how nor is it easy to increase the amount food at a coral reef or tropical rain forest. Mesocosm experiments, in which scientists creates an artificial system like a miniature ocean in a beaker or aquarium, provide exciting opportunities. My friend and colleague, Allen Hurlburt, conducted once such experiment in which he manipulated the amount of banana in containers.  Fruit flies collected in the rainforest where then allowed to colonize. It remains a beautiful and elegant experiment demonstrating the importance of food in controlling diversity. Allen’s study served as the inspiration for the wood-fall experiment.

Wood falls are the perfect experimental system to test mo’ food, mo’ species hypotheses. Each of the dead pieces of wood on the deep-sea floor represent little food islands. The background and typical deep-sea, muddy bottom is a food desert. The species occurring on wood falls are ultimately dependent on only the wood for nutrition. By ultimately controlling the size of the wood fall, we can control the amount of food the community of species receives.

In 2005, Jim Barry and I chunked 32 Acacia log into the deep ocean off the Central California coast. In actuality, we placed them with an ROV at spot over 3 kilometers deep.

Then we waited.

Five years later we collected half of the wood falls. Two years after that we returned for the other half.

Ten years after initially deploying the wood falls, the main paper from this work is now available as preprint. The nearly decade this experiment took to realize actually results in part reflected the length of the experiment.  However, even once collected a considerable amount of effort was need.  In the last three years, I spent countless hours meticulously sorting all the animals, nearly 13,000 individuals, from the wood falls. Taxonomists, all coauthors on the paper, spent many hours identifying these to species. With the analyses taken over a year plus the writing of the manuscript…well it adds up.

Wood fall, the results

Thankfully, with increased wood-fall size, i.e. increased food, the number of species actually increased. Strikingly, no individual hypothesis was the smoking gun for this increase in diversity.

Rather the mo’ food, mo’ species relationship reflects a combination of routes. In accordance with the mo’ individuals, mo’ species hypothesis, the total number of individuals increased with wood fall size, and was concordant with rises in the number of species. As predicted by the nothing-special hypothesis, the species on smaller wood falls, i.e. food poor, were just subsets of those species occurring on larger wood falls, i.e. mo’ food.   Increasing wood-fall size also lead to increased rare species, supporting the diva species/unique and special snowflake hypothesis. Increased larval connections between small and large wood falls also seemed to ameliorate the mo’ food, mo’ species relationship in conjunction with the tourist hypothesis.

I am just finishing examining body sizes of all the wood-fall species, but interestingly my pet hypothesis about miniatures and giants does not seem to hold. The pattern is far more interesting. Thanks to the many who supported my crowdfund project (I still love that video), David Honig and I are beginning to construct the food web through stable isotope analyses.

Notorious B.I.G., Mase, and Puff Daddy lamented the rise of problems with more money. However, to all three of these artists the reasons why this occurred were pretty straightforward. Haters gonna hate. People gonna covet your yacht. The biological world is much more complex. As simple as mo’ food, mo’ species is, the reasons why this elegant pattern exists represents a variety of interacting processes, only some we are beginning to understand.

McClain, C., Barry, J., Eernisse, D., Horton, T., Judge, J., Kakui, K., Mah, C., & Warén, A. (2015). Multiple Processes Generate Productivity-Diversity Relationships in Experimental Wood-Fall Communities Ecology DOI: 10.1890/15-1669.1

The post More Food, More Species first appeared on Deep Sea News.

Everyone knows I despise charismatic megafauna (especially dolphins). I will now secretly admit that I also don’t care much for charismatic invertebrates. I mean, Yeti crabs are pretty much the Lindsay Lohan of marine creatures – they’re just too damn attention-seeking with their bristly claws and all. And they’re everywhere…

What I do love are cryptic species – nondescript, gooey specimens that all look the same, but have surprisingly distinct genomes. Candlelight and soul forever, I dream of myself and them together!

Looking at the DNA of microscopic animals is full of mystery and intrigue – it feels a bit like solving a crime (albeit a PG-13, Nancy Drew type of crime). Traditional taxonomy just doesn’t have that thill for me – it is slow and steady, requires hours under the microscope, and has an unsettling degree of subjectivity. DNA, on the other hand, is extremely objective – you can’t argue* with good data sequenced from a trustworthy spot in the genome. Those ATCGs just don’t lie.

But that doesn’t mean DNA is a magic bullet. DNA provides a new type of evidence for making decisions about species, but that evidence still has to be robustly analyzed and interpreted in the context of historical knowledge (taxonomic classifications and anatomical features of specimens).

A recent paper by Jörger et al. (2012) displays the power of DNA to differentiate amongst gelatinous blobs. The authors analyzed molecular evidence alongside body features to investigate sea slug species in the genus Pontohedyle, a group which taxonomists thought they had described LIKE A BOSS. Anatomy didn’t tell much of an exiting story – specimens could be lumped into two different groups based on appearance, and both these species were presumed to live pretty much anywhere in the ocean. [Sidenote: this is a pretty common assumption for microscopic animals and is known as the “meiofaunal paradox”. Victorian scientists would think “Oh, they all look the same, so lets describe these as the same species.” because they didn’t have any badass knowledge about DNA, and they didn’t have a time machine. But nowadays, this thinking is in direct conflict with our knowledge about these species–microscopic animals have been shown to have limited ability to move around, even during larval stages. They pretty much get stuck in the marine neighborhood where they grew up, so how can they spread their sweet DNA all around the world?]

The researchers started to look a little bit closer, baby, and study how sea slugs get it on, get it on. Because…

Uncovering putative cryptic lineages is fundamental not only for our advances in understanding speciation processes in meiofaunal taxa [microscopic multicellular animals <1mm long, such as nematodes, copepods, and tardigrades], but also to understanding historical biogeography.

Jörger et al. analyzed the sea slug DNA in every way they could think of. First off, they looked at the story from three different genes: Cytocrhome c Oxidase subunit 1 (the “barcoding” locus in the mitochondrial genome), 16S rRNA (a gene encoding a ribosome subunit in the mitochondria), and 28S rRNA (a ribosome subunit gene in the nuclear genome).

All three genes told the same story. The results of different data analysis methods were consistent. And wow, they sure threw all the data analysis acronyms they could think of at that DNA:

…we apply four independent methods of molecular based species delineation: General Mixed Yule Coalescent model (GMYC), statistical parsimony, Bayesian Species Delineation (BPP) and Automatic Barcode Gap Discovery (ABGD). The secondary species hypothesis (SSH) is gained by relying only on uncontradicted results of the different approaches (‘minimum consensus approach’).

In the end, 2 morphological species became 12 cryptic species (each color in the this tree below representing a different cryptic species):

The power of antatomical features was, er, not so powerful after all.

Previously used external morphological characters such as the shape of oral tentacles, body length and width, or color of the digestive gland (e.g., [68]) depend highly on the stage of contraction and nutrition, and are variable through time for each individual [40,41] and therefore inappropriate for species delineation.

The color of the digestive gland?! Really, guys?

So think about what this means for our understanding of biodiversity on earth. This is just one study, from one genus out of thousands in the taxonomic classification of animals (and there’s still a lot of microscopic critters we haven’t even described). Evidence like this comes out all the time. For example, a study focused on the nematode Pellioditis marina (a well known estuarine species living in Northern Europe) found that this “species” is actually a complex of at least 4 genetically distinct cryptic species. Just when we think we’re making good progress on taxonomy, DNA is routinely telling us that we probably have to split every known microbial eukaryote species into 3-4 cryptic entities.

And on top of that, Jörger et al. remind us of how little of the earth’s surface we’ve actually sampled:

Although we present the first study on meiofaunal slugs with representative worldwide taxon sampling, we know our dataset is likely to represent only a fragment of the hidden diversity in the genus because a) tropical sands still are largely unsampled, b) suitable habitats are patchy and disjunct, and c) the indication of accumulated diversity in geographically small areas (e.g., three distinct genetic Pontohedyle lineages on the island of Moorea).

Scientists–and humans–are on an eternal quest to talk about species. It helps us organize our knowledge of the world, and helps us to understand historical processes which have influenced how things evolve and how they are distributed geographically. There’s always a lot of press surrounding the latest paper claiming the official and absolute estimate of the number of species on earth (here’s one hyped up example). Personally, I don’t take much stock in these, because I don’t think we have nearly enough information to even make ballpark guesses. We have NO genetic information about most microscopic animals on earth. Hell, the Guinea Worm can’t even get its genome sequenced. For small non-parasitic wormy things, we’re just lumping similar-looking blobs into categories after a quick peek down the microscope. Its like saying all blonde haired people belong to one species, and all redheads belong to another – a.k.a, surface appearances take precedence, end of story.

Next time you hear a “global species estimate”, don’t say you believe it, please don’t say you believe it!

*Ok, well you can argue, and people do. But that is another blog post for another day. Just work with me here, people.

Reference:
Jörger KM, Norenburg JL, Wilson NG, Schrödl M. (2012) Barcoding against a paradox? Combined molecular species delineations reveal multiple cryptic lineages in elusive meiofaunal sea slugs. BMC Evol Biol,12(1):245.

The post When 2 becomes 12: Cryptic species need some love like they’ve never needed love before first appeared on Deep Sea News.

Ken described the project (funded by the US National Science foundation) in a recent e-mail:

We left Punta Arenas Chile Jan 1st, 2013 and arrive into McMurdo Station, Antarctica Feb 7th. The purpose of this cruise is to study genetic patterns of biodiversity in the Bellingshausen, Amundsen and Ross Seas. These are some of the most remote waters on the planet. Given the rapidly changing environment in this region due to climate change, we also want to establish an understanding of where different species currently occur.

You can follow their cruise on Twitter (@Icy_Inverts_AU and  @CMU_Antarctica), and find more information at the websites listed below. Just remember guys, Cabin Fever and/or extended periods of sleeplessness DO NOT MIX WELL with Tweeting.

Blog/web pages:

Icy Inverts 2013 – Shipboard Blog

Icy Inverts 2013 – Project portal at Auburn University

Biology in Antarctica – Project portal at Central Michigan University

YouTube video describing the project:

Auburn University – Icy Inverts 2013 – sorry DSN readers, I couldn’t embed the video here because of the privacy settings :(

The post “Icy Inverts” 2013 Cruise – Scientific Adventures in Antarctic Waters first appeared on Deep Sea News.

Tongue biters have been in my inbox a few times lately.  If you’ve managed never to come across these interesting little isopods before, they are members of a wholly parasitic group called the Cymothoidae.  For regular readers of Deep Sea News, you can think about them as smaller versions of Bathynomus, which they resemble a lot, the main difference being, you know, that whole sucking-the-life-out-of-a-fish-through-its-tongue thing.  There’s quite a few species and they are widely distributed around the world in fishes from salt water and fresh water alike.  What really interests me about these perennial visitors to my newsfeed is that people seem to be singularly horrified by them, whereas I don’t find them the least bit repulsive or even surprising in any way.  To me, they are just another critter that has found a niche to occupy; I guess that’s the parasitologist in me (long before I studied whale sharks, I studied the ecology of parasitism).

In any sort of systematic parasitology training, you quickly realize – or are explicitly taught – that the presence of critters like the tongue biter is not unusual.  Indeed, most wild fish harbour several species of parasites simultaneously and this is totally and completely normal.  This seems to be a really hard concept for a lot of people to wrap their heads around.  Parasites are assumed to be unusual and bad, a sign that things are seriously amiss.  It’s tempting to look at the host of that tongue biter and think “there goes an evolutionary loser – an animal that fell prey to a repulsive little parasite”.  But that’s not how it works at all.  In fact, if you can survive and thrive despite your parasite burden, then you are an evolutionary winner, an idea that was formally codified as the Hamilton-Zuk hypothesis, based on studies of parasitism and plumage in birds.  The corollary of this is that parasitism is a constant and normal part of the evolutionary pressures acting on an animal, and for that to be the case, parasitism has to be not only normal but positively common.  And so it is.  We just don’t notice it, because for the most part parasites are cryptic, they are literally out of sight and out of mind.  It’s only when something as glaringly obvious as a tongue biter comes along that we even notice parasites at all, even though that same fish may well host a half a dozen other species  at the same time.

No fish is an island.  When I snorkel on a Pacific reef, I don’t swim along and see mother-in-law Diagramma labiosum, I see one of the superstars of parasitology.  When I used to study these drabbest of reef fishes in the lab of my PhD advisor Tom Cribb, we had counted sixteen different trematode worm species in the digestive tract alone.  There were also monogenean worms on the outside: a different species for each fin, several on the gills and even one that specialized on the pharyngeal tooth pads (a tough place to live indeed). There were also parasitic copepods of several varieties and a dozen protozoans of varied flavours throughout the tissues.  Oh yeah, there was also an enormous amphilinid – a bizarre worm distantly related to tapeworms – that lived in the body cavity.  All in all, every individual Diagramma was a swimming hotspot of parasite biodiversity, and seeing a school of them together was like looking at a rainforest; you just needed a dissecting scope and some iris scissors so you could see the trees in the forest.

In my PhD studies (which seem to be receding in the rearview mirror altogether too fast these days!), I looked at far more modest critters.  While a Diagramma might weigh a good 5-10lbs, the fishes I did for my dissertation were little goby-like and minnow-like fresh water jobbies that occur in Australia’s species poor temperate rivers.  Even there, the average parasite richness in a 5 cm/2 inch fish was close to five species per individual.  Fish size does make a difference, but the truth is that if there is a fish swimming, then one, and more likely many more, parasite species has made its home there.  I have never heard of a fish that does not host any parasites at all and I doubt that such a fish exists.

The implications of this for global diversity are profound.  If there are 28,000 species of bony fishes, and each has at least 5 unique parasite species, then those 28,000 fishes scale up to 140,000 species of parasites.  If you use more aggressive (I would argue realistic) estimates of parasite richness, then it’s easy to get estimates of a quarter of a million species of fish parasites or more.

This is surprising to many people, not least to my fish and fisheries biologist friends.  “Where are they all?”, they say.  When they dissect fish for diet studies or anatomy, they don’t see all the things a parasitologist sees.  The truth is that the majority of parasites are missed unless the person doing the dissection has been trained to look in the right way.  Freezing fish, for example, which is bog-standard practice for diet studies, is basically a total bust for parasites.  To really see everything, you need to dissect fish fresh, immediately after death, and preferably immersed in saline (for internal organs) or the relevant water (for external surfaces), under a dissecting scope.  Only then can you appreciate the delicate form and characteristic movements than can reveal a tiny trematode among strands of mucus and strips of intestinal epithelium.  You also have to look in the right places.  Not just the obvious places like the intestine and gills, but inside the heart chambers, in the gall bladder, in the nares and inside the eyeballs, just for instance.

My aim here is to help break the notion that parasitism is in any way unusual in the sea, or anywhere else  for that matter (those cute fluffy kangaroos? Yuppers – DOZENS of roundworm species each).  To that end, here’s a graphic that I hope helps to show that your average fish is, to parasites, a diverse palette of microhabitats, all of which are ripe for the exploiting for the cost of a few specialized adaptations.  If you look hard enough, you’ll find something living in most of these microhabitats, in most species of fishes.  You can find figures like this in many animal parasitology textbooks, but I made this one special for you lot.  So, enjoy, and use as you see fit (click twice to embiggenate)

The post No fish is an island first appeared on Deep Sea News.

The post The Biodiverse Universe first appeared on Deep Sea News.

Mark Gibson is a divemaster, social scientist, and independent writer living in Washington, DC. He can be found blogging at Breaching the Blue. You can find Mark on twitter @breachingblue. The following post is cross-posted at his blog here.

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How many marine species are there?  It is a question that stumped even the Census of Marine Life (CoML), a 10-year long research project that involved thousands of researchers.

Yet now a far smaller team of former CoML scientists has statistically estimated that there are about 2.2 million marine species, and a grand total of just under 9 million species on the entire planet.

At the outset, the CoML “logically estimated” there were 1-10 million marine species – essentially a guesstimate.  The hope was that research cruises and a universal catalogue would yield enough information to generate a statistically-rigorous estimate.  But this estimate proved elusive as the rates of discovery remained linear.  The CoML noted this challenge in their 2010 capstone report, Highlights of a Decade of Discovery:

Census researchers tried statistical methods to estimate how many forms of marine life remain to be discovered. Alas, or perhaps wonderfully, the eventual number remains unknown. The upward curve of accumulation of new species for most taxa and regions has yet to bend enough to calculate a firm plateau.

One might think this was because of the myriad species remaining to be discovered in the ocean’s depths.  But this would be wrong.  Dr. Ian Poiner, Chair of the CoML Scientific Steering Committee, explained to me that while there is much to learn about the deep sea, the other ocean regions hold similar secrets:

Much of the deep sea is unexplored and there is a very high rate of discovery of new species. For example, of some 680 specimens of copepods collected on CoML CeDAMar cruise (DIVA 2) to the south-eastern Atlantic only seven could be identified; 99 percent were new to science. However there is a lot of our oceans unexplored and there is a high rate of discovery of new species wherever we go -shallow, deep, cold, hot. For some areas, like the vast middle waters of our oceans, have virtually not been sampled. (email to author)

So after all the work of the CoML, how is it that five scientists from Dalhousie University and the University of Hawaii (and formerly of the CoML) have finally provided a statistical estimate?  The trick lies in Linnaean taxonomy.

The scientists reasoned that we have probably already found most higher taxonomic groupings (i.e. kingdoms, classes, orders, etc) as their rates of discovery are quite low.  And since the number of groups found at each hierarchical level tends to rise as you move down the hierarchy, the researchers could estimate how many species might remain based on well-studied species groups.

An analysis of the Catalogue of Life and the World Register of Marine Species ultimately revealed reliable numerical relationships between the more complete higher taxonomic levels and the species level.

The CoML was a path-breaking endeavor that increased the number of known marine species from about 230,000 to nearly 250,000.  Combined with this new study, we learn that there are about 2 million species left to discover.

For those of us in the marine community, the ocean has long been a fascinating, mysterious, and exciting place, and I don’t think a jump in the numbers changes that.  But it does provide us a measure of how far we really have to travel to understand our deep blue home, as well as how much we stand to lose if we cannot protect it.

—

Note: These numbers refer to eukaryote species, organisms whose cells contain complex structures enclosed within membranes.  The authors estimated the total number of prokaryote species, but expressed low-confidence as taxonomic discovery was still quite high.  Microorganisms and viruses were not examined.

Reference:

Camilo Mora, Derek P. Tittensor, Sina Adl, Alastair G. B. Simpson & Boris Worm (2011). How Many Species Are There on Earth and in the Ocean? PLoS Biology, 9 (8) : 10.1371/journal.pbio.1001127

The post New Innovative Estimate of Total Marine Species first appeared on Deep Sea News.

On December 26^th 2004, a 9.0 earthquake struck off northern Sumatra in Indonesia.  This triggered a massive tsunami that affected Indonesia, India, Malaysia, Maldives, Sri Lanka, Thailand, and Africa. What was the lasting environmental impact of the tsunami and what might we expect from the recent Honshu Tsunami?

The environmental impacts of tsunami can be broken down in to sixt major categories. Examples are given from the 2004 tsunami.

1. Solid Waste, Disaster Debris, and Sewage: The size of a tsunami disaster results in principalities being unable to adequately deal with the sheer magnitude of debris.  This increases the likelihood that waste will be disposed of in an environmentally inappropriate manner (open dumping, air burning, dumping in new areas).  Hazardous materials, sewage, and toxic substances may also be mixed with ordinary debris.
2. Contamination of soil and water: This includes salinization of rivers, wells, lakes, and groundwater aquifers.  Sewage may impact water supplies and impact natural aquatic systems.  In the Maldives, one of the most significant impacts of the tsunami was on groundwater.  Salt-water intrusion, leaking septic tanks and debris contaminated water wells quickly impacted the groundwater that lies just below the surface. Salination and debris contamination may also lower soil fertility.
3. Loss of Infrastructure and Facilities:  UNEP reported extensive damage to environmental infrastructure, buildings and industrial sites. These include water and sanitation systems, solid waste disposal sites, and waste treatment centers. Oil storage facilities released oil and wastes into the environment which subsequently was not handled properly during clean-up.
4. Loss of Natural Ecosystems: Coral reefs, mangroves, coastal areas, wetlands, agricultural fields and forests, and aquaculture areas can be badly damaged. Indonesia’s State Ministry of National Development Planning’s damage assessment estimated that 20% of sea grass beds, 30% of coral reefs, and 25-35% of wetlands, and 50% of sandy beaches of the west coast, have been damaged. In some local areas, 90% damage was reported to mangroves and coastal forests. In Thailand, 15 to 20% of the coral reefs were affected by the tsunami primarily due to siltation and sand infiltration. In the Nicobar Islands 51-100% of mangrove systems, 41-100% of coral reefs, and 6.5-27% of forest ecosystems were damaged. Mangrove systems near river mouths and channels appear particularly susceptible to loss due to heightened flow concentrated at river mouths and inundation of mangrove forests through river channels. Of course, the disappearance and relocation of beaches was also common.
5. Nutrification of Coastal Waters: Material can be transported from land back to sea.  This material can be heavy in nutrients and trace elements that lead to phytoplankton blooms and increases in populations of secondary consumers.  With extreme nutrification, hypoxic conditions may be possible.
6. Impact to Biological Communities and Species Due to Factors Above: Inside forests, heavy deposition of sediments on the forest floor may lead changes in the species composition of the organism living on or in the soil. One study suggests mangroves forests were slower to recover. Four years after the tsunami, intertidal and offshore communities appear to be recovered with similar species and number of individuals. However, 1-2 years afterwards a study of non-vegetated area, i.e. sand and mud flats, displayed a considerable reduction in both biodiversity and abundances of species.  The rapid recovery of these systems reflects that they are naturally highly variable. In a species of heart urchin some individuals survived the tsunami, but overall juveniles dominated the population. The Nicobar Scrub Fowl, listed as vulnerable on the IUCN Redlist, dwindled from 2,318-4,056 to 395-790 breeding pairs after the tsunami, a decline of 70%.  The tsunami also adversely influenced Nicobar Scrub Fowl nest-sites because of loss of suitable habitat. After the tsunami, Long-Tailed Macaques displayed fewer numbers near the coast. Juveniles were also more prevalent in the population.  It is hypothesized this reflects the destruction of coastal fruit trees used by the monkeys. Freshwater ponds and peat swamps are also heavily impacted due to salinization.  After the tsunami, many impacted ponds and swamps showed no sign to returning to their original species composition.

Although macabre, wildlife may fare better after a tsunami if the human population is greatly reduced.  This is particularly true of fisheries.

More than 13,000 fishermen were killed and another 5,000 evacuated in Sri Lanka alone, with 80% of the fishing fleet lost or severely damaged. On the Thai coast, according to the UN Food and Agriculture Organization, 4,500 fishing vessels were smashed, jeopardizing the livelihoods of 120,000 people in fishing villages there.

UPDATE: Jason Goldman has a nice write up about the some of the early environmental impacts from the Honshu Tsunami at Scientific American.

M. Sanjayan of The Nature Conservancy in Arlington, Virginia, told ScienceInsiderthat the biggest impact on wildlife would be on shorebirds nesting on small islands throughout the Pacific, rather than on the Japanese mainland. Indeed, the majority of wildlife-related news of the tsunami has come from small Pacific islands such as those in the Midway Atoll National Wildlife Refuge…The US Fish and Wildlife Service is nowestimating that the Midway Atoll National Wildlife Refuge sustained losses of that more than 110,000 Laysan Albatross chicks – representing approximately 22% of chicks born this year – along with an estimated two thousand adults. In addition, thosands of Bonin petrels were buried alive, and thousands of fish were washed ashore where they suffocated on Eastern Island.

Sources:

• http://www.gdrc.org/uem/disasters/disenvi/tsunami.html
• http://www.project-syndicate.org/commentary/jernelov5/English
• http://www.unep.org/tsunami/reports/tsunami_indonesia_layout.pdf
• Srinivas, H., & Nakagawa, Y. (2008). Environmental implications for disaster preparedness: Lessons Learnt from the Indian Ocean Tsunami Journal of Environmental Management, 89 (1), 4-13 DOI: 10.1016/j.jenvman.2007.01.054
• Szczuciński, W., Niedzielski, P., Rachlewicz, G., Sobczyński, T., Zioła, A., Kowalski, A., Lorenc, S., & Siepak, J. (2005). Contamination of tsunami sediments in a coastal zone inundated by the 26 December 2004 tsunami in Thailand Environmental Geology, 49 (2), 321-331 DOI: 10.1007/s00254-005-0094-z
• http://www.ias.ac.in/currsci/jul102005/195.pdf
• http://www.cabdirect.org/abstracts/20093094216.html
• http://www.cabdirect.org/abstracts/20093094212.html
• Sivakumar, K. (2009). Impact of the 2004 tsunami on the Vulnerable Nicobar megapode Megapodius nicobariensis Oryx, 44 (01) DOI: 10.1017/S0030605309990810
• Whanpetch, N., Nakaoka, M., Mukai, H., Suzuki, T., Nojima, S., Kawai, T., & Aryuthaka, C. (2010). Temporal changes in benthic communities of seagrass beds impacted by a tsunami in the Andaman Sea, Thailand Estuarine, Coastal and Shelf Science, 87 (2), 246-252 DOI: 10.1016/j.ecss.2010.01.001
• http://www.italian-journal-of-mammalogy.it/article/view/4484/pdf
• http://rmbr.nus.edu.sg/rbz/biblio/58/58rbz329-348.pdf

The post From the Editor’s Desk: The Environmental Impacts of Tsunamis first appeared on Deep Sea News.

Despite the isolation experienced by the deep-sea, the climate does have an effect in this seemingly remote environment.

via Frontiers: The deep sea and climate | Uncharted Atolls.

The post Climate Change and the Deep Sea first appeared on Deep Sea News.

As part of our NSF RAPID grant studying the impact of the Deepwater Horizon spill, our group is busy organizing an outreach workshop for undergrads entitled the “Bioinformatics of Biodiversity”. We’ll be giving a small group of students the down-low on traditional taxonomy as well as high-throughput sequencing of sediment communities–especially emphasizing the interdependence between the two for inferring complex interactions within marine ecosystems. While preparing material for these workshop sessions, I’ve been thinking a lot about what it means to be a marine biologist in the 21st century–I’m really not joking about the scripting.

On any given day, I may extract nematodes from some deep-sea mud, PCR up some 18S genes, build a quick phylogeny, help someone prep environmental RNA for transcriptome analysis, write and run perl scripts, fiddle around with Linux dependencies, and outline some complex data processing needs to my colleagues in the computer science department. Once in a while I go down to the beach to collect some fresh, writhing worms.

“You hear that Mr. Anderson? That is the sound of inevitability.”

I still consider myself a marine biologist at heart, but my goal as a postdoc is to be marketable. Academia is a crowded island, and if I want to survive I need to adapt and find my niche.

Now, we are truly living a data-driven life. One proposal I read succinctly noted the “twin revolutions in information/computing and in the biological sciences”. Computers are getting faster and DNA sequencing is becoming ever more high-throughput (with the pace of the latter far outstripping the former). With the plummeting cost of high-throughput sequencing technology and the impacts of climate change already manifesting, reverse taxonomy is becoming the only cost-effective option for describing the biodiversity on Earth: sequence environmental DNA first, then search out biological patterns, and eventually stick a formal species name on the taxa with the most interesting ecology. Taxonomy is always going to be important, but the problem is we could never do it fast enough. Scientists who study microbes are already taking an alternative approach–realizing that the functional role of organisms in an environment (e.g. expressed genes) can be more important than who is actually there.

In fact, given the vast number of uncultivated microbes, it may be that a DNA-centric approach, in which genes are linked to habitats (locations), is more useful than the species-centric view [Field et al. (2010) Nat Biotech 26(5):541]

I’m currently in beautiful San Diego to participate in the Biodiversity Working Group of the Genomic Standards Consortium. We’ll be discussing the current challenges facing high-throughput biodiversity research—how to anticipate and plan for future research needs, particularly the need for diverse fields to unite and share computational resources and workflows. The data problem is too big (and cyberinfrastructure is too costly) for disparate groups to try and tackle alone—thus, today’s scientific community is poised to become more integrative than ever (common computational hurdles mean that disciplines must unite to overcome them). Not only do scientists need robust data storage facilities, but researchers need to access and analyze large DNA datasets (and their associated metadata) in order to tease out patterns across biological communities.

Young biologists who can grasp this overarching zeitgeist and gain a broad scientific background–both computational and ecological–will be well poised for future success. You don’t necessarily need to walk the walk, but you definitely need to talk the talk. And maybe stumble around in the dark (for your own skill development?) if anyone asked you to actually try and walk the walk. I can talk about relational databases to computer scientists, but I could never actually sit down and construct one–well I could, but it would involve much swearing and lots of caffeine.

The post A 21st century view of Marine Biology first appeared on Deep Sea News.