pelagic | Deep Sea News https://deepseanews.com All the news on the Earth's largest environment. Wed, 20 May 2015 19:28:06 +0000 en-US hourly 1 https://wordpress.org/?v=7.0 Release the Glaucus! https://deepseanews.com/2015/05/release-the-glaucus/ Wed, 20 May 2015 19:28:06 +0000 https://www.deepseanews.com/?p=54784 Aliens? Squishies? Deformed Plastic? Jellyfish? Many descriptors have accompanied the emails, texts, and Facebook messages that have recently flooded my cellular device, all describing one unique…

The post Release the Glaucus! first appeared on Deep Sea News.

]]>
Aliens? Squishies? Deformed Plastic? Jellyfish?

Many descriptors have accompanied the emails, texts, and Facebook messages that have recently flooded my cellular device, all describing one unique ocean beastie…

Exhibit A.

Screen Shot 2015-05-20 at 11.28.12 AM

 

With Spring alterations in wind patterns, hoards of blue, planktonic sailors known as Velella velella have raided the Western seaboard of the United States by the billions. Though commonly confused as jellyfish, Velella are actually upside floating ships of doom of hydroids. Think a colony living under one Pringle-shaped roof, rather than an individual.

Though Velella do sting, you will not necessarily feel their harpoons of death, aka nematocysts, pierce your skin. (However, No promises if you were to try to lick one….) Last year, our very own RR Helm even posted an amazing video compiled by the masterminds of MBARI perfectly describing the secret lives of these colonial creatures.

gcblIo8The one question that remains unanswered…what in the heck are we going to do with all of them now that they are here?! Summer is coming and we can’t very well have the beach looking like this when all the tourists come!

The only viable answer I could come up with…

Release the Glaucus!

 

I know what you’re thinking. An army of bright, blue, squishy, ocean pokemon might not seem like a viable option. And to that I label you a dream crusher. In fact, these aeolid nudibranchs, known as Glaucus atlanticus, LUURRRVVVEEEE to nom all the Velella they can eat! They even steal the Velella‘s super stinging powers and make them their own. And what’s better than getting ANOTHER even crazier alien-like ocean creature to do your bidding?

hpop1788
The end is near! The end is near! 

Needless to say, this half-hatched “Velella Clean-up Plan (v 1.0)”  is still in the Development Stage as Glaucus don’t typically make their way here to the Best West Coast. They are often found in more tropical regions destroying those Velella. We could plausibly use the pelagic snail Janthina as our master villain too…but the tagline “Release the Janthina!” just doesn’t have the same ring to it. For now we are just brainstorming….but for precautionary measures DSN has begun recruitment of our very own Glaucus army. Be afraid.

The post Release the Glaucus! first appeared on Deep Sea News.

]]>
We don't know the ocean https://deepseanews.com/2014/11/we-dont-know-the-ocean/ https://deepseanews.com/2014/11/we-dont-know-the-ocean/#comments Wed, 05 Nov 2014 18:37:20 +0000 https://www.deepseanews.com/?p=53690 This is not the ocean: This is not the ocean: Indeed, even THIS is not the ocean: Before you start thinking that the folks at…

The post We don't know the ocean first appeared on Deep Sea News.

]]>
This is not the ocean:

shutterstock_89486707This is not the ocean:

shutterstock_115897093

Indeed, even THIS is not the ocean:

shutterstock_102961433

Before you start thinking that the folks at DSN are losing their marbles, bear with me!  The truth is that none of these three all-too-familiar and quintessentially marine images reflects the actual reality of what most of the ocean is like.  Here’s why.  At their most basic, the above three images can be represented like this (respectively):

Coastal
Coast
Benthic
Bottom
Surface

Our experience of the ocean is almost entirely defined by our interactions along its margins: along the coast, sitting the bottom or floating on the surface.  More often, it’s some combination of these, like a coral reef, which can be all three: coastal, benthic and also in reach of or transcending the surface at least some of the time.  In all of these marginal habitats, life is heavily influenced by the margin itself: benthic things have specific adaptations to interacting with the substrate, while pelagic things have adaptations for interacting with the surface, and so on.  In many of these places it’s sunny, it’s warm and there are lots of animals, at least relatively speaking.   The point of my post is that the rest of the ocean, an overwhelming majority in fact, looks like this:

Bathyal

That’s because the part of the oceans not included in coastal zones, on the bottom, or within sunlight’s reach of the surface make’s up about 94% of the volume of the ocean (and of course, the other 6% looks like this at night time, or 50% of the time!).  Average ocean depth is around 12,100 feet, with sunlight penetrating the top 650 feet or so.  The other 11,450 feet consists of pitch dark and perpetual blackness, with no margin or structure to disrupt the inky 3-dimensional void.  It’s also uniformly and numbingly cold; below the reach of sunlight it is about 4°C or 39°F everywhere in the world, regardless of whether you are off Greenland or Hawaii.  About the only thing that isn’t uniform throughout this habitat is pressure, which varies greatly with the depth of any given cube of water, but is generally a great deal more than any experienced along coasts or at the surface, although it must be said that bottom-dwelling communities in the deepest parts of the ocean experience the greatest pressures of all.

There are animals in the void too, of course, but they are sparse in the extreme and without extrinsic light and without any habitat structures they are foreign in form.  Often delicate and flimsy, diaphanous or gelatinous, they exist in a world without walls, floor or ceiling, without any structure at all to define the boundaries of their environment or even to serve as some spatial point of reference.  There are animals here that will not during their lifetime experience a solid surface, or even a fluid one such as the boundary where water meets air; they and their ancestors appear and disappear from the void, never alighting on anything.  To them, a wall might be as incomprehensible as a black hole is to us.  They are born, live out their life histories and die in a frigid, timeless, structureless void.

I’m not a religious guy, but the bible opens with a statement to the effect that “the earth was formless and empty, darkness was over the surface of the deep” and I can’t help but be struck that the world described by this passage, before God supposedly created light and began to shape the world, bears a striking resemblance to the vast majority of the oceans that exist today.  We think we know the oceans, but we don’t, not really, because the majority of the oceans are an icy black void inhabited by creatures as alien as any we can expect to find in that other unceasing void, the one we call space.

 

 

 

The post We don't know the ocean first appeared on Deep Sea News.

]]>
https://deepseanews.com/2014/11/we-dont-know-the-ocean/feed/ 6
How do you figure out how much plastic is in the ocean? https://deepseanews.com/2013/12/how-do-you-figure-out-how-much-plastic-is-in-the-ocean/ https://deepseanews.com/2013/12/how-do-you-figure-out-how-much-plastic-is-in-the-ocean/#comments Mon, 02 Dec 2013 19:36:41 +0000 https://www.deepseanews.com/?p=23447 Nobody ever told me that becoming a marine biologist would involve spending four years figuring out how to count. Because, seriously, how hard can counting…

The post How do you figure out how much plastic is in the ocean? first appeared on Deep Sea News.

]]>
Nobody ever told me that becoming a marine biologist would involve spending four years figuring out how to count. Because, seriously, how hard can counting be? Well, it turns out, when you’re trying to count tiny pieces of plastic in the ocean, it gets complicated really fast.

When I went out to the North Pacific Subtropical Gyre in 2009 and 2010, part of the goal was to figure out how much plastic debris was actually there. That’s the first step to understanding what impact it might be having the ecosystem, after all. So we towed a net around on the surface, and towed a net underwater, and made visual counts of the plastic floating by on the ocean’s surface. Between the two cruises, we had measurements of plastic quantity over 6,000 miles of ocean – we were all set, right?

Double rainbow in the Gyre! Everything's under control! Until we get back to shore...
Double rainbow in the Gyre! Everything’s under control! Until we get back to shore…

But when we started to analyze the data, things got complicated. The quantity of trash was hugely variable. Tows taken right next to each other, or taken in around the same location a year apart, had very different quantities of plastic. In order to get a handle on why this was, I teamed up with Andrew Titmus, an ornithologist who did the visual counts of floating plastic on our 2009 cruise, and Mike Ford, a NOAA oceanographer who was Chief Scientist on the 2010 cruise. The results were published in PLOS ONE last week, and NOAA has a brief writeup here.

The paper was hard to write, because it’s essentially “here’s a bunch of things that you should know about where plastic is in the quote-unquote garbage patch,” or, as I very scientifically referred to it on Twitter, a giant BLORT of data. I’m going to highlight a couple major points, but feel free to check out the paper yourself and ask more questions below.

1. Wind matters. 

When the ocean is really calm, the plastic bobs to the surface and there’s a lot of it. When the wind kicks up and the ocean gets choppy, the plastic gets mixed below the surface, and you can’t capture it in a surface-towed net (which is the standard way to measure plastic). Our plastic counts go way down once the wind gets to a certain point, regardless of where we are in the ocean. Giora Proskurowski & colleagues found a similar phenomenom in the Atlantic.

 

Quarter-meter square made out of PVC with fleck of microplastic on a calm ocean.
On a flat-calm day, tons of these little flecks of microplastic float to the surface. You can see them around the quadrat that I’m holding. (For all you benthic ecologists out there, yes indeed, I am pretty sure I AM the only person to use a quadrat while floating in the middle of the ocean, thank you very much.)
Me on a rough day, leaning over the side of a ship, towing a net.
On this rough day, most of the plastic (and zooplankton) got mixed below the surface. No, I didn’t get much work done. Yes, it was a super fun day.

2. Filtering tiny amounts of plastic out of the ocean takes out a lot of life, too. 

For every 1000 grams (2 lbs) of plastic bits we removed from the water, we took out 731 grams (1.6 lbs) of ocean life, primarily zooplankton and baby fish. That’s a lot of critters, particularly since life is relatively sparse in the North Pacific Gyre. Remediation schemes will have to be sure that they are not causing more damage than they’re solving. For more on that, check out the Open Ocean Cleanup Guidelines.

Plastic intermixed with jellyfish and other zooplankton.
Zooplankton, y u so small? Photo by J. Leichter.

3. Since plastic varies so much, it’s going to take a lot of work to figure out whether it’s increasing or decreasing. 

We used our data to create an imaginary future where plastic had increased between 10% and 100%. It turns out that it’s really hard to detect even relatively large increases in plastic with reasonable certainty. On the 2009 cruise, we worked our butts off for three weeks to take 119 surface samples (and it took me over a year, a lot of bad R code, and the help of awesome volunteers to convert jars of plankton and plastic into data). Unfortunately, it would take 250 surface samples to detect a 50% increase in microplastic with 80% probability. We’re going to have to figure out a better way to do that, or we won’t be able to tell if the problem is getting better, or getting worse.

Figure 6 from Goldstein et al. 2013, PLOS ONE.
This is a figure from the paper. The top shows how many samples you’d have to take to figure out how much plastic has increased, with various levels of statistical certainty (red is good). The bottom shows how many samples you’d have to take to reduce the variability as much as it can be reduced.

So, what’s the take-home of this paper? We can’t go waltzing into the Gyre wanting to do everything at once (like I did in 2009 *cough cough*). To be effective, expeditions on the science of plastic debris need to think about what their specific objectives are. Want to study the animals growing right on the plastic? Target the rarer large floating objects. Want to get a glimpse of how the widest array of ocean life is interacting with plastic? Seek out trash stuck in eddies, where temporary pulses of high-nutrient water cause plankton to grow and attract fish.

If you want more, data from this paper is archived online at the CCE LTER Datazoo, and figures that didn’t quite fit into the paper, such as the types of plastic we collected, can be found over on Figshare. Want to know more about what all this plastic is doing to marine life? Check out Chelsea’s guest post and new paper on what happens when fish eat plastic, and Mark Browne’s new paper (with BBC article!) on lugworms. And as always, I’m happy to answer your questions in the comment thread.

 

The post How do you figure out how much plastic is in the ocean? first appeared on Deep Sea News.

]]>
https://deepseanews.com/2013/12/how-do-you-figure-out-how-much-plastic-is-in-the-ocean/feed/ 25
Solving the Mystery of the Placental Jellyfish https://deepseanews.com/2012/05/solving-the-mystery-of-the-placental-jellyfish/ https://deepseanews.com/2012/05/solving-the-mystery-of-the-placental-jellyfish/#comments Thu, 10 May 2012 00:06:17 +0000 https://www.deepseanews.com/?p=17350 Yesterday the DSN crew first saw the video above.  What is this large floating sheet of goo?  Is it alive? Was it once alive? The…

The post Solving the Mystery of the Placental Jellyfish first appeared on Deep Sea News.

]]>

Yesterday the DSN crew first saw the video above.  What is this large floating sheet of goo?  Is it alive? Was it once alive?

The two leading contenders seems to be that it is A) an old whale placenta or B) a rare and enigmatic deep-sea jellyfish.  And the answer is…. B)

A) So why is not an old whale placenta?  The video is from approximately 5000 feet (1500 m). A placenta would need to sink to this depth without any other organism consuming it.  Unlikely given that its rate of decent would have been slow and any organic food source in the deep sea is unlikely to last long.

B) So why is it a jellyfish?* In 1967, F.S. Russell described a very enigmatic deep-sea jellyfish, Deepstaria enigmatica.

During Dive 159 of the U.S. research submersible Deepstar 400 on 22 October 1966 Dr. Eric G. Barham, Dr. George Pickwell, and Mr. Ronald Church collected a remarkable scyphomedusan at a depth of about 723 m in the San Diego Trough…when first noted, the jellyfish’s margin was collapsed and the [outer, convex surface of the umbrella] indented.

In other words it didn’t look like much of a jellyfish.  Sound familiar?

On opposite sides of the umbrella are two large tubular shaped processes…It has a yellowish brown tinge…The radial canal system is most striking.  It consists of a meshwork, likened by Dr. Barham to wire-netting.

The meshwork, wire-netting like, radial canal system of Deepstaria enigmatica

The gonads are situated along the margins of fan-shape mesenteries, and tend to be broken up into several isolated processes with incurved edges.

Gonads on a fan shaped protrusion
Figure from Russell 1967
Specimen of Deepstaria enigmatica described by Russell 1967

In 1988 Larson and colleagues published further work describing this rare group of jellyfish.  They too noted the unique canal system.

But it is these researcher’s behavioral notes that I find most interesting.

These two species of Deepstaria display some unique behaviour; peristaltic locomotion and pursing of the bell margin are unknown in other medusae. Probably the peristaltic locomotion is necessary because the umbrella is too thin and the subumbrella musculature too diffuse to support more rapid pulsation. Our observations of both species of Deepstaria suggest that they usually hang  motionless with the umbrella open…It seems probable to us that medusae in this genus are large ambush predators in the meso- and bathypelagic environment…we speculate that the feeding behaviour might be as follows. The medusae usually hang vertically and motionless with the bell open; occasional peristaltic contractions probably enable them to swim slowly, at least enough to retard sinking. Because the area of the subumbrella is so large, upward-swimming prey occasionally would swim into it. Once prey enter the large subumbrellar chamber, the contact stimulates rapid contraction of the coronal muscle, pursing the umbrella shut and trapping the prey. As the prey attempts to escape, it contacts nematocysts on the subumbrella, being repeatedly stung until weakened. It may additionally become covered with mucus and further immobilized. Then peristalsis and ciliary movement could transport the prey towards the mouth where the oral arms could grasp and engulf it…’Bagging’ prey in this way is not known in other medusae.

Plate 4 One of the large gelatinous organisms, Deepstaria enigmatica, that have been recently found to be very abundant in mesopelagic waters of the world ocean. This medusa was photographed in Monterey Bay by Kevin Raskoff © MBARI, 1998.

Russell, F. S. (1967). “On a remarkable new scyphomedusan Deepstaria enigmatica”. Journal of the Marine Biological Association of the UK 47: 469-473.

Larson, R.; Madin L., Harbison, G. (1988). “In situ observations of deep water medusae of the genus Deepstaria, with a description of D. reticulum sp. nov.”. Journal of the Marine Biological Association of the UK 68: 689-699.

*UPDATE: This has now also been confirmed by Dr. Steven Haddock of the Monterey Bay Aquarium Research Center, an expert on deep-sea and pelagic creatures.

UPDATE2: Steven Haddock provides some much better photos of Deepstaria engimatica on the Jellyfish Watch Facebook page.

UPDATE3: Several comments below suggest the species is Deepstaria reticulum.  Important thing is that it is still a jellyfish and already known.

The post Solving the Mystery of the Placental Jellyfish first appeared on Deep Sea News.

]]>
https://deepseanews.com/2012/05/solving-the-mystery-of-the-placental-jellyfish/feed/ 58
Big text files can tell you how the ocean works https://deepseanews.com/2011/09/big-text-files-can-tell-you-how-the-ocean-works/ https://deepseanews.com/2011/09/big-text-files-can-tell-you-how-the-ocean-works/#comments Sat, 03 Sep 2011 18:18:44 +0000 https://www.deepseanews.com/?p=15130 …because “High-throughput sequencing confers a deep view of seasonal community dynamics in pelagic marine environments”, however appropriate a title, seems far too dry and technical…

The post Big text files can tell you how the ocean works first appeared on Deep Sea News.

]]>
ResearchBlogging.org…because “High-throughput sequencing confers a deep view of seasonal community dynamics in pelagic marine environments”, however appropriate a title, seems far too dry and technical for a blog.  I mean, I want people to read my posts, right? Don’t be fooled by the title, though: I am going to give you some seriously elegant science here.

Because of my own research, I try to keep pretty up-to-date with the wider world of high-throughput DNA sequencing—keeping tabs on other scientists who, like myself, use millions of DNA sequences to study complex species assemblages in different types of ecosystems.  A couple recent papers relayed results from a 6-year investigation of microbial communities in the Western English Channel waters near Plymouth, UK.

Gilbert et al. (2011, 2010) show that even in bacterial communities, there are definite seasonal patterns and peaks in community diversity.  Figuring out what causes these patterns is sometimes surprisingly easy – it looks like shifting day length accounts for 65% of the changes in bacterial diversity (I’m sure the authors’ jaws dropped when they saw this result…).  Even more ridiculous (in a good way), the specific bacterial assemblage—the ‘fingerprint’ of species present in the community—could predict the month with 100% accuracy.   And no surprise, only 2% of the 100 most abundant taxa they observed could be identified down to species level.  (Previously undiscovered diversity is so old hat these days.  But still cool).

Microbial community in the Western English Channel surface waters near Plymouth, UK. The larger the circle, the more abundant the species. Colors represent the persistence of taxa over time (e.g. the number of samples they were found in; orange = 5%, yellow = 16%, green = 35%, blue = 66%, red = 100%) From Gilbert et al, 2011

Network analysis indicates that communities are driven from the “bottom-up”: the environment determines the bacterial taxa that thrive (differential responses to temperature, light availability, etc), and then the eukaryotic taxa may then sneak in depending on what yummy bacteria there are to eat:

“Reginald, I do fancy some Gammaproteobacteria for supper on this fine afternoon – what do you say”

“Tickety-boo old chap, lets get swimming”

Over time there were occasional blooms of rare taxa – all of a sudden one species would become perplexingly abundant.  These types of spikes are very exciting – as a scientist, I dream of the day where we can link a specific taxon to a specific environmental change (invasion of predators, an oil spill, or an invisible pollutant). As more studies like these are published, my dream may soon become a reality.

Seasonal patterns in surface water microbial communities, grouped as an average of 3 seasons. Lines represent taxonomic assemblages grouped at the level of Order. From Gilbert et al. 2011

The coolest thing is that these patterns are consistent no matter what type of data you look at (Gilbert et al. 2010) – whether you’re looking at one gene sequenced from all species (metagenetics), random genomic fragments from the community (metagenomics), or only the community gene expression (metatranscritpomics).  From gene expression data, Gilbert et al. additionally found important genes which turn on and off according to season and time of day – but these show NO resemblance to any known genes.  Which is pretty exciting, because we’ve sequenced a lot of genomes at this point, and functionally important genes are pretty conserved (and easy to spot) across the tree of life.  Microbes are obviously doing something important in the environment—maybe producing an unknown protein which recycles nutrients such as Nitrogen or Phosphorus—but all we can do is scratch our heads at this point.  New studies like this are constantly turning the science world upside down—like, we scientists thought we knew how the Nitrogen cycle worked…but apparently we didn’t.

Although Gilbert et al. (2011) focused on UK waters, their observations of seasonal patterns were surprisingly congruent with a previous study off the California coast (Fuhrman et al. 2006).  To me, the fact that microbial communities can be so similar, despite being so geographically far apart, is completely amazing.  But like any good scientific study, the results seem to generate more questions than answers.  Now that we’re building a deep and accurate view of marine ecosystems (thank you, high-throughput sequencing), we can start to dig further and ask questions about what exactly drives these patterns.  I can’t wait to find out!

References:

Gilbert JA, Steele JA, Caporaso JG, Steinbrück L, Reeder J, Temperton B, Huse S, McHardy AC, Knight R, Joint I, Somerfield P, Fuhrman JA, & Field D (2011a). Defining seasonal marine microbial community dynamics. The ISME journal PMID: 21850055

Gilbert, J., Field, D., Swift, P., Thomas, S., Cummings, D., Temperton, B., Weynberg, K., Huse, S., Hughes, M., Joint, I., Somerfield, P., & Mühling, M. (2010). The Taxonomic and Functional Diversity of Microbes at a Temperate Coastal Site: A ‘Multi-Omic’ Study of Seasonal and Diel Temporal Variation PLoS ONE, 5 (11) DOI: 10.1371/journal.pone.0015545

Fuhrman JA, Hewson I, Schwalbach MS, Steele JA, Brown MV, & Naeem S (2006). Annually reoccurring bacterial communities are predictable from ocean conditions. Proceedings of the National Academy of Sciences of the United States of America, 103 (35), 13104-9 PMID: 16938845

The post Big text files can tell you how the ocean works first appeared on Deep Sea News.

]]>
https://deepseanews.com/2011/09/big-text-files-can-tell-you-how-the-ocean-works/feed/ 1
If I had my way, we’d just sequence everything https://deepseanews.com/2010/07/if-i-had-my-way-wed-just-sequence-everything/ https://deepseanews.com/2010/07/if-i-had-my-way-wed-just-sequence-everything/#comments Wed, 28 Jul 2010 20:13:36 +0000 https://www.deepseanews.com/?p=9327 Sometimes I find it really frustrating that all we ever talk about is species (granted, I am very guilty of this too).  Is it new? …

The post If I had my way, we’d just sequence everything first appeared on Deep Sea News.

]]>
ResearchBlogging.org
Sometimes I find it really frustrating that all we ever talk about is species (granted, I am very guilty of this too).  Is it new?  Where is it found? Where isn’t it found?   Where do we put it on the tree of life? Does it need protection? Zzzzzzzzzzzzzz…

The question I wished we asked more is: what is this species doing?  When I look at marine sediments under a microscope, my mind buzzes with the thought of millions of unknown genetic pathways all ecologically intertwined yet inherently isolated in each individual organism.  In the old days (circa 2005 and boho-chic fashions), understanding gene expression was limited to single species—common model organisms—scrutinized in highly artificial settings (hmm, which gene do I want to knock out of this mouse today?).  Oh, and you had to have previously sequenced the entire genome for said organism if you ever wanted a shot in hell at understanding your data.

Fast forward to the present, and researchers are embracing a new field: Metatrascriptomics.  Try to say that three times fast.  Transcriptomics of any variety is the study of RNA molecules (messenger RNAs, ribosomal RNAs, transcript RNAs and non-coding RNAs) present in a cell at any given time.  By sequencing RNA molecules, we can get a snapshot of the genes being expressed in a cell, tissue, organism, or even whole community of organisms at a given place and time.  These type of studies used to be carried out in a limited fashion using quantitative PCR (qPCR) or microarrays, but new sequencing technologies (454, Illumina) now allow us to sequence RNA at a much grander scale: we’re getting more sequences than ever (millions at a time) and can cover a huge taxonomic breadth (whole microbial communities).

How to sequence a metatranscriptome, taken from Moran, 2009

In the past few years, Metatranscriptomics has revealed some really neat stuff about marine environments, which Mary Ann Moran has summarized in a stellar review article.  For example, Hewson et al. described the expression profile of a key cyanobacteria species (Crocosphaera watsonii) whose biology was poorly known but played a key role in nitrogen fixation in marine environments.  In another study, Poretsky et al. analysed mRNA transcripts to describe the activity Pacific bacterioplankton communities across day and night.  They found evidence that these organisms invest heavily in energy acquisition and metabolism when the sun is shining, but shift over to producing important molecular components (amino acids, vitamins, membranes) once immersed in darkness.  How cool is that?

Transcription activities of ocean microbes during the day (top bars) versus night (bottom bars) samples; Viridiplanteae (green), photosynthetic Chromist algae (yellow), and other Chromist (red), after Poretsky et al. 2009

These new approaches are once again highlighting how little we know (when isn’t that the case in science?).   It appears that any typical pelagic microbial transcriptome currently contains a huge proportion of previously unknown gene products—Gilbert et al. reported a whopping 91% of large gene families that appeared to be novel!

These studies just reinforce my (somewhat compulsive) desire to sequence everything in sight.  That, and remind me to start carrying around an emergency pipetting kit, just in case.

References:

Gilbert, J., Field, D., Huang, Y., Edwards, R., Li, W., Gilna, P., & Joint, I. (2008). Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities PLoS ONE, 3 (8) DOI: 10.1371/journal.pone.0003042

Hewson, I., Poretsky, R., Beinart, R., White, A., Shi, T., Bench, S., Moisander, P., Paerl, R., Tripp, H., Montoya, J., Moran, M., & Zehr, J. (2009). In situ transcriptomic analysis of the globally important keystone N2-fixing taxon Crocosphaera watsonii The ISME Journal, 3 (5), 618-631 DOI: 10.1038/ismej.2009.8

Moran, M.A. (2009). Metatranscriptomics: Eavesdropping on complex microbial communities Microbe, 4 (7), 329-335 Open-Access PDF

Poretsky, R., Hewson, I., Sun, S., Allen, A., Zehr, J., & Moran, M. (2009). Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre Environmental Microbiology, 11 (6), 1358-1375 DOI: 10.1111/j.1462-2920.2008.01863.x

The post If I had my way, we’d just sequence everything first appeared on Deep Sea News.

]]>
https://deepseanews.com/2010/07/if-i-had-my-way-wed-just-sequence-everything/feed/ 2
Interactions in the Dark Ocean https://deepseanews.com/2010/07/interactions-in-the-dark-ocean/ https://deepseanews.com/2010/07/interactions-in-the-dark-ocean/#comments Mon, 05 Jul 2010 17:01:11 +0000 https://www.deepseanews.com/?p=8823 The deep sea, a vast, dark realm featuring disticntive organisms and serving as a massive reservoir of carbon, is the largest and leas explored ecosystem on Earth.…

The post Interactions in the Dark Ocean first appeared on Deep Sea News.

]]>
Fig 1 from Steinberg and Hansell (2010) DSRIIThe recent of issue of Deep-Sea Research II is out and focuses on the ecological and biogeochemical interactions in the dark ocean. Perhaps the best summary of why this is an important contribution is from the editor of the volume themselves...

The deep sea, a vast, dark realm featuring disticntive organisms and serving as a massive reservoir of carbon, is the largest and leas explored ecosystem on Earth.  At a time when the ocean is responding to anthropogenic forcings, we note that considerably less is known about ecological and biogeochemical processes in the dark ocean (the dim mesopelagic or ‘twilight zone” plus the aphotic bathypelagic zone below) than in the euphotic zone-the focus of several prior major interdsciplinary studies.  The biological pump connects surfaces processes to the deepest ocean layers…These deep layers are characterized by significant decomposition, recycling, and repackaging of particulate and dissolved organic matter. thus, the interplay between biological and geochemical processes at depth can have significant affects on the magnitude and efficiency of the biological pump, which regulates in part atmospheric CO2 and, hence climate.

This volume contains many excellent contributions including: Major contribution of autotrophy to microbial carbon cycling in the deep North Atlantic’s interior; Assessing the apparent imbalance between geochemical and biochemical indicators of meso- and bathypelagic biological activity: What the @$#! is wrong with present calculations of carbon budgets? (discussed previously at DSN); and the great reviews Emerging concepts on microbial processes in the bathypelagic ocean – ecology, biogeochemistry, and genomics and Mesopelagic zone ecology and biogeochemistry – a synthesis.  Despite the paper not being open access, they are worth a read.

The post Interactions in the Dark Ocean first appeared on Deep Sea News.

]]>
https://deepseanews.com/2010/07/interactions-in-the-dark-ocean/feed/ 1
TGIF: Vampire Squid https://deepseanews.com/2010/02/tgif-vampire-squid/ https://deepseanews.com/2010/02/tgif-vampire-squid/#comments Fri, 05 Feb 2010 02:48:43 +0000 https://www.deepseanews.com/?p=7065 The vampire squid (Vampyroteuthis infernalis) lives in the deep ocean, home to the largest ecosystems on our planet. A “living fossil,” this animal has remained…

The post TGIF: Vampire Squid first appeared on Deep Sea News.

]]>

The vampire squid (Vampyroteuthis infernalis) lives in the deep ocean, home to the largest ecosystems on our planet. A “living fossil,” this animal has remained relatively unchanged for hundreds of millions of years. The deep ocean contains what may be the greatest number of animal species, the greatest biomass, and the greatest number of individual organisms in the living world. Humans have explored the deep ocean for about 150 years, and most of what is known is based on studies of the deep seafloor. In contrast, the water column above the deep seabed comprises more than 90% of the living space, yet less than 1% of this biome has been explored. The deep pelagic biota is the largest and least-known major faunal group on Earth despite its obvious importance at the global scale. Pelagic species represent an incomparable reservoir of biodiversity. Although we have yet to discover and describe the majority of these species, the threats to their continued existence are numerous and growing. Conserving deep pelagic biodiversity is a problem of global proportions that has never been addressed comprehensively. The potential effects of these threats include the extensive restructuring of entire ecosystems, changes in the geographical ranges of many species, large-scale elimination of taxa, and a decline in biodiversity at all scales. This review provides an initial framework of threat assessment for confronting the challenge of conserving deep pelagic biodiversity; and it outlines the need for baseline surveys and protected areas as preliminary policy goals.

The post TGIF: Vampire Squid first appeared on Deep Sea News.

]]>
https://deepseanews.com/2010/02/tgif-vampire-squid/feed/ 2
Life in the Deep Sea: Only the Fragile Survive https://deepseanews.com/2009/12/life-in-the-deep-sea-only-the-fragile-survive/ https://deepseanews.com/2009/12/life-in-the-deep-sea-only-the-fragile-survive/#comments Fri, 11 Dec 2009 21:24:32 +0000 https://www.deepseanews.com/?p=6405 At this year’s National Association for Biology Teachers conference, Steve Haddock from the Monterey Bay Aquarium Research Institute, spoke on deep ocean habitats.   The National…

The post Life in the Deep Sea: Only the Fragile Survive first appeared on Deep Sea News.

]]>

At this year’s National Association for Biology Teachers conference, Steve Haddock from the Monterey Bay Aquarium Research Institute, spoke on deep ocean habitats.   The National Evolutionary Synthesis Center sponsored the session on extreme environments and are now making all the videos available.  Steve’s excellent and visually impressive talk is above and demonstrates the wonder and beauty of the deep-sea pelagic zone.  Definitely a must watch for both information and entertainment.

And due to popular request we will be bringing back the TGIF.  Links for ocean related videos are always welcome.  Make suggestions in the comments below.

Text from Youtube on Steve’s Talk:

The deep ocean is the largest living space on Earth, abundant with diverse alien-looking life forms despite the fact that it is dark, cold, has limited resources and exerts high pressures. In response to these environmental challenges and unique ecological constraints, organisms have evolved a variety of forms and functions including transparent dome eye covers, cloaks of invisibility, and the ability to communicate by making bioluminescent light. Because there are few surfaces, morphologies have diversified in unconstrained manner resulting in 40-meter long jellies and diaphanous comb jellies that propel themselves with eyelash-like cilia. Many of these deep-sea species are not yet described, and current research involves understanding the diversity and relationships of these animals, as well as the genetic underpinnings of their unique bio-optical properties. Although they are obscure even to marine biologists and live in some of most unexplored habitats on the planet, these animals actually can occur as close as a few kilometers from a large city. This paradox underscores how much we have yet to learn about life on this planet.

The post Life in the Deep Sea: Only the Fragile Survive first appeared on Deep Sea News.

]]>
https://deepseanews.com/2009/12/life-in-the-deep-sea-only-the-fragile-survive/feed/ 2
More Mercury Deeper https://deepseanews.com/2009/08/more-mercury-deeper/ https://deepseanews.com/2009/08/more-mercury-deeper/#comments Thu, 20 Aug 2009 18:20:00 +0000 https://www.deepseanews.com/?p=5667 Mercury is distributed across the earth whether it is in the atmosphere, biosphere, or geosphere.  In the marine realm, the methylated form of mercury (CH3Hg+)…

The post More Mercury Deeper first appeared on Deep Sea News.

]]>
Figure 2 from Drazen et al. 2009. Log-transformed mean THg concentrations (μg/kg) at the mean log(mass) of 4.24 or approximately 17.4 kg plotted as a function of median depth of occurrence for 9 species of pelagic fishes.
Figure 2 from Choy et al. 2009. Log-transformed mean THg concentrations (μg/kg) at the mean log(mass) of 4.24 or approximately 17.4 kg plotted as a function of median depth of occurrence for 9 species of pelagic fishes.

ResearchBlogging.org

Mercury is distributed across the earth whether it is in the atmosphere, biosphere, or geosphere.  In the marine realm, the methylated form of mercury (CH3Hg+) is the form of mercury most easily bioaccumulated. But let’s take a step back and ask how the oceans got mercury in the first place.  One source may be from the atmosphere.  Fifty percent of atmospheric concentrations originate from volcanic activity and recently, the other fifty percent from anthropogenic sources such as mining activities and manufacturing.  Some input may also occur from terrestrial sources such as rivers and groundwater carrying inorganic mercury into coastal regions. Recent work suggests that biomediated methylation of mercury occurs in the oceans by sulfate-reducing bacteria living in low oxygen regions. The study suggests that these bacteria sink to mid-depths, where they decompose and release methylmercury. This biomethylated mercury accounts for as much as 29% of all mercury in subsurface ocean waters of the Pacific.  Methylated mercury concentrations are highest below the thermocline and nearly undetectable in surface waters. Findings for another groups largely corroborate this model for the Mediterranean, i.e. not all methylated mercury comes directly from coastal or river sources .  But the relative contribution of all these sources, whether the methylated form that enters into the ocean or formed in situ, and many other specifics of the process are either unknown or only recently understood.

A recent study by Choy et. al in PNAS begins to look at these depth related patterns in mercury concentration for bioaccumlation in 9 predatory pelagic fish and 56 species of their prey (cephalopods, fishes, and crustaceans) in the Pacific.  After accounting for age and size, both positively correlated with methylmercury concentrations, the researchers can explain 76% of mercury concentrations with depth where both prey and predator species spends most of their time.  This deeper depth, 600-1000 meters, corresponds to the low oxygen depths in the Pacific.

These results lend support for both the in situ biomethylation of mercury in the open oceans and that it is enhanced in oxygen poor depths.  Choy et. al’s data support recent conclusions that the main source of methylmercury in the open ocean is from the deep water column and not export from coastal regions or the euphotic zone.”

Of course, this also suggests that eating deep-sea fish may also put you at a much greater risk of mercury poisoning.  Just one of the many reasons not to eat our deep-sea brethren.

Source Wikipedia Commons: This chart shows the level of atmospheric mercury deposition detected in ice cores from the Upper Fremont Glacier in Wyoming. Heightened deposition rates correspond to volcanic and anthropogenic events over the past 270 years. Preindustrial deposition rates can be conservatively extrapolated to present time (4 ng/L; in green) to illustrate the increase during the past 100 years (in red) and significant decreases in the past 15-20 years.
Source Wikipedia Commons: This chart shows the level of atmospheric mercury deposition detected in ice cores from the Upper Fremont Glacier in Wyoming. Heightened deposition rates correspond to volcanic and anthropogenic events over the past 270 years. Pre-industrial deposition rates can be conservatively extrapolated to present time (4 ng/L; in green) to illustrate the increase during the past 100 years (in red) and significant decreases in the past 15-20 years.

Sunderland, E., Krabbenhoft, D., Moreau, J., Strode, S., & Landing, W. (2009). Mercury sources, distribution, and bioavailability in the North Pacific Ocean: Insights from data and models Global Biogeochemical Cycles, 23 (2) DOI: 10.1029/2008GB003425 (see also Cossa et. al 2009)

Choy, C., Popp, B., Kaneko, J., & Drazen, J. (2009). The influence of depth on mercury levels in pelagic fishes and their prey Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0900711106

The post More Mercury Deeper first appeared on Deep Sea News.

]]>
https://deepseanews.com/2009/08/more-mercury-deeper/feed/ 3