2010 Ecology Edition

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sph res2010

E D I T I ON 0 3

E c ol o gy

COOPERATIVE INSTITUTE FOR RESEARCH IN ENVIRONMENTAL SCIENCES

BeetleManiaAt risk: forests, watersheds,water quality and air.Will Western forests recoverfrom the pine beetle epidemic?

Forecastinglethal coralbleaching

Tracked byyour bacterialfingerprints

The Vaticanand life beyond

planet Earth


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04 Bleach alert! To protect coral, CIRES and NOAA researchers start forecasting deadly warm water episodes.05 A climate for pikas The Western Water Assessment helps evaluate the plight of the pika.06 Touchy subjectWere all continents of microscopic ecological zonesespecially women.08 Gales and res and beetlesoh, my!CIRES Carol Wessman studies the recovery of forests beset by wind, logging, re, and pine beetles.10 Dont count on the treesWarmer temperatures mean longer growing seasons and better carbon uptake by trees, right? Maybe not.11 Pine beetles impact leaves the ground, affects the air The Innovative Research Program brings diverse scientists together to scrutinize beetle epidemic.

12Dead trees dont drinkPine beetles, and steps to control them, could imperil crucial processes in Colorados watersheds.

14 Mystery of the smelly purple lake The unique ecology of Little Gaynor Lake has scientists scratching their heads. And holding their noses.16 On the wing and listening for waterfallsMigrating birds might navigate by the sounds of waterfalls along their route.19 Wheres Waldothe seal?Pioneering research uses remote-controlled planes to study ice oes and the creatures that inhabit them.

20Evolving a speedy microbe to clean up a chemical messPCP, still in use in the United States as a wood preservative, might meet its match in a microscopic janitor.

21 The Vatican City workshop on life beyond planet EarthA unique meeting takes place in Vatican City to discuss the origins of life.22 MySphere: the Fierer lab The punchy crew of the Fierer lab lend a little insightand comic reliefto their workspace.

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On the cover A pine beetle stuck by the sap that a tree used to expel it. Morgan Heim/CIRES


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Researchers have begunying Unmanned Aircraft

Systems (UAS) with cameras to help them track seal populations inthe rapidly changing Arctic. Can you nd the seals in this image? Getthe answer and read more about the research onpage 19.

See the seals?

11 millionpounds

8,200feet

of chemical pentachlorophenol(PCP) had been produced in theUnited States as of 2002.The chemical is still used asa wood preservative;many other uses havebeen restricted.Source: U.S. EPA

E e e w w w

w w w !

The average

human hand

has about 150

species ofbacteria

living on it.

Source: Fierer 2009

During a mountain pine beetleepidemic, beetles emerging froman infested tree can kill at leasttwo trees the following year.Source: Colorado State University Extension Service

The elevation below which American pikararely live in the southern portion of their range(including parts of New Mexico, Nevada, and

California). In the northern portion of theirrange, American pika have been observed nearsea level. Source: U.S. Fish and Wildlife Service

The Vati an has a nhist ry f interest inastr n my. The idea that ifemi ht be f und e sewhere... w u d be nsideredas eviden e f g dsma ni en e.

Read more about Shelley CopleysVatican visit onpage 21.

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Bleach Alert!NoAA/cIRES t ives advan ewarnin f ra -stressin heat

Warm water can kill coral, and the bleaching of coral reefsaround the world, often associated with heat stress, has becomea critical problem in reef ecosystems. Bleaching occurs whenstressed corals expel symbiotic organisms that give corals theircolor and help provide them with food. So CIRES researchersand colleagues developed a new tool to forecast warm waterepisodes. The still-experimental Coral Bleaching Outlook isa companion to NOAA Coral Reef Watchs real-time satellitemonitoring of ocean temperatures. The Outlook uses models andobservations of sea surface temperatures to forecast temperaturesone week to three months in advance. NOAA and CIRES

researchers won a Silver Medal for their work on the outlook.

Learn moreVisit cires.colorado.edu/about/accomplishments/performanceto learn more about CIRES awards.

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Re ent resear h

sh ws that were a

wa kin mi r bia

habitats ... w men

just a itt e m re s

Touchy subje

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When running around the playground as kids, itwas usually the boys who were thought to havemore cooties. But a new study shows that when itcomes to a handshake, women harbor more variedbacteria than men.

Noah Fierer, a CIRES Fellow and assistant professorof ecology and evolutionary biology at the Universityof Colorado at Boulder (CU-Boulder), looked at themicrobial colonies making their homeson human hands. He found more than4,700 species of bacteria distributedacross 51 people. The average palm, hediscovered, hosts about 150 differentbacteria species. And when separatedalong gender lines, women, well, theyhouse up to about 30 percent more kindsof microbes than guys.

Inevitable jokes aside, Fierers study,co-authored by Micah Hamady of CU-

Boulders computer science department,Christian Lauber of CIRES and RobKnight of CU-Boulders chemistry and biochemistrydepartment, illustrates the magnitude of bacterialbiodiversity on the human body.

I view humans as continents of microscopicecological zones with the kind of diversity compa-rable to deep oceans or tropical jungles, Fierer said.

Today we have the ability to answer large-scalequestions about these complex microbial communi-ties and their implications for human health that wewerent even asking six months or a year ago.

By focusing on a technique known as metagenom-icssampling DNA directly from the microbe com-munityFierer zoomed in on the lives of bacteriawith a high-powered sequencing machine, distin-

guishing about 100 times more genesequences than found in previous studiesof skin bacteria. Standard skin culturingmisses many of the microbial hitchhik-ers, his study shows.

No need to go nuts with the hand sani-tizer, however. Most bacteria dont causeillness, and can even help protect againstgetting sick, said study co-author Knight.

As for the gender gap of microbial dis-tribution, there could be several reasons

for the difference. Women tend to applymore moisturizer and makeup, bothof which could be sources of microbes especiallybecause they tend be reused. Nature has its roletoo, including differences in sweat and oil glands,hormones, and pH. One things for sure, whether onthe palm of woman or man, people are planets whenit comes to bacteria.

TheScience

DNA sequen ina ws resear herst zer in n theparti u ar ba teria

vera e n a

pers ns b dy.

A bu s-eye view n the w r d

We leavebehindbacterial trailsso distinct, thetraces couldpotentiallybe used like angerprint.

For bacteria, getting respect can be hard. A bit of aboost came recently when Wisconsin declared Lac-tococcus lactis , the bug responsible for making allthat yummy cheese, the state microbe. Now the littlecritters are getting more cred from CIRES. Here are afew of the ways CIRES scientists are upping the WOWfactor of the microbial world.

Human bodies, microbial planetsMicrobial diversity doesnt just apply to a persons

hands. A bacterium that lives on the forehead mightturn its agellum up at real estate on the elbow. CU-Boulders Rob Knight, Noah Fierer, and colleaguesmapped bacterial communities across 27 sites onthe human body and found that different zones hostunique types of microbes. Not only that, but one per-sons bacterial makeup likely differs from another.

Bacterial crime ghtersTurns out when we touch things such as a computer

keyboard or mouse, we leave behind an identifyingtrace of bacteria. These buggy clues could eventuallyplay a role in solving who-done-its, as the microbeswe leave behind are so distinct they act like a bacterial

ngerprint. Theres still work to do in order to sort outthe details, such as distinguishing between multipleusers of an object. But lawbreakers beware: some dayinvestigators might nail suspects after swabbing forbacteria in crime scenes clean of prints or DNA.

The leafy loyalty of plant microbes

Trees, too, boast their own bacterial signatures, sug-gesting that trees and their bugs share a close sym-biotic relationship. Noah Fierer and his team sampledbacteria from trees of several species and found eachspecies with its own consistent microbial community.Unlike people, whose skin bacterial communities maydiffer from person to person, trees of the same specieslikely harbor similar types of bacteria, even if thosetrees live on different continents from one another.

Steve Miller/CIRES


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When re decimates the site of an experiment, someresearchers might throw their hands up in dismay. Notso for CIRES Fellow and profesor of ecology and evolu-tionary biology Carol Wessman.

My rst thought was, This is cool, said Wessman.Now things are getting really interesting.

Wessmans research is focused on the impacts of mul-tiple disturbances on forest ecosystems. Until 2003, shehad been studying a region in the Routt National Forest

of northwestern Colo-rado that had suffered acatastrophic blowdown

in 1997, and had thenbeen partially salvagelogged in 1999. Wess-man was comparingmetrics of forest recov-ery between the two.

Then came the re.The 2002 Mt. Zirkel

Complex Fire, whichconsumed more than12,500 hectares, mayhave destroyed Wess-mans experiment. But

she simply took it as an opportunity to investigate a keyecological question: just how much can a forest stand?

I am interested to see if there is a limit to the num-ber of severe disturbances that a forest can experiencebefore its ability to regenerate breaks down, said Wess-man. Do the effects of different disturbances accumu-

late? Do the disturbances interact?Wessmans research is critical for those who want to

understand the future of forests and the services theyprovide, from biodiversity to clean water and car-bon storage. Climate change and other human-forestinteractions are expected to disturb forests with greaterfrequency, extent, and intensity. The effects of suchdisturbances are likely to have far reaching economicand social consequences. Better understanding of howforests will respond could help forest managers betterplan for the potential stormy waters ahead.

Studying forest regeneration

Since the re, Wessman and her students have beenvisiting the differently affected regions of the forest tometiculously log the ne details of forest regrowth. Theymeasure the soil temperature, water content and nitro-gen availability at 23 sites, and map the location, height,and species of every new seedling.

Prior to the re, Wessman had found that regrowth inthe areas that had been logged after the blowdown wasslower than that in the blowdown only regions; fewernew seedlings were observed and the rate of growth forexisting seedlings was reduced. It appeared that whilethe forest could recover from a single disturbance, mul-tiple disturbances proved more challenging.

After the re, however, some interesting and contradic-tory results began to emerge. Wessman found seedlingsand new growth in the sites where the salvage logginghad taken place, but not in the areas where just theblowdown had occurreda reversal of previous results.

Gales, res, and beetlesoh mE ist car Wessman: h w mu h an a f rest stand?

TheScience

After a b wd wn,in , a re,

and a pine beet einfestati n, h w dth se events a e ta f rest e systemsre very fr m ne ra f ur?


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The research has provided a really good example ofthe cumulative and interactive effects of the disturbanc-es. The various permutations of the disturbances interactquite differently and produce quite different measurableresults, said Wessman.

Predicting the impacts of beetle kill

While Wessmans besieged experimental plots werestruggling to recover from the effects of multiple distur-bances, the Routt National Forestwith many other for-ests in the Western United Stateswas hit with anothercatastrophe: beetle kill. The mountain pine beetle hasdevastated large regions in the Routt National Forest andDistrict Rangers estimate 600 acres of the forest land arelogged a month to remove affected trees. Moreover, thebeetles have impacted both Wessmans control forestand regions where the re was less severe, effectivelyburrowing their way into her research.

Wessman, however, believes the latest disturbance

simply adds another layer to her experiment. The ques-tion is how will the beetle kill interact with the otherrecent disturbances as it hits along the margins and inthe remaining areas of green forest? The whole area isundergoing change, she said.

Wessman also hopes that the insights gleaned so farwill provide useful information in predicting how thesesubalpine ecosystems will recover from the beetle kill.Forest regeneration and nitrogen cycling in beetle-killedstands may parallel the blowdown areas in some ways,because in both cases the overstory is dead, she said.

Ultimately, however, she hopes that her researchwill inform some of the questions faced in a climateof unpredictable change brought about by warmingtemperatures.

How resilient are our forests to more frequent, andperhaps more extreme, disturbances? And how dowe (humans) have to adjust to accommodate thosechanges?

StudentFocus: Brian BumaCarol Wessmans graduate student Brian Buma

is studying ecological diversity patterns followingmajor disturbances in forests.

We suspect more diversity or less diversity isa function of how much disturbance a site hasaccrued, said Buma. How do communitiesreorganize after disturbances? What sort of plantscome in?

To gain a large-scale perspective on thosequestions, Buma analyzes remote-sensing dataobtained from aerial surveys by the U.S. ForestService, to determine the relationships betweenthe different disturbances across the landscape.

Its good to get concrete numbers in a spatialsense over the whole landscape, said Buma.Then you can draw these large-scale interpreta-

tions which is really hard to do when you are juststanding on the ground.

Brian Buma earned a graduateStudent Resear h Fe wship f r hisw rk. cIRES ers tw raduatefe wships, ran in in supp rt fr ma summer r sin e semester t f uryears. Visit urwebsite t earnm re ab ut cIRESfe wships.

Learnmore

about CIRES fellowships atcires.colorado.edu/education.

Photos/Jane Palmer


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Contrary to conventional belief, as the climatewarms and growing seasons lengthen, subalpineforests will soak up less carbon dioxide (CO 2) thanthey used to, according to research by CIRES Fel-low and biology professor Russell Monson and hisgraduate student, Jia Hu.

As a result, more of the greenhouse gas will beleft to concentrate in the atmosphere.Our ndings contradict studies from other

ecosystems that conclude longer growing seasonsactually increase plant carbon uptake, said Jia Hu,a graduate student in the University of Colorado atBoulders Department of Ecology and EvolutionaryBiology.

Working with Monson, Hu found that whilesmaller snowpacks tended to advance the onset ofspring and extend the growing season, they alsoreduced the amount of water available to forestslater in the summer and fall. The water-stressedtrees were then less effective in converting CO 2 into biomass. Summertime rains were unable tomake up the difference.

Snow is much more effective than rain indelivering water to these forests, said Monson.If a warmer climate brings more rain, this wontoffset the carbon uptake potential being lost due todeclining snowpacks, he said.

Drier trees also are more susceptible to beetleinfestations and wild res, Monson said.

The researchers found that even as late into theseason as September and October, 60 percent ofthe water in stems and needles collected from sub-alpine trees along Colorados Front Range could betraced back to spring snowmelt. They were able todistinguish between spring snow and summertimerain in plant matter by analyzing slight variations inthe water molecules hydrogen and oxygen atoms.

The results suggest subalpine trees, such aslodgepole pine, subalpine r, and Englemannspruce depend largely on snowmelt throughout the

growing season.As snowmelt in these high-elevation forests is

predicted to decline, the rate of carbon uptake willlikely follow suit, said Hu.

Subalpine forests currently make up an estimated70 percent of the western United States carbonsink. Their geographic range includes much of theRocky Mountains, Sierra Nevada, and high-eleva-tion Paci c Northwest.

Dont counton the treesF rests n t ike y t

untera t warmin

cIRES Inn vative Resear h Pr ramis desi ned t stimu ate reative and

ab rative resear h. IRP pr je tsften pr du e re ative y qui k resu ts

that f rm the f undati n f a pr p saf r a m re substantia rant.


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Pine beetles impact leav

the ground, affects the aiA famous U.S. politician oncequipped, Trees cause more pollutionthan automobiles do. The statementwas widely derided, but it contained akernel of truth: trees and the soil sur-rounding their roots do produce carboncompounds called volatile organiccompounds (VOCs). VOCs can interactwith anthropogenic emissionsnitro-

gen compounds from car tailpipes andpower plant stacks, for exampletoform lung-damaging ozone smog.

CIRES researchers aretrying to understand howVOC emissions fromColorados high-countryforests will change asmountain pine beetlesinvade, killing lodge-pole pines and droppingneedles and branches tothe ground.

When you have asigni cant part of the stateoverrun with beetles,as Colorado is, its going to affect theatmosphere, said CIRES Fellow Joost deGouw. The question is, how?

De Gouw is working with CIRES Fel-lows Russ Monson and Noah Fierer totake advantage of a decade-long historyof forest experiments at the University of

Colorados Mountain Research Stationnear Nederland, Colorado. Mountainpine beetles are just beginning to arriveat the site, but Monsons group has beenworking there for more than 10 years,trying to understand how climate changealters the carbon dioxide (CO 2) cycle inforests.

Part of the ecological research hasinvolved girdling groups of treesre-moving wide strips of bark to slowly killtrees by breaking the link between theirneedles and roots. The idea was to dis-tinguish between CO 2 emissions by treerootswhich would be affected by gir-dlingand emissions by soil microbes,which would not.

Serendipitously, the research createda timeline of beetle-like disturbances,with some of the trees girdled a decade

ago (theyre now dead); and othersgirdled just last year (stressed, but stillalive).

It seemed like an ideal setup for study-ing how VOC emissions change as treesdie, Monson said. Joost had pioneeredthe development of an instrument thatpretty much captures the whole range ofVOCs, and he had the experience with

similar data. We had the site, and Noah(Fierer) had a graduate student who wasinterested.

The three Fellows ap-plied for and received anInnovative Research Grantfrom CIRES, and set up aproton transfer reactionmass spectrometer to col-lect emissions data frommountain forests during thesummer of 2009.

CIRES graduate studentChris Gray is beginningto pore through the data.In theory, he said, one

might expect VOC emissions from soilsto spike up as trees drop needles andbranches and microbes in the soil beginto decompose some of that litter. Theressome evidence, from other studies, thatplants under certain kinds of stress emitmore VOC.

Within a few years, as the easy-to-decompose material is broken down,VOC emissions may drop back downagain, Gray hypothesized. But this is allkind of new research, so were not sure,he said.

Monson said its still not certain thatthe current beetle outbreak is a resultof climate change, but there is strongreason to believe that trees that are morestressed are more vulnerable to attackby beetles. He and others suspect thatincreasing temperature and decreasingmoisture availability in the mountains arestressing the treesand girdling clearlyhas stressed them, too, Monson said.

During the summer of 2009, he and agraduate student found beetles ze-roed in on the trees that had just beengirdled... those trees acted like magnets.

TheScience

cIRES resear hersstudy h w a pinebeet e utbreak maya e t as emissi ns bytrees, itter,and s i mi r bes.

11

Learnmore

Visit cires.colorado.edu/science/pro/irp.

Steve Miller/CIRES


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Tiny beetles barely the size of agrain of rice have wreaked havoc onwestern forests in the United Statesand Canada during the last decade.An outbreak of mountain pine beetles,Dendroctonus ponderosae , has turnedwhole mountainsides of once-greenforests brown, brittle, and dead.

CIRES ecologists James McCutchan(Associate Director of CIRES Centerfor Limnology) and Suzanne vanDrunick (CIRES Associate Directorfor Science) are trying to understandhow those changesand peoples at-

tempts to control the beetle outbreakwith chemicalsare affecting re-gional water quality and ecosystems.

Their work is funded by the WesternWater Assessment, a joint project ofCIRES and NOAA.

Vegetation in a watershed affectsthe quality and quantity of water,McCutchan said. If the pine beetles

kill the trees, then one link in a com-plex system has been taken out. Wedlike to understand what that means.

Growing forests intercept some ofthe precipitation and nutrients thatfall within a watershed. Tree andother plant roots pull up water thatpercolates through soil, and removephosphorous, nitrogen, and othernutrients. As trees die, more nitrogenor carbon may ow downstream, forexample, affecting communities ofaquatic algae, plants, insects, and even

sh. If more phosphorous ows down-

hill, McCutchan said, it could affectdrinking water quality downstream.Some mountain reservoirssuch asDillon Reservoirare required to keepphosphorous below certain levels, andoften come close to surpassing them.

When human activities add chemi-cal insecticides to the mixcarba-mates or pyrethroids are the key ones

Dead trees dont drinkHow will mountain pine beetlesand attempts tocontrol themaffect aquatic ecosystems?TheScience

H w are c rad sdrinkin water andthe e systems inthe watersheds thatpr vide it, impa tedby beet e ki and the

hemi a s meant tmiti ate it?

Morgan Heim/CIRES


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used to ght pine beetlesthere maybe further effects on aquatic ecosys-tems, van Drunick said.

McCutchan and van Drunick will fo-cus their research in Rocky MountainNational Park, for two key reasons:the park is home to the headwaters ofmany river basins critical for drink-ing water in Colorado, and workingin the relatively pristine park elimi-nates some potentially confoundingeffectsseptic systems, for example,which can add nutrients to a system.

For the pesticide work, van Drunickand her colleagues will collect watersamples in the spring of 2010thepeak of the tree-spraying seasonfrom areas immediately downstreamof treated trees. The park has focusedits limited spray campaign to less-toxic carbaryl, one type of carbamate,in high-priority areas, such as nearcampgrounds. Homeowners living inscattered private inholdings within thepark may also be spraying trees, withpotential consequences on aquaticecosystems.

Initially, well look at areas likelyto have the highest concentrations ofpesticides, van Drunick said. If the

samples show high levels of carbarylor other pesticides, then she and hercolleagues can plan further sampling.

We certainly dont expect to seeenough carbaryl to at-out kill sh,van Drunick said, but we can moni-tor carbaryl to determine if concen-trations are high enough to causesublethal effects such as changes inrespiration or swimming performancein sh, or changes in the compositionof aquatic invertebrate communities,which could, in turn, affect sh.

McCutchan will measure a suite ofnutrients in water samples collectedfrom montane streams in the parkduring several times of yearinclud-ing samples from the 2009 and 2010Water Blitz, a collaboration withRocky Mountain National Park sci-entists interested in monitoring waterquality in the park. The single-dayBlitz, conducted with the help of doz-

ens of Park Service employees andvolunteers, generates a water qualitysnapshot in time, McCutchan said.

We hope that by putting togethersnapshots with more intensive timesampling, we can go beyond monitor-ing to analysis, and to understandingthe system in a more complete way,he said.

U.S. Forest Service 13


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Mystery of the smeTheScience

Unp easant as it maybe, the e y atw rk in litt e gayn rlake u d havep sitive imp i ati nsf r bi fue pr du ti n.

14

Ah! The sun is shining. The day is warm, and afriendly breeze sweeps by just enough to tease at yourhat. On days like these, theres nothing like a nicespring or summer afternoon by the lake. But wait.Something else came in on the breeze, something thatdoesnt go with good times or fresh air and summerswims. It smells like rotten eggs. And the lake ripplespurple across the way, looking like Kool-Aid gone bad.

This is Little Gaynor Lake, a small, naturally occurringbasin called a prairie pothole. The lake is one of twopotholes in Boulder County. As ice melts and water

warms, the lake periodically turns purple and beginsto emit an unsavory odor, an odor that so offendedthe neighbors that Boulder County Open Space askedCIRES researchers Prof. William Lewis and Dr. JamesMcCutchan to gure out what was going on with thiswatering hole. The answer might not be welcomenews for the surrounding residents, but could bodewell for biofuel research.


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purple lake

15

The source of the dilemma appears to be a naturaland rare phenomenon. As far as we know, theresno overland source of pollution because theres notributary to this lake, said Dr. Lewis. So even if therewere no people around, the lake would probably stillbe doing this.

A lake with only a small amount of groundwaterowing through it has become a sulfur-rich environ-

ment. With that distinguishing character comes anunusual ecology. Organisms specially adapted to ex-ploit oxygen-poor waters have colonized the lake. An

alga, Anabaenopsis elenkenii , produces organic matterthat uses up oxygen near the lake bottom and leads tothe formation of sul de. One bacterium, Chromatium ,uses sul de for photosynthesis and is responsible forthe lakes occasional purple color. When wind churnsthe water, the smelly sul de rises to the top, and,coupled with light, fuels photosynthesis by the purple-colored bacteria.

That the unusual lake is natural raises uncertaintyabout what, if anything, Boulder County should doto x it. The upside is that the organisms responsiblefor the smelly, purple lake could offer clues to a newform of biofuel production. The alga is hardy, continu-ing to grow and release energy even in environmentsdeprived of light and oxygen. That makes it a goodcandidate for biofuel.

The fact that the alga is so abundant is another plus.The theoretical cap on chlorophyll concentrations, anindicator for algae densities, for a lake of this size is

about 300 mg/L. Little Gaynor Lake showed concen-trations upwards of 2,000 mg/L. When we saw thatwe said, Wow! We havent seen concentrations thathigh before, said McCutchan.

Need another reason to like this odorous environ-ment? The algas af nity for salty waters could aidbiofuel production in places where agriculture isotherwise off-limits.

C I R E S p h o t o s


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Migrating birds could put the most state-of-the-art GPS to shame with their arsenal of built-innavigation sensors. These frequent yers usetools, such as Earths magnetic eld, the sunsorientation, visual cues, and weather to navigate

migration routessometimesspanningthousandsof miles andmultiplecontinents. Nowa new study inprogress looksat the possibilitythat waterfallsmight offer

another clue asto how birdsstay on track.Waterfalls sendout distinct sound

signatures, so CIRES and NOAA/ESRL scientistAlfred J. Bedard is comparing the soundscape ofNiagara Falls with the hearing power of pigeonsand migration patterns of birds traveling alongthe Atlantic Flyway. If Bedards suspicions provecorrect, this would be the rst evidence thatbirds use waterfalls as navigation beacons whileon migration.

On the wing

and listeningfor waterfalls

TheScience

New resear hsu ests that birdsuse their hearinin additi n ts ar rientati n,weather, and visua

ues t navi atemi rati n r utes.

North American ywaysThere are four major geographic routes along which birds migratenorth and south over North America.

P a c i c F l y w

a y

C e n t r a l F l y w

a y

M i s s i s s i p p i F l y w

a y

A t l a n t i c F l y w

a y

iStockphotoCIRES/migration.pwnet.org


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iStockphoto

For map lovers, digital elevation models (DEMs) are the perfectvirtual exploration tool. Zoom in to Alaskas King Cove to seehow the sea oor drops off just south of the island. Pan over tothe Gulf of Mexico to check out the shallows west of Florida.These maps dont just allow for detailed tours. For a couple ofyears, researchers have used DEMs to monitor tsunami impacts.Now, theyre also helping scientists keep an eye on the health of

ecosystems.

CIRES researchers and colleagueswith NOAAs National GeophysicalData Center have spent the last fewyears producing 10-meter resolutionDEMs of dozens of coastal areasaround the country, from Hawaii toMaine.

These are primarily for tsunamimitigation, to serve forecast andwarning programs, said CIRES BarryEakins, science lead of the CoastalScience Team producing the models.NOAAs Lisa Taylor directs the team.Emergency managers trying to plan

for potential tsunami inundation events need precise elevationinformation, she said.

DEMs can also be used for ecosystem modeling, to predict stormsurges associated with hurricanes, to understand coastal upwelling,and to characterize sh habitat, Eakins said.

To produce the technical models, Eakins, Taylor, and colleaguesuse every source of elevation data availablerecent data fromsophisticated remote-sensing instrumentation on satellites,airplanes, or boats; or from historic maps produced by federal,

state, and local institutions. DEMs are used operationally, inNOAAs Tsunami Forecast and Warning System, and theyrebeginning to reach ecosystem managers.

CIRES graduate student Jason Caldwell is using DEMs forhis Ph.D. research on salmon in the Central Valley Projectof California. Caldwell, whose advisor is CIRES Fellow BalajiRajagopalan, said the projects overall goal is to improve thedecision-making tools relied on by water resource and sheriesmanagers in the Sacramento River Basin, to reduce sh mortalityfrom higher stream temperatures in summer months.

In 2004, the National Marine Fisheries Service identi edlimitations in the regions water allocation decision-supportsystems. Water managers had insuf cient information aboutstream temperature uctuations in space and time (warm streamtemperatures are harmful to sh, but streams can be cooled withcontrolled releases from dams). So Caldwell is linking ne-scaleDEMs of the region to hydrology and weather models to betterunderstand when and where water temperatures are likely toexceed critical thresholds for sh mortality. In theory, his workbuilding better decision-support tools can be applied in otherlocations as well.

Mapping the seaooraids tsunami, coastal

ecosystem monitoring

TheScienceMaps f the sea

r used tpredi t tsunamiimpa ts a spr ve usefuin m nit rin

e systems.


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Field biologists tend to collect fascinating stories. Thetime a gorilla charged. The time someone stepped on awasps nest. That harrowing ight to the research station.

It can be dif cult to keep tabs on living things, particu-larly when they live in very remote areas, yet doing so isoften critical for conservation decisions. CIRES scientistBetsy Weatherhead is helping NOAA use unmanned

aircraft systems (UAS), originally developed for militaryuse, to meet NOAAs mission involving ecology of iceseals in the Arctic.

The sealsringed, ribbon, spotted,and beardedall fall under NOAAsprotection, and they each rely in someway on oating patches of sea iceforbreeding, foraging, or to escape preda-tors. That makes the animals potentiallyvulnerable to climate change, which iswhittling away at Arctic sea ice. Andit makes the seals dif cult to study,Weatherhead said. Seals occur overvast areas of the Arctic, and accessingthese areas safely is challenging usingcurrent vessel-based and aerial surveytechnologies.

So Weatherhead and several other NOAA colleagues,including Robyn Angliss, Deputy Director of NOAAsNational Marine Mammal Laboratory in Seattle, Wash-ington, spearheaded the development and support of aproject to send a UAS over sea ice, to see if the tech-nique could be used to identify ice seals and monitor

populations.In May and June of 2009, years of planning culminated

in the launching of a Scan Eagle UAS, with a 10-footwingspan, from the NOAA vessel MacArthur II in theBering Sea west of Alaska. The UAS, which is ownedby the University of Alaska-Fairbanks and operated byGreg Walker, carried a video camera and a digital still

camera, which captured about 25,000 images during 10ights over sea ice in the Bering Sea.Viewed from 300 feet above the surface, a ribbon seal

can look like a shadow, or a puddle of dark water on alight-colored oe of ice, and the sheer number of imagesthat require processing is daunting. Now, Weather-head and her colleagues are trying to gure out how to

quickly and automatically retrieve data from the imagesthey obtained.Theyre beginning to talk with image

processing companiesgroups thatwrite face recognition software, forexampleto help pick out seals fromshadow.

The researchers have pored throughenough of the images to know thatthey will be useful, Angliss said. Wehave been impressed by the quality ofthe digital still images, said Angliss.Based on preliminary review, we candetermine ice seal species, relative age,and gender for some ice seal species.This technology may be useful in thefuture to monitor ice seal populations

across the Arctic.Occasionally, its possible to learn even more about

the seals environment. In some images collected usingUAS in other parts of the Arctic, you can see the foot-prints of polar bears, Weatherhead said. Weatherhead,an atmospheric physicist who studies climate change

and variability, especially in the Arctic, said shes de-lighted to be working closely with population biologistson the project.

Here we have ecologists counting animals andphysicists studying sea ice in the same places, Weath-erhead said. Its terri c to be working together onthese same images.

Wheres Waldo...the seacIRES resear her he ps e ists with pi neerin te hn y

TheScience

Physi ists ande ists team upt use unmannedair raft t study

rem te Ar ti i e andthe reatures that ait h me.

Photos/NOAAAn unmanned aircraft system (UAS) is launched from a ship in the Arctic.

Two seals among the cracks and shadows on the sea ice. NOAA


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Few bacteria would choose the hazardous man-made chemical pentachlorophenol (PCP) from themenu of microbial delights. But one bug is givingit a shot. Its the best-described of only a handful ofbacteria known to break down the pollutant. Oneproblem though: its not particularly good at its job,yet.

Theres a chance that modern science could help thismicrobe sort out its digestive problems. Thats whyCIRES Fellow and Professor of molecular, cellular, anddevelopmental biology Shelley Copley is leading aresearch team aimed at engineering a more ef cientform of the bacterium. The goal is not just to makea better bug, but to understand what it took to makeit happen, said Copley. How do you evolve newenzymes and new metabolic pathways? We want tounderstand the process on a molecular level.

If Copley can do that, PCP, long considered dif cultto destroy, may have reason to start shaking in its

chlorine bonds. Introduced in 1936, PCP worked asan herbicide, algicide, fungicide, and insecticide, andwas a widely used wood preservative and disinfectantuntil it was largely banned in the United States in1987. Today its used for mainly industrial tasks: tomake utility poles, railroad ties, and wharf pilings last.Exposure to high levels of PCP can induce fever, dam-age the liver and immune system, and possibly causecancer. Because PCP is both highly chlorinated and

man-made, it is dif cult for nature to clean up.One natural exception is the bacterium Sphingomo-

nas chlorophenolicum , which likely developed itspathway for breaking down PCP in the few decadessince the chemicals introduction. The process iscumbersome, requiring several enzymes that run intoproblems along the way. One intermediate product iseven more toxic than the original pollutant and canbe harmful to the bacterium. The enzymes dont doa good job, probably because they just havent hadenough time to evolve, said Copley. They donthave good control over the chemistry.

Some genetic engineering could smooth out the pro-cess. Students and post-docs from Copleys group arecloning the genes that encode the chomping enzymesand putting them into the bacterium E. coli . They areusing in vitro evolution techniques to generate tensof thousands of variations of the enzymes to identifywhich ones do the best job. Through this process, Co-

pley hopes to select for better enzymes that can thenbe put back into the original bacterium. If Copley andher team succeed, S. chlorophenolicum may becomethe PCP-eating champion of the world.

This is a novel pathway that has evolved veryrecently, offering a rare glimpse into evolution in ac-tion, said Copley. It represents an exciting opportu-nity to both study evolution and help solve a humanhealth and environmental problem.

Evolving a speedy microbeto clean up a chemical mess

TheScience

The perni i ushemi a

penta h r phena ,r PcP, is sti

wide y used t treatw d f r te eph nep es r rai r adties. can an enzymebe en ineeredt redu e PcPs

envir nmentaimpa ts?

iStockphoto


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The Vati an city w rksh pand ife bey nd p anet EarthIn 2009, cIRES Fe w She ey c p ey was am n the s ientists invited t dis uss ife and its

p ssibi ities utside ur s ar system durin a unique meetin in Vati an city.

This was a gathering to discuss astrobiology. Can youtell us about this relatively new area of scienti c studyand how you became involved in it?

NASA de nes astrobiology as the study of the origin,evolution, distribution, and future of life in the universe.Its a fascinating interdisciplinary endeavor that bringstogether astrophysicists, planetary scientists, geologists,chemists, biologists, and even philosophers.

My interest in astrobiology stemmed from my workon the evolution of enzymes and metabolic pathways.Thinking about the origin of the sophisticated proteinenzymes and robust metabolic networks found in extantlife inevitably led me to thinking about the characteris-tics of the earliest life forms on Earth, and then to think-ing about how they arose from the collection of smallorganic molecules available on the early Earth.

What was it like giving a talk of this nature in a placelike Vatican City?

It was surreal. In many ways, it was a typical scienti cmeeting. There were excellent talks from top scientists indiverse areas of astrobiology, and fascinating discus-sions over coffee and meals. Our hosts were priests, butthe meeting wasnt about religion, or the relationshipbetween religion and scienceit was all about thescience. The Vatican has a long history of interestin astronomy. The idea that life might be foundelsewhere in the Universe is quite acceptable tothe Church, and indeed would be considered asevidence of Gods magni cence.

You spoke about catalysts as essential forlife to emerge. Can you tell us a littlemore about this relationship?

Almost every reaction that occursin living organisms is catalyzed byan enzyme. This is critical for lifebecause these reactions would

otherwise be terribly slow. Catalysts were also critical forthe emergence of life, not only because they acceleratedthe rates of certain reactions, but because they dictatedthe types of reactions that would be incorporated intomodern metabolic networks.

Were there any other topics that stood out for you? The topic that really grabbed my interest was the

amazing increase in the rate of discovery of extra-solar

planetsthere are now several hundred known extra-solar planets! Also, the ability to detect planets in thehabitable zones is improving. This is harder because itrequires detection of smaller planets closer to stars, butit is starting to happen, so we can now be sure that thereare habitable planets out there.

What did you get out of this experience? I came away with a renewed sense of excitement

about working on a Really Big Questionthe origin oflifeand a profound respect for the power of interdisci-plinary science.

Where do things go from here? Life on other planets? Abetter understanding of life on Earth?

There are so many important unanswered questions.We know of only one example of life at this point,

and we have a poor understanding of how life origi-nated on this planet. That makes it dif cult to pre-dict what life might look like on other planets, whattypes of planets (and moons) might support life, and

how we should look for life elsewhere. Thereis a lot of interest in what exotic forms of life

might look like. A big challenge is guring

out how best to look for life, given theuncertainties about what were lookingfor, the vast distances involved, andthe high cost of big telescopes and

the higher cost of space missions.

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MySphere

A vacuum pumpit really sucks.

Protocol posted in mid-air so as to be resistantto note-taking.

Flammables cabinetdoubles as tiny graduatestudent of ce.

Timer used to see how long it takes for a) ex-periment step to nish, b) donuts to disappear.

H w pe p e w rk,resear h, and re ax at cIRES

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Fierer Lab

Why are microbes cool?

Because theyre like tiny little people!Gaddy

Because theyre everywhere; theyreancient, and 99 percent of describedspecies are unculturable, which means nofeeding, no tanks to clean, and no poopto pick up. Garrett

Microbes make the world go round,some give us the runs while others giveus a buzz! Bob

The immense number of microbes,although individually small, affectchemical cycles on a global scale.Chris G.

Because there arent many things thatcan produce both cheese and diarrhea.Chris L.

Theyve ruled the world for billions of

years, and theyre incredibly diverse,but weve only just begun to crack theirsecrets. Kate

Polymerase chain reaction (helps look atDNA) cleanup kit with components missingto provide additional fun when working underdeadlines.

The barhelps make the cocktail reagentsfor samples.

Multichannel pipette for measuring outsamples.

Tip jar for used micropipette tips lls up inless than ve minutes, sometimes even fasterwhen Donnas well-caffeinated.

Assistant Ashley blending in with lab equip-ment.

Sample wellswhere thousands of little DNAslive. Equals $5,000 in samples and one Ph.D.disseration (no joke).

Latex gloves stuffed back in box after failed at-tempt to get the prize inside. Used to preventcontamination.

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Morgan Heim/CIRES

From Left: Chris Lauber, Donna Berg-Lyons,Scott Bates, Ashley Grimaldi

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2010 Ecology Edition

Documents

Transcript of 2010 Ecology Edition