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Researchers Strive to MainstreamMolecular Tools

r. Seuss probably wasn't in a system, but finding a particular professor at Northwestern Universitythinking about genetic-based organism requires molecular tools that (Evanston, Ill.).molecular tools when he identify the organism by its genetic

wrote Horton Hears a Who, but the simi- material. Quick Startlarity between the story and the tech- Molecular tools could produce quick Molecular techniques were born innology are striking. In the story, Horton and meaningful results, avoid indicator 1972 with the discovery of recombinanthears a speck of dust talking. What he organism requirements, and det~rmine DNA and hybridization -the joining ofdiscovers is that an entire world lives whether pathogens are alive or dead, two complementary strands of geneticin that speck. Only Horton -with his said Charles Bott, an environmental en- material in which one strand is used as aespecially sensitive ears -could hear gineer at Parsons Corp. (Pasadena, probe to detect the other, said Danielthe Who's shouts. Calif.). Despite such benefits, however, Oerther, assistant professor in the

Everyone could see the speck and molecular tools still reside mostly in the Department of Civil and Environmentalnotice its movements, but without research arena. Whether these methods Engineering at the University ofHorton's sensitive ears, they could not ever will be viable for typical wastewater Cincinnati. Then in 1983, Bott said, thetell what was on it. Similarly, tradi- treatment has been a perennial discus- polymerase chain reaction (PCR) -ational wastewater measurements can sion for researchers, noted Bruce technique to amplify a strand of DNAassess the overall effect of organisms Rittmann, an environmental engineering and detect a defined sequence of genes

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-was developed, and a new method ecule attached to the probe to detect The fingerprinting techniques, on theof protein analysis caused the molecular the microorganism. other hand, enable researchers to iden-biology movement to take off. The ASH method involves attaching a tify (or at least document) the DNA of

The application of molecular tools to fluorescent molecule to the genetic probe any microorganism. "This deals with thethe wastewater treatment field has been and exposing the probe to microorgan- reality that we've only isolated and se-evolving for the past 10 to 12 years, but isms in the sample (in situ), he said. quenced a very tiny fraction of all the or-in the last 2 to 5 years it has exploded, Researchers then use a fluorescent mi- ganisms that are interesting," RittmannOerther said. Currently, molecular tech- croscope to identify the microorganisms, noted.niques are used to identify which mi- Rittmann said. However, he noted, onecroorganisms are present, Rittmann said. must know which organisms are present Early LeadsThe two classical methods are dot-blot in order to choose the proper genetic Some typical uses for molecular tech-hybridization and fluorescent in situ hy- probes for either classical method. niques in biological wastewater treat-bridization (FISH), he noted, while the ASH also can help researchers learn ment applications include identifying fil-two fingerprinting techniques are dena- about spatial relationships among dif- amentous bacteria as the cause ofturing gradient gel electrophoresis ferent organisms, Rittman noted. ASH foaming and bulking, evaluating the ef-(DGGE) and terminal restriction frag- preserves the grouping patterns and fects of microbial stress responses, andment length polymorphism (T -RFLP). aggregates of organisms in a treatment understanding the microbiology of en-

In short, Rittman explained, the system, he said, and its results star- hanced biological phosphorus removal,dot-blot method extracts a microor- tIed researchers a few years ago, when Bott said.ganism's RNA, attaches it to filter pa- FISH revealed that nitrifying bacteria "One of the most exciting areas forper, and exposes it to genetic probes generally form extremely dense group- molecular tools is the identification andthat stick to certain parts of the RNA. ings inside larger aggregates of mi- evaluation of nitrifying bacteria," BottThe method relies on a radioactive mol- croorganisms. said. "So, 'who's there, where are they,

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and what are they doing?' are the ques- ploit, but on the other hand, it's hard toJ tions we're asking, and using these tools keep up."

to answer." The bigger problem, however, is mak-Rittman agreed. In the past few years, ing water quality professionals aware of

he noted, researchers have been pushing the tools available. Understanding biol-, beyond "who's there" type molecular ogy using molecular tools is fundamen-tools to begin developing methods that tally different than biology before mole-determine what various bugs are doing. cular tools, Oerther said. While most

scientific advancements evolve over gen-J erations of scientists, molecular biolo-

-' gy has exploded onto the scene in only~~ 25 years, he noted. The result of such~ quick development is that most people, ~ at the height of their careers today lack~ any formal training in this area...>z~. Gaining Ground

r E To help move molecular tools out of~ the research lab and into practical use,~ researchers are taking molecular tech- How would you like to tackle this guy's~ niques to managers in the wastewater complaints about your lift station odors wafting~ field. into his backyard? .if you have a Biocube

r U Fo r e am I 0 th d N Odor Control System in place, you'll never

Th . d ~ l . h shows how fI x p e, er er an ancyIS '61'" mlCrograp uorescenc:e ...need worry.

in situ hybridization can identify individual ceIs Love, an associate professor of CIVIl andof Acinetobactercakoaceticus (green) and environmental engineering at Virginia Biocube has tackled histheir level of growU1 activity as measured by Tech (Blacksburg), organized a work- problem, and hundredsprecursor 165 rRNA-targeted oligonucleotide shop in 2002 so researchers and practi- like it, with our patentedprobe hybridization (red). tioners could discuss the merits of mol- biofiltration technology.

ecular tools. Funded by the National From minor nuisanceI "A microorganism can do many, Science Foundation, the 2-day workshop odors arou,nd manholes

many different things, but it doesn't do had IS participants who discussed four and vent pipes, to moreall of them at once," Rittman said. As a overarching questions: malodorous problemsmicroorganism does a given task, it ac- .Can faculty establish careers work- like lift stations and treatment plants,

r tivates the needed DNA, and molecular ing on molecular biology? Bioc~be pre~ents quiet, effec~ive andtools can read the activated DNA. How should molecular tools be stan- practically maintenance-free solutions. Ourstrands, he noted. dardized? ~re-engineered systems can be easily

.. H h Id I I I b .,. Installed by your own staff. Once in place,.ow s ou mo ecu ar too s e, ,

~ Fast P ace h ? Blocube Systems run for years without any

taugt. d' h d ' h I "Ime la c ange out an Wit on y minima

Molecular techniques are advancing. What are the practical applications ' t t I t ' ' t b' ,dmain enance, rans a Ing In 0 Ig savings an

very quickly. While current molecular of the molecular tools? 'C quicker return on your investment,tests readily identify microorganisms, At press time, Oerther said the jour- ~

.they are not yet good at counting them, nal Re/Views in Environmental Science ~ Avoid heavy confrontations

.Rittmann said. However, in the last 2 or and Bio/Technology had accepted an ar- '~ and lighten the air with3 years, researchers have begun to de- ticle detailing the workshop results, ~ your customers.velop quantitative techniques, Also, kits And last year, Rittman organized a ~ Contact Biocubeare now available that make FISH-based special issue of the peer-reviewed journal m today and specify I,t t. h f t d . h .d II!' E . R h rs ~ an odor controles mg muc as er an easler, e Sal. ..ater nvlronment esearc "eptem- c

Wh ' l ...0 solution that willI e new advancements are ""11- her/October 2002), which Included sev- 0).. th h I " . h ' f I I I ' turn them intomg m e 0 es, sometimes t e m or- era papers on mo ecu ar technIques ~ b ' f" u your Iggest ans.

matlon almost flows too quickly. "One that had been presented at WEFTEC,OI" c3, of the great strengths and also one of in Atlanta. c"

the great challenges of the business is WEFTEC.03" will feature several op. ~ B i O)C~ ~ .that it's changing so fast," Rittmann portunities to learn more about the de- E 'L-/" ,InC.

said. "It's great that we're getting these sign and application of molecular tools in .e E ' t II E ' d Od E'" ,5 nvlronmen a y nglneere or Imlnatlon

new technIques and more thIngs to ex- the wastewater treatment process. On QI

0 toll free: (877) 299-2108~ www.biocube.com0u.. Visit our WEFTEC@ Booth 5853.

and what are they doing?' are the ques- ploit, but on the other hand, it's hard tor tions we're asking, and using these tools keep up."

to answer." The bigger problem, however, is mak-Rittman agreed. In the past few years, ing water quality professionals aware of

he noted, researchers have been pushing the tools available. Understanding biol-r beyond "who's there" type molecular ogy using molecular tools is fundamen-

tools to begin developing methods that tally different than biology before mole-determine what various bugs are doing. cular tools, Oerther said. While most

scientific advancements evolve over gen-r erations of scientists, molecular biolo-

-' gy has exploded onto the scene in only~~ 25 years, he noted. The result of such~ quick development is that most people

r ~ at the height of their careers today lack~ any formal training in this area.~z~ Gaining Ground

r ~ To help move molecular tools out of~ the research lab and into practical use,~ researchers are taking molecular tech- How would you like to tackle this guy'sffi niques to managers in the wastewater complaints about your lift station odors wafting~ field. into his backyard? .If you have a Biocube

r uF I 0 th d N Odor Control System in place, you'll never

Th . d ~ l . h shows howfl or examp e, er er an ancyIS '6"" mlCrograp uorescenc:e ...need worry.

in situ hybridization can identify individual ceIs Love, an associate professor of CIVIl andof Acinetobactercakoaceticus (green) and environmental engineering at Virginia Biocube has tackled histheir level of growth activity as measured by Tech (Blacksburg), organized a work- problem, and hundredsprecursor 165 rRNA-targeted oligonucleotide shop in 2002 so researchers and practi- like it, with our patentedprobe hybridization (red). tioners could discuss the merits of mol- biofiltration technology.

ecular tools. Funded by the National From minor nuisanceI "A microorganism can do many, Science Foundation, the 2-day workshop odors arou,nd manholes

many different things, but it doesn't do had 15 participants who discussed four and vent pipes, to moreall of them at once," Rittman said. As a overarching questions: malodorous problemsmicroorganism does a given task, it ac- .Can faculty establish careers work- like lift stations and treatment plants,

r tivates the needed DNA, and molecular ing on molecular biology? Bioc~be pre~ents quiet, effec~ive andtools can read the activated DNA. How should molecular tools be stan- practically maintenance-free solutions. Our

~ strands, he noted. dardized? ~re-engineered systems can b~ easily!

H h Id I I I b Installed by your own staff. Once In place,.ow s ou mo ecu ar too s e" "

~\ Fast Pa ce h ? Blocube Systems run for years without any

taugt. d" h t d "h I "" Ime la c ange ou an Wit on y minima:, Molecular techniques are advancing. What are the practical applications ' t t I t" " t b' "

d.main enance, rans a Ing In 0 Ig savings anvery quickly. While current molecular of the molecular tools? 'C quicker return on your investment"tests readily identify microorganisms, At press time, Oerther said the jour- ~

.they are not yet good at counting them, nal Re/Views in Environmental Science ~ Avoid heavy confrontations

.Rittmann said. However, in the last 2 or and Bio/Technology had accepted an ar- .~ and lighten the air with3 years, researchers have begun to de- ticle detailing the workshop results. ~ your customers.velop quantitative techniques. Also, kits And last year, Rittman organized a ~ Contact Biocubeare now availabie that make FISH-based special issue of the peer-reviewed journal m today and specify

J t t. h f t d . h .d '" E . R h rs ~ an odor controles mg muc as er an easler, e Sal. ffater nvlronment esearc "eptem- cWh ' l ...0 solution that will

I e new advancements are "flll- her/October 2002), which Included sev- 0).. th h I " t. h . f I I I .turn them intomg m e 0 es, some Imes t e m or- era papers on mo ecu ar technIques ~ b " f" u your Iggest ans.mati on almost flows too quickly. "One that had been presented at WEFTEC.OI" i3, of the great strengths and also one of in Atlanta. c.

the great challenges of the business is WEFTEC.03" will feature several op- ~ B i O)C~ ~ .that it's changing so fast," Rittmann portunities to learn more about the de- ~ 'L--""" ,InC.

said. "It's great that we're getting these sign and application of molecular tools in .e E " t II E . Od E'"' .." c nvlronmen a y nglneered or Imlnatlon

new technIques and more things to ex- the wastewater treatment process. On "Q;

0 toll free: (877) 299-2108~ www.biocube.com0~ Visit our WEFTEC@ Booth 5853.

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Sunday, Oct. 12, Oerther will lead attending Session 20: Bulking and FlocWorkshop 115: FISHing in Activated Structure on Tuesday, Oct. 14, andSludge, which will present basics, pros Session 59: Application of Molecularand cons, and potential uses of genetic Tools on Wednesday, Oct. 15. Bott,techniques. The workshop is based on a who will moderate both sessions, said100week molecular biology course geared that he is especially looking forwardtoward postgraduate engineering stu- to the papers titied Quantifying Species

DAF (Dissolved Air Flotation) dents. In addition to interactive pres en- -Specific Filamentous BulkingRemoves F.O.G.'s, suspended tations, participants will be able to work Thresholds Using Molecular and Reactorsolids, BOD's and COD's. with molecular tools to characterize Studies and A New Molecular+Flow rates from 10 to 1100 gpm wastewater samples from their own Respirometry Method for Identifying+"V" bottom with sludge auger is treatment plants, Oerther said. Bacteria and Detennining Their Growthstandard ..

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