Posts in category Microbial & Environmental Genomics

We Had Fun with Genomics!!

Published by Lisa McDonald on 16 March 2010 in Education and Microbial & Environmental Genomics.

BEWiSE March 6 & 13 at JCVI

BEWiSE March 6 & 13 at JCVI

Wow! It’s been an exciting week!! Crystal Snowden and I flew to San Diego Friday, March 5th – jumped off the plane and the fun began!  We went straight to the lab and set up for BEWiSE and prepped for Expanding Your Horizons (EYH).  We are really fortunate to have such a great team in the San Diego facility.

Saturday started early with Crystal Snowden heading out to EYH at University of San Diego.  I did not go, but Crystal said it was an AWESOME time.  She worked with 45 young ladies.  The students learned about Winograsky columns and how the environmental organisms contributed to the microbial fuel cells and waste water treatment.  They prepared microscope slides by staining bacteria and viewed them under the microscopes.  The participants ranged in age from 12 to 16.  Unfortunately, Crystal was too busy to take pictures!  The quote of the day was, “This is AWESOME!”

Pipetting in the lab

Pipetting in the lab

While Crystal was busy at USD, Orianna Bretschger, Shino Ishii, Angela Wu, Eric Son and I hosted 16 young ladies from BEWiSE. Our day started early too at 9:00, running through 2:30.  We learned about genomics, microbial fuel cells and waste water treatment.  In the labs, the girls mastered pipetting and DNA extraction culminating with DNA isolation from the Winograsky columns.  The day ended with setting up PCR of the DNA isolates.  It was like riding a lab train.

Orianna Bretschger is helping get the mud samples - stinky!!

Orianna Bretschger is helping get the mud samples - stinky!!

During the week, Crystal finished the students’ samples through library construction and the second PCR.  The samples then traveled east to Rockville for sequencing, where Monica Thomas picked up the process.  She prepped them for sequencing and came in at 3:00AM Saturday morning to pull the data off the sequencers for us.  Wow! That is team work AND dedication.

We started again Saturday, March 13th early at 9:00AM.  I knew the samples worked, but the BEWiSE participants didn’t.  We poured our agarose gels, used a new buffer that enables the gels to run faster, checked out the transformation plates – ending with a BLAST search of their sequence DATA.    Of the eight groups, six had data – the sequencing of the 16s RNA gene matched uncultured bacteria.  Cool!  Some were related to Cyanobacteria – even cooler!  It was a great time for young ladies and JCVI staff.  We get invigorated too!!!

How could the week get better? In the middle of the week, we also exhibited at the San Diego Science Alliance High Tech Fair as I noted in my last posting.  We brought the Winograsky columns, the sediment tanks and the microscopes.  We recruited a few more JCVI staff and scientists to help – Sue Fields, Greg Wanger, Jeff McLean, Adi Ramon and Jeff McQuaid.  Under the scopes we had some estuary water with algae, small bacteria and paramecium – cool.  For our younger guests, we also had Daphnia to look at.  With the scopes, we were able to draw participants’ interest and then talk about our batteries and water reclamation.  Tuesday night, we had participants of all ages – 800 in two-hours.  Wednesday, there were at least 1,000 students being bus’d in from all over San Diego.  The booth was rockin’ and rollin’ – and it wasn’t just because the booth next to us had Guitar Hero™.
Orianna Brestchger at the SDSA High Tech Fair!

Orianna Bretschger at the SDSA High Tech Fair!

I flew back to Maryland Sunday – exhausted.  It was a GREAT week!  I hope to see all the BEWiSE girls applying for internships in the next year or two.  Don’t forget to tell your teachers what you did!

For more pictures – visit our Facebook page.

Watch for us at the SD Science Festival on MARCH 27th!!

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Scientist Spotlight: Orianna Bretschger

Published by Laura Sheahan on 11 March 2010 in Microbial & Environmental Genomics.

Most of us have never thought about how to make more water or cleaner water or develop unique sources of energy but that’s exactly what Orianna Bretschger does at JCVI.  She is working at the intersection of engineering, physics, and biology to design small machines powered by bacteria that can purify wastewater and generate electricity at the same time.

Orianna Bretschger

Orianna Bretschger

Working in alternative energy was a natural career choice for Orianna since she grew up in the desert in Arizona where water was a precious and finite commodity. She also lived in places without electricity or plumbing.  One place, that holds fond memories for her, had an old-fashioned windmill that was used to pump water into an open tank for cattle.

Orianna always had an interest in science, especially astronomy, and with that interest, coupled to good teachers who always inspired her, she found her way to where she is now.

At an early age, Orianna entered the Young Astronauts program.  She had been introduced to the program by the school director, who happened to be a nun, who was at one time on the short list for the “teacher in space program.”  By junior high Orianna had attended two International Young Astronauts conferences, toured the Johnson and Kennedy Space Centers, and travelled to the former USSR with her mentors and another student to help build relationships with Young Kosmonauts; a trip that solidified her love of science.

In high school she expanded her science interests to physics and planetary science, and had the opportunity to present a poster at a Lunar and Planetary Science conference at the Johnson Space Center in Houston.  Incidentally, her teacher for these courses was also her cross-country coach – he encouraged her to go to school at Northern Arizona University, in Flagstaff, AZ (where the “dwarf planet” Pluto was discovered) where she earned a merged degree in physics and astronomy.

After her undergraduate education, Orianna went into industry, landing a job at Raytheon Missile Systems in Tucson, Arizona. There she worked on guidance systems, supporting projects in the Electro-optical subsystems department for two years, something she considers to be a great experience.  As part of her work there on the Algorithm and Analysis team she developed algorithms for the guidance systems and began the efforts to test and validate the system. As part of her job she got to fly in old military planes, collecting and analyzing flight data and system performance.

At the end of two years at Raytheon, she still had not made the decision to attend graduate school but instead headed to Authenti-Corp, a company that is involved in biometrics evaluation (e.g. facial and voice recognition devices, fingerprint and iris scanners, digital signature verification, smart cards etc.)  where her primary job was working with the Department of the Army Biometrics Task Force to develop policies and procedures for biometric systems testing and implementation. She decided that government contracting was not for her, and subsequently worked various jobs for a couple of years, including bartending in her time off, to prepare for grad school.

Orianna decided on University of Southern California, where she was accepted into the Materials Science Ph.D. program in the School of Engineering. She spent her first semester working in a Carbon Composites lab, and later met Ken Nealson in the Biology Department where she began working on microbial fuel cells (MFCs) in Ken’s laboratory.   Graduate work was focused on identifying the specific genes in the organism Shewanella oneidensis MR-1 involved with electrical current production, and solid-phase manganese and iron oxide reduction. She also led the effort to characterize the power performance, fuel flexibility, and metabolic activity of several other Shewanella wild-type strains and environmental enrichments. Throughout these projects she was given the opportunity to learn and practice microbial physiology, reactor design, electrochemistry, analytical chemistry, and environmental engineering.  She graduated in the summer of 2008 and then joined JCVI with Ken.

Orianna really enjoys the diversity of science at JCVI and according to her the wonderful people make for a terrific work environment. Specifically her interests are to extend the technology for sustainable wastewater treatment, energy recovery, and develop MFC systems for the study of microbial physiology.  Ten years from now she hopes to be tenured faculty, and believes her work with engineered and biological systems will ultimately contribute to developing healthy and sustainable water management practices throughout the Southwest and worldwide.

Note: Adapted from the original article written by Karen Nelson, Director of JCVI’s Rockville campus.

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Having Fun with Genomics

Published by Lisa McDonald on 3 March 2010 in Education and Microbial & Environmental Genomics.

I am the generation after landing on the moon. As a child, I don’t recall having any science inspiration. I was fortunate to have parents that made it possible for me and my siblings to get a very good education. I went to a small parochial school outside of Washington, DC. It was a great school but we had no labs and so my exposure to science was limited at best.  I always liked school and did well, especially in math.

Then I went to Elizabeth Seton High School and had a bumpy road of it. I had two strong teachers mentoring me, Sr. Lani, my homeroom teacher, and Sr. Mary Marguerite in Pre Calculus and Calculus. Though I still had no real strong interest in science, I decided to take AP Biology in senior year. Ms. D’Apolito made us read science journals. Wow! That was unbelievably hard!! I struggled. But in this class, Ms. D’Apolito brought her love of science and research experience into the classroom. I vividly remember reading a journal article about E. coli and thought, “This is so cool! I want to go into research.” And my friends thought I was crazy. So off to college I went, majoring in nursing.

Staying locally, I entered the Catholic University of America, planning to concentrate in nursing. My first year chemistry was taught by this incredible teacher, Dr. Diane Bunce, who is currently a Nifty Fifty with the USA Science and Engineering Festival. She made chemistry exciting and alive!! My second semester, I knew I really wanted to study science. Through many discussions with Dr. Bunce, I realized with a chemistry degree I could do anything from make new plastics to make new cosmetics (her sister worked at a major cosmetic company). Finally, I decided I really wanted Biochemistry – I love photosynthesis!! From there, I continued to work with Dr. Bunce who specialized in chemistry education. I was a teaching assistant (TA) for her professional development in the summer – working with high school chemistry teachers – and I TA’d in her non-science major chemistry class. Dr. Bunce is one of my greatest mentors.

From there, I graduated and had another extraordinary opportunity to come to work in what was described as a “controversial” lab at NIH. I had no idea what I was walking into – but am extremely grateful that Dr. Venter gave me the opportunity to work in his lab. From there, you can read Dr. Venter’s book. I participated in the greatest scientific revolution – the beginnings of genomics!! Furthermore, I have gotten back to my roots – I get to work with teachers, students and “non-science” community to excite them about science and genomics.

Why do I share my story? To explain the difference between my school science experience and the opportunities that exists today for kids of all ages. I never had the opportunity to participate in science enrichment programs because very few existed then. This coming week, JCVI is presenting at two awesome events and hosting a group of young women for a special program in San Diego. First, March 6 and 13, we will be hosting BEWiSE, Better Education for Women in Science & Engineering. BEWiSE is a program of the San Diego Science Alliance and makes a difference for talented young women who are encouraged to contribute to science and engineering professions. Twenty 9th graders will have the opportunity to explore the microbial diversity from soil in a sediment battery by working with JCVI’s Orianna Bretschger. Wow! I never did this in high school or college.

We are also presenting on March 6th at the “Expanding Your Horizon Conference” at the University of San Diego. My colleague, Crystal Snowden, will be hosting a workshop discussing the sediment fuel cell and exploring the bacteria present. This conference reaches out to young girls too! What fun to see the critters under the microscope!

Finally, we will be exhibiting along with several other organizations in the area at the San Diego Science Alliance High Tech Fair. Here, we will have the sediment batteries, microscopes for viewing sea water microbes and soil bacteria, plus slides of diatoms found in Antarctica. Did you really think that electricity could be generated from mud, let alone, sludge??

I wish I had the opportunity to go to programs like this when I was young! You never know when that spark will be lit – in a classroom, at a science festival, watching the waves or a discussion over dinner. Finally, a big thank you goes to all my mentors I’ve had in my life: Sr. Lani, Sr. Mary Marguerite, Ms. D’Apolito, Dr. Bunce and Dr. Venter!

Have you thanked your teachers and mentors lately?

Watch for pictures next week.

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AGBT, Marco Island 2010

Published by Samuel Payne on 3 March 2010 in Bioinformatics and Microbial & Environmental Genomics.

I just got back from AGBT in Marco Island, Florida and I am still in awe. As noted in the name, this conference highlights advances in both genome biology and technology.  The biology seemed to be very human genome centric.  Many of the talks presented full genome sequences of cancer genomes or familial cohorts.  Some of the numbers that people threw around were shocking. It was only a short time ago that Craig Venter came out with the first personal genome, and now sequencing centers like Washington University in St. Louis and the Broad are talking about sequencing hundreds of human genomes in a year.  I was really impressed by a talk from Wash-U where they sequenced 4 exomes for Miller’s syndrome – two normal parents and two affected children – and discovered the causative gene.  They were also very honest about their efforts not being as readily successful in a variety of other Mendelian autosomal recessive traits.

One of the more interesting fallouts from all this sequencing is that everyone is submitting to dbSNP; I think that soon nearly every base will have a SNP.  Unfortunately people are currently using dbSNP to filter out candidate SNPs for their study.  Their logic runs something like, “If it’s in dbSNP then it must be benign.”  You can easily see that with the sequencing of several hundred cancer genomes, this proposition will no longer hold.  dbSNP will hold a vast array of deleterious SNPs.  What it needs to transform into is not just a database of ‘Chr17:2345656 A->T’, but rather something that keeps track of frequency and phenotype. Also there was a discussion about false-discovery rates, and how to keep databases clean.  Some of these studies were going to submit 18 million new SNPs, with a 10% FDR. That’s 2 million false positives :(

The technology portion of the conference was amazing.  There were new instruments being rolled out by numerous companies, and they were all promising. I loved sitting and listening to the clever new set-ups. There were several single molecule sequencers which I am very excited for – because we can hopefully get past metagenomic pools and on to metagenomic genomes.

I was lucky to be chosen as a presenter in the Genome Informatics session on Thursday evening.  There were lots of talks about RNA-seq and getting more out of your sequencing data.  So I felt like a bit of an outsider not talking about sequencing.  My presentation was on proteogenomics, which uses proteomic data to improve genome annotation.  Then major thrust for this audience is that genome annotation is far from perfect, and proteomics evidence can reveal many novel proteins in every genome that I’ve come across. I think that as biology expands past E. coli and B. subtilis into the vastness of genome diversity, we are seeing genes that look nothing like we’ve ever imagined.  Rather, as I point out in the talk, we are often NOT seeing these new genes because gene predictors fail to recognize them.  I’ve attached the slides to the post for your viewing pleasure (Payne.AGBT.2010).  Let me know what you think.

Sam

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High Impact Science in Antarctica

Published by Jeff McQuaid on 28 February 2010 in Education and Microbial & Environmental Genomics.

The Mertz Glacier as seen in 2007, extending 75 km out into the Southern Ocean

Antarctica was in the news this weekend when a 97 kilometer long iceberg the size of Luxembourg collided with the floating Mertz Glacier, breaking the famous glacier off at the base and generating a 2500 sq. kilometer iceberg. Each of these behemoths weigh several hundred billion tons, so the impact must have been quite a crunch!

Iceberg B9B collides with Mertz Glacier Tongue

At right is an image taken February 20th, several days after the impact: the broken Mertz Glacier Tongue is on the left side of the photo, and the colliding B9B iceberg is near the center-right.   The Mertz Glacier, which was sheared off at the base, was a significant barrier to westward drifting sea ice.  The Mertz Glacier is on the George V coast of East Antarctica, a region is famous for its high-velocity katabatic winds: sustained wind velocities at nearby Dumont D’Urville have reached 199 m.p.h!  These winds blow the pack ice out to sea, and because of the blocking geometry of the Mertz Glacier, this area generally remains ice-free all winter.

Fluorescence map of the Mertz Polynya in December 2007 (mertz Glacier is in lower right). Surface blooms are in red, and marine metagenomic samples were taken in areas marked with a star.

In the Austral summer of 2007, scientists from the J. Craig Venter Institute visited this ice-free area, or polynya, as part of the International Polar Year’s Census of Antarctic Marine Life (CAML). Because sunlight can freely penetrate the water column, polynyas are areas of enhanced productivity. Diatoms and other phytoplankton form massive springtime blooms, supporting whales, penguins, and much of the Antarctic food chain.  Above is a fluorescence ‘bloom map’ of the Mertz Polynya, just west of the Mertz Glacier. Our expedition on board the Aurora Australis attempted to capture a biological snapshot of the entire region, and Jeff Hoffman and I were able to collect samples ranging from thick blooms of  Phaeocystis antarctica to oligotrophic cold-water upwellings at the base of the Mertz Glacier.

CTD Rosette being deployed at the base of the Mertz Glacier to collect a sample from 1320m deep

CTD Rosette being deployed at the base of the Mertz Glacier to collect a sample from 1320m in depth

The region around the Mertz Glacier is equally famous as one of three regions where Antarctic Bottom Water is formed (the other two are the Ross and Weddell Seas).  Bottom water is created where saline water is extruded from newly formed sea ice.  This cold dense water sinks from the surface and becomes distributed into all of the world’s major ocean basins. Because the sea-ice in a polynya is continuously formed and blown out to sea, there is near continual production of brine and bottom water.  While in the Mertz Ploynya, Jeff and I used the ships 24-bottle CTD rosette to sample some of this bottom water, and one of the samples came from Buchanan Bay, right next to the area where the glacier split.  This sample came from a depth of 1320m, and may yield insight into bacterial activities at the base of the water column.  Additional deep water samples were taken in the Adelie Depression , the Mertz Bank, and the Mertz Depression, and one sample came from a depth of 3,690 m in the Southern Ocean.

Almost half of the water samples we collected have been sequenced using 454 sequencing technology and are in the process of annotation.  This biological data will form an important baseline as this region undergoes rapid change: loss of the protective geometry of the Mertz Glacier will likely cause changes in the formation of the Mertz Polynya, influencing both the biology of the annual spring bloom and the dynamics of bottom water formation.  Stay tuned for more updates on this exciting event and on the microbiology of the region.

Tafelbergs floating in the morning light, Mertz Polynya, December 2007

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New ways to analyze metagenomics data

Published by Johannes Goll on 4 February 2010 in Bioinformatics and Microbial & Environmental Genomics.

Are you looking for new tools to analyze your metagenomics data? Are you using  MG-RAST, IMG/M or MEGAN for your daily metagenomics work?

JCVI is working on a user friendly alternative that you might be looking for -  a new  tool kit  for metagenomics data visualization and analysis  built using the latest web 2.0 technologies.

JCVI’s Metagenomics Reports (METAREP) is a user friendly web interface designed to help scientists browse, compare, view,  and query annotation data derived from ORFs called on metagenomics reads. It supports both functional (Gene Ontology, Enzyme Commission Classification) and browsing of taxonomic assignments. When performing a search, users can either specify fields or logical combinations of fields to flexibly filter datasets on the fly. METAREP provides lists and pie charts of top functional and taxonomic categories for browse and search results. Tools are being developed that focus on the comparative analysis of multiple datasets. The system is optimized to be user friendly and fast .

Currently, an alpha version of METAREP  is used and tested internally at JCVI. In April 2010 , we will release the beta version to a limited set of interested external users.

If you like to see the tool in action,  join us  at the DOE Genomic Science Workshop ( February 9-10, 2010) for our web and poster presentation (5:30 – 8:00 pm on each day) or sign up to become part of the beta testing process at www.jcvi.org/metarep .

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DNA microarrays vs RNAseq — The winner and new heavyweight champion is?… It’s a draw.

Published by Scott Peterson on 3 February 2010 in Infectious Disease, Microbial & Environmental Genomics and Sequencing.

In the past year or so there have been several articles stating that the death of microarray technology is growing near. These proclamations are due to the more recently introduced methodology referred to as RNAseq. At first glance I wrote these claims off as being silly and premature. Over time though I am starting to appreciate that while the claim is still clearly wrong, the issue isn’t about technology displacement at all. My group works on a wide variety of gene expression problems ranging from the simple in vitro microbial gene expression studies to problems involving metagenomic samples of enormous complexity (http://pfgrc.jcvi.org). In my experience, the decision of whether to use DNA microarrays or RNAseq seems straight-forward and unambiguous. In reality the two technologies couldn’t be more complementary. Given the simple in vitro gene expression study as an example, the low cost, short turn-around time, exceptional quantitative accuracy and ease of data generation all make the glass slide microarray the clear choice.

About three years ago our laboratory began thinking about how to examine gene expression of pathogenic bacteria in the context of host infection. The challenge here is related to assay sensitivity since any RNA preparation derived from such an infection will yield host RNAs in an abundance 100 to 1000 times greater than that obtained from the infectious agent. Labeled RNAs from such an experiment would yield little useful information about the bacterial gene expression using standard DNA microarray procedures. This represents a clear case for RNAseq. The bewildering number of sequence reads we have come to enjoy from NextGen sequencing platforms is only going to get better. The extra bonus of applying RNAseq is that both the host and infectious agent can be profiled at the same time. There are still many technical problems to work out for routine use of RNAseq, such as effective rRNA removal and the development of appropriate data analysis tools, but the effort required seems quite justifiable.

I can think of only one application that is beginning to take on momentum where an investigator may truly ponder which strategy makes the most sense to apply. The approach is one that mimics EST sequencing as a means of defining genes and gene limits. Our ability to properly identify coding DNA sequences (CDS) in genomes ranges from, very good to relatively poor, depending on the genome in question. Members of the parasite research community, to name one, have struggled with this problem often. Generally speaking, substantial over-calling of genes occurs making it difficult for scientists to begin down the path of functional characterization of their favorite genome. We have worked with such groups recently to provide an independent means of substantiating gene calls via evidence of RNA expression. The design of such studies involves generating RNAs from a wide variety of experimental conditions to enhance the frequency for evidence based gene calls. DNA microarrays designed as a low or high density tiling array can be acquired at a reasonable cost and with good experimental outcomes. The case for applying RNAseq rests on the increased ability to detect transcripts that are expressed at low levels that defy routine detection using DNA microarrays.

In summary, I find very few instances where one might reasonably stop to wonder which technology are best suited for the biological/technical problem at hand. When sensitivity isn’t limiting, use DNA microarrays. When sensitivity is everything, look toward the short read sequencing technologies. In the end it turns out that it wasn’t really a contest at all. We should all feel fortunate that each strategy has its appropriate time and place for use. Those researchers, like myself, that have invested much time and effort working with DNA microarrays have nothing to fear, we just have more options now. This is a good thing to say the least. Most of our gene expression work is supported through a contract from NIAID to the PFGRC under contract N01-A115447.

Scott Peterson http://www.jcvi.org/cms/about/bios/speterson/

Professor, JCVI

Scientific Director, PFGRC at JCVI

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Science Festivals

Published by Lisa McDonald on 2 February 2010 in Education and Microbial & Environmental Genomics.

With spring around the corner (or at least we hope), there are several upcoming science festivals. These festivals are designed to provide students and families opportunities to find out what is happening in local science research institutes, universities and companies. These organizations are expanding the text books beyond our imaginations. These are EXCITING times in science – we are just scratching the surface of understanding the diversity of life on our planet, beginning to understand how to boot up synthetic cell, and how to better care for us and our planet.

SDSA High Tech Fair 2009: Dr. Bretschger and students

We are looking forward to participating in the SDSA High Tech Fair, March 9 & 10. Stop by our booth. It should be easy to find – with a unique sulfur odor coming from the sediment battery Dr. Bretschger created related to her work. At the end of March, we will exhibit with SD Science Festival Expo Day, March 27, which brings together over 150 hands-on science activities and stage performances for people of all ages and interest levels!

Switching coasts, April 25, JCVI will be participating at the Rockville Science Day. Another fun day of hands-on science activities and demonstrations! Look for the Mobile Lab there!!

DiscoverGenomics! Mobile Lab

DiscoverGenomics! Mobile Lab

Finally, this fall, we are excited to participate in the first ever USA Science & Engineering Festival Expo on the National Mall! The Mobile Lab will be there with other labs for a mobile lab CONVOY!! Well, maybe not as security might not like that, but we will be there.  Explore science & engineering with hundreds of free, hands-on activities and over 40 science shows on three different stages. The two-day Expo is perfect for teens, children and their families, and anyone with a curious mind who is looking for a weekend of fun and discovery. Build an underwater robot, chat with a Nobel Laureate, explore the science behind the magic of Hogwarts Academy and see a car that drives itself. From bugs to birds, kitchen chemistry to computer games, environmental monitoring to electronic music – the Expo has something for everyone and is completely free of charge. The Expo is the pinnacle event of the inaugural USA Science & Engineering Festival to be held in the greater Washington D.C. area October 10-24, 2010. The USA Science & Engineering Festival is a collaboration of over 500 of the nation’s leading science and engineering organizations. For more information on all Festival events and how you can get involved, visit www.usasciencefestival.org

I hope everyone can make it out to these great events.  If you are scientists or have a science-related career, please be sure to get out there and volunteer.  National Lab Day has provided a great national portal to volunteer.  There are never enough science fair judges, career speakers or mentors, so contact your local school to find out how you can help.

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Waste-to-Electricity?

Published by Orianna Bretschger on 22 January 2010 in Microbial & Environmental Genomics.

Many of us don’t spend a lot of time pondering wastewater treatment unless we absolutely have to.  However, we may need to start rethinking this dirty job.   In the United States wastewater treatment is a multi-billion dollar industry that is facing major challenges in the coming years including an ageing infrastructure, increasing populations, changing environmental regulations, and limited water resources.  Globally, the problem is much worse.  According to the United Nations, over 2 billion people are without access to adequate sanitation or safe drinking water; a reality that has led to devastating mortality rates among children under the age of five.  These present and future challenges demand innovative and sustainable solutions for wastewater treatment and water recycling technologies.  That is where microbial fuel cells come in…

The Electromicrobiology group at JCVI-West is developing new and innovative microbial fuel cells (MFCs) for wastewater treatment using only the metabolic action of microorganisms that naturally exist in wastewater streams.  Not only can MFC systems remove a majority of the organics contained in wastewater samples in half of the time required for traditional anaerobic systems, but they can also: (1) reduce waste-gas emissions, such as methane production; (2) significantly decrease sludge volumes (the left-over biomass and organic material from wastewater treatment); and (3) recover energy via direct electricity production.  All of these benefits lead to a water treatment system that could be deployed anywhere in the world without the need for an energy grid.

How does it work?  The answer is extracellular electron transfer.

Extracellular electron transfer results from a need to breathe.  Many microorganisms have evolved mechanisms to move electrons outside of the cellular membrane to facilitate respiration.  These mechanisms may involve the use of bacterial nanowires, outer-membrane-bound metalloproteins, and/or soluble electron shuttles.  Whatever the mechanism(s) may be, the result is an energy metabolism that allows “electrogenic” microorganisms to survive by respiring solid surfaces.  If the solid surface is the electrode of a MFC, we are able to capture some of the electrons resulting from respiration, and move them across a circuit to produce electricity.  This rapid movement of electrons away from the microbial community is what diverts energy away from methanogenesis and biomass production, resulting in a more efficient and sustainable treatment process.

By measuring electron flow across the circuit, i.e. electrical current, we are also able to directly monitor microbial respiration and use the MFCs as tools for studying electron transfer mechanisms in pure cultures and mixed consortia.   Microbial fuel cells and other bio-electrochemical systems offer many opportunities for studying microbial energy metabolism; and may also serve as unique cultivation devices.   These systems could be a useful tool for microbial enrichment and selecting for new organisms that can be sequenced and used for reference genomes.

Every bit of knowledge we gain about the fundamental processes associated with microbial energy metabolism brings us closer to optimizing MFC systems for technology applications, such as wastewater treatment.  In the Electromicrobiology group, we hope to further promote the merger between biological and engineered systems to ultimately provide MFCs that can be practically employed as cost-effective and sustainable wastewater treatment devices worldwide.

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300 Papers

Published by Matthew LaPointe on 13 January 2010 in Microbial & Environmental Genomics.

Congratulations to Ken Nealson for publishing his 300th paper! Ken has been a driving force in microbiology for 40 years having published several seminal papers in microbial ecology. In the 1980s he helped to pioneer the field of geobiology and discovered bacteria that thrive on metal.

Dr. Kenneth H. Nealson

Dr. Kenneth H. Nealson

Dr. Nealson is a fellow of the American Academy of Microbiology, he has chaired several National Academy of Sciences committees, and has received numerous awards including from the American Society for Microbiology and the Society for Industrial Microbiology.

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