W3: Genomic surveillance to track microbial fate and activity in natural and engineered environments

Summary

Dr. O from the UF Howard T. Odum Center for Wetlands presents his research on environmental genomic surveillance, explaining its application in understanding microbial water quality and addressing environmental challenges. His work emphasizes the difference between natural and engineered water systems, and the development of monitoring tools for real-time microbial surveillance. Dr. O highlights the complexities of genomic surveillance compared to clinical samples, underlining the importance of spatial and temporal data. He discusses ongoing projects related to microbial activity in aquifers and the impact of storms on antimicrobial resistance genes, as well as tools to improve genomic surveillance techniques.

Highlights

• Dr. O introduced the concept of environmental genomic surveillance as a cutting-edge research tool aimed at addressing ecological and public health issues 🧬.
• He discussed the role of DNA and RNA in tracking microbial abundance and activities in various water systems 🌊.
• Dr. O's research includes developing an automated system for sampling and analysis, enhancing real-time data collection 🕒.
• A key case study involves tracking antimicrobial resistance spread due to hurricanes, highlighting climate impacts on microbial activity 🌪.
• Dr. O also explored nitrous oxide production in karst aquifers, underlining its role as a significant greenhouse gas 🌿.
• The work around biofilm monitoring in drinking water systems points to significant public health implications 🚰.

Key Takeaways

• Environmental genomic surveillance is crucial for understanding microbial activities in different environments 🧬.
• Dr. O's research focuses on both natural and engineered water systems and their microbial interactions 🌊.
• The seminar emphasized the difference between DNA stability and the variability of mRNA under environmental conditions 🔬.
• Dr. O aims to design an automated system for molecular analysis on-site, highlighting the importance of big data in environmental sciences 📊.
• Ongoing projects involve studying antimicrobial resistance in hurricane-affected areas and microbial activities in karst aquifers 🌀.
• Research also targets improving genomic surveillance methods and tools for broader applications in environmental engineering 🛠.

Overview

Dr. O, part of the University of Florida's faculty, specializes in environmental genomic surveillance. His research primarily investigates how microbial water quality impacts both natural and engineered water systems. During his seminar, he elaborated on the innovative methodologies aiming to bridge the understanding of pathogens' fate and transit within these environments. This included the challenges of analyzing mixed environmental samples, as opposed to single-host clinical samples.

Central to his talk was the development of technologies for environmental monitoring. Dr. O described an envisioned automated sampling and analysis system that could operate on-site, aiming to revolutionize real-time microbial data gathering. This system would enhance the ability to monitor changes in microbial communities, significantly impacting both environmental health strategies and responses to events like pandemics.

His presentation also touched on specific projects looking at microbial resistance gene transfer during hurricane events, and studying greenhouse gas production in karst aquifers. Collaborations with different departments within the university are crucial for advancing these studies. Ultimately, Dr. O's research highlights the integration of genomic tools with environmental science to address complex challenges in managing water resources.

Chapters

• 00:00 - 00:30: Introduction The chapter titled 'Introduction' begins with a greeting to the audience joining via Zoom and YouTube for the Water Wetlands and Watershed seminar series in spring 2025. This is the penultimate seminar in the series. The presenter, Dr. Chamto, also known as Cham, is introduced. Although he is not feeling well, he is able to present virtually from a different location.
• 00:30 - 01:00: Speaker Introduction The chapter titled "Speaker Introduction" provides an overview of Dr. O, an assistant professor at the University of Florida's Department of Environmental Engineering Sciences. It mentions his educational background, including his BS and MS from Soul National University in South Korea and his PhD from the University of Illinois at Urbana-Champaign. The introduction highlights his research focus on environmental genomic surveillance and microbial water quality, with an aim to understand the fate and transport of pathogens.
• 01:00 - 01:30: Research Focus This chapter discusses the growing interest in antimicrobial resistant genes and microbial interactions in both engineered and natural water systems. Listeners are encouraged to consider the differences and intersections between these two types of systems. Additionally, it highlights efforts in developing rapid online monitoring tools for real-time microbial surveillance in water infrastructure, which has garnered increasing attention.
• 01:30 - 02:00: Genomic Surveillance Overview The chapter 'Genomic Surveillance Overview' introduces the concept of using genomic surveillance methods in environmental contexts, specifically focusing on tracking COVID-19 in wastewater. The speaker, despite having a cold, articulates the importance of employing these novel techniques as a means to monitor the virus's spread within communities. The chapter highlights the emerging nature of this scientific approach and sets the stage for further discussions on its applications and benefits in public health.
• 02:00 - 03:00: Microbial Activities In the chapter 'Microbial Activities', the speaker introduces a research tool used to address environmental issues. The outline of the talk includes an introduction to environmental genomics and surveillance systems, followed by a discussion on ongoing research topics. The goal is to present environmental genomic surveillance, although the chapter will only briefly touch upon this aspect.
• 03:00 - 04:30: Challenges and Goals The chapter titled 'Challenges and Goals' focuses on discussing various research topics rather than delving deeply into one specific area. It aims to highlight the different types of environmental issues that can be addressed using emerging research tools. The ultimate research goal emphasized is to mitigate the impact of microbial activity on public health and the economy. The chapter notes the numerous ways in which microbes influence our lives, although it specifies that only two examples will be presented in detail.
• 04:30 - 06:00: Improving Genomic Surveillance The chapter discusses how pathogens can contaminate water sources, including recreational and drinking water, leading to infections. It highlights the adaptability of microbes to their environments, which allows them to thrive and perform metabolic activities. These activities result in the transformation of chemical species, highlighting the complex interaction between pathogens and their environments in the context of genomic surveillance.
• 06:00 - 09:00: Antimicrobial Resistance and Hurricanes The chapter explores the intersection of antimicrobial resistance and hurricanes, focusing on the role and importance of microbes in the context of environmental changes.
• 09:00 - 15:00: Nitrous Oxide in Aquifers The chapter titled 'Nitrous Oxide in Aquifers' explores the role of microbial activity in the transformation and presence of nitrous oxide within aquifers. It details how genes are transcribed into mRNA, which is then used to translate proteins, highlighting that what is referred to as microbial activity is essentially the collective effect of protein activity. The chapter emphasizes that microbial processes are deeply interconnected with DNA presence and mRNA transcription, noting that all microorganisms possess one or more of these functions.
• 15:00 - 21:00: Biofilm Monitoring in Water Systems The chapter discusses the monitoring of biofilms in water systems, emphasizing the role of DNA and mRNA in understanding microbial activity. While DNA remains stable throughout a microbe's lifecycle, mRNA levels can fluctuate based on environmental conditions. This variability allows microbes to adapt and respond to changes by transcribing or degrading mRNA as needed, which helps in identifying microbial activity in different environments.
• 21:00 - 25:30: Conclusion and Acknowledgments The chapter defines 'environmental genomic surveillance' as the systematic collection and analysis of environmental samples of DNA and RNA. This approach is used to monitor and understand how microbial communities respond to environmental changes, which is termed 'microbial activities.' The chapter underscores the importance of analyzing RNA to determine microbial response to changing environmental conditions.
• 25:30 - 35:30: Question and Answer The chapter discusses the challenges involved in environmental genomic surveillance, comparing it to clinical genomic surveillance. In clinical genomic surveillance, genomic analysis is performed on clinical samples taken from mostly one host. However, environmental samples are a mixture of various elements. The chapter uses the analogy of 'colored microbes' to represent targets in environmental samples, highlighting the complexity and difficulty in targeting specific elements.
• 35:30 - 37:30: Closing Remarks The chapter titled 'Closing Remarks' focuses on the complexity and diversity of microbes. It highlights that microbes, even within the same species, display significant genetic diversity akin to how humans are all homo sapiens but individually different. Furthermore, the chapter discusses the challenge posed by complex microbial communities that coexist with target microbes, making it difficult to precisely define or isolate target microbes.

W3: Genomic surveillance to track microbial fate and activity in natural and engineered environments Transcription

• 00:00 - 00:30 oh thanks Kathy and recording all right greetings everyone on Zoom greetings out there on YouTube thanks for coming this is our second to last water wetlands and wershed seminar for fall uh spring 2025 um and we're really happy to have uh our own colleague here Dr chamto or Cham he's in the room sort of there over on on Zoom and was not doing well today who's presenting virtually so give a
• 00:30 - 01:00 brief introduction and then Sham the floor is yours so Dr o is an assistant professor in the department of environmental engineering sciences here at the University of Florida he has his BS and MS degrees both from Soul National University in South Korea and then he has his PhD from the University of Illinois at Urbana Champagne and as we'll hear about today Dr o's research focuses on environmental genomic surveillance and we'll understand a little bit more by the end of today what that means and microbial water quality his work aims to better understand the fate and transport of pathogens
• 01:00 - 01:30 antimicrobial resistant genes which a lot of folks are getting more and more uh we'll say interested in nowadays and microbial interactions in engineered and natural water systems and so maybe as you're listening today either online or here in the room try to think about what are the differences between engineered and natural systems and and where they might cross over he's also leading efforts to develop uh monitoring tools also like rapid online monitoring tools for real-time microbial surveillance in water infrastructure which also we've been hearing a lot more about ever since
• 01:30 - 02:00 basically COVID tracking in the wastewater supply so Cham the floor is yours and uh have at it thank you very much uh hello every hi everyone so I have a cold i really wanted to make it in person so please uh forgive me not uh presenting there or my unpleasant voices so what I wanted to present today is about environmental uh genomic surveillance and this is quite emerging
• 02:00 - 02:30 research tool and I want to introduce what this new tool is and how we can utilize this tool to address environmental issues so this is outline of my talk today i first introduce environment genomics uh surveillance system and um then I will move on to introducing my ongoing research topics as my goal today is to introduce environmental genomic surveillance so I will briefly skim
• 02:30 - 03:00 through uh different research topics rather than focusing on one topic in depth uh I want to highlight what types of environmental issues we can address with this emerging research tool so my ultimate research goal is to mitigate the impact of microbial activity in the environment on public health and economy and you can name numerous reasons how microbes affect our life but I like to present the two
• 03:00 - 03:30 reasons so pathogens can contaminate recreational water such as river or coastal water or contaminate drinking water sources that result in uh pathogen infection and microbes also designed to survive and thrive at uh where they are so for that purpose they do metabolic activities and these activities transform chemical species of substances and because carbon and
• 03:30 - 04:00 nitrogen are important nutrients for the microbes they play a critical role in global carbon and nitrogen cycle then how can genomic surveillance help us understand those microbial activities i'd like to explain what microbial activities are with these illustrations so all living creatures have DNA dna consist of hundred or thousands of genes which are depicted in
• 04:00 - 04:30 red uh piece and each gene can be transcribed into mRNA and this mRNA can be used to translate proteins and what we call microbial activity is actually the result of group activity of proteins so microbial activity involves the presence of uh DNA and transcription of mRNA all microorganisms have one or few
• 04:30 - 05:00 DNA and the number of DNA remains stable throughout their life cycle on the other hand mRNA level can vary significantly depending on environmental conditions when microbes are under certain conditions that result in doing some activities then they uh what microbes do is transcribe mRNA and if if the situation change and they need to reduce or stop the reactions then they degrade mRNA so DNA can represent microbial
• 05:00 - 05:30 abundance in the environment and RNA can represent how microbes respond to the environmental change conditions which I call microbial activities with that I'd like to define environmental uh genomic surveillance as systematic collection of environmental samples and analysis of DNA and RNA in order to track the fate and activity of microbes in the environment
• 05:30 - 06:00 environmental genomic surveillance involves many challenges i like to compare environmental genomic surveillance to clinical genomic surveillance they perform genomic analysis on clinical samples clinical samples are from mostly one host whereas environmental samples are mixtures of everything which is look like this now let's assume the colored microbes here are our target in many cases our target
• 06:00 - 06:30 microbes present at low prevalence and they are genetically diverse this means even though they are in one species they are not identical like we are all homo sapiens but are not identical on top of that our target microbes exist together with complex microbial communities so it's challenging to define our target microbes here green things in the illustration uh present impurities such
• 06:30 - 07:00 as organic matters or ions that could interfere with molecular analysis more importantly our target environmental field lies on a large area so we have to strategically take samples to understand the spatial dynamics i believe environmental engineers and scientists are well qualified to track these challenges because basically what we are doing is to understand fate and
• 07:00 - 07:30 transport of matters in the environment we've learned and studied a physiochemical uh reactions uh in the environment for example we understand surface charge of uh particles and the absorption disorption reactions which is the key information to understand the interactions with other particles and we know how hydraological conditions decide like whether or not certain particles
• 07:30 - 08:00 flow through the streams or settle down to the bottom we also know um weather and climate conditions affect these substances furthermore we can think all these reactions on different scales from micro to a global scale and I believe environmental genomic surveillance is simply replacing our target matter with genomic materials like DNA and RNA so
• 08:00 - 08:30 what I want to emphasize on this slide is although we are not a microbiologist but we can make unique contributions to this field of study now let's move on to next chapter um I will show you how uh these unique contributions look like the first uh research topic is about improving environmental genomic surveillance itself and the other three will be
• 08:30 - 09:00 presented to show what environmental issues we can address uh environment genomic surveillance involves roughly these three steps first um for genomic surveillance someone has to go out to the field to take samples and they need to bring this sample back to laboratories and with this sample we have to increase our target genetic materials and reduce
• 09:00 - 09:30 impurities once this processing is done the samples are ready for molecular analysis researchers uh including myself has made a effort focusing on improving the simple processing and analysis our target DNA and RNA however based on my experience uh going out to the field to take samples would be the most challenging and timeconsuming labor intensive
• 09:30 - 10:00 works and I personally are tired of uh sampling as well so what I've been imagining so far is to develop a certain system that we can install in the field and that system can take samples process and analyze samples on site and just send the data back to me because I'm a big fan of big data and I believe as long as we have high resolution spatial temporary data with an aid of AI
• 10:00 - 10:30 technology we'll be able to uh better understand what's going on in the environment and this is the simple design of what I have in mind and first module will be designed to take sample from environment like coastal water or river to take um microorganisms and then uh it's designed to take DNA RNA out of the cells which I
• 10:30 - 11:00 call microbialis and these uh RNA and DNA will be isolated ated from all impurities and purified in the absorbance and these purified genomic materials will be conveyed to the second module which is which is PCR and the basic approaches to this system is to taking a large volume of raw samples if you have to bring your sample to laboratory your sample volumes
• 11:00 - 11:30 are limited to like one liter or so but because we'll install this system on site we can process the water however we want like 100 gallons if we need it and we'll design processing method as mild as possible such as heating the water with salt which is sufficient to discharge the processed sample back to the site although these mild processes uh will have a decent DNA and RNA recovery
• 11:30 - 12:00 efficiency we expect the lower efficiency will be compensated by the large volume of the input sample and this rough calculation about the processing efficiency tells us the if the first mild purification process can recover 10% from large volume of the sample and if needed we can um add advanced technology to improve the efficiency and if we achieve um a 50%
• 12:00 - 12:30 from the second uh second process the result uh concentration will be uh 10,000 times higher than the raw sample and um we are currently working on this PCR module so this is the PCR design of our PCR pcr has pretty simple design it has thermal cycler and a fluoresence uh
• 12:30 - 13:00 measurement and as shown in this drawing there is a reactor in the center which is surrounded by uh a heating block and this uh copper block is attached to the pelium module to control the reaction temperature and we have excitation light source here and emission light detector on the bottom and the temperature and the fluoresence can be monitored as shown in the photo and the image on the
• 13:00 - 13:30 right hand side we're still optimizing the prototype of this PCR but what makes this PCR system different from conventional PCR is this will be automated continuous flow PCR system what I mean is the reactor here will be connected to the programmable pump so that we can convey the exact volume of PCR reagent and nucleate acid purified
• 13:30 - 14:00 from the first module at the determined time frame so this PCR system doesn't need personnel to operate this system all right um let's move on to other research topics i'd like to introduce what types of envir issues we can address with this environmental genomic surveillance first topic is about tracking the spread of antimicrobial resistance genes due to hurricanes Hen
• 14:00 - 14:30 and Milton if you still remember these two hurricanes made landfalls in Florida last year just two weeks apart after Helen we tried our best to clean up the debris and pollutants but the cleaning capacity was its max and many uh of the g uh garbage or pollutants were just temporarily piled up without being properly secured and hurricane Milton just
• 14:30 - 15:00 redistributed what we piled up and uh which ended up in uh coastal water and center for coastal solutions under the leadership of Dr angelini found this situation serious and we went out for taking samples ranging from um Tampa Bay through the um Punta Gorda as shown on the map and what my laboratory found with these samples are the elevated
• 15:00 - 15:30 intercostal levels which indicates the fal contamination so this is the evidence showing the untreated waste water and non-point source pollutants were discharged from inland and what is this makes um this situation makes worse is the outbreaks of vibrio volicus which shows the u high m mortality like 20% florida public uh health department
• 15:30 - 16:00 reported doubled cases of biboponicus when the the hurricane milton hit the Florida through the collaboration with Dr morrison and Dr jung in the department of environmental engineering sciences we hypothesize this decision the freshwater bacteria that can contains high abundance of antimicrobial resistance genes which is denoted in the red circle can form
• 16:00 - 16:30 bofilm on microlastics which will confirm the elevated concentration and the um the once the uh once this bacteria can form bofilm and this bofilm could be the place where antimicrobial resence gene are transferred to indigenous marine bacteria if that happens antimicrobial resence gene could establish in the
• 16:30 - 17:00 coastal water and the negative impact from the storm surge due to the hurricanes can last much longer than we initially thought so fortunately NSA bought our hypothesis and support our uh sample analysis and this is what we're going to do with these samples our goal is to find the evidence showing horizontal gene transfer um allows a
• 17:00 - 17:30 piece of genes to be transferred to other microbes however there will be another mechanism of gene transfer which is called vertical gene transfer where the whole genome will be replicated and inherited in the same microbial species so we'll examine antimicrobial resence genes with identical sequences like this red color and then we'll look
• 17:30 - 18:00 into the adjacent reasons and if we the if the adjacent regions are also identical then this is the uh evidence for the volical gene transfer and if the adjacent regions are not identical while the uh while having the same AMR then this will be the app does for hyster gene transfer we just initiated this project so I hope to share uh some interesting
• 18:00 - 18:30 result soon next topic is about a nitrous oxide production in car aquifer it's been one and a half year since I moved to Florida and I'm so happy with such a beautiful nature in Florida here and I love spending time with my family at springs like um itchoni springs in this
• 18:30 - 19:00 picture but these pristine springs uh more specifically Florida aquifer or carsted oifers may be a hot spot for nitrous oxide nitrous oxide is third most significant greenhouse gases and many researcher research group have reported high concentrations of nitrous oxide at car stock occipers and this uh study has been collaborated by Dr shan Yun in the department of geological
• 19:00 - 19:30 sciences let me briefly explain what could happen in car oifer car landscape comprises about 20% of all ice free uh landscape and a carifer has soluble rocks such as carbonate with easily dissolved by water so the car stock first looks like porous media and depending on the geological feature they could form conduit which is like a large water
• 19:30 - 20:00 channel if the water flow of the surface water increases then the surface water can infiltrate into this car stockifer through the conduits and the pores media and replace the groundwater in this car stockifer and because groundwater typically shows unarobic conditions while surface water shows aerobic conditions the car stockifer will go through frequent transition between
• 20:00 - 20:30 aerobic and unarobic conditions and this is the microbiological nitrogen transformation pathway when anthropogenic activities like using fertilizers at agriculture fields discharge ammonia and nitrate into water and these um nitrogen species go through these transformation processes and these nitrogen species can be transformed to
• 20:30 - 21:00 nitrite nitrous oxide and nitrogen gas um depending on the environmental conditions so we want to learn how hydraological conditions like this affect microbiological activities uh as introduced here we chose a Santa Fe river sink and rice system in Florida which is about one way uh one hour from here we believe this is ideal site to study
• 21:00 - 21:30 the relationship between hydraological conditions and microbial activities because as you can see in this map Santa Fe river f flow uh like this and but suddenly the river disappear at river sink and what actually happens is the water flows through the underground conduits uh as shown in yellow uh color and the Department of Geological Sciences at UF have investigated this
• 21:30 - 22:00 site a lot and now we have clear understanding how conduits looks as shown in this illustrations and the water uh forms a river again uh at the river rise and USGS installed water stations at river sink and river rise so we know um the exact volume of the water that recharges in cars aquifer and there are two
• 22:00 - 22:30 monitoring sites which uh we can analyze the water quality in the uh carifer there was a quite big rainfall in the past January and we go out went out for sampling throughout the rainfall event here uh the black solid line shows the surface water flow rate to oifer so if the line is above zero this means the surface water fills the car
• 22:30 - 23:00 stockifer so we confirm this rainfall event induced a surface uh water infiltration into the car stockifer we also measured the nitrous oxide um during the during the rainfall event and we found the similar trend with the time lag and what this means is the uh car stockifer conditions for changed from unarobic to aerobic and this uh
• 23:00 - 23:30 induced the micro the promoted nitrous oxide production and you hypothesize that this is because mild aerobic conditions um disrupted this microbial transformation pathway from nitrous oxide to nitrogen gas which is called incomplete denitrification so we analyze microbial
• 23:30 - 24:00 community through 16 RNA and 16 RDNA sequencing and this PCA analysis shows how microbial community changed during the rainfall event uh this W31 data points represent initial microbial profile and the microwave profile shows significant change throughout the rainfall events and the last sample W36
• 24:00 - 24:30 uh uh represent the microbial profile at the last sample uh shows the the microbial characteristics return back to the initial states of the um uh microbial profile and this data indicates um rainfall events somehow impacted microbial activity and abundances
• 24:30 - 25:00 and we also quantified this NIR and NOS gene and if the NI over NOS gene is large that means the Nitrous oxide production is dominant pathway and if the NI over NOS is small then nitrous oxide consumption is the dominant pathway and here this grand graph on the bottom shows NI over NOS ratio over time and as
• 25:00 - 25:30 you can see the the trend of this ratio followed the trend of N2 production so we believe this is the evidence showing the microbial activities indeed caused N2 production now that we know microbial nitrogen transformation is the key mechanism for nitrous production in
• 25:30 - 26:00 cartoifer we wanted to evaluate these microbial activities in a more quantitative way dr yun and I are working on developing bio micrfluidic system to unveil microville and two production mechanisms this system is basically a micro fluidic system where we can fabricate any designs of chips so that we can mimic different car occupers and we have two uh water
• 26:00 - 26:30 channels that represent surface water flow through the conduits and groundwater flow through the uh car oifer that what my laboratory is doing is to design bacteria to produce green fluoresence when nitrous oxide production is the dominant pathway and produce red fluoresence when um nitrous oxide consumption is the dominant
• 26:30 - 27:00 pathway and we'll grow this bacteria on this microfidic system so we'll see the color change depending on the hydraological conditions and with that data we'll explore how hydraological conditions affects microbial activities all right uh the previous two topics were about microbes uh in the nature and this last topic is about
• 27:00 - 27:30 microbes in the uh engineer the system uh the title for the last topic is uh monitoring bofilm dispersion from the um drinking water distribution systems and this study has been collaborated with Dr hanzago from Soultech there were two at least 200 drinking water associated outbreaks in the United States from 2015 to 2020
• 27:30 - 28:00 this may be a huge number if you think we are living in one of the most developed countries and I'm confident with the water treatment technology and I'll be happy to drink the water discharged from the drinking water treatment plants however um when when they convey the water to each household the water passes through the drinking water distribution system where there are biofilms in it and these
• 28:00 - 28:30 biofilms are biomolecules biomolelecular complex where microbes including pathogens can thrive and this biofilm protect microbes from residual disinfectant so pathogens they present uh at low level when they discharge from the drinking water treatment plants can increase the concentration in the drinking water distribution system to the level they
• 28:30 - 29:00 can infect human beings through uh drinking water consumptions because taking sample from inner surface of the pipe disrupt water supply it's not easy to regularly monitor bofilm in drinking water distribution system so our approach uh to address this issue is to analyze microbes in the tab effluent but let me briefly introduce a
• 29:00 - 29:30 biofilm life cycle in drinking water distribution system the planktonic bacteria from water treatment plants can bind to the surface wa sur inner surface of the drinking water distribution system and they produce sticky chemicals that strongly bind themselves to the uh to the pipe surface and then bofilm can start growing from the surface and once they are matured then bacteria can
• 29:30 - 30:00 release back into the bur solutions s and if we analyze microbes in the tap water there will be the plantonic bacteria from water treated plants and bacteria released from the drinking water distribution system I will call plantonic bacteria um and this as a bofilm bacteria for just for the convenience so our research question is
• 30:00 - 30:30 how can we differentiate biofilm bacteria from plantonic bacteria in the tab effort our approach is to focus on quarum sensing uh process which is bacteria communication mechanisms so believe or not bacteria can communicate each other bacteria produces chrome chrome sensing signals to the surrounding environment
• 30:30 - 31:00 and at the same time they can sense the concentration of these chemicals and these chemical upregulate the corum sensing reactions meaning they can produce more chemicals when they detect the corum sensing signals and once this signal exceed the certain level then they initiate the downstream gene expressions including the bofilm formation so quum sensing is population
• 31:00 - 31:30 density dependent microbial reactions and it's involved in um bofilm formation cell density varies significantly depending on two bacterial mode of growth which are plantonic bacterial growth and bofuel growth on the left hand side you can see the plantonic bacteria can replicate in bark solution the cell density increase is like just changing from rural area to
• 31:30 - 32:00 suburban areas but bofilm growth is like complex apartment in mega cities the cell density of bofilm bacteria is um two to three orders of magnitude higher than that of plankton bacteria so we hypothesize the quorum sensing related mRNA will be produced more in this bacteria compared to plantonic cells and we
• 32:00 - 32:30 chose last eye gene which is uh because this is a wellstudied um this is one of the quum sensing uh related gene to test our hypothesis we grew bacteria in two reactor s with different specific surface areas the small reactor has 18 times higher specific surface area than the large reactors and we analyze loss I mRNA uh
• 32:30 - 33:00 in the cells from these two reactors because the planktonic uh bacteria grow in bulk solution while bofilm bacteria grow on surfaces we assume the small reactors will have higher impact from bofilm bacteria and the result shows that the bacteria from the large reactor which is shown in red circle did not show a
• 33:00 - 33:30 significant lossy gene expression as population density increased however small reactors um where has more bofilm impact showed a lassi gene expressions we also grew bacteria in tubing system under under flow conditions and we flow tap water through the tubing with bofuel
• 33:30 - 34:00 uh what this data on the right hand side shows is the last eye mRNA in in the affluent shows a strong correlation with the mRNA of the bofilm uh in the tubing so given all together what our study shows is um we can investigate bofilm dispersion from the drinking water distribution systems by analyzing
• 34:00 - 34:30 the course and seeing mRNA in tap effluent so I've just skimmed through all um our ongoing research if the presentation was too busy I'm sorry about that but uh through this seminar what I wanted to introduce is environmental genomic surveillance and what type of environmental challenges we can address with this tool so this is the take a take-home
• 34:30 - 35:00 message for you investigating DNA and RNA in the environment helps us understand how microbes impact both environmental and public health so this is all I prepared um I'd like to shout out uh all uh type of supports for uh for our study uh especially all uh students from my laboratory who are highly motivated
• 35:00 - 35:30 and um they work really hard thank you very much if you have any questions I'll be happy to take from audiences but uh you can reach out through different channels uh for further discussions thank you very much thank you Cham thanks Dr o for sharing with us despite your your uh voice and everything so sorry it was very clear so we'll start with some questions in the room and then we'll check on YouTube i
• 35:30 - 36:00 know many of our students are watching on the YouTube stream right now so please pop your questions in the chat there we'll start with questions from the room okay I'll ask a question okay so so Cham you the the study that was most uh you know relevant to the work I've been seeing recently is this the nitrous oxide production in the aquifer Vantoo and I think one of the major challenges we have when we think about you know nutrient pollution at the land surface
• 36:00 - 36:30 and especially after it recharges the aquifer and then maybe one year five year 30 years later is emerges from the spring and we want to understand what the load of nitrate from the land surface how much is denitrified along the pathway and even what is the what like how do we model it first order zero order second order is any of the work that you're doing right now uh able to help us understand what are basically the half-life something simple like a
• 36:30 - 37:00 halflife or a denitrification rate constant uh um an an area or volume weighted removal rate constant that we can use to because not every molecule of nitrate that enters the aquifer leaves and some portion is ditrified and is not becoming pollution for downstream water resources right great uh great question so if I understand your question correctly there um so there are the water flow underground will show
• 37:00 - 37:30 different um time scale and actually the department of geological sciences uh has investigated a lot about that and what they found is um the relationship with the isotope uh analysis what they found is the the nutrients of carbon or nitrogen that are injected into infiltrate into the aquifer will
• 37:30 - 38:00 um uh show show us like decade or from decade to like days if the geological feature allows the water coming out of the aquifer to the through the spring then they could uh impact us like day within days but if the geological feature allows the the water flow through the long journey through the uh carifer then the impact will um come out after like decades so it highly depends
• 38:00 - 38:30 on geological feature and the reduction mechanism is mostly uh because of the microbial activities and that microbial activity also depends on the hydraolog geological feature that I just described on this slide so it really highly dependent on the uh environmental conditions right so assuming we know the travel time distributions which we often do at least through models right so we have the overall proportion of water that
• 38:30 - 39:00 spends one week one day 10 years 100 years so we have the travel time distribution and we want to basically apply some kind of removal rate coefficient to if it spends a week it has a shorter time but the removal rate constant is whatever negative 3.7 and if it spends 100 years it's a longer time but the removal rate constant is still first order negative same number so what I'm looking for is like how can we get a better feel for the spatial variation right overall capacity of the alpha if
• 39:00 - 39:30 we assume The uh primary mechanism for the nitro side transformation is microbial activities that microbial activity really depends on the environmental conditions so what we wanted to reveal with this um biomicidic system is we want to provide a more quantitative way to evaluate the reduction of uh of these the denitification processes because the so of course we can average all the
• 39:30 - 40:00 hydraological um processes like with the average precipitation but u the precipitation events really depends on case by case so we'll what we are going to explore through this system is the the strength of the rainfall event and how that uh strength affects uh with the geological feature
• 40:00 - 40:30 like conduits and porous uh porosity of the porous media um uh collectively affects the microbial activities okay okay thank you CH i want to follow up with you on about that a little bit later some potential ideas other questions from the room youtube is very quiet okay if no other questions then
• 40:30 - 41:00 let's give Dr o another round of applause let him get a nap or something thank you so much Chad we appreciate you for having me here presenting despite the illness so next week we have our final seminar of the semester we have Dr bibil is coming and I believe he's um going to be presenting virtually as well one moment let me just check to be sure um I've caught up if you're in the environmental engineering sciences section I've mostly caught up on the grading i know there was some confusion with the due dates and some of them were
• 41:00 - 41:30 like from in the deep past and so that's all updated if there was confusion about what you uploaded for which week don't worry I can see them all and so I'm um I've gone through and graded those yes so next week we have um Himeante Bayil from Agon Bioengineering and I think he's going to be here in person so we'll see you all next week and until then um be well thanks everyone cheers thank you