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Muruleedhara (Murulee) N Byappanahalli, PhD

I am a Staff Scientist (Research Microbiologist) with the USGS Great Lakes Science Center’s Lake Michigan Ecological Research Station in Chesterton, Indiana, conducting research in restoration and conservation biology programs, with projects in aquatic and terrestrial ecosystems. Emerging technologies, such as eDNA, high throughput sequencing, and microbiome, are routinely used in these projects.

My research at the Great Lakes Science Center’s (GLSC) Lake Michigan Ecological Research Station (GLSC-LMERS) spans across aquatic and terrestrial ecosystems, focusing on restoration and conservation biology programs. Environmental microbiology and environmental genomics are key disciplines in these projects. 

In previous work, I studied the distribution and population characteristics of enteric bacteria in Great Lakes watersheds (streams and riparian soils, beach sand, aquatic vegetation) and their impacts on beneficial use impairments such as water quality. I also explored the best management practices to restore these degraded waterways. 

My microbial research in terrestrial programs is a collaborative effort devoted to understanding the biology of plant invasion. Specifically, I am exploring how soil microorganisms (bacteria, fungi) might augment or diminish this invasive process, using the Asiatic bittersweet (Celastrus orbiculatus) as a model plant species. Much of this his research is conducted in public lands within the Indiana Dunes National Park. 
 
My research in environmental genomics, which is collaborative, brings an array of emerging technologies in support of ongoing fisheries assessment and conservation programs. I use environmental DNA (eDNA), autonomous sample processors, and high throughput sequencing (HTS) methods, including metabarcoding and shotgun sequencing, in conjunction with traditional surveys (e.g., trawling). 

Recently, I have been applying eDNA and HTS tools to identify pollinator species (bees and bee communities) in grasslands from different geographical areas, by capturing eDNA left behind by pollinators visiting flowering plants. The main goal of this Ecosystem Mission Area (EMA) funded project, which involves multiple USGS Science Centers (including GLSC-LMERS), is to develop new DNA-based tools to improve existing monitoring programs for pollinators, including listed/endangered species. 

Professional Experience

  • 2001-Present: Research Microbiologist, Great Lakes Science Center, Lake Michigan Ecological Research Station, Chesterton, Indiana

Education and Certifications

  • Ph.D. (Microbiology, 2000): University of Hawaii at Manoa, Honolulu, Hawaii

  • MS (Microbiology, 1996): University of Hawaii at Manoa, Honolulu, Hawaii

  • MSc (Agricultural Microbiology, 1982): University of Agricultural Sciences, Bengaluru, India

  • BSc (Agriculture, 1979): University of Agricultural Sciences, Bengaluru, India

Affiliations and Memberships*

  • American Society for Microbiology (ASM), Washington, D.C.

  • Soil Science Society of America (SSSA), Madison, Wisconsin

Science and Products

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Bumblebee on Phacelia flower

Using Pollinator Environmental DNA to Assess the Ecological Resilience of America’s Grasslands

Scientists from six USGS science centers are collaborating with USDA, university, and Tribal partners, and Department of the Interior land managers, to assess the status of pollinator communities and the distribution of species of conservation concern using environmental DNA. These methods will be used to improve assessments of habitat quality and pollinator responses to restoration, including...
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Species Management Research Program, Eastern Ecological Science Center, Forest and Rangeland Ecosystem Science Center, Great Lakes Science Center, Northern Prairie Wildlife Research Center, Northern Rocky Mountain Science Center, Upper Midwest Environmental Sciences Center, Pacific Northwest Environmental DNA Laboratory
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Using Pollinator Environmental DNA to Assess the Ecological Resilience of America’s Grasslands

Scientists from six USGS science centers are collaborating with USDA, university, and Tribal partners, and Department of the Interior land managers, to assess the status of pollinator communities and the distribution of species of conservation concern using environmental DNA. These methods will be used to improve assessments of habitat quality and pollinator responses to restoration, including...
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A metal box beside a creek contains equipment that collects and filters water samples

READI-Net: Providing Tools for the Early Detection and Management of Aquatic Invasive Species

The USGS has developed the Rapid environmental (e)DNA Assessment and Deployment Initiative & Network (READI-Net) to accelerate the implementation of environmental DNA (eDNA) analysis as a best practice for the early detection of aquatic biological threats. READI-Net provides tools and a strategy to collect and deliver early detection data for natural resource managers and public health protection...
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Ecosystems Mission Area, Biological Threats and Invasive Species Research Program, Columbia Environmental Research Center, Eastern Ecological Science Center, Forest and Rangeland Ecosystem Science Center, New York Water Science Center, Northern Rocky Mountain Science Center, Upper Midwest Environmental Sciences Center, Wetland and Aquatic Research Center , Wyoming-Montana Water Science Center, Pacific Northwest Environmental DNA Laboratory
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READI-Net: Providing Tools for the Early Detection and Management of Aquatic Invasive Species

The USGS has developed the Rapid environmental (e)DNA Assessment and Deployment Initiative & Network (READI-Net) to accelerate the implementation of environmental DNA (eDNA) analysis as a best practice for the early detection of aquatic biological threats. READI-Net provides tools and a strategy to collect and deliver early detection data for natural resource managers and public health protection...
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Data releases by this scientist

Eutrophication and plankton communities (Cyanobacteria and eukaryotic algae) in the Grand Calumet River Area of Concern, Indiana, 2021

The data being released were part of a project funded by the United States Environmental Protection Agency (USEPA). This study sought to identify the planktonic communities (cyanobacteria, eukaryotic algae) potentially contributing to eutrophication within the Grand Calumet River Area of Concern (AOC) in northern Indiana along the southern shore of Lake Michigan. In 2021, triplicate water samples
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Great Lakes Science Center

Environmental DNA detection and survival, influence of sediment, and stream transport in a Lake Michigan watershed, 2018

The data released are associated with an examination of eDNA from round goby fish (Neogobius melanostomus) in a series of field sample collections (lake nearshore and stream transport) and in vitro laboratory experiments. The round goby was used as a model for our source of eDNA in the field collections and mesocosm experiments. The field samples for lake nearshore (water and sediment) were collec
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Great Lakes Science Center

Identify sources of high E. coli concentrations, beaches of southern Lake Michigan, 2015, (version 2.0, July 2020)

Data were collected as part of a study to identify sources of E. coli contamination at several beaches located in the Grand Calumet River Areas of Concern, located in northern Indiana on Lake Michigan. Water samples were collected at each site (Jeorse Park 1, Jeorse Park 2, Hammond East, Hammond West, Whihala East, and the Grand Calumet River) three times a week for thirteen weeks and analyzed for
By
Great Lakes Science Center

Microbial communities and bacterial indicators for shoreline sand, sediment, and water in Racine, Wisconsin; Chicago, Illinois; and East Chicago, Indiana; 2016-2017

The data associated with the following data release were collected between 2016 and 2017 at three locations on Lake Michigan: Racine, WI; Chicago, IL; and East Chicago, IN. Individual water samples were collected one day a week for ten weeks between June and August. Samples were collected from eight specific sites made up of two river and six shoreline type environments. Sampling was completed at
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Great Lakes Science Center

Quantification of nitrogen-fixing microorganisms (targeting nifH gene) in Cladophora algae by quantitative polymerase chain reaction (qPCR)

Data were collected to determine the abundance of nitrogen-fixing microorganisms in Cladophora algae growing on rocks, breakwall structures, or submerged dreissenid mussel beds around southern Lake Michigan. Cladophora samples (N=33) were collected between June and September 2015 from three urban areas: (a) Jeorse Park, East Chicago, Indiana, (b) Calumet Beach, Chicago, Illinois, and (c) North Bea
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Great Lakes Science Center

16S rRNA gene sequencing and E. coli for shorelines and the Grand Calumet River, Indiana, 2015

Data were collected in August and September 2015 for analysis of bacteria communities of the Grand Calumet River and associated shorelines. Water samples were collected on three occasions corresponding to one rain-related (wet) events and two non-rain (dry) events. Water samples were collected in the Grand Calumet River, at the mouth of the river, at offshore locations around the peninsular impoun
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Great Lakes Science Center

16S rRNA gene sequencing and E. coli for shorelines and the Grand Calumet River, Indiana, 2015

Data were collected in August and September 2015 for analysis of bacteria communities of the Grand Calumet River and associated shorelines. Water samples were collected on three occasions corresponding to one rain-related (wet) events and two non-rain (dry) events. Water samples were collected in the Grand Calumet River, at the mouth of the river, at offshore locations around the peninsular impoun
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Great Lakes Science Center

Quantitative polymerase chain reaction (qPCR): An alternative, rapid water quality monitoring tool at a National Park on Lake Michigan.

Data were collected to evaluate the efficacy of quantitative polymerase chain reaction (qPCR) as a rapid, alternative method for monitoring recreational water at select beaches and rivers of Sleeping Bear Dunes National Lakeshore (SLBE), in Empire, Michigan. Water samples were collected between August 4 and September 18, 2014 (N=297) from four locations (Esch Rd, Otter Creek, Platte Bay, and Platt
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Great Lakes Science Center

Multimedia related to this scientist

Researchers at a workbench in a lab
Pollinator Experiment Assembly Line
Pollinator Experiment Assembly Line
Researchers at a workbench in a lab

Pollinator Experiment Assembly Line

Pollinator Experiment Assembly Line

USGS scientists busy developing methods for identifying pollinators using environmental-DNA. Photo credit: Dawn Shively, USGS (contractor).

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Great Lakes Science Center, Great Lakes Science Center
Researchers at a workbench in a lab

Pollinator Experiment Assembly Line

Pollinator Experiment Assembly Line

USGS scientists busy developing methods for identifying pollinators using environmental-DNA. Photo credit: Dawn Shively, USGS (contractor).

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Great Lakes Science Center, Great Lakes Science Center
Researchers in a Laboratory
Running a Polymerase Chain Reaction
Running a Polymerase Chain Reaction
Researchers in a Laboratory

Running a Polymerase Chain Reaction

Running a Polymerase Chain Reaction

Aaron Aunins (Eastern Ecological Science Center, Leetown, West Virginia) prepares samples for polymerase chain reaction (PCR) as Kasia Kelly (left) and Dawn Shively (middle) (both from Great Lakes Science Center, Chesterton, Indiana) observe and document the procedure. Photo credit: Murulee Byappanahalli, USGS.

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Great Lakes Science Center
Researchers in a Laboratory

Running a Polymerase Chain Reaction

Running a Polymerase Chain Reaction

Aaron Aunins (Eastern Ecological Science Center, Leetown, West Virginia) prepares samples for polymerase chain reaction (PCR) as Kasia Kelly (left) and Dawn Shively (middle) (both from Great Lakes Science Center, Chesterton, Indiana) observe and document the procedure. Photo credit: Murulee Byappanahalli, USGS.

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Great Lakes Science Center

Publications by this scientist

Filter Total Items: 65

Bacteria common to rhizosphere communities of Asiatic bittersweet across a post-glacial landscape

Invasive plants such as Asiatic bittersweet (Celastrus orbiculatus Thunb.) are a significant problem for land managers as they impact plant species composition, disrupt nutrient dynamics and structure of native ecosystems, and are difficult to eradicate. As a result of the increasing abundance of Asiatic bittersweet across the eastern U.S., we have been investigating underlying factors potentially
Authors
Cindy H. Nakatsu, Noel B. Pavlovic, Muruleedhara Byappanahalli
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Ecosystems Mission Area, Great Lakes Science Center

Microbial source tracking and evaluation of best management practices for restoring degraded beaches of Lake Michigan

Attempts to mitigate shoreline microbial contamination require a thorough understanding of pollutant sources, which often requires multiple years of data collection (e.g., point/nonpoint) and the interacting factors that influence water quality. Because restoration efforts can alter shoreline or beach morphology, revisiting source inputs is often necessary. Microbial source tracking (MST) using so
Authors
Meredith B. Nevers, Paul M. Buszka, Muruleedhara Byappanahalli, Travis Cole, Steven R. Corsi, P. Ryan Jackson, Julie L. Kinzelman, Cindy H Nakatsu, Mantha S. Phanikumar
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Ecosystems Mission Area, Land Management Research Program, Great Lakes Science Center

Gut microbiota associated with different sea lamprey (Petromyzon marinus) life stages

Sea lamprey (SL; Petromyzon marinus), one of the oldest living vertebrates, have a complex metamorphic life cycle. Following hatching, SL transition into a microphagous, sediment burrowing larval stage, and after 2–10+ years, the larvae undergo a dramatic metamorphosis, transforming into parasitic juveniles that feed on blood and bodily fluids of fishes; adult lamprey cease feeding, spawn, and die
Authors
Prince P Mathai, Muruleedhara Byappanahalli, Nicholas S. Johnson, Michael J. Sadowsky
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Ecosystems Mission Area, Great Lakes Science Center

Influence of filter pore size on composition and relative abundance of bacterial communities and select host-specific MST markers in coastal waters of southern Lake Michigan

Water clarity is often the primary guiding factor in determining whether a prefiltration step is needed to increase volumes processed for a range of microbial endpoints. In this study, we evaluate the effect of filter pore size on the bacterial communities detected by 16S rRNA gene sequencing and incidence of two host-specific microbial source tracking (MST) markers in a range of coastal waters fr
Authors
Muruleedhara Byappanahalli, Meredith B. Nevers, Dawn Shively, Cindy H Nakatsu, Julie L. Kinzelman, Mantha S. Phanikumar
By
Ecosystems Mission Area, Great Lakes Science Center

Sequestration of microfibers and other microplastics by green algae, Cladophora, in the US Great Lakes

Daunting amounts of microplastics are present in surface waters worldwide. A main category of microplastics is synthetic microfibers, which originate from textiles. These microplastics are generated and released in laundering and are discharged by wastewater treatment plants or enter surface waters from other sources. The polymers that constitute many common synthetic microfibers are mostly denser
Authors
Julie R. Peller, Meredith B. Nevers, Muruleedhara Byappanahalli, Cassie Nelson, Bharath Ganesh Babu, Mary Anne Evans, Eddie Kostelnik, Morgan Keller, Jenna Johnston, Sarah Shidler
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Ecosystems Mission Area, Great Lakes Science Center

Influence of sediment and stream transport on detecting a source of environmental DNA

Environmental DNA (eDNA) can be used for early detection, population estimations, and assessment of potential spread of invasive species, but questions remain about factors that influence eDNA detection results. Efforts are being made to understand how physical, chemical, and biological factors—settling, resuspension, dispersion, eDNA stability/decay—influence eDNA estimations and potentially popu
Authors
Meredith B. Nevers, Katarzyna Przybyla-Kelly, Dawn A. Shively, Charles C. Morris, Joshua Dickey, Muruleedhara Byappanahalli
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Ecosystems Mission Area, Great Lakes Science Center

Evaluating the impacts of foreshore sand and birds on microbiological contamination at a freshwater beach

Beaches along the Great Lakes shorelines are important recreational and economic resources. However, contamination at the beaches can threaten their usage during the swimming season, potentially resulting in beach closures and/or advisories. Thus, understanding the dynamics that control nearshore water quality is integral to effective beach management. There have been significant improvements in t
Authors
Ammar Saffaie, Chelsea J. Weiskerger, Meredith B. Nevers, Muruleedhara Byappanahalli, Mantha S. Phanikumar
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Ecosystems Mission Area, Great Lakes Science Center

Utilization of multiple microbial tools to evaluate efficacy of restoration strategies to improve recreational water quality at a Lake Michigan Beach (Racine, WI)

Hydro-meteorological conditions facilitate transport of fecal indicator bacteria (FIB) to the nearshore environment, affecting recreational water quality. North Beach (Racine, Wisconsin, United States), is an exemplar public beach site along Lake Michigan, where precipitation-mediated surface runoff, wave encroachment, stormwater and tributary outflow were demonstrated to contribute to beach advis
Authors
Julie Kinzelman, Muruleedhara Byappanahalli, Meredith B. Nevers, Dawn Shively, Stephan Kurdas, Cindy H Nakatsu
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Ecosystems Mission Area, Great Lakes Science Center

Interaction of bacterial communities and indicators of water quality in shoreline sand, sediment, and water of Lake Michigan

Shoreline sand harbors high concentrations of fecal indicator bacteria (FIB) that may be resuspended into the water column through washing and resuspension. Studies have explored coastal processes that influence this sand-water flux for FIB, but little is known about how microbial markers of contamination or the bacterial community interact in the sand-water interface. In this study, we take a thr
Authors
Meredith B. Nevers, Muruleedhara Byappanahalli, Cindy H. Nakatsu, Julie L. Kinzelman, Mantha S. Phanikumar, Dawn Shively, Ashley Spoljaric
By
Ecosystems Mission Area, Great Lakes Science Center

Quantifying microplastics in Indiana’s Lake Michigan watershed and submerged aquatic vegetation

Environmental breakdown of plastics produces synthetic microfibers, a class of microplastics that are most prevalent in surface waters. A main source of these pollutants is wastewater treatment plants which discharge into surface waters, including those that flow into Lake Michigan. Microplastics can settle into aquatic sediment or exist for lengths of time in the swash zone of the lakes; they can
Authors
Julie R. Peller, Meredith B. Nevers, Muruleedhara Byappanahalli, Mary Anne Evans
By
Ecosystems Mission Area, Great Lakes Science Center

Real-time water quality monitoring at a Great Lakes National Park

Quantitative polymerase chain reaction (qPCR) was used by the USEPA to establish new recreational water quality criteria in 2012 using the indicator bacteria enterococci. The application of this method has been limited, but resource managers are interested in more timely monitoring results. In this study, we evaluated the efficacy of qPCR as a rapid, alternative method to the time-consuming membra
Authors
Muruleedhara Byappanahalli, Meredith B. Nevers, Dawn Shively, Ashley Spoljaric, Christopher Otto
By
Ecosystems Mission Area, Great Lakes Science Center

Identifying and eliminating sources of recreational water quality degradation along an urban coast

Restoration of highly degraded urban coastal waters often requires large-scale, complex projects, but in the interim, smaller-scale efforts can provide immediate improvements to water quality conditions for visitor use. We examined short-term efforts to improve recreational water quality near the Grand Calumet River (GC) in the Laurentian Great Lakes. Identified as an Area of Concern (AOC) by the
Authors
Meredith B. Nevers, Muruleedhara Byappanahalli, Dawn Shively, Paul M. Buszka, P. Ryan Jackson, Mantha S. Phanikumar
By
Ecosystems Mission Area, Great Lakes Science Center

Non-USGS Publications**

Fujioka, R.S., Byappanahalli, M.N., 2001. Microbial ecology controls the establishment of fecal bacteria in tropical soil environment.  In Advances in Water and Wastewater Treatment Technology: Molecular Technology, Nutrient Removal, Sludge Reduction and Environmental Health. Matsuo, T., Hanaki, K., Takizawa, S., Satoh, H. (eds.). Amsterdam, the Netherlands: Elsevier, pp. 273-283.
Byappanahalli, M.N., Fujioka, R.S., 1998. Evidence that tropical soil environment can support the growth of Escherichia coli. Water Sci. Technol. 38, 171-174.
Habte, M., B. N. Muruleedhara, and H. Ikawa. 1993. Response of neem, (Azadirachta indica) to soil P concentration and mycorrhizal fungi. Arid Soil Research and Rehabilitation 7(4):327-333. https://doi.org/10.1080/15324989309381365
Habte, M. and M. N. Byappanahalli. 1994. Dependency of cassava (Manihot esculenta) on vesicular-arbuscular mycorrhizal fungi. Mycorrhiza 4(6):241-245. https://doi.org/10.1007/BF00206771.
Habte, M., M. N. Byappanahalli, J. Ram. 1994. Response of Sauropus androgynous to soil P concentration and mycorrhizal colonization. Journal of Plant Nutrition 17(2-3):511-521. https://doi.org/10.1080/01904169409364745.
Fujioka, R. S., and M. N. Byappanahalli. 1996. Assessing the applicability of recreational water quality standards to Hawaii and other tropical islands. Project completion report (WRRC-96-01) to the Department of Health, State of Hawaii. 50 pp. http://scholarspace.manoa.hawaii.edu/handle/10125/21922.
Byappanahalli, M. N. and R. S. Fujioka. 1998. Evidence that tropical soil environment can support the growth of Escherichia coli. Water Science & Technology 38(12):171-174. DOI: https://doi.org/10.1016/S0273-1223(98)00820-8.
Fujioka, R. S., and M. N. Byappanahalli. 1998. Do fecal indicator bacteria multiply in the soil environments of Hawaii? Project completion report (WRRC-98-04) to the U.S. EPA Grant Administration Division, Washington, D.C., and RARE Program, Region IX, San Francisco, California. 85 pp. http://scholarspace.manoa.hawaii.edu/handle/10125/21939
Habte, M. and B. N. Byappanahalli. 1998. Influence of pre-storage drying conditions and duration of storage on the effectiveness of root inoculum of Glomus aggregatum. Journal of Plant Nutrition 21(7):1375-1389. https://doi.org/10.1080/01904169809365490.
Fujioka, R. S. and M. N. Byappanahalli. 2001. Microbial ecology controls the establishment of fecal bacteria in tropical soil environment, p. 273-283. In T. Matsuo, K. Hanaki, S. Takizawa, and H. Satoh, editors. Advances in Water and Wastewater Treatment Technology: Molecular Technology, Nutrient Removal, and Environmental Health. Elsevier, Amsterdam, the Netherlands. https://doi.org/10.1016/B978-044450563-7/50211-0.
Brinkman, N. E., R. A. Haugland, L. J. Wymer, M. Byappanahalli, R. L. Whitman, and S. J. Vesper. 2003. Evaluation of a rapid, quantitative real-time PCR method for enumeration of pathogenic Candida cells in water. Applied and Environmental Microbiology 69(3):1775-1782. doi: 10.1128/AEM.69.3.1775-1782.2003.
Fujioka, R. S., and M. N. Byappanahalli. 2003. Proceedings and Report of Tropical Water Quality Indicator Workshop, Honolulu, Hawaii, March 1-2, 2001. Special Report SR-2004-01, University of Hawaii at Manoa, Water Resources Research Center, Honolulu, Hawaii. 95pp. https://www2.hawaii.edu/~kirs/report.pdf

**Disclaimer: The views expressed in Non-USGS publications are those of the author and do not represent the views of the USGS, Department of the Interior, or the U.S. Government.

News about this scientist

Przybyla-Kelly Delivers Virtual Poster Presentation Workshop Hosted by Government eDNA Working Group

Przybyla-Kelly Delivers Virtual Poster Presentation Workshop Hosted by Government eDNA Working Group

Comparing round goby eDNA concentrations in water, sediment, and algae with abundance estimates by divers in four Great Lakes.

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Byappanahalli, Kelly, and Shively Visit EESC for Training and Collaboration

Byappanahalli, Kelly, and Shively Visit EESC for Training and Collaboration

LMERS scientists dedicated time to training in new techniques including High Throughput Sequencing, Bioinformatics, and discussing ongoing projects...

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GLSC Hosts Congressmen Mrvan (IN) And Neguse (CO) During NPS Tour

GLSC Hosts Congressmen Mrvan (IN) And Neguse (CO) During NPS Tour

Congressional Staff Learn About Lake Michigan Ecological Research Station Work In Support of National Park Service

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GLSC Cladophora Research Featured in Environmental Health News

GLSC Cladophora Research Featured in Environmental Health News

Microplastics in Algae

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Students visit GLSC Chesterton lab to learn about microbiology applications

Students visit GLSC Chesterton lab to learn about microbiology applications

Students from Indiana University Northwest visited the Lake Michigan Ecological Research Station (GLSC, Chesterton, Indiana).

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Science and Products

*Disclaimer: Listing outside positions with professional scientific organizations on this Staff Profile are for informational purposes only and do not constitute an endorsement of those professional scientific organizations or their activities by the USGS, Department of the Interior, or U.S. Government