Ashvini Chauhan, Ph.D.
School of the Environment
1515 MLK Boulevard, Suite 305 B, Building FSHSRC
Florida A&M University,Tallahassee, Florida- 32307
Phone: (Office); 850-599-8895 (Lab); FAX: 850-561-2248
Laboratory Web site: http://www.famu.edu/index.cfm?environmentalscience&Faculty
Link to CV
The overall rationale of my research is to obtain a comprehensive understanding on the causes and consequences of microbial biodiversity in both coastal and terrestrial ecosystems. My research is divided into three fundamental areas: the response of microbial diversity as a function of environmental change, such as global warming, microbial ecology of anthropogenically altered environments and exploitation of microorganisms and algae for biobased products such as biofuel production.
Previously, both animal and plant diversity shifts have been utilized as indicators of ecological integrity and assessment following anthropogenic disturbance(s). However, recent applications of genomic and transcriptomic approaches are fast leading to paradigm shifts towards understanding microorganisms in their ecosystem context. To accomplish these objectives, my laboratory applies cutting-edge tools including metagenomics, transcriptomics, bar-coded pyrosequencing, catalyzed reporter deposition fluorescent in-situ hybridization (CARD-FISH), DNA/RNA Stable Isotope Probing (SIP), functional gene arrays (FGAs) and qPCR to obtain a comprehensive understanding of bacterial, archaeal, fungal and algal communities in different environments. We are also heavily engaged in the development of emergent bioanalytical techniques that facilitate publishing in top science journals. For example, our finding on the marine microbial loop processes using a novel adaptation of SIP in estuarine systems was published in Proceedings of the National Academy of Sciences, USA (Chauhan et al., Proc. Natl. Acad. Sci. USA 106(11): 4301-4306). With this publication, FAMU became one of only two minority schools to have published in this prestigious journal (ISI Thompson Sciences). More recently, we have reported a novel application of Femtosecond Laser-induced breakdown spectroscopy (LIBS), which provides for a precise ‘fingerprint’ of trace elements contained in biological samples. This has enabled us to discriminate microorganisms isolated from environmental samples, including pathogenic bacteria. In addition to detection, quantification, and characterization of microbial communities, there is a significant interest in assessing gene expression in order to further understand the ecological functions of microorganisms. As an example, in a DoD funded project, we are characterizing degradation of naphthalene metabolism in a Gram-positive Rhodococcus opacus strain M213, isolated from fuel-oil contaminated sediments in northern Idaho. Previously described biochemical pathways for bacterial degradation of naphthalene include formation of salicylic acid as a key intermediate metabolite. Our findings suggest that this is not true for strain M213; it does not grow on salicylic acid, but grows well on o-phthalic acid, 4 hydroxyphthalic acid, 3-hydroxybenzoic acid and protocatechuic acid. In concentrated cell suspensions of M213 containing 0.1% of naphthalene, we identified several transiently occurring metabolites by reversed phase HPLC and confirmed by high resolution electrospray ionization (ESI) time-of-flight (TOF) mass spectrometry in the negative ion mode. The metabolites identified over a 3 day incubation period included o-phthalic acid, 4 hydroxyphthalic acid, 3-hydroxybenzoic acid and 3,4-dihydroxybenzoic acid. Conversely, salicylic acid, the key metabolite formed in previously described naphthalene degradative pathways, was formed in only in minor concentration.
To understand the genetics of naphthalene degradation in strain M213, we performed pulse-field gel electrophoresis (PFGE) which showed the presence of three distinct genomic fractions- chromosomal DNA, 750Kb megaplasmid, and 350Kb megaplasmid DNA. These fractions were then amplified by narAa and narAb genes encoding the α and β subunits of the naphthalene dioxygenase (NDO) catalytic component iron-sulfur protein (ISPNAR), which is involved in the first stage of naphthalene biodegradation into 1,2-dihydronaphthalene. Surprisingly, all three DNA fractions showed the presence of narAa and narAb genes; nucleotide sequence of both strands of putative nar-like fragments revealed an overall 96-98% homology to narAa and narAb of the recently isolated strain B2-1, from the Verkhnekamsk salt mining region of Russia. Moreover, qPCR analysis indicated that there were 2-3-fold higher gene copy numbers of both narAa and narAb genes on the 750KB megplasmid compared with chromosomal and the 350KB megaplasmid, respectively. Our data suggests that there may be several distinct genes for naphthalene degradation in strain M213 that likely originated by reshuffling of genetic modules and genomic rearrangements. We are currently sequencing the genome from strain M213 by a transposase mediated Roche 454 pyrosequencing and Illumina sequencing which will yield further information on the genetics of naphthalene degradation through previously undescribed pathways in contaminated environments.
In a recently completed study funded by NSF, we have investigated short-term response of estuarine microbiota over a tidal cycle. Briefly, marine dissolved organic matter (DOM) is one of the largest active reservoirs of reduced carbon at the earth’s surface. In any given system, the fate of DOM is a function of the physiological status and taxonomic composition of the native bacterial communities as well as the relative lability of the DOM, all of which vary both spatially and temporally. To a large extent, as the primary consumers of DOM, heterotrophic bacteria control its persistence in the marine system (i.e. remineralization back to CO2 vs. assimilation and potential trophic transfer. DOM that is assimilated into bacterial biomass is potentially available for trophic transfer via the microbial loop, which is one of the major carbon cycling pathways in oceans representing approximately one-half of the oceanic primary production. Microbial diversity has long been considered to be a function of bottom up substrate supply and top down factors including protistan grazing and viral lysis. In addition to the ‘top’ down and ‘bottom up’ controls, we discovered rapidly functioning ‘sideways’ control via bacterial predators- the Bdellovibrio-like organisms (BLOs) which likely have critical impacts on pathways through which autochthonous and allochthonous nutrients are mineralized by aquatic microbiota, thereby impacting climate change and ocean acidification processes. As an extension of this project, we are collaborating with Dr Jason Hall-Spencer, from the School of Marine Science and Engineering at University of Plymouth, UK. The world’s oceans take up roughly 30% of the current anthropogenic CO2 emissions; this increased dilution of CO2 in seawater results in a decrease of pH as well as a dilution of carbonates. The dramatic effects, especially on calcifying plankton, can already be observed globally. In this project, we are studying water, algal and sediments collected from a naturally occurring CO2 vent- Castello Aragonese, part of a 132,000 y old volcano at the northeastern side of Ischia Island in Italy. At this site, gas vents occur in shallow waters and gas bubbles-up at about 1.4 x 106 l/ d comprising of 90-95% CO2. The site is microtidal (0.5 m range) and the CO2 vents lack sulfur; they acidify normal salinity and alkalinity seawater along a pH gradient from 8.17 down to 6.57 for 300 m running parallel to the rocky shore. Hall-Spencer et al. found a total of 64 macrobenthic taxa at the vent areas, where reductions in biodiversity of adult populations are caused by lowered pH. There is however no information on the potential impacts of changes in pH on marine microbial communities, which play critical roles in the nutrient cycling and global productivity of oceans.Because even a slight change in ocean pH will likely cause major biodiversity losses, in this project, we are investigating ecological tipping points of prokaryotes (bacteria, archaeal) and eukaryotes (algae, fungi, protists) at the genetic, taxonomical and functional scales along pH gradients. Benthic microbial diversity, biomass, community composition, abundance as well as functional changes in the ecosystem are being studied using a toolkit of diverse molecular techniques (e.g. 16S rRNA, and functional gene sequencing, ARISA, qPCR, and metagenomics). Furthermore, community-shifts as well as ecosystem resistance and resilience, are experimentally investigated as a function of pH, temperature, and CO2 variations. Analogous to metagenomics, environmental transcriptomic analysis involves retrieval of mRNAs from environmental systems without prior knowledge of what genes might be expressed by the community. Thus it provides the most unbiased perspective on community gene expression in situ. We are also analyzing gene expression of marine bacterioplankton communities by the direct retrieval and analysis of microbial transcripts from the water, sediment and plankton samples collected from the CO2 volcanic vent, Italy. Data obtained from this project will be used to develop predictive models on how oceanic pH changes will affect the microbial loop functioning and thus overall marine productivity.
In a related project, funded by BP/FIO, we are investigating how carbon flow between phytoplankton and bacteria change as a function of hydrocarbons from the Deepwater Horizon oil spill. Microcosms spiked with oil, oil + Corexit and controls were studied using 3H-leucine incorporation, CARD-FISH and pyrosequencing. It was clear that phytoplankton were rapidly killed by even less than 1% oil concentration. Conversely, marine microorganisms rapidly changed from a diverse community to those that have the propensity to degrade oil such as Oceanospirillaceae, Alcanivoracaceae and Sphingomonadaceae. Further, unassembled (raw) reads were compared to a novel database of proteins involved in hydrocarbon degradation using the tblastx algorithm from NCBI. Proteins involved in alkane degradation, including methane, were more abundant in the oil + corexit microcosms relative to oil and control microcosms. Simultaneously, we are also utilizing three recently developed bacterial gene constructs from the laboratory of Dr. Jan Van Der Meer, University of Lausanne, Switzerland to quantify bioavailable fractions of Deepwater Horizon hydrocarbons spilled into the Gulf waters, sediments and oyster reefs such that recommendations on adequate restoration measures of these environments can be obtained.
In terrestrial systems, we are investigating denitrification processes within agroecosystems being fed by nutrient-rich municipal recycled wastewater to grow plants for animal feed. As a function of wastewater loading, the north Florida aquifers system has become polluted with excess nitrate. Much of north Florida is dependent on this freshwater resource, and our study is providing biotechnological and environmentally sustainable solutions for wastewater reuse. In another recently completed study, we studied the impact of mining activities on soil microbiota. Specifically, we assessed rehabilitation success in three chronosequence sites; our study suggests that, in tandem with geochemical methods, microbial communities can be used as sensitive bioindicators of soil health. Additionally, comparisons obtained between un-mined and 03, 13 and 23 year old rehabilitated soils provide conclusive evidence that mining operations resulted in severe perturbations to the soils such that impacted soils were significantly low in soil microbiota including Proteobacteria, Acidobacteria, Bacteroidetes, and high G+C Gram-positives. These microbial groups are critical to maintaining soil productivity and their low abundance and activity in the post-mined soils likely caused poor quality and low productivity of the Jamaican soils.
One of my long term interests is to study the anthropogenic nutrient loading on wetlands. Wetlands are significant contributors of methane, which is much more potent than CO2 as a greenhouse gas. To this end, we have obtained significant findings on the genotypic and phenotypic characterization of anaerobic carbon cycling microbial guilds, with an emphasis on fermentative bacteria, syntrophs, methanogens and methanotrophs. Using cutting edge molecular tools, including functional gene arrays, stable isotope probing and metagenomics, we have thus far been able to link the structure to the function of complex soil/rhizosphere microbial communities of Florida Everglades, which clearly indicate that eutrophication results in a complex change in the microbial guilds leading to divergent pathways of methane formation. Because anaerobic processes can be exploited to produce bioenergy and other value added products, we are beginning a new project funded by DoD to couple wastewater nutrients to obtain algal biomass and other value added biobased products.
EVR6064, Principles of Ecology (Graduate; 3 cr)
EVS5028, Environmental Biotechnology (Graduate; 3 cr) OR EVR 5068, Marine Microbial Ecology (Graduate, 4 cr)
EVS2920, Environmental Science Foum and Colloiquim (1 cr)
EVS5027, Environmental Microbiology with lab (Graduate; 4 cr), OR EVS5673, Bioremediation Application and Techniques (Graduate; 3 cr)
EVS2920, Environmental Science Foum and Colloiquim (1 cr)
EVS5028, Molecular Biology Techniques with lab (Graduate; 3 cr)
EVS5930, Special Topics Course “Theory and Applications of Tools in Microbial Ecology (Graduate; 3 cr)
New Courses being developed:
Applied Microbial Processes with lab (Undergraduate; 3 cr)
Bioenery (Graduate; 4 cr)
A. Aquatic Microbial Ecology:
B. Soil Microbial Ecology:
C. Biodegradation and Bioremediation:
D. Book Chapter/Review (Peer-reviewed and by invitation only):
Scholarships, Awards and Merits:
Students Currently being Advised:
1. PI, $558,472 (2011-2014): Phycoremediation of military wastewater pollutants and nutrients to generation of environmentally sustainable biobased products. Funded by DoD.
2. PI, $373,248 (2010-2013), Characterization of a novel naphthalene metabolic pathway in R. opacus M213 and comparative ecology of associated degradative gene(s) in contaminated military sites. DoD.
3. Co-PI, $215,021: Uncoupling of autotrophy and heterotrophy: effects of the Deepwater Horizon Oil Spill on microbial food webs. BP/FIO; Co-PIs: Dr. Jennifer Cherrier (FAMU); Dr. Wade Jeffrey (UWF). Funded by BP/FIO.
4. Co-PI, 255,968 (2009), the US-Brazil Environmental and Business Cross Cultural initiative: Sustainability Challenges and Attractiveness of Investments in Biofuels Production.
5. PI, $95,000 (August 2007- 2008): Microbial Communities as Sensitive Indicators of Ecosystem Health and Processes in Bauxite Soils of Jamaica. Funded by Alcoa.
6. PI, $11,000 (August 2007- 2008): Bdellovibrio-and like organisms (BALOs) as new generation of antibiotic agents. RCMI Drug Discovery Program, NIH.
7. CO-PI, $269,496 (July 15 2007- July 14 2008). Reduction of Vibrio vulnificus in oysters by treatment with Bdellovibrio and Like Organisms (BALOs) and viruses. CSREES (USDA).
8. Co-PI, $998,820. NSF HBCU-RISE, Tracing Carbon Flow in the Apalachicola Bay-A Case Study. Nov 1, 2005-Oct 31, 2008.
9. PI, $65,612 (2002-2003): NASA Space Biotechnology and Commercial Applications project (NAG10-316) titled "The molecular microbial ecology of closed systems supporting rice growth and waste treatment". Co-PI: Andrew Ogram, University of Florida
Membership of Professional Societies:
Collaborators and Co-PIs: