# positions[].organizations[].parent[].label
College of Agriculture and Life Sciences

# overview
Plants are in constant interactions with a large diversity of microorganisms, that belong to various biological kingdoms including archaea, bacteria, fungi and protista. In nature, these inter-kingdom interactions can be both cooperative and detrimental to the host-plants. My major research focus is to understand the dynamics of inter-kingdom microbiome-interactions and how it affects the crop production. We use cutting-edge culture-independent (metagenomics, metatranscriptomics and metabolomics) and culture-dependent (culturomics) methods combined with computational biology. We especially employ a systematics-based approach, so that we can identify individual organisms involved in these interactions, their biological functions, impacts on neighboring niches, and metabolic activity.

Current research projects

The research has several direct biotechnological applications, and the research in our lab focuses on the following:

1. Develop bioferlitizers/biopesticides: By disentangling the microbial functions that are essential for different growth stages of crop plants, we intend to develop "soil probiotics" to improve crop health. In order to achieve this, we study natural ecosystems and wild plants related to crops. The technology developed will be sustainable and environmentally friendly. Our current research focuses on developing microbial inoculum assemblages from teosinte (ancestor of modern maize) and transferring the microbiota to maize to improve pest and pathogen resistance.

2. Pathobiomes of plants: The concept of pathobiome is an emerging field in pathogen biology. In recent times, it has been noted that pathogens do not act alone in natural ecosystems, but along with a mob of other microorganisms. Deciphering the interaction between a plant pathogen and its associated microbiomes is necessary to understand pathogensis and also to design control measures. Research in my lab specifically focusses on mycosphere bacterial microbiota of pathogenic fungi. Our recent research focusses on pathobiomes associated with Fusarium wilt of cotton.

3. Indicators of microbial dysbiosis: Dysbiosis is a microbial imbalance caused by perturbation in an ecosystem or a niche. Plant microbiomes experience dysbiosis during biotic (disease) and abiotic (drought, flooding, heat etc) stress. We study dysbiosis to understand shift in microbial processes, detect stress indicators and design stress alleviation measures including developing microbial inoculum (biofertilizers).

# keywords[]
3102 Bioinformatics And Computational Biology

# keywords[]
30 Agricultural, Veterinary And Food Sciences

# keywords[]
<italic>fusarium Proliferatum </italic>

# keywords[]
<italic>fusarium Incarnatum-equiseti </italic>

# keywords[]
<italic>fusarium Incarnatum </italic>

# keywords[]
<italic>oryza Latifolia</italic>

# keywords[]
<italic>oryza Sativa</italic>

# keywords[]
<italic>sarocladium Oryzae</italic>

# keywords[]
<italic>fusarium Equiseti </italic>

# keywords[]
3102 Bioinformatics And Computational Biology

# keywords[]
30 Agricultural, Veterinary And Food Sciences

# keywords[]
30 Agricultural, Veterinary And Food Sciences

# keywords[]
30 Agricultural, Veterinary And Food Sciences

# keywords[]
<italic>magnaporthe Oryzae</italic>

# keywords[]
<italic>epicoccum Sorghinum</italic>

# keywords[]
<italic>alternaria Padwickii</italic>

# keywords[]
<italic>cochliobolus Miyabeanus</italic>

# keywords[]
Magnaporthe Oryzae<italic></italic><italic></italic>

# keywords[]
<italic>epicoccum Sorghimum</italic>

# keywords[]
<italic>curvularia Hawaiiensis</italic>

# educationAndTraining[].organization.label
Newcastle University - (Newcastle upon Tyne, United Kingdom)

# publications[].label
Draft Genome Resources of Seven Strains of Tilletia horrida , Causal Agent of Kernel Smut of Rice

# publications[].label
Microbiome differentiation between micro-sympatric maize and teosinte reveals domestication-driven functional erosion of the microbiome across plant compartments

# publications[].label
Hyphosphere bacteria modify phenotypic traits of the cotton Fusarium wilt pathogen

# publications[].label
The Distinguished Microbiome: Differentiating Microbial Dysbiosis and the Pathobiome of Banana Fusarium Tropical Race 4

# publications[].label
Biosystematics of alkaliphilic streptomycetes isolated from seven locations across a beach and dune sand system.

# publications[].label
Complete Genome Sequence of Geobacter sp. Strain FeAm09, a Moderately Acidophilic Soil Bacterium.

# publications[].label
Effects of ozone exposure on the xerophilic fungus, Eurotium amstelodami IS-SAB-01, isolated from naan bread.

# publications[].label
Microbial Community of Saline, Alkaline Lakes in the Nebraska Sandhills Based on 16S rRNA Gene Amplicon Sequence Data.

# publications[].label
A modular, low-cost, configurable, and opensource automated irrigation system to regulate soil water content in plant microbiome studies

# publications[].label
Rhizosphere pathobiome of Fusarium wilt in tomato and cascading effects within the soil metabolome

# publications[].label
Multiple Streptomyces species with distinct secondary metabolomes have identical 16S rRNA gene sequences.

# publications[].label
First Report of Fusarium Sheath Rot of Rice Caused by Fusarium incarnatum-equiseti Species Complex in the United States.

# publications[].label
Temporal changes of bacterial communities in the Tuber melanosporum ectomycorrhizosphere during ascocarp development.

# publications[].label
Effect of maize domestication and breeding on rhizosphere and phyllosphere microbial communities and network assembly

# publications[].label
Multi-Locus Sequence Analysis Reveals Diversity of the Rice Kernel Smut Populations in the United States.

# publications[].label
Littoral lichens as a novel source of potentially bioactive Actinobacteria.

# publications[].label
Black truffle-associated bacterial communities during the development and maturation of Tuber melanosporum ascocarps and putative functional roles.

# publications[].label
Seed endophytic microbial populations between organically and conventionally grown rice are taxonomically and functionally

# publications[].label
Effect of ozone on spore germination, spore production and biomass production in two Aspergillus species.

# publications[].label
An improved method compatible with metagenomic analyses to extract genomic DNA from soils in Tuber melanosporum orchards.

# publications[].label
Computer-assisted numerical analysis of colour-group data for dereplication of streptomycetes for bioprospecting and ecological purposes.

# publications[].label
Draft Genomes of Five Fusarium oxysporum f. sp. niveum Strains Isolated from Infected Watermelon from Texas with Temporal and Spatial Differences

# publications[].label
Aeroponic approach for nondestructive root exudate collection and simulation of variable water stress trialed on cotton (Gossypium hirsutum).

# publications[].label
Characterization of Differences of Seed Endophytic Microbiome in Conventional and Organic Rice by Amplicon-based Sequencing and Culturing Methods

# publications[].label
Multiple Biosynthetic Gene Pathways are Revealed in Whole-Genome Sequence of Endophytic Biocontrol Strain Pantoea stewartii subsp. indologenes ST25.

# publications[].label
Progressive drought alters the root exudate metabolome and differentially activates metabolic pathways in cotton (Gossypium hirsutum).

# publications[].label
Pharmacological activity of Costus spicatus in experimental Bothrops atrox envenomation.

# publications[].label
Fusarium cotton wilt pathogen Fusarium oxysporum f. sp. vasinfectum race 4 (FOV4) supports a diverse aerobic and anaerobic bacterium on its hyphae

# publications[].label
De novo genome sequence of endophytic biocontrol strain Bacillus sp. ST24 isolated from rice seed.

# publications[].label
Nondestructive root exudate sampling using aeroponics throughout progressive drought stress and recovery

# publications[].label
Individual variation in 3-methylbutanal: a putative link between human leukocyte antigen and skin microflora.

# publications[].label
Core hyphosphere microbiota of Fusarium oxysporum f. sp. niveum

# publications[].label
Genetic and phenotypic evidence for Streptomyces griseus ecovars isolated from a beach and dune sand system.

# publications[].label
Genetic variation of rice kernel smut populations in the United States

# publications[].label
Core hyphosphere microbiota of Fusarium oxysporum f. sp. niveum.

# publications[].label
Purification and characterization of an extracellular lipase from a novel strain Penicillium sp DS-39 (DSM 23773)

# publications[].label
Ecology and molecular typing of L. monocytogenes in a processing plant for cold-smoked salmon in the Republic of Ireland

# publications[].label
First Report and Characterization of Propiconazole Resistance in Tilletia horrida Causing Kernel Smut in Rice.

# publications[].label
Ecology and molecular typing of L. monocytogenes in a processing plant for cold-smoked salmon in the Republic of Ireland

# publications[].label
Core bacteria associated with hyphosphere of Fusarium oxysporum f. sp. niveum over spatial and temporal differences

# publications[].label
Characterization of differences in seed endophytic microbiome in conventional and organic rice by amplicon-based sequencing and culturing methods.

# publications[].label
First Report of Leaf Spot of Rice Caused by Epicoccum sorghinum in the United States.

# publications[].label
First Report of Brown Leaf Spot of Rice Caused by Curvularia hawaiiensis in the United States.

# researcherOn[].label
Getting to the root of drought: Unlocking plant-soil-microbiome interactions in the rhizosphere that regulate drought responses

# researcherOn[].awardedBy.label
National Institute of Food and Agriculture - (Washington D.C., District of Columbia, United States)

# researcherOn[].label
Endophytic Microbial Culture-Collection For Pest Management In Maize

# researcherOn[].awardedBy.label
National Institute of Food and Agriculture - (Washington D.C., District of Columbia, United States)

# researcherOn[].label
Deciphering microbial functions to improve plant productivity and sustainable agriculture

# researcherOn[].awardedBy.label
National Institute of Food and Agriculture - (Washington D.C., District of Columbia, United States)

# researcherOn[].label
Interaction between biotic and abiotic determinants of epidemic dynamics in the cotton-Fusarium soilborne pathosystem

# researcherOn[].awardedBy.label
National Institute of Food and Agriculture - (Washington D.C., District of Columbia, United States)

# researcherOn[].label
Optimizing teosinte to maize microbiome transplant strategies to enhance insect resistance in maize

# researcherOn[].awardedBy.label
National Institute of Food and Agriculture - (Washington D.C., District of Columbia, United States)

# researcherOn[].label
Partners in Crime: Pathobiome of Fusarium Cotton Wilt Pathogen

# researcherOn[].awardedBy.label
National Institute of Food and Agriculture - (Washington D.C., District of Columbia, United States)

# organizations[]
College of Agriculture and Life Sciences

# schools[]
College of Agriculture and Life Sciences

# etdChairOf[].label
Qin, Kuan (2022-08). Application of Lignite-Derived Humic Substances in Vegetable Production Systems. Doctoral Dissertation.