People

Trent Northen

Understanding the dynamic processes by which microbial community metabolism transform biopolymers and metabolites within their environment

We are interested how microbial communities are structured by the biopolymers and metabolites in their environment and the dynamic and reciprocal processes by which they transform these pools. Central to these efforts are the development of mass spectrometry approaches to study these processes including exoenzyme activity profiling, exometabolomics and mass spectrometry imaging. Together these allow us to comprehensively characterize metabolic activities, dynamics and localization within complex cellular systems to predict responses and design interventions.

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EcoFAB

Ben Bowen

Understanding biological mechanisms associated with change

Understanding complex, dynamic metabolic networks in an environmental context will require utilization of emerging technologies. These datasets generated are often large-scale both in terms of complexity and raw-size making them difficult to mine for biological insight. Ben is leading several computational efforts including Metabolite Atlas and OpenMSI to make the most high-performance, advanced data management, model building, analysis and visualization resources for mass spectrometry accessible to all scientists via the web.

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OpenMSI

Metabolite Atlas

Peter Andeer

Nutrient turnover in grassland soils

Grassland soils contain a significant portion of the Earth’s carbon, yet the mechanisms that influence nutrient cycling in these ecosystems are not well understood. In collaboration with the laboratories of Prof. Jill Banfield (UC Berkeley) and Dr. Chongle Pan (Oak Ridge National Laboratory) we are performing multi-omics analyses of soils at Angelo Coastal Reserve to examine the interrelationships between microbial communities and metabolites surrounding Fall rainfalls. I am then using stable isotope probing to determine direct linkages between the sequenced microbial communities and the compounds identified using untargeted exometabolomics.

Markus de Raad

Increasing throughput: developing high throughput mass spectrometry-based assays

Traditional LC/GC-MS methods are often low-throughput. Nanostructure-initiator mass spectrometry (NIMS) presents a powerful alternative to standard LC/GC-MS methods. NIMS has extremely high sensitivity and lateral resolution, which allows the disposition and analysis of ~10,000 samples. I am developing novel high-throughput mass spectrometry assays by integrating nanoscale sample deposition methods into NIMS. I apply these assays, for example, on activity screening of peptoid/peptide libraries and small molecule uptake/synthesis in microbial/cellular systems.

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LinkedIn

Suzanne Kosina

Using exometabolomics to predict microbial interactions

In many ecological systems, microorganisms exist in communities. What drives the interactions between these organisms and with their environments is of great interest for predicting the effects that changes to environmental conditions (rainfall, temperature and flora/fauna) will have on soil fertility, green house gas sequestration/release, community structure, etc. I use mass spectrometry based exometabolomics data and total organic carbon analysis to understand how individual microorganisms transform their environments and use this information to predict and test interactions between microorganisms.

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Katherine Louie

JGI Metabolomics User Program

As part of the Metabolomics group at JGI, we characterize the metabolite profile of organisms to gain insight and create linkages between sequence and function.

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Connor Tomaka

Utilizing EcoFabs and Metabolomics to uncover biogeochemical implications of microbial processes on the rhizosphere

I am a Research Associate at the Northen Lab developing and conducting EcoFab and exometabolomic experiments. My research intersects fields of biogeochemistry, agroecology, microbial ecology, and applied plant biology.

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Thomas Harwood

JGI Metabolomics User Program

As part of the Metabolomics group at JGI, we characterize the metabolite profile of organisms to gain insight and create linkages between sequence and function.

Amber Golini

Fabricated ecosystem (EcoFAB) development and metabolomics sample processing

As part of the Metabolomics group at JGI, I assist with the development of fabricated ecosystem (EcoFAB) technology and with the preparation, processing, and analysis of metabolomic samples using mass spectrometry based methods.

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MiMi Lynde

Yezhang Ding

Exploring plant-microbe interactions through metabolites

Plants utilize chemicals to communicate with microorganisms, favoring beneficial microbes and killing harmful ones. I am interested in using integrative approaches, including metabolomics, genetics, transcriptomics, proteomics and others to identify novel secondary metabolites involved in plant microbe interactions and explore how plants use these metabolites to benefit their own.

Kateryna Zhalnina

The role of microorganisms in the rhizosphere priming of soil organic matter decomposition

I am interested in physiological, biochemical and evolutionary aspects of plant-microbial interactions and how these interactions mediate biogeochemical cycles. Plant-soil-microbial crosstalk is operated through complex nutrient exchanges, where plant-released exudates can be consumed by rhizosphere communities. This can mediate microbial metabolism triggering microbial response that may be involved in nutrient stabilization/destabilization in soils – rhizosphere priming. I am using genomic analysis of a rhizosphere community to define metabolic traits that outline mutualistic relationships between microorganisms and plants in soil (e.g. extracellular enzymes, nutrient transporters). I am also using exometabolomic analysis and profiling of exoenzymes activities to evaluate what microbes uptake from the plant-exuded compounds, and how they respond to the plant exudation through release of metabolites and changing exoenzymatic activities.

Albina Khasanova

Researching the impact of genetics and environment on plant roots and shoots

My current research interests center around the impact of genetics and environment on variation in root and shoot traits that effect plant establishment, growth, and resource use efficiency. I am currently utilizing the developing C4 perennial grass model system, Panicum hallii and its close relative switchgrass (P. virgatum, a leading biofuel candidate) to understand the genetic architecture of root traits and their relationship with shoot traits in order to develop a more complete picture of the adaptive differences that arise between ecotypes in response to abiotic and biotic changes in the environment. At the Northen lab, I will be working on profiling the root exudate composition of P. hallii ecotypes in the presence of synthetic microbial communities in order to investigate plant exudate/microbiome relationships and examine the impact of select microbiomes on plant productivity.

Yuntao Hu

Algal metabolism and interactions between plants, microbes, and soil

I am a chemist with research experience on mass spectrometry, metabolomics, programming, and modeling. My project focuses on understanding the metabolism of bioenergy precursor production from green algae. I am also investigating plant-microbe-soil interaction using metabolomic and isotope tracing approaches.

Vlastimil Novak

Investigating the nutrient-exometabolome-rhizobiome interactions in plants

The effective use of natural resources will require the growth of bioenergy crops on marginal soils with minimal input of synthetic N fertilizers. Experimental evidence suggests that root exudation plays an important role in recruiting beneficial soil microbiome. However, the full role of exometabolites in mechanisms of plant-microbe interaction and N cycling in the rhizosphere remains cryptic. To gains insight into these dynamic processes, I use the combination of stable isotope techniques, metabolomics, and model grasses grown in fabricated plant ecosystems (EcoFAB). Mechanistic understanding of grass-microbe interactions will allow the building of predictive models, which will lead to the identification of new breeding targets and microbial amendment strategies for improved plant nitrogen use efficiency.

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ORCID

Ying Wang

Unraveling metabolic interactions within microbial communities

I am an environmental scientist with multidisciplinary training and research experience in environmental chemistry, microbiology, toxicology, and nanotechnology. I am broadly interested in addressing soil health and sustainable agriculture under global change. My current research aims to probe interactions within soil microbial communities using advanced techniques including exometabolomics. Such a mechanistic understanding of microbial metabolic interactions will contribute to predicting (and further managing) microbial community responses to changing environments and harnessing microbes for enhancing soil fertility and agricultural productivity.

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Qing Zheng

Host-microbe interactions in biocrusts

I am a soil microbial ecologist with research experience in soil microbial carbon cycling and soil biogeochemistry. I am currently working on a biocrust project, focusing on comparing microbial assembly in biocrust cyanosphere and plant rhizosphere using synthetic microbial communities and exometabolomics.

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ResearchGate

Edi Wipf

Characterizing plant-archaea interactions and determining their involvement in nitrogen availability in soils and increasing carbon capture

As some of the earliest and most resilient lifeforms on Earth, archaea are ubiquitous, diverse, and enigmatic in how much remains to be known of their existence and interactions with our world. One group of particular importance is ammonia oxidizing archaea, which are thought to significantly contribute to biogeochemical cycling, comprise approximately 1-5% of all prokaryotes in soils, and have indirect and broad interactions with a variety of organisms.

With a background in plant evolutionary ecology and environmental microbiology and as part of the Zhalnina group, I am using controlled laboratory ecosystems, synthetic biology, microscopy, comparative genomics, metabolomics, and transcriptome analysis to better understand the mechanisms by which archaea and plants interact and impact nitrogen and carbon cycling.

In addition to this research, I am interested and involved in mentoring, teaching, and equity and inclusion efforts.

Please reach out with any inquiries and requests; thank you!

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Kshitiz Gupta

Employing micro/nanofluidic technologies and developing fabricated ecosystems (EcoFAB) for studying plant-microbe interactions

Plants and microbes live together in a harmonious community. This interdependence is enabled through various microscale interactions/communication, which are carried out through different chemical compounds (metabolites). I'm developing a fabricated ecosystem platform called EcoFAB to create a controlled environment for studying these interactions. Additionally, I am interested in developing microfluidic technologies to enable high-throughput NIMS-based screening of the metabolites.

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Margaret Lozano

Vanessa Brisson

Researching the role of metabolites in the microbial communities of plants and algae

My research centers around microbial communities associated with two biofuels relevant systems: algae and switchgrass. I am investigating the role of metabolite exudation in beneficial microbial community recruitment and structuring by algae and plants. I am using a combination of targeted and untargeted metabolomics approaches to understand metabolite exchange and interactions within these systems.

Kai Deng

Development of high throughput enzyme assays to study glycoside hydrolases and lignases

Enzymes play the central role in converting celluloses (hemicelluoses) into simple fermentable sugars and in the deconstruction of lignin. I am developing new assays and high-throughput assay platforms to provide functional annotations for various enzymes and enzyme-variants. This involves the utilization of surface-based nanostructure-initiator mass spectrometry (NIMS), Labman, Biomek automation workstation and microscale liquid handling by acoustic printer. The goal is to provide rapid feedback of the activities of enzymes of interest and help the development of high performance strains.

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JBEI

Spencer Diamond

Metagenomics and metabolomics of grassland soils

I am using a combinatoral approach of genomics and untargeted metabolomics to asses how metabolites are cycled in the terrestrial subsurface of grassland soils. This research means to asses how bacteria on a species level respond to rainfall events, as well as increased rainfall in our study area (the Angelo Coast Reserve). This study is a collaboration between the Northern laboratory and the laboratory of Prof. Jill Banfield at UC Berkeley.

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LinkedIn

Jenny Onley

Characterization of lignin-modifying enzymes using NIMS

Lignin is a complex and recalcitrant macromolecule in plant cell walls. Lignin can be broken down into smaller molecules suitable for the production of biofuels and other valuable end products. My work focuses on characterizing lignin-modifying enzymes, which degrade or modify lignin. Enzyme assays are performed with nanostructure-initiator mass spectrometry (NIMS) with high sensitivity, specificity, and in a high throughput manner.

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Meghana Faltane