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.

Links:

Publications

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.

Links:

Publications

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.

Links:

Publications

LinkedIn

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.

Links:

LinkedIn

La Zhen Han

Fabricated ecosystem development and sample processing

I assist with the development of fabricated ecosystem (EcoFAB) technology and processing of metabolomic samples.

Links:

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.

Links:

Publications

Andrea Kuftin

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.

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.

Links:

Publications

Daniel Treen

Custom Metabolomics Analysis Tools

I am an associate software developer at the Northen Lab developing, maintaining, and using our metabolomics data analysis tools. My current research revolves around the intersection of machine learning, LC/MS data, and cheminformatics.

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.

Noel Ha

High-throughput screening of metabolites and enzyme activity via microfluidics

Combinatorial screening of massive scale enzyme libraries through metabolite detection has the potential to discover new enzymes and multi-step metabolic pathways. I am developing a novel droplet microfluidic device that can be directly coupled with a nanostructure-initiator mass spectrometry (NIMS), to create a new approach for rapid screening of enzyme activities at a massive scale up to 100,000 metabolite analyses on a single microfluidic chip. We envision broad applications of this microfluidic system in discovery of new enzymes to support synthetic biology and biomass deconstruction as well as drug development.

Links:

Publications

JBEI

LinkedIn

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.

Lauren Jabusch

How can plants thrive under stress?

In order to feed and fuel our planet, grasses need to thrive under harsh conditions like low quantity and quality plant nutrients and high levels of salt in soil. Using our EcoFAB technology, I am interested in what microbes live in grass roots and how they contribute to plant growth.

Andrew Osborn

Genome mining of secondary metabolites

My research is focused on the genome mining of secondary metabolite gene clusters to discover new compounds. I am interested in how these secondary metabolites are formed, what roles they have in biological systems, and their development into useful compounds.

Nicholas Saichek

High-throughput approaches for investigation of microbial interactions within synthetic microbial communities

There is an urgent need to improve our understanding of the connections between microbial community composition and interactions to their in situ activities. As a means of accomplishing this, my research focuses on the development of new tools and techniques that allow us to link biomarker-based proteomics with metabolomics in order to get a complete understanding of microbial dynamics in simple synthetic communities (SynComs).

Links:

LinkedIn

Marc Van Goethem

Linking metagenomics and metabolomics in soil biocrust

Biological soil crusts (biocrust) cover a substantial proportion of the Earth’s terrestrial surface. These microbe-dominated soil communities face uncertain futures given expected shifts in precipitation quantity and frequency against the backdrop of a warming climate scenario. My research links metagenomics of entire biocrust communities to their produced metabolites in order to consolidate our understanding of these important photosynthetic consortia in desert ecosystems under the changing environment.

Links:

Publications

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.

Links:

Publications

LinkedIn

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.

Links:

ResearchGate

Zoila Aponte

Investigating microbial interactions and communities through grasses

I’m a first-year microbiology Ph.D. student at UC Berkeley. My main research interest is in microbial metabolic interactions and their impact on community establishment and dynamics. During my rotation in the Northen lab, I’m working to further understand interactions between Brachypodium distachyon and single bacteria and bacterial communities. We can do this by studying plant metabolic exudation and phenotypes in the presence or absence of bacteria, as well as by measuring the impact of plant exudates on bacterial growth.

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.

Anita Silver

Quantifying interactions between microbes using exometabolomic data

I am using concepts from community ecology, mechanistic modelling and statistics to develop quantitative metrics for predicting interactions between microbe strains from the exometabolomic data of individual strains. The data I am working with comes from the Web of Microbes, a database created by the Northen Lab, which contains changes in metabolite concentrations associated with individual microbes in different environments.

Margaret Lozano

Jane Tanamachi

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.

Links:

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.

Links:

Publications

ResearchGate

LinkedIn

Johan Leveau

Understanding plant health and disease from studying plant-microbe interactions at micrometer scales

The field of microbial ecology is experiencing a revolution in the types of tools that have become available to study how microorganisms interact with one another and with their biotic and abiotic environment at scales that are most relevant to them. Part of this revolution is the development and use of artificial theaters of microbial activity, such as Dr. Northen’s EcoFABs. These are designed to mimic the natural environment at microscopic resolution and to allow precise manipulation of the environment and its microbiota to test hypotheses relevant to the question whether macroscale outcomes (such as plant health and disease) can be predicted from microscale interactions. In this collaboration with the Leveau Lab at the University of California Davis, EcoFABS are exploited to study plant-beneficial bacteria from the genus Collimonas and their ability to maintain root health and stimulate root growth in the face of biotic and abiotic stresses.

Links:

Leveau Lab