Both carbon and nitrogen stable isotope analyses in lake sediments provide crucial insights into past environmental conditions and biological processes. Marine and lacustrine carbonate minerals capture carbon cycle information, and their δ13C values are key to reconstructing paleoenvironmental changes. We have used stable isotope analyses, metagenomics, and geochemical modeling to demonstrate that carbonate spherules and micrite from Kiritimati's hypersaline lake have distinct δ13C values due to local biological processes, particularly photosynthesis.

Journal paper: Chen et al., Geobiology, 2022

Nitrogen stable isotope ratios (δ15N) in lake sediments are also crucial for interpreting historical nutrient sources and trophic status but can yield conflicting productivity interpretations. We have used metagenomics to show that variations in δ15N values in Kiritimati's hypersaline lake sediments are influenced by microbial processes, with high δ15N values linked to denitrification and low values to assimilatory nitrate reduction and ammonification.

Journal paper: Chen et al., Journal of Paleolimnology, 2021

Understanding the adaptive strategies of microbial communities in fluctuating environments is crucial for comprehending their survival mechanisms. Biofilms help bacteria adhere to surfaces and are essential for survival in challenging conditions, but their formation mechanisms in fluctuating subsurface conditions are not well understood. We have examined 16 Rhodanobacter strains under various conditions, finding that biofilms grow significantly under low pH and aluminum stress, and identified genetic traits associated with biofilm formation and metal tolerance, including the loss of flagella and the presence of the Type VI secretion system.

Journal paper: Chen et al., the ISME journal, 2024

Additionally, salinity influences microbial communities and functional groups in lacustrine sediments, with dynamic changes observed in response to temporal variability. An examination of geochemistry and functional gene data from 13 lakes in Kiritimati revealed shifts from more halophilic microorganisms in 2014 to more mesohaline, marine, or halotolerant microorganisms in 2019, driven by salinity changes due to the El Niño-Southern Oscillation. Together, these findings underscore the complex interplay of environmental factors and microbial adaptations in diverse ecosystems.

Journal paper: Chen et al., Scientific Reports, 2023

Partnering with Drs. Seiji Nakagawa, Stanislav Glubokovskikh, and Wenming Dong (LBNL), we are pioneering investigations into the biofilm formation behaviors of H2-utilizing microbes within sandstones located over 1 km underground. Using field-relevant sandstone samples in lab experiments, our research aims to understand the influence of these microbial activities on the geophysical properties of the sandstones. 

The rhizosphere microbiome is vital for plant productivity and ecosystem functions, but its complexity makes studying microbial interactions difficult. We have developed a design framework to create Reduced Complexity Consortia (RCC) from Brachypodium roots, demonstrating that microbial communities enriched with carbon substrates and transferred across generations form stable, functionally distinct consortia with key plant growth-promoting traits. We further present a robust methodology to create a stable 15-member synthetic microbial community from Brachypodium distachyon's rhizobiome, demonstrating plant growth-promoting traits and enhanced drought resilience in controlled experiments.

Journal paper: Chen et al., Frontiers in Microbiology, 2024
Yadav*, Chen*, et al., Plant, cell, and environment, 2024 (in prep)

My current collaboration with Dr. Marcin Joachimiak (LBNL) employs machine learning to innovatively design optimal microbial consortia for degrading PFAS (Per- and polyfluorinated substances) contaminants. Given their widespread use and resulting persistent pollution, PFAS pose significant health risks due to their tendency to accumulate in biological tissues. This method marks a substantial improvement over traditional remediation techniques by enhancing the speed, efficacy, and efficiency of environmental cleanup. 

The role of microbial necromass (nonliving microbial biomass), a significant component of belowground organic carbon, in nutrient cycling and its impact on the dynamics of microbial communities in subsurface systems remains poorly understood. I have been working on characterizing the metabolites from the microbial necromass and their impacts on microbial communities. We are currently working on charactering the necromass generated from different death pathways, and their ability to bind with common minerals from the field (quartz, clay, iron oxides, etc). We are also trying to look at the microbial communities to utilize the mineral-associated organic matter.

Journal paper: Finley, ..., Chen, et al., ISME Communication, 2024 (in review)