Public Abstract

DE-SC0019119: RESPONSE OF SUBSURFACE NITROGEN-CYCLING MICROBIAL COMMUNITIES TO ENVIRONMENTAL FLUCTUATIONS

Award Status: Inactive

Institution: Board of Trustees of the Leland Stanford Junior University, Redwood City, CA
UEI: HJD6G4D6TJY5
DUNS: 009214214

Most Recent Award Date: 10/25/2023
Number of Support Periods: 3
PM: Kulkarni, Resham

Current Budget Period: 09/15/2020 - 09/14/2024
Current Project Period: 09/15/2018 - 09/14/2024
PI: Francis, Christopher

Supplement Budget Period: N/A

Public Abstract

*Response of Subsurface Nitrogen-Cycling Microbial Communities to Environmental Fluctuations* Christopher Francis, Stanford University (Principal Investigator) Nicholas Bouskill, Lawrence Berkeley National Laboratory (co-Principal Investigator) PUBLIC ABSTRACT Floodplains are hot spots for biological productivity that drive biogeochemical reactions and moderate ground and surface water quality, carbon turnover, and regional land-atmosphere interactions. Within the semi-arid upper Colorado River Basin (CRB) and intermountain west, a large fraction of shallow subsurface organic carbon (C) is believed to reside within organic-enriched, fine-grained sediments embedded within low-productivity coarse organic-poor sand-and-cobble alluvium. These organic-rich sediments support sulfate-reducing conditions and are consequently referred to as ‘naturally-reduced zones’ (NRZs). Oxygen is highly reactive with sulfides, which are abundant in NRZs, and thus does not readily penetrate into NRZs. Consequently, respiration of these large pools of reduced carbon may be controlled by the availability of alternative electron acceptors, notably nitrate. NRZs contain large inventories of nitrogen (N) and uranium (U) in the numerous contaminated DOE legacy site floodplains in the upper CRB, locations of former ore-processing activity. Concentration of these elements within NRZs slows carbon decomposition and chemically stabilizes U as U(IV). Microbial N cycling has the capability to “unlock” the biogeochemical nutrient supply stored within NRZs, drive C cycling, and cause U to be released to the aquifers. Nitrification links organic matter decomposition to the production of nitrite and ultimately nitrate, an oxidant of U(IV) and the primary electron acceptor for denitrification. While heterotrophic denitrification couples the oxidation of organic matter to the reduction of nitrate to gaseous products, chemoautotrophic denitrifiers can couple the oxidation of inorganic compounds like Fe²⁺ or sulfide (which are highly-enriched within NRZs) to nitrate reduction. Nitrification and denitrification are believed to help mediate C turnover in NRZ sediments and are the primary sources of the potent greenhouse gas, N₂O. Despite their biogeochemical importance, remarkably little is currently known regarding N-cycling microbial communities within NRZs. To address this critical knowledge gap, we plan to examine microbial N cycling at a site within the shallow floodplain of Riverton, WY, which is being developed by the SLAC Groundwater Quality SFA program as a primary research site to study the impact of transient redox biogeochemistry coupled to transient transport processes on groundwater quality. This SFA is focused primarily on sulfur-iron-phosphorus-contaminant interactions. However, the large redox variations imply that the abundance and composition of soluble reactive N pools (NH₄⁺, NO₂^-, and NO₃^-) will be highly variable throughout the year, highlighting the need to examine N transformations induced by hydrological transitions of organic-rich sediments. The overarching goal of our project is to determine how shifts in key environmental parameters and gradients impact microbial N-cycling communities/processes within subsurface sediments of Riverton, WY. To meet this goal, we will employ a powerful combination of molecular, meta-omic, biogeochemical, and modeling approaches to pursue three specific objectives: (1) to associate in situ environmental drivers of N cycling with distinct functional guilds using field measurements of pore water geochemistry and GHG fluxes from unperturbed sediment cores coupled to (bio)geochemical profiling, high-resolution sequence-based profiling, metagenomics and metatranscriptomics of microbial communities over time and space; (2) determine the guild response to variation in key ecosystem drivers by using microcosms to examine the effect of environmentally-relevant conditions/perturbations on microbial community structure, transcription, and N-cycling activity; and (3) develop a dynamic ecosystem model that captures the diverse N metabolisms within the Riverton subsurface and their response to environmental pressures by utilizing the extensive community genomic and biogeochemical data obtained in Objectives 1-2. Ultimately, the proposed work will not only yield unprecedented insights into the microbial and molecular mechanisms of subsurface N-cycling, but also strongly support and build out (but not duplicate) the SLAC Groundwater Quality SFA program.

Response of Subsurface Nitrogen-Cycling Microbial Communities to Environmental Fluctuations

Christopher Francis, Stanford University (Principal Investigator)

Nicholas Bouskill, Lawrence Berkeley National Laboratory (co-Principal Investigator)

PUBLIC ABSTRACT

Floodplains are hot spots for biological productivity that drive biogeochemical reactions and moderate ground and surface water quality, carbon turnover, and regional land-atmosphere interactions. Within the semi-arid upper Colorado River Basin (CRB) and intermountain west, a large fraction of shallow subsurface organic carbon (C) is believed to reside within organic-enriched, fine-grained sediments embedded within low-productivity coarse organic-poor sand-and-cobble alluvium. These organic-rich sediments support sulfate-reducing conditions and are consequently referred to as ‘naturally-reduced zones’ (NRZs). Oxygen is highly reactive with sulfides, which are abundant in NRZs, and thus does not readily penetrate into NRZs. Consequently, respiration of these large pools of reduced carbon may be controlled by the availability of alternative electron acceptors, notably nitrate. NRZs contain large inventories of nitrogen (N) and uranium (U) in the numerous contaminated DOE legacy site floodplains in the upper CRB, locations of former ore-processing activity. Concentration of these elements within NRZs slows carbon decomposition and chemically stabilizes U as U(IV).

Microbial N cycling has the capability to “unlock” the biogeochemical nutrient supply stored within NRZs, drive C cycling, and cause U to be released to the aquifers. Nitrification links organic matter decomposition to the production of nitrite and ultimately nitrate, an oxidant of U(IV) and the primary electron acceptor for denitrification. While heterotrophic denitrification couples the oxidation of organic matter to the reduction of nitrate to gaseous products, chemoautotrophic denitrifiers can couple the oxidation of inorganic compounds like Fe²⁺ or sulfide (which are highly-enriched within NRZs) to nitrate reduction. Nitrification and denitrification are believed to help mediate C turnover in NRZ sediments and are the primary sources of the potent greenhouse gas, N₂O. Despite their biogeochemical importance, remarkably little is currently known regarding N-cycling microbial communities within NRZs.

To address this critical knowledge gap, we plan to examine microbial N cycling at a site within the shallow floodplain of Riverton, WY, which is being developed by the SLAC Groundwater Quality SFA program as a primary research site to study the impact of transient redox biogeochemistry coupled to transient transport processes on groundwater quality. This SFA is focused primarily on sulfur-iron-phosphorus-contaminant interactions. However, the large redox variations imply that the abundance and composition of soluble reactive N pools (NH₄⁺, NO₂^-, and NO₃^-) will be highly variable throughout the year, highlighting the need to examine N transformations induced by hydrological transitions of organic-rich sediments. The overarching goal of our project is to determine how shifts in key environmental parameters and gradients impact microbial N-cycling communities/processes within subsurface sediments of Riverton, WY.

To meet this goal, we will employ a powerful combination of molecular, meta-omic, biogeochemical, and modeling approaches to pursue three specific objectives: (1) to associate in situ environmental drivers of N cycling with distinct functional guilds using field measurements of pore water geochemistry and GHG fluxes from unperturbed sediment cores coupled to (bio)geochemical profiling, high-resolution sequence-based profiling, metagenomics and metatranscriptomics of microbial communities over time and space; (2) determine the guild response to variation in key ecosystem drivers by using microcosms to examine the effect of environmentally-relevant conditions/perturbations on microbial community structure, transcription, and N-cycling activity; and (3) develop a dynamic ecosystem model that captures the diverse N metabolisms within the Riverton subsurface and their response to environmental pressures by utilizing the extensive community genomic and biogeochemical data obtained in Objectives 1-2. Ultimately, the proposed work will not only yield unprecedented insights into the microbial and molecular mechanisms of subsurface N-cycling, but also strongly support and build out (but not duplicate) the SLAC Groundwater Quality SFA program.