Seasonal Hydrogeochemical Changes Influence Nitrogen Cycling Genes in Microbes Found in River Sediments

Seasonal changes affect microbiome communities, genes, and subsurface  biogeochemical pathways differently.

The Science

U.S. Department of Energy (DOE) researchers investigated the role of microbial genetic diversity in two major subsurface biogeochemical processes: nitrification and denitrification. Results show that across different seasons only a few microbe species, namely Nitrosoarchaeum, carry out nitrification functions—demonstrating high resistance to environmental change. However, denitrification genes, which are more broadly distributed in the community, displayed a variety of diversity patterns and abundance dynamics—demonstrating greater microbial interactions as conditions change.

The Impact

There is little research connecting microbiomes at the genetic level to hydro-biogeochemical modeling. This research uncovers the importance of gene diversity and dynamics in microbial communities involved in key elemental cycling pathways. For example, under extreme environmental conditions an entire biochemical pathway could be altered or eliminated if a single step in that pathway has low genetic diversity in the microbial population, and its loss could not be replaced.


The Pacific Northwest National Laboratory research team, led by Bill Nelson, found that major environmental processes—specifically nitrification and denitrification—are maintained through a variety of diversity strategies. Historically, the bulk of biogeochemical research has focused on microbial communities at the organismal level. But this research focused on the importance of genetic distribution and diversity.

In their recent PLOS ONE paper, the researchers discuss the roles microbes play in ecological functions, the novelty of the genetic makeup of these microbes, and future research opportunities to determine which organisms are genetically expressing nitrogen cycling functions.

The novelty of this study comes from examining the temporal dynamics of diversity at the gene level. To evaluate all genes in the nitrification and denitrification pathways, novel Hidden Markov Models (HMMs) were developed that can recognize the broad diversity found in environmental samples. The team found that, while different environmental conditions impair microbiome growth and the gene expression of some populations, at the same time, those conditions can stimulate other genes and their associated microbes. High biodiversity at the organism or genetic level creates more resiliency, and the microbiome community can respond more rapidly to environmental changes.

In the future, researchers hope to more fully evaluate how diversity dynamics affect community metabolism function, including the role of metatranscriptomes or metaproteomes. The results of such future studies could help determine which organisms are expressing nitrogen cycling functions, and they could be incorporated into biogeochemical models of ecosystem function.

Principal Investigator(s)

Bill Nelson
Pacific Northwest National Laboratory


This research was supported by the Office of Biological and Environmental Research (BER), within the U.S. Department of Energy (DOE) Office of Science , as part of the Subsurface Biogeochemical Research Scientific Focus Area (SFA) at Pacific Northwest National Laboratory (PNNL).