Nitrogen cycling and microbial cooperation in the terrestrial subsurface

Abstract

The nitrogen cycle plays a major role in aquatic nitrogen transformations, including in the terrestrial subsurface. However, the variety of transformations remains understudied. To determine how nitrogen cycling microorganisms respond to different aquifer chemistries, we sampled groundwater with varying nutrient and oxygen contents. Genes and transcripts involved in major nitrogen-cycling pathways were quantified from 55 and 26 sites, respectively, and metagenomes and metatranscriptomes were analyzed from a subset of oxic and dysoxic sites (0.3-1.1 mg/L bulk dissolved oxygen). Nitrogen-cycling mechanisms (e.g. ammonia oxidation, denitrification, dissimilatory nitrate reduction to ammonium) were prevalent and highly redundant, regardless of site-specific physicochemistry or nitrate availability, and present in 40% of reconstructed genomes, suggesting that nitrogen cycling is a core function of aquifer communities. Transcriptional activity for nitrification, denitrification, nitrite-dependent anaerobic methane oxidation and anaerobic ammonia oxidation (anammox) occurred simultaneously in oxic and dysoxic groundwater, indicating the availability of oxic-anoxic interfaces. Concurrent activity by these microorganisms indicates potential synergisms through metabolite exchange across these interfaces (e.g. nitrite and oxygen). Fragmented denitrification pathway encoding and transcription was widespread among groundwater bacteria, although a considerable proportion of associated transcriptional activity was driven by complete denitrifiers, especially under dysoxic conditions. Despite large differences in transcription, the capacity for the final steps of denitrification was largely invariant to aquifer conditions, and most genes and transcripts encoding N2O reductases were the atypical Sec-dependant type, suggesting energy-efficiency prioritization. Results provide insights into the capacity for cooperative relationships in groundwater communities, and the richness and complexity of metabolic mechanisms leading to the loss of fixed nitrogen.

Identification and Characterization of a Bacterial Periplasmic Solute Binding Protein That Binds l-Amino Acid Amides

“…The conservation of both ligand-binding and Ca 2+ -coordinating residues in the group of 610 amidase-associated uncharacterized proteins from the SSN used to identify Me Ami suggests a shared biochemical requirement for amino acid amides in the species from which these genes were identified. The prevalence of Gram-negative nitrogen-fixing soil bacteria within this group, some of which are known to thrive on short chain amines, suggests an evolutionary advantage for soil bacteria capable of catalyzing amidase reactions on l -amino acid amides. This would metabolize them to the respective l -amino acid and ammonia, facilitating access to amino acid utilization pathways such as the citric acid cycle and ammonia assimilation pathways such as the glutamine synthetase–glutamate synthase pathway .…”

Differential contribution of nitrifying prokaryotes to groundwater nitrification

“…However, it remains unclear if the major energy source to sustain cell metabolism originated from complete ammonium oxidation or rather from nitrite oxidation. In fact, a recent subsurface study detected transcriptional activity in association with nitrite oxidation but not ammonium oxidation for a CMX-related MAG [65], while CMX Nitrospira in water from rapid sand filters did not prefer to oxidize external nitrite alone [7]. As we found NO 2 - transporters in representative groundwater MAGs from both CMX clades, the cells may also be capable of taking up the NO 2 - formed by AOB, supporting their primary role as nitrite oxidizers along with Nitrosomonas ureae and Nitrosospira sp.…”

Microbial dynamics in soils of the Damma glacier forefield show succession in the functional genetic potential

“…Overall, we did find changes in the abundance of N‐cycling genes along the Damma glacier forefield: OD&S dominated N‐cycling processes during the process of soil development, genes involved in nitrogen fixation were more abundant in the vegetated soils, and genes related to nitrification were enriched in the barren soils. Despite having distinct requirements (e.g., for oxygen), many reactions in the N‐cycle tend to co‐occur in the environment, leading to efficient N recycling, competition for the same resource (e.g., nitrate) and coupled processes, such as nitrification and denitrification (Mosley et al, 2022). Brankatschk et al (2011) suggested, however, that the number of genes involved in major N‐cycling pathways may not be consistent with the corresponding enzyme activity, so a deeper understanding of N‐cycling genes at the transcriptional and translational level may still be necessary in the Damma glacier forefield.…”