Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification

Abstract

Competition between nitrate-reducing bacteria (NRB) and sulfate-reducing bacteria (SRB) for resources in anoxic environments is generally thought to be governed largely by thermodynamics. It is now recognized that intermediates of nitrogen and sulfur cycling (e.g., hydrogen sulfide, nitrite, etc.) can also directly impact NRB and SRB activities in freshwater, wastewater, and sediment and therefore may play important roles in competitive interactions. Here, through comparative transcriptomic and metabolomic analyses, we have uncovered mechanisms of hydrogen sulfide- and cysteine-mediated inhibition of nitrate respiratory growth for the NRB Intrasporangium calvum C5. Specifically, the systems analysis predicted that cysteine and hydrogen sulfide inhibit growth of I. calvum C5 by disrupting distinct steps across multiple pathways, including branched-chain amino acid (BCAA) biosynthesis, utilization of specific carbon sources, and cofactor metabolism. We have validated these predictions by demonstrating that complementation with BCAAs and specific carbon sources relieves the growth inhibitory effects of cysteine and hydrogen sulfide. We discuss how these mechanistic insights give new context to the interplay and stratification of NRB and SRB in diverse environments. IMPORTANCE Nitrate-reducing bacteria (NRB) and sulfate-reducing bacteria (SRB) colonize diverse anoxic environments, including soil subsurface, groundwater, and wastewater. NRB and SRB compete for resources, and their interplay has major implications on the global cycling of nitrogen and sulfur species, with undesirable outcomes in some contexts. For instance, the removal of reactive nitrogen species by NRB is desirable for wastewater treatment, but in agricultural soils, NRB can drive the conversion of nitrates from fertilizers into nitrous oxide, a potent greenhouse gas. Similarly, the hydrogen sulfide produced by SRB can help sequester and immobilize toxic heavy metals but is undesirable in oil wells where competition between SRB and NRB has been exploited to suppress hydrogen sulfide production. By characterizing how reduced sulfur compounds inhibit growth and activity of NRB, we have gained systems-level and mechanistic insight into the interplay of these two important groups of organisms and drivers of their stratification in diverse environments.

Draft genome sequence of Intrasporangium sp. DVR, an actinobacterium of the family Intrasporangiaceae isolated from soil in Japan

“…The genus Intrasporangium belongs to the phylum Actinomycetota and comprises five species, that is, I. calvum , I. chromatireducens , I. flavum , I. mesophilum , and I. oryzae ( 1 ). They are known as Gram-positive aerobic bacteria but sometimes show capacities for nitrate reduction under anaerobic growth conditions ( 2 , 3 ). Thus, this taxonomic group may catalyze anaerobic metabolisms in nature.…”

Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes

“…We were able to identify signatures of specific growth phases in 20-40% of the abundant bacterial populations in the guts of these four individuals. We describe how our growth phase inference approach can serve to inform more accurate mechanistic modeling of flow-through ecosystems (e.g., community-scale metabolic models, which usually assume exponential growth), which could have broad implications for the gut microbiome and host health [8, 33, 34], flow-through agricultural systems [35, 36], climate change [35, 37, 38], and industrial bioreactor production processes [39, 40].…”

“…We describe how our growth phase inference approach can serve to improve statistical inferences derived from microbiome data and to inform more accurate mechanistic modeling of flow-through ecosystems (e.g., community-scale metabolic models, which usually assume exponential growth), which could have broad implications for human health 8,34,35 , agricultural systems 36,37 , climate change 36,38,39 , and industrial bioreactor production processes 40,41 .…”

“…Furthermore, we were able to identify specific growth phase signatures in abundant bacterial populations in the guts of four individuals with long and dense metagenomic time series by analyzing paired replication rate and abundance trajectories. We describe how our growth phase inference approach can serve to improve statistical inferences derived from microbiome data and to inform more accurate mechanistic modeling of flow-through ecosystems (e.g., community-scale metabolic models, which usually assume exponential growth), which could have broad implications for human health 8, 34, 35 , agricultural systems 36, 37 , climate change 36, 38, 39 , and industrial bioreactor production processes 40, 41 .…”