Dechloromonasand close relatives prevail during hydrogenotrophic denitrification in stimulated microcosms with oxic aquifer material

Abstract

Globally occurring nitrate pollution in groundwater is harming the environment and human health. In situ hydrogen addition to stimulate denitrification has been proposed as a remediation strategy. However, observed nitrite accumulation and incomplete denitrification are severe drawbacks that possibly stem from the specific microbial community composition. We set up a microcosm experiment comprising sediment and groundwater from a nitrate polluted oxic oligotrophic aquifer. After the microcosms were sparged with hydrogen gas, samples were taken regularly within 122 h for nitrate and nitrite measurements, community composition analysis via 16S rRNA gene amplicon sequencing and gene and transcript quantification via qPCR of reductase genes essential for complete denitrification. The highest nitrate reduction rates and greatest increase in bacterial abundance coincided with a 15.3-fold increase in relative abundance of Rhodocyclaceae, specifically six ASVs that are closely related to the genus Dechloromonas. The denitrification reductase genes napA, nirS and clade I nosZ also increased significantly over the observation period. We conclude that taxa of the genus Dechloromonas are the prevailing hydrogenotrophic denitrifiers in this nitrate polluted aquifer and the ability of hydrogenotrophic denitrification under the given conditions is species-specific.

Genotypic and phenotypic characterization of hydrogenotrophic denitrifiers

“…The multiple isolation of D . denitrificans and close relatives during the second isolation support their importance in hydrogenotrophic denitrification in oxic, nitrate‐polluted oligotrophic aquifers (Duffner et al ., 2021). While it is unclear which species prevails under which conditions, both Dechloromonas (and close relatives) and Hydrogenophaga obviously play an important role in hydrogenotrophic denitrification.…”

“…australiensis and D98 of a so far not described species were incapable of hydrogenotrophic denitrification supports the finding of Duffner et al . (2021) that the ability for hydrogenotrophic denitrification among the family Rhodocyclaceae is species‐specific.…”

“…The different outcome could be due to high mineral nutrient concentrations in the MM that was used for the first isolation or due to the different sampling time points because seasonal differences in the bacterial community composition of aquifers are well-known (Chik et al, 2020). The multiple isolation of D. denitrificans and close relatives during the second isolation support their importance in hydrogenotrophic denitrification in oxic, nitrate-polluted oligotrophic aquifers (Duffner et al, 2021). While it is unclear which species prevails under which conditions, both Dechloromonas (and close relatives) and Hydrogenophaga obviously play an important role in hydrogenotrophic denitrification.…”

“…Location and sampling methods are described in Duffner et al . (2021). Samples were stored at 4°C for 1 day until the enrichment incubations started.…”

Complete Genome Sequences of Hydrogenotrophic Denitrifiers

“…We isolated three hydrogenotrophic denitrifiers after enrichment from sediment (H3) and groundwater (D110 and F76) samples from a highly nitrate-polluted aquifer in the Hohenthann region of southeast Germany ( 1 ). Samples were obtained as described ( 2 ). Enrichment and isolation were performed under anoxic conditions with a 60% H 2 /10% CO 2 /30% N 2 atmosphere.…”