Metabolic diversity and aero-tolerance in anammox bacteria from geochemically distinct aquifers

Abstract

Background: Anaerobic ammonium oxidation (anammox) is important for converting bioavailable nitrogen into dinitrogen gas, particularly in carbon poor environments. Yet, the diversity and prevalence of anammox bacteria in the terrestrial subsurface – a typically oligotrophic environment – is little understood across different geochemical conditions. To determine the distribution and activity of anammox bacteria across a range of aquifer lithologies and physicochemistries, we analysed 16S rRNA genes, metagenomes and metatranscriptomes, and quantified hydrazine synthase genes and transcripts sampled from 59 groundwater wells distributed over 1 240 km2. Results: Data indicate that anammox-associated bacteria (class Brocadiae) and the anammox process are prevalent in aquifers (identified in aquifers with sandy-gravel, sandsilt and volcanic lithologies). While Brocadiae diversity decreased with increasing DO, Brocadiae 16S rRNA genes and hydrazine synthase genes and transcripts (hydrazine synthase, hzsB) were detected across a wide range of bulk groundwater dissolved oxygen (DO) concentrations (0 – 10 mg/L). Anammox genes and transcripts (hzsB) correlated significantly with those involved in bacterial and archaeal ammonia oxidation (ammonia monooxygenase, amoA), which could represent a major source of nitrite for anammox. Differences in anammox community composition were strongly associated with DO and bore depth (and to a lesser extent pH and phosphate), revealing niche differentiation among anammox bacteria in groundwater that was largely driven by water oxygen contents, and not ammonium/nitrite. Eight Brocadiae genomes (63-95% estimated completeness) reconstructed from a subset of groundwater sites belong to 2 uncharacterized families and 6 novel species (based on average nucleotide identity). Distinct groups of these genomes dominated the anammox-associated community at dysoxic and oxic sites, further reflecting the influence of DO on Brocadiae composition. Six of the genomes (dominating dysoxic or oxic sites) have genes characteristic of anammox (hydrazine synthase and/or dehydrogenase). These genes, in addition to aerotolerance genes, belonging to four Brocadiae genomes, were transcriptionally active, although transcript numbers clearly highest in dyoxic groundwater. Conclusions: Our findings indicate anammox bacteria contribute to loss of fixed N across diverse anoxic-to-oxic aquifer conditions, and that this is likely supported by nitrite from aerobic ammonia oxidation. Results provide an insight into the distribution and activity of anammox bacteria across distinct aquifer physicochemisties.

Co-occurrence and cooperation between comammox and anammox bacteria in a full-scale attached growth municipal wastewater treatment process

“…While recent studies have suggested that anammox bacteria are most likely oxygen tolerant rather than strictly anaerobic 53,54 , the comparatively high abundance of anammox in the attached phase could also be due to anaerobic zones deeper in the biofilm. Further, transcriptional activity of anammox genes associated with Brocadia were found in aquifers with anoxic-to-oxic conditions suggesting anammox bacteria are able to contribute to nitrogen loss in a diverse range of oxygen environments 55 .…”

Metatranscriptomic analysis reveals synergistic activities of comammox and anammox bacteria in full-scale attached growth nitrogen removal system

“…Research into anammox located in deep sea anoxic nitrate-ammonium transition zones observed expression of full gene sets for flagella mobility despite limited energy for mobility, suggesting flagellar activity is linked to in situ growth 72 . Similarly, other Planctomycetes bacteria have shown increased flagella mobility in highly rich media 73 suggesting AMX may utilize chemotaxis within high nutrient concentrations as opposed to mobility to avoid oxygen stress 74 .…”

Predicted metabolic roles and stress responses provide insights into candidate phyla Hydrogenedentota and Sumerlaeota as members of the rare biosphere in biofilms from various environments

“…Studies that reported abundances found that organisms of this candidate phylum always constituted <1% of the community. Currently, there is only one Hydrogenedentota MAG available from Shark Bay (Skoog et al, 2022), but MAGs of Hydrogenedentota have been assembled from other environments including subsurface waters (Momper et al, 2018;Mosley et al, 2022;Tully et al, 2018), hot spring water and sediments (Liew et al, 2022;Zhou et al, 2020), marine sediment (Zhou, Mara, et al, 2022), freshwater sediment (Hahn et al, 2022;Jaffe et al, 2023), hydrothermal vents (Speth et al, 2021;Zhong et al, 2022;Zhou, St. John, et al, 2022), anaerobic digesters and annamox bioreactors (Campanaro et al, 2020;Lin et al, 2021;Nobu et al, 2015;Pabst et al, 2022;Rinke et al, 2013;Suarez et al, 2022;Wang et al, 2020;Wang et al, 2022;Zhang et al, 2022), wastewater (Grégoire et al, 2023;Haryono et al, 2022;Huang et al, 2021;Parks et al, 2017) and saline and hypersaline sediments (Uzun et al, 2020;Vavourakis et al, 2019). Of these studies, only one characterized this organism and identified Ca.…”