Ultra-small bacteria and archaea exhibit genetic flexibility towards groundwater oxygen content, and adaptations for attached or planktonic lifestyles.

Aquifers are populated by highly diverse microbial communities, including unusually small bacteria and archaea. The recently described Patescibacteria (or Candidate Phyla Radiation) and DPANN radiation are characterized by ultra-small cell and genomes sizes, resulting in limited metabolic capacities and probable dependency on other organisms to survive. We applied a multi-omics approach to characterize the ultra-small microbial communities over a wide range of aquifer groundwater chemistries. Results expand the known global range of these unusual organisms, demonstrate the wide geographical range of over 11,000 subsurface-adapted Patescibacteria, Dependentiae and DPANN archaea, and indicate that prokaryotes with ultra-small genomes and minimalistic metabolism are a characteristic feature of the terrestrial subsurface. Community composition and metabolic activities were largely shaped by water oxygen content, while highly site-specific relative abundance profiles were driven by a combination of groundwater physicochemistries (pH, nitrate-N, dissolved organic carbon). We provide insights into the activity of ultra-small prokaryotes with evidence that they are major contributors to groundwater community transcriptional activity. Ultra-small prokaryotes exhibited genetic flexibility with respect to groundwater oxygen content, and transcriptionally distinct responses, including proportionally greater transcription invested into amino acid and lipid metabolism and signal transduction in oxic groundwater, along with differences in taxa transcriptionally active. Those associated with sediments differed from planktonic counterparts in species composition and transcriptional activity, and exhibited metabolic adaptations reflecting a surface-associated lifestyle. Finally, results showed that groups of phylogenetically diverse ultra-small organisms co-occurred strongly across sites, indicating shared preferences for groundwater conditions.

Nitrogen cycling and microbial cooperation in the terrestrial subsurface.

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.

Metabolic Diversity and Aero-Tolerance in Anammox Bacteria from Geochemically Distinct Aquifers.

Anaerobic ammonium oxidation (anammox) is important for converting bioavailable nitrogen into dinitrogen gas, particularly in carbon-poor environments. However, the diversity and prevalence of anammox bacteria in the terrestrial subsurface-a typically oligotrophic environment-are little understood. To determine the distribution and activity of anammox bacteria across a range of aquifer lithologies and physicochemistries, we analyzed 16S rRNA genes and quantified hydrazine synthase genes and transcripts sampled from 59 groundwater wells and metagenomes and metatranscriptomes from an oxic-to-dysoxic subset. Data indicate that anammox and anammox-associated bacteria (class "Candidatus Brocadiae") are prevalent in the aquifers studied, and that anammox community composition is strongly differentiated by dissolved oxygen (DO), but not ammonia/nitrite. While "Candidatus Brocadiae" diversity decreased with increasing DO, "Candidatus Brocadiae" 16S rRNA genes and hydrazine synthase (hzsB) genes and transcripts were detected across a wide range of bulk groundwater DO concentrations (0 to 10 mg/L). Anammox genes and transcripts correlated significantly with those involved in aerobic ammonia oxidation (amoA), potentially representing a major source of nitrite for anammox. Eight "Candidatus Brocadiae" genomes (63 to 95% complete), representing 2 uncharacterized families and 6 novel species, were reconstructed. Six genomes have genes characteristic of anammox, all for chemolithoautotrophy. Anammox and aerotolerance genes of up to four "Candidatus Brocadiae" genomes were transcriptionally active under oxic and dysoxic conditions, although activity was highest in dysoxic groundwater. The coexpression of nrfAH nitrite reductase genes by "Candidatus Brocadiae" suggests active regeneration of ammonia for anammox. Our findings indicate that anammox bacteria contribute to loss of fixed N across diverse anoxic-to-oxic aquifer conditions, which is likely supported by nitrite from aerobic ammonia oxidation. IMPORTANCE Anammox is increasingly shown to play a major role in the aquatic nitrogen cycle and can outcompete heterotrophic denitrification in environments low in organic carbon. Given that aquifers are characteristically oligotrophic, anammox may represent a major route for the removal of fixed nitrogen in these environments, including agricultural nitrogen, a common groundwater contaminant. Our research confirms that anammox bacteria and the anammox process are prevalent in aquifers and occur across diverse lithologies (e.g., sandy gravel, sand-silt, and volcanic) and groundwater physicochemistries (e.g., various oxygen, carbon, nitrate, and ammonium concentrations). Results reveal niche differentiation among anammox bacteria largely driven by groundwater oxygen contents and provide evidence that anammox is supported by proximity to oxic niches and handoffs from aerobic ammonia oxidizers. We further show that this process, while anaerobic, is active in groundwater characterized as oxic, likely due to the availability of anoxic niches.

Defining natural baselines for rates of change in New Zealand's groundwater quality: Dealing with incomplete or disparate datasets, accounting for impacted sites, and merging into state of the-environment reporting.

To effectively manage sustainably groundwater bodies, it is essential to establish what the naturally occurring ranges of chemical concentrations in groundwaters are and how they change over time. We defined baseline trends for New Zealand groundwaters using: 1) pattern recognition techniques to deal with inconsistent monitoring suites between the national (110 sites) and the denser regional network (>1000 sites), and 2) multivariate statistics to identify and remove impacted sites from the enhanced dataset. Rates of changes were calculated for 13 parameters between January 2005 and December 2014 at more than 1000 groundwater quality monitoring sites. The resulting dataset included 262 complete cases (CC), which was enhanced using Machine-Learning (ML) techniques to a total of 607 sites. Hierarchical cluster analysis was used to identify trend clusters that were consistent between the CC, ML-enhanced datasets and a 2006 study based on solely on the national network. The largest cluster (WR) consisted of low magnitude changes across all parameters and was attributed to water-rock interaction processes. The second largest cluster (I) exhibited fast changes particularly for parameters linked to human-induced impact. The third largest cluster (D) comprised decreases of all parameters and was associated with dilution processes. Trend clusters were further refined using groundwater quality state information, enabling the identification of impacted sites outside of Cluster I in the ML-enhanced and CC datasets. Corresponding trend baselines were subsequently derived at unimpacted sites using univariate quantile distribution (5th and 95th percentile thresholds). Finally, we developed classifications combining baselines (state and trend) and natural variability to enhance state of the environment reporting. This allowed the new identification of deteriorating trends at sites where groundwater quality state is not yet affected in addition to trend reversals. These classifications can be adapted to incorporate new knowledge or align with surface water quality reporting.

Are methylmercury concentrations in the wetlands of Kejimkujik National Park, Nova Scotia, Canada, dependent on geology?

In the relatively pristine ecosystem in Kejimkujik Park, Nova Scotia, methylmercury (MeHg) concentrations in loons, Gavia immer, are among the highest recorded anywhere in the world. This study investigated the influence of bedrock lithology on MeHg concentrations in wetlands. Twenty-five different wetland field sites were sampled over four different bedrock lithologies; Kejimkujik monzogranite, black sulfidic slate, gray slate, and greywacke. Soil samples were analyzed for ethylmercury (EtHg), MeHg, total Hg, acid-volatile sulfides (AVS), organic matter, and water content as well as the biological parameters, mercury methyltransferase (HgMT) activity, sulfate reduction rates, fatty acid methyl ester (FAME) composition, and acidity. Methylmercury concentrations in the wetlands were highly dependent (P < 0.08) on lithology with no significant difference between bogs, fens, and swamps. Methylmercury concentrations in wetland soils developed on Kejimkujik monzogranite averaged 900 ng kg(-1) compared with only 300 ng kg(-1) in wetland soils developed on black sulfidic slate. Fatty acid methyl ester composition was also lithologically dependent (P < 0.001) with biomarkers for Desulfobulbus spp. discriminating between sites containing high and low MeHg concentrations. Levels of MeHg in wetlands were predicted mainly (41% of the sum of squares) by HgMT activity that differed (P < 0.009) between wetlands, with activity in bogs almost three times that present in swamps. Wetland MeHg concentrations are highly dependent on the lithology on which they have developed for largely biological reasons.