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1. Microbial Nitrogen Metabolism in Chloraminated Drinking Water Reservoirs

   https://doi.org/10.1128/mSphere.00274-20  

   Potgieter, Sarah C.; Dai, Zihan; Venter, Stephanus N.; Sigudu, Makhosazana; Pinto, Ameet J.; McMahon, Katherine (April 2020, mSphere)

   ABSTRACT Ammonia availability due to chloramination can promote the growth of nitrifying organisms, which can deplete chloramine residuals and result in operational problems for drinking water utilities. In this study, we used a metagenomic approach to determine the identity and functional potential of microorganisms involved in nitrogen biotransformation within chloraminated drinking water reservoirs. Spatial changes in the nitrogen species included an increase in nitrate concentrations accompanied by a decrease in ammonium concentrations with increasing distance from the site of chloramination. This nitrifying activity was likely driven by canonical ammonia-oxidizing bacteria (i.e., Nitrosomonas ) and nitrite-oxidizing bacteria (i.e., Nitrospira ) as well as by complete-ammonia-oxidizing (i.e., comammox) Nitrospira -like bacteria. Functional annotation was used to evaluate genes associated with nitrogen metabolism, and the community gene catalogue contained mostly genes involved in nitrification, nitrate and nitrite reduction, and nitric oxide reduction. Furthermore, we assembled 47 high-quality metagenome-assembled genomes (MAGs) representing a highly diverse assemblage of bacteria. Of these, five MAGs showed high coverage across all samples, which included two Nitrosomonas, Nitrospira, Sphingomonas , and Rhizobiales -like MAGs. Systematic genome-level analyses of these MAGs in relation to nitrogen metabolism suggest that under ammonia-limited conditions, nitrate may be also reduced back to ammonia for assimilation. Alternatively, nitrate may be reduced to nitric oxide and may potentially play a role in regulating biofilm formation. Overall, this study provides insight into the microbial communities and their nitrogen metabolism and, together with the water chemistry data, improves our understanding of nitrogen biotransformation in chloraminated drinking water distribution systems. IMPORTANCE Chloramines are often used as a secondary disinfectant when free chlorine residuals are difficult to maintain. However, chloramination is often associated with the undesirable effect of nitrification, which results in operational problems for many drinking water utilities. The introduction of ammonia during chloramination provides a potential source of nitrogen either through the addition of excess ammonia or through chloramine decay. This promotes the growth of nitrifying microorganisms and provides a nitrogen source (i.e., nitrate) for the growth for other organisms. While the roles of canonical ammonia-oxidizing and nitrite-oxidizing bacteria in chloraminated drinking water systems have been extensively investigated, those studies have largely adopted a targeted gene-centered approach. Further, little is known about the potential long-term cooccurrence of complete-ammonia-oxidizing (i.e., comammox) bacteria and the potential metabolic synergies of nitrifying organisms with their heterotrophic counterparts that are capable of denitrification and nitrogen assimilation. This study leveraged data obtained for genome-resolved metagenomics over a time series to show that while nitrifying bacteria are dominant and likely to play a major role in nitrification, their cooccurrence with heterotrophic organisms suggests that nitric oxide production and nitrate reduction to ammonia may also occur in chloraminated drinking water systems. 

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2. Comammox Nitrospira bacteria outnumber canonical nitrifiers irrespective of electron donor mode and availability in biofiltration systems

   https://doi.org/10.1093/femsec/fiac032  

   Vilardi, Katherine J; Cotto, Irmarie; Sevillano, Maria; Dai, Zihan; Anderson, Christopher L; Pinto, Ameet (April 2022, FEMS Microbiology Ecology)

   Abstract Complete ammonia oxidizing bacteria coexist with canonical ammonia and nitrite oxidizing bacteria in a wide range of environments. Whether this is due to competitive or cooperative interactions, or a result of niche separation is not yet clear. Understanding the factors driving coexistence of nitrifiers is critical to manage nitrification processes occurring in engineered and natural ecosystems. In this study, microcosm-based experiments were used to investigate the impact of nitrogen source and loading on the population dynamics of nitrifiers in drinking water biofilter media. Shotgun sequencing of DNA followed by co-assembly and reconstruction of metagenome assembled genomes revealed clade A2 comammox bacteria were likely the primary nitrifiers within microcosms and increased in abundance over Nitrosomonas-like ammonia and Nitrospira-like nitrite oxidizing bacteria irrespective of nitrogen source type or loading. Changes in comammox bacterial abundance did not correlate with either ammonia or nitrite oxidizing bacterial abundance in urea-amended systems, where metabolic reconstruction indicated potential for cross-feeding between strict ammonia and nitrite oxidizers. In contrast, comammox bacterial abundance demonstrated a negative correlation with nitrite oxidizers in ammonia-amended systems. This suggests potentially weaker synergistic relationships between strict ammonia and nitrite oxidizers might enable comammox bacteria to displace strict nitrite oxidizers from complex nitrifying communities. 

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3. Comparing DNA, RNA and protein levels for measuring microbial dynamics in soil microcosms amended with nitrogen fertilizer

   https://doi.org/10.1038/s41598-019-53679-0  

   Orellana, Luis H.; Hatt, Janet K.; Iyer, Ramsunder; Chourey, Karuna; Hettich, Robert L.; Spain, Jim C.; Yang, Wendy H.; Chee-Sanford, Joanne C.; Sanford, Robert A.; Löffler, Frank E.; et al (November 2019, Scientific Reports)

   Abstract To what extent multi-omic techniques could reflectin situmicrobial process rates remains unclear, especially for highly diverse habitats like soils. Here, we performed microcosm incubations using sandy soil from an agricultural site in Midwest USA. Microcosms amended with isotopically labeled ammonium and urea to simulate a fertilization event showed nitrification (up to 4.1 ± 0.87 µg N-NO₃⁻g⁻¹dry soil d⁻¹) and accumulation of N₂O after 192 hours of incubation. Nitrification activity (NH₄⁺ → NH₂OH → NO → NO₂^- → NO₃⁻) was accompanied by a 6-fold increase in relative expression of the 16S rRNA gene (RNA/DNA) between 10 and 192 hours of incubation for ammonia-oxidizing bacteriaNitrosomonasandNitrosospira, unlike archaea and comammox bacteria, which showed stable gene expression. A strong relationship between nitrification activity and betaproteobacterial ammonia monooxygenase and nitrite oxidoreductase transcript abundances revealed that mRNA quantitatively reflected measured activity and was generally more sensitive than DNA under these conditions. Although peptides related to housekeeping proteins from nitrite-oxidizing microorganisms were detected, their abundance was not significantly correlated with activity, revealing that meta-proteomics provided only a qualitative assessment of activity. Altogether, these findings underscore the strengths and limitations of multi-omic approaches for assessing diverse microbial communities in soils and provide new insights into nitrification. 

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4. The Role of Carbon to Nitrogen Ratio on the Performance of Denitrifying Biocathodes for Decentralized Wastewater Treatment

   https://doi.org/10.3390/w14193076  

   Castro, Cynthia J; Taha, Kamal; Kenney, Itzé; Yeh, Daniel H (October 2022, Water)

   Bioelectrochemical systems with denitrifying biocathodes have been of interest for the removal of nitrate in decentralized wastewater treatment applications. Only a few studies have directly focused on this application, but the removal rates have been very low. This study evaluated the operational parameters that affect the nitrate removal of two-chambered microbial fuel cells (MFCs) with a biocathode, particularly, the carbon to nitrogen ratio (C:N) and proton diffusivity across electrode chambers. The results show that proton diffusion across a proton exchange membrane is not a limiting step in nitrogen removal performance. At C:N ratios of 4 and 8, biocathodes with a continuously supplied carbon source at the anode were able to achieve complete nitrogen removal at a rate of 0.97 ± 0.21 and 1.15 ± 0.13 mg N L−1 d−1, respectively. However, as the C:N ratio increased from 4, 8, 16, and 32, the electrode potentials decreased accordingly. Ratio 4 C:N had a cathodic reduction potential of +66.1 ± 5.3 mV vs. SHE and dropped to −78.6 ± 9.8 mV vs. SHE at 32 C:N. The cathode electrode potential can be controlled by way of the carbon concentrations at the anode, which can have major indirect implications on the evolution of cathodic microbial communities that have preference to particular ranges of reduction potentials. The cathodic biofilms in this study were dominated by the phyla Proteobacteria, Acidobacteria, Bacteroidetes and Nitrospirae, which are known to have key denitrifying microorganisms. The genus Stenotrophomonas was found in abundance within the attached cathode biofilm and to a lesser extent in the suspended biomass. Vibrio, Acidobacteria_Gp4, Nitrosomonas, and Candidatus Competibacter were also cultivated in both the suspended and attached biomass. Nitrospira was only found in the attached biofilm. Regardless of operational scheme, nitrogen removal was improved at low C:N ratios, with 8 C:N having the best performance overall. This indicates that higher C:N ratios than were previously explored (>4 C:N) provide sufficient coulombs to facilitate denitrification at the cathode even while the anodic CEs remain low. Reactor design modifications should be considered to fully support robust denitrifying communities, enhancing the overall nitrogen removal for decentralized wastewater treatment applications. 

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5. Exploring the Meta-regulon of the CRP/FNR Family of Global Transcriptional Regulators in a Partial-Nitritation Anammox Microbiome

   https://doi.org/10.1128/mSystems.00906-21  

   Beach, Natalie K.; Myers, Kevin S.; Owen, Brian R.; Seib, Matt; Donohue, Timothy J.; Noguera, Daniel R. (October 2021, mSystems)

   Lindemann, Stephen R. (Ed.)

   ABSTRACT Microorganisms must respond to environmental changes to survive, often by controlling transcription initiation. Intermittent aeration during wastewater treatment presents a cyclically changing environment to which microorganisms must react. We used an intermittently aerated bioreactor performing partial nitritation and anammox (PNA) to investigate how the microbiome responds to recurring change. Meta-transcriptomic analysis revealed a dramatic disconnect between the relative DNA abundance and gene expression within the metagenome-assembled genomes (MAGs) of community members, suggesting the importance of transcriptional regulation in this microbiome. To explore how community members responded to cyclic aeration via transcriptional regulation, we searched for homologs of the catabolite repressor protein/fumarate and nitrate reductase regulatory protein (CRP/FNR) family of transcription factors (TFs) within the MAGs. Using phylogenetic analyses, evaluation of sequence conservation in important amino acid residues, and prediction of genes regulated by TFs in the MAGs, we identified homologs of the oxygen-sensing FNR in Nitrosomonas and Rhodocyclaceae , nitrogen-sensing dissimilative nitrate respiration regulator that responds to nitrogen species (DNR) in Rhodocyclaceae , and nitrogen-sensing nitrite and nitric oxide reductase regulator that responds to nitrogen species (NnrR) in Nitrospira MAGs. Our data also predict that CRP/FNR homologs in Ignavibacteria , Flavobacteriales , and Saprospiraceae MAGs sense carbon availability. In addition, a CRP/FNR homolog in a Brocadia MAG was most closely related to CRP TFs known to sense carbon sources in well-studied organisms. However, we predict that in autotrophic Brocadia , this TF most likely regulates a diverse set of functions, including a response to stress during the cyclic aerobic/anoxic conditions. Overall, this analysis allowed us to define a meta-regulon of the PNA microbiome that explains functions and interactions of the most active community members. IMPORTANCE Microbiomes are important contributors to many ecosystems, including ones where nutrient cycling is stimulated by aeration control. Optimizing cyclic aeration helps reduce energy needs and maximize microbiome performance during wastewater treatment; however, little is known about how most microbial community members respond to these alternating conditions. We defined the meta-regulon of a PNA microbiome by combining existing knowledge of how the CRP/FNR family of bacterial TFs respond to stimuli, with metatranscriptomic analyses to characterize gene expression changes during aeration cycles. Our results indicated that, for some members of the community, prior knowledge is sufficient for high-confidence assignments of TF function, whereas other community members have CRP/FNR TFs for which inferences of function are limited by lack of prior knowledge. This study provides a framework to begin elucidating meta-regulons in microbiomes, where pure cultures are not available for traditional transcriptional regulation studies. Defining the meta-regulon can help in optimizing microbiome performance. 

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