Betaproteobacteria are a key component of surface water biofilters that maintain sustained manganese removal in response to fluctuations in influent water temperature.

The health risks associated with manganese (Mn) in drinking water, and an improved understanding of Mn accumulation within, and subsequent release from, distribution systems, have increased the need for robust, sustainable treatment options to minimize Mn concentrations in finished water. Biofiltration is an established and effective method to remove Mn in groundwater however, Mn removal in surface water biofilters is an emerging treatment process that has not been extensively studied. Seasonal variations in water temperature can present an operational challenge for surface water biofilters which may see reduced Mn removal under colder conditions. This study examined the microbiomes of surface water biofilters at three utilities (ACWD WTP, WTP B, and WTP D) which all experienced similar seasonal fluctuations in influent water temperature. High Mn removal was observed at the ACWD WTP for much of the year, but Mn removal decreased with a concurrent decrease in the influent water temperature (58% ± 22%). In contrast, both WTP B and WTP D achieved year-round Mn removal (84% ± 5% and 93% ± 8% respectively). Marker gene (16S rRNA) sequencing analysis of the biofilter microbiomes identified a high abundance of Betaproteobacteria in WTP B and WTP D (37% ± 12% and 21% ± 3% respectively), but a low abundance of Betaproteobacteria in the ACWD WTP (2% ± 2%). The microbiomes of new bench-scale biofilters, in operation at the ACWD WTP, were also investigated. The abundance of Betaproteobacteria was significantly greater (p < 0.05) after the biofilters had acclimated than before acclimation, and differential abundance analysis identified 6 genera within the Betaproteobacteria class were enriched in the acclimated microbiome. Additionally, the acclimated biofilters were able to maintain high Mn removal performance (87% ± 10%) when the influent water temperature decreased to 10 °C or less. Further analysis of previously published studies found the abundance of Betaproteobacteria was also significantly greater (p < 0.001) in biofilters with sustained Mn removal than in biofilters which did not treat for Mn as a contaminant, despite differences in design scale, source water, and media type. Microbiome network analysis identified multiple co-occurrence relationships between Betaproteobacteria and Mn oxidizing bacteria in the WTP B and WTP D biofilters, suggesting indirect contributions by Betaproteobacteria to biological Mn oxidation. These co-occurrence relationships were not present in the full-scale ACWD WTP microbiome. Whether the role of Betaproteobacteria in biological Mn oxidation is direct, indirect, or a combination of both, they are consistently present at a high abundance in both groundwater and surface water biofilters with sustained Mn removal, and their absence may contribute to the seasonal fluctuations in Mn removal observed at the ACWD WTP. This new insight to Betaproteobacteria and their role in Mn biofiltration could contribute to water innovation and design that would improve the reliability of Mn removal.

Biological and physico-chemical mechanisms accelerating the acclimation of Mn-removing biofilters.

This study investigated treatment strategies which accelerated the acclimation of new Mn-removing biofilters to help utilities respond to changing Mn regulations, such as the recent introduction of a health-based maximum acceptable concentration and a reduction in the aesthetic objective for Mn in drinking water by Health Canada. Bench-scale filters of either GAC or anthracite media were fed with applied water containing Mn (17-61 µg/L) from a full-scale plant over 294 days. Treatment strategies included the addition of H2O2 (1 mg/L) and/or an increase in pH from 6.8 to 7.5 through the addition of NaOH. The potential physico-chemical and biological mechanisms responsible for accelerated biofilter acclimation under the various redox conditions were investigated through thermodynamic modelling, to predict homogeneous Mn oxide formation, and 16S rRNA gene amplicon sequencing, to characterize the microbial community within the filters. GAC filters treated with NaOH, and both H2O2 and NaOH, were the first to acclimate (< 20 µg/L Mn in filter effluent) after 59 and 63 days respectively, while the ambient GAC filter took almost 3 times as long to acclimate (168 days), and the anthracite filters which received the same chemically adjusted water took almost 4 times as long (226 and 251 days, respectively). The accelerated acclimation in the treated GAC filters was likely due to physico-chemical oxidation via three potential mechanisms: (1) homogeneous oxidation of dissolved Mn(II) to Mn(III)/Mn(IV) oxides and the subsequent removal of oxides from solution through adherence to the GAC surface, (2) adsorption of dissolved Mn(II) to GAC and subsequent homogeneous or biological oxidation, or (3) formation of colloidal Mn(III)/Mn(IV) oxides and subsequent adsorption of dissolved Mn(II) to the Mn colloids. In the untreated GAC filter and all anthracite filters, which did not benefit from improved redox conditions or an active surface, physico-chemical mechanisms alone were insufficient for consistent Mn removal to less than 20 µg/L. Acclimation in these filters was delayed until a microbiome enriched with bacteria capable of biological nitrification and Mn oxidation evolved within the filters. The acclimated microbiome was consistent between GAC and anthracite filters and was significantly different from the non-acclimated microbiome (p < 0.001) initially formed during the early operation of the filters. Interestingly, treatment with NaOH, and NaOH and H2O2, which accelerated physico-chemical oxidation in GAC filters, was observed to delay the development of biological oxidation in anthracite filters, and thus deferred acclimation. Although some filters took longer to acclimate than others, once acclimation was reached all filters had a similar microbiome and were able to consistently remove Mn to below 20 µg/L.

Discovery of an expanded set of avian leukosis subgroup E proviruses in chickens using Vermillion, a novel sequence capture and analysis pipeline [corrected].

Transposable elements (TEs), such as endogenous retroviruses (ERVs), are common in the genomes of vertebrates. ERVs result from retroviral infections of germ-line cells, and once integrated into host DNA they become part of the host's heritable genetic material. ERVs have been ascribed positive effects on host physiology such as the generation of novel, adaptive genetic variation and resistance to infection, as well as negative effects as agents of tumorigenesis and disease. The avian leukosis virus subgroup E family (ALVE) of endogenous viruses of chickens has been used as a model system for studying the effects of ERVs on host physiology, and approximately 30 distinct ALVE proviruses have been described in the Gallus gallus genome. In this report we describe the development of a software tool, which we call Vermillion, and the use of this tool in combination with targeted next-generation sequencing (NGS) to increase the number of known proviruses belonging to the ALVE family of ERVs in the chicken genome by 4-fold, including expanding the number of known ALVE elements on chromosome 1 (Gga1) from the current 9 to a total of 40. Although we focused on the discovery of ALVE elements in chickens, with appropriate selection of target sequences Vermillion can be used to develop profiles of other families of ERVs and TEs in chickens as well as in species other than the chicken.