Protozoa graze on the 2,6-dichlorobenzamide (BAM)-degrading bacterium Aminobacter sp. MSH1 introduced into waterworks sand filters

How bioaugmentation for pesticide removal influences the microbial community in biologically active sand filters

Removing pesticides from biological drinking water filters is challenging due to the difficulty in activating pesticide-degrading bacteria within the filters. Bioaugmented bacteria can alter the filter's microbiome, affecting its performance either positively or negatively, depending on the bacteria used and their interaction with native microbes. We demonstrate that adding specific bacteria strains can effectively remove recalcitrant pesticides, like metaldehyde, yielding compliance to regulatory standards for an extended period. Our experiments revealed that the Sphingobium CMET-H strain was particularly effective, consistently reducing metaldehyde concentrations to levels within regulatory compliance, significantly outperforming Acinetobacter calcoaceticus E1. This success is attributed to the superior acclimation and distribution of the Sphingobium strain within the filter bed, facilitating more efficient interactions with and degradation of the pesticide, even when present at lower population densities compared to Acinetobacter calcoaceticus E1. Furthermore, our study demonstrates that the addition of pesticide-degrading strains significantly impacts the filter's microbiome at various depths, despite these strains making up less than 1% of the total microbial community. The sequence in which these bacteria are introduced influences the system's ability to degrade pesticides effectively. This research shows the potential of carefully selected and dosed bioaugmented bacteria to improve the pesticide removal capabilities of water filtration systems, while also highlighting the dynamics between bioaugmented and native microbial communities. Further investigation into optimizing bioaugmentation strategies is suggested to enhance the resilience and efficiency of drinking water treatment systems against pesticide contamination.

Cooperative interactions between invader and resident microbial community members weaken the negative diversity-invasion relationship

The negative diversity-invasion relationship observed in microbial invasion studies is commonly explained by competition between the invader and resident populations. However, whether this relationship is affected by invader-resident cooperative interactions is unknown. Using ecological and mathematical approaches, we examined the survival and functionality of Aminobacter niigataensis MSH1 to mineralize 2,6-dichlorobenzamide (BAM), a groundwater micropollutant affecting drinking water production, in sand microcosms when inoculated together with synthetic assemblies of resident bacteria. The assemblies varied in richness and in strains that interacted pairwise with MSH1, including cooperative and competitive interactions. While overall, the negative diversity-invasion relationship was retained, residents engaging in cooperative interactions with the invader had a positive impact on MSH1 survival and functionality, highlighting the dependency of invasion success on community composition. No correlation existed between community richness and the delay in BAM mineralization by MSH1. The findings suggest that the presence of cooperative residents can alleviate the negative diversity-invasion relationship.

Toward Improved Bioremediation Strategies: Response of BAM-Degradation Activity to Concentration and Flow Changes in an Inoculated Bench-Scale Sediment Tank

Compound-specific isotope analysis (CSIA) can reveal mass-transfer limitations during biodegradation of organic pollutants by enabling the detection of masked isotope fractionation. Here, we applied CSIA to monitor the adaptive response of bacterial degradation in inoculated sediment to low contaminant concentrations over time. We characterized Aminobacter sp. MSH1 activity in a flow-through sediment tank in response to a transient supply of elevated 2,6-dichlorobenzamide (BAM) concentrations as a priming strategy and took advantage of an inadvertent intermittence to investigate the effect of short-term flow fluctuations. Priming and flow fluctuations yielded improved biodegradation performance and increased biodegradation capacity, as evaluated from bacterial activity and residual concentration time series. However, changes in isotope ratios in space and over time evidenced that mass transfer became increasingly limiting for degradation of BAM at low concentrations under such stimulated conditions, and that activity decreased further due to bacterial adaptation at low BAM (μg/L) levels. Isotope ratios, in conjunction with residual substrate concentrations, therefore helped identifying underlying limitations of biodegradation in such a stimulated system, offering important insight for future optimization of remediation schemes.

The complete genome of 2,6-dichlorobenzamide (BAM) degrader Aminobacter sp. MSH1 suggests a polyploid chromosome, phylogenetic reassignment, and functions of plasmids

Aminobacter sp. MSH1 (CIP 110285) can use the pesticide dichlobenil and its recalcitrant transformation product, 2,6-dichlorobenzamide (BAM), as sole source of carbon, nitrogen, and energy. The concentration of BAM in groundwater often exceeds the threshold limit for drinking water, requiring additional treatment in drinking water treatment plants or closure of the affected abstraction wells. Biological treatment with MSH1 is considered a potential sustainable alternative to remediate BAM-contamination in drinking water production. We present the complete genome of MSH1, which was determined independently in two institutes at Aarhus University and KU Leuven. Divergences were observed between the two genomes, i.e. one of them lacked four plasmids compared to the other. Besides the circular chromosome and the two previously described plasmids involved in BAM catabolism, pBAM1 and pBAM2, the genome of MSH1 contained two megaplasmids and three smaller plasmids. The MSH1 substrain from KU Leuven showed a reduced genome lacking a megaplasmid and three smaller plasmids and was designated substrain MK1, whereas the Aarhus variant with all plasmids was designated substrain DK1. A plasmid stability experiment indicate that substrain DK1 may have a polyploid chromosome when growing in R2B medium with more chromosomes than plasmids per cell. Finally, strain MSH1 is reassigned as Aminobacter niigataensis MSH1.

Successional trophic complexity and biogeographical structure of eukaryotic communities in waterworks' rapid sand filters

As groundwater-fed waterworks clean their raw inlet water with sand filters, a variety of pro- and eukaryotic microbial communities develop on these filters. While several studies have targeted the prokaryotic sand filter communities, little is known about the eukaryotic communities, despite the obvious need for knowledge of microorganisms that get in contact with human drinking water. With a new general eukaryotic primer set (18S, V1-V3 region), we performed FLX-454 sequencing of material from 21 waterworks' sand filters varying in age (3-40 years) and geographical location on a 250 km east-west axis in Denmark, and put the data in context of their previously published prokaryotic communities. We find that filters vary highly in trophic complexity depending on age, from simple systems with bacteria and protozoa (3-6 years) to complex, mature systems with nematodes, rotifers and turbellarians as apex predators (40 years). Unlike the bacterial communities, the eukaryotic communities display a clear distance-decay relationship that predominates over environmental variations, indicating that the underlying aquifers feeding the filters harbor distinct eukaryotic communities with limited dispersal in between. Our findings have implications for waterworks' filter management, and offer a window down to the largely unexplored eukaryotic microbiology of groundwater aquifers.

A novel hybrid concept for implementation in drinking water treatment targets micropollutant removal by combining membrane filtration with biodegradation

Groundwater extracted for drinking water production is commonly treated by aeration and sand filtration. However, this simple treatment is typically unable to remove pesticide residues. As a solution, bioaugmentation of sand filter units (i.e., the addition of specific degrader strains) has been proposed as an alternative "green" technology for targeted pesticide removal. However, the introduced degraders are challenged by (i) micropollutant levels of target residue, (ii) the oligotrophic environment and (iii) competition and predation by the native microorganisms, leading to loss of population and degradation potential. To overcome these challenges, we propose the introduction of a novel hybrid treatment step to the overall treatment process in which reverse osmosis filtration and biodegradation are combined to remove a target micropollutant. Here, the reverse osmosis produces a concentrated retentate that will act as a feed to a dedicated biofilter unit, intended to promote biodegradation potential and stability of an introduced degrader. Subsequently, the purified retentate will be re-mixed with the permeate from reverse osmosis, for re-mineralization and downstream consumption. In our study, we investigated the effect of reverse osmosis retentates on the degradation potential of an introduced degrader. This paper provides the first promising results of this hybrid concept using the 2,6-dichlorobenzamide (BAM)-degrading bacteria Aminobacter sp. MSH1 in batch experiments, spiked with radiolabeled BAM. The results showed an increased degradation potential of MSH1 in retentate waters versus untreated water. Colony-forming units and qPCR showed a stable MSH1 population, despite higher concentrations of salts and metals, and increased growth of native bacteria.

Bioaugmentation of rapid sand filters by microbiome priming with a nitrifying consortium will optimize production of drinking water from groundwater

Ammonium oxidation to nitrite and then to nitrate (nitrification) is a key process in many waterworks treating groundwater to make it potable. In rapid sand filters, nitrifying microbial communities may evolve naturally from groundwater bacteria entering the filters. However, in new filters this may take several months, and in some cases the nitrification process is never sufficiently rapid to be efficient or is only performed partially, with nitrite as an undesired end product. The present study reports the first successful priming of nitrification in a rapid sand filter treating groundwater. It is shown that nitrifying communities could be enriched by microbiomes from well-functioning rapid sand filters in waterworks and that the enriched nitrifying consortium could be used to inoculate fresh filters, significantly shortening the time taken for the nitrification process to start. The key nitrifiers in the enrichment were different from those in the well-functioning filter, but similar to those that initiated the nitrification process in fresh filters without inoculation. Whether or not the nitrification was primed with the enriched nitrifying consortium, the bacteria performing the nitrification process during start-up appeared to be slowly outcompeted by Nitrospira, the dominant nitrifying bacterium in well-functioning rapid sand filters.

Groundwater contamination with 2,6-dichlorobenzamide (BAM) and perspectives for its microbial removal

The pesticide metabolite 2,6-dichlorobenzamide (BAM) is very persistent in both soil and groundwater and has become one of the most frequently detected groundwater micropollutants. BAM is not removed by the physico-chemical treatment techniques currently used in drinking water treatment plants (DWTP); therefore, if concentrations exceed the legal threshold limit, it represents a sizeable problem for the stability and quality of drinking water production, especially in places that depend on groundwater for drinking water. Bioremediation is suggested as a valuable strategy for removing BAM from groundwater by deploying dedicated BAM-degrading bacteria in DWTP sand filters. Only a few bacterial strains with the capability to degrade BAM have been isolated, and of these, only three isolates belonging to the Aminobacter genus are able to mineralise BAM. Considerable effort has been made to elucidate degradation pathways, kinetics and degrader genes, and research has recently been presented on the application of strain Aminobacter sp. MSH1 for the purification of BAM-contaminated water. The aim of the present review was to provide insight into the issue of BAM contamination and to report on the current status and knowledge with regard to the application of microorganisms for purification of BAM-contaminated water resources. This paper discusses the prospects and challenges for bioaugmentation of DWTP sand filters with specific BAM-degrading bacteria and identifies relevant perspectives for future research.