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

Destabilization mechanisms of Semi-aerobic aged refuse biofilters under harsh treatment conditions: Evidence from fluorescence and microbial characteristics

Semi-aerobic aged refuse biofilters (SAARB) are commonly-used biotechnologies for treating landfill leachate. In actual operation, SAARB often faces harsh conditions characterized by high concentrations of chemical oxygen demand (COD) and Cl-, as well as a low carbon-to-nitrogen ratio (C/N), which can disrupt the microbial community within SAARB, leading to operational instability. Maintaining the stable operation of SAARB is crucial for the efficient treatment of landfill leachate. However, the destabilization mechanism of SAARB under harsh conditions remains unclear. To address this, the study simulated the operation of SAARB under three harsh conditions, namely, high COD loading (H-COD), high chloride ion (Cl-) concentration environment (H-Cl-), and low C/N ratio environment (L-C/N). The aim is to reveal the destabilization mechanism of SAARB under harsh conditions by analyzing the fluorescence characteristics of effluent DOM and the microbial community in aged refuse. The results indicate that three harsh conditions have different effects on SAARB. H-COD leads to the accumulation of proteins; H-Cl- impedes the reduction of nitrite nitrogen; L-C/N inhibits the degradation of humic substances. These outcomes are attributed to the specific effects of different factors on the microbial communities in different zones of SAARB. H-COD and L-C/N mainly affect the degradation of organic matter in aerobic zone, while H-Cl- primarily impedes the denitrification process in the anaerobic zone. The abnormal enrichment of Corynebacterium, Castellaniella, and Sporosarcina can indicate the instability of SAARB under three harsh conditions, respectively. To maintain the steady operation of SAARB, targeted acclimation of the microbial community in SAARB should be carried out to cope with potentially harsh operating conditions. Besides, timely mitigation of loads should be implemented when instability characteristics emerge, and carbon sources and electron donors should be provided to restore treatment performance effectively.

Bioaugmentation has temporary effect on anaerobic pesticide biodegradation in simulated groundwater systems

Groundwater is the most important source for drinking water in The Netherlands. Groundwater quality is threatened by the presence of pesticides, and biodegradation is a natural process that can contribute to pesticide removal. Groundwater conditions are oligotrophic and thus biodegradation can be limited by the presence and development of microbial communities capable of biodegrading pesticides. For that reason, bioremediation technologies such as bioaugmentation (BA) can help to enhance pesticide biodegradation. We studied the effect of BA using enriched mixed inocula in two column bioreactors that simulate groundwater systems at naturally occurring redox conditions (iron and sulfate-reducing conditions). Columns were operated for around 800 days, and two BA inoculations (BA1 and BA2) were conducted in each column. Inocula were enriched from different wastewater treatment plants (WWTPs) under different redox-conditions. We observed a temporary effect of BA1, reaching 100% removal efficiency of the pesticide 2,4-D after 100 days in both columns. In the iron-reducing column, 2,4-D removal was in general higher than under sulfate-reducing conditions demonstrating the influence of redox conditions on overall biodegradation. We observed a temporary shift in microbial communities after BA1 that is relatable to the increase in 2,4-D removal efficiency. After BA2 under sulfate-reducing conditions, 2,4-D removal efficiency decreased, but no change in the column microbial communities was observed. The present study demonstrates that BA with a mixed inoculum can be a valuable technique for improving biodegradation in anoxic groundwater systems at different redox-conditions.

Investigating eukaryotic and prokaryotic diversity and functional potential in the cold and alkaline ikaite columns in Greenland

The ikaite columns in the Ikka Fjord, SW Greenland, represent a permanently cold and alkaline environment known to contain a rich bacterial diversity. 16S and 18S rRNA gene amplicon and metagenomic sequencing was used to investigate the microbial diversity in the columns and for the first time, the eukaryotic and archaeal diversity in ikaite columns were analyzed. The results showed a rich prokaryotic diversity that varied across columns as well as within each column. Seven different archaeal phyla were documented in multiple locations inside the columns. The columns also contained a rich eukaryotic diversity with 27 phyla representing microalgae, protists, fungi, and small animals. Based on metagenomic sequencing, 25 high-quality MAGs were assembled and analyzed for the presence of genes involved in cycling of nitrogen, sulfur, and phosphorous as well as genes encoding carbohydrate-active enzymes (CAZymes), showing a potentially very bioactive microbial community.

Inoculation with adapted bacterial communities promotes development of full scale slow sand filters for drinking water production

Gravity-driven filtration through slow sand filters (SSFs) is one of the oldest methods for producing drinking water. As water passes through a sand bed, undesired microorganisms and chemicals are removed by interactions with SSF biofilm and its resident microbes. Despite their importance, the processes through which these microbial communities form are largely unknown, as are the factors affecting these processes. In this study, two SSFs constructed using different sand sources were compared to an established filter and observed throughout their maturation process. One SSF was inoculated through addition of sand scraped from established filters, while the other was not inoculated. The operational and developing microbial communities of SSFs, as well as their influents and effluents, were studied by sequencing of 16S ribosomal rRNA genes. A functional microbial community resembling that of the established SSF was achieved in the inoculated SSF, but not in the non-inoculated SSF. Notably, the non-inoculated SSF had significantly (p < 0.01) higher abundances of classes Armatimonadia, Elusimicrobia, Fimbriimonadia, OM190 (phylum Planctomycetota), Parcubacteria, Vampirivibrionia and Verrucomicrobiae. Conversely, it had lower abundances of classes Anaerolineae, Bacilli, bacteriap25 (phylum Myxococcota), Blastocatellia, Entotheonellia, Gemmatimonadetes, lineage 11b (phylum Elusimicrobiota), Nitrospiria, Phycisphaerae, subgroup 22 (phylum Acidobacteriota) and subgroup 11 (phylum Acidobacteriota). Poor performance of neutral models showed that the assembly and dispersal of SSF microbial communities was mainly driven by selection. The temporal turnover of microbial species, as estimated through the scaling exponent of the species-time relationship, was twice as high in the non-inoculated filter (0.946 ± 0.164) compared to the inoculated filter (0.422 ± 0.0431). This study shows that the addition of an inoculum changed the assembly processes within SSFs. Specifically, the rate at which new microorganisms were observed in the biofilm was reduced. The reduced temporal turnover may be driven by inoculating taxa inhibiting growth, potentially via secondary metabolite production. This in turn would allow the inoculation community to persist and contribute to SSF function.

Microbial ecology of drinking water from source to tap

As drinking water travels from its source, through various treatment processes, hundreds to thousands of kilometres of distribution network pipes, to the taps in private homes and public buildings, it is exposed to numerous environmental changes, as well as other microbes living in both water and on surfaces. This review aims to identify the key locations and factors that are associated with changes in the drinking water microbiome throughout conventional urban drinking water systems from the source to the tap water. Over the past 15 years, improvements in cultivation-independent methods have enabled studies that allow us to answer such questions. As a result, we are beginning to move towards predicting the impacts of disturbances and interventions resulting ultimately in management of drinking water systems and microbial communities rather than mere observation. Many challenges still exist to achieve effective management, particularly within the premise plumbing environment, which exhibits diverse and inconsistent conditions that may lead to alterations in the microbiota, potentially presenting public health risks. Finally, we recommend the establishment of global collaborative projects on the drinking water microbiome that will enhance our current knowledge and lead to tools for operators and researchers alike to improve global access to high-quality drinking water.

Exploring microbial diversity in Greenland Ice Sheet supraglacial habitats through culturing-dependent and -independent approaches

The microbiome of Greenland Ice Sheet supraglacial habitats is still underinvestigated, and as a result there is a lack of representative genomes from these environments. In this study, we investigated the supraglacial microbiome through a combination of culturing-dependent and -independent approaches. We explored ice, cryoconite, biofilm, and snow biodiversity to answer: (1) how microbial diversity differs between supraglacial habitats, (2) if obtained bacterial genomes reflect dominant community members, and (3) how culturing versus high throughput sequencing changes our observations of microbial diversity in supraglacial habitats. Genomes acquired through metagenomic sequencing (133 high-quality MAGs) and whole genome sequencing (73 bacterial isolates) were compared to the metagenome assemblies to investigate abundance within the total environmental DNA. Isolates obtained in this study were not dominant taxa in the habitat they were sampled from, in contrast to the obtained MAGs. We demonstrate here the advantages of using metagenome SSU rRNA genes to reflect whole-community diversity. Additionally, we demonstrate a proof-of-concept of the application of in situ culturing in a supraglacial setting.

Combination of partial nitrification and microbial fuel cell for simultaneous ammonia reduction, organic removal, and energy recovery

The chemical oxygen demand (COD) in municipal wastewater has become an obstacle for anammox in mainstream applications. In this study, the single chamber microbial fuel cell (MFC) was installed as an influent device for a partial nitrification-sequencing batch reactor (PN-SBR) to realize integrating COD removal and partial nitrification. After 80 days of operation, the nitrite accumulation rate reached 93%, while the COD removal efficiency was 56%. The output voltage and the power density of MFC were 66.62 mV and 2.40 W/m3, respectively. The content of EPS, especially polysaccharides in the stable phase, has increased compared with the seed sludge. The most dominant genus in MFC anode biofilm and SBR granular sludge was Thauera, which has organic compounds degradation capacity and could degrade nitrate. This study revealed the microbial interaction between MFC and partial nitrification and provided a new strategy for stable ammonia and nitrite supply for mainstream anammox plants.

Microbial Diversity in Four Rhizocompartments (Bulk Soil, Rhizosphere, Rhizoplane, and Endosphere) of Four Winter Wheat Varieties at the Fully Emerged Flag Leaf Growth Stage

Community composition and recruitment are important elements of plant-microbe interactions and may provide insights for plant development and resilience. The results of 16S rRNA amplicon sequencing from four rhizocompartments for four wheat cultivars grown under controlled conditions and sampled after flag leaf emergence are provided. Data demonstrate differences in microbial communities according to rhizocompartment.

Exploring organic micropollutant biodegradation under dynamic substrate loading in rapid sand filters

Microbial removal of trace organic micropollutants (OMPs) from drinking water sources remains challenging. Nitrifying and heterotrophic bacteria in rapid sand filters (RSFs) are capable of biodegrading OMPs while growing on ammonia and dissolved organic matter (DOM). The loading patterns of ammonia and DOM may therefore affect microbial activities as well as OMP biodegradation. So far, there is very limited information on the effect of substrate loading on OMP biodegradation at environmentally relevant concentrations (∼ 1 µg/L) in RSFs. We investigated the biodegradation rates of 16 OMPs at various substrate loading rates and/or empty bed contact times (EBCT). The presence of DOM improved the biodegradation of paracetamol (41.8%) by functioning as supplementary carbon source for the heterotrophic degrader, while hindering the biodegradation of 2,4-D, mecoprop and benzotriazole due to substrate competition. Lower loading ratios of DOM/benzotriazole benefited benzotriazole biodegradation by reducing substrate competition. Higher ammonia loading rates enhanced benzotriazole removal by stimulating nitrification-based co-metabolism. However, stimulating nitrification inhibited heterotrophic activity, which in turn inhibited the biodegradation of paracetamol, 2,4-D and mecoprop. A longer EBCT promoted metformin biodegradation as it is a slowly biodegradable compound, but suppressed the biodegradation of paracetamol and benzotriazole due to limited substrate supply. Therefore, the optimal substrate loading pattern is contingent on the type of OMP, which can be chosen based on the priority compounds in practice. The overall results contribute to understanding OMP biodegradation mechanisms at trace concentrations and offer a step towards enhancing microbial removal of OMPs from drinking water by optimally using RSFs.

Microbial ecology of biofiltration used for producing safe drinking water

Abstract

Biofiltration is a water purification technology playing a pivotal role in producing safe drinking water. This technology attracts many interests worldwide due to its advantages, such as no addition of chemicals, a low energy input, and a high removal efficiency of organic compounds, undesirable taste and odours, and pathogens. The current review describes the microbial ecology of three biofiltration processes that are routinely used in drinking water treatment plants, i.e. (i) rapid sand filtration (RSF), (ii) granular activated carbon filtration (GACF), and (iii) slow sand filtration (SSF). We summarised and compared the characteristics, removal performance, and corresponding (newly revealed) mechanisms of the three biofiltration processes. Specifically, the microbial ecology of the different biofilter processes and the role of microbial communities in removing nutrients, organic compounds, and pathogens were reviewed. Finally, we highlight the limitations and challenges in the study of biofiltration in drinking water production, and propose future perspectives for obtaining a comprehensive understanding of the microbial ecology of biofiltration, which is needed to promote and optimise its further application.

Key points

• Biofilters are composed of complex microbiomes, primarily shaped by water quality.

• Conventional biofilters contribute to address safety challenges in drinking water.

• Studies may underestimate the active/functional role of microbiomes in biofilters.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-022-12013-x.

Metagenomic Research of Infectious Diseases in Archaeological Contexts: Evidence from the Hospital Real de Todos-os-Santos (Portugal)

Syphilis is one of the most exciting diseases explored in paleopathology and, therefore, tracing back its origin and development has provided a prolific debate. The combination of paleopathological data with historical sources, iconography, and archaeological contexts were the primary sources used to reconstruct its historical path. However, there are some limitations to paleopathological diagnosis due to the nature of bone reaction to stimuli. In addition, historical sources are subjected to a bias of social and cultural nature and the knowledge of those who wrote them. Hence, ancient DNA analysis offers the possibility of acquiring proof of cause by identifying pathogens in an organism. We undertook a metagenomic study of a skeleton exhumed from the Royal Hospital of All Saints (Portugal), renowned for treating syphilis from the 16th century onwards. The skeleton had previously been diagnosed with syphilis according to paleopathological analysis. However, the metagenomics analysis showed no presence of the pathogen associated with syphilis (i.e., Treponema pallidum) but revealed pathogenic microorganisms related to respiratory diseases (pneumonia), nonspecific bone infections (osteomyelitis), and oral bacterial pathologies as well as Hansen’s disease (also known as leprosy). The results are exciting and demand a reappraisal of the observed bone changes, recontextualizing their characterization as syphilis related. They prove that past reconstruction of health and disease diagnoses based on assessing human osteological remains of known context (such as a syphilitic hospital) may bias interpretations and, therefore, caution is recommended, not forgetting that the absence of evidence is not evidence of absence (in this case of syphilis) in life.

Diversity and Structure of Bacterial Communities in Different Rhizocompartments (Rhizoplane, Rhizosphere, and Bulk) at Flag Leaf Emergence in Four Winter Wheat Varieties

Understanding basic interactions at the plant-soil interphase is critical if we are to exploit natural microbial communities for improved crop resilience. We report here 16S amplicon sequencing data from 3 rhizocompartments of 4 wheat cultivars grown under controlled greenhouse conditions. We observed that rhizocompartments and cultivar affect the community composition.

Can we shape microbial communities to enhance biological activated carbon filter performance?

A new focus on biofiltration has emerged that aims to shape microbial communities to improve treatment efficacy. It is therefore necessary to understand the linkages between microbial community structure and biofilter function. However, the assembly and interaction of microbial communities in biological activated carbon (BAC) filters are unknown. In this study, we selected one coal-based granular activated carbon (GAC), GAC-13, with simultaneously developed micropore and micro-level macropore volume used for a bench-scale BAC column experiment, and compared it with other coal-based GACs and wood-based GAC in terms of the dissolved organic carbon (DOC) removal and microbial community characteristics. The results showed that there was no difference between the DOC removal efficiency of BAC-13 and the other two coal-based BAC filters with high iodine value in the period dominated by adsorption, while the DOC removal efficiency of BAC-13 (64.7±0.6%) was significantly higher than that of other BAC filters (36.3±0.8-54.1±0.4%) with a difference of 0.3-0.7 mg/L in DOC during the steady state. The bacterial communities were strongly assembled by deterministic rather than stochastic factors, where the surface polarity of GAC had a greater effect on the microbial communities than its physical properties. The corresponding co-occurrence network revealed that microbes in the BAC filter may be more cooperative than competitive. The keystone bacterium Hyphomicrobium, which had a relatively low abundance, contributed 0.3-1% more to the most abundant functions and produced 5-21 proteins/(g·GAC) more than the dominant bacterium Sphingobium. The metaproteomic-based approach could provide more accurate information regarding the contributions of different species to metabolic functions. The pore size distribution of GAC was found to be an important factor in determining BAC filter performance; the most important pore sizes were micropores and micro-level macropores (0.2-10 μm and >100 μm in diameter), and the latter impacted the abundance of keystone species. Overall, our findings provide new insights into shaping microbial communities by optimizing pore size structure to improve BAC performance, especially the abundance of keystone species.

Effects of treatment processes on AOC removal and changes of bacterial diversity in a water treatment plant

The effectiveness of different treatment processes on assimilable organic carbon (AOC) removal and bacterial diversity variations was evaluated in a water treatment plant. The van der Kooij technique was applied for AOC analysis and responses of bacterial communities were characterized by the metagenomics assay. Results show that the AOC concentrations were about 93, 148, 43, 51, 37, and 38 μg acetate-C/L in effluents of raw water basin, preozonation, rapid sand filtration (RSF), ozonation, biofiltration [biological activated carbon (BAC) filtration], and chlorination (clear water), respectively. Increased AOC concentrations were observed after preozonation, ozonation, and chlorination units due to the production of biodegradable organic matters after the oxidation processes. Results indicate that the oxidation processes were the main causes of AOC formation, which resulted in significant increases in AOC concentrations (18-59% increment). The AOC removal efficiencies were 47, 28, and 60% in the RSF, biofiltration, and the whole system, respectively. RSF and biofiltration were responsible for the AOC treatment and both processes played key roles in AOC removal. Thus, both RSF and biofiltration processes would contribute to AOC treatment after oxidation. Sediments from the raw water basin and filter samples from RSF and BAC units were collected and analyzed for bacterial communities. Results from scanning electron microscope analysis indicate that bacterial colonization was observed in filter materials. This indicates that the surfaces of the filter materials were beneficial to bacterial growth and AOC removal via the adsorption and biodegradation mechanisms. Next generation sequencing analyses demonstrate that water treatment processes resulted in the changes of bacterial diversity and community profiles in filters of RSF and BAC. According to the findings of bacterial composition and interactions, the dominant bacterial phyla were Proteobacteria (41% in RSF and 56% in BAC) followed by Planctomycetes and Acidobacteria in RSF and BAC systems, which might affect the AOC biodegradation efficiency. Results would be useful in developing AOC treatment and management processes in water treatment plants.

Unravelling the contribution of nitrifying and methanotrophic bacteria to micropollutant co-metabolism in rapid sand filters

The presence of organic micropollutant (OMP) in groundwater threatens drinking water quality and public health. Rapid sand filter (RSF) rely on biofilms with nitrifying and methanotrophic bacteria to remove ammonia and methane during drinking water production. Previous research observed the partial removal of OMPs with active nitrification and methane oxidation due to co-metabolic conversion of OMPs. However, the contribution of indigenous nitrifying and methanotrophic communities from RSF has yet to be fully explored. Accordingly, experiments were carried out with biofilm-covered sand collected from field-scale RSF, to assess the removal of nine OMPs by nitrifying and methanotrophic bacteria. Results indicated that stimulating nitrification resulted in significantly more removal of caffeine, 2,4-dichlorophenoxyacetic acid and bentazone. Stimulating methanotrophic conditions enhanced the removal of caffeine, benzotriazole, 2,4-dichlorophenoxyacetic acid and bentazone. Microbial community analysis based on 16 S rRNA gene sequencing revealed Nitrosomonas and Nitrospira are the dominant genus in the community under nitrifying conditions. The three genera Methylobacter, Methylomonas and Methylotenera were enriched under methanotrophic conditions. This study highlights that nitrifying and methanotrophic bacteria play important roles during OMP removal in field RSF. Furthermore, results suggest that bioaugmentation with an enriched nitrifying and methanotrophic culture is a promising approach to improve OMP removal in RSF.

Acylase enzymes disrupting quorum sensing alter the transcriptome and phenotype of Pseudomonas aeruginosa, and the composition of bacterial biofilms from wastewater treatment plants

Biofilms represent an essential way of life and colonization of new environments for microorganisms. This feature is regulated by quorum sensing (QS), a microbial communication system based on autoinducer molecules, such as N-acyl-homoserine lactones (AHLs) in Gram negative bacteria. In artificial ecosystems, like Wastewater Treatment Plants (WWTPs), biofilm attachment in filtration membranes produces biofouling. In this environment, the microbial communities are mostly composed of Gram-negative phyla. Thus, we used two AHLs-degrading enzymes, obtained from Actinoplanes utahensis (namely AuAAC and AuAHLA) to determine the effects of degradation of QS signals in the biofilm formation, among other virulence factors, of a Pseudomonas aeruginosa strain isolated from a WWTP, assessing molecular mechanisms through transcriptomics. Besides, we studied the possible effects on community composition in biofilms from activated sludge samples. Although the studied enzymes only degraded the AHLs involved in one of the four QS systems of P. aeruginosa, these activities produced the deregulation of the complete QS network. In fact, AuAAC -the enzyme with higher catalytic efficiency- deregulated all the four QS systems. However, both enzymes reduced the biofilm formation and pyocyanin and protease production. The transcriptomic response of P. aeruginosa affected QS related genes, moreover, transcriptomic response to AuAAC affected mainly to QS related genes. Regarding community composition of biofilms, as expected, the abundance of Gram-negative phyla was significantly decreased after enzymatic treatment. These results support the potential use of such AHLs-degrading enzymes as a method to reduce biofilm formation in WWTP membranes and ameliorate bacterial virulence.

Relevance of Candidatus Nitrotoga for nitrite oxidation in technical nitrogen removal systems

Abstract

Many biotechnological applications deal with nitrification, one of the main steps of the global nitrogen cycle. The biological oxidation of ammonia to nitrite and further to nitrate is critical to avoid environmental damage and its functioning has to be retained even under adverse conditions. Bacteria performing the second reaction, oxidation of nitrite to nitrate, are fastidious microorganisms that are highly sensitive against disturbances. One important finding with relevance for nitrogen removal systems was the discovery of the mainly cold-adapted Cand. Nitrotoga, whose activity seems to be essential for the recovery of nitrite oxidation in wastewater treatment plants at low temperatures, e.g., during cold seasons. Several new strains of this genus have been recently described and ecophysiologically characterized including genome analyses. With increasing diversity, also mesophilic Cand. Nitrotoga representatives have been detected in activated sludge. This review summarizes the natural distribution and driving forces defining niche separation in artificial nitrification systems. Further critical aspects for the competition with Nitrospira and Nitrobacter are discussed. Knowledge about the physiological capacities and limits of Cand. Nitrotoga can help to define physico-chemical parameters for example in reactor systems that need to be run at low temperatures.

Key points

• Characterization of the psychrotolerant nitrite oxidizer Cand. Nitrotoga

• Comparison of the physiological features of Cand. Nitrotoga with those of other NOB

• Identification of beneficial environmental/operational parameters for proliferation

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-021-11487-5.

Characterization of the synergistic relationships between nitrification and microbial regrowth in the chloraminated drinking water supply system

Deterioration of water quality is commonly found in secondary water supply systems (SWSSs), especially the growth of microbes. To explore the metabolic mechanism for rapid microbial regrowth in SWSSs, a regrowth potential assessment, flow cytometry, and quantitative PCR were conducted. Metagenomic and 16S rRNA gene sequencing were performed to better understand the microbial communities and metabolism. It was found that the increased biomass in the SWSS was significantly higher than that in the drinking water distribution system (DWDS). Statistical analysis revealed that ammonia oxidation was the dominant driver of increased biomass in the SWSS. The abundances of ammonia oxidation bacteria, concentration of nitrogen species, and related enzymes demonstrated that ammonia oxidation in the SWSS was more vigorous than that in the DWDS. In the SWSS, the metabolism of the ammonia oxidation cluster was more vigorous, and ammonia-oxidizing bacteria (AOB) were the dominant nitrifying bacteria. Incomplete nitrification products were involved in the metabolism of heterotrophic bacteria and promoted the growth of heterotrophic bacteria in the SWSS. More attention should be given to controlling incomplete nitrification to improve tap water quality.

Performance and microbial ecology of a novel moving bed biofilm reactor process inoculated with heterotrophic nitrification-aerobic denitrification bacteria for high ammonia nitrogen wastewater treatment

To overcome long start-up time, poor ammonia tolerance and removal performance of traditional moving bed biofilm reactor (MBBR) inoculated with activated sludge for high-ammonia wastewater treatment, a novel MBBR based on heterotrophic nitrification-aerobic denitrification (HN-AD) was proposed. Start-up of MBBR was firstly performed via inoculated with HN-AD bacteria. Start-up time was shortened from 39 d to 15 d, NH₄⁺ tolerance was enhanced from 200 mg/L to 1000 mg/L, and TN removal was increased from 30.4% to 80.7%. The carrier types and NH₄⁺ concentration had significant effects on nitrogen removal and microbial ecology. When the NH₄⁺ concentration was increased to 900 mg/L in MBBR using polyvinyl alcohol gel as carrier, the TN removal, the abundance of HN-AD bacteria Acinetobacter, Pseudomonas and Paracoccus, which played a key role in TN removal and ammonia tolerance, and the abundance of genes related to nitrogen removal were much higher than those of MBBR using kaldness.

Use of Newly Designed Primers for Quantification of Complete Ammonia-Oxidizing (Comammox) Bacterial Clades and Strict Nitrite Oxidizers in the Genus Nitrospira

Complete ammonia-oxidizing (comammox) bacteria play key roles in environmental nitrogen cycling and all belong to the genus Nitrospira, which was originally believed to include only strict nitrite-oxidizing bacteria (sNOB). Thus, differential estimation of sNOB abundance from that of comammox Nitrospira has become problematic, since both contain nitrite oxidoreductase genes that serve as common targets for sNOB detection. Herein, we developed novel comammox Nitrospira clade A- and B-specific primer sets targeting the α-subunit of the ammonia monooxygenase gene (amoA) and a sNOB-specific primer set targeting the cyanase gene (cynS) for quantitative PCR (qPCR). The high coverage and specificity of these primers were checked by use of metagenome and metatranscriptome data sets. Efficient and specific amplification with these primers was demonstrated using various environmental samples. Using the newly designed primers, we successfully estimated the abundances of comammox Nitrospira and sNOB in samples from two chloramination-treated drinking water systems and found that, in most samples, comammox Nitrospira clade A was the dominant type of Nitrospira and also served as the primary ammonia oxidizer. Compared with other ammonia oxidizers, comammox Nitrospira had a higher abundance in process water samples in these two drinking water systems. We also demonstrated that sNOB can be readily misrepresented by an earlier method, calculated by subtracting the comammox Nitrospira abundance from the total Nitrospira abundance, especially when the comammox Nitrospira proportion is relatively high. The new primer sets were successfully applied to comammox Nitrospira and sNOB quantification, which may prove useful in understanding the roles of Nitrospira in nitrification in various ecosystems.IMPORTANCENitrospira is a dominant nitrite-oxidizing bacterium in many artificial and natural environments. The discovery of complete ammonia oxidizers in the genus Nitrospira prevents the use of previously identified primers targeting the Nitrospira 16S rRNA gene or nitrite oxidoreductase (nxr) gene for differential determination of strict nitrite-oxidizing bacteria (sNOB) in the genus Nitrospira and among comammox bacteria in this genus. We designed three novel primer sets that enabled quantification of comammox Nitrospira clades A and B and sNOB with high coverage, specificity, and accuracy in various environments. With the designed primer sets, sNOB and comammox Nitrospira were differentially estimated in drinking water systems, and we found that comammox clade A predominated over sNOB and other ammonia oxidizers in process water samples. Accurate quantification of comammox Nitrospira and sNOB by use of the newly designed primers will provide essential information for evaluating the contribution of Nitrospira to nitrification in various ecosystems.

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.

Metagenomics Unravels Differential Microbiome Composition and Metabolic Potential in Rapid Sand Filters Purifying Surface Water Versus Groundwater

Designed for retaining suspended particles, rapid sand filters (RSFs) are widely used in drinking water treatment. There is increasing evidence that microbial processes within RSFs contribute to the transformation and removal of organic carbon, nitrogen, and metal pollutants. Here, we linked microbial composition and functional profiles with the treatment performance of 12 different RSFs that significantly removed influent ammonium and manganese (Mn). Metagenomic analyses showed that chemoautotrophic or methanotrophic bacteria were prevalent in the groundwater filters, and chemoheterotrophic bacteria encoding more carbohydrate- and xenobiotic-metabolizing genes were more abundant in the surface water filters. Approximately 92% of ammonium was transformed into nitrate, with a critical contribution from comammox Nitrospira. The composition of comammox amoA differed between groundwater and surface water filters, with clade A dominating groundwater filters (78.0 ± 12.0%) and clade B dominating surface water filters (91.9 ± 8.9%). Further, we identified six bacterial genera encoding known Mn(II)-oxidizing genes in the RSFs, with Pseudomonas accounting for 71.1%. These Mn(II)-oxidizing bacteria might promote Mn(II) oxidation and thus increase the removal of influent Mn. Overall, our study gave a comprehensive investigation of microbiome in RSFs and highlighted the roles of comammox and Mn(II)-oxidizing bacteria in water purification.

Tuning up microbiome analysis to monitor WWTPs' biological reactors functioning

Wastewater treatment plants (WWTPs) are necessary to protect ecosystems quality and human health. Their function relies on the degradation of organic matter and nutrients from a water influent, prior to the effluent release into the environment. In this work we studied the bacterial community dynamics of a municipal WWTP with a membrane bioreactor through 16S rRNA gene sequencing. The main phyla identified in the wastewater were Proteobacteria, Bacteroidetes, Chloroflexi, Planctomycetes and Actinobacteria. The WWTP is located in Spain and, like other studied WWTP in temperate climate zones, the temperature played a major role in community assembly. Seasonal community succession is observed along the two years sampling period, in addition to a continual annual drift in the microbial populations. The core community of the WWTP bioreactor was also studied, where a small fraction of sequence variants constituted a large fraction of the total abundance. This core microbiome stability along the sampling period and the likewise dissimilarity patterns along the temperature gradient makes this feature a good candidate for a new process control in WWTPs.

Fast start-up strategies of MBBR for mariculture wastewater treatment

Moving bed biofilm reactor (MBBR) is widely used for ammonia removal in saline recirculating aquaculture systems but often faces a slow start-up problem. The aim of this study was to develop a strategy for the rapid start-up of MBBR treating synthetic mariculture wastewater. Changes in nitrification performance, biofilm characteristics and bacterial community were assessed in response to various start-up strategies: R1 as the control; R2 with step-decrease of inlet NH₄⁺-N; R3 with step-increase of inlet salinity; R4 added with particulate organic matter (POM) and R5 inoculated with nitrifying bacteria. Results show that nitrification was completed on day 63 for R3, 16-18 days faster than the other strategies. The highest protein (28.2 ± 5.1 mg/g·VS) and polysaccharide (59.4 ± 0.4 mg/g·VS) contents were observed in R3, likely linked to the faster biofilm formation. Fourier Transform infrared spectroscopy (FTIR) analysis confirmed the typical constituents of carbohydrates, proteins, lipids and DNA in biofilms. Moreover, along with the biofilm development in R3, the intensity of the peak at 1400 cm^-1 (assigned to specific amides) decreased. Pyrosequencing of 16s rRNA revealed that Gammaproteobacteria was the predominating microbial community at class level (35.6%) in R3. qPCR analysis further verified the significantly higher gene copies of amoA (1.57 × 10⁴ copies/μL) and nxrB (5.51 × 10³ copies/μL) in R3. Results obtained make the elevated salinity strategy a promising alternative for the rapid nitrification start-up of saline wastewater.

Looking at the Origin: Some Insights into the General and Fermentative Microbiota of Vineyard Soils

In winemaking processes, there is a current tendency to develop spontaneous fermentations taking advantage of the metabolic diversity of derived from the great microbial diversity present in grape musts. This enological practice enhances wine complexity, but undesirable consequences or deviations could appear on wine quality. Soil is a reservoir of important microorganisms for different beneficial processes, especially for plant nutrition, but it is also the origin of many of the phytopathogenic microorganisms that affect vines. In this study, a meta-taxonomic analysis of the microbial communities inhabiting vineyard soils was realized. A significant impact of the soil type and climate aspects (seasonal patterns) was observed in terms of alpha and beta bacterial diversity, but fungal populations appeared as more stable communities in vineyard soils, especially in terms of alpha diversity. Focusing on the presence and abundance of wine-related microorganisms present in the studied soils, some seasonal and soil-dependent patterns were observed. The Lactobacillaceae family, containing species responsible for the malolactic fermentation, was only present in non-calcareous soils samples and during the summer season. The study of wine-related fungi indicated that the Debaryomycetaceae family dominates the winter yeast population, whereas the Saccharomycetaceae family, containing the most important fermentative yeast species for winemaking, was detected as dominant in summer.

Enhanced diuron remediation by microorganism-immobilized silkworm excrement composites and their impact on soil microbial communities

In response to the potential threats stemming from the constantly increasing consumption of herbicides, bioremediation offers a beneficial technology for reducing the widespread herbicide contamination. In order to facilitate the in-situ degradation of diuron, Arthrobacter globiformis D47 is captured onto a biocompatible carrier to assemble the microorganism-immobilized silkworm excrement (MSE) composites. By characterization, bacterial cells are intensively entrapped in/onto the carriers, showing high survival and stable catalytic degradation of target pollutants. Meanwhile, MES composites display excellent adaptiveness and feasibility under different conditions, and the average half-life of diuron is shortened to 7.69 d in sugarcane field where diuron is regularly sprayed for weed management. Importantly, we assess that the use of MSE may generally boost the overall xenobiotic-degrading ability, likely due to the slight alternation of the diversity and composition of soil microbial communities. Taking together, the presented MSE provides an attractive in situ approach for the efficient diuron removal as well as for the more feasible utilization of various pollutant-degrading microorganisms.

Low Temperature and Neutral pH Define "Candidatus Nitrotoga sp." as a Competitive Nitrite Oxidizer in Coculture with Nitrospira defluvii

Nitrification is an essential process for N removal in activated sludge to avoid toxicity of ammonium and nitrite. Besides Nitrospira, "Candidatus Nitrotoga" has been identified as a key nitrite-oxidizing bacterium (NOB) performing the second step of nitrification, nitrite oxidation to nitrate, in wastewater treatment plants (WWTPs). However, the driving forces for the dominance of Nitrotoga in certain plants have often remained unclear and could not be explained solely by temperature effects. In this study, we characterized the physiology of the ammonium-dependent Nitrotoga sp. BS with regard to temperature and pH variations and evaluated its competitiveness against Nitrospira defluvii Both NOB originated from the same WWTP and shared a comparable pH optimum of 7.3. Based on these results, coculturing experiments with these NOB were performed in batch reactors operated at either 17°C or 22°C to compare their abundances under optimal (pH 7.4) or suboptimal (pH 6.4) conditions using 1 mM nitrite. As revealed by quantitative PCR (qPCR), fluorescence in situ hybridization (FISH), and 16S amplicon sequencing, Nitrotoga sp. BS was clearly favored by its optimal growth parameters and dominated over Ns. defluvii at pH 7.4 and 17°C, whereas a pH of 6.4 was more selective for Ns. defluvii Our synthetic communities revealed that niche differentiation of NOB is influenced by a complex interaction of environmental parameters and has to be evaluated for single species.IMPORTANCE "Ca. Nitrotoga" is a NOB of high environmental relevance, but physiological data exist for only a few representatives. Initially, it was detected in specialized niches of low temperature and low nitrite concentrations, but later on, its ubiquitous distribution revealed its critical role for N removal in engineered systems like WWTPs. In this study, we analyzed the competition between Nitrotoga and Nitrospira in bioreactors and identified conditions where the K strategist Ns. defluvii was almost replaced by Nitrotoga sp. BS. We show that the pH value is an important factor that regulates the composition of the nitrite-oxidizing enrichment with a dominance of Nitrotoga sp. BS versus Ns. defluvii at a neutral pH of 7.4 in combination with a temperature of 17°C. The physiological diversity of novel Nitrotoga cultures improves our knowledge about niche differentiation of NOB with regard to functional nitrification under suboptimal conditions.

Quantitative and qualitative evaluation of the impact of the G2 enhancer, bead sizes and lysing tubes on the bacterial community composition during DNA extraction from recalcitrant soil core samples based on community sequencing and qPCR

Soil DNA extraction encounters numerous challenges that can affect both yield and purity of the recovered DNA. Clay particles lead to reduced DNA extraction efficiency, and PCR inhibitors from the soil matrix can negatively affect downstream analyses when applying DNA sequencing. Further, these effects impede molecular analysis of bacterial community compositions in lower biomass samples, as often observed in deeper soil layers. Many studies avoid these complications by using indirect DNA extraction with prior separation of the cells from the matrix, but such methods introduce other biases that influence the resulting microbial community composition. To address these issues, a direct DNA extraction method was applied in combination with the use of a commercial product, the G2 DNA/RNA Enhancer, marketed as being capable of improving the amount of DNA recovered after the lysis step. The results showed that application of G2 increased DNA yields from the studied clayey soils from layers from 1.00 to 2.20 m. Importantly, the use of G2 did not introduce bias, as it did not result in any significant differences in the biodiversity of the bacterial community measured in terms of alpha and beta diversity and taxonomical composition. Finally, this study considered a set of customised lysing tubes for evaluating possible influences on the DNA yield. Tubes customization included different bead sizes and amounts, along with lysing tubes coming from two suppliers. Results showed that the lysing tubes with mixed beads allowed greater DNA recovery compared to the use of either 0.1 or 1.4 mm beads, irrespective of the tube supplier. These outcomes may help to improve commercial products in DNA/RNA extraction kits, besides raising awareness about the optimal choice of additives, offering opportunities for acquiring a better understanding of topics such as vertical microbial characterisation and environmental DNA recovery in low biomass samples.

Stochastic processes govern invasion success in microbial communities when the invader is phylogenetically close to resident bacteria

Despite recent efforts in identifying the determinants of invasion in microbial communities, experimental observations across different ecosystems are inconclusive. While relationships between resident community diversity and invasion success are often noted, community diversity says little about community assembly processes. Community assembly processes may provide a more inclusive framework to explain-and potentially prevent or facilitate-invasion. Here we let replicate nitrite-oxidizing bacterial guilds assemble under different conditions from a natural source community and study their compositional patterns to infer the relative importance of the assembly processes. Then, an invader strain from that same guild was introduced at one of three propagule pressures. We found no significant correlation between community diversity and invasion success. Instead, we observed that the effect of selection on invasion success was surpassed by the effect of drift, as inferred from the substantial influence of propagule pressure on invasion success. This dominance of drift can probably be generalized to other invasion cases with high phylogenetic similarity between invader and resident community members. In these situations, our results suggest that attempting to modulate the invasibility of a community by altering its diversity is futile because stochastic processes determine the invasion outcome. Increasing or reducing propagule pressure is then deemed the most efficient avenue to enhance or limit invasion success.

Dynamics and Functional Potential of Stormwater Microorganisms Colonizing Sand Filters

Stormwater management is increasingly relying on engineered infiltration systems (EIS) to reduce the volume and improve the quality of managed stormwater. Yet, EIS in the field will be colonized by a diverse array of environmental microorganisms that change the physiochemical properties of the EIS and provide a habitat for microorganisms with harmful or beneficial qualities. Understanding factors influencing the composition and stability of microbial communities could open up strategies for more efficient management of stormwater. Here, we analyzed the potential pathogenic and metabolic capabilities of stormwater microorganisms colonizing idealized EIS (i.e., sand columns) under laboratory conditions over time. The diversity of microbial communities was analyzed using 16S rRNA gene sequencing, and potential pathogens and denitrifying microbes were identified from taxonomic match to known species. Denitrification potential as determined by nosZ abundance was also assessed with quantitative polymerase chain reaction PCR. Our findings demonstrate that replicate microbial communities colonizing sand columns change in a similar way over time, distinct from control columns and the source community. Potential pathogens were initially more abundant on the columns than in the stormwater but returned to background levels by 24 days after inoculation. The conditions within sand columns select for potential denitrifying microorganisms, some of which were also potential pathogens. These results demonstrate that a diverse suite of stormwater microorganisms colonize sand filters, including a transient population of potential pathogens and denitrifiers. Manipulating the inoculating microbial community of EIS could prove an effective mechanism for changing both potential pathogens and denitrifying bacteria.