Article

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

Authors:
  • Harbin Institute of Technology at Shenzhen
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Abstract

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 treatment performance of 12 different RSFs that significantly removed influent ammonium and manganese (Mn). Metagenomic analyses showed 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 the Mn(II) oxidation and thus increase the removal of influent Mn. Overall, our study gave a comprehensive investigation on microbiome in RSFs and highlighted the roles of comammox and Mn(II)-oxidizing bacteria in water purification.

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... Rapid sand filter (RSF) is a widely applied technology for treatment of groundwater at DWTPs, where different pollutants can be removed by an interplay of biological and chemical processes. Organic and inorganic particles are retained in a sand bed (Teunissen et al., 2008;Craft, 1966), while ammonia and methane are oxidized by nitrifying and methanotrophic bacteria (Gülay et al., 2016;Hu et al., 2020;Papadopoulou et al., 2019). In addition, Fe(II), Mn(II) and As(III) can be removed by biological or/and chemical oxidation (van Beek et al., 2012;Vries et al., 2017;Gude et al., 2016). ...
... Consistent with previous research (Poghosyan et al., 2020), the genera Nitrosomonas and Nitrospira were widely identified in the field RSF. In addition, Hu et al. (2020) found that Nitrospira was the genera carrying the comammox amoA genes, which accounts for 64.0% of amoA genes in average in RSF, emphasizing the important role of Nitrospira in microbial ammonia oxidation in RSF Fig. 5. Bacterial density measured by qPCR under different microcosm conditions. a) The abundance of nitrifying bacteria was assessed by quantification of amoA gene copies; b) the abundance of methanotrophic bacteria was assessed by quantification of pmoA gene copies. ...
... **p-value is 0.001-001; ***p-value is 0.0001-0001; ****p-value is 0.00001-00001. (Poghosyan et al., 2020;Hu et al., 2020). In addition, previous investigations reported that the Nitrosomonas europaea was able to degrade steroidal estrogens, triclosan and bisphenol A (Shi et al., 2004;Roh et al., 2009), suggesting that the nitrifying bacteria found in this study were capable of OMP biodegradation. ...
Article
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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.
... A relative abundance of nxrB genes of NOB was also detected between 2 and 4 % in selected filters (Fig. 5). The presence of AOB (Nitrosomonas) and NOB (Nitrospira) was commonly found in other full-scale water treatment SFs (Albers et al., 2015;Hu et al., 2020;Palomo et al., 2016;Poghosyan et al., 2020), but the remarkable occurrence of AOA is a unique finding for the household SFs of our study. Quantification of functional genes of AOA and NOB along the filter depths suggested their widespread abundance along the sand filters, even in deeper sand layer (below 15 cm) (Fig. S9) where we observed a depletion of AOB. ...
... The results indicated that each factor of Fe, Mn, As, and NH 4 + inflow concentrations can influence microbial communities in sand filters between 15 and 20 % (Fig. 6B, Table S3). This finding is also in line with Hu et al., 2020, which revealed that Fe, Mn, NH 4 + and PO 4 3− were strongly influencing the microbial communtiy variation in rapid sand filters. We noticed that in SFs B3 and C17, fed by groundwater enriched with Fe(II) (Fe concentration of 21 and 30 mg L −1 respectively) and depleted in As(III) (As concentrations of 3.3 and 16.97 μg L −1 , respectively), Sideroxydans was present as the most dominant potential Fe(II)-oxidizer, with a relative abundance of up to 8.8 and 13.2 %, respectively (Fig. 4A). ...
Article
Household sand filters (SFs) are widely applied to remove iron (Fe), manganese (Mn), arsenic (As), and ammonium (NH4⁺) from groundwater in the Red River delta, Vietnam. Processes in the filters probably include a combination of biotic and abiotic reactions. However, there is limited information on the microbial communities treating varied groundwater compositions and on whether biological oxidation of Fe(II), Mn(II), As(III), and NH4⁺ contributes to the overall performance of SFs. We therefore analyzed the removal efficiencies, as well as the microbial communities and their potential activities, of SFs fed by groundwater with varying compositions from low (3.3 μg L⁻¹) to high (600 μg L⁻¹) As concentrations. The results revealed that Fe(II)-, Mn(II)-, NH4⁺-, and NO2⁻-oxidizing microorganisms were prevalent and contributed to the performance of SFs. Additionally, groundwater composition was responsible for the differences among the present microbial communities. We found i) microaerophilic Fe(II) oxidation by Sideroxydans in all SFs, with the highest abundance in SFs fed by low-As and high-Fe groundwater, ii) Hyphomicropbiaceae as the main Mn(II)-oxidizers in all SFs, iii) As sequestration on formed Fe and Mn (oxyhydr)oxide minerals, iv) nitrification by ammonium-oxidizing archaea (AOA) followed by nitrite-oxidizing bacteria (NOB), and v) unexpectedly, the presence of a substantial amount of methane monooxygenase genes (pmoA), suggesting microbial methane oxidation taking place in SFs. Overall, our study revealed diverse microbial communities in SFs used for purifying arsenic-contaminated groundwater and our data indicate an important contribution of microbial activities to the key functional processes in SFs.
... 25 In the 13 C-MMI−SIP microcosms, some cells exhibited remarkable red shifts from 1001 to 967 cm −1 and from 1660 to 1624 cm −1 (Raman shift extents of 34 and 36 cm −1 , respectively), consistent with the findings in previous studies. 25,47 Therefore, these cells were the active PHE degraders incorporating 13 C-PHE. ...
... These two vibrational bands have previously been used as fingerprint biomarkers to identify the microcosms incorporated with 13 Clabeled compounds, such as 13 C-glucose and 13 C-phenylalanine. 25,47,51 Accordingly, our MMI−SIP−RACS approach overcomes the limitations of each technology; it efficiently identifies the active PHE degraders, linking their identities and functions at the single-cell level. ...
... Several manganese oxidizing bacteria (MnOB) have been identified on filter materials and in the water phase, including Pseudomonas sp., Streptomyces sp., and Leptothrix sp. (Bruins et al., 2014;Hu et al., 2020). The Mn and Fe oxides (MnOx and FeOx) formed and retained in RSF are able to remove OMPs by adsorption (Forrez et al., 2011) or by catalyzing chemical oxidation (Jian et al., 2019;Manoli et al., 2017) (Figure 2). ...
... In raw groundwater, the concentrations of ammonium and methane are at hundreds mg/L, even several mg/L (Papadopoulou et al., 2019;Tatari et al., 2013). These compounds are typically removed by a combination of aeration and removal by autotrophic nitrifying and methane oxidizing bacteria (Hu et al., 2020;Papadopoulou et al., 2019). In addition to ammonium and methane removal, these autotrophic organisms also show OMPs biotransformation capacity (Batt et al., 2006;Papadopoulou et al., 2019). ...
Article
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A cost-effective approach for efficient organic micropollutants (OMPs) removal is to optimize existing infrastructure at drinking water treatment plants. A promising option is rapid sand filtration (RSF), as OMPs removal has been observed in this treatment technology. However, the mechanisms and pathways involved are not fully understood and strategies to optimize removal have yet to be thoroughly explored. Therefore, this article firstly described basic RSF functions that can support OMPs removal. OMPs can be removed by chemical and biological Mn/Fe oxides or degraded co-metabolically by ammonia oxidizing bacteria and methane oxidizing bacteria. In addition, heterotrophic bacteria can metabolically transform OMPs and their transformation products. Then, we reviewed current literatures described OMPs removal in RSF, showing biodegradation can contribute significantly to OMPs removal. Thereafter, we presented strategies to improve OMPs biodegradation, including bioaugmentation, optimizing hydraulic conditions by adjusting contact time and backwashing intensity, and adding biocarriers to retain biomass during rapid flow rates. Finally, we provided recommendations for further research towards optimizing and maintaining OMPs removal in RSF for safe drinking water production. This review therefore gives a critical evaluation of RSF-based technologies for OMPs removal from drinking water and provides recommendations for further improving OMPs removal in RSF.
... Rapid sand filters (RSF), widely used to produce drinking water from groundwater, are useful model systems. They are characterized by stable conditions, including active growth, primarily driven by the oxidation of ammonia, methane, and other inorganic compounds present at low concentrations in the influent water, large populations (10 9 to 10 10 cells/g), significant mixing (due to backwashing), continuous but limited immigration from prokaryotes in the influent water, and no dispersal between separate sand filters (resulting in allopatric populations) (5)(6)(7)(8). In addition, the microbial communities inhabiting these systems, which are usually stable across time (9), have been broadly described, showing a general dominance of complete ammonia oxidizers (comammox) (6,10,11). ...
Article
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Microbial species interact with each other and their environment (ecological processes) and undergo changes in their genomic repertoire over time (evolutionary processes). How these two classes of processes interact is largely unknown, especially for complex communities, as most studies of microbial evolutionary dynamics consider single species in isolation or a few interacting species in simplified experimental systems.
... Results show that in RSF and BAC samples, some bacterial species were able to oxide sulfide and ammonia (Hu et al., 2019;Abu Hasan et al., 2020;Poghosyan et al., 2020) and some bacteria could utilize organic compounds (e.g., lactate, glutamate, citrate, carbohydrates) as energy and carbon sources (Cermakova et al., 2017;Korotta-Gamage and Sathasivan, 2017;Greenstein et al., 2018b;Hu et al., 2020). Thus, these bacteria might be also responsible to the AOC removal. ...
Article
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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.
... The α diversity of bacterial communities has been investigated in lake ecosystems (Hu et al. 2020), river ecosystems (Luo et al. 2020), and marine ecosystems (Hoshino et al. 2020). Some aquaculture ecosystem bacterial communities have similar α diversity values ). ...
Article
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The integrated multitrophic aquaculture (IMTA) pond represents a unique ecosystem in which various species of aquatic organisms with different trophic levels are co-cultured together, achieving ecological and economic effects by using ecological principles. This study was designed to investigate the composition pattern of the bacterial communities and potential drivers in IMTA ponds of Penaeus japonicus-Portunus trituberculatus (SC) and P. japonicus-P. trituberculatus-Sinonovacula constricta (SCC). SC and SCC sediments were collected in July, October, and December and used to sequence the 16S rRNA gene and analyze physical and chemical indicators. The α diversity of the bacterial community was not significantly different between the sediments of SC and SCC. The dominant phyla of bacterial communities in sediments of SC and SCC shared a large number of common members. Bacterial members involved in denitrification were biomarkers in the sediment of SC, while biomarkers involved in nitrification, assimilatory nitrate reduction, and nitrogen fixation were found in the sediment of SCC. The β diversity was significantly different between SC and SCC. The bacterial community composition dissimilarity was significantly correlated with environmental factors, which were driven by pH, NH4⁺ concentration in the sediment (S_ NH4⁺), and NO2⁻ concentration in the sediment (S_ NO2⁻) in July, and pH was the most important explanatory variable for the community composition dissimilarity (P < 0.05). The dissimilarity was driven by oxidation–reduction potential (ORP) and NO2⁻ concentration in the pore water of sediments (P_ NO2⁻) in October, and P_ NO2⁻ was the most important variable (P < 0.05). The S_ NH4⁺, S_ NO2⁻, and pH exhibited interactions for the dissimilarity in December, and the S_ NH4⁺ was the most important variable (P < 0.05). Additionally, the pH was significantly correlated with the S_ NH4⁺ and S. constricta densities (P < 0.05). These results indicated that the co-culture of S. constricta in shrimp-crab ponds may cause specific composition patterns of bacterial communities by influencing pH and inorganic nitrogen sources, resulting in an increase in bacterial mineralization and nutrient catabolism and a shift in the nitrogen cycling processes from denitrification to nitrification, assimilatory nitrate reduction, and nitrogen fixation in the sediment. Graphical abstract
... A recent study found no significant correlations between Mn(II)-oxidizing gene abundance in rapid sand filters and the influent or filter Mn(II) content. 78 It should be noted that the sand filters investigated received feed water from different water sources that could have various bacterial species and water quality, probably making some other factors, rather than the Mn(II) concentration, play a dominant role in shaping the bacterial communities in the filters. In the present study, the Mn(II) concentration difference (0 and 100 μg/L) was the main difference between pipe systems. ...
... mg-N/L and ~0.01-0.035 mg-N/L, respectively, clade B comammox Nitrospira dominated the nitrifying microbial populations Hu et al., 2020). A recent study also reported that nitrification activity in forest and paddy soils when subjected to ammonium limitation is associated with clade B rather than clade A comammox Nitrospira (Wang et al., 2019). ...
Article
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Elevated concentrations of ammonium and methane in groundwater are often associated with microbiological, chemical and sanitary problems during drinking water production and distribution. To avoid their accumulation, raw water in the Netherlands and many other countries is purified by sand filtration. These drinking water filtration systems select for microbial communities that mediate the biodegradation of organic and inorganic compounds. In this study, the top layers and wall biofilm of a Dutch drinking water treatment plant (DWTP) were sampled from the filtration units of the plant over three years. We used high-throughput sequencing in combination with differential coverage and sequence composition-based binning to recover 56 near-complete metagenome-assembled genomes (MAGs) with an estimated completion of ≥70% and with ≤10% redundancy. These MAGs were used to characterize the microbial communities involved in the conversion of ammonia and methane. The methanotrophic microbial communities colonizing the wall biofilm (WB) and the granular material of the primary rapid sand filter (P-RSF) were dominated by members of the Methylococcaceae and Methylophilaceae. The abundance of these bacteria drastically decreased in the secondary rapid sand filter (S-RSF) samples. In all samples, complete ammonia-oxidizing (comammox) Nitrospira were the most abundant nitrifying guild. Clade A comammox Nitrospira dominated the P-RSF, while clade B was most abundant in WB and S-RSF, where ammonium concentrations were much lower. In conclusion, the knowledge obtained in this study contributes to understanding the role of microorganisms in the removal of carbon and nitrogen compounds during drinking water production. We furthermore found that drinking water treatment plants represent valuable model systems to study microbial community function and interaction.
... Given the high abundance, ubiquity, and important functions of microbes in aquaculture ecosystems, it is important to determine the main drivers of microbial patterns in these ecosystems. Studies have shown that the distribution patterns of microbial structures and functions in shrimp ponds are governed by one or multiple factors [6,7]. Some studies have indicated that temperature, pH, and N, or their interactions, mainly affect the microbial structure and function in some shrimp farming models [8,9], which hint at the optimal conditions for microbial structure and function and the ecological lifestyles of specific taxonomic communities in shrimp ponds. ...
Article
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The microbial structure and metabolic potential, particularly with regard to nitrogen (N) cycling, in integrated multitrophic aquaculture (IMTA) ponds with shrimp remain unclear. In this study, an analysis of microbial community taxonomic diversity and a metagenomic analysis of N-related genes were performed in a shrimp-crab pond (Penaeus japonicus-Portunus trituberculatus, SC) and a shrimp-crab-clam pond (P. japonicus-P. trituberculatus-Sinonovacula constricta, SCC) to evaluate microbial structure and N transformation capacities in these two shrimp IMTA ponds. The composition of the microbial communities was similar between SC and SCC, but the water and sediments shared few common members in either pond. The relative abundances of N cycling genes were significantly higher in sediment than in water in both SC and SCC, except for assimilatory nitrate reduction genes. The main drivers of the differences in the relative abundances of N cycling genes in SC and SCC were salinity and pH in water and the NO2- and NH4+ contents of pore water in sediment. These results indicate that the coculture of S. constricta in a shrimp-crab pond may result in decreased N cycling in sediment. The reduced N flux in the shrimp IMTA ponds primarily originates within the sediment, except for assimilatory nitrate reduction.
... SFs are mainly responsible for removing ammonia from drinking water source (Lee et al. 2014). While nitri cation is a simple but effective biological process to remove the ammonia in SFs (Hu et al. 2020b). To the best of our knowledge, nitri cation is traditionally considered to be a two-step process, consisting of ammonia oxidation and nitrite oxidation. ...
Preprint
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Sand filter (SFs) are common treatment processes for nitrogen pollutants removal in drinking water treatment plants (DWTPs). However, the mechanisms on the nitrogen-cycling role of SFs are still unclear. In this study, 16S rRNA gene amplicon sequencing was used to characterise the diversity and composition of the bacterial community in SFs from DWTPs. Additionally, metagenomics approach was used to determine the functional microorganisms involved in nitrogen cycle in SFs. Our results showed that Proteobacteria, Acidobacteria, Nitrospirae, and Chloroflexi dominated in SFs. Subsequently, 85 high-quality metagenome-assembled genomes (MAGs) were retrieved from metagenome datasets of selected SFs involving nitrification, assimilatory nitrogen reduction, and denitrification processes. Read mapping to reference genomes of Nitrospira and the phylogenetic tree of the ammonia monooxygenase subunit A gene, amoA, suggested that Nitrospira is abundantly found in SFs. Furthermore, according to their genetic content, a nitrogen metabolic model in SFs was proposed using representative MAGs and pure culture isolates. Quantitative real-time polymerase chain reaction (PCR) showed that ammonia-oxidising bacteria (AOB) and archaea (AOA), and complete ammonia oxidisers (comammox) were ubiquitous in the SFs, with the abundance of comammox being higher than that of AOA and AOB. Moreover, we identified a bacterial strain with a high NO3-N removal rate as Pseudomonas sp., which could be applied in the bioremediation of micro-polluted drinking water sources. Our study provides insights into functional nitrogen-metabolising microbes in SFs of DWTPs.
... The overall taxonomy accounts for 17 ASVs assigned to Archaea while the remaining 1239 were assigned to Bacteria. Despite some differences in relative abundance the community is overall conserved in the dataset and mostly composed by Aminobacter, Comamonadaceae, Pseudomonas, Zooglea, Curvibacter, Gallionella, Arthrobacter, and Sediminibacterium, which are commonly found in waterworks sand filters (Albers et al., 2015a;Ellegaard-Jensen et al., 2020;Gülay et al., 2018;Hu et al., 2020). The major visible difference is due to the depletion of Aminobacter from Nevtraco after Day 3 (Beginning in Fig. 4c). ...
Article
Groundwater contamination by recalcitrant organic micropollutants such as pesticide residues poses a great threat to the quality of drinking water. One way to remediate drinking water containing micropollutants is to bioaugment with specific pollutant degrading bacteria. Previous attempts to augment sand filters with the 2,6-dichlorobenzamide (BAM) degrading bacterium Aminobacter niigataensis MSH1 to remediate BAM-polluted drinking water initially worked well, but the efficiency rapidly decreased due to loss of degrader bacteria. Here, we use pilot-scale augmented sand filters to treat retentate of reverse osmosis treatment, thus increasing residence time in the biofilters and potentially nutrient availability. In a first pilot-scale experiment, BAM and most of the measured nutrients were concentrated 5-10 times in the retentate. This did not adversely affect the abundances of inoculated bacteria and the general prokaryotic community of the sand filter presented only minor differences. On the other hand, the high degradation activity was not prolonged compared to the filter receiving non-concentrated water at the same residence time. Using laboratory columns, it was shown that efficient BAM degradation could be achieved for >100 days by increasing the residence time in the sand filter. A slower flow may have practical implications for the treatment of large volumes of water, however this can be circumvented when treating only the retentate water equalling 10-15% of the volume of inlet water. We therefore conducted a second pilot-scale experiment with two inoculated sand filters receiving membrane retentate operated with different residence times (22 versus 133 minutes) for 65 days. While the number of MSH1 in the biofilters was not affected, the effect on degradation was significant. In the filter with short residence time, BAM degradation decreased from 86% to a stable level of 10-30% degradation within the first two weeks. The filter with the long residence time initially showed >97% BAM degradation, which only slightly decreased with time (88% at day 65). Our study demonstrates the advantage of combining membrane filtration with bioaugmented filters in cases where flow rate is of high importance.
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Microbial life on Earth commonly occurs in diverse and complex communities where species interact, and their genomic repertoires evolve over time. Our understanding of species interaction and evolution has increased during last decades, but most studies of evolutionary dynamics are based on single species in isolation or experimental systems composed of few interacting species. Here, we use the microbial ecosystem found in groundwater-fed sand filters as a model to avoid this limitation. In these systems, diverse microbial communities experience relatively stable conditions, and the coupling between chemical and biological processes is generally well defined. Metagenomic analysis of 12 sand filters revealed systematic co-occurrence of at least five comammox Nitrospira species, favoured by low ammonium concentrations. Nitrospira species showed intra-population sequence diversity, although possible clonal expansion was detected in few abundant local comammox populations. Nitrospira populations were separated by gene flow boundaries, suggesting natural and cohesive populations. They showed low homologous recombination and strong purifying selection, the latest process being especially strong in genes essential in energy metabolism. Positive selection was detected on genes related to resistance to foreign DNA and phages. Additionally, we analysed evolutionary processes in populations from different habitats. Interestingly, our results suggest that in comammox Nitrospira these processes are not an intrinsic feature but greatly vary depending on the habitat they inhabit. Compared to other habitats, groundwater fed sand filters impose strong purifying selection and low recombination. Together, this study improves understanding of interactions and evolution of species in the wild, and sheds light on the environmental dependency of evolutionary processes.
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Phragmites reeds are widely used in constructed wetlands (CWs) for treating wastewater. The enrichment of microorganisms and Fe/Mn plaque in Phragmites rhizospheres largely contributes to pollutant removal. However, their interactions and potential synergistic roles in water purification are poorly understood. To address the issue, we first compared the microbial community traits in the Phragmites rhizosphere and adjacent bulk soil in six long-term operated CWs. Results showed that enriched microbes and functional genes in the Phragmites rhizosphere were largely involved in Mn oxidation, resulting in a two to three times enrichment of Mn oxides in the rhizosphere. In turn, the enriched Mn oxides played significant roles in driving microbial community composition and function. To further understand the biological manganese oxidation in the rhizosphere, we identified Mn-oxidizing bacteria using genome-centric analysis and found that 92% of identified Mn-oxidizing bacteria potentially participated in nitrogen cycling. We then conducted relationships between Mn-oxidizing genes and different nitrogen cycling genes and found Mn-oxidizing gene abundance was significantly correlated with ammonia oxidation gene amoA (R = 0.65). Remarkably, complete ammonia oxidation (comammox) Nitrospira, accounting for 39.11% of ammonia oxidizers, also positively correlated with Mn-oxidizing microbes. Based on the above observations, we inferred that the use of Mn oxides as a substrate in CWs may enhance ammonia oxidation. To apply this to actual engineering, we explored treatment performance in a pilot-scale Mn-amending CW. As expected, ammonia removal capacity improved by 23.34%, on average, in the Mn-amending CW. In addition, the abundance of amoA genes increased significantly in the Mn-amending CW, indicating improved biological processes rather than chemical reactions.
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The discovery of a complete ammonia oxidizer (comammox Nitrospira) challenged the traditional theory of two step nitrification. Comammox Nitrospira co-occurred and competed with traditional ammonia oxidizers in many habitats. However, the ubiquitous existence and high abundance of comammox Nitrospira in drinking-water treatment plants (DWTPs) suggested that this habitat could lead to niche partitioning among ammonia oxidizers. Thus, revealing the potential mechanisms could explain where and how comammox Nitrospira dominated ammonia oxidation. In this study, investigations of in situ DWTPs and ex situ bioreactors were combined to reveal the mechanisms. Results indicated that comammox Nitrospira was the most abundant (79%–97%) and most active (66%–86%) ammonia oxidizer in attached growth tanks of DWTPs, which was 1.3–1.7 times higher than that in the suspended growth system. Furthermore, to confirm whether attached growth was the key to the dominance of comammox Nitrospira, two bioreactors, with quartz sand and hollow sphere as fillers (fillers used in DWTPs), were operated for 390 days. Results showed that comammox Nitrospira was the primary contributor (52.5%–90.4%) to ammonia oxidation in both reactors. The combination of network analysis and genome bins showed that comammox Nitrospira could create a two-way physiological feeding by exchanging self-produced cobalamin with amino acids from co-occurrent partners. Thus, comammox Nitrospira would dominate ammonia oxidation in an attached growth system. Based on its greater adaptability to low substrate concentrations, comammox Nitrospira may be the core of a new bioprocess and play an important role in drinking water treatment.
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The co-existence of volatile chlorinated hydrocarbons (VCHs) and nitrate pollution in groundwater is prominent, but how nitrate exposure affects weak-electrical stimulated bio-dechlorination activity of VCH is largely unknown. Here, by establishing weak-electrical stimulated trichloroethylene (TCE) dechlorination systems, the influence on TCE dechlorination by exposure to the different concentrations (25–100 mg L⁻¹) of nitrate was investigated. The existence of nitrate in general decreased TCE dechlorination efficiency to varying degrees, and the higher nitrate concentration, the stronger the inhibitory effects, verified by the gradually decreased transcription levels of tceA. Although the TCE dechlorination kinetic rate constant decreased by 36% the most, under all nitrate concentration ranges, TCE could be completely removed within 32 h and no difference in generated metabolites was found, revealing the well-maintained dechlorination activity. This was due to the quickly enriched bio-denitrification activity, which removed nitrate completely within 9 h, and thus relieved the inhibition on TCE dechlorination. The obvious bacterial community structure succession was also observed, from dominating with dechlorination genera (e.g., Acetobacterium, Eubacterium) to dominating with both dechlorination and denitrification genera (e.g., Acidovorax and Brachymonas). The study proposed the great potential for the in situ simultaneous denitrification and dehalogenation in groundwater contaminated with both nitrate and VCHs.
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Granular activated carbon (GAC) filtration impacts pathogen colonization and bacterial communities in drinking water. However, the effects of ozone and heterogeneous Fenton oxidation on microbial community composition, in particular opportunistic pathogens (OPs), and their metabolic potential in biofilms and effluents from GAC filtration are not fully understood. The results of our pilot-scale test indicated that Fenton-GAC filtration removed more dissolved organic carbon (DOC, 1.25 mg/L) than ozone-GAC filtration (0.98 mg/L). Excitation-emission matrix (EEM) results showed that Fenton-GAC removed more tyrosine-like proteins and fulvic acid-like materials, while ozone-GAC removed more humic acid-like compounds and tryptophan-like proteins. Illumina HiSeq analysis indicated that Curvibacter and Hydrogenophaga dominated in the Fenton-GAC biofilm, while Bradyrhizobium, Aquabacterium and Limnobacter were predominant in the ozone-GAC biofilm. Functional prediction suggested that the microbial functional gene related to glyoxylate and dicarboxylate metabolism (the pathway for carbohydrate metabolism) was higher in the Fenton-GAC biofilm, resulting in higher contents of protein in extracellular polymeric substances (EPS) in the Fenton-GAC biofilm. Therefore, there were fewer bacteria that detached from the biofilm into the water during the Fenton-GAC filtration process. The lower EPS content in the effluents from Fenton-GAC resulted in bacteria, including OPs, being easier to remove by chlorine. However, ozone oxidation removed more bacteria, including different OPs, than Fenton oxidation, which contributed to fewer bacteria and OPs in the effluents from ozone-GAC. Overall, our results provide a Fenton-GAC treatment process to remove DOC and control OPs in drinking water systems, the cost of which was comparable to that of ozone-GAC.
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Background: The study of microbiomes using whole-metagenome shotgun sequencing enables the analysis of uncultivated microbial populations that may have important roles in their environments. Extracting individual draft genomes (bins) facilitates metagenomic analysis at the single genome level. Software and pipelines for such analysis have become diverse and sophisticated, resulting in a significant burden for biologists to access and use them. Furthermore, while bin extraction algorithms are rapidly improving, there is still a lack of tools for their evaluation and visualization. Results: To address these challenges, we present metaWRAP, a modular pipeline software for shotgun metagenomic data analysis. MetaWRAP deploys state-of-the-art software to handle metagenomic data processing starting from raw sequencing reads and ending in metagenomic bins and their analysis. MetaWRAP is flexible enough to give investigators control over the analysis, while still being easy-to-install and easy-to-use. It includes hybrid algorithms that leverage the strengths of a variety of software to extract and refine high-quality bins from metagenomic data through bin consolidation and reassembly. MetaWRAP's hybrid bin extraction algorithm outperforms individual binning approaches and other bin consolidation programs in both synthetic and real data sets. Finally, metaWRAP comes with numerous modules for the analysis of metagenomic bins, including taxonomy assignment, abundance estimation, functional annotation, and visualization. Conclusions: MetaWRAP is an easy-to-use modular pipeline that automates the core tasks in metagenomic analysis, while contributing significant improvements to the extraction and interpretation of high-quality metagenomic bins. The bin refinement and reassembly modules of metaWRAP consistently outperform other binning approaches. Each module of metaWRAP is also a standalone component, making it a flexible and versatile tool for tackling metagenomic shotgun sequencing data. MetaWRAP is open-source software available at https://github.com/bxlab/metaWRAP .
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Taxonomy is an organizing principle of biology and is ideally based on evolutionary relationships among organisms. Development of a robust bacterial taxonomy has been hindered by an inability to obtain most bacteria in pure culture and, to a lesser extent, by the historical use of phenotypes to guide classification. Culture-independent sequencing technologies have matured sufficiently that a comprehensive genome-based taxonomy is now possible. We used a concatenated protein phylogeny as the basis for a bacterial taxonomy that conservatively removes polyphyletic groups and normalizes taxonomic ranks on the basis of relative evolutionary divergence. Under this approach, 58% of the 94,759 genomes comprising the Genome Taxonomy Database had changes to their existing taxonomy. This result includes the description of 99 phyla, including six major monophyletic units from the subdivision of the Proteobacteria, and amalgamation of the Candidate Phyla Radiation into a single phylum. Our taxonomy should enable improved classification of uncultured bacteria and provide a sound basis for ecological and evolutionary studies.
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The objective of this study was to investigate whether arsenic-oxidising bacteria (AsOB) will grow and survive in rapid sand filters. Additionally, the interdependence of other groundwater constituents (Fe(II), Mn(II), NH4) with biological As(III) oxidation was investigated. For this purpose As(III) oxidation was monitored in pilot-scale filter sand columns fed with raw groundwater, as well as treated groundwater (drinking water) with spikes of either As(III), Mn(II) or NH4. It was concluded that biological As(III) oxidation rapidly developed in the rapid sand filter columns. With a typical lag and log phase, decreasing As(III) and increasing As(V) concentrations in the effluent of the sand columns were observed in a timeframe of weeks. The growth of biomass in the sand columns was confirmed with ATP analysis. ATP concentrations on the sand grains increased from 0.7 ng/g to 16, 8 and 2 ng/g filter sand stratified from the top of the sand filter to the bottom, respectively. Additionally, a microbial community analysis (16S rRNA) showed a high relative abundance of α- and β-Proteobacteria; the same classes where most AsOB are phylogenetically placed. This study establishes that AsOB are able to grow and maintain their population on low As(III) concentrations, either in presence, or absence, of other common groundwater bacteria and mineral precipitates, directly leading to an increased As removal in the filter bed.
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Little is known about the forces that determine the assembly of diverse bacterial communities inhabiting drinking water treatment filters and how this affects drinking water quality. Two contrasting ecological theories can help to understand how natural microbial communities assemble; niche theory and neutral theory, where environmental deterministic factors or stochastic factors predominate respectively. This study investigates the development of the microbial community on two common contrasting filter materials (quartz sand and granular activated carbon-GAC), to elucidate the main factors governing their assembly, through the evaluation of environmental (i.e. filter medium type) and stochastic forces (random deaths, births and immigration). Laboratory-scale filter columns were used to mimic a rapid gravity filter; the microbiome of the filter materials, and of the filter influent and effluent, was characterised using next generation 16S rRNA gene amplicon sequencing and flow-cytometry. Chemical parameters (i.e. dissolved organic carbon, trihalomethanes formation) were also monitored to assess the final effluent quality. The filter communities seemed to be strongly assembled by selection rather than neutral processes, with only 28% of those OTUs shared with the source water detected on the filter medium following predictions using a neutral community model. GAC hosted a phylogenetically more diverse community than sand. The two filter media communities seeded the effluent water, triggering differences in both water quality and community composition of the effluents. Overall, GAC proved to be better than sand in controlling microbial growth, by promoting higher bacterial decay rates and hosting less bacterial cells, and showed better performance for putative pathogen control by leaking less Legionella cells into the effluent water.
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Drinking water treatment processes remove undesirable chemicals and microorganisms from source water, which is vital to public health protection. The purpose of this study was to investigate the effects of treatment processes and configuration on the microbiome by comparing microbial community shifts in two series of different treatment processes operated in parallel within a full-scale drinking water treatment plant (DWTP) in Southeast China. Illumina sequencing of 16S rRNA genes of water samples demonstrated little effect of coagulation/sedimentation and pre-oxidation steps on bacterial communities, in contrast to dramatic and concurrent microbial community shifts during ozonation, granular activated carbon treatment, sand filtration, and disinfection for both series. A large number of unique operational taxonomic units (OTUs) at these four treatment steps further illustrated their strong shaping power towards the drinking water microbial communities. Interestingly, multidimensional scaling analysis revealed tight clustering of biofilm samples collected from different treatment steps, with Nitrospira, the nitrite-oxidizing bacteria, noted at higher relative abundances in biofilm compared to water samples. Overall, this study provides a snapshot of step-to-step microbial evolvement in multi-step drinking water treatment systems, and the results provide insight to control and manipulation of the drinking water microbiome via optimization of DWTP design and operation.
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There is increasing interest in employing shotgun sequencing, rather than amplicon sequencing, to analyze microbiome samples. Typical projects may involve hundreds of samples and billions of sequencing reads. The comparison of such samples against a protein reference database generates billions of alignments and the analysis of such data is computationally challenging. To address this, we have substantially rewritten and extended our widely-used microbiome analysis tool MEGAN so as to facilitate the interactive analysis of the taxonomic and functional content of very large microbiome datasets. Other new features include a functional classifier called InterPro2GO, gene-centric read assembly, principal coordinate analysis of taxonomy and function, and support for metadata. The new program is called MEGAN Community Edition (CE) and is open source. By integrating MEGAN CE with our high-throughput DNA-to-protein alignment tool DIAMOND and by providing a new program MeganServer that allows access to metagenome analysis files hosted on a server, we provide a straightforward, yet powerful and complete pipeline for the analysis of metagenome shotgun sequences. We illustrate how to perform a full-scale computational analysis of a metagenomic sequencing project, involving 12 samples and 800 million reads, in less than three days on a single server. All source code is available here: https://github.com/danielhuson/megan-ce.
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Importance: The identity of the Mn(II) oxidase enzyme inP. putidaGB-1 has been a long-standing question in the field of bacterial Mn(II) oxidation. In this current work, we demonstrate thatP. putidaGB-1 employs both the MCO- and AHP-mediated pathways for the oxidation of Mn(II), rendering this model organism relevant to the study of both types of Mn(II) oxidase enzymes. The presence of three oxidase enzymes inP. putidaGB-1 deepens the mystery of why microorganisms oxidize Mn(II), while providing the field with the tools necessary to address this question. The initial identification of MopA as a Mn(II) oxidase in this strain required the deletion of FleQ, a regulator involved in both flagella and biofilm synthesis inP. aeruginosa Therefore, these results are also an important step towards understanding the regulation of Mn(II) oxidation.
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Here, we document microbial communities in rapid gravity filtration units, specifically serial rapid sand filters (RSFs), termed prefilters (PFs) and after- filters (AFs), fed with anoxic groundwaters low in organic carbon to prepare potable waters. A comprehensive 16S rRNA-based amplicon sequencing survey revealed a core RSF microbiome comprising few bacterial taxa (29–30 genera) dominated by Nitrospirae, Proteobacteria and Acidobacteria, with a strikingly high abundance (75–87±18%) across five examined waterworks in Denmark. Lineages within the Nitrospira genus consistently comprised the second most and most abundant fraction in PFs (27±23%) and AFs (45.2±23%), respectively, and were far more abundant than typical proteobacterial ammonium-oxidizing bacteria, suggesting a physiology beyond nitrite oxidation for Nitrospira. Within the core taxa, sequences closely related to types with ability to oxidize ammonium, nitrite, iron, manganese and methane as primary growth substrate were identified and dominated in both PFs (73.6±6%) and AFs (61.4±21%), suggesting their functional importance. Surprisingly, operational taxonomic unit richness correlated strongly and positively with sampling location in the drinking water treatment plant (from PFs to AFs), and a weaker negative correlation held for evenness. Significant spatial heterogeneity in microbial community composition was detected in both PFs and AFs, and was higher in the AFs. This is the first comprehensive documentation of microbial community diversity in RSFs treating oligotrophic groundwaters. We have identified patterns of local spatial heterogeneity and dispersal, documented surprising energy–diversity relationships, observed a large and diverse Nitrospira fraction and established a core RSF microbiome.
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BlastKOALA and GhostKOALA are automatic annotation servers for genome and metagenome sequences, which perform KEGG Orthology (KO) assignments to characterize individual gene functions and reconstruct KEGG pathways, BRITE hierarchies and KEGG modules to infer high-level functions of the organism or the ecosystem. Both servers are made freely available at the KEGG website (http://www.kegg.jp/blastkoala/). In BlastKOALA the KO assignment is done by a modified version of the internally used KOALA algorithm after the BLAST search against a non-redundant dataset of pangenome sequences at the species, genus or family level, which is generated from the KEGG GENES database by retaining the KO content of each taxonomic category. In GhostKOALA, which utilizes more rapid GHOSTX for database search and is suitable for metagenome annotation, the pangenome dataset is supplemented with CD-HIT clusters including those for viral genes. The result files may be downloaded and manipulated for further KEGG Mapper analysis, such as comparative pathway analysis using multiple BlastKOALA results.
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Rapid sand filtration is essential at most waterworks that treat anaerobic groundwater. Often the filtration depends on microbiological processes but the microbial communities of the filters are largely unknown. We determined the prokaryotic community structures of 11 waterworks receiving groundwater from different geological settings by 16S rRNA gene based 454 pyrosequencing and explored their relationships to filtration technology and raw water chemistry. Most of the variation in microbial diversity observed between different waterworks sand filters could be explained by the geochemistry of the inlet water. In addition, our findings suggested four features of particular interest: (1) Nitrospira dominated over Nitrobacter at all waterworks, suggesting that Nitrospira is a key nitrifying bacterium in groundwater-treating sand filters. (2) Hyphomicrobiaceae species were abundant at all waterworks, where they may be involved in manganese oxidation. (3) Six of eleven waterworks had significant concentrations of methane in their raw water and very high abundance of the methanotrophic Methylococcaceae. (4) The iron-oxidizing bacteria Gallionella was present at all waterworks suggesting that biological iron-oxidation is occurring in addition to abiotic iron-oxidation. Elucidation of key members of the microbial community in groundwater-treating sand filters has practical potential, for example when methods are needed to improve filter function.
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Manganese(II) contamination is naturally occurring in many groundwater and surface water sources. Moreover, industrial wastewater is also responsible for much of the Mn(II) contamination. Nowadays, Mn(II) contamination has become a serious environmental problem in some regions of the world. To explore a biological approach for removing excessive amounts of aqueous Mn(II) from water, we found a new biocatalyst multicopper oxidase CueO, which was firstly proved to catalyze the oxidation of Mn(II) both in vitro and in vivo. Subsequently, we established a CueO-mediated catalysis system to prepare biogenic Mn oxide (BioMnOx), which was confirmed to be γ-Mn3O4 by X-ray diffraction. This newly prepared BioMnOx consisted of 53.6% Mn(II), 18.4% Mn(III) and 28.0% Mn(IV) characterized by X-ray photoelectron spectroscopy. It exhibited distinct polyhedral structure with nanoparticles of 150-350 nm diameters observed by transmission electron microscopy. Importantly, CueO could remove 35.7% of Mn(II) after a seven-day reaction, and on the other hand, the cueO-overexpressing Escherichia coli strain (ECueO) could also oxidize 58.1% dissolved Mn(II), and simultaneously remove 97.7% Mn(II). Based on these results, we suggest that ECueO strain and CueO enzyme have potential applications on Mn(II) decontamination in water treatment.
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The role of microbial consortia on the removal of manganese (Mn) was examined on sand from three different Belgian rapid sand filters for the treatment of ground water. Microorganisms closely associated with deposits of Fe and amorphous Mn precipitates were observed by SEM and EDAX techniques on sand from the filters able to remove Mn efficiently. Bacterial counts were performed. Of the CFU enumerated on PYM-medium, 25–33% displayed Mn-oxidizing activity. Batch cultures were set up by inoculating a Mn-containing, low organic medium with sand from one of the filters. Microbial growth resulted in the formation of Mn-removing bacterial flocs and a pH increase. Suppression of microbial growth by addition of azide, kanamycin, or by autoclaving reduced removal of Mn2+ from 0.5 mM/day to 0.05–0.11 mM/day. Buffering the pH of the medium at 7.5 (0.1 mM Hepes) decelerated the Mn removal but did not halt it, whereas microelectrode measurements revealed a clear pH drop of about 0.7 units inside bacterial flocs. In the absence of Mn2+, the pH drop was only 0.4 units. The auto-catalytic removal of Mn by the Mn oxide coated filter sand was not sufficient to explain the Mn removal observed. Inactivated cells were not capable of a pronounced autocatalytic Mn removal. Experiments with enrichment cultures indicated that the Mn-removing capacity of the microbial sand filter consortia was not constitutive but was promoted by preadaptation and the presence of a substratum. These results clearly link Mn oxidation in rapid sand filters to microbial processes.
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A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at the phylum level. Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria.
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While sand filters are widely used to treat drinking water, the role of sand filter associated microorganisms in water purification has not been extensively studied. In the current investigation, we integrated molecular (based on metagenomic) and physicochemical analyses to elucidate microbial community composition and function in a common sand filter used to treat groundwater for potable consumption. The results revealed that the biofilm developed rapidly within 2 days (reaching ∼10(11) prokaryotes per gram) in the sand filter along with abiotic and biotic particulates accumulated in the interstitial spaces. Bacteria (up to 90%) dominated the biofilm microbial community, with Alphaproteobacteria being the most common class. Thaumarchaeota was the sole phylum of Archaea, which might be involved in ammonia oxidation. Function annotation of metagenomic datasets revealed a number of aromatic degradation pathway genes, such as aromatic oxygenase and dehydrogenase genes, in the biofilm, suggesting a significant role for microbes in the breakdown of aromatic compounds in groundwater. Simultaneous nitrification and denitrification pathways were confirmed as the primary routes of nitrogen removal. Dissolved heavy metals in groundwater, e.g. Mn(2+) and As(3+), might be biologically oxidized to insoluble or easily adsorbed compounds and deposited in the sand filter. Our study demonstrated that the role of the microbial community in the sand filter treatment system are critical to effective water purification in drinking water.
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This revised and updated edition focuses on constrained ordination (RDA, CCA), variation partitioning and the use of permutation tests of statistical hypotheses about multivariate data. Both classification and modern regression methods (GLM, GAM, loess) are reviewed and species functional traits and spatial structures analysed. Nine case studies of varying difficulty help to illustrate the suggested analytical methods, using the latest version of Canoco 5. All studies utilise descriptive and manipulative approaches, and are supported by data sets and project files available from the book website: Http://regent.prf.jcu.cz/maed2/. Written primarily for community ecologists needing to analyse data resulting from field observations and experiments, this book is a valuable resource to students and researchers dealing with both simple and complex ecological problems, such as the variation of biotic communities with environmental conditions or their response to experimental manipulation.
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Summary: CD-HIT is a widely used program for clustering biological sequences to reduce sequence redundancy and improve the performance of other sequence analyses. In response to the rapid increase in the amount of sequencing data produced by the next-generation sequencing technologies, we have developed a new CD-HIT program accelerated with a novel parallelization strategy and some other techniques to allow efficient clustering of such datasets. Our tests demonstrated very good speedup derived from the parallelization for up to ∼24 cores and a quasi-linear speedup for up to ∼8 cores. The enhanced CD-HIT is capable of handling very large datasets in much shorter time than previous versions.Availability: http://cd-hit.org.Contact: liwz@sdsc.eduSupplementary information: Supplementary data are available at Bioinformatics online.
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Although earlier circumstantial observations have suggested the presence of iron oxidizing bacteria (IOB) in groundwater-fed rapid sand filters (RSF), ferrous iron (Fe(II)) oxidation in this environment is often considered a chemical process due to the highly oxic and circumneutral pH conditions. Due to the low water temperature (5–10°C), typical of groundwaters, on the other hand, rates of chemical Fe(II) oxidation may be reduced, which may allow IOB to grow and compete with chemical Fe(II) oxidation. Hence, we hypothesized that IOB are active and abundant in groundwater-fed RSFs. Here, we applied a combination of cultivation and molecular techniques to isolate, quantify, and confirm the growth of IOB from groundwater-fed rapid sand filters, operated at different influent Fe(II) concentrations. Isolates related to Undibacterium and Curvibacter were identified as novel lineages of IOB. Gallionella spp. were dominant in all waterworks, whereas Ferriphaselus and Undibacterium were dominant at pre-filters of those receiving groundwaters with high (>2 mg/l) Fe(II) concentrations. The high density and diversity of IOB in groundwater-fed RSFs suggest that neutrophilic iron oxidizers may not be limited to oxic/anoxic interfaces.
Article
Motivation: The nitrogen (N) cycle is a collection of important biogeochemical pathways in the Earth ecosystem and has gained extensive foci in ecology and environmental studies. Currently, shotgun metagenome sequencing has been widely applied to explore gene families responsible for N cycle processes. However, there are problems in applying publically available orthology databases to profile N cycle gene families in shotgun metagenomes, such as inefficient database searching, unspecific orthology groups, and low coverage of N cycle genes and/or gene (sub)families. Results: To solve these issues, this study built a manually curated integrative database (NCycDB) for fast and accurate profiling of N cycle gene (sub)families from shotgun metagenome sequencing data. NCycDB contains a total of 68 gene (sub)families and covers eight N cycle processes with 84,759 and 219,146 representative sequences at 95% and 100% identity cutoffs, respectively. We also identified 1,958 homologous orthology groups and included corresponding sequences in the database to avoid false positive assignments due to "small database" issues. We applied NCycDB to characterize N cycle gene (sub)families in 52 shotgun metagenomes from the Global Ocean Sampling expedition. Further analysis showed that the structure and composition of N cycle gene families were most strongly correlated with latitude and temperature. NCycDB is expected to facilitate N cycle studies via shotgun metagenome sequencing approaches in various environments. The framework developed in this study can be served as a good reference to build similar knowledge-based functional gene databases in various processes and pathways. Availability: NCycDB database files are available at https://github.com/qichao1984/NCyc. Supplementary information: Supplementary data are available at Bioinformatics online.
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Drinking water treatment plants based on groundwater may suffer from incomplete ammonium removal, which deteriorates drinking water quality and constrains water utilities in the operation of their plants. Ammonium is normally removed through nitrification in biological granular media filters, and recent studies have demonstrated that dosing of copper can stimulate the removal of ammonium. Here, we investigated if copper dosing could generically improve ammonium removal of biofilters, at treatment plants with different characteristics. Copper was dosed at ≤1.5 μg Cu/L to biofilters at 10 groundwater treatment plants, all of which had displayed several years of incomplete nitrification. Plants exceeded the Danish national water quality standard of 0.05 mg NH4+/L by a factor of 2-12. Within only 2-3 weeks of dosing, ammonium removal rates increased significantly (up to 150%). Nitrification was fully established, with ammonium effluent concentrations of <0.01 mg NH4+-N/L at most plants, regardless of the differences in raw water chemistry, ammonium loading rates, filter design and operation, or treatment plant configuration. However, for filters without primary filtration, it took longer time to reach complete ammonium removal than for filters receiving prefiltered water, likely due to sorption of copper to iron oxides, at plants without prefiltration. With complete ammonium removal, we subjected two plants to short-term loading rate upshifts, to examine the filters' ability to cope with loading rate variations. After 2 months of dosing and an average loading rate of 1.0 g NH4+-N/m3 filter material/h, the loading rate was upshifted by 50%. Yet, a filter managed to completely remove all the influent ammonium, showing that with copper dosing the filter had extra capacity to remove ammonium even beyond its normal loading rates. Depth sampling revealed that the ammonium removal rate of the filter's upper 10 cm increased more than 7-fold from 0.67 to 4.90 g NH4+-N/m3/h, and that nitrite produced from increased ammonium oxidation was completely oxidized further to nitrate. Hence, no problems with nitrite accumulation or breakthrough occurred. Overall, copper dosing generically enhanced nitrification efficiency and allowed a range of quite different plants to meet water quality standards, even at increased loading rates. The capacity increase is highly relevant in practice, as it makes filters more robust towards sudden ammonium loading rate variations.
Article
The recent discovery of completely nitrifying Nitrospira demands a re-examination of nitrifying environments to evaluate their contribution to nitrogen cycling. To approach this challenge, tools are needed to detect and quantify comammox Nitrospira. We present primers for the simultaneous quantification and diversity assessement of both comammox Nitrospira clades. The primers cover a wide range of comammox diversity, spanning all available high quality sequences. We applied these primers to 12 groundwater-fed rapid sand filters, and found comammox Nitrospira to be abundant in all filters. Clade B comammox comprise the majority (∼75%) of comammox abundance in all filters. Nitrosomonadaceae were present in all filters, though at low abundance (mean=1.8%). Ordination suggests that temperature impacts the structure of nitrifying communities, and in particular that increasing temperature favours Nitrospira. The nitrogen content of the filter material, sulfate concentration, and surface ammonium loading rates shape the structure of the comammox guild in the filters. This work provides an assay for simultaneous detection and diversity assessment of clade A and B comammox Nitrospira, expands our current knowledge of comammox Nitrospira diversity, and demonstrates a key role for comammox Nitrospira in nitrification in groundwater-fed biofilters. This article is protected by copyright. All rights reserved.
Article
Biodegradable organic matter (BOM), found in all surface waters, is a challenge for drinking water utilities because it can lead to distribution system bio-regrowth, react to form disinfection by-products, or be a specific compound of concern. A critical review of BOM (occurrence and oxidant effects) and rapid-rate biofiltration performance (preozonation, backwashing with an oxidant, empty bed contact time (EBCT) and temperature) was carried out. An extensive literature data analysis (n = 100) found total organic carbon (TOC) in nonozonated water is comprised of 20% (median) biodegradable organic carbon (BDOC) and 3% (median) assimilable organic carbon (AOC). For ozonated waters (n = 103), these values increased to 30% (median) BDOC and 9% (median) AOC. For all operation conditions (n = 117), biofilters (12 min average EBCT) removed 12% (median) of the influent TOC with higher removals for ozonated waters, 15% (median), compared to nonozonated waters, 10% (median). As temperature increased from ≤10 °C to ≥20 °C, TOC removal increased from 10% to 17% (median). This review demonstrates biofiltration can be an efficient treatment technology to remove a portion of the BOM from the filter influent and should be optimized to achieve maximum removal.
Article
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.
Article
The herbicide bentazone is recalcitrant in aquifers and is therefore frequently detected in wells used for drinking water production. However, bentazone degradation has been observed in filter sand from a rapid sand filter at a waterworks with methane-rich groundwater. Here, the association between methane oxidation and removal of bentazone was investigated with a methanotrophic enrichment culture derived from methane-fed column reactors inoculated with that filter sand. Several independent lines of evidence obtained from microcosm experiments with the methanotrophic enrichment culture, tap water and bentazone at concentrations below 2 mg/L showed methanotrophic co-metabolic bentazone transformation: The culture removed 53% of the bentazone in 21 days in presence of 5 mg/L of methane, while only 31% was removed in absence of methane. Addition of acetylene inhibited methane oxidation and stopped bentazone removal. The presence of bentazone partly inhibited methane oxidation since the methane consumption rate was significantly lower at high (1 mg/L) than at low (1 μg/L) bentazone concentrations. The transformation yield of methane relative to bentazone normalized by their concentration ratio ranged from 58 to 158, well within the range for methanotrophic co-metabolic degradation of trace contaminants calculated from the literature, with normalized substrate preferences varying from 3 to 400. High-resolution mass spectrometry revealed formation of the transformation products (TPs) 6-OH, 8-OH, isopropyl-OH and di-OH-bentazone, with higher abundances of all TPs in the presence of methane. Overall, we found a suite of evidence all showing that bentazone was co-metabolically transformed to hydroxy-bentazone by a methanotrophic culture enriched from a rapid sand filter at a waterworks.
Article
Microorganisms inhabiting filtration media of a drinking water treatment plant can be beneficial, because they metabolize biodegradable organic matter from source waters and those formed during disinfection processes, leading to the production of biologically stable drinking water. However, which microbial consortia colonize filters and what metabolic capacity they possess remain to be investigated. To gain insights into these issues, we performed metagenome sequencing and analysis of microbial communities in three different filters of a full-scale drinking water treatment plant (DWTP). Filter communities were sampled from a rapid sand filter (RSF), granular activated carbon filter (GAC), and slow sand filter (SSF), and from the Schmutzdecke (SCM, a biologically active scum layer accumulated on top of SSF), respectively. Analysis of community phylogenetic structure revealed that the filter bacterial communities significantly differed from those in the source water and final effluent communities, respectively. Network analysis identified a filter-specific colonization pattern of bacterial groups. Bradyrhizobiaceae were abundant in GAC, whereas Nitrospira were enriched in the sand-associated filters (RSF, SCM, and SSF). The GAC community was enriched with functions associated with aromatics degradation, many of which were encoded by Rhizobiales (∼30% of the total GAC community). Predicting minimum generation time (MGT) of prokaryotic communities suggested that the GAC community potentially select fast-growers (<15 h of MGT) among the four filter communities, consistent with the highest dissolved organic matter removal rate by GAC. Our findings provide new insights into the community phylogenetic structure, colonization pattern, and metabolic capacity that potentially contributes to organic matter removal achieved in the biofiltration stages of the full-scale DWTP.
Article
We investigated the density and distribution of total bacteria, canonical Ammonia Oxidizing Bacteria (AOB) (Nitrosomonas plus Nitrosospira), Ammonia Oxidizing Archaea (AOA), as well as Nitrobacter and Nitrospira in rapid sand filters used for groundwater treatment. To investigate the spatial distribution of these guilds, filter material was sampled at four drinking water treatment plants (DWTPs) in parallel filters of the pre- and after-filtration stages at different locations and depths. The target guilds were quantified by qPCR targeting 16S rRNA and amoA genes. Total bacterial densities (ignoring 16S rRNA gene copy number variation) were high and ranged from 10(9) to 10(10) per gram (10(15) to 10(16) per m(3)) of filter material. All examined guilds, except AOA, were stratified at only one of the four DWTPs. Densities varied spatially within filter (intra-filter variation) at two of the DWTPs and in parallel filters (inter-filter variation) at one of the DWTPs. Variation analysis revealed random sampling as the most efficient strategy to yield accurate mean density estimates, with collection of at least 7 samples suggested to obtain an acceptable (below half order of magnitude) density precision. Nitrospira was consistently the most dominant guild (5-10% of total community), and was generally up to 4 orders of magnitude more abundant than Nitrobacter and up to 2 orders of magnitude more abundant than canonical AOBs. These results, supplemented with further analysis of the previously reported diversity of Nitrospira in the studied DWTPs based on 16S rRNA and nxrB gene phylogeny (Gülay et al., 2016; Palomo et al., 2016), indicate that the high Nitrospira abundance is due to their comammox (complete ammonia oxidation) physiology. AOA densities were lower than AOB densities, except in the highly stratified filters, where they were of similar abundance. In conclusion, rapid sand filters are microbially dense, with varying degrees of spatial heterogeneity, which requires replicate sampling for a sufficiently precise determination of total microbial community and specific population densities. A consistently high Nitrospira to bacterial and archaeal AOB density ratio suggests that non-canonical pathways for nitrification may dominate the examined RSFs.
Article
The number of microbial genomes sequenced each year is expanding rapidly, in part due to genome-resolved metagenomic studies that routinely recover hundreds of draft-quality genomes. Rapid algorithms have been developed to comprehensively compare large genome sets, but they are not accurate with draft-quality genomes. Here we present dRep, a program that reduces the computational time for pairwise genome comparisons by sequentially applying a fast, inaccurate estimation of genome distance, and a slow, accurate measure of average nucleotide identity. dRep achieves a 28 × increase in speed with perfect recall and precision when benchmarked against previously developed algorithms. We demonstrate the use of dRep for genome recovery from time-series datasets. Each metagenome was assembled separately, and dRep was used to identify groups of essentially identical genomes and select the best genome from each replicate set. This resulted in recovery of significantly more and higher-quality genomes compared to the set recovered using co-assembly.
Article
The top layer of natural rapid sand filtration was found to effectively oxidise arsenite (As(III)) in groundwater treatment. However, the oxidation pathway has not yet been identified. The aim of this study was to investigate whether naturally formed manganese oxide (MnO2), present on filter grains, could abiotically be responsible for As(III) oxidation in the top of a rapid sand filter. For this purpose As(III) oxidation with two MnO2 containing powders was investigated in aerobic water containing manganese(II) (Mn(II)), iron(II) (Fe(II)) and/or iron(III) (Fe(III)). The first MnO2 powder was a very pure - commercially available - natural MnO2 powder. The second originated from a filter sand coating, produced over 22 years in a rapid filter during aeration and filtration. Jar test experiments showed that both powders oxidised As(III). However, when applying the MnO2 in aerated, raw groundwater, As(III) removal was not enhanced compared to aeration alone. It was found that the presence of Fe(II)) and Mn(II) inhibited As(III) oxidation, as Fe(II) and Mn(II) adsorption and oxidation were preferred over As(III) on the MnO2 surface (at pH 7). Therefore it is concluded that just because MnO2 is present in a filter bed, it does not necessarily mean that MnO2 will be available to oxidise As(III). However, unlike Fe(II), the addition of Fe(III) did not hinder As(III) oxidation on the MnO2 surface; resulting in subsequent effective As(V) removal by the flocculating hydrous ferric oxides.
Article
High concentrations of iron (Fe(II)) and manganese (Mn(II)) often occur simultaneously in groundwater. Previously, we demonstrated that Fe(II) and Mn(II) could be oxidized to biogenic Fe-Mn oxides (BFMO) via aeration and microbial oxidation, and the formed BFMO could further oxidize and adsorb other pollutants (e.g., arsenic (As(III)) and antimony (Sb(III))). To apply this finding to groundwater remediation, we established four quartz-sand columns for treating groundwater containing Fe(II), Mn(II), As(III), and Sb(III). A Mn-oxidizing bacterium (Pseudomonas sp. QJX-1) was inoculated into two parallel bioaugmented columns. Long-term treatment (120 d) showed that bioaugmentation accelerated the formation of Fe-Mn oxides, resulting in an increase in As and Sb removal. The bioaugmented columns also exhibited higher overall treatment effect and anti-shock load capacity than that of the non-bioaugmented columns. To clarify the causal relationship between the microbial community and treatment effect, we compared the biomass of active bacteria (reverse-transcribed real-time PCR), bacterial community composition (Miseq 16S rRNA sequencing) and community function (metagenomic sequencing) between the bioaugmented and non-bioaugmented columns. Results indicated that the QJX1 strain grew steadily and attached onto the filter material surface in the bioaugmented columns. In general, the inoculated strain did not significantly alter the composition of the indigenous bacterial community, but did improve the relative abundances of xenobiotic metabolism genes and Mn oxidation gene. Thus, bioaugmentation intensified microbial degradation/utilization for the direct removal of pollutants and increased the formation of Fe-Mn oxides for the indirect removal of pollutants. Our study provides an alternative method for the treatment of groundwater containing high Fe(II), Mn(II) and As/Sb.
Article
The biokinetic behavior of NH4+ removal was investigated at different depths of a rapid sand filter treating groundwater for drinking water preparation. Filter materials from the top, middle and bottom layers of a full-scale filter were exposed to various controlled NH4+ loadings in a continuous-flow lab-scale assay. NH4+ removal capacity, estimated from short term loading up-shifts, was at least 10 times higher in the top than in the middle and bottom filter layers, consistent with the stratification of Ammonium Oxidizing Bacteria (AOB). AOB density increased consistently with the NH4+ removal rate, indicating their primarily role in nitrification under the imposed experimental conditions. The maximum AOB cell specific NH4+ removal rate observed in the bottom was at least 3 times lower compared to the top and middle layers. Additionally, a significant up-shift capacity (4.6 and 3.5 times) was displayed from the top and middle layers, but not from the bottom layer at increased loading conditions. Hence, AOB with different physiological responses were active at the different depths. The biokinetic analysis predicted that despite the low NH4+ removal capacity at the bottom layer, the entire filter is able to cope with a 4-fold instantaneous loading increase without compromising the effluent NH4+. Ultimately, this filter up-shift capacity was limited by the density of AOB and their biokinetic behavior, both of which were strongly stratified.
Article
Rapid gravity sand filtration is a drinking water production technology widely used around the world. Microbially catalyzed processes dominate the oxidative transformation of ammonia, reduced manganese and iron, methane and hydrogen sulfide, which may all be present at millimolar concentrations when groundwater is the source water. In this study, six metagenomes from various locations within a groundwater-fed rapid sand filter (RSF) were analyzed. The community gene catalog contained most genes of the nitrogen cycle, with particular abundance in genes of the nitrification pathway. Genes involved in different carbon fixation pathways were also abundant, with the reverse tricarboxylic acid cycle pathway most abundant, consistent with an observed Nitrospira dominance. From the metagenomic data set, 14 near-complete genomes were reconstructed and functionally characterized. On the basis of their genetic content, a metabolic and geochemical model was proposed. The organisms represented by draft genomes had the capability to oxidize ammonium, nitrite, hydrogen sulfide, methane, potentially iron and manganese as well as to assimilate organic compounds. A composite Nitrospira genome was recovered, and amo-containing Nitrospira genome contigs were identified. This finding, together with the high Nitrospira abundance, and the abundance of atypical amo and hao genes, suggests the potential for complete ammonium oxidation by Nitrospira, and a major role of Nitrospira in the investigated RSFs and potentially other nitrifying environments.The ISME Journal advance online publication, 29 April 2016; doi:10.1038/ismej.2016.63.
Article
We present kallisto, an RNA-seq quantification program that is two orders of magnitude faster than previous approaches and achieves similar accuracy. Kallisto pseudoaligns reads to a reference, producing a list of transcripts that are compatible with each read while avoiding alignment of individual bases. We use kallisto to analyze 30 million unaligned paired-end RNA-seq reads in <10 min on a standard laptop computer. This removes a major computational bottleneck in RNA-seq analysis.
Article
As(III&V), Mn(II), and Fe(II) may occur simultaneously in some groundwater and surface water. Studying their redox reactions and interactions is essential to unravel the biogeochemical cycles of these metal ions in aquatic ecosystems and to find effective methods to remove them simultaneously in drinking water treatment. Here, the formation of biogenic Fe-Mn oxides (BFMO, defined as a mixture of biogenic Mn oxide (BMO) and Fe oxide) as well as its oxidation and adsorption of As in a Fe(II)-Mn(II)-As(III&V)-Mn-oxidizing microbe (Pseudomonas sp. QJX-1) system were investigated. Batch experiments and structure characterization revealed that the BFMO was formed via a sequential precipitation of Fe oxide and BMO. The first formed Fe oxide was identified as FeOOH (lepidocrocite) and the latter formed BMO was identified as MnO2 (similar to hexagonal birnessite). In the BFMO mixture, the BMO part was mainly responsible for As(III) oxidation, and the Fe oxide part dominated As adsorption. Remarkably, the BMO could oxidize Fe(II) to form FeOOH, which may improve As adsorption. The optimum Mn(II)/Fe(II) ratio for As removal was approximately 1:3 (mol/mol). Taken together, in Fe(II)-Mn(II)-As(III&V)-Mn-oxidizing microbe ecosystems, the in situ formation of BFMO could eliminate or decrease Fe(II), Mn(II), and As(III&V) species simultaneously. Therefore, based on this study, new approaches may be developed for As removal from water containing high concentrations of Fe(II) and Mn(II).
Article
The study of metagenomics has been much benefited from low-cost and high-throughput sequencing technologies, yet the tremendous amount of data generated make analysis like de novo assembly to consume too much computational resources. In late 2014 we released MEGAHIT v0.1 (together with a brief note of Li et al. (2015) [1]), which is the first NGS metagenome assembler that can assemble genome sequences from metagenomic datasets of hundreds of Giga base-pairs (bp) in a time- and memory-efficient manner on a single server. The core of MEGAHIT is an efficient parallel algorithm for constructing succinct de Bruijn Graphs (SdBG), implemented on a graphical processing unit (GPU). The software has been well received by the assembly community, and there is interest in how to adapt the algorithms to integrate popular assembly practices so as to improve the assembly quality, as well as how to speed up the software using better CPU-based algorithms (instead of GPU).
Article
Nitrification is a two-step process where ammonia is first oxidized to nitrite by ammonia-oxidizing bacteria and/or archaea, and subsequently to nitrate by nitrite-oxidizing bacteria. Already described by Winogradsky in 1890, this division of labour between the two functional groups is a generally accepted characteristic of the biogeochemical nitrogen cycle. Complete oxidation of ammonia to nitrate in one organism (complete ammonia oxidation; comammox) is energetically feasible, and it was postulated that this process could occur under conditions selecting for species with lower growth rates but higher growth yields than canonical ammonia-oxidizing microorganisms. Still, organisms catalysing this process have not yet been discovered. Here we report the enrichment and initial characterization of two Nitrospira species that encode all the enzymes necessary for ammonia oxidation via nitrite to nitrate in their genomes, and indeed completely oxidize ammonium to nitrate to conserve energy. Their ammonia monooxygenase (AMO) enzymes are phylogenetically distinct from currently identified AMOs, rendering recent acquisition by horizontal gene transfer from known ammonia-oxidizing microorganisms unlikely. We also found highly similar amoA sequences (encoding the AMO subunit A) in public sequence databases, which were apparently misclassified as methane monooxygenases. This recognition of a novel amoA sequence group will lead to an improved understanding of the environmental abundance and distribution of ammonia-oxidizing microorganisms. Furthermore, the discovery of the long-sought-after comammox process will change our perception of the nitrogen cycle.
Article
Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be a two-step process catalysed by chemolithoautotrophic microorganisms oxidizing either ammonia or nitrite. No known nitrifier carries out both steps, although complete nitrification should be energetically advantageous. This functional separation has puzzled microbiologists for a century. Here we report on the discovery and cultivation of a completely nitrifying bacterium from the genus Nitrospira, a globally distributed group of nitrite oxidizers. The genome of this chemolithoautotrophic organism encodes the pathways both for ammonia and nitrite oxidation, which are concomitantly activated during growth by ammonia oxidation to nitrate. Genes affiliated with the phylogenetically distinct ammonia monooxygenase and hydroxylamine dehydrogenase genes of Nitrospira are present in many environments and were retrieved on Nitrospira-contigs in new metagenomes from engineered systems. These findings fundamentally change our picture of nitrification and point to completely nitrifying Nitrospira as key components of nitrogen-cycling microbial communities.
Rapid sand filtration (RSF) is an economical way to treat anoxic groundwater around the world. It consists of groundwater aeration followed by passage through a sand filter. The oxidation and removal of ferrous iron, which is commonly found in anoxic groundwaters, is often believed to be a fully physicochemical process. However, persistently low temperatures in RSF across Denmark may negatively affect the kinetics of chemical oxidation. The slower chemical oxidation of ferrous iron may increase the chances for iron bioconversion by neutrophilic iron-oxidizing bacteria (FeOB), which are found naturally in many environments. In this study, we used a combination of a cultivation-based opposing gradient enrichment technique and 16S rRNA gene targetedmolecular tools to isolate, quantify and identify FeOB froma RSF. Themicroscopic quantification of selectively enriched FeOB cells revealed that in RSF, neutrophilic iron oxidizers were present at the level of up to 7 × 105 cells g1 sediment. The spatial abundance and diversity of FeOB inferred by denaturing gradient gel electrophoresis fingerprinting differed greatly both between andwithin individual sand filters. The results suggest a larger than assumed role of FeOB in iron removal at waterworks using RSF technologies.
Article
The efficiency of manganese removal in conventional groundwater treatment consisting of aeration followed by rapid sand filtration, strongly depends on the ability of filter media to promote auto-catalytic adsorption of dissolved manganese and its subsequent oxidation. Earlier studies have shown that the compound responsible for the auto-catalytic activity in ripened filters is a manganese oxide called Birnessite. The aim of this study was to determine if the ripening of manganese removal filters and the formation of Birnessite on virgin sand is initiated biologically or physico-chemically. The ripening of virgin filter media in a pilot filter column fed by pre-treated manganese containing groundwater was studied for approximately 600 days. Samples of filter media were taken at regular time intervals, and the manganese oxides formed in the coating were analysed by Raman spectroscopy, Electron Paramagnetic Resonance (EPR) and Scanning Electron Microscopy (SEM). From the EPR analyses, it was established that the formation of Birnessite was most likely initiated via biological activity. With the progress of filter ripening and development of the coating, Birnessite formation became predominantly physico-chemical, although biological manganese oxidation continued to contribute to the overall manganese removal. The knowledge that manganese removal in conventional groundwater treatment is initiated biologically could be of help in reducing typically long ripening times by creating conditions that are favourable for the growth of manganese oxidizing bacteria. Copyright © 2014 Elsevier Ltd. All rights reserved.
Article
The alignment of sequencing reads against a protein reference database is a major computational bottleneck in metagenomics and data-intensive evolutionary projects. Although recent tools offer improved performance over the gold standard BLASTX, they exhibit only a modest speedup or low sensitivity. We introduce DIAMOND, an open-source algorithm based on double indexing that is 20,000 times faster than BLASTX on short reads and has a similar degree of sensitivity. © 2014 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.
Article
STAMP is a graphical software package that provides statistical hypothesis tests and exploratory plots for analysing taxonomic and functional profiles. It supports tests for comparing pairs of samples or samples organized into two or more treatment groups. Effect sizes and confidence intervals are provided to allow critical assessment of the biological relevancy of test results. A user-friendly graphical interface permits easy exploration of statistical results and generation of publication-quality plots. Availability and implementation: STAMP is licensed under the GNU GPL. Python source code and binaries are available from our website at: http://kiwi.cs.dal.ca/Software/STAMP Contact: donovan.parks{at}gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.
Article
Biological rapid sand filters are often used to remove ammonium from groundwater for drinking water supply. They often operate under dynamic substrate and hydraulic loading conditions, which can lead to increased levels of ammonium and nitrite in the effluent. To determine the maximum nitrification rates and safe operating windows of rapid sand filters, a pilot scale rapid sand filter was used to test short-term increased ammonium loads, set by varying either influent ammonium concentrations or hydraulic loading rates. Ammonium and iron (flock) removal were consistent between the pilot and the full-scale filter. Nitrification rates and ammonia-oxidizing bacteria and archaea were quantified throughout the depth of the filter. The ammonium removal capacity of the filter was determined to be 3.4 g NH4-N m(-3) h(-1), which was 5 times greater than the average ammonium loading rate under reference operating conditions. The ammonium removal rate of the filter was determined by the ammonium loading rate, but was independent of both the flow and influent ammonium concentration individually. Ammonia-oxidizing bacteria and archaea were almost equally abundant in the filter. Both ammonium removal and ammonia-oxidizing bacteria density were strongly stratified, with the highest removal and ammonia-oxidizing bacteria densities at the top of the filter. Cell specific ammonium oxidation rates were on average 0.6 × 10(2) ± 0.2 × 10(2) fg NH4-N h(-1) cell(-1). Our findings indicate that these rapid sand filters can safely remove both nitrite and ammonium over a larger range of loading rates than previously assumed.
Article
Indigenous bacterial communities are essential for biofiltration processes in drinking water treatment systems. In this study, we examined the microbial community composition and abundance of three different biofilter types (rapid sand, granular activated carbon, and slow sand filters) and their respective effluents in a full-scale, multi-step treatment plant (Zürich, CH). Detailed analysis of organic carbon degradation underpinned biodegradation as the primary function of the biofilter biomass. The biomass was present in concentrations ranging between 2-5 × 10(15) cells/m(3) in all filters but was phylogenetically, enzymatically and metabolically diverse. Based on 16S rRNA gene-based 454 pyrosequencing analysis for microbial community composition, similar microbial taxa (predominantly Proteobacteria, Planctomycetes, Acidobacteria, Bacteriodetes, Nitrospira and Chloroflexi) were present in all biofilters and in their respective effluents, but the ratio of microbial taxa was different in each filter type. This change was also reflected in the cluster analysis, which revealed a change of 50-60% in microbial community composition between the different filter types. This study documents the direct influence of the filter biomass on the microbial community composition of the final drinking water, particularly when the water is distributed without post-disinfection. The results provide new insights on the complexity of indigenous bacteria colonizing drinking water systems, especially in different biofilters of a multi-step treatment plant.
Article
Biologically stable water does not promote the growth of microorganisms during its distribution. This article combines microbiological theory and European practice to demonstrate how biological processes within a water treatment plant can remove the organic and inorganic substrates that cause or contribute to biological instability. Theory and practice indicate that ammonium and manganese ions and biodegradable organic compounds can be removed by attached-growth processes such as fixed bed, fluidized bed, and rapid sand filters. Low temperatures do not preclude good treatment. A quantitative kinetic model, which accurately describes field results, provides a sound basis for successful design and operation of biological water treatment processes. Following a biological process with conventional processes is recommended to provide multiple barriers against the escape of microorganisms into the finished water. El agua biologicamente estable no fomenta el crecimiento de microorganismos en el proceso de distribución. Este artículo combina teoría de microbiología con la práctica en Europa para demostrar como procesos biológicos dentro de una planta de tratamiento de agua pueden remover substratos orgánicos e inorgánicos que causan o contribuyen a la inestabilidad biológica. La teoría y práctica indican que los iones de amonio y manganeso y componentes orgánicos biodegradables pueden ser removidos por medio de procesos de crecimiento por adheción tales como filtros de lecho fijo, de lecho fluidificado, y filtros de arena rápidos. Temperaturas bajas no imposibilitan el buen tratamiento. Un modelo cinético cuantitativo, que describe con precisión los resultados de campo, provee una base sólida para el diseño y operación con éxito de procesos biológicos de tratamiento de agua. Se recomienda que un proceso biológico sea seguido de un proceso convencional para proveer barreras múltiples contra el escape de microorganismos al agua tratada.
Article
Biological stability refers to the inability of drinking water to support microbial growth. This phenomenon was studied in a full-scale drinking water treatment and distribution system of the city of Zurich ( Switzerland). The system treats lake water with successive ozonation and biological filtration steps and distributes the water without any disinfectant residuals. Chemical and microbiological parameters, notably dissolved organic carbon (DOC), assimilable organic carbon (AOC), heterotrophic plate counts (HPC) and flow-cytometric total cell concentration (TCC), were measured over an 18-month period. We observed a direct correlation between changes in the TCC, DOC and AOC concentrations during treatment; an increase in cell concentration was always associated with a decrease in organic carbon. This pattern was, however, not discerned with the conventional HPC method. The treated water contained on average a TCC of 8.97 x 10(4) cells ml(-1), a DOC concentration of 0.78 mgl(-1) and an AOC concentration of 32 mu g(-1), and these parameters hardly changed in the distribution network, suggesting that the treated water had a high level of biological stability. This study highlights the descriptive value of alternative parameters such as flow-cytometric TCC for drinking water analysis, and pinpoints some of the key aspects regarding biological stability in drinking water without disinfectant residuals.
Article
The bacterial community structure of a drinking water microbiome was characterized over three seasons using 16S rRNA gene based pyrosequencing of samples obtained from source water (a mix of a groundwater and a surface water), different points in a drinking water plant operated to treat this source water, and in the associated drinking water distribution system. Even though the source water was shown to seed the drinking water microbiome, treatment process operations limit the source water's influence on the distribution system bacterial community. Rather, in this plant, filtration by dual media rapid sand filters played a primary role in shaping the distribution system bacterial community over seasonal time scales as the filters harbored a stable bacterial community that seeded the water treatment processes past filtration. Bacterial taxa that colonized the filter and sloughed off in the filter effluent were able to persist in the distribution system despite disinfection of finished water by chloramination and filter backwashing with chloraminated backwash water. Thus, filter colonization presents a possible ecological survival strategy for bacterial communities in drinking water systems, which presents an opportunity to control the drinking water microbiome by manipulating the filter microbial community. Grouping bacterial taxa based on their association with the filter helped to elucidate relationships between the abundance of bacterial groups and water quality parameters and showed that pH was the strongest regulator of the bacterial community in the sampled drinking water system.