Pyrosequencing analysis of the bacterial community in drinking water wells

Tracking the microbial communities from the farm to the processing facility of a washed-rind cheese operation

Milk residue and the accompanying biofilm accumulation in milking systems can compromise the microbial quality of milk and the downstream processes of cheese production. Over a six-month study, the microbial ecosystems of milk (n = 24), tap water (n = 24) and environmental swabs (n = 384) were cultured by plating decimal dilutions to obtain viable counts of total aerobic mesophilic lactose-utilizing bacteria (lactose-M17), lactic acid bacteria (MRS), yeasts and molds (Yeast, Glucose, Chloramphenicol (YGC) medium). Viable aerobic lactose-M17 plate counts of milk remained well below 4.7 log CFU/ml over five of the months, except for 1 week in November where milk at the facility exceeded 5 log CFU/ml. Swab samples of the farm milking equipment showed consistent viable counts after sanitation, while the bulk tank swabs contained the lowest counts. Viable counts from swabs of the facility were generally below the detection limit in the majority of samples with occasional residual contamination on some food contact surfaces. Extracted DNA was amplified using primers targeting the V3-V4 region of the 16S rRNA gene, and the amplicons were sequenced by MiSeq to determine the shared microbiota between the farm and the processing facility (8 genera). Culture independent analysis of bacterial taxa in milk, water and residual contamination after sanitation with swab samples revealed the shared and distinct microbiota between the sample types of both facilities. Amplicon sequence variants (ASVs) of the V3-V4 region of the 16S rRNA gene revealed that the microbiota of milk samples had lower diversity than water or environmental swabs (279 ASVs compared to 3,444 in water and 8,747 in environmental swabs). Brevibacterium and Yaniella (both Actinomycetota) were observed in all sampling types. Further studies will include whole genome sequencing of Brevibacterium spp. isolates to determine their functionality and diversity within the system.

Spatial and Temporal Shifts of Endophytic Bacteria in Conifer Seedlings of Abies religiosa (Kunth) Schltdl. & Cham

Endophytes play an important role in plant development, survival, and establishment, but their temporal dynamics in young conifer plants are still largely unknown. In this study, the bacterial community was determined by metabarcoding of the 16S rRNA gene in the rhizoplane, roots, and aerial parts of 1- and 5-month-old seedlings of natural populations of Abies religiosa (Kunth) Schltdl. & Cham. In 1-month-old seedlings, Pseudomonas dominated aerial parts (relative abundance 71.6%) and roots (37.9%). However, the roots exhibited significantly higher bacterial species richness than the aerial parts, with the dissimilarity between these plant sections mostly explained by the loss of bacterial amplification sequence variants. After 5 months, Mucilaginibacter dominated in the rhizoplane (9.0%), Streptomyces in the roots (12.2%), and Pseudomonas in the aerial parts (18.1%). The bacterial richness and community structure differed significantly between the plant sections, and these variations were explained mostly by 1-for-1 substitution. The relative abundance of putative metabolic pathways significantly differed between the plant sections at both 1 and 5 months. All the dominant bacterial genera (e.g., Pseudomonas and Burkholderia-Caballeronia-Paraburkholderia) have been reported to have plant growth-promoting capacities and/or antagonism against pathogens, but what defines their role for plant development has still to be determined. This investigation improves our understanding of the early plant-bacteria interactions essential for natural regeneration of A. religiosa forest.

Understanding the impacts of intermittent electro field on the bioelectrochemical aniline degradation system: Performance, microbial community and functional enzyme

On account of the lack of a sustainable electron donor source and the inhibitory effect of aniline on denitrogenation make it tough to achieve simultaneous removal of aniline and nitrogen. Herein, the strategy of adjusting electric field mode was applied to the electro-enhanced sequential batch reactors (E-SBRs: R1 (continuous ON), R2 (2 h-ON/2 h-OFF), R3 (12 h-ON/12 h-OFF), R4 (in the aerobic phase ON), R5 (in the anoxic phase ON)) to treat aniline wastewater. Aniline removal rate reached approximately 99% in the five systems. Decreasing electrical stimulation interval from 12 to 2 h significantly improved the electron utilization efficiency for aniline degradation and nitrogen metabolism. The total nitrogen removal was achieved from 70.31% to 75.63%. Meanwhile, the hydrogenotrophic denitrifiers of Hydrogenophaga, Thauera, and Rhodospirillales, enriched in reactors of minor electrical stimulation interval. Accordingly, the expression of functional enzyme related to electron transport was incremental with the proper electrical stimulation frequency.

Organic carbon release, denitrification performance and microbial community of solid-phase denitrification reactors using the blends of agricultural wastes and artificial polymers for the treatment of mariculture wastewater

This paper explored the possibility of heterotrophic denitrification driven by composite solid carbon sources in low carbon/nitrogen ratio marine recirculating aquaculture wastewater. In this study, two agricultural wastes, reed straw (RS), corn cob (CC) and two artificial polymers, polycaprolactone (PCL), poly3-hydroxybutyrate-hydroxypropionate (PHBV) were mixed in a 1:1 ratio to compare the carbon release characteristics of the four composite carbon sources (RS+PCL, RS+PHBV, CC+PCL, and CC+PHBV) and their effects on improving the mariculture wastewater for denitrification. Dissolved organic carbon (DOC) after carbon source release (4.96-1.07 mg/g), total organic carbon/chemical oxygen demand (1.9-0.79) and short-chain fatty acids (SCFAs) (4.23-0.21 mg/g) showed that all the four composite solid carbon sources had excellent organic carbon release ability, and the CC+PCL group had the highest release of DOC and SCFAs. Energy-dispersive X-ray spectroscopy, scanning electron microscopy, and Fourier-transform infrared spectroscopy were used to observe the changes in the surface characteristics of the composite carbon source before and after application. And results showed that the stable internal structure enabled CC+PCL group to have continuous carbon release performance and achieved the maximum denitrification efficiency (93.32 %). The NRE results were supported by the abundance of the Proteobacteria microbial community at the phylum level and Marinobacter at the genus level. Quantitative real-time PCR (q-PCR) indicated CC-containing composite carbon source groups have good nitrate reduction ability, while PCL-containing composite carbon source groups have better nitrite reduction level. In conclusion, the carbon source for agricultural wastes and artificial polymers can be used as an economic and effective solid carbon source for denitrification and treatment of marine recirculating aquaculture wastewater.

Enhanced denitrification of dispersed swine wastewater using Ca(OH)2-pretreated rice straw as a solid carbon source

In a pilot-scale packed bed reactor, the denitrification performance and microbial community structure of the dispersed swine wastewater treatment using calcium hydroxide (Ca(OH)₂) pretreated rice straw as a carbon source were investigated. In a Ca(OH)₂-pretreated rice straw supported denitrification system (Ca(OH)₂-RS), the removal efficiency of NO₃^--N was 96.39% at an influent NO₃^--N load of 0.04 kg/(m³•d). Meanwhile, there was no obvious accumulation of NO₂^--N or chemical oxygen demand (COD) in the effluent of Ca(OH)₂-RS. The contents of soluble microbial byproduct-like substances and tryptophan-like substances in the effluent of Ca(OH)₂-RS were reduced by 46.2% and 43.4%, respectively, compared with the influent. Overall, the Ca(OH)₂-pretreated rice straw system had a strong resistance to fluctuations in water quality conditions, such as influent NO₃^--N and COD concentrations. According to the microbial assay results, the Ca(OH)₂ pretreatment enriched more denitrifying bacteria. Among them, Proteobacteria (42.33%) and Bacteroidetes (35.28%) were the dominant bacteria. Moreover, the main denitrifying functional bacteria, generanorank_f_Saprospiraceae (13.32%), norank_f_Porphyromonadaceae (4.22%), and Flavobacterium (3.25%), were enriched in Ca(OH)₂-RS. This suggested that using Ca(OH)₂-pretreated rice straw as a carbon source was a stable and efficient technology to enhance the denitrification performance of dispersed swine wastewater.

Co-occurrence of autotrophic and heterotrophic denitrification in electrolysis assisted constructed wetland packing with coconut fiber as solid carbon source

Aiming at the problems of lack of carbon sources for nitrogen removal and low phosphorus removal efficiency of constructed wetlands (CWs) in treating wastewater treatment plant (WWTP) effluent, an electrolysis assisted constructed wetland (E-CW) with coconut fiber as substrate and solid carbon sources was constructed. The synthetic secondary effluent was used as the influent of the E-CW with a wastewater treatment capacity of 140 L d^-1. The total nitrogen (TN) and the total phosphorus (TP) removal efficiency of the E-CW with coconut fiber treating WWTP effluent were 69.4% and 93.3%, respectively, which were 54.3% and 88.2% higher than those of CW with coconut fiber and no electrolysis. The removal efficiency of TN was 39.9% higher than that of E-CW with gravel. The current intensity had significant effect on nitrogen removal efficiency and the release of carbon sources from coconut fiber. When current intensity increased from 0.25 A to 1.00 A, the TN removal efficiency and nitrate removal rate increased by 21.1% and 0.21 mg L^-1 h^-1, respectively, and the volatile fatty acids (VFAs) released from coconut fiber increased by 57.7 mg L^-1. The 16S rRNA high-throughput sequencing results indicated that the main functional nitrogen-removing microbes were Hydrogenophaga, Thauera, Rhodanobacteraceae_norank, Xanthobacteraceae_norank, etc. Multiple paths including autotrophic denitrification with hydrogen and Fe²⁺ as electron donors and heterotrophic denitrification were achieved in the system. Meanwhile, the main functional lignocellulose degradation microbes were enriched in the system, including Cytophaga_xylanolytica_group, and Caldilineaceae. Because electrolysis created a favorable environment for them to release carbon sources from coconut fiber. This study provided a new perspective for advanced nutrients removal of WWTP effluent in CWs.

Impact of secondary salts, temperature, and pH on the colloidal stability of graphene oxide in water

The stability of graphene oxide (GO) in water is extremely relevant because of its application as an adsorbent material, as well as for its fate and behavior in the environment. Zeta potential was used to study the effect of secondary salts (carbonate, sulfate, and phosphate), temperature (20 to 60 °C), and pH (5 to 9) on the stability of six different GOs produced from natural, synthetic, and amorphous graphite-with and without the use of attrition milling. Generally, GOs produced with attrition-milled graphites had lower ζ-potentials than their unmilled counterparts because of their smaller particle sizes and higher concentration of oxygen-containing functional groups. It was observed that GO produced from graphite and synthetic graphite had ζ-potential values lower than -30 mV, even at 30 °C. However, it was observed that all the GOs studied were unstable in the presence of carbonate and sulfate salts at concentrations between 170 and 1695 mg L^-1, as they reached a ζ-potential of -4.1 mV. Density-functional theory electronic structure calculations suggested that the instability of GO in the presence of carbonate and sulfate was caused by the abstraction of a proton resulting in interaction energies E _int of 28.3 and 168.9 kJ mol^-1, respectively. Our results suggest that temperatures above 30 °C, as well as carbonate and sulfate salts at concentrations relevant to arid and semi-arid regions, could promote the formation of agglomerates of GO, thus limiting its use and mobility in water.

Bacteria in (vermi)composted organic wastes mostly survive when applied to an arable soil cultivated with wheat (Triticum sp. L.)

Composting and vermicomposting are an environmentally friendly way to reduce pathogens in organic wastes and generate a valuable product that provides nutrients for crops. However, how the bacterial community structure changes during these different processes and if the bacteria applied with the (vermi)composted products survive in an arable cultivated soil is still largely unknown. In this study, we monitored how the bacterial community structure changed during conditioning, composting with and without Eisenia fetida, and when the end-product was applied to arable soil cultivated with wheat Triticum sp. L. The organic wastes used were biosolid, cow manure, and a mixture of both. Large changes occurred in the relative abundance of some of the most abundant bacterial genera during conditioning, but the changes were much smaller during composting or vermicomposting. The bacterial community structure was significantly different in the organic wastes during conditioning and (vermi)composting but adding E. fetida had no significant effect on it. Changes in the relative abundance of the bacterial groups in the (vermi)composted waste applied to the arable soil cultivated with wheat were small, suggesting that most survived even after 140 days. As such, applying (vermi)composted organic wastes not only adds nutrients to a crop but also contributes to the survival of plant growth-promoting bacteria found in the (vermi)compost. However, putative human pathogens found in the biosolid also survived in the arable soil, and their relative abundance remained high but mixing the biosolid with cow manure reduced that risk. It was found that applying (vermi)composted organic wastes to an arable soil not only provides plant nutrients and adds bacteria with plant growth-promoting capacities, but some putative pathogens also survived.

Microbial diversity in extreme environments

A wide array of microorganisms, including many novel, phylogenetically deeply rooted taxa, survive and thrive in extreme environments. These unique and reduced-complexity ecosystems offer a tremendous opportunity for studying the structure, function and evolution of natural microbial communities. Marker gene surveys have resolved patterns and ecological drivers of these extremophile assemblages, revealing a vast uncultured microbial diversity and the often predominance of archaea in the most extreme conditions. New omics studies have uncovered linkages between community function and environmental variables, and have enabled discovery and genomic characterization of major new lineages that substantially expand microbial diversity and change the structure of the tree of life. These efforts have significantly advanced our understanding of the diversity, ecology and evolution of microorganisms populating Earth's extreme environments, and have facilitated the exploration of microbiota and processes in more complex ecosystems.

High removal efficiencies of antibiotics and low accumulation of antibiotic resistant genes obtained in microbial fuel cell-constructed wetlands intensified by sponge iron

Using microbial fuel cells with constructed wetlands (MFC-CWs) for eliminating antibiotics has recently attracted extensive attention. However, antibiotic removal efficiencies in MFC-CWs must be enhanced, and the accumulation of antibiotic resistant genes (ARGs) remains an unmanageable issue. This study tries to enhance the antibiotic removal in synthetic wastewater and reduce ARGs by adding sponge iron (s-Fe⁰) and calcium peroxide to the anode and cathode of MFC-CWs, respectively, and/or simultaneously. The results demonstrated that adding s-Fe⁰ and calcium peroxide to MFC-CWs could improve the removal efficiencies of sulfamethoxazole (SMX) and tetracycline (TC) by 0.8-1.3% and 6.0-8.7%. Therein, s-Fe⁰ also significantly reduced 84.10-94.11% and 49.61-60.63% of total sul and tet genes, respectively. Furthermore, s-Fe⁰ improved the voltage output, power density, columbic efficiency, and reduced the internal resistance of reactors. The intensification to the electrode layers posed a significant effect on the microbial community composition and functions, which motivated the shift of antibiotic removal, accumulation of ARGs and bioelectricity generation in MFC-CWs. Given the overall performance of MFC-CWs, adding s-Fe⁰ to the anode region of MFC-CWs was found to be an effective strategy for removing antibiotics and reducing the accumulation of ARGs.

Effect of simulated tidal cycle on DOM, nitrogen and phosphorus release from sediment in Dagu River-Jiaozhou Bay estuary

Tide drives salt mixing processes, erosion, deposition, and nutrient circulation in sediments, which is critical to the estuarine systems. This study aims to investigate the effects of tidal cycle intensity on sediment dissolved organic matter (DOM), nitrogen and phosphorus release. In this study, the effects of tide are investigated by simulating different intensity of tidal disturbance with tidal simulator devices. The microbial community changes under different tidal cycle are disclosed to explain the mechanism of nutrient release. In addition, the short-term release of nitrogen and phosphorus under simulated tidal cycle is predicted by stepwise regression method. Results show that the higher the tidal cycle intensity, the stronger the DOM mineralization in sediments and diffusion into overlying water, leading to a sustained increase of fluorescence intensity in DOM. Besides, the tidal disturbance promotes the NH₄⁺-N and NO₃^--N release and the tidal disturbance is helpful for ammonification. While the greater the tidal intensity, the lower the NO₃^--N release. Content of released total phosphorus (TP) maintains at a low level and fluctuates over time under different simulated tidal intensity. In addition, tidal cycle greatly changes the microbial richness and diversity. Gammaproteobactere has the ability of denitrification and can reduce nitrate to nitrite. Besides, tidal environment greatly affects the abundance of Marinobacter which can enhance the N, P, and C migration transformation ability. The research on microbial community further explains the mechanism of nutrient release. The model of nitrogen and phosphorus release contributes to providing basic data for predicting the short-term release of nutrients under different simulated tidal intensity.

Bacterial Communities in Alkaline Saline Soils Amended with Young Maize Plants or Its (Hemi)Cellulose Fraction

We studied three soils of the former lake Texcoco with different electrolytic conductivity (1.9 dS m-1, 17.3 dS m-1, and 33.4 dS m-1) and pH (9.3, 10.4, and 10.3) amended with young maize plants and their neutral detergent fibre (NDF) fraction and aerobically incubated in the laboratory for 14 days while the soil bacterial community structure was monitored by means of 454-pyrosequencing of their 16S rRNA marker gene. We identified specific bacterial groups that showed adaptability to soil salinity, i.e., Prauseria in soil amended with young maize plants and Marinobacter in soil amended with NDF. An increase in soil salinity (17.3 dS m-1, 33.4 dS m-1) showed more bacterial genera enriched than soil with low salinity (1.9 dS m-1). Functional prediction showed that members of Alfa-, Gamma-, and Deltaproteobacteria, which are known to adapt to extreme conditions, such as salinity and low nutrient soil content, were involved in the lignocellulose degradation, e.g., Marinimicrobium and Pseudomonas as cellulose degraders, and Halomonas and Methylobacterium as lignin degraders. This research showed that the taxonomic annotation and their functional prediction both highlighted keystone bacterial groups with the ability to degrade complex C-compounds, such as lignin and (hemi)cellulose, in the extreme saline-alkaline soil of the former Lake of Texcoco.

Implications of Climate Change: How Does Increased Water Temperature Influence Biofilm and Water Quality of Chlorinated Drinking Water Distribution Systems?

Temperature variation can promote physico-chemical and microbial changes in the water transported through distribution systems and influence the dynamics of biofilms attached to pipes, thus contributing to the release of pathogens into the bulk drinking water. An experimental real-scale chlorinated DWDS was used to study the effect of increasing temperature from 16 to 24°C on specific pathogens, bacterial-fungal communities (biofilm and water samples) and determine the risk of material accumulation and mobilisation from the pipes into the bulk water. Biofilm was developed for 30 days at both temperatures in the pipe walls, and after this growth phase, a flushing was performed applying 4 gradual steps by increasing the shear stress. The fungal-bacterial community characterised by Illumina MiSeq sequencing, and specific pathogens were studied using qPCR: Mycobacterium spp., Mycobacterium avium complex, Acanthamoeba spp., Pseudomonas aeruginosa, Legionella pneumophilia, and Stenotrophomonas maltophilia. Sequencing data showed that temperature variation significantly modified the structure of biofilm microbial communities from the early stages of biofilm development. Regarding bacteria, Pseudomonas increased its relative abundance in biofilms developed at 24°C, while fungal communities showed loss of diversity and richness, and the increase in dominance of Fusarium genus. After the mobilisation phase, Pseudomonas continued being the most abundant genus at 24°C, followed by Sphingobium and Sphingomonas. For biofilm fungal communities after the mobilisation phase, Helotiales incertae sedis and Fusarium were the most abundant taxa. Results from qPCR showed a higher relative abundance of Mycobacterium spp. on day 30 and M. avium complex throughout the growth phase within the biofilms at higher temperatures. The temperature impacts were not only microbial, with physical mobilisation showing higher discolouration response and metals release due to the increased temperature. While material accumulation was accelerated by temperature, it was not preferentially to either stronger or weaker biofilm layers, as turbidity results during the flushing steps showed. This research yields new understanding on microbial challenges that chlorinated DWDS will undergo as global temperature rises, this information is needed in order to protect drinking water quality and safety while travelling through distribution systems.

Profiles of antibiotic resistome and microbial community in groundwater of CKDu prevalence zones in Sri Lanka

The chronic kidney disease of unknown etiology (CKDu) prevalent in certain regions of Sri Lanka poses a serious threat to human health. Previous epidemiological studies focused on the search of causative agents for CKDu etiology from the viewpoint of groundwater composition, but how CKDu prevalence affected the groundwater microbial composition, especially the antibiotic resistome, has never been illuminated. This study investigated the response of microbial community and antibiotic resistome to CKDu prevalence in the groundwater through the high throughput sequencing and qPCR (HT-qPCR), respectively. Results showed that CKDu prevalence significantly influenced the distribution of antibiotic resistome and microbial community composition. The mexF dominated in all the groundwater samples and could be considered as an intrinsic ARG, and the β-lactamase cphA was specially enriched and closely associated with the antibiotics used for CKDu patients. The Acinetobacter was a potential human pathogen common in the groundwater of CKDu affected regions, while CKDu prevalence specially enriched the Aeromonas. Statistical analysis indicated that CKDu prevalence impacted antibiotic resistome through the microbial community as a whole, and MGEs contributed to the occurrence of mexF, while the enrichment of cphA could be attributed to the increase of Aeromonas.

Linkage Between Dissolved Organic Matter Transformation, Bacterial Carbon Production, and Diversity in a Shallow Oligotrophic Aquifer: Results From Flow-Through Sediment Microcosm Experiments

Aquifers are important reservoirs for organic carbon. A fundamental understanding of the role of groundwater ecosystems in carbon cycling, however, is still missing. Using sediment flow-through microcosms, long-term (171d) experiments were conducted to test two scenarios. First, aquifer sediment microbial communities received dissolved organic matter (DOM) at low concentration and typical to groundwater in terms of composition (DOM-1x). Second, sediments received an elevated concentration of DOM originating from soil (DOM-5x). Changes in DOM composition were analyzed via NMR and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Carbon production, physiological adaptations and biodiversity of groundwater, and sediment prokaryotic communities were monitored by total cell counts, substrate use arrays, and deep amplicon sequencing. The experiments showed that groundwater microbial communities do not react very fast to the sudden availability of labile organic carbon from soil in terms of carbon degradation and biomass production. It took days to weeks for incoming DOM being efficiently degraded and pronounced cell production occurred. Once conditioned, the DOM-1x supplied sediments mineralized 294(±230) μgC L⁻¹_sed d⁻¹, 10-times less than the DOM-5x fed sediment communities [2.9(±1.1) mgC L⁻¹_sed d⁻¹]. However, the overall biomass carbon production was hardly different in the two treatments with 13.7(±4.8) μgC L⁻¹_sed d⁻¹ and 14.3(±3.5) μgC L⁻¹_sed d⁻¹, respectively, hinting at a significantly lower carbon use efficiency with higher DOM availability. However, the molecularly more diverse DOM from soil fostered a higher bacterial diversity. Taking the irregular inputs of labile DOM into account, shallow aquifers are assumed to have a low resilience. Lacking a highly active and responsive microbial community, oligotrophic aquifers are at high risk of contamination with organic chemicals.

Unravelling the composition of tap and mineral water microbiota: Divergences between next-generation sequencing techniques and culture-based methods

The complex and highly diverse microbial environment of drinking water, consisting mainly of bacteria at different metabolic states, is still underexplored. The aim of this work was to characterize the bacterial communities in tap water and bottled mineral water, the two predominant sources of drinking water in modern societies. A total of 11 tap water samples from a range of locations and distribution networks and 10 brands of bottled natural mineral water were analysed using two approaches: a) heterotrophic plate counts by matrix-assisted laser desorption/ionization time of flight mass-spectrometry (MALDI-TOF MS) for the culturable heterotrophic communities, and b) Illumina amplicon sequencing for total bacteria including non-culturable bacteria. Culturable heterotrophic bacteria were isolated in WPCA (ISO) agar at 22 ± 2 °C for 72 h and 2046 isolates were identified using MALDI-TOF MS. The Bruker Daltonics Library and a previously customized library (Drinking Water Library) were used as reference databases. For the total bacteria fraction, DNA was extracted from 6 L of water and submitted to Illumina 16S rRNA sequencing of the v4 region. Significant differences were observed between mineral and tap water, with a general dominance of Alphaproteobacteria (mainly the genus Blastomonas) in tap water and Gammaproteobacteria in mineral water with Acidovorax being the dominant genus in 3 out of 7 mineral water brands. The bacterial communities in the different brands of mineral water were highly diverse and characteristic of each one. Moreover, the season in which the water was bottled also affected the species distribution, with some of them identified in only one season. Among the culturable bacteria, the most abundant phylum was Proteobacteria (around 85% of the isolates), followed by Actinobacteria, Firmicutes and Bacteroidetes. Proteobacteria was also the most abundant phylum detected with Illumina sequencing (>99% of the reads). The two methods gave distinct results at the different taxonomic levels and could therefore have a complimentary application in the study of microbiota in mineral water environments. MALDI-TOF MS is a promising method for the rapid identification of heterotrophic bacteria in routine water analysis in the bottling industry. SIGNIFICANCE AND IMPACT OF THE STUDY: The complementarity of MALDI-TOF MS and NGS in the assessment of bacterial community diversity has been demonstrated in water intended for human consumption. The two methods are suitable for routine use in the water industry for water quality management.

Advanced treatment of effluent from municipal wastewater treatment plant by strengthened ecological floating bed

The performance of eological floating bed (EFB) with novel carbon source (CS) and reed biochar substrate (RBS) derived from reed straw (RS) was evaluated for the advanced treatment of effluent from wastewater treatment plants (WWTPs). The average carbon releasing capacity of CS was 4.50 mg/g, and the P adsorption capacity of RBS was 0.39 mg/g. The additional CS and RBS increased the average removal efficiencies of total nitrogen (TN) and total phosphorus (TP) by 57.6% and 46.7%, respectively. Furthermore, the high-throughput sequencing results revealed significantly different microbial species richness and diversity due to the CS and RBS. Some genera related to nitrogen removal, such as Pseudomonas, Rhodobacter, Hydrogenophaga, Bradyrhizobium, Acinetobacter and Thiobacillus, were enriched in the EFB with CS and RBS. This study provided a suitable method for effectively treating low C/N wastewater such as WWTPs effluent using EFB strengthened by processed wetland plant.

Research on efficient denitrification system based on banana peel waste in sequencing batch reactors: Performance, microbial behavior and dissolved organic matter evolution

Nitrate pollution presents a serious threat to the environment and public health. As an excellent heterotrophic denitrification carbon source, banana peel (a kind of agricultural waste) provides a feasible alternative to deal with the persistent high concentrations of nitrate pollution. Although the feasibility and economy of banana peel for denitrification have already been reported, the long-term stability and mechanism were still unclear. The coupling mechanism of organic matters and microorganism in the denitrification process was systematically investigated through a 17-cycle experiment. The results showed that significant NO₃^--N removal load and rate of 164.42 mg/g and 4.69 mg/(L·h) after long-term tests could be obtained. Organic matter analysis and 16S rRNA sequencing showed that the evolution of organic matter was dominated by Anaerolineaceae (fermenting bacteria), and, in the final step, the humification of organic matter was realized. Moreover, the presence of Lentimicrobium (denitrifying bacteria) was indispensable for the continuous removal of high concentrations of nitrate. The main functional gene of nitrogen transformation in this reaction system was NirS (haem-containing). This lab-scale heterotrophic denitrification process could contribute to a better understanding of the carbon and nitrogen cycles in the biogeochemical cycles to some extent, and it also provides a reference for the construction of highly efficient nitrate degradation reactors, based on agricultural wastes.

Biodiversity of organisms inhabiting the water supply network of Wroclaw. Detection of pathogenic organisms constituting a threat for drinking water recipients

The objective of the article was to present the diversity of organisms inhabiting the water supply network with particular consideration of pathogenic organisms that can cause an epidemiological threat, with the application of high throughput sequencing (HTS). The study material was water sampled from 15 points in the water supply system. High species diversity of bacteria was evidenced, as well as the presence of microorganisms from genus Clostridium and family Enterobacteriaceae. No presence of bacteria Clostridium perfringens was recorded, which suggests proper performance of water treatment processes. Owing to advanced techniques of molecular biology, the article also presents species very similar to pathogenic bacteria the detection of which is not possible by means of standard water analysis (plate culture). Based on literature data and very high similarity of the genome of the bacteria to that of pathogenic bacteria, the species are considered to potentially show the same negative character towards the recipient, and cause a serious epidemiological threat. Therefore, the performed analyses show that classic methods of assessment of sanitary quality of water are not fully sufficient, and HTS analysis should be performed as an auxiliary tool to provide the complete image of the community in the existing network.

Myriophyllum elatinoides growth and rhizosphere bacterial community structure under different nitrogen concentrations in swine wastewater

In this study, Myriophyllum elatinoides growth under different nitrogen (N) concentrations (2, 250, 300, 350 and 400 mg L^-1) and changes in rhizosphere bacterial community structure were investigated. High N (>300 mg L^-1) concentrations caused reduction in M. elatinoides biomass. Growth tended to stabilize at 49 days. N concentration in roots were higher than that in stems and leaves under high N conditions. TN and NH₄⁺ removal efficiencies reached 84.0% and 87.2%, respectively, in M. elatinoides surface flow constructed wetlands (SFCWs). Rhizosphere bacterial diversity increased over time. Proteobacteria, Firmicutes, Cyanobacteria, and Bacteroidetes dominated at the phylum level. Genera Turicibacter, Allochromatium, and Methylocystis increased at low N (<300 mg L^-1) concentrations, while Pseudomonas increased at high N concentrations over the experimental period. Redundancy analysis showed that pH was strongly correlated with changes in rhizosphere bacterial community structure. These findings helped to insight into N removal mechanism in M. elatinoides.

Biodiversity and ecology of microorganisms in high pressure membrane filtration systems

High-pressure membrane filtration (reverse osmosis and nanofiltration) is used to purify different water sources, including wastewater, surface water, groundwater and seawater. A major concern in membrane filtration is the accumulation and growth of micro-organisms and their secreted polymeric substances, leading to reduced membrane performance and membrane biofouling. The fundamental understanding of membrane biofouling is limited despite years of research, as the means of microbial interactions and response to the conditions on the membrane surface are complicated. Here, we discuss studies that investigated the microbial diversity of fouled high-pressure membranes. High-throughput amplicon sequencing of the 16S rRNA gene have shown that Burkholderiales, Pseudomonadales, Rhizobiales, Sphingomonadales and Xanthomonadales frequently obtain a high relative abundance on fouled membranes. The bacterial communities present in the diverse feed water types and in pre-treatment compartments are different from the communities on the membrane, because high-pressure membrane filtration provides a selective environment for certain bacterial groups. The biofilms that form within the pre-treatment compartments do not commonly serve as an inoculum for the subsequent high-pressure membranes. Besides bacteria also fungi are detected in the water treatment compartments. In contrast to bacteria, the fungal community does not change much throughout membrane cleaning. The stable fungal diversity indicates that they are more significant in membrane biofouling than previously thought. By reviewing the biodiversity and ecology of microbes in the whole high pressure membrane filtration water chain, we have been able to identify potentials to improve biofouling control. These include modulation of hydrodynamic conditions, nutrient limitation and the combination of cleaning agents to target the entire membrane microbiome.

Behavior of selected organophosphate flame retardants (OPFRs) and their influence on rhizospheric microorganisms after short-term exposure in integrated vertical-flow constructed wetlands (IVCWs)

Considering its ubiquitous occurrence and potential adverse effects of organophosphorus flame retardant (OPFR), it is urgent to explore the efficient treatment for OPFRs wastewater. Thus, integrated vertical-flow constructed wetlands (IVCWs) were set up to comparatively evaluate their nitrogen removal capacity under tidal flow operations and to investigate environmental behavior and rhizosphere microbial responses after short-term exposure to three OPFRs. The results show that IVCWs have an excellent TN removal rate (628.13 ± 110.63 mg m^-2 d^-1) and moderate mitigation efficiencies (48.37 ± 9.52 to 82.28 ± 7.48%) for target OPFRs when treating low-C/N ratio wastewater. Moreover, the sorption of selected OPFRs to soil (28.85-308.41 ng g^-1, dry weight (dw)), igneous rock (659.85-970.80 ng g^-1 dw) and zeolite (1045.60-1351.70 ng g^-1 dw) and accumulation in tissues of C. alternifolius (0-289.68 ng g^-1 dw) and P. australis (0.56-108.22 ng g^-1 dw) showed a hydrophobicity-specific feature. Namely, the highly hydrophobic compound tricresyl phosphate (TCrP) partitioned preferentially to sediment, and the chlorinated analytes were more easily taken up and then translocated into the plant body. Simultaneously, further mass balance analysis revealed the fate of OPFRs in IVCW components. A total of 53.25% of the highly hydrophobic TCrP inflow mass settled in sediment, while tris (2-chloroethyl) phosphate (TCEP) and tris (1-chloro-2-propyl) phosphate (TCPP) were more liable to discharge (35.33-50.89%) and other pathways (38.77-39.87%). Furthermore, the abundance of aerobic denitrifying bacteria (AD) in rhizosphere soil (2.25-5.12%), jointly with the prevalence of nitrobacteria (NOBs, 1.84-13.60%) and denitrifying bacteria (DNBs, 5.84-7.89%) in sublayer matrices, was responsible for superior TN removal. Additionally, the rhizosphere microbial richness, diversity and nitrogen-related microorganisms were clearly influenced by the presence of OPFRs. Notably, the genera Pseudomonas and Sphingobium might be the functional microorganisms for mixture OPFRs biodegradation.

Response of the Bacterial Community and Antibiotic Resistance in Overnight Stagnant Water from a Municipal Pipeline

Although drinking water safety has raised considerable concern, to date, the hidden health risks in newly released overnight water from a municipal pipeline have seldom received attention. In this study, bacterial community composition and the response of antibiotic-resistant bacteria (ARB) to ciprofloxacin, azithromycin, tetracycline, penicillin, and cephalosporin in overnight stagnant water were analyzed. With increases in heterotrophic bacteria plate count (HPC) during water stagnation, the numbers of ARB and the ARB/HPC ratios for the five antibiotics in resident water were observed to increase, which illustrated that the prevalence of ARB rose in the pipe network water during stagnation time (ST). Furthermore, during water stagnation for 12 h, an increase in bacteria related to fermentation was also observed. When the ST rose to 48 h, the fermentation bacteria become non-significant, and this was related to the exchange of pipe network water during daytime stagnation within the 48-h period. The antibiotic resistance index (ARI) showed that tetracycline had the highest resistance level in fresh water, and then decreased during water stagnation. When ST increased to 12 h, all ARI values of the five antibiotics were low, which was associated with changes in parameters during water retention and reduced resistance during short-term stagnation. When the ST increased to 24 and 48 h, the resistance to most antibiotics (except for tetracycline) increased, which showed that increasing antibiotic resistance is caused by the formation of biofilms in the pipeline during water stagnation.

Seasonal changes in the bacterial community structure of three eutrophicated urban lakes in Mexico city, with emphasis on Microcystis spp

Artificial urban lakes commonly have physicochemical conditions that contribute to rapid anthropogenic eutrophication and development of cyanobacterial blooms. Microcystis is the dominat genus in most freshwater bodies and is one of the main producter of microcystins. Using 454-pyrosequencing we characterized the bacterial community, with special emphasis on Microcystis, in three recreational urban lakes from Mexico City in both wet and dry seasons. We also evaluated some physicochemical parameters that might influence the presence of Microcystis blooms, and we associated the relative abundance of heterotrophic and autotrophic bacterial communities with their possible metabolic capacities. A total of 14 phyla, 18 classes, 39 orders, 53 families and 48 bacterial genera were identified in both seasons in the three urban lakes. Cyanobacteria had the highest relative abundance followed by Proteobacteria and Actinobacteria. Microcystis was the dominant taxon followed by Arthrospira, Planktothrix and Synechococcus. We also found heterotrophic bacteria associated with the blooms, such as Rhodobacter, Pseudomonas, Sphingomonas and, Porphyrobacter. The highest richness, diversity and dominance were registered in the bacterial community of the Virgilio Uribe Olympic Rowing-Canoeing Track in both seasons, and the lowest values were found in the Chapultepec Lake. The canonical correspondence analysis showed that dissolved oxygen and NO₃-N concentrations might explain the presence of Microcystis blooms. The metabolic prediction indicated that these communities are involved in photosynthesis, oxidative phosphorylation, methane metabolism, carbon fixation, and nitrogen and sulfur metabolism. The lakes studied had a high prevalence of Microcystis, but average values of microcystins did not exceed the maximum permissible level established by the United States Environmental Protection Agency for recreational and cultural activities. The presence of cyanobacteria and microcystins at low to moderate concentrations in the three lakes could result in ecosystem disruption and increase animal and human health risks.

Effect of the degree of oxidation of graphene oxide on As(III) adsorption

The study of the interaction between graphene oxide (GO) and arsenic is of great relevance not only in the design of adsorbent materials to remove this contaminant but also in the understanding of its combined nanotoxicity. In this work, we show that As(III) adsorption, primarily H₃AsO₃, by graphene oxide is affected by its degree of oxidation. Three types of GO with C/O ratios between 1.35 and 1.98 were produced, resulting in important variations in the concentration of COH and COC functional groups. The less oxidized material reached a maximum As(III) adsorption capacity of 123 mg/g, whereas the GO with the highest degree of oxidation reached a value of 288 mg/g at pH 7, the highest reported in the literature. We also show that sulfates and carbonates present in water strongly inhibit As(III) adsorption. The interaction between graphene oxide and As(III) was also studied by Density Functional Theory (DFT) computer models showing that graphene oxide interacts with As(III) primarily through hydrogen bonds, having interaction energies with the hydroxyl and epoxide groups of 1508.6 and 1583.6 kJ/mol, respectively. Finally, cytotoxicity tests showed that the graphene oxide maintained cellular viability of 57% with 50 μg/ml, regardless of its degree of oxidation.

Dietary effects on gut microbiota of the mesquite lizard Sceloporus grammicus (Wiegmann, 1828) across different altitudes

BACKGROUND

High-altitude ecosystems are extreme environments that generate specific physiological, morphological, and behavioral adaptations in ectotherms. The shifts in gut microbiota of the ectothermic hosts as an adaptation to environmental changes are still largely unknown. We investigated the food ingested and the bacterial, fungal, and protistan communities in feces of the lizard Sceloporus grammicus inhabiting an altitudinal range using metabarcoding approaches.

RESULTS

The bacterial phyla Bacteroidetes and Firmicutes, and the genera Bacteroides and Parabacteroides dominated the core fecal bacteriome, while Zygomycota and Ascomycota, and the species Basidiobolus ranarum and Basidiobolus magnus dominated the core fecal mycobiome. The diet of S. grammicus included 29 invertebrate families belonging to Arachnida, Chilopoda, and Insecta. The diversity and abundance of its diet decreased sharply at high altitudes, while the abundance of plant material and Agaricomycetes was significantly higher at the highest site. The composition of the fecal microbiota of S. grammicus was different at the three altitudes, but not between females and males. Dietary restriction in S. grammicus at 4150 m might explain the high fecal abundance of Akkermansia and Oscillopira, bacteria characteristic of long fasting periods, while low temperature favored B. magnus. A high proportion of bacterial functions were digestive in S. grammicus at 2600 and 3100, while metabolism of aminoacids, vitamins, and key intermediates of metabolic pathways were higher at 4150 m. Different assemblages of fungal species in the lizard reflect differences in the environments at different elevations. Pathogens were more prevalent at high elevations than at the low ones.

CONCLUSIONS

Limiting food resources at high elevations might oblige S. grammicus to exploit other food resources and its intestinal microbiota have degradative and detoxifying capacities. Sceloporus grammicus might have acquired B. ranarum from the insects infected by the fungus, but its commensal relationship might be established by the quitinolytic capacities of B. ranarum. The mycobiome participate mainly in digestive and degradative functions while the bacteriome in digestive and metabolic functions.

Bioenergy generation and simultaneous nitrate and phosphorus removal in a pyrite-based constructed wetland-microbial fuel cell

This study investigates the performance of a pyrite-based constructed wetland-microbial fuel cell (PCW-MFC) in chemical oxygen demand (COD), nitrate (NO₃^--N), total inorganic nitrogen (TIN), and total phosphorus (TP) removal and bioelectricity generation, and explores the mechanisms involved. Four microcosms were used: a constructed wetland (CW), a pyrite-based constructed wetland (PCW), a constructed wetland-microbial fuel cell (CW-MFC), and a PCW-MFC. After 180 days' operation, the PCW-MFC exhibited enhanced simultaneous nitrate and phosphorus removal and bioelectricity output. The maximum COD, NO₃^--N, TIN, and TP removal efficiencies in the PCW-MFC were 71.9%, 70.1%, 63.2%, and 91.2%, respectively, for a hydraulic retention time (HRT) of 6 h. The mean bioelectricity output of the PCW-MFC was 19.0-28.4% higher than that of the CW-MFC. The nitrate removal rate constant of the PCW-MFC was 1.04 d^-1, which is significantly higher than those of the others. Geobacter and sulfate-reducing bacteria were enriched in the PCW-MFC.

High-throughput DNA sequencing technologies for water and wastewater analysis

Conventional microbiological water monitoring uses culture-dependent techniques to screen indicator microbial species such as Escherichia coli and fecal coliforms. With high-throughput, second-generation sequencing technologies becoming less expensive, water quality monitoring programs can now leverage the massively parallel nature of second-generation sequencing technologies for batch sample processing to simultaneously obtain compositional and functional information of culturable and as yet uncultured microbial organisms. This review provides an introduction to the technical capabilities and considerations necessary for the use of second-generation sequencing technologies, specifically 16S rDNA amplicon and whole-metagenome sequencing, to investigate the composition and functional potential of microbiomes found in water and wastewater systems.

Modified solid carbon sources with nitrate adsorption capability combined with nZVI improve the denitrification performance of constructed wetlands

In this study, various modified agricultural wastes (modified canna leaves (MCL), modified rice straw (MRS) and modified peanut shells (MPS)) as solid carbon sources (SCSs) were used to remove nitrate in constructed wetlands (CWs). Then, modified SCSs combined with nZVI (SCSN) as co-electrons further enhanced both heterotrophic denitrification (HD) and autotrophic denitrification (AD) performance of CWs. The results showed that NO₃^--N removal efficiencies in CWs with SCSNs (75.3-91.1%) and in CWs with SCSs (63.3-65.5%) were significantly higher than that in CK-CW (47.0%). The presence of SCSs reduced the accumulation of NO₂^--N in CWs. Compared to the addition of SCSs, the addition of SCSNs decreased the effluent COD concentration in CWs, avoiding secondary pollution. In addition, the solid-phase denitrifiers Silanimonas and Thauera were enriched in MPS-CW. Thermomonas, an autotrophic denitrifying bacteria (ADB), and Azospira, a nitrate-reducing Fe (II) oxidation bacteria (NRFOB), exhibited high relative abundance in MPN-CW.

Microbial community dynamics during aerobic granulation in a sequencing batch reactor (SBR)

Microorganisms in aerobic granules formed in sequencing batch reactors (SBR) remove contaminants, such as xenobiotics or dyes, from wastewater. The granules, however, are not stable over time, decreasing the removal of the pollutant. A better understanding of the granule formation and the dynamics of the microorganisms involved will help to optimize the removal of contaminants from wastewater in a SBR. Sequencing the 16S rRNA gene and internal transcribed spacer PCR amplicons revealed that during the acclimation phase the relative abundance of Acinetobacter reached 70.8%. At the start of the granulation phase the relative abundance of Agrobacterium reached 35.9% and that of Dipodascus 89.7% during the mature granule phase. Fluffy granules were detected on day 43. The granules with filamentous overgrowth were not stable and they lysed on day 46 resulting in biomass wash-out. It was found that the reactor operation strategy resulted in stable aerobic granules for 46 days. As the reactor operations remained the same from the mature granule phase to the end of the experiment, the disintegration of the granules after day 46 was due to changes in the microbial community structure and not by the reactor operation.

Application of sewage sludge to agricultural soil increases the abundance of antibiotic resistance genes without altering the composition of prokaryotic communities

The application of sewage sludge as soil amendment is a common agricultural practice. However, wastewater treatment plants, sewage sludge and sewage sludge-amended soils have been reported as hotspots for the appearance and dissemination of antibiotic resistance, driven, among other factors, by selection pressure exerted by co-exposure to antibiotics and heavy metals. To address this threat to environmental and human health, soil samples from a long-term (24 years) field experiment, carried out to study the impact of thermally dried and anaerobically digested sewage sludge (at different doses and frequencies of application) on agricultural soil quality, were investigated for the presence of genes encoding antibiotic resistance (ARGs) and mobile genetic elements (MGEs). Sewage sludge-induced changes in specific soil physicochemical and microbial properties, as indicators of soil quality, were also investigated. The application of sewage sludge increased the total concentration of copper and zinc in amended soils, but without affecting the bioavailability of these metals, possibly due to the high values of soil pH and organic matter content. Soil microbal quality, as reflected by the value of the Soil Quality Index, was higher in sewage sludge-amended soils. Similarly, the application of sewage sludge increased soil microbial activity and biomass, as well as the abundance of ARGs and MGE genes, posing a risk of dissemination of antibiotic resistance. In contrast, the composition of soil prokaryotic communities was not significantly altered by the application of sewage sludge. We found correlation between soil Cu and Zn concentrations and the abundance of ARGs and MGE genes. It was concluded that sewage sludge-derived amendments must be properly treated and managed if they are to be applied to agricultural soil.

Intensified heterotrophic denitrification in constructed wetlands using four solid carbon sources: Denitrification efficiency and bacterial community structure

Biodenitrification using solid carbon sources is a cost-effective way for nitrate removal. In the study, wheat straw, cotton, poly(butylene succinate), and newspaper was chosen as the carbon source to compare the denitrification efficiency and bacterial communities in constructed wetlands. Parameters including COD, NO₃^--N, NO₂^--N and total nitrogen (TN) were analyzed. Results indicated that newspaper provided significantly higher NO₃^--N and TN removal efficiency than the other three solid carbon sources in low-temperature condition. Moreover, both newspaper and wheat straw allowed high NO₃^--N and TN removal efficiency in high-temperature condition. According to pyrosequencing analysis, denitrifying bacteria Dechloromonas and Thauera were the predominant genus in the anaerobic zone of CO- (3.92 and 2.35%, respectively), WS- (1.97 and 1.02%, respectively) and NP-CWs (1.71 and 1.31%, respectively). Genus of Levilinea was enriched in NP- (1.02%) and WS-CWs (0.91%). Furthermore, genus Paludibacter (2.69%) and Saccharofermentans (3.14%) showed high relative abundance in WS-CWs.

Effects of pipe material on nitrogen transformation, microbial communities and functional genes in raw water transportation

Raw water transportation pipelines are vital in an urban water supply system for transporting raw water to drinking water treatment plants. This study investigated the effects of pipe material on nitrogen transformation, microbial communities and characteristics of related function genes in paint-lined steel pipe (PLSP) and cement-lined steel pipe (CLSP) raw water model systems. We established quantitative relationships between specific functional genes and change rates of nitrogen pollutants, which were verified by field investigation on nitrogen pollutant transformations in real raw water transportation systems. The results showed that the CLSP produced higher ammonia nitrogen (NH₄⁺-N) transformation rates and higher effluent concentrations of nitrate nitrogen (NO₃^--N) and dissolved organic nitrogen (DON) than the PLSP. Both pipes achieved high and stable nitrite nitrogen (NO₂^--N) and low total nitrogen (TN) removal efficiency. Nitrification was found to be the dominant process in both model systems, especially in the CLSP. Characteristics of microbial communities and nitrogen functional genes, which were analysed by high-throughput pyrosequencing and quantitative polymerase chain reaction (qPCR), respectively, varied between the two pipe systems. Nitrogen transformation pathways, identified by path analysis, were also different between the PLSP and CLSP due to different microbial community characteristics and synergistic effects of nitrogen functional genes. In the CLSP, (NH₄⁺-N→NO₂^--N) with part denitrification, was the primary transformation pathway of ammonia nitrogen (NH₄⁺-N), while only ammonia oxidization contributed to NH₄⁺-N transformation in the PLSP. (NO₂^--N→NO₃^--N) was the main pathway involved in NO₂^--N transformation and NO₃^--N accumulation. The TN removal showed complex relationships with nitrification, denitrification and nitrogen fixation processes. These findings provided molecular-level insights into nitrogen pollutant transformations during the transportation of raw water through different types of pipes and technical support for the selection of raw water pipe materials. In our study area, the Taihu basin, China, PLSP was better than CLSP for distributing raw water in a short transportation distance, due to the lower effluent concentrations of DON and NO₃^--N and less abundance of microorganisms.

Characterization of the bacterial community composition in water of drinking water production and distribution systems in Flanders, Belgium

The quality of drinking water is influenced by its chemical and microbial composition which in turn may be affected by the source water and the different processes applied in drinking water purification systems. In this study, we investigated the bacterial diversity in different water samples from the production and distribution chain of thirteen drinking water production and distribution systems from Flanders (Belgium) that use surface water or groundwater as source water. Water samples were collected over two seasons from the source water, the processed drinking water within the production facility and out of the tap in houses along its distribution network. 454‐pyrosequencing of 16S ribosomal RNA gene sequences revealed a total of 1,570 species‐level bacterial operational taxonomic units. Strong differences in community composition were found between processed drinking water samples originating from companies that use surface water and other that use groundwater as source water. Proteobacteria was the most abundant phylum in all samples. Yet, several phyla including Actinobacteria were significantly more abundant in surface water while Cyanobacteria were more abundant in surface water and processed water originating from surface water. Gallionella, Acinetobacter, and Pseudomonas were the three most abundant genera detected. Members of the Acinetobacter genus were even found at a relative read abundance of up to 47.5% in processed water samples, indicating a general occurrence of Acinetobacter in drinking water (systems).

Gut Bacterial Communities of Dendroctonus valens and D. mexicanus (Curculionidae: Scolytinae): A Metagenomic Analysis across Different Geographical Locations in Mexico

Dendroctonus bark beetles are a worldwide significant pest of conifers. This genus comprises 20 species found in North and Central America, and Eurasia. Several studies have documented the microbiota associated with these bark beetles, but little is known regarding how the gut bacterial communities change across host range distribution. We use pyrosequencing to characterize the gut bacterial communities associated with six populations of Dendroctonus valens and D. mexicanus each across Mexico, determine the core bacteriome of both insects and infer the metabolic pathways of these communities with Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) to evaluate whether these routes are conserved across geographical locations. Our results show that the β-diversity with UniFrac unweighted varies among locations of both bark beetles mainly due to absence/presence of some rare taxa. No association is found between the pairwise phylogenetic distance of bacterial communities and geographic distance. A strict intraspecific core bacteriome is determined for each bark beetle species, but these cores are different in composition and abundance. However, both bark beetles share the interspecific core bacteriome recorded previously for the Dendroctonus genus consisting of Enterobacter, Pantoea, Providencia, Pseudomonas, Rahnella, and Serratia. The predictions of metabolic pathways are the same in the different localities, suggesting that they are conserved through the geographical locations.

Amplicon Sequencing Reveals Microbiological Signatures in Spent Nuclear Fuel Storage Basins

Water quality is an important determinant for the structural integrity of alloy cladded fuels and assemblies during long-term wet storage. Detailed characterization of a water filled storage basin for spent nuclear reactor fuel was performed following the formation and proliferation of an amorphous white flocculent. White precipitant was sampled throughout the storage basin for chemical and spectroscopic characterization, and environmental DNA was extracted for 454 pyrosequencing of bacterial 16S rRNA gene diversity. Accordingly, spectroscopic analyses indicated the precipitant to be primarily amorphous to crystalline aluminum (oxy) hydroxides with minor associated elemental components including Fe, Si, Ti, and U. High levels of organic carbon were co-localized with the precipitant relative to bulk dissolved organic concentrations. Bacterial densities were highly variable between sampling locations and with depth within the water filled storage basin; cell numbers ranged from 4 × 10³to 4 × 10⁴ cells/mL. Bacterial diversity that was physically associated with the aluminum (oxy) hydroxide complexes exceeded an estimated 4,000 OTUs/amplicon library (3% cutoff) and the majority of sequences were aligned to the families Burkholderiaceae (23%), Nitrospiraceae (23%), Hyphomicrobiaceae (17%), and Comamonadaceae (6%). We surmise that episodic changes in the physical and chemical properties of the basin contribute to the polymerization of aluminum (oxy) hydroxides, which in turn can chemisorb nutrients, carbon ligands and bacterial cells from the surrounding bulk aqueous phase. As such, these precipitants should establish favorable microhabitats for bacterial colonization and growth. Comparative analyses of 16S rRNA gene amplicon libraries across a selection of natural and engineered aquatic ecosystems were performed and microbial community and taxonomic signatures unique to the spent nuclear fuel (SNF) storage basin environment were revealed. These insights could spur the development of tractable bio-indicators that are specific of and diagnostic for water quality at discrete locations and finer scales of resolution, marking an important contribution for improved water quality and management of SNF storage facilities.

Comparative Analysis of the Gut Bacterial Community of Four Anastrepha Fruit Flies (Diptera: Tephritidae) Based on Pyrosequencing

Fruit flies are the most economically important group of phytophagous flies worldwide. Whereas the ecological role of bacteria associated with tephritid fruit fly species of the genera Bactrocera and Ceratitis has been demonstrated, the diversity of the bacterial community in Anastrepha has been poorly characterized. This study represents the first comprehensive analysis of the bacterial community in the gut of larvae and adults of Anastrepha ludens, A. obliqua, A. serpentina, and A. striata using 454 pyrosequencing. A total of four phyla, seven classes, 11 families, and 27 bacterial genera were identified. Proteobacteria was the most represented phylum, followed by Firmicutes, Actinobacteria, and Deinococcus-Thermus. The genera Citrobacter, Enterobacter, Escherichia, Klebsiella, and Raoultella were dominant in all samples analyzed. In general, the bacterial community diversity in adult flies was higher in species with a broader diet breadth than species with a restricted number of hosts, whereas it was also higher in adults versus larvae. Differences in bacterial communities in adults might be determined by the number of fruit species infested. Lastly, the predictive functional profile analysis suggested that community members may participate in metabolic pathways related to membrane transport and metabolism of carbohydrates, amino acids, cofactors, and lipids. These results provide the basis for the study of unexplored functional roles of bacteria in this insect group.

Bacteriome from Pinus arizonica and P. durangensis: Diversity, Comparison of Assemblages, and Overlapping Degree with the Gut Bacterial Community of a Bark Beetle That Kills Pines

Symbioses between plants and microorganims have been fundamental in the evolution of both groups. The endophytic bacteria associated with conifers have been poorly studied in terms of diversity, ecology, and function. Coniferous trees of the genera Larix, Pseudotsugae, Picea and mainly Pinus, are hosts of many insects, including bark beetles and especially the Dendroctonus species. These insects colonize and kill these trees during their life cycle. Several bacteria detected in the gut and cuticle of these insects have been identified as endophytes in conifers. In this study, we characterized and compared the endophytic bacterial diversity in roots, phloem and bark of non-attacked saplings of Pinus arizonica and P. durangensis using 16S rRNA gene pyrosequencing. In addition, we evaluated the degree of taxonomic relatedness, and the association of metabolic function profiles of communities of endophytic bacteria and previously reported gut bacterial communities of D. rhizophagus; a specialized bark beetle that colonizes and kills saplings of these pine species. Our results showed that both pine species share a similar endophytic community. A total of seven bacterial phyla, 14 classes, 26 orders, 43 families, and 51 genera were identified. Enterobacteriaceae was the most abundant family across all samples, followed by Acetobacteraceae and Acidobacteriaceae, which agree with previous studies performed in other pines and conifers. Endophytic communities and that of the insect gut were significantly different, however, the taxonomic relatedness of certain bacterial genera of pines and insect assemblages suggested that some bacteria from pine tissues might be the same as those in the insect gut. Lastly, the metabolic profile using PICRUSt showed there to be a positive association between communities of both pines and insect gut. This study represents the baseline into the knowledge of the endophytic bacterial communities of two of the major hosts affected by D. rhizophagus.

Microbial community structure in aerobic and fluffy granules formed in a sequencing batch reactor supplied with 4-chlorophenol at different settling times

Toxic compounds, such as 4-chlorophenol (4-CP), which is a common pollutant in wastewater, are removed efficiently from sequencing batch reactors (SBRs) by microorganisms. The bacterial community in aerobic granules formed during the removal of 4-CP in a SBR was monitored for 63days. The SBR reactor was operated with a constant filling and withdrawal time of 7 and 8min and decreasing settling time (30, 5, 3 and 2min) to induce the formation of aerobic granules. During the acclimation period lasting 15days (30min settling time) had a strong effect on the bacterial community. From day 18 onwards, Sphingobium and Comamonadaceae were detected. Rhizobiaceae were dominant from day 24 to day 28 when stable aerobic granules were formed. At day 35, fluffy granules were formed, but the bacterial community structure did not change, despite the changes in the reactor operation to inhibit filamentous bacteria growth. This is the first report on changes in the bacterial community structure of aerobic and fluffy granules during granulation process in a reactor fed with 4-CP and the prediction of its metabolic pathways.

Biological treatment of N-nitrosodimethylamine (NDMA) and N-nitrodimethylamine (NTDMA) in a field-scale fluidized bed bioreactor

The ex situ treatment of N-nitrosodimethylamine (NDMA) and N-nitrodimethylamine (NTDMA) in groundwater was evaluated in a field-scale fluidized bed bioreactor (FBR). Both of these compounds, which originally entered groundwater at the test site from the use of liquid rocket propellant, are suspected human carcinogens. The objective of this research was to examine the application of a novel field-scale propane-fed fluidized bed bioreactor as an alternative to ultraviolet irradiation (UV) for treating NDMA and NTDMA to low part-per-trillion (ng/L) concentrations. Previous laboratory studies have shown that the bacterium Rhodococcus ruber ENV425 can biodegrade NDMA and NTDMA during growth on propane as a primary substrate and that the strain can effectively reduce NDMA concentrations in propane-fed bench-scale bioreactors of different design. R. ruber ENV425 was used as a seed culture for the FBR, which operated at a fluidization flow of ∼19 L-per-min (LPM) and received propane, oxygen, and inorganic nutrients in the feed. The reactor effectively treated ∼1 μg/L of influent NDMA to effluent concentrations of less than 10 ng/L at a hydraulic residence time (HRT) of only 10 min. At a 20 min HRT, the FBR reduced NDMA to <4.2 ng/L in the effluent, which was the discharge limit at the test site where the study was conducted. Similarly, NTDMA was consistently treated in the FBR from ∼0.5 μg/L to <10 ng/L at an HRT of 10 min or longer. Based on these removal rates, the average NDMA and NTDMA elimination capacities achieved were 2.1 mg NDMA treated/m³ of expanded bed/hr of operation and 1.1 mg NTDMA treated/m³ of expanded bed/hr of operation, respectively. The FBR system was highly resilient to upsets including power outages. Treatment of NDMA, but not NTDMA, was marginally affected when trace co-contaminants including trichloroethene (TCE) and trichlorofluoromethane (Freon 11) were initially added to feed groundwater, but performance recovered over a few weeks in the continued presence of these compounds. Strain ENV425 appeared to be replaced by native propanotrophs over time based on qPCR analysis, but contaminant treatment was not diminished. The results suggest that a FBR can be a viable alternative to UV treatment for removing NDMA from groundwater.

Archaeal and Bacterial Community Structure in an Anaerobic Digestion Reactor (Lagoon Type) Used for Biogas Production at a Pig Farm

Biogas production from animal waste is an economically viable way to reduce environmental pollution and produce valuable products, i.e<i>.</i>, methane and a nutrient-rich organic waste product. An anaerobic digestion reactor for biogas production from pig waste was sampled at the entrance, middle (digestion chamber), and exit of a digester, while the bacterial and archaeal community structure was studied by 16S rRNA gene metagenomics. The number of bacterial operational taxonomic units (OTU)-97% was 3-7 times larger than that of archaeal ones. Bacteria and Archaea found in feces of animals (e.g., Clostridiaceae, Lachnospiraceae, Ruminococcaceae, <i>Methanosarcina</i>, <i>Methanolobus</i>, <i>Methanosaeta</i>, and <i>Methanospirillum</i>) dominated the entrance of the digester. The digestion chamber was dominated by anaerobic sugar-fermenting OP9 bacteria and the syntrophic bacteria <i>Candidatus</i> Cloacamonas (Waste Water of Evry 1; WWE1). The methanogens dominant in the digestion chamber were the acetoclastic <i>Methanosaeta</i> and the hydrogenothrophic <i>Methanoculleus</i> and <i>Methanospirillum</i>. Similar bacterial and archaeal groups that dominated in the middle of the digestion chamber were found in the waste that left the digester. Predicted functions associated with degradation of xenobiotic compounds were significantly different between the sampling locations. The microbial community found in an anaerobic digestion reactor loaded with pig manure contained microorganisms with biochemical capacities related to the 4 phases of methane production.

Bacterial biomes and potential human pathogens in irrigation water and leafy greens from different production systems described using pyrosequencing

AIMS

To investigate the influence of irrigation water microbial quality on leafy green vegetables produced in commercial and small-scale farms as well as homestead gardens using pyrosequencing.

METHODS AND RESULTS

Next generation sequencing analysis of the V1-V3 hypervariable region of bacterial 16S rDNA was used to compare bacterial diversity in irrigation water sources and on leafy vegetables. In all samples (12) analysed, the phylum Proteobacteria (64·5%), class Gammaproteobacteria (56·6%) and genus Aeromonas (14·4%) were found to be dominant. Of the total Escherichia sequences detected in tested samples, lettuce (16·3%) from the one commercial farm harboured more sequences than cabbage from the small-scale farm (1·3%) or homestead gardens (1·9%). Escherichia sequences were detected in both irrigation water (4·6%) and on cabbage (1·3%) samples from the small-scale farm. The genus Salmonella was absent in borehole water but was detected in the holding dam water (<1%) from commercial farm A. Salmonella sequences were present in river water (<1%) and on cabbages (1·9%) from the small-scale farm but were not detected on cabbage samples from the one commercial farm or the homestead gardens.

CONCLUSION

Water sources quality used for irrigation greatly influences the microbial dynamics of the irrigated crop.

SIGNIFICANCE AND IMPACT OF THE STUDY

Microbial biomes in irrigation water and on leafy greens were described with pyrosequencing and revealed insights into prevalence of potential and opportunistic pathogens across different production systems.

Structure and dynamics of the gut bacterial microbiota of the bark beetle, Dendroctonus rhizophagus (Curculionidae: Scolytinae) across their life stages

Bark beetles play an important role as agents of natural renovation and regeneration in coniferous forests. Several studies have documented the metabolic capacity of bacteria associated with the gut, body surface, and oral secretions of these insects; however, little is known about how the bacterial community structure changes during the life cycle of the beetles. This study represents the first comprehensive analysis of the bacterial community of the gut of the bark beetle D. rhizophagus during the insect’s life cycle using 454 pyrosequencing. A total of 4 bacterial phyla, 7 classes, 15 families and 23 genera were identified. The α-diversity was low, as demonstrated in previous studies. The dominant bacterial taxa belonged to the Enterobacteriaceae and Pseudomonadaceae families. This low α-diversity can be attributed to the presence of defensive chemical compounds in conifers or due to different morpho-physiological factors in the gut of these insects acting as strong selective factors. Members of the genera Rahnella, Serratia, Pseudomonas and Propionibacterium were found at all life stages, and the first three genera, particularly Rahnella, were predominant suggesting the presence of a core microbiome in the gut. Significant differences in β-diversity were observed, mainly due to bacterial taxa present at low frequencies and only in certain life stages. The predictive functional profiling indicated metabolic pathways related to metabolism of amino acids and carbohydrates, and membrane transport as the most significant in the community. These differences in the community structure might be due to several selective factors, such as gut compartmentalization, physicochemical conditions, and microbial interactions.

Bacteria in drinking water sources of a First Nation reserve in Canada

Approximately 20% of the 600 First Nations reserves across Canada are under a drinking water advisory, often due to unacceptable levels of bacteria. In this study, we detected fecal bacteria at an alarmingly high frequency in drinking water sources in a fly-in First Nations community, most notably in buckets/drums of homes without running water where Escherichia coli levels ranged from 20 to 62,000CFU/100mL. The water leaving the water treatment plant was free of E. coli and its free residual chlorine concentration (0.67mg/L) was within the range typically observed for treated water in Canada. Water samples from taps in homes served by cisterns, and those sampled from the water truck and community standpipe, always showed unacceptable levels of E. coli (1 to 2100CFU/100mL) and free residual chlorine concentrations below the 0.2mg/L required to prevent bacterial regrowth. Samples from taps in homes served by piped water had lower levels of E. coli (0 to 2CFU/100mL). DNA- and RNA-based 16S rRNA Illumina sequencing demonstrated that piped and cisterns water distribution systems showed an abundance of viable cells of Alphaproteobacteria indicative of biofilm formation in pipes and cisterns. The alpha diversity, based on observed OTUs and three other indices, was lowest in water truck samples that supplied water to the cistern and the low free residual chlorine concentration (0.07mg/L) and predominance of Betaproteobacteria (63% of viable cells) that were immediately detected after the truck had filled up at the water treatment plant was indicative of contamination by particulate matter. Given these findings, First Nation residents living without running water and relying on inadequate water distribution systems are at higher risk of contracting water-born illnesses. We urge all governments in Canada to expand their investments in supporting and sustaining water as a human right in Canada's First Nations communities.

Unraveling the microbial community of a cold groundwater catchment system

The abundance, diversity and composition of bacterial communities in water wells with low groundwater temperatures were assessed. The drinking water catchment system, equipped with subsurface groundwater treatment for iron- and manganese removal, is located within a continental influenced veldt landscape type in eastern Russia, close to the border to China. In this study, the bacterial communities in 22 different water wells of the catchment system were analyzed and correlated to operating conditions and environmental factors. The investigated bacterial treated and groundwater populations differed from those in central European groundwater. Large variations between the investigated samples were observed, and DGGE profiles of water samples from the beginning and the end of the abstraction phases revealed two distinct fingerprint clusters with about 82% similarity to each other corresponding to the operation mode of the wells. Sequence data analysis from 454 pyrosequencing indicated Rhodoferax and Gallionella as the most abundant genera within the catchment system. The abundance of the OTU Methylotenera was statistically significant when correlated to the beginning of the abstraction phases, while no indicator OTUs could be determined for the end of the pumping phases. ACK-M1 cluster was proofed as indicator OTU for operating wells, whereas the Gallionella OTUs were correlated with non operating wells. Well operation and resultant oxygen entry could serve as factors that altered the bacterial community structure and composition the most. Quantitative PCR analysis showed that genes related to the iron-reducing Rhodoferax genus were present in nearly all of the samples. This study clearly showed an alteration within the bacterial communities dependent on the operation mode of the water wells.

Bacterial Communities Associated with Different Anthurium andraeanum L. Plant Tissues

Plant-associated microbes have specific beneficial functions and are considered key drivers for plant health. The bacterial community structure of healthy Anthurium andraeanum L. plants was studied by 16S rRNA gene pyrosequencing associated with different plant parts and the rhizosphere. A limited number of bacterial taxa, i.e., Sinorhizobium, Fimbriimonadales, and Gammaproteobacteria HTCC2089 were enriched in the A. andraeanum rhizosphere. Endophytes were more diverse in the roots than in the shoots, whereas all shoot endophytes were found in the roots. Streptomyces, Flavobacterium succinicans, and Asteroleplasma were only found in the roots, Variovorax paradoxus only in the stem, and Fimbriimonas 97%-OTUs only in the spathe, i.e., considered specialists, while Brevibacillus, Lachnospiraceae, Pseudomonas, and Pseudomonas pseudoalcaligenes were generalist and colonized all plant parts. The anaerobic diazotrophic bacteria Lachnospiraceae, Clostridium sp., and Clostridium bifermentans colonized the shoot system. Phylotypes belonging to Pseudomonas were detected in the rhizosphere and in the substrate (an equiproportional mixture of soil, cow manure, and peat), and dominated the endosphere. Pseudomonas included nine 97%-OTUs with different patterns of distribution and phylogenetic affiliations with different species. P. pseudoalcaligenes and P. putida dominated the shoots, but were also found in the roots and rhizosphere. P. fluorescens was present in all plant parts, while P. resinovorans, P. denitrificans, P. aeruginosa, and P. stutzeri were only detected in the substrate and rhizosphere. The composition of plant-associated bacterial communities is generally considered to be suitable as an indicator of plant health.

Microbiome profiling of drinking water in relation to incidence of inflammatory bowel disease

The etiology of inflammatory bowel disease (IBD) is unknown; current research is focused on determining environmental factors. One consideration is drinking water: water systems harbour considerable microbial diversity, with bacterial concentrations estimated at 10(6)-10(8) cells/L. Perhaps differences in microbial ecology of water sources may impact differential incidence rates of IBD. Regions of Manitoba were geographically mapped according to incidence rates of IBD and identified as high (HIA) or low (LIA) incidence areas. Bulk water, filter material, and pipe wall samples were collected from public buildings in different jurisdictions and their population structure analyzed using 16S rDNA sequencing. At the phylum level, Proteobacteria were observed significantly less frequently (P = 0.02) in HIA versus LIA. The abundance of Proteobacteria was also found to vary according to water treatment distribution networks. Gammaproteobacteria was the most abundant class of bacteria and was observed more frequently (P = 0.006) in LIA. At the genus level, microbes found to associate with HIA include Bradyrhizobium (P = 0.02) and Pseudomonas (P = 0.02). Particular microbes were found to associate with LIA or HIA, based on sample location and (or) type. This work lays out a basis for further studies exploring water as a potential environmental source for IBD triggers.

Microbial analysis of in situ biofilm formation in drinking water distribution systems: implications for monitoring and control of drinking water quality

Biofilm formation in drinking water distribution systems (DWDS) is influenced by the source water, the supply infrastructure and the operation of the system. A holistic approach was used to advance knowledge on the development of mixed species biofilms in situ, by using biofilm sampling devices installed in chlorinated networks. Key physico-chemical parameters and conventional microbial indicators for drinking water quality were analysed. Biofilm coverage on pipes was evaluated by scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM). The microbial community structure, bacteria and fungi, of water and biofilms was assessed using pyrosequencing. Conventional wisdom leads to an expectation for less microbial diversity in groundwater supplied systems. However, the analysis of bulk water showed higher microbial diversity in groundwater site samples compared with the surface water site. Conversely, higher diversity and richness were detected in biofilms from the surface water site. The average biofilm coverage was similar among sites. Disinfection residual and other key variables were similar between the two sites, other than nitrates, alkalinity and the hydraulic conditions which were extremely low at the groundwater site. Thus, the unexpected result of an exceptionally low diversity with few dominant genera (Pseudomonas and Basidiobolus) in groundwater biofilm samples, despite the more diverse community in the bulk water, is attributed to the low-flow hydraulic conditions. This finding evidences that the local environmental conditions are shaping biofilm formation, composition and amount, and hence managing these is critical for the best operation of DWDS to safeguard water quality.