Bacterial diversity from the source to the tap: a comparative study based on 16S rRNA gene-DGGE and culture-dependent methods

Two-year Monitoring of Microbiological Water Quality in Small Water Supply Systems: Implications for Microbial Risk Management

Small water supply systems (SWSSs) are often more vulnerable to waterborne disease outbreaks. In Japan, many SWSSs operate without regulation under the Waterworks Law, yet there is limited investigation into microbial contamination and the associated health risks. In this study, the microbiological water quality of four SWSSs that utilize mountain streams as water sources and do not install water treatment facilities were monitored for over 2 years. In investigated SWSSs, the mean heterotrophic plate counts were below 350 CFU/mL, and the total bacterial loads (16S rDNA concentration) ranged from 4.71 to 5.35 log10 copies/mL. The results also showed the consistent presence of fecal indicator bacteria (FIB), i.e., Escherichia coli and Clostridium perfringens, suggesting the potential of fecal pollution. E. coli was then utilized as an indicator to assess the health risk posed by E. coli O157:H7 and Campylobacter jejuni. The results indicated that the estimated mean annual risk of infection and disability-adjusted life years (DALYs) exceeded acceptable levels in all SWSSs for the two reference pathogens. To ensure microbial water safety, implementing appropriate water treatment facilities with an estimated mean required reduction of 5-6 log10 was necessary. This study highlighted the potential microbial contamination and health risk level in SWSSs that utilize mountain streams as water sources, even though the water sources were almost not affected by human activities. Furthermore, this study would also be helpful in supporting risk-based water management to ensure a safe water supply in SWSSs.

Antimicrobial Resistance Elements in Coastal Water of Llanquihue Lake, Chile

Antimicrobial resistance has been stated to be a global health problem. In Chile, the use of antibiotics should be declared by medical prescription, but it is unknown what happens to the drugs once the treatment ends. Among the possibilities for their disposal are the trash or the drain; regardless of which scenario arises, antibiotics could accumulate in the environment, stimulating the emergence of antimicrobial resistance mechanisms and their transfer between microorganisms. Unfortunately, sometimes wastewater ends up in bodies of water, due to the dragging of elements by rain, or by the presence of illegal water discharges. In this work, shotgun metagenomics was used to elucidate the functional and microbial composition of biohazard elements in the bay of Puerto Varas City, Chile. As expected, a high diversity of microorganisms was found, including bacterial elements described as human or animal pathogens. Also, a diverse repertory of antimicrobial resistant genes (ARGs) was detected, which confers mainly resistance to macrolides, beta-lactams, and tetracyclines, consistent with the families of antibiotics most used in Chile. Similar ARGs were identified in DNA mobile elements. In addition, we tested the antimicrobial susceptibility in 14 bacterial strains isolated from Llanquihue Lake. This is the first report of the presence of genomic elements that could constitute a health problem, considering the importance of the interconnection between environmental, animal, and human health, a concept known as One Health.

Effect of household pipe materials on formation and chlorine resistance of the early-stage biofilm: various interspecific interactions exhibited by the same microbial biofilm in different pipe materials

Microbial community biofilm exists in the household drinking water system and would pose threat to water quality. This paper explored biofilm formation and chlorination resistance of ten dual-species biofilms in three typical household pipes (stainless steel (SS), polypropylene random (PPR), and copper), and investigated the role of interspecific interaction. Biofilm biomass was lowest in copper pipes and highest in PPR pipes. A synergistic or neutralistic relationship between bacteria was evident in most biofilms formed in SS pipes, whereas four groups displayed a competitive relationship in biofilms formed in copper pipe. Chlorine resistance of biofilms was better in SS pipes and worse in copper pipes. It may be helped by interspecific relationships, but was more dependent on bacteria and resistance mechanisms such as more stable extracellular polymeric substance. The corrosion sites may also protect bacteria from chlorination. The findings provide useful insights for microbial control strategies in household drinking water systems.

Bacterial diversity across four drinking water distribution systems in Croatia: impacts of water management practices and disinfection by-products

Several factors may impact bacterial diversity in drinking water distribution systems (DWDSs) including the origin of the raw water, the water treatment technologies, and the disinfection practices applied. 16S rRNA metabarcoding was used for the in-depth characterization of bacterial communities in the four studied Croatian DWDSs (A, B, C, D) two of which had residual disinfectant (A, B) and two were without (C, D), while only B utilized the conventional water treatment technology. Significantly higher diversity and species richness were evidenced in non-disinfected DWDSs (p<0.05) compared to disinfected DWDSs. The phylum Proteobacteria was the most abundant in all the DWDSs, being proportionately higher in non-disinfected systems (p<0.05). The most abundant genera in DWDS-A Mycobacterium and Sphingomonas both positively correlated, whereas Lactobacillus negatively correlated with the concentration of disinfection by-products (DBPs) as a sum of haloacetic acids (HAAs). Conversely, the genus Ralstonia positively correlated with the individual DBP dichloroacetic acid. These results indicate that genera Sphingomonas, Mycobacterium, Lactobacillus and Ralstonia could have an effect on promoting the formation of DBPs, in a similar manner to how negatively correlated taxa may influence their degradation.

Microbial Community Structure and Diversity in Drinking Water Supply, Distribution Systems as well as Household Point of Use Sites in Addis Ababa City, Ethiopia

Understanding ecology of microbiomes in drinking water distribution systems is the most important notion in delivering safe drinking water. Drinking water distribution systems harbor various microbiota despite efforts made in improving water infrastructures in the water industry, especially, in developing countries. Intermittent water supply, long time of water storage, low water pressure, and contaminated source water are among many of the factors responsible for poor drinking water quality affecting health of people. The aim of this study was to explore microbial diversity and structure in water samples collected from source water, treated water, reservoirs, and household points of use locations (taps). High-throughput Illumina sequencing technology was employed by targeting the V4 region of the 16S rRNA gene and the V1-V3 region of the 18S rRNA gene to analyze the microbial community structure. Proteobacteria followed by Firmicutes, Bacteroidetes, and Actinobacteria were the core dominating taxa. Gammaproteobacteria was also dominant among other proteobacterial classes across all sampling points. Opportunistic bacterial genera such as Pseudomonas, Legionella, Klebsiella, Escherichia, and Actinobacteria, as well as eukaryotic microbes like Cryptosporidium, Hartmannella, Acanthamoeba, Aspergillus, and Candida were also abundant taxa found along the distribution systems. The shift in microbial community structure from source to point of use locations was influenced by basic factors such as residual chlorine, intermittent water supply, and long-time storage at the household. The complex microbiota detected in different sampling sites in this study brings drinking water quality problem which further causes significant health problems to both human and animal health. Treatment ineffectiveness, disinfection inefficiency, poor maintenance actions, leakage of sewage, and other domestic wastes are few among many other factors responsible for degraded drinking water quality in this study putting health at high risk. Findings of this research provide important and baseline information to understand the microbial profiles of drinking water along source water and distribution systems. Moreover, knowing the microbial profile will help to design proper water quality assurance approaches.

Distribution, Diversity and Antibiotic Resistance of Pseudomonas spp. Isolated from the Water Dams in the North of Tunisia

Natural environment is one of the important reservoirs to disseminate antibiotic resistance, most of the antibiotics resistance researches were focused on clinical isolates. Thus, this work aimed to analyze surface water samples collected from dams and rivers in the north of Tunisia. Pseudomonas species were confirmed using biochemical and molecular identifications. Resistance was studied by testing their susceptibility against 19 antibiotics using the disc diffusion method moreover the virulence factors were studied by PCR targeting 13 genes. 104 isolates were confirmed as Pseudomonas genera distributed into 21 species. The most abundant species is P. aeruginosa (22.11%), followed by P. protegens (12.5%). No resistance phenotypes were observed towards imipenem, meropenem, ceftazidime, colistin, ciprofloxacin and amikacin. A high resistance level was observed against cefoxitin (94.23%), amoxicillin-clavulanic acid (67.31%), nalidixic acid (62.5%), streptomycin (57.69%), ticarcillin (43.27%), fosfomycin (64.42%) and tetracycline (23.08%). A low rate of resistance was observed against cefotaxime (16.35%) and gentamicin (7.69%). The majority (70.19%) of isolates were Multidrug-resistant (MDR). 12 of virulence genes were found in all P. aeruginosa isolates. Our results showed that Pseudomonas isolates could be an important reservoir of antibiotic resistance from environment sites.

The Presence of Opportunistic Premise Plumbing Pathogens in Residential Buildings: A Literature Review

Opportunistic premise plumbing pathogens (OPPP) are microorganisms that are native to the plumbing environment and that present an emerging infectious disease problem. They share characteristics, such as disinfectant resistance, thermal tolerance, and biofilm formation. The colonisation of domestic water systems presents an elevated health risk for immune-compromised individuals who receive healthcare at home. The literature that has identified the previously described OPPPs (Aeromonas spp., Acinetobacter spp., Helicobacter spp., Legionella spp., Methylobacterium spp., Mycobacteria spp., Pseudomonas spp., and Stenotrophomonas spp.) in residential drinking water systems were systematically reviewed. By applying the Preferred reporting items for systematic reviews and meta-analyses guidelines, 214 studies were identified from the Scopus and Web of Science databases, which included 30 clinical case investigations. Tap components and showerheads were the most frequently identified sources of OPPPs. Sixty-four of these studies detected additional clinically relevant pathogens that are not classified as OPPPs in these reservoirs. There was considerable variation in the detection methods, which included traditional culturing and molecular approaches. These identified studies demonstrate that the current drinking water treatment methods are ineffective against many waterborne pathogens. It is critical that, as at-home healthcare services continue to be promoted, we understand the emergent risks that are posed by OPPPs in residential drinking water. Future research is needed in order to provide consistent data on the prevalence of OPPPs in residential water, and on the incidence of waterborne homecare-associated infections. This will enable the identification of the contributing risk factors, and the development of effective controls.

Monitoring antibiotic resistance genes in wastewater environments: The challenges of filling a gap in the One-Health cycle

Antibiotic resistance (AR) is a global problem requiring international cooperation and coordinated action. Global monitoring must rely on methods available and comparable across nations to quantify AR occurrence and identify sources and reservoirs, as well as paths of AR dissemination. Numerous analytical tools that are gaining relevance in microbiology, have the potential to be applied to AR research. This review summarizes the state of the art of AR monitoring methods, considering distinct needs, objectives and available resources. Based on the overview of distinct approaches that are used or can be adapted to monitor AR, it is discussed the potential to establish reliable and useful monitoring schemes that can be implemented in distinct contexts. This discussion places the environmental monitoring within the One-Health approach, where two types of risk, dissemination across distinct environmental compartments, and transmission to humans, must be considered. The plethora of methodological approaches to monitor AR and the variable features of the monitored sites challenge the capacity of the scientific community and policy makers to reach a common understanding. However, the dialogue between different methods and the production of action-oriented data is a priority. The review aims to warm up this discussion.

Detection of Yeast-like Symbionts in Brown Planthopper Reared on Different Resistant Rice Varieties Combining DGGE and Absolute Quantitative Real-Time PCR

Simple Summary

The brown planthopper (BPH) is an important pest that causes huge losses in rice production. The promotion and use of insect-resistant rice varieties is an important way to control BPH. However, in practice, BPH can adapt to resistant rice within several generations. Endosymbionts may be one of the reasons for the rapid adaptation of BPH to resistant rice. The BPH harbor yeast-like symbionts (YLS) in their abdomen, and YLS are essential for the nutrition, development, and reproduction of BPH. Our previous report showed that among the YLS communities detected in BPH, Ascomycetes symbionts, Pichia-like symbionts, and Candida-like symbionts were the three dominant populations of YLS. In this study, PCR-DGGE and absolute quantitative real-time PCR were used to detect the variations of three dominant YLS in BPH across different nymph ages and on different resistant rice varieties. The results showed that the total number of YLS gradually increased from the first instar to adulthood, but decreased in the fifth instar nymph, when BPH were reared on the susceptible rice variety TN1. The rice-resistant varieties, Mudgo, ASD7, and RH have more significant inhibitory effects on the three dominant YLS in the first and second generations of BPH. However, the numbers of the three dominant YLS were all recovered from the third generation of BPH. Ascomycetes symbionts were the most dominant strain among the three YLS.

Abstract

The brown planthopper (BPH), Nilaparvata lugens, is a serious pest of rice throughout Asia. Yeast-like symbionts (YLS) are endosymbionts closely linked with the development of BPH and the adapted mechanism of BPH virulence to resistant plants. In this study, we used semi-quantitative DGGE and absolute quantitative real-time PCR (qPCR) to quantify the number of the three YLS strains (Ascomycetes symbionts, Pichia-like symbionts, and Candida-like symbionts) that typically infect BPH in the nymphal stages and in newly emerged female adults. The quantities of each of the three YLS assessed increased in tandem with the developing nymphal instar stages, peaking at the fourth instar stage, and then declined significantly at the fifth instar stage. However, the amount of YLS present recovered sharply within the emerging adult females. Additionally, we estimated the quantities of YLS for up to eight generations after their inoculation onto resistant cultivars (Mudgo, ASD7, and RH) to reassociate the dynamics of YLS with the fitness of BPH. The minimum number of each YLS was detected in the second generation and gradually increased from the third generation with regard to resistant rice varieties. In addition, the Ascomycetes symbionts of YLS were found to be the most abundant of the three YLS strains tested for all of the development stages of BPH.

Microbial diversity in full-scale water supply systems through sequencing technology: a review

The prevalence of microorganisms in full-scale water supply systems raises concerns about their pathogenicity and threats to public health. Clean tap water is essential for public health safety. The conditions of the water treatment process from the source water to tap water, including source water quality, water treatment processes, the drinking water distribution system (DWDS), and building water supply systems (BWSSs) in buildings, greatly influence the bacterial community in tap water. Given the importance of drinking water biosafety, the study of microbial diversity from source water to tap water is essential. With the development of molecular biology methods and bioinformatics in recent years, sequencing technology has been applied to study bacterial communities in full-scale water supply systems. In this paper, changes in the bacterial community and the influence of each treatment stage on microbial diversity in full-scale water supply systems are classified and analyzed. Microbial traceability analysis and control are discussed, and suggestions for future drinking water biosafety research and its prospects are proposed.

Twenty-first century molecular methods for analyzing antimicrobial resistance in surface waters to support One Health assessments

Antimicrobial resistance (AMR) in the environment is a growing global health concern, especially the dissemination of AMR into surface waters due to human and agricultural inputs. Within recent years, research has focused on trying to understand the impact of AMR in surface waters on human, agricultural and ecological health (One Health). While surface water quality assessments and surveillance of AMR have historically utilized culture-based methods, culturing bacteria has limitations due to difficulty in isolating environmental bacteria and the need for a priori information about the bacteria for selective isolation. The use of molecular techniques to analyze AMR at the genetic level has helped to overcome the difficulties with culture-based techniques since they do not require advance knowledge of the bacterial population and can analyze uncultivable environmental bacteria. The aim of this review is to provide an overview of common contemporary molecular methods available for analyzing AMR in surface waters, which include high throughput real-time polymerase chain reaction (HT-qPCR), metagenomics, and whole genome sequencing. This review will also feature how these methods may provide information on human and animal health risks. HT-qPCR works at the nanoliter scale, requires only a small amount of DNA, and can analyze numerous gene targets simultaneously, but may lack in analytical sensitivity and the ability to optimize individual assays compared to conventional qPCR. Metagenomics offers more detailed genomic information and taxonomic resolution than PCR by sequencing all the microbial genomes within a sample. Its open format allows for the discovery of new antibiotic resistance genes; however, the quantity of DNA necessary for this technique can be a limiting factor for surface water samples that typically have low numbers of bacteria per sample volume. Whole genome sequencing provides the complete genomic profile of a single environmental isolate and can identify all genetic elements that may confer AMR. However, a main disadvantage of this technique is that it only provides information about one bacterial isolate and is challenging to utilize for community analysis. While these contemporary techniques can quickly provide a vast array of information about AMR in surface waters, one technique does not fully characterize AMR nor its potential risks to human, animal, or ecological health. Rather, a combination of techniques (including both molecular- and culture-based) are necessary to fully understand AMR in surface waters from a One Health perspective.

Effects of bacterial community composition and structure in drinking water distribution systems on biofilm formation and chlorine resistance

Community-intrinsic properties affect the composition and function of a microbial community. Understanding the microbial community-intrinsic properties in drinking water distribution systems (DWDS) could help to select disinfection strategies and aid in the prevention of waterborne infectious diseases. In this study, we investigated the formation of multi-species biofilms in six groups, each consisting of four or five mixed bacterial strains isolated from a simulated DWDS, at different incubation times (24, 48, and 72 h). We then evaluated the chlorine resistance of the 72-h multi-species biofilms in the presence of 0.3, 0.6, 1, 2, 4, and 10 mg/L residual chlorine. Microbacterium laevaniformans inhibited the formation of multi-species biofilms, Sphingomonas sp., Acinetobacter sp. and A. deluvii had the effect of promoting their growth, and B. cereus has little effect on the growth of multi-species biofilms. However, these inhibition and promotion effects were weak and inadequate to completely control the growth of multi-species biofilms. All multi-species produced strong biofilms after 72 h incubation, which could be due to microbial community-intrinsic properties. Community-intrinsic properties could maintain high EPS production and cell-to-cell connections in multi-species biofilms, and could affect the formation of multi-species biofilms. The chlorine resistance of multi-species biofilms was significantly improved by B. cereus, but significantly reduced by M. laevaniformans. These results indicated that the microbial community-intrinsic properties were influenced by the environment. At a relatively low disinfectant concentration (<2 mg/L residual chlorine), the community-intrinsic properties were maintained; however, when the disinfectant concentration was increased to 2-4 mg/L residual chlorine, the community-intrinsic properties weakened, and significantly affected the resistance of the microbial communities to the disinfectant. With further increases in concentration, to >4 mg/L residual chlorine, no significant difference was observed in the disinfectant resistance of the microbial community.

Differential prevalence and host-association of antimicrobial resistance traits in disinfected and non-disinfected drinking water systems

Antimicrobial resistance (AMR) in drinking water has received less attention than its counterparts in the urban water cycle. While culture-based techniques or gene-centric PCR have been used to probe the impact of treatment approaches (e.g., disinfection) on AMR in drinking water, to our knowledge there is no systematic comparison of AMR trait distribution and prevalence between disinfected and disinfectant residual-free drinking water systems. We used metagenomics to assess the associations between disinfectant residuals and AMR prevalence and its host association in full-scale drinking water distribution systems (DWDSs) with and without disinfectant residuals. While the differences in AMR profiles between DWDSs were associated with the presence or absence of disinfectant, they were also associated with overall water chemistry and more importantly with microbial community structure. AMR genes and mechanisms differentially abundant in disinfected systems were primarily associated with nontuberculous mycobacteria (NTM). Finally, evaluation of metagenome assembled genomes (MAGs) also suggests that NTM possessing AMR genes conferring intrinsic resistance to key antibiotics were prevalent in disinfected systems, whereas such NTM genomes were not detected in disinfectant residual free DWDSs. Altogether, our findings provide insights into the drinking water resistome and its association with potential opportunistic pathogens, particularly in systems with disinfectant residual.

The destruction of Escherichia coli adhered to pipe surfaces in a model drinking water distribution system via various antibiofilm agents

The aim of the study is to estimate the effectiveness of three antibiofilm agents against Escherichia coli biofilm that formed in six different types of pipelines. A laboratory-scale water system was built for this work to allow for the creation of biofilm in the pipelines studied. The level of the growth rate of E. coli biofilm cells was monitored over 90 days on those tested pipe materials. The results of bacterial cell densities displayed that the highest biofilm growth was observed in the biofilm formed on the iron (Fe) pipe. In contrast, the biofilm formation rate was significantly lower on copper (Cu) pipe compared to other materials. Three antibiofilm agents, including chlorine, silver ions (Ag⁺ ), and silver nanoparticles (AgNPs), were employed to eradicate the biofilm cells. E. coli counts indicated that AgNPs are more efficient in destructing any formed biofilm cells on all tested materials. At the same time, the chlorine was only useful in the case of biofilm developed on plastic and Cu. However, the antibiofilm efficiency of Ag⁺ performs similarly to chlorine against E. coli biofilm cells. Ultimately, AgNPs are considred the most powerful antibiofilm agent among the other agents toward the biofilm cells in their maturation stage, which offers an encouraging way for the long-term functioning of water systems. PRACTITIONER POINTS: The growth rate of E. coli biofilm cells was investigated on different materials. The count of biofilm cells developed on iron pipes was higher than other materials. The E. coli biofilm on iron pipe could resist chlorine and AgNPs to a large extent. The developed biofilm on copper pipe was more sensitive to chlorine, Ag⁺ . and AgNPs. The biofilm cells could be easily eradicated from plastic-based materials with all tested disinfectants.

Evolution of gentamicin and arsenite resistance acquisition in Ralstonia pickettii water isolates

Ralstonia pickettii are ubiquitous in water environments. Members of this species are frequently, but not always, resistant to both gentamicin and arsenite. Gentamicin and arsenite co-resistance and the putative molecular mechanisms were investigated. A group of 37 R. pickettii strains isolated from drinking water and hospital wastewater were characterized for gentamicin and arsenite resistance phenotypes, the number and size of plasmids, and screened for genetic elements associated with arsenite tolerance, Integrative and Conjugative Elements (ICEs), among other. The genomes of three representative strains were compared. Most gentamicin resistant (GR) isolates (32/33) were resistant to arsenite, and harbored ICE- and ars operon-related genes. These genetic elements were not detected in any of the five arsenite susceptible strains, regardless of the GR (n = 1) or gentamicin susceptibility (GS) (n = 4) phenotype. The comparison of the genomes of two GR (one resistant and one susceptible to arsenite) and one GS strains suggested that these phenotypes correspond to three phylogroups, distinguished by presence of some genes only in GR isolates, in addition to point mutations in functional genes. The presence of ICEs and ars operon-related genes suggest that arsenite resistance might have been acquired by GR lineages.

Acinetobacter spp. in food and drinking water - A review

Acinetobacter spp. has emerged as a pathogen of major public health concern due to their increased resistance to antibiotics and their association with a wide range of nosocomial infections, community-acquired infections and war and natural disaster-related infections. It is recognized as a ubiquitous organism however, information about the prevalence of different pathogenic species of this genus in food sources and drinking water is scarce. Since the implementation of molecular techniques, the role of foods as a source of several species, including the Acinetobacter baumannii group, has been elucidated. Multidrug resistance was also detected among Acinetobacter spp. isolated from food products. This highlights the importance of foods as potential sources of dissemination of Acinetobacter spp. between the community and clinical environments and reinforces the need for further investigations on the potential health risks of Acinetobacter spp. as foodborne pathogens. The aim of this review was to summarize the published data on the occurrence of Acinetobacter spp. in different food sources and drinking water. This information should be taken into consideration by those responsible for infection control in hospitals and other healthcare facilities.

Distribution of Antibiotic-Resistant Enterobacteriaceae Pathogens in Potable Spring Water of Eastern Indian Himalayas: Emphasis on Virulence Gene and Antibiotic Resistance Genes in Escherichia coli

Every year millions of people die due to fatal waterborne diseases around the world especially in developing countries like India. Sikkim, a northeastern state of India, greatly depends on natural water sources. About 80% of the population of Sikkim depends on natural spring water for domestic as well as agricultural use. Recent waterborne disease outbreaks in the state raises a concerning question on water quality. In this study, we analyzed water quality especially for the detection of Enterobacteriaceae members from four districts of the state. Isolation with selective culture media techniques and taxonomic characterization of Enterobacteriaceae bacteria with 16S rRNA gene showed the prevalence of Escherichia coli (37.50%), Escherichia fergusonii (29.41%), Klebsiella oxytoca (36.93%), Citrobacter freundii (37.92%), Citrobacter amalonaticus (43.82%), Enterobacter sp. (43.82%), Morganella morganii (43.82%), Hafnia alvei (32.42%), Hafnia paralvei (38.74%), and Shigella flexneri (30.47%) in the spring water of Sikkim. Antibiotic susceptibility test (AST) showed resistance of the isolates to common antibiotics like ampicillin, amoxicillin as well as to third generation antibiotics like ceftazidime and carbapenem. None of the isolates showed resistance to chloramphenicol. E. coli isolated from spring water of Sikkim showed presence of different virulence genes such as stx1 (81.81%), elt (86.66%), and eae (66.66%) along with resistance gene for ampicillin (CITM) (80%), quinolones (qnrB) (44.44%), tetracycline (tetO) (66.66%), and streptomycin (aadA1) (66.66%). The data indicates a high incidence rate of multiple antibiotic resistant enteric bacteria in the spring water of Sikkim. Additionally, the presence of enteric bacteria in the water samples indicates widespread fecal contamination of the spring water.

Multi-parametric assessment of biological stability of drinking water produced from groundwater: Reverse osmosis vs. conventional treatment

Although water produced by reverse osmosis (RO) filtration has low bacterial growth potential (BGP), post-treatment of RO permeate, which is necessary prior to distribution and human consumption, needs to be examined because of the potential re-introduction of nutrients/contaminants. In this study, drinking water produced from anaerobic groundwater by RO and post-treatment (ion exchange, calcite contactors, and aeration) was compared with that produced by conventional treatment comprising (dry) sand filtration, pellet softening, rapid sand filtration, activated carbon filtration, and UV disinfection. The multi-parametric assessment of biological stability included bacterial quantification, nutrient concentration and composition as well as bacterial community composition and diversity. Results showed that RO permeate remineralised in the laboratory has an extremely low BGP (50 ± 12 × 10³ ICC/mL), which increased to 130 ± 10 × 10³ ICC/mL after site post-treatment. Despite the negative impact of post-treatment, the BGP of the finished RO-treated water was >75% lower than that of conventionally treated water. Organic carbon limited bacterial growth in both RO-treated and conventionally treated waters. The increased BGP in RO-treated water was caused by the re-introduction of nutrients during post-treatment. Similarly, OTUs introduced during post-treatment, assigned to the phyla of Proteobacteria and Bacteroidetes (75-85%), were not present in the source groundwater. Conversely, conventionally treated water shared some OTUs with the source groundwater. It is clear that RO-based treatment achieved an extremely low BGP, which can be further improved by optimising post-treatment, such as using high purity calcite. The multi-parametric approach adopted in this study can offer insights into growth characteristics including limiting nutrients (why) and dominating genera growing (who), which is essential to manage microbiological water quality in water treatment and distribution systems.

Spatiotemporal Changes of Antibiotic Resistance and Bacterial Communities in Drinking Water Distribution System in Wrocław, Poland

Antibiotic resistance of bacteria is an emerging problem in drinking water treatment. This paper presents the comparison of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) prevalence during the summer and winter season in a full-scale drinking water distribution system (DWDS) supplied by two water treatment plants (WTPs). The effect of distance from WTP and physical–chemical water parameters on its microbial properties was also tested. Bacterial consortia dwelling in bulk tap water were additionally compared by means of denaturating gradient gel electrophoresis (DGGE). The results showed that among ARB, bacteria resistant to ceftazidime (CAZ) were the most abundant, followed by bacteria resistant to amoxicillin (AML), ciprofloxacin (CIP), and tetracycline (TE). Numerous ARGs were detected in tested tap water samples. Only CAZ resistant bacteria were more prevalent in the season of increased antibiotic consumption, and only AML resistant bacteria relative abundances increase was statistically significant with the distance from a WTP. The investigated tap water meets all legal requirements. It is therefore safe to drink according to the law. Nevertheless, because antibiotic resistance could pose a threat to consumer health, it should be further monitored in DWDSs.

Assessing the impact of source water on tap water bacterial communities in 46 drinking water supply systems in China

Drinking water purification and distribution processes shape the bacterial community in tap water; however, this study calls attention to the impact of source water on tap water bacterial community. Herein, paired source and tap water samples were collected from 46 drinking water supply systems in different watersheds across China, and high-throughput sequencing delineated that bacterial richness and diversity decreased and biogeographical distribution pattern weakened in tap water compared to source water. Despite the great changes of bacteria from source to tap, Bayesian-based SourceTracker analysis still verified that the proportional contributions of source water to shaping the tap water bacterial community ranged from 0% to 92.8% (49.73% ± 30.22% on average). This indelible contribution was further confirmed by the Mantel test (P < 0.001), Procrustes test (P < 0.001) and variance partition analysis, which showed that the source water together with geographical location explained 40.11% of tap water bacterial community variation. To explore the potential reasons that explain the great differences in the impact of source water among different samples, the universal shift pattern of bacterial communities from source to tap was summarized as a classification of dominant bacterial taxa: "sensitive taxa" versus "resistant taxa". The taxa including Planctomycetes, Verrucomicrobia, Acidobacteria, Chloroflexi, and δ-Proteobacteria could act as biomarkers to distinguish samples between source and tap water, and were classified as sensitive taxa. In contrast, α-Proteobacteria, β-Proteobacteria, γ-Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, and Cyanobacteria were classified as resistant taxa. The abundance of sensitive taxa was negatively correlated with the SourceTracker proportion, while the abundance of resistant taxa was positively correlated with the SourceTracker proportion (P < 0.01). Thus, variation in source water bacterial community could be responsible for the degree of impact on tap water. Our findings give notice that the impact of source water microbiomes must be taken more seriously, and sufficient source water protection and engineering control strategies should be implemented to prevent the biological consequences of source water on tap water.

Presence of Legionella spp. in cooling towers: the role of microbial diversity, Pseudomonas, and continuous chlorine application

Legionnaires' disease (LD) is a severe pneumonia caused by several species of the genus Legionella, most frequently by Legionella pneumophila. Cooling towers are the most common source for large community-associated outbreaks. Colonization, survival, and proliferation of L. pneumophila in cooling towers are necessary for outbreaks to occur. These steps are affected by the chemical and physical parameters of the cooling tower environment. We hypothesize that the bacterial community residing in the cooling tower could also affect the presence of L. pneumophila. A 16S rRNA gene targeted amplicon sequencing approach was used to study the bacterial community of cooling towers and its relationship with the Legionella spp. and L. pneumophila communities. The results indicated that the water source shaped the bacterial community of cooling towers. Several taxa were enriched and positively correlated with Legionella spp. and L. pneumophila. In contrast, Pseudomonas showed a strong negative correlation with Legionella spp. and several other genera. Most importantly, continuous chlorine application reduced microbial diversity and promoted the presence of Pseudomonas creating a non-permissive environment for Legionella spp. This suggests that disinfection strategies as well as the resident microbial population influences the ability of Legionella spp. to colonize cooling towers.

Biofilm formation potential and chlorine resistance of typical bacteria isolated from drinking water distribution systems

Biofilms are the main carrier of microbial communities throughout drinking water distribution systems (DWDSs), and strongly affect the safety of drinking water. Understanding biofilm formation potential and chlorine resistance is necessary for exploring future disinfection strategies and preventing water-borne diseases. This study investigated biofilm formation of five bacterial strains isolated from a simulated DWDS at different incubation times (24 h, 48 h, and 72 h), then evaluated chlorine resistance of 72 h incubated biofilms under chlorine concentrations of 0.3, 0.6, 1, 2, 4, and 10 mg L⁻¹. All five bacterial strains had biofilm formation potential when incubated for 72 h. The biofilm formation potential of Acinetobacter sp. was stronger than that of Bacillus cereus, Microbacterium sp. and Sphingomonas sp. were moderate, and that of Acidovorax sp. was weak. In contrast, the order of chlorine resistance was Bacillus sp. > Sphingomonas sp. > Microbacterium sp. > Acidovorax sp. > Acinetobacter sp. Thus, the chlorine resistance of a single-species biofilm has little relation with the biofilm formation potential. The biofilm biomass is not a major factor affecting chlorine resistance. Moreover, the chlorine resistance of a single-species biofilm is highly related to the physiological state of bacterial cells, such as their ability to form spores or secrete extracellular polymeric substances, which could reduce the sensitivity of the single-species biofilm to a disinfectant or otherwise protect the biofilm.

Biofilms are the main carrier of microbial communities throughout drinking water distribution systems (DWDSs), and strongly affect the safety of drinking water.

Betaproteobacteria are predominant in drinking water: are there reasons for concern?

Betaproteobacteria include some of the most abundant and ubiquitous bacterial genera that can be found in drinking water, including mineral water. The combination of physiology and ecology traits place some Betaproteobacteria in the list of potential, yet sometimes neglected, opportunistic pathogens that can be transmitted by water or aqueous solutions. Indeed, some drinking water Betaproteobacteria with intrinsic and sometimes acquired antibiotic resistance, harbouring virulence factors and often found in biofilm structures, can persist after water disinfection and reach the consumer. This literature review summarises and discusses the current knowledge about the occurrence and implications of Betaproteobacteria in drinking water. Although the sparse knowledge on the ecology and physiology of Betaproteobacteria thriving in tap or bottled natural mineral/spring drinking water (DW) is an evidence of this review, it is demonstrated that DW holds a high diversity of Betaproteobacteria, whose presence may not be innocuous. Frequently belonging to genera also found in humans, DW Betaproteobacteria are ubiquitous in different habitats, have the potential to resist antibiotics either due to intrinsic or acquired mechanisms, and hold different virulence factors. The combination of these factors places DW Betaproteobacteria in the list of candidates of emerging opportunistic pathogens. Improved bacterial identification of clinical isolates associated with opportunistic infections and additional genomic and physiological studies may contribute to elucidate the potential impact of these bacteria.

Comparison of Culture- and Quantitative PCR-Based Indicators of Antibiotic Resistance in Wastewater, Recycled Water, and Tap Water

Standardized methods are needed to support monitoring of antibiotic resistance in environmental samples. Culture-based methods target species of human-health relevance, while the direct quantification of antibiotic resistance genes (ARGs) measures the antibiotic resistance potential in the microbial community. This study compared measurements of tetracycline-, sulphonamide-, and cefotaxime-resistant presumptive total and fecal coliforms and presumptive enterococci versus a suite of ARGs quantified by quantitative polymerase chain reaction (qPCR) across waste-, recycled-, tap-, and freshwater. Cross-laboratory comparison of results involved measurements on samples collected and analysed in the US and Portugal. The same DNA extracts analysed in the US and Portugal produced comparable qPCR results (variation <28%), except for bla_OXA-1 gene (0%–57%). Presumptive total and fecal coliforms and cefotaxime-resistant total coliforms strongly correlated with bla_CTX-M and intI1 (0.725 ≤ R² ≤ 0.762; p < 0.0001). Further, presumptive total and fecal coliforms correlated with the Escherichia coli-specific biomarkers, gadAB, and uidA, suggesting that both methods captured fecal-sourced bacteria. The genes encoding resistance to sulphonamides (sul1 and sul2) were the most abundant, followed by genes encoding resistance to tetracyclines (tet(A) and tet(O)) and β-lactams (bla_OXA-1 and_,bla_CTX-M), which was in agreement with the culture-based enumerations. The findings can help inform future application of methods being considered for international antibiotic resistance surveillance in the environment.

The cooling tower water microbiota: Seasonal dynamics and co-occurrence of bacterial and protist phylotypes

Cooling towers for heating, ventilation and air conditioning are ubiquitous in the built environment. Often located on rooftops, their semi-open water basins provide a suitable environment for microbial growth. They are recognized as a potential source of bacterial pathogens and have been associated with disease outbreaks such as Legionnaires' disease. While measures to minimize public health risks are in place, the general microbial and protist community structure and dynamics in these systems remain largely elusive. In this study, we analysed the microbiome of the bulk water from the basins of three cooling towers by 16S and 18S rRNA gene amplicon sequencing over the course of one year. Bacterial diversity in all three towers was broadly comparable to other freshwater systems, yet less diverse than natural environments; the most abundant taxa are also frequently found in freshwater or drinking water. While each cooling tower had a pronounced site-specific microbial community, taxa shared among all locations mainly included groups generally associated with biofilm formation. We also detected several groups related to known opportunistic pathogens, such as Legionella, Mycobacterium, and Pseudomonas species, albeit at generally low abundance. Although cooling towers represent a rather stable environment, microbial community composition was highly dynamic and subject to seasonal change. Protists are important members of the cooling tower water microbiome and known reservoirs for bacterial pathogens. Co-occurrence analysis of bacteria and protist taxa successfully captured known interactions between amoeba-associated bacteria and their hosts, and predicted a large number of additional relationships involving ciliates and other protists. Together, this study provides an unbiased and comprehensive overview of microbial diversity of cooling tower water basins, establishing a framework for investigating and assessing public health risks associated with these man-made freshwater environments.

Identification of Factors Affecting Bacterial Abundance and Community Structures in a Full-Scale Chlorinated Drinking Water Distribution System

Disentangling factors influencing suspended bacterial community structure across distribution system and building plumbing provides insight into microbial control strategies from source to tap. Water quality parameters (residence time, chlorine, and total cells) and bacterial community structure were investigated across a full-scale chlorinated drinking water distribution system. Sampling was conducted in treated water, in different areas of the distribution system and in hospital building plumbing. Bacterial community was evaluated using 16S rRNA gene sequencing. Bacterial community structure clearly differed between treated, distributed, and premise plumbing water samples. While Proteobacteria (60%), Planctomycetes (20%), and Bacteroidetes (10%) were the most abundant phyla in treated water, Proteobacteria largely dominated distribution system sites (98%) and taps (91%). Distributed and tap water differed in their Proteobacteria profile: Alphaproteobacteria was dominant in distributed water (92% vs. 65% in tap waters), whereas Betaproteobacteria was most abundant in tap water (18% vs. 2% in the distribution system). Finally, clustering of bacterial community profiles was largely explained by differences in chlorine residual concentration, total bacterial count, and water residence time. Residual disinfectant and hydraulic residence time were determinant factors of the community structure in main pipes and building plumbing, rather than treated water bacterial communities.

Metagenomic study on the composition of culturable and non-culturable bacteria in tap water and biofilms at intensive care units

Bacterial community diversity of bulk water and corresponding biofilms of four intensive care units' (ICUs) drinking water systems were studied and compared using 16S rRNA gene amplicons and next generation sequencing. Proteobacteria, mainly Alphaproteobacteria and Betaproteobacteria were dominant in the bulk water and biofilms. Principal component analysis showed different bacterial communities characterizing each of the bulk water and the biofilms in three of the studied ICUs. Taxonomic classification and comparison of different genera between samples highlighted the dominance of Aquabacterium (80%) and Novosphingobium (72%) in bulk water while biofilms harbored different bacteria affiliated to Pelomonas (97%) and Caulobacter (96%), Porphyrobacter (78%) and Staphylococcus (74%). Staphylococcus aureus was the only possible pathogen found with low percentage (2.32%) in three of the ICUs' biofilm and only in one of the ICU's bulk water. This study sheds light on the prevalence of unculturable bacterial flora in the biofilm ignored by the microbiological standard methods. This study was performed on tap and bulk water from ICUs; however, it indicates the need for further studies to investigate the function and activity of the microbial diversity in order to assess the real risk presented by this water microflora on patients' health.

Xylo-oligosaccharides display a prebiotic activity when used to supplement wheat or corn-based diets for broilers

It is now well established that exogenous β-1,4-xylanases improve the nutritive value of wheat-based diets for poultry. Among other factors, the mechanism of action of exogenous enzymes may involve a microbial route resulting from the generation of prebiotic xylo-oligosaccharides (XOS) in the birds' gastro-intestinal (GI) tract. In a series of three experiments, the effect of XOS on the performance of broilers fed wheat or corn-based diets was investigated. In experiment 1, birds receiving diets supplemented with XOS displayed an increased weight gain (P = 0.08). The capacity of XOS to improve the performance of animals during a longer trial (42 d) was investigated (Experiment 2). The data revealed that diet supplementation with XOS, tested at two incorporation rates (0.1 and 1 g/kg), or with an exogenous β-1,4-xylanase resulted in an increased nutritive value of the wheat-based diet. An improvement in animal performance was accompanied by a shift in the microbial populations colonizing the upper portions of the GI tract. XOS were also able to improve the performance of broilers fed a corn-based diet, although the effects were not apparent at incorporation rates of 10 g/kg. Together these studies suggest that in some cases the capacity of β-1,4-xylanases to improve the nutritive value of wheat-based diets is more related to their ability to produce prebiotic XOS than to their ability to degrade arabinoxylans. The extremely low quantities of XOS used in this study also challenge the depiction of a prebiotic being a quantitatively fermented substrate. These data also bring into question the validity of the "cell wall" mechanism, as XOS elicited an effect with clearly no action on endosperm cell wall integrity and yet the performance effects noted were equivalent or superior to the added enzymes.

Habitat fragmentation is linked to cascading effects on soil functioning and CO2 emissions in Mediterranean holm-oak-forests

We studied key mechanisms and drivers of soil functioning by analyzing soil respiration and enzymatic activity in Mediterranean holm oak forest fragments with different influence of the agricultural matrix. For this, structural equation models (SEM) were built including data on soil abiotic (moisture, temperature, organic matter, pH, nutrients), biotic (microbial biomass, bacterial and fungal richness), and tree-structure-related (basal area) as explanatory variables of soil enzymatic activity and respiration. Our results show that increased tree growth induced by forest fragmentation in scenarios of high agricultural matrix influence triggered a cascade of causal-effect relations, affecting soil functioning. On the one hand, soil enzymatic activity was strongly stimulated by the abiotic (changes in pH and microclimate) and biotic (microbial biomass) modifications of the soil environment arising from the increased tree size and subsequent soil organic matter accumulation. Soil CO₂ emissions (soil respiration), which integrate releases from all the biological activity occurring in soils (autotrophic and heterotrophic components), were mainly affected by the abiotic (moisture, temperature) modifications of the soil environment caused by trees. These results, therefore, suggest that the increasing fragmentation of forests may profoundly impact the functioning of the plant-soil-microbial system, with important effects over soil CO₂ emissions and nutrient cycling at the ecosystem level. Forest fragmentation is thus revealed as a key albeit neglected factor for accurate estimations of soil carbon dynamics under global change scenarios.

Reduced Chlorine in Drinking Water Distribution Systems Impacts Bacterial Biodiversity in Biofilms

In drinking water distribution systems (DWDS), a disinfectant residual is usually applied to limit bacterial regrowth. However, delivering water with no or reduced chlorine residual could potentially decrease the selection for antimicrobial resistant microorganisms, favor bacterial regrowth and result in changes in bacterial populations. To evaluate the feasibility of water reduction in local DWDS while ensuring water safety, water quality was measured over 2 months in two different networks, each of them harboring sub-areas with normal and reduced chlorine. Water quality remained good in chlorine reduced samples, with limited development of total flora and absence of coliforms. Furthermore, 16S rRNA amplicon-based metagenomics was used to investigate the diversity and the composition of microbial communities in the sub-networks. Taxonomic classification of sequence reads showed a reduced bacterial diversity in sampling points with higher chlorine residuals. Chlorine disinfection created more homogeneous bacterial population, dominated by Pseudomonas, a genus that contains some major opportunistic pathogens such as P. aeruginosa. In the absence of chlorine, a larger and unknown biodiversity was unveiled, also highlighted by a decreased rate of taxonomic classification to the genus and species level. Overall, this experiment in a functional DWDS will facilitate the move toward potable water delivery systems without residual disinfectants and will improve water taste for consumers.

Recent progress and perspectives in biotrickling filters for VOCs and odorous gases treatment

Pollution caused by volatile organic compounds (VOCs) and odorous pollutants in the air can produce severe environmental problems. In recent years, the emission control of VOCs and odorous pollutants has become a crucial issue owing to the adverse effect on humans and the environment. For treating these compounds, biotrickling filter (BTF) technology acts as an environment friendly and cost-effective alternative to conventional air pollution control technologies. Besides, low concentration of VOCs and odorous pollutants can also be effectively removed using BTF systems. However, the VOCs and odorants removal performance by BTF may be limited by the hydrophobicity, toxicity, and low bioavailability of these pollutants. To solve these problems, this review summarizes the design, mechanism, and common analytical methods of recent BTF advances. In addition, the operating conditions, mass transfer, packing materials and microorganisms (which are the critical parameters in a BTF system) were evaluated and discussed in view of improving the removal performance of BTFs. Further research on these specific topics, together with the combination of BTF technology with other technologies, should improve the removal performance of BTFs.

Impact of chlorine dioxide disinfection of irrigation water on the epiphytic bacterial community of baby spinach and underlying soil

The contamination of pathogenic bacteria through irrigation water is a recognized risk factor for fresh produce. Irrigation water disinfection is an intervention strategy that could be applied to reduce the probability of microbiological contamination of crops. Disinfection treatments should be applied ensuring minimum effective doses, which are efficient in inhibiting the microbial contamination while avoiding formation and accumulation of chemical residues. Among disinfection technologies available for growers, chlorine dioxide (ClO₂) represents, after sodium hypochlorite, an alternative disinfection treatment, which is commercially applied by growers in the USA and Spain. However, in most of the cases, the suitability of this treatment has been tested against pathogenic bacteria and low attention have been given to the impact of chemical residues on the bacterial community of the vegetable tissue. The aim of this study was to (i) to evaluate the continual application of chlorine dioxide (ClO₂) as a water disinfection treatment of irrigation water during baby spinach growth in commercial production open fields, and (ii) to determine the subsequent impact of these treatments on the bacterial communities in water, soil, and baby spinach. To gain insight into the changes in the bacterial community elicited by ClO₂, samples of treated and untreated irrigation water as well as the irrigated soil and baby spinach were analyzed using Miseq® Illumina sequencing platform. Next generation sequencing and multivariate statistical analysis revealed that ClO₂ treatment of irrigation water did not affect the diversity of the bacterial community of water, soil and crop, but significant differences were observed in the relative abundance of specific bacterial genera. This demonstrates the different susceptibility of the bacteria genera to the ClO₂ treatment. Based on the obtained results it can be concluded that the phyllosphere bacterial community of baby spinach was more influenced by the soil bacteria community rather than that of irrigation water. In the case of baby spinach, the use of low residual ClO₂ concentrations (approx. 0.25 mg/L) to treat irrigation water decreased the relative abundance of Pseudomonaceae (2.28-fold) and Enterobacteriaceae (2.5-fold) when comparing treated versus untreated baby spinach. Members of these two bacterial families are responsible for food spoilage and foodborne illnesses. Therefore, a reduction of these bacterial families might be beneficial for the crop and for food safety. In general it can be concluded that the constant application of ClO₂ as a disinfection treatment for irrigation water only caused changes in two bacterial families of the baby spinach and soil microbiota, without affecting the major phyla and classes. The significance of these changes in the bacterial community should be further evaluated.

Assessing the origin of bacteria in tap water and distribution system in an unchlorinated drinking water system by SourceTracker using microbial community fingerprints

The general consensus is that the abundance of tap water bacteria is greatly influenced by water purification and distribution. Those bacteria that are released from biofilm in the distribution system are especially considered as the major potential risk for drinking water bio-safety. For the first time, this full-scale study has captured and identified the proportional contribution of the source water, treated water, and distribution system in shaping the tap water bacterial community based on their microbial community fingerprints using the Bayesian "SourceTracker" method. The bacterial community profiles and diversity analyses illustrated that the water purification process shaped the community of planktonic and suspended particle-associated bacteria in treated water. The bacterial communities associated with suspended particles, loose deposits, and biofilm were similar to each other, while the community of tap water planktonic bacteria varied across different locations in distribution system. The microbial source tracking results showed that there was not a detectable contribution of source water to bacterial community in the tap water and distribution system. The planktonic bacteria in the treated water was the major contributor to planktonic bacteria in the tap water (17.7-54.1%). The particle-associated bacterial community in the treated water seeded the bacterial community associated with loose deposits (24.9-32.7%) and biofilm (37.8-43.8%) in the distribution system. In return, the loose deposits and biofilm showed a significant influence on tap water planktonic and particle-associated bacteria, which were location dependent and influenced by hydraulic changes. This was revealed by the increased contribution of loose deposits to tap water planktonic bacteria (from 2.5% to 38.0%) and an increased contribution of biofilm to tap water particle-associated bacteria (from 5.9% to 19.7%) caused by possible hydraulic disturbance from proximal to distal regions. Therefore, our findings indicate that the tap water bacteria could possibly be managed by selecting and operating the purification process properly and cleaning the distribution system effectively.

Antibiotic resistance in wastewater treatment plants: Tackling the black box

Wastewater is among the most important reservoirs of antibiotic resistance in urban environments. The abundance of carbon sources and other nutrients, a variety of possible electron acceptors such as oxygen or nitrate, the presence of particles onto which bacteria can adsorb, or a fairly stable pH and temperature are examples of conditions favouring the remarkable diversity of microorganisms in this peculiar habitat. The wastewater microbiome brings together bacteria of environmental, human and animal origins, many harbouring antibiotic resistance genes (ARGs). Although numerous factors contribute, mostly in a complex interplay, for shaping this microbiome, the effect of specific potential selective pressures such as antimicrobial residues or metals, is supposedly determinant to dictate the fate of antibiotic resistant bacteria (ARB) and ARGs during wastewater treatment. This paper aims to enrich the discussion on the ecology of ARB&ARGs in urban wastewater treatment plants (UWTPs), intending to serve as a guide for wastewater engineers or other professionals, who may be interested in studying or optimizing the wastewater treatment for the removal of ARB&ARGs. Fitting this aim, the paper overviews and discusses: i) aspects of the complexity of the wastewater system and/or treatment that may affect the fate of ARB&ARGs; ii) methods that can be used to explore the resistome, meaning the whole ARB&ARGs, in wastewater habitats; and iii) some frequently asked questions for which are proposed addressing modes. The paper aims at contributing to explore how ARB&ARGs behave in UWTPs having in mind that each plant is a unique system that will probably need a specific procedure to maximize ARB&ARGs removal.

Spatiotemporal changes in bacterial community and microbial activity in a full-scale drinking water treatment plant

To gain insight into the bacterial dynamics present in drinking water treatment (DWT) systems, the microbial community and activity in a full-scale DWT plant (DWTP) in Guangzhou, South China, were investigated using Illumina Hiseq sequencing analyses combined with cultivation-based techniques during the wet and dry seasons. Illumina sequencing analysis of 16S rRNA genes revealed a large shift in the proportion of Actinobacteria, Proteobacteria and Firmicutes during the treatment process, with the proportion of Actinobacteria decreased sharply, whereas that of Proteobacteria and Firmicutes increased and predominated in treated water. Both microbial activity and bacterial diversity during the treatment process showed obvious spatial variation, with higher levels observed during the dry season and lower levels during the wet season. Clustering analysis and principal component analysis indicated dramatic shifts in the bacterial community after chlorination, suggesting that chlorination was highly effective at influencing the bacterial community. The bacterial community structure of finished water primarily comprised Pseudomonas, Citrobacter, and Acinetobacter, and interestingly showed high similarity to biofilms on granular activated carbon. Additionally, the abundance of bacterial communities was relatively stable in finished water and did not change with the season. A large number of unique operational taxonomic units were shared during treatment steps, indicating the presence of a diverse core microbiome throughout the treatment process. Opportunistic pathogens, including Pseudomonas, Acinetobacter, Citrobacter, Mycobacterium, Salmonella, Staphylococcus, Legionella, Streptococcus and Enterococcus, were detected in water including finished water, suggesting a potential threat to drinking-water safety. We also detected bacteria isolated from each treatment step using the pure-culture method. In particular, two isolates, identified as Mycobacterium sp. and Blastococcus sp., which belong to the phylum Actinobacteria, were obtained from finished water during the dry season. Together, these results provided evidence of spatial and temporal variations in DWTPs and contributed to the beneficial manipulation of the drinking water microbiome.

Exploring the Cultivable Ectocarpus Microbiome

Coastal areas form the major habitat of brown macroalgae, photosynthetic multicellular eukaryotes that have great ecological value and industrial potential. Macroalgal growth, development, and physiology are influenced by the microbial community they accommodate. Studying the algal microbiome should thus increase our fundamental understanding of algal biology and may help to improve culturing efforts. Currently, a freshwater strain of the brown macroalga Ectocarpus subulatus is being developed as a model organism for brown macroalgal physiology and algal microbiome studies. It can grow in high and low salinities depending on which microbes it hosts. However, the molecular mechanisms involved in this process are still unclear. Cultivation of Ectocarpus-associated bacteria is the first step toward the development of a model system for in vitro functional studies of brown macroalgal–bacterial interactions during abiotic stress. The main aim of the present study is thus to provide an extensive collection of cultivable E. subulatus-associated bacteria. To meet the variety of metabolic demands of Ectocarpus-associated bacteria, several isolation techniques were applied, i.e., direct plating and dilution-to-extinction cultivation techniques, each with chemically defined and undefined bacterial growth media. Algal tissue and algal growth media were directly used as inoculum, or they were pretreated with antibiotics, by filtration, or by digestion of algal cell walls. In total, 388 isolates were identified falling into 33 genera (46 distinct strains), of which Halomonas (Gammaproteobacteria), Bosea (Alphaproteobacteria), and Limnobacter (Betaproteobacteria) were the most abundant. Comparisons with 16S rRNA gene metabarcoding data showed that culturability in this study was remarkably high (∼50%), although several cultivable strains were not detected or only present in extremely low abundance in the libraries. These undetected bacteria could be considered as part of the rare biosphere and they may form the basis for the temporal changes in the Ectocarpus microbiome.

Heterotrophic monitoring at a drinking water treatment plant by matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry after different drinking water treatments

The aim of this work was to assess the suitability of matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) for routine heterotrophic monitoring in a drinking water treatment plant. Water samples were collected from raw surface water and after different treatments during two campaigns over a 1-year period. Heterotrophic bacteria were studied and isolates were identified by MALDI-TOF MS. Moreover, the diversity index and the coefficient of population similarity were also calculated using biochemical fingerprinting of the populations studied. MALDI-TOF MS enabled us to characterize and detect changes in the bacterial community composition throughout the water treatment plant. Raw water showed a large and diverse population which was slightly modified after initial treatment steps (sand filtration and ultrafiltration). Reverse osmosis had a significant impact on the microbial diversity, while the final chlorination step produced a shift in the composition of the bacterial community. Although MALDI-TOF MS could not identify all the isolates since the available MALDI-TOF MS database does not cover all the bacterial diversity in water, this technique could be used to monitor bacterial changes in drinking water treatment plants by creating a specific protein profile database for tracking purposes.

Ubiquitous and persistent Proteobacteria and other Gram-negative bacteria in drinking water

Drinking water comprises a complex microbiota, in part shaped by the disinfection and distribution systems. Gram-negative bacteria, mainly members of the phylum Proteobacteria, represent the most frequent bacteria in drinking water, and their ubiquity and physiological versatility raises questions about possible implications in human health. The first step to address this concern is the identification and characterization of such bacteria that is the first objective of this study, aiming at identifying ubiquitous or persistent Gram-negative bacteria, Proteobacteria or members of other phyla, isolated from tap water or from its source. >1000 bacterial isolates were characterized and identified, and a selected group (n=68) was further analyzed for the minimum inhibitory concentrations (MIC) to antibiotics (amoxicillin and gentamicin) and metals (copper and arsenite). Total DNA extracts of tap water were examined for the presence of putatively acquired antibiotic resistance or related genes (intI1, bla_TEM, qnrS and sul1). The ubiquitous tap water genera comprised Proteobacteria of the class Alpha- (Blastomonas, Brevundimonas, Methylobacterium, Sphingobium, Sphingomonas), Beta- (Acidovorax, Ralstonia) and Gamma- (Acinetobacter and Pseudomonas). Persistent species were members of genera such as Aeromonas, Enterobacter or Dechloromonas. Ralstonia spp. showed the highest MIC values to gentamicin and Acinetobacter spp. to arsenite. The genes intI1, bla_TEM or sul1 were detected, at densities lower than 2.3×10⁵copies/L, 2.4×10⁴copies/L and 4.6×10²copies/L, respectively, in most tap water samples. The presence of some bacterial groups, in particular of Beta- or Gammaproteobacteria (e.g. Ralstonia, Acinetobacter, Pseudomonas) in drinking water may deserve attention given their potential as reservoirs or carriers of resistance or as opportunistic pathogens.

Proteobacteria become predominant during regrowth after water disinfection

Disinfection processes aim at reducing the number of viable cells through the generation of damages in different cellular structures and molecules. Since disinfection involves unspecific mechanisms, some microbial populations may be selected due to resilience to treatment and/or to high post-treatment fitness. In this study, the bacterial community composition of secondarily treated urban wastewater and of surface water collected in the intake area of a drinking water treatment plant was compared before and 3-days after disinfection with ultraviolet radiation, ozonation or photocatalytic ozonation. The aim was to assess the dynamics of the bacterial communities during regrowth after disinfection. In all the freshly collected samples, Proteobacteria and Bacteroidetes were the predominant phyla (40-50% and 20-30% of the reads, respectively). Surface water differed from wastewater mainly in the relative abundance of Actinobacteria (17% and <5% of the reads, respectively). After 3-days storage at light and room temperature, disinfected samples presented a shift of Gammaproteobacteria (from 8 to 10% to 33-65% of the reads) and Betaproteobacteria (from 14 to 20% to 31-37% of the reads), irrespective of the type of water and disinfection process used. Genera such as Pseudomonas, Acinetobacter or Rheinheimera presented a selective advantage after water disinfection. These variations were not observed in the non-disinfected controls. Given the ubiquity and genome plasticity of these bacteria, the results obtained suggest that disinfection processes may have implications on the microbiological quality of the disinfected water.

Multidrug resistance phenotypes are widespread over different bacterial taxonomic groups thriving in surface water

The environment is the original and most ancient source of the antibiotic resistance determinants that threat the human health nowadays. In the environment, water is a privileged habitat and mode of dissemination of bacteria of different origins. Freshwater bodies that cross urban areas are supposed to hold a complex mixture of both human/animal origin and strictly environmental bacteria. In this study, we were interested in unveiling the bacterial diversity in urban river transects and, simultaneously, investigate the occurrence of antibiotic resistant bacteria, in particular the multidrug resistant (MDR). With this aim, water and sediments of two rivers were sampled from an urban transect and the bacterial diversity was assessed based on 16S rRNA gene-based community analysis and, simultaneously, total heterotrophic bacteria were isolated in the presence and in the absence of antibiotics. The three predominant phyla were Proteobacteria, Bacteroidetes and Actinobacteria, in water, or Acidobacteria, in sediments. MDR bacteria were observed to belong to the predominant phyla observed in water, mostly of the classes Gamma- and Betaproteobacteria (Proteobacteria) and Sphingobacteriia and Flavobacteriia (Bacteroidetes) and belonged to genera of ubiquitous (Pseudomonas, Acinetobacter, Stenotrophomonas) or mainly environmental (Chitinophaga, Chryseobacterium) bacteria. The observation that MDR bacteria are widespread in the environment and over distinct phylogenetic lineages has two relevant implications: i) the potential of environmental bacteria as source or facilitators for antibiotic resistance acquisition; ii) the need to complement culture-independent methods with culture-based approaches in order to identify major sources of MDR profiles.

Cry1Ac Transgenic Sugarcane Does Not Affect the Diversity of Microbial Communities and Has No Significant Effect on Enzyme Activities in Rhizosphere Soil within One Crop Season

Cry1Ac transgenic sugarcane provides a promising way to control stem-borer pests. Biosafety assessment of soil ecosystem for cry1Ac transgenic sugarcane is urgently needed because of the important role of soil microorganisms in nutrient transformations and element cycling, however little is known. This study aimed to explore the potential impact of cry1Ac transgenic sugarcane on rhizosphere soil enzyme activities and microbial community diversity, and also to investigate whether the gene flow occurs through horizontal gene transfer. We found no horizontal gene flow from cry1Ac sugarcane to soil. No significant difference in the population of culturable microorganisms between the non-GM and cry1Ac transgenic sugarcane was observed, and there were no significant interactions between the sugarcane lines and the growth stages. A relatively consistent trend at community-level, represented by the functional diversity index, was found between the cry1Ac sugarcane and the non-transgenic lines. Most soil samples showed no significant difference in the activities of four soil enzymes: urease, protease, sucrose, and acid phosphate monoester between the non-transgenic and cry1Ac sugarcane lines. We conclude, based on one crop season, that the cry1Ac sugarcane lines may not affect the microbial community structure and functional diversity of the rhizosphere soil and have few negative effects on soil enzymes.

Antibiotic resistance in urban aquatic environments: can it be controlled?

Over the last decade, numerous evidences have contributed to establish a link between the natural and human-impacted environments and the growing public health threat that is the antimicrobial resistance. In the environment, in particular in areas subjected to strong anthropogenic pressures, water plays a major role on the transformation and transport of contaminants including antibiotic residues, antibiotic-resistant bacteria, and antibiotic resistance genes. Therefore, the urban water cycle, comprising water abstraction, disinfection, and distribution for human consumption, and the collection, treatment, and delivery of wastewater to the environment, is a particularly interesting loop to track the fate of antibiotic resistance in the environment and to assess the risks of its transmission back to humans. In this article, the relevance of different transepts of the urban water cycle on the potential enrichment and spread of antibiotic resistance is reviewed. According to this analysis, some gaps of knowledge, research needs, and control measures are suggested. The critical rationale behind the measures suggested and the desirable involvement of some key action players is also discussed.

Microbial community analysis in a combined anaerobic and aerobic digestion system for treatment of cellulosic ethanol production wastewater

This study investigated the microbial diversity established in a combined system composed of a continuous stirred tank reactor (CSTR), expanded granular sludge bed (EGSB) reactor, and sequencing batch reactor (SBR) for treatment of cellulosic ethanol production wastewater. Excellent wastewater treatment performance was obtained in the combined system, which showed a high chemical oxygen demand removal efficiency of 95.8% and completely eliminated most complex organics revealed by gas chromatography-mass spectrometry (GC-MS). Denaturing gradient gel electrophoresis (DGGE) analysis revealed differences in the microbial community structures of the three reactors. Further identification of the microbial populations suggested that the presence of Lactobacillus and Prevotella in CSTR played an active role in the production of volatile fatty acids (VFAs). The most diverse microorganisms with analogous distribution patterns of different layers were observed in the EGSB reactor, and bacteria affiliated with Firmicutes, Synergistetes, and Thermotogae were associated with production of acetate and carbon dioxide/hydrogen, while all acetoclastic methanogens identified belonged to Methanosaetaceae. Overall, microorganisms associated with the ability to degrade cellulose, hemicellulose, and other biomass-derived organic carbons were observed in the combined system. The results presented herein will facilitate the development of an improved cellulosic ethanol production wastewater treatment system.

Impact of disinfection on drinking water biofilm bacterial community

Disinfectants are commonly applied to control the growth of microorganisms in drinking water distribution systems. However, the effect of disinfection on drinking water microbial community remains poorly understood. The present study investigated the impacts of different disinfectants (chlorine and chloramine) and dosages on biofilm bacterial community in bench-scale pipe section reactors. Illumina MiSeq sequencing illustrated that disinfection strategy could affect both bacterial diversity and community structure of drinking water biofilm. Proteobacteria tended to predominate in chloraminated drinking water biofilms, while Firmicutes in chlorinated and unchlorinated biofilms. The major proteobacterial groups were influenced by both disinfectant type and dosage. In addition, chloramination had a more profound impact on bacterial community than chlorination.

Hydromonas duriensis gen. nov., sp. nov., isolated from freshwater

An aerobic, Gram-stain-negative rod, designated strain A2P5T, was isolated from the Douro river, in Porto, Portugal. Cells were catalase- and oxidase-positive. Growth occurred at 15–30 °C, at pH 6–8 and in the presence of 1 % (w/v) NaCl. The major respiratory quinone was Q8, the genomic DNA had a G+C content of 47 ± 1 mol%, and phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol were amongst the major polar lipids. On the basis of 16S rRNA gene sequence analysis, strain A2P5T was observed to be a member of the family Burkholderiaceae, but could not be identified as a member of any validly named genus. The low levels of 16S rRNA gene sequence similarity to other recognized taxa ( < 91 %), together with the comparative analysis of phenotypic and chemotaxonomic characteristics, supported the proposal of a novel species of a new genus within the family Burkholderiaceae. The name Hydromonas duriensis gen. nov., sp. nov. is proposed. The type strain of Hydromonas duriensis is A2P5T ( = LMG 28428T = CCUG 66137T).

Habitat Fragmentation can Modulate Drought Effects on the Plant-soil-microbial System in Mediterranean Holm Oak (Quercus ilex) Forests

Ecological transformations derived from habitat fragmentation have led to increased threats to above-ground biodiversity. However, the impacts of forest fragmentation on soils and their microbial communities are not well understood. We examined the effects of contrasting fragment sizes on the structure and functioning of soil microbial communities from holm oak forest patches in two bioclimatically different regions of Spain. We used a microcosm approach to simulate the annual summer drought cycle and first autumn rainfall (rewetting), evaluating the functional response of a plant-soil-microbial system. Forest fragment size had a significant effect on physicochemical characteristics and microbial functioning of soils, although the diversity and structure of microbial communities were not affected. The response of our plant-soil-microbial systems to drought was strongly modulated by the bioclimatic conditions and the fragment size from where the soils were obtained. Decreasing fragment size modulated the effects of drought by improving local environmental conditions with higher water and nutrient availability. However, this modulation was stronger for plant-soil-microbial systems built with soils from the northern region (colder and wetter) than for those built with soils from the southern region (warmer and drier) suggesting that the responsiveness of the soil-plant-microbial system to habitat fragmentation was strongly dependent on both the physicochemical characteristics of soils and the historical adaptation of soil microbial communities to specific bioclimatic conditions. This interaction challenges our understanding of future global change scenarios in Mediterranean ecosystems involving drier conditions and increased frequency of forest fragmentation.