Bacterial characterization of Beijing drinking water by flow cytometry and MiSeq sequencing of the 16S rRNA gene

Anthropogenic impact on airborne bacteria of the Tibetan Plateau

The Tibetan Plateau is a pristine environment with limited human disturbance, with its aerosol microbiome being primarily influenced by the monsoon and westerly circulations. Additionally, the diversity and abundance of airborne microorganisms are also affected by anthropogenic activities, such as animal farming, agriculture, and tourism, which can lead to increased risks to the ecosystem and human health. However, the impact of anthropogenic activities on airborne microbes on the Tibetan Plateau has been rarely studied. In this work, we investigated the airborne bacteria of areas with weak (rural glacier) and strong human disturbance (urban building), and found that anthropogenic activities increased the diversity of airborne bacteria, and the concentration of potential airborne pathogens. Moreover, airborne bacteria in rural aerosols demonstrated significant differences in their community structure during monsoon- and westerly-affected seasons, while this pattern was weakened in urban aerosols. Additionally, urban aerosols enriched Lactobacillus sp. (member of genus Lactobacillus), which are potential pathogens from anthropogenic sources, whereas rural aerosols enriched A. calcoaceticus (member of genus Acinetobacter) and E. thailandicus (member of genus Enterococcus), which are both speculated to be sourced from surrounding animal farming. This study evaluated the impact of human activities on airborne bacteria in the Tibetan Plateau and contributed to understanding the enrichment of airborne pathogens in natural and anthropogenic background.

Effect of NaClO and ClO2 on the bacterial properties in a reclaimed water distribution system: efficiency and mechanisms

Extensive application of reclaimed water alleviated water scarcity obviously. Bacterial proliferation in reclaimed water distribution systems (RWDSs) poses a threat to water safety. Disinfection is the most common method to control microbial growth. The present study investigated the efficiency and mechanisms of two widely used disinfectants: sodium hypochlorite (NaClO) and chlorine dioxide (ClO₂) on the bacterial community and cell integrity in effluents of RWDSs through high-throughput sequencing (Hiseq) and flow cytometry, respectively. Results showed that a low disinfectant dose (1 mg/L) did not change the bacterial community basically, while an intermediate disinfectant dose (2 mg/L) reduced the biodiversity significantly. However, some tolerant species survived and multiplied in high disinfectant environments (4 mg/L). Additionally, the effect of disinfection on bacterial properties varied between effluents and biofilm, with changes in the abundance, bacterial community, and biodiversity. Results of flow cytometry showed that NaClO disturbed live bacterial cells rapidly, while ClO₂ caused greater damage, stripping the bacterial membrane and exposing the cytoplasm. This research will provide valuable information for assessing the disinfection efficiency, biological stability control, and microbial risk management of reclaimed water supply systems.

16S rRNA Based Profiling of Bacterial Communities Colonizing Bakery-Production Environments

Conventional culture-based techniques are largely inadequate in elucidating the microbiota contained in an environment, due to low recovery within a complex bacterial community. This limitation has been mitigated by the use of next-generation sequencing (NGS)-based approaches thereby facilitating the identification and classification of both culturable and uncultivable microorganisms. Amplicon targeted NGS methods, such as 16S ribosomal RNA (16S rRNA) and shotgun metagenomics, are increasingly being applied in various settings such as in food production environments to decipher the microbial consortium therein. Even though multiple food matrices/food production environments have been studied, the low-moisture environment associated with bakery food production remains to be investigated. To address this knowledge gap, in this study, we investigated the microbiome associated with two bakery production sites (designated as A and B) located in Ireland using 16S rRNA-amplicon-based sequencing. Amplicons corresponding to a hypervariable region contained within the 16S rRNA gene were amplified from DNA samples purified from environmental swabs and ingredients collected at both sites at various stages (preparation, production, postproduction, and storage) across the bakery production chain, over three seasons (winter, spring, and summer). These amplicons were sequenced, and data were analyzed using the mothur pipeline and visualized using MicrobiomeAnalyst and a series of R packages. The top seven bacterial phyla identified at both sites were composed of Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, Deinococcus-Thermus, Patescibacteria, and Verrucomicrobia. In addition, the phyla Tenericutes (Mycoplasmatota) and Acidobacteria were observed only in samples taken at site B. Different bacterial compositions were identified at each stage of production. These same bacteria were also found to be present in the final processed food suggesting the influence of the environment on the food matrix. This study is the first demonstration of the utility of 16S rRNA amplicon-based sequencing to describe the microbiota associated with bakery processing environments.

Monitoring Bacterial Community Dynamics in a Drinking Water Treatment Plant: An Integrative Approach Using Metabarcoding and Microbial Indicators in Large Water Volumes

Monitoring bacterial communities in a drinking water treatment plant (DWTP) may help to understand their regular operations. Bacterial community dynamics in an advanced full-scale DWTP were analyzed by 16S rRNA metabarcoding, and microbial water quality indicators were determined at nine different stages of potabilization: river water and groundwater intake, decantation, sand filtration, ozonization, carbon filtration, reverse osmosis, mixing chamber and post-chlorination drinking water. The microbial content of large water volumes (up to 1100 L) was concentrated by hollow fiber ultrafiltration. Around 10 million reads were obtained and grouped into 10,039 amplicon sequence variants. Metabarcoding analysis showed high bacterial diversity at all treatment stages and above all in groundwater intake, followed by carbon filtration and mixing chamber samples. Shifts in bacterial communities occurred downstream of ozonization, carbon filtration, and, more drastically, chlorination. Proteobacteria and Bacteroidota predominated in river water and throughout the process, but in the final drinking water, the strong selective pressure of chlorination reduced diversity and was clearly dominated by Cyanobacteria. Significant seasonal variation in species distribution was observed in decantation and carbon filtration samples. Some amplicon sequence variants related to potentially pathogenic genera were found in the DWTP. However, they were either not detected in the final water or in very low abundance (<2%), and all EU Directive quality standards were fully met. A combination of culture and high-throughput sequencing techniques may help DWTP managers to detect shifts in microbiome, allowing for a more in-depth assessment of operational performance.

The baseline oral microbiota predicts the response of locally advanced oral squamous cell carcinoma patients to induction chemotherapy: A prospective longitudinal study

PURPOSE

Among oral squamous cell carcinoma (OSCC) patients who receive docetaxel, cisplatin, and 5-fluorouracil (TPF) induction chemotherapy, those with a favorable pathological response tend to obtain satisfactory clinical outcomes, while the total population exhibit no survival benefit. Thus, there is an urgent need to improve the therapeutic effect of TPF by applying personalized treatment according to distinct biomarkers.

METHODS AND MATERIALS

In the present study, we collected oral rinse samples from 44 OSCC patients enrolled in our prospective multicenter random phase II trial before TPF induction chemotherapy to conduct 16S rRNA gene sequencing and metagenomic analysis. Patients were administrated with two cycles of TPF induction chemotherapy (75 mg/m² cisplatin and 75 mg/m² docetaxel on day 1 and 750 mg/m² fluorouracil from the first to the fifth day), and then divided into responsive and nonresponsive groups according to the Response Evaluation Criteria in Solid Tumors (RECIST) version 1.1.

RESULTS

In the 16S rRNA gene sequence analysis, Fusobacterium and Mycoplasma were more enriched in the nonresponsive group, while Slackia was more enriched in the responder group at the genus level. In the metagenomic shotgun sequencing analysis, Fusobacterium nucleatum was more enriched in the nonresponsive group. Functional analysis showed that the platinum drug resistance pathway and microRNAs in cancer and RNA degradation pathways were remarkably associated with patient sensitivity to induction chemotherapy.

CONCLUSIONS

Our data suggest that the oral microbiome may play an important role in the OSCC patient sensitivity to TPF induction chemotherapy and offer novel potential biomarkers for predicting the response to TPF induction chemotherapy.

Chlorination effects on DNA based characterization of water microbiomes and implications for the interpretation of data from disinfected systems

Quantitative PCR (qPCR) and next generation sequencing (NGS) are nucleic acid based microbiology techniques that provide new insights into drinking water quality, but considerable uncertainty remains around their correct interpretation. We noticed the presence of bacterial DNA from various putative pathogens, including from faecal indicator bacteria (FIB), in disinfected water, when culturable FIB were absent. To understand these observations better we studied the effect of chlorination on conventional and DNA based microbial water quality assessments. Surface water chlorination reduced plate counts for various FIB by up to >6 log units, intact cell counts by flow cytometry by 3.3 log units, and 16S rRNA gene copies by qPCR by 1.5 and 1.6 log units for total bacteria and total coliforms, respectively. Nanopore sequencing of 16S rRNA amplicons with the portable MinION device revealed the DNA from several families containing putative pathogens appeared to be more resistant than that of other bacteria to degradation by chlorine disinfection. For instance, 16S rRNA genes assigned to the Enterobacteriaceae family, members of which are mostly the target of coliform tests, increased in relative abundance from 0.001 ± 0.0002% to 0.0036 ± 0.003% after chlorine treatment. Hence, metagenomic drinking water data needs to be interpreted with caution. Plate counts and flow cytometry in combination with DNA based analysis provide more robust insight than NGS or qPCR alone.

The impact of UV treatment on microbial control and DBPs formation in full-scale drinking water systems in northern China

To manage potential microbial risks and meet increasingly strict drinking water health standards, UV treatment has attracted increasing attention for use in drinking water systems in China. However, the effects of UV treatment on microbial control and disinfection by-products (DBPs) formation in real municipal drinking water systems are poorly understood. Here, we collected water samples from three real drinking water systems in Beijing and Tianjin to investigate the impacts of UV treatment on microbial control and DBP formation. We employed heterotrophic plate count (HPC), flow cytometry (FCM), quantitative PCR analysis, and high-throughput sequencing to measure microorganisms in the samples. Different trends were observed between HPC and total cell count (measured by FCM), indicating that a single indicator could not reflect the real degree of biological re-growth in drinking water distribution systems (DWDSs). A significant increase in the 16S rRNA gene concentration was observed when the UV system was stopped. Besides, the bacterial community composition was similar at the phylum level but differed markedly at the genera level among the three DWDSs. Some chlorine-resistant bacteria, including potential pathogens (e.g., Acinetobacter) showed a high relative abundance when the UV system was turned off. It can be concluded that UV treatment can mitigate microbial re-growth to some extent. Finally, UV treatment had a limited influence on the formation of DBPs, including trihalomethanes, haloacetic acids, and nitrogenated DBPs. The findings of this study may help to understand the performance of UV treatment in real drinking water systems.

Dependency of DNA extraction efficiency on cell concentration confounds molecular quantification of microorganisms in groundwater

Quantification of microbes in water systems is essential to industrial practices ranging from drinking water and wastewater treatment to groundwater remediation. While quantification using DNA-based molecular methods is precise, the accuracy is dependent on DNA extraction efficiencies. We show that the DNA yield is strongly impacted by the cell concentration in groundwater samples (r = -0.92, P < 0.0001). This has major implications for industrial applications using quantitative polymerase chain reaction (qPCR) to determine cell concentrations in water, including bioremediation. We propose a simple normalization method using a DNA recovery ratio, calculated with the total cell count and DNA yield. Application of this method to enumeration of bacteria and archaea in groundwater samples targeting phylogenetic markers (16S rRNA) demonstrated an increased goodness of fit after normalization (7.04 vs 0.94 difference in Akaike's information criteria). Furthermore, normalization was applied to qPCR quantification of functional genes and combined with DNA sequencing of archaeal and bacterial 16S rRNA genes to monitor changes in abundance of methanogenic archaea and sulphate-reducing bacteria in groundwater. The integration of qPCR and DNA sequencing with appropriate normalization enables high-throughput quantification of microbial groups using increasingly affordable and accessible techniques. This research has implications for microbial ecology and engineering research as well as industrial practice.

Spatio-temporal survey of opportunistic premise plumbing pathogens in the Paris drinking water distribution system

Opportunistic premise plumbing pathogens present in drinking water are linked to a significant number of infections for health compromised patients. However, their monitoring is not required in current water potability standards and they have been poorly studied in a full-scale network. In this study, we quantified, by qPCR, three opportunistic pathogens, Mycobacterium spp., Legionella pneumophila, Pseudomonas aeruginosa throughout the Paris drinking water network over a one-year sampling campaign. While Mycobacteria spp. seemed ubiquitous whatever the distribution system and the time of the year, the occurrence of L. pneumophila and P. aeruginosa showed seasonal variations. Unlike L. pneumophila and P. aeruginosa, the concentration (copies number/L) of Mycobacterium spp. varied between sampling sites. The variation in microbial numbers did not demonstrate any correlations with temperature, pH, chlorine, conductivity, orthophosphate or nitrate levels. In conclusion, Mycobacterium spp. are common inhabitants of the Paris network while L. pneumophila and P. aeruginosa presence fluctuate over space and time. Such qPCR approach would help to better understand the behaviour of opportunistic premise plumbing pathogens.

Flow cytometry applications in water treatment, distribution, and reuse: A review

Ensuring safe and effective water treatment, distribution, and reuse requires robust methods for characterizing and monitoring waterborne microbes. Methods widely used today can be limited by low sensitivity, high labor and time requirements, susceptibility to interference from inhibitory compounds, and difficulties in distinguishing between viable and non-viable cells. Flow cytometry (FCM) has recently gained attention as an alternative approach that can overcome many of these challenges. This article critically and systematically reviews for the first time recent literature on applications of FCM in water treatment, distribution, and reuse. In the review, we identify and examine nearly 300 studies published from 2000 to 2018 that illustrate the benefits and challenges of using FCM for assessing source-water quality and impacts of treatment-plant discharge on receiving waters, wastewater treatment, drinking water treatment, and drinking water distribution. We then discuss options for combining FCM with other indicators of water quality and address several topics that cut across nearly all applications reviewed. Finally, we identify priority areas in which more work is needed to realize the full potential of this approach. These include optimizing protocols for FCM-based analysis of waterborne viruses, optimizing protocols for specifically detecting target pathogens, automating sample handling and preparation to enable real-time FCM, developing computational tools to assist data analysis, and improving standards for instrumentation, methods, and reporting requirements. We conclude that while more work is needed to realize the full potential of FCM in water treatment, distribution, and reuse, substantial progress has been made over the past two decades. There is now a sufficiently large body of research documenting successful applications of FCM that the approach could reasonably and realistically see widespread adoption as a routine method for water quality assessment.

Occurrence and Fate of Ultramicrobacteria in a Full-Scale Drinking Water Treatment Plant

Ultramicrobacteria (UMB) are omnipresent and numerically dominate in freshwater, as microbes can present in drinking water systems, however, the UMB communities that occur and their removal behaviors remain poorly characterized in drinking water treatment plants (DWTPs). To gain insights into these issues, we profiled bacterial cell density, community structure and functions of UMB and their counterpart large bacteria (LB) using flow cytometry and filtration paired with 16S rRNA gene high-throughput sequencing in a full-scale DWTP. Contrary to the reduction of bacterial density and diversity, the proportion of UMB in the total bacteria community increased as the drinking water treatment process progressed, and biological activated carbon facilitated bacterial growth. Moreover, UMB were less diverse than LB, and their community structure and predicted functions were significantly different. In the DWTP, UMB indicator taxa were mainly affiliated with α/β/γ-Proteobacteria, Deinococcus-Thermus, Firmicutes, Acidobacteria, and Dependentiae. In particular, the exclusive clustering of UMB at the phylum level, e.g., Parcubacteria, Elusimicrobia, and Saccharibacteria, confirmed the fact that the ultra-small size of UMB is a naturally and evolutionarily conserved trait. Additionally, the streamlined genome could be connected to UMB, such as candidate phyla radiation (CPR) bacteria, following a symbiotic or parasitic lifestyle, which then leads to the observed high connectedness, i.e., non-random intra-taxa co-occurrence patterns within UMB. Functional prediction analysis revealed that environmental information processing and DNA replication and repair likely contribute to the higher resistance of UMB to drinking water treatment processes in comparison to LB. Overall, the study provides valuable insights into the occurrence and fate of UMB regarding community structure, phylogenetic characteristics and potential functions in a full-scale DWTP, and it is a useful reference for beneficial manipulation of the drinking water microbiome.

Application of Cytosense flow cytometer for the analysis of airborne bacteria collected by a high volume impingement sampler

Characterization of airborne bacterial cells requires efficient collection, concentration, and analysis techniques, particularly to overcome the challenge of their dilute nature in outdoor environments. This study aims to establish a rapid and reliable approach for quantification of bacteria in air samples. To do this, a high volume impingement sampler was applied to collect airborne bacteria from a wastewater treatment plant (WWTP). The bacterial cell density was estimated by a Cytosense flow cytometer (Cytobouy) and compared to quantitative PCR (qPCR) data based on 16S rRNA genes. The average bacterial cell density measured by Cytosense ranged from 1.1 to 2.5 × 10⁴ cells m^-3 of air and that estimated by qPCR ranged from 0.08 to 3.8 × 10⁴ cells m^-3 of air. Regression analysis showed no systematic difference in bacterial cell densities between two methods applied when the cells were analyzed in vivo, and statistical tests confirmed that Cytosense counts of unfixed samples provided realistic values. Bacterial cell densities and the amount of DNA extracted from the sample were significantly correlated with relative humidity on a sampling day. The results showed that the present method was reliable to estimate bacteria densities from the outdoor environment, and the analysis given by Cytosense was faster and more sensitive than qPCR method. In addition, the Cytosense gave valuable information about cell characteristics at different sampling conditions.

Investigation of Detection Limits and the Influence of DNA Extraction and Primer Choice on the Observed Microbial Communities in Drinking Water Samples Using 16S rRNA Gene Amplicon Sequencing

In recent years, 16S rRNA gene amplicon sequencing has been widely adopted for analyzing the microbial communities in drinking water (DW). However, no comprehensive attempts have been made to illuminate the inherent method biases specifically relating to DW communities. In this study, we investigated the impact of DNA extraction and primer choice on the observed microbial community, and furthermore estimated the detection limit of the 16S rRNA gene amplicon sequencing in these experimental settings. Of the two DNA extraction kits investigated, the PowerWater DNA Isolation Kit resulted in higher yield, better reproducibility and more OTUs identified compared to the FastDNA SPIN Kit for Soil, which is also commonly used within DW microbiome research. The use of three separate primer-sets targeting the V1-3, V3-4, and V4 region of the 16S rRNA gene revealed large differences in OTU abundances, with some of the primers unable to detect entire phyla. Estimations of the detection limit were based on bacteria-free water samples (1 L) spiked with Escherichia coli cells in different concentrations [10¹–10⁶ cells/ml]. E.coli could be detected in all samples, however, samples with ∼10¹ cells/ml had several contaminating OTUs constituting approximately 8% of the read abundances. Based on our findings, we recommend using the PowerWater DNA Isolation Kit for DNA extraction in combination with PCR amplification of the V3-4 or V4 region for DW samples if a broad overview of the microbial community is to be obtained.

Identifying the underlying causes of biological instability in a full-scale drinking water supply system

Changes in bacterial concentration and composition in drinking water during distribution are often attributed to biological (in)stability. Here we assessed temporal biological stability in a full-scale distribution network (DN) supplied with different types of source water: treated and chlorinated surface water and chlorinated groundwater produced at three water treatment plants (WTP). Monitoring was performed weekly during 12 months in two locations in the DN. Flow cytometric total and intact cell concentration (ICC) measurements showed considerable seasonal fluctuations, which were different for two locations. ICC varied between 0.1-3.75 × 10⁵ cells mL^-1 and 0.69-4.37 × 10⁵ cells mL^-1 at two locations respectively, with ICC increases attributed to temperature-dependent bacterial growth during distribution. Chlorinated water from the different WTP was further analysed with a modified growth potential method, identifying primary and secondary growth limiting compounds. It was observed that bacterial growth in the surface water sample after chlorination was primarily inhibited by phosphorus limitation and secondly by organic carbon limitation, while carbon was limiting in the chlorinated groundwater samples. However, the ratio of available nutrients changed during distribution, and together with disinfection residual decay, this resulted in higher bacterial growth potential detected in the DN than at the WTP. In this study, bacterial growth was found to be higher (i) at higher water temperatures, (ii) in samples with lower chlorine residuals and (iii) in samples with less nutrient (carbon, phosphorus, nitrogen, iron) limitation, while this was significantly different between the samples of different origin. Thus drinking water microbiological quality and biological stability could change during different seasons, and the extent of these changes depends on water temperature, the water source and treatment. Furthermore, differences in primary growth limiting nutrients in different water sources could contribute to biological instability in the network, where mixing occurs.

Initial evenness determines diversity and cell density dynamics in synthetic microbial ecosystems

The effect of initial evenness on the temporal trajectory of synthetic communities in comprehensive, low-volume microcosm studies remains unknown. We used flow cytometric fingerprinting and 16S rRNA gene amplicon sequencing to assess the impact of time on community structure in one hundred synthetic ecosystems of fixed richness but varying initial evenness. Both methodologies uncovered a similar reduction in diversity within synthetic communities of medium and high initial evenness classes. However, the results of amplicon sequencing showed that there were no significant differences between and within the communities in all evenness groups at the end of the experiment. Nevertheless, initial evenness significantly impacted the cell density of the community after five medium transfers. Highly even communities retained the highest cell densities at the end of the experiment. The relative abundances of individual species could be associated to particular evenness groups, suggesting that their presence was dependent on the initial evenness of the synthetic community. Our results reveal that using synthetic communities for testing ecological hypotheses requires prior assessment of initial evenness, as it impacts temporal dynamics.

Dissemination of antibiotic resistance genes and their potential removal by on-farm treatment processes in nine swine feedlots in Shandong Province, China

This work investigated the dissemination of antibiotic resistance genes (ARGs) encoding resistance to sulfonamide and tetracycline antibiotics in nine swine feedlots located in Shandong Province of China, and examined their potential removal by various on-farm treatment processes. Results indicate that the target ARGs were widely distributed in swine wastes, with mean relative abundances ranging from 3.3 × 10^-5 (tetC) to 5.2 × 10^-1 (tetO) in swine manure and from 7.3 × 10^-3 (tetC) to 1.7 × 10^-1 (tetO) in swine wastewater. The mean relative ARG abundances ranged from 9.9 × 10^-5 (tetW) to 1.1 × 10^-2 (tetO) in soils and from 3.1 × 10^-4 (tetW) to 1.1 × 10^-2 (sul2) in receiving river sediments, indicating that the farmland application of swine manure compost and the discharge of swine wastewater promoted the dissemination of ARGs into adjacent environments. Microbial fermentation bed (MFB) could reduce the relative ARG abundances by 0-1.18 logs. However, septic tank, biogas digester and natural drying methods were relatively ineffective for ARG removal, and the relative abundances of some ARGs (i.e., tetC, tetG, sul1, and sul2) even increased by 0.74-3.90 logs in treated wastes. Bacterial diversity analysis indicates that the evolution of bacterial communities in the MFB played a crucial role in eliminating the ARGs. This study helps the effective assessment and management of ecological risks arising from ARGs in swine feedlots.