Characterizing community dynamics and exploring bacterial assemblages in two activated sludge systems

Ammonium oxidizing bacterial populations in South African activated sludge wastewater treatment plants

This is the first study that describes ammonium oxidizing bacterial populations and correlations of these populations with a range of criteria in activated sludge wastewater treatment plants in South Africa. In this study, not only the influent but also the activated sludge chemistry was comprehensively characterized. Multivariate statistical analyses were used to determine the relative significances of the geographical location (factor: site), wastewater treatment plant process (factor: configuration), seasonality (factor: season), and environmental parameters on the ammonium oxidizing bacterial genera in six municipal activated sludge wastewater treatments plants from two sites (the cities of Cape Town and Ekurhuleni). The geographical location (site) was significant for selection of the ammonium oxidizing genera (Global ANOSIM R value = 0.538, p = 0.001). It was established that the inter-site differences were not climatic in origin, nor related to the composition of the influent, but were rather driven by the activated sludge chemistry. It was found using BEST analysis that the activated sludge ammonia, activated sludge total phosphate, and activated sludge total chemical oxygen demand were the most significant (p < 0.001) drivers for ammonium oxidizing bacterial selection (ANOSIM Global R value 0.419) and were significantly higher in the activated sludge from the City of Cape Town wastewater treatment plants. Nitrosospira was the most abundant ammonium oxidizing bacterial genus, with notably higher relative and estimated actual abundances in the City of Cape Town wastewater treatment plants than the City of Ekurhuleni wastewater treatment plants. The strong selection of Nitrosospira in the City of Cape Town wastewater treatment plants with higher nutrient concentrations strongly suggests that high concentrations of activated sludge ammonia, activated sludge total phosphate, and activated sludge total chemical oxygen demand are key selective drivers for this genus. PRACTITIONER POINTS: First comprehensive study describing ammonium oxidizing bacterial populations in Southern African domestic activated sludge wastewater treatment plants. The geographical location (site) was significant for selection of different ammonium oxidizing genera (Global ANOSIM R value = 0.538, p = 0.001). Inter-site differences driven by the activated sludge chemistry, not climate or influent wastewater composition. Selection of Nitrosospira driven by high concentrations of activated sludge ammonia, total phosphate and total chemical oxygen demand.

Integration of taxa abundance and occurrence frequency to identify key gut bacteria correlated to clinics in Crohn's disease

Bacteria abundance alternation in the feces or mucosa of Crohn's disease (CD) patients has long been applied to identify potential biomarkers for this disease, while the taxa occurrence frequency and their correlations with clinical traits were understudied. A total of 97 samples from the feces and gut mucosa were collected from CD patients and healthy controls (HCs), 16S rRNA-based analyses were performed to determine the changes in taxa abundance and occurrence frequency along CD and to correlate them with clinical traits. The results showed that bacteria communities were divergent between feces and mucosa, while the taxa abundance and occurrence frequency in both partitions showed similar exponential correlations. The decrease of specific fecal bacteria was much more effective in classifying the CD and HCs than that of the mucosal bacteria. Among them, Christensenellaceae_R-7_group and Ruminococcus were predicted as biomarkers by using random forest algorithm, which were persistently presented (> 71.40% in frequency) in the feces of the HCs with high abundance, whereas transiently presented in the feces (< 5.5% in frequency) and mucosa (< 18.18% in frequency) of CD patients with low abundance. Co-occurrence network analysis then identified them as hub taxa that drive the alternations of other bacteria and were positively correlated to the circuiting monocytes. The loss of specific bacteria in the healthy gut may cause great disturbance of gut microbiota, causing gut bacteria dysbiosis and correlated to immune disorders along CD, which might not only be developed as effective noninvasive biomarkers but also as therapy targets.

Variations of bile bacterial community alongside gallstone disease progression and key taxa involved in poor outcomes after endoscopic surgery

Gallstone disease is a prevalent biliary disease worldwide, and bacteria play vital roles in the disease development and progression, as well as the prognosis after endoscopic surgery. However, there have been limited studies to explore the key taxa involved. In this study, bile samples from healthy controls (HCs, liver donors without hepatobiliary disease) and three diseased groups, namely patients with gallbladder stones (GBS), patients with common bile duct stones (CBDS), and patients with stricture in the common bile duct (SCBD), were collected and analyzed. Bacterial community characterization based on 16S rRNA amplicon sequencing showed that bacterial diversities did not change significantly alongside gallstone disease development and progression. The predominant phyla in each group were Proteobacteria, Firmicutes, Bacteroidota, and Fusobacteriota, representing over 80% in abundance of the biliary bacteria community. Specifically, the abundance of Proteobacteria decreased greatly while that of Firmicutes and Bacteroidota increased greatly in the diseased groups when compared to that in HCs. Moreover, linear discriminant analysis identified several genera highly represented in the diseased groups. Among them, Klebsiella, Prevotella, Pseudomonas and Veillonella are persistent in both the HCs group and the diseased groups, indicating an enrichment of local bile bacteria in the diseased bile; while Lachnoanerobaculum, Atopobium, Oribacterium, and Stomatobaculum, those aligned to oral cavity taxa, are persistent in the diseased groups but are transient in the HCs group, and their abundances sequentially increased with the disease development and progression (HCs→GBS→CBDS→SCBD), implying a translocation and colonization of the oral cavity bacteria in the diseased bile. Moreover, co-occurrence network analysis revealed that bacterial infection (e.g., Photobacterium and Plesiomonas) from the intestine was developed during endoscopic surgery with reduced bile bacteria diversity. The results of this study revealed that the bile bacterial community is relatively stable and dominated by a few persistent taxa. Moreover, we hypothesized that translocation and colonization of specific bacteria from the oral cavity happens alongside gallstone disease development and progression, and bacterial infection from the intestinal tract results in poor outcomes after endoscopic surgery.

Influence of seasonality, wastewater treatment plant process, geographical location and environmental parameters on bacterial community selection in activated sludge wastewater treatment plants treating municipal sewage in South Africa

This is the first comprehensive study that focusses on the correlation between the bacterial community composition and a range of previously identified selective criteria in activated sludge wastewater treatment plants on the African continent. Multivariate statistical analyses were used to determine the relative significance of the geographical location (factor: site), wastewater treatment plant process (factor: configuration), seasonality (factor: season), and environmental parameters on the bacterial communities in nine wastewater treatments plants from two sites in South Africa using terminal restriction fragment length polymorphism as a screening tool to rationalize the number of samples (to 50 samples) for high throughput (Illumina MiSeq) sequencing. Site was the most significant factor (Global ANOSIM R value = 0.91, p = 0.001), and it was established that the inter-site differences were not climatic in origin but related to differences in the composition of the influent and activated sludge. Previous studies that have reported associations between microbial community structure and environmental parameters have measured influent chemistry, and this is the first time, to our knowledge, that the comprehensive chemical character of activated sludge itself has been included in this type of study. It was found using BEST analysis that the activated sludge ammonia, activated sludge total phosphate and influent chemical oxygen demand were the most significant (p < 0.001) drivers for inter-site bacterial community selection (ANOSIM Global R values of 0.862, 0.782 and 0.428, respectively). This link would not have been established with only influent chemical analyses as there was no significant difference (t-test, p > 0.05) in the average influent phosphate concentrations between the 2 sites, but there was a highly significant difference (p < 0.001, t (15.5)>t-crit (2.01)) in the activated sludge total phosphate concentrations (20.8 ± 17.0 and 127.8 ± 40.2 mg/L). This is notable for all future studies on a global level aimed at identifying factors for selection of microbial communities in activated sludge.

Monthly dynamics of microbial communities and variation of nitrogen-cycling genes in an industrial-scale expanded granular sludge bed reactor

Introduction

The expanded granular sludge bed (EGSB) is a major form of anaerobic digestion system during wastewater treatment. Yet, the dynamics of microbial and viral communities and members functioning in nitrogen cycling along with monthly changing physicochemical properties have not been well elucidated.

Methods

Here, by collecting the anaerobic activated sludge samples from a continuously operating industrial-scale EGSB reactor, we conducted 16S rRNA gene amplicon sequencing and metagenome sequencing to reveal the microbial community structure and variation with the ever-changing physicochemical properties along within a year.

Results

We observed a clear monthly variation of microbial community structures, while COD, the ratio of volatile suspended solids (VSS) to total suspended solids (TSS) (VSS/TSS ratio), and temperature were predominant factors in shaping community dissimilarities examined by generalized boosted regression modeling (GBM) analysis. Meanwhile, a significant correlation was found between the changing physicochemical properties and microbial communities (p <0.05). The alpha diversity (Chao1 and Shannon) was significantly higher (p <0.05) in both winter (December, January, and February) and autumn (September, October, and November) with higher organic loading rate (OLR), higher VSS/TSS ratio, and lower temperature, resulting higher biogas production and nutrition removal efficiency. Further, 18 key genes covering nitrate reduction, denitrification, nitrification, and nitrogen fixation pathways were discovered, the total abundance of which was significantly associated with the changing environmental factors (p <0.05). Among these pathways, the dissimilatory nitrate reduction to ammonia (DNRA) and denitrification had the higher abundance contributed by the top highly abundant genes narGH, nrfABCDH, and hcp. The COD, OLR, and temperature were primary factors in affecting DNRA and denitrification by GBM evaluation. Moreover, by metagenome binning, we found the DNRA populations mainly belonged to Proteobacteria, Planctomycetota, and Nitrospirae, while the denitrifying bacteria with complete denitrification performance were all Proteobacteria. Besides, we detected 3,360 non-redundant viral sequences with great novelty, in which Siphoviridae, Podoviridae, and Myoviridae were dominant viral families. Interestingly, viral communities likewise depicted clear monthly variation and had significant associations with the recovered populations (p <0.05).

Discussion

Our work highlights the monthly variation of microbial and viral communities during the continuous operation of EGSB affected by the predominant changing COD, OLR, and temperature, while DNRA and denitrification pathways dominated in this anaerobic system. The results also provide a theoretical basis for the optimization of the engineered system.

Community Composition and Function of Bacteria in Activated Sludge of Municipal Wastewater Treatment Plants

Municipal wastewater treatment plants (WWTPs) use functional microorganisms in activated sludge (AS) to reduce the environmental threat posed by wastewater. In this study, Illumina NovaSeq sequencing of 16S rRNA genes was performed to explore the microbial communities of AS at different stages of the two WWTP projects in Shenzhen, China. Results showed that Proteobacteria, Bacteroidetes, Acidobacteria, Firmicutes, and Nitrospirae were the dominant phyla in all the samples, with Proteobacteria being the most abundant and reaching a maximum proportion of 59.63%. There was no significant difference in biodiversity between the two water plants, but Stage 1 and Stage 2 were significantly different. The Mantel test indicated that nitrate, total nitrogen (TN), chemical oxygen demand (COD), and nutrients were essential factors affecting the bacterial community structure. FAPROTAX analysis emphasized that the leading functional gene families include nitrification, aerobic nitrite oxidation, human pathogens, and phototrophy. This study reveals changes in the community structure of AS in different treatment units of Banxuegang WWTP, which can help engineers to optimize the wastewater treatment process.

Tropical and temperate wastewater treatment plants assemble different and diverse microbiomes

The diversity and assembly of activated sludge microbiomes play a key role in the performances of municipal wastewater treatment plants (WWTPs), which are the most widely applied biotechnological process systems. In this study, we investigated the microbiomes of municipal WWTPs in Bangkok, Wuhan, and Beijing that respectively represent tropical, subtropical, and temperate climate regions, and also explored how microbiomes assembled in these municipal WWTPs. Our results showed that the microbiomes from these municipal WWTPs were significantly different. The assembly of microbiomes in municipal WWTPs followed deterministic and stochastic processes governed by geographical location, temperature, and nutrients. We found that both taxonomic and phylogenetic α-diversities of tropical Bangkok municipal WWTPs were the highest and were rich in yet-to-be-identified microbial taxa. Nitrospirae and β-Proteobacteria were more abundant in tropical municipal WWTPs, but did not result in better removal efficiencies of ammonium and total nitrogen. Overall, these results suggest that tropical and temperate municipal WWTPs harbored diverse and unique microbial resources, and the municipal WWTP microbiomes were assembled with different processes. Implications of these findings for designing and running tropical municipal WWTPs were discussed. KEY POINTS: • Six WWTPs of tropical Thailand and subtropical and temperate China were investigated. • Tropical Bangkok WWTPs had more diverse and yet-to-be-identified microbial taxa. • Microbiome assembly processes were associated with geographical location.