The functional and taxonomic richness of wastewater treatment plant microbial communities are associated with each other and with ambient nitrogen and carbon availability

Comparison of nitrification performance in SBR and SBBR with response to NaCl salinity shock: Microbial structure and functional genes

Ammonia removal by nitrifiers at the extremely high salinity poses a great challenge for saline wastewater treatment. Sequencing batch reactor (SBR) was conducted with a stepwise increase of salinity from 10 to 40 g-NaCl·L-1, while sequencing batch biofilm reactor (SBBR) with one-step salinity enhancement, their nitrification performance, microbial structure and interaction were evaluated. Both SBR and SBBR can achieve high-efficiency nitrification (98% ammonia removal) at 40 g-NaCl·L-1. However, SBBR showed more stable nitrification performance than SBR at 40 g-NaCl·L-1 after a shorter adaptation period of 4-15 d compared to previous studies. High-throughput sequencing and metagenomic analysis demonstrated that the abundance and capability of conventional ammonia-oxidizing bacteria (Nitrosomonas) were suppressed in SBBR relative to SBR. Gelidibacter, Anaerolineales were the predominant genus in SBBR, which were not found in SBR. NorB and nosZ responsible for reducing NO to N2O and reducing N2O to N2 respectively had s strong synergistic effect in SBBR. This study will provide a valuable reference for the startup of nitrification process within a short period of time under the extremely high NaCl salinity.

Effects of dietary metabolizable energy level on hepatic lipid metabolism and cecal microbiota in aged laying hens

Lipid metabolic capacity, feed utilization, and the diversity of gut microbiota are reduced in the late laying stage for laying hens. This experiment aimed to investigate the effects of different levels of dietary metabolizable energy (ME) on hepatic lipid metabolism and cecal microbiota in late laying hens. The 216 Peking Pink laying hens (57-wk-old) were randomly assigned to experimental diets of 11.56 (HM = high ME), 11.14 (MM = medium ME), or 10.72 (LM = low ME) MJ of ME/kg, with each dietary treatment containing 6 replicates per group and 12 chickens per replicate. The HM group showed higher triglyceride (TG), total cholesterol (T-CHO), and low-density lipoprotein cholesterol (LDL-C) concentrations in the liver compared with the LM group; second, the HM group showed higher TG concentration and the LM group showed lower T-CHO concentration compared with MM group; finally, the HM group showed a lower hepatic lipase (HL) activity compared with the MM and LM groups (P < 0.05). There was a significant difference in the microbial community structure of the cecum between the HM and MM groups (P < 0.05). The decrease of dietary ME level resulted in a gradual decrease relative abundance of Proteobacteria. At the genus level, beneficial bacteria were significantly enriched in the LM group compared to the MM group, including Faecalibacterium, Lactobacillus, and Bifidobacterium, (linear discriminant analysis [LDA] >2, P <0.05). In addition, at the species level, Lactobacillus crispatus, Parabacteroides gordonii, Blautia caecimuris, and Lactobacillus johnsonii were significantly enriched in the LM group (LDA>2, P < 0.05). The HM group had a higher abundance of Sutterella spp. compared to the LM group (LDA>2, P <0.05). In conclusion, this research suggests that the reduction in dietary energy level did not adversely affect glycolipid metabolism or low dietary ME (10.72 MJ/kg). The findings can be helpful for maintaining intestinal homeostasis and increasing benefit for gut microbiota in late laying hens.

Influence of redox condition and inoculum on micropollutant biodegradation by soil and activated sludge communities

Micropollutant biodegradation is selected by the interplay among environmental conditions and microbial community composition. This study investigated how different electron acceptors, and different inocula with varying microbial diversity, pre-exposed to distinct redox conditions and micropollutants, affect micropollutant biodegradation. Four tested inocula comprised of agricultural soil (Soil), sediment from a ditch in an agricultural field (Ditch), activated sludge from a municipal WWTP (Mun AS), and activated sludge from an industrial WWTP (Ind AS). Removal of 16 micropollutants was investigated for each inoculum under aerobic, nitrate reducing, iron reducing, sulfate reducing, and methanogenic conditions. Micropollutant biodegradation was highest under aerobic conditions with removal of 12 micropollutants. Most micropollutants were biodegraded by Soil (n = 11) and Mun AS inocula (n = 10). A positive correlation was observed between inoculum community richness and the number of different micropollutants a microbial community initially degraded. The redox conditions to which a microbial community had been exposed appeared to positively affect micropollutant biodegradation performance more than pre-exposure to micropollutants. Additionally, depletion of the organic carbon present in the inocula resulted in lower micropollutant biodegradation and overall microbial activities, suggesting that i) an additional carbon source is needed to promote micropollutant biodegradation; and ii) overall microbial activity can be a good indirect indicator for micropollutant biodegradation activity. These results could help to develop novel micropollutant removal strategies.

Dietary metabolizable energy and crude protein levels affect pectoral muscle composition and gut microbiota in native growing chickens

The experiment aimed to study effects of dietary metabolizable energy (ME) and crude protein (CP) levels alone and in interaction on performance, pectoral muscle composition and gut microbiota in native growing chickens. A total of 648 10-wks-old Beijing-You Chicken (BYC) female chickens were randomly allocated to 9 groups with 6 replicates per group and 12 chickens per replicate, and the chickens were fed with a 3 × 3 factorial diets (3 levels of dietary ME: 11.31 MJ/kg, 11.51 MJ/kg, 11.71 MJ/kg; and 3 levels of dietary CP: 14%, 15%, 16%). The results showed that dietary ME and CP levels didn't affect average feed intake (AFI), body weight gain, feed gain ratio (P > 0.05), but ME level significantly affected the AFI (P < 0.05); mortality rate of 11.31 MJ/kg group was the highest (P < 0.05). Dietary ME, CP levels, and the interaction significantly affected pectoral CP and crude fat (CF) content of the growing chickens (P < 0.01). Dietary CP level had opposite effects on pectoral CP and CF content (P < 0.01). The 16% CP increased the pectoral CF content, which may have a negative impact on meat flavor. Dietary ME level affected 11 types of pectoral free amino acids (FAA) contents, including aspartic acid, L-threonine (P < 0.05), also amino acid classification, for example, total amino acid (TAA) and essential amino acid (EAA) content (P < 0.05). The 11.51 MJ/kg group had the highest TAA, EAA, delicious amino acid (DAA) content and EAA percentage (P < 0.05), while 11.31 MJ/kg group had the lowest bitter amino acid (BAA) content and BAA percentage and the highest fresh and sweet amino acid (FSAA) percentage (P < 0.05). Dietary CP level significantly affected glutamine and tyrosine content (P < 0.05). The interaction of dietary ME and CP level affected C20:3n6 content, saturated fatty acid (SFA), and unsaturated fatty acid (UFA) percentage (P < 0.05). The CP level significantly affected SFA percentage (P < 0.05). The 16% CP level increased the diversity of gut microbiota, but at the same time increased the relative abundance of Proteobacteria (P < 0.05), which is a sign of microbiota disorder. The increase of dietary ME level resulted in a gradual decrease in the diversity and relative abundance of gut microbiota. In conclusion, the present study suggested that the medium dietary ME (11.51 MJ/kg) and low CP (14-15%) levels can be helpful for enhancing pectoral muscle composition, increase meat quality such as flavor and nutritional value, and benefit for gut microbiota in native growing chickens.

Rumen and Fecal Microbiota Characteristics of Qinchuan Cattle with Divergent Residual Feed Intake

Residual feed intake (RFI) is one of the indicators of feed efficiency. To investigate the microbial characteristics and differences in the gastrointestinal tract of beef cattle with different RFI, a metagenome methodology was used to explore the characteristics of the rumen and fecal microbiota in 10 Qinchuan cattle (five in each of the extremely high and extremely low RFI groups). The results of taxonomic annotation revealed that Bacteroidetes and Firmicutes were the most dominant phyla in rumen and feces. Prevotella was identified as a potential biomarker in the rumen of the LRFI group by the LEfSe method, while Turicibacter and Prevotella might be potential biomarkers of the HRFI and LRFI group in feces, respectively. Functional annotation revealed that the microbiota in the rumen of the HRFI group had a greater ability to utilize dietary polysaccharides and dietary protein. Association analysis of rumen microbes (genus level) with host genes revealed that microbiota including Prevotella, Paraprevotella, Treponema, Oscillibacter, and Muribaculum, were significantly associated with differentially expressed genes regulating RFI. This study discovered variances in the microbial composition of rumen and feces of beef cattle with different RFIs, demonstrating that differences in microbes may play a critical role in regulating the bovine divergent RFI phenotype variations.

Influence of metabolism and microbiology on organic micropollutants biotransformation in anoxic heterotrophic reactors

There is scarce information about the biotransformation of organic micropollutants (OMPs) under anoxic conditions. In this study, a heterotrophic denitrifying bioreactor was set up to study the fate of several OMPs from metabolic and microbiological points of view. Primary metabolic activity was increased by adding progressively higher nitrogen loading rates during the operation (from 0.075 to 0.4 g N-NO₃^- L^-1 d^-1), which resulted in an important shift in the microbial population from a specialized biomass to a more diverse community. Such a change provoked a significant increase in the removal efficiency of erythromycin (ERY), roxithromycin (ROX) and bisphenol-A (BPA), and some bacterial taxa, such as Rhodoplanes, were identified as possible indicators related to the biodegradation of these compounds. The increasing primary metabolic activity in the reactor did not enhance the OMP-specific removal rates, suggesting that the bacterial composition is more influential than cometabolism.

Scientific concepts and methods for moving persistence assessments into the 21st century

The evaluation of a chemical substance's persistence is key to understanding its environmental fate, exposure concentration, and, ultimately, environmental risk. Traditional biodegradation test methods were developed many years ago for soluble, nonvolatile, single-constituent test substances, which do not represent the wide range of manufactured chemical substances. In addition, the Organisation for Economic Co-operation and Development (OECD) screening and simulation test methods do not fully reflect the environmental conditions into which substances are released and, therefore, estimates of chemical degradation half-lives can be very uncertain and may misrepresent real environmental processes. In this paper, we address the challenges and limitations facing current test methods and the scientific advances that are helping to both understand and provide solutions to them. Some of these advancements include the following: (1) robust methods that provide a deeper understanding of microbial composition, diversity, and abundance to ensure consistency and/or interpret variability between tests; (2) benchmarking tools and reference substances that aid in persistence evaluations through comparison against substances with well-quantified degradation profiles; (3) analytical methods that allow quantification for parent and metabolites at environmentally relevant concentrations, and inform on test substance bioavailability, biochemical pathways, rates of primary versus overall degradation, and rates of metabolite formation and decay; (4) modeling tools that predict the likelihood of microbial biotransformation, as well as biochemical pathways; and (5) modeling approaches that allow for derivation of more generally applicable biotransformation rate constants, by accounting for physical and/or chemical processes and test system design when evaluating test data. We also identify that, while such advancements could improve the certainty and accuracy of persistence assessments, the mechanisms and processes by which they are translated into regulatory practice and development of new OECD test guidelines need improving and accelerating. Where uncertainty remains, holistic weight of evidence approaches may be required to accurately assess the persistence of chemicals. Integr Environ Assess Manag 2022;18:1454-1487. © 2022 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).

Influence of Eimeria maxima coccidia infection on gut microbiome diversity and composition of the jejunum and cecum of indigenous chicken

Coccidiosis is an economically significant protozoan disease and an intracellular parasite that significantly impacts poultry production. The gastrointestinal tract microbiota plays a central role in host health and metabolism, and these microbes enhance chickens’ immune systems and nutrient absorption. In this study, we analyzed the abundance and diversity of microbiota of the jejunum and cecum of a dual-purpose indigenous Horro chicken following Eimeria maxima infection. We compared microbial abundance, composition, and diversity at the 4- and 7- days post-infection using 16S rRNA gene sequencing. We obtained, on average, 147,742 and 132,986 high-quality sequences per sample for jejunum and cecum content, respectively. Firmicutes, Proteobacteria, Campilobacterota and Bacteroidota were the major microbial phylum detected in the jejunum content. Firmicutes were the dominant phylum for 4- and 7-days jejunum control groups accounting for (>60% of the sequences). In the infected group Campilobacterota was the dominant phylum in the jejunum (> 24% of sequences) at 4-and 7-days post-infection groups, while Proteobacteria was predominant at 4- and 7-days post-infection of the cecum (> 40% of the sequences). The microbial genus Lactobacillus and Helicobacter were found in the jejunum, while Alistipes, Barnesiella and Faecalibacterium were detected in the cecum. In the jejunum, Helicobacter was dominant at 4 -and-7 days post-infection (≥24%), and Lactobacillus was dominant at 4 -and 7- days in the control group (> 50%). In 4- and 7-days post-infection, Alistipes genus was the more prevalent (> 38%) in the cecum. Thus, clear differences were observed in the bacterial microbiota distribution and abundance between the jejunum and cecum, as well as between infected and control groups for both tissues. The results indicate that chicken intestinal microbial imbalance (dysbiosis) is associated with Eimeria parasite infection and will likely affect the host-microbial non-pathogenic and pathogenic molecular interactions.

Metagenomic Analysis Reveals Changes in Bacterial Communities and Antibiotic Resistance Genes in an Eye Specialty Hospital and a General Hospital Before and After Wastewater Treatment

The spread of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in hospital wastewater poses a great threat to public health, and wastewater treatment plants (WWTPs) play an important role in reducing the levels of ARB and ARGs. In this study, high-throughput metagenomic sequencing was used to analyze the bacterial community composition and ARGs in two hospitals exposed to different antibiotic use conditions (an eye specialty hospital and a general hospital) before and after wastewater treatment. The results showed that there were various potential pathogenic bacteria in the hospital wastewater, and the abundance and diversity of the influent ARGs in the general hospital were higher than those in the eye hospital. The influent of the eye hospital was mainly composed of Thauera and Pseudomonas, and sul1 (sulfonamide) was the most abundant ARG. The influent of the general hospital contained mainly Aeromonas and Acinetobacter, and tet39 (tetracycline) was the most abundant ARG. Furthermore, co-occurrence network analysis showed that the main bacteria carrying ARGs in hospital wastewater varied with hospital type; the same bacteria in wastewater from different hospitals could carry different ARGs, and the same ARG could also be carried by different bacteria. The changes in the bacterial community and ARG abundance in the effluent from the two hospitals showed that the activated sludge treatment and the direct chlorination disinfection can effectively remove some bacteria and ARGs in wastewater but have limitations. The species diversity increased significantly after the activated sludge treatment, while the direct chlorination disinfection did not increase the diversity. The activated sludge treatment has a better effect on the elimination of ARGs than the direct chlorination disinfection. In summary, we investigated the differences in bacterial communities and ARGs in wastewater from two hospitals exposed to different antibiotic usage conditions, evaluated the effects of different wastewater treatment methods on the bacterial communities and ARGs in hospital wastewater, and recommended appropriate methods for certain clinical environments.

Metagenomics Insights Into the Microbial Diversity and Microbiome Network Analysis on the Heterogeneity of Influent to Effluent Water

Sanitizing the water sources of local communities is important to control the spread of microbial resistance genes, especially those for water-borne illnesses. The activities of antibiotic resistance gene (ARG)-host pathogens pose a threat to public health, and it has been estimated that the infection will lead up to 10 million deaths globally by the year 2050. Hence, in this study, we aim to analyze the efficiency of our municipal wastewater treatment plant (WWTP) process in producing pathogen-free water by investigating the microbial composition between influent and effluent water sites. Shotgun metagenomics sequencing using the Illumina platform was performed on the influent and effluent samples of six different WWTP sites located in Johore, Malaysia. After raw data pre-processing, the non-redundant contigs library was then aligned against BLASTP for taxonomy profiling and the Comprehensive Antibiotic Resistance Database for ARG annotation. Interestingly, the alpha-diversity result reported that effluent site samples showed higher abundance and diverse heterogeneity compared to the influent site. The principal component analysis (PCA) and non-metric multidimensional scaling (NMDS) plots also suggested that effluent sites showed high variation in the genetic material due to loosely clustered sample plots, as compared to the tightly clustered influent samples. This study has successfully identified the top three abundant phyla in influent-Proteobacteria, Firmicutes, and Bacteroidetes-and effluent-Proteobacteria, Actinobacteria, and Bacteroidetes-water. Despite the overlap within the top three abundant phyla in influent and effluent sites (Proteobacteria and Bacteroidetes), the ARG composition heat map and drug class phenotype plot bar exhibits a general trend of a downward shift, showing the efficiency of WWTP in reducing opportunistic pathogens. Overall, it was demonstrated that our municipal WWTP efficiently eliminated pathogenic microbes from the influent water before its total discharge to the environment, though not with the total elimination of microorganisms. This metagenomics study allowed for an examination of our water source and showed the potential interaction of species and ARGs residing in the influent and effluent environment. Both microbial profile structure and co-occurrence network analysis provide integrated understanding regarding the diversity of microorganisms and interactions for future advanced water sanitation treatments.

Insight into impact of sewage discharge on microbial dynamics and pathogenicity in river ecosystem

Direct sewage discharge could cause copious numbers of serious and irreversible harm to the environment. This study investigated the impacts of treated and raw sewage on the river ecosystem. Through our analysis, sewage carried various nutrients into the river, leading to changes in the microbial community in the river and reducing the diversity and richness of bacteria. The relative abundances of Hydrogenophaga, Thauera, Planctomyces, Zoogloea, and Pseudomonas boosted from 0.25, 0.01, 0.00, 0.05, and 0.08% to 3.33, 3.43, 0.02, 6.28, and 2.69%, before and after raw sewage discharge, respectively. The gene abundance of pathogenic bacteria significantly increased after raw sewage discharge. For instance, the gene abundance of Vibrio, Helicobacter, Tuberculosis, and Staphylococcus augmented from 4055, 3797, 13,545, 33 reads at Site-1 to 23,556, 13,163, 19,887, 734 reads at Site-2, respectively. In addition, according to the redundancy analysis (RDA), the infectious pathogens were positively related to the environmental parameters, in which COD showed the highest positive correlation with Mycobacterium tuberculosis. Additionally, river self-purification may contribute to improving water quality and reducing pathogenicity. The outcomes of this study showed that direct discharge brought pathogens and changed microbial community structure of the river.

MOVIS: A multi-omics software solution for multi-modal time-series clustering, embedding, and visualizing tasks

Thanks to recent advances in sequencing and computational technologies, many researchers with biological and/or medical backgrounds are now producing multiple data sets with an embedded temporal dimension. Multi-modalities enable researchers to explore and investigate different biological and physico-chemical processes with various technologies. Motivated to explore multi-omics data and time-series multi-omics specifically, the exploration process has been hindered by the separation introduced by each omics-type. To effectively explore such temporal data sets, discover anomalies, find patterns, and better understand their intricacies, expertise in computer science and bioinformatics is required. Here we present MOVIS, a modular time-series multi-omics exploration tool with a user-friendly web interface that facilitates the data exploration of such data. It brings into equal participation each time-series omic-type for analysis and visualization. As of the time of writing, two time-series multi-omics data sets have been integrated and successfully reproduced. The resulting visualizations are task-specific, reproducible, and publication-ready. MOVIS is built on open-source software and is easily extendable to accommodate different analytical tasks. An online version of MOVIS is available under https://movis.mathematik.uni-marburg.de/ and on Docker Hub (https://hub.docker.com/r/aanzel/movis).

Environmental structure impacts microbial composition and secondary metabolism

Determining the drivers of microbial community assembly is a central theme of microbial ecology, and chemical ecologists seek to characterize how secondary metabolites mediate these assembly patterns. Environmental structure affects how communities assemble and what metabolic pathways aid in that assembly. Here, we bridged these two perspectives by addressing the chemical drivers of community assembly within a spatially structured landscape with varying oxygen availability. We hypothesized that structured environments would favor higher microbial diversity and metabolite diversity. We anticipated that the production of a compound would be more advantageous in a structured environment (less mixing) compared to an unstructured environment (more mixing), where the molecule would have a diminished local effect. We observed this to be partially true in our experiments: structured environments had similar microbial diversity compared to unstructured environments but differed significantly in the metabolites produced. We also found that structured environments selected for communities with higher evenness, rather than communities with higher richness. This supports the idea that when characterizing the drivers of community assembly, it matters less about who is there and more about what they are doing. Overall, these data contribute to a growing effort to approach microbial community assembly with interdisciplinary tools and perspectives.

Sugar profile regulates the microbial metabolic diversity in Chinese Baijiu fermentation

Cereals are widely used as raw material for food fermentation, and they can provide a variety of sugars in the fermentation via saccharification. However, the effect of sugar profile on microbial metabolism in spontaneous food fermentation is still unclear. Here, this work studied the regulation of sugar profile on the diversity of microbiota and their metabolism in Chinese Baijiu fermentation using sorghum as raw material. Six sugars were detected during Baijiu fermentation with 6 different cultivars of sorghum. The diversity of microbiota (ANOSIM: bacteria: P = 0.001, R = 0.77; fungi: P = 0.009, R = 0.33) and metabolites (ANOSIM: P = 0.001, R = 0.50) had different profiles during Baijiu fermentation. Among these sugars, glucose, fructose, and arabinose were identified as key sugars driving both the microbial and the metabolic diversity during Chinese Baijiu fermentation, and the metabolic diversity was positively correlated with the microbial diversity (P < 0.05). Hence, response surface methodology was used to establish a predictive model for regulating the metabolic diversity with the combination of three key sugars. The metabolic diversity significantly increased to 0.42 with the optimized levels of glucose (31.82 g/L), fructose (4.81 g/L), and arabinose (0.20 g/L), compared with unoptimized low-level average metabolic diversity (0.29). This work would provide a strategy to control microbial metabolism in spontaneous food fermentation, hence to improve the quality of fermented foods.

Shotgun metagenomic analysis reveals the prevalence of antibiotic resistance genes and mobile genetic elements in full scale hospital wastewater treatment plants

Wastewater treatment plants are considered as hotspots of emerging antimicrobial genes and mobile genetic elements. We used a shotgun metagenomic approach to examine the wide-spectrum profiles of ARGs (antibiotic resistance genes) and MGEs (mobile genetic elements) in activated sludge samples from two different hospital trains at the wastewater treatment plants (WWTPs) in Daegu, South Korea. The influent activated sludge and effluent of two trains (six samples in total) at WWTPs receiving domestic sewage wastewater (SWW) and hospital wastewater (HWW) samples collected at multiple periods were subjected to high throughput 16S rRNA metagenome sequencing for microbial community diversity. Cloacibacterium caeni and Lewinella nigricans were predominant in SWW effluents, while Bacillus subtilis and Staphylococcus epidermidis were predominant in HWW effluents based on the Miseq platform. Totally, 20,011 reads and 28,545 metagenomic sequence reads were assigned to 25 known ARG types in the SWW2 and HWW5 samples, respectively. The higher abundance of ARGs, including multidrug resistance (>53%, MDR), macrolide-lincosamide-streptogramin (>9%, MLS), beta-lactam (>3.3%), bacitracin (>4.4%), and tetracycline (>3.4%), confirmed the use of these antibiotics in human medicine. In total, 190 subtypes belonging to 23 antibiotic classes were detected in both SWW2 and HWW5 samples. RpoB2, MacB, and multidrug (MDR) ABC transporter shared the maximum matched genes in both activated sludge samples. The high abundance of MGEs, such as a gene transfer agent (GTA) (four times higher), transposable elements (1.6 times higher), plasmid related functions (3.8 times higher), and phages (two times higher) in HWW5 than in SWW2, revealed a risk of horizontal gene transfer in HWW. Domestic wastewater from hospital patients also influenced the abundance of ARGs and MGEs in the activated sludge process.

Integrated metagenomic and metatranscriptomic analyses of ultraviolet disinfection effects on antibiotic resistance genes and bacterial communities during wastewater treatment

Ultraviolet (UV) disinfection is now widely implemented in wastewater treatment plants (WWTPs) worldwide, but its effect on antibiotic resistome of the surviving bacteria remains unclear. In this study, we employed high-throughput sequencing-based metagenomic and metatranscriptomic approaches to comprehensively elucidate the effects of UV disinfection on the shifts of bacterial community and antibiotic resistance genes (ARGs) on both DNA and mRNA levels in one WWTP. Metagenomic analyses revealed an insignificant change in the bacterial community after UV disinfection, while metatranscriptomic analyses showed that UV disinfection significantly changed the abundance of 13.79% of phyla and 10.32% of genera. In total, 38 ARG-like open reading frames (ORFs) and 327 ARG-like transcripts were identified in the DNA and RNA samples, respectively. The relative abundances of the total ARGs, each ARG type, and each ARG subtype also varied after UV disinfection. Additionally, UV disinfection significantly reduced the expression of total ARGs from 49.40 transcripts per kilobase of exon model per million mapped reads (TPM) to 47.62 TPM, and significantly changed the expression of 10.75% of ARG subtypes in wastewater (p < 0.05). Notably, the significant increase in the expression and obvious increase in the relative abundance of macrolide-lincosamide-streptogramin B (MLSB) resistance genes revealed that UV disinfection increases the potential health risk of MLSB resistance genes in wastewater. Moreover, potential host analyses of ARGs revealed the different preferences of antibiotic resistant bacteria (ARB) to ARGs. This study may shed new light on the underlying mechanism of the UV disinfection effect on antibiotic resistance.

Deciphering the microbial patterns of anammox process under hexavalent chromium stress: Abundant and rare subcommunity respond differently

This study aims to unravel the microbial responses to Cr(VI) stress in anaerobic ammonium oxidation (anammox) reactor. The result showed that anammox process could tolerate 2 mg/L Cr(VI) after acclimation, while 5 mg/L Cr(VI) stress resulted in significant inhibition on anammox bacterial activity. Ca. Jettenia was the predominant anammox genus, whose abundance showed a decreasing tendency with increasing Cr(VI) dosage. Cr(VI) addition resulted in significant and irreversible changes in microbial community structure, and increased the relative influence of stochastic processes on community assembly. Furthermore, rare subcommunity contributed greatly to biodiversity of whole community (90.35%), while abundant subcommunity were more similar to the whole community. Importantly, Cr(VI) exposure caused greater variations in rare subcommunity compared with abundant one, indicating that rare taxa were more sensitive to Cr(VI) stress. This was further confirmed by ABT model, which showed higher relative influence of Cr(VI) on rare subcommunity. In addition, results suggested that rare taxa play essential roles in whole community stability, because of their great contribution to species richness and community variations, and keystone roles in ecosystem network. Moreover, network analysis showed that conditionally rare taxa frequently and positively interacted with abundant taxa, which may contribute to the community resilience to Cr(VI) stress.

Community composition of cecal microbiota in commercial yellow broilers with high and low feed efficiencies

The cecal microbiota plays important roles in host food digestion and nutrient absorption, which may in part affect feed efficiency (FE). To investigate the composition and functional differences of cecal microbiota between high (n = 30) and low (n = 29) feed conversion ratio (FCR; metric for FE) groups, we performed 16S rRNA gene sequencing and predicted the metagenome function using Phylogenetic Investigation of Communities by Reconstruction of Unobserved Species in yellow broilers. The results showed that the 2 groups had the same prominent microbes but with differing abundance. Firmicutes, Bacteroidetes, and Actinobacteria were 3 prominent bacterial phyla in the cecal microbial community. Although there were no differences in microbial diversity, compositional differences related to FCR were found via linear discriminant analysis (LDA) effect size; the genus Bacteroides had a significantly higher abundance (LDA >2) in the high FE (HFE) group than in the low FE group. Furthermore, genus Bacteroides had a negative FCR-associated correlation (P < 0.05). Oscillospira was positively correlated with Bacteroides in both groups, whereas Dorea was negatively correlated with Bacteroides in the HFE group. Predictive functional analysis revealed that metabolic pathways such as “starch and sucrose metabolism,” “phenylalanine, tyrosine and tryptophan biosynthesis,” and “carbohydrate metabolism” were significantly enriched in the HFE group. The relatively subtle differences in FE-associated cecal microbiota composition suggest a possible link between cecal microbiota and FE. Moreover, Bacteroides may potentially be used as biomarkers for FE to improve growth performance in yellow broilers.

A Review of Current and Emerging Approaches for Water Pollution Monitoring

The aquatic ecosystem is continuously threatened by the infiltration and discharge of anthropogenic wastewaters. This issue requires the unending improvement of monitoring systems to become more comprehensive and specific to targeted pollutants. This review intended to elucidate the overall aspects explored by researchers in developing better water pollution monitoring tools in recent years. The discussion is encircled around three main elements that have been extensively used as the basis for the development of monitoring methods, namely the dissolved compounds, bacterial indicator, and nucleic acids. The latest technologies applied in wastewater and surface water mapped from these key players were reviewed and categorized into physicochemical and compound characterizations, biomonitoring, and molecular approaches in taxonomical and functional analyses. Overall, researchers are continuously rallying to enhance the detection of causal source for water pollution through either conventional or mostly advanced approaches focusing on spectrometry, high-throughput sequencing, and flow cytometry technology among others. From this review’s perspective, each pollution evaluation technology has its own advantages and it would be beneficial for several aspects of pollutants assessments to be combined and established as a complementary package for better aquatic environmental management in the long run.

Microbial invasions in sludge anaerobic digesters

Among processes that control microbial community assembly, microbial invasion has received little attention until recently, especially in the field of anaerobic digestion. However, knowledge of the principles regulating the taxonomic and functional stability of microbial communities is key to truly develop better predictive models and effective management strategies for the anaerobic digestion process. To date, available studies focus on microbial invasions in digesters feed with activated sludge from municipal wastewater treatment plants. Herein, this review summarizes the importance of invasions for anaerobic digestion management, the ecological theories about microbial invasions, the traits of activated sludge microorganisms entering the digesters, and the resident communities of anaerobic reactors that are relevant for invasions and the current knowledge about the success and impacts of invasions, and discusses the research needs on this topic. The initial data indicate that the impact of invasions is low and only a small percentage of the mostly aerobic microorganisms present in the activated sludge feed are able to become stablished in the anaerobic digesters. However, there are still numerous unknowns about microbial invasions in anaerobic digestion including the influence of anaerobic feedstocks or process perturbances that new approaches on microbial ecology could unveil. KEY POINTS: • Microbial invasions are key processes to develop better strategies for digesters management. • Knowledge on pathogen invasions can improve anaerobic digestion microbial safety. • To date, the number of successful invasions on anaerobic digesters from activated sludge organisms is low. • Feed organisms detected in digesters are mostly inactive residual populations. • Need to expand the range of invaders and operational scenarios studied.

Association between Aquatic Micropollutant Dissipation and River Sediment Bacterial Communities

Assessment of micropollutant biodegradation is essential to determine the persistence of potentially hazardous chemicals in aquatic ecosystems. We studied the dissipation half-lives of 10 micropollutants in sediment-water incubations (based on the OECD 308 standard) with sediment from two European rivers sampled upstream and downstream of wastewater treatment plant (WWTP) discharge. Dissipation half-lives (DT50s) were highly variable between the tested compounds, ranging from 1.5 to 772 days. Sediment from one river sampled downstream from the WWTP showed the fastest dissipation of all micropollutants after sediment RNA normalization. By characterizing sediment bacteria using 16S rRNA sequences, bacterial community composition of a sediment was associated with its capacity for dissipating micropollutants. Bacterial amplicon sequence variants of the genera Ralstonia, Pseudomonas, Hyphomicrobium, and Novosphingobium, which are known degraders of contaminants, were significantly more abundant in the sediment incubations where fast dissipation was observed. Our study illuminates the limitations of the OECD 308 standard to account for variation of dissipation rates of micropollutants due to differences in bacterial community composition. This limitation is problematic particularly for those compounds with DT50s close to regulatory persistence criteria. Thus, it is essential to consider bacterial community composition as a source of variability in regulatory biodegradation and persistence assessments.

Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance

The development of reliable, mixed-culture biotechnological processes hinges on understanding how microbial ecosystems respond to disturbances. Here we reveal extensive phenotypic plasticity and niche complementarity in oleaginous microbial populations from a biological wastewater treatment plant. We perform meta-omics analyses (metagenomics, metatranscriptomics, metaproteomics and metabolomics) on in situ samples over 14 months at weekly intervals. Based on 1,364 de novo metagenome-assembled genomes, we uncover four distinct fundamental niche types. Throughout the time-series, we observe a major, transient shift in community structure, coinciding with substrate availability changes. Functional omics data reveals extensive variation in gene expression and substrate usage amongst community members. Ex situ bioreactor experiments confirm that responses occur within five hours of a pulse disturbance, demonstrating rapid adaptation by specific populations. Our results show that community resistance and resilience are a function of phenotypic plasticity and niche complementarity, and set the foundation for future ecological engineering efforts.

Herold et al. present an integrated meta-omics framework to investigate how mixed microbial communities, such as oleaginous bacterial populations in biological wastewater treatment plants, respond with distinct adaptation strategies to disturbances. They show that community resistance and resilience are a function of phenotypic plasticity and niche complementarity.

Exploring the Specificity of Extracellular Wastewater Peptidases to Improve the Design of Sustainable Peptide-Based Antibiotics

New antimicrobial peptides are emerging as promising alternatives to conventional antibiotics because of their specificity for target pathogens and their potential to be rapidly hydrolyzed (i.e., inactivated) by extracellular peptidases during biological wastewater treatment, thereby limiting the emergence and propagation of antibiotic resistance in the environment. However, little is known about the specificity of extracellular peptidases derived from wastewater microbial communities, which is a major impediment for the design of sustainable peptide-based antibiotics that can be hydrolyzed by wastewater peptidases. We used a set of natural peptides to explore the specificity of dissolved extracellular wastewater peptidases. We found that enzyme-catalyzed hydrolysis occurred at specific sites and that a subset of these hydrolyses was conserved across enzyme pools derived from three independent wastewater microbial communities. An analysis of the amino-acid residues flanking the hydrolyzed bonds revealed a set of residue motifs that were linked to enzyme-catalyzed hydrolysis and are therefore candidates for incorporation into new and sustainable peptide-based antibiotics.

A brief guide for the measurement and interpretation of microbial functional diversity

The importance of functional diversity for the functioning and behaviour of microbial communities is clear, yet the widespread incorporation of functional diversity measurements into environmental microbiology study designs remains surprisingly limited. This may, at least to some extent, be a consequence of the unique conceptual and methodological challenges to measuring functional diversity in microbial communities. To facilitate the increased incorporation of functional diversity measurements into environmental microbiology study designs, we review here the process and some key caveats for measuring functional diversity and provide specific examples. We highlight three main decision points and provide guidance to making these decisions based on the underlying mechanisms for how functional diversity relates to an ecosystem process or property of interest. We discuss the selection of an appropriate type of functional trait, selection of the specificity at which functional diversity will be measured, and selection of an appropriate metric for estimating functional diversity from quantitative measures of those traits. We further discuss decisions regarding the use of one- or multi-dimensional measures of functional diversity and how advances in the field of trait-based community ecology could be applied or adapted to address questions in environmental microbiology.

Metagenomic analysis of sludge and early-stage biofilm communities of a submerged membrane bioreactor

Biofilm formation on membranes in activated sludge membrane bioreactors (MBR), commonly identified as biofouling, is a significant problem for MBR operations. A better understanding of microbial species involved in the biofilm formation is needed to develop anti-biofilm measures. A read-based and genome-resolved shotgun metagenomic approach was applied to characterize the composition and functional potential of the sludge and early stage biofilm microbial communities in an MBR process. Read-based analysis revealed that the prevalence of different phyla are relatively similar in both the sludge and biofilm samples, with Proteobacteria as the most dominant, followed by Chloroflexi, Bacteroidetes and Planctomycetes. However, the relative abundance of these phyla slightly varies between the sludge and biofilm. Phyla such as Actinobacteria, bacterial candidate phyla, Chlamydiae, Cyanobacteria/Melainabacteria and Firmicutes are 2 to 4 times more abundant in the biofilm than in the sludge. At the genus level, genera belonging to Proteobacteria (Legionella, Caulobacter, Sphingomonas, Acinetobacter and Rhizobium), Cyanobacteria (Hassallia), and Spirochaetes (Turneriella) are at least twice more abundant in the biofilm. These genera, especially those belonging to Phylum Proteobacteria, are known to play an important role in the formation of biofilms on surfaces. The Alpha diversity is found slightly higher in the biofilm, compared with sludge samples. Functional classification of reads through the SEED subsystem shows that functional classes such as those involved in the metabolism of various molecules are significantly different in the biofilm and sludge. A phylogenomic analysis of the six extracted metagenome assembled genomes (MAGs) shows that three MAGs belong to Proteobacteria, and one MAG belong to each of Chloroflexi, Bacteroidetes and Planctomycetes. The relative abundance of the MAG belonging to Alphaproteobacteria is higher in the biofilm. A functional potential analysis of the MAGs reveals their potential to metabolize carbon and nitrogen sources, as well as the prevalence of antibiotic resistance genes.

Enrichment of Denitrifying Bacterial Community Using Nitrite as an Electron Acceptor for Nitrogen Removal from Wastewater

This work aimed to enrich a denitrifying bacterial community for economical denitrification via nitrite to provide the basic objects for enhancing nitrogen removal from wastewater. A sequencing batch reactor (SBR) with continuous nitrite and acetate feeding was operated by reasonably adjusting the supply rate based on the reaction rate, and at a temperature of 20 ± 2 °C, pH of 7.5 ± 0.2, and dissolved oxygen (DO) of 0 mg/L. The results revealed that the expected nitrite concentration can be achieved during the whole anoxic reaction period. The nitrite denitrification rate of nitrogen removal from synthetic wastewater gradually increased from approximately 10 mg/(L h) to 275.35 mg/(L h) over 12 days (the specific rate increased from 3.83 mg/(g h) to 51.80 mg/(g h)). Correspondingly, the chemical oxygen demand/nitrogen (COD/N) ratio of reaction decreased from 7.9 to 2.7. Both nitrite and nitrate can be used as electron acceptors for denitrification. The mechanism of this operational mode was determined via material balance analysis of substrates in a typical cycle. High-throughput sequencing showed that the main bacterial community was related to denitrification, which accounted for 84.26% in the cultivated sludge, and was significantly higher than the 2.16% in the seed sludge.

Shifts in the Microbial Community of Activated Sludge with Different COD/N Ratios or Dissolved Oxygen Levels in Tibet, China

In this study, we examined the influence of the organic carbon-to-nitrogen ratio (chemical oxygen demand (COD/N)) and dissolved oxygen (DO) levels on the removal efficiency of pollutants and on the change in total microflora in the cyclic activated sludge system (CASS) in the Nyingchi prefecture in Tibet. The results demonstrated that the treatment performance was the best when the COD/N ratio was 7:1 or the DO levels were 2–2.5 mg/L in comparison with four different tested COD/N ratios (4:1, 5:1, 7:1, and 10:1) and DO concentrations (0.5–1, 1–2, 2–2.5, and 2.5–3.5 mg/L). The treatment performance can be explained by the relative operational taxonomic unit richness and evenness of the microbial communities in activated sludge. Evident microbial variance was observed, especially different COD/N ratios and DO concentrations, which were conducive to the disposal of urban sewage in plateaus. The results help to understand sewage treatment under different COD/N ratios or DO concentrations on plateaus. This work provides practical guidance for the operation of any wastewater treatment plant on a plateau.

Microbial residence time is a controlling parameter of the taxonomic composition and functional profile of microbial communities

A remaining challenge within microbial ecology is to understand the determinants of richness and diversity observed in environmental microbial communities. In a range of systems, including activated sludge bioreactors, the microbial residence time (MRT) has been previously shown to shape the microbial community composition. However, the physiological and ecological mechanisms driving this influence have remained unclear. Here, this relationship is explored by analyzing an activated sludge system fed with municipal wastewater. Using a model designed in this study based on Monod-growth kinetics, longer MRTs were shown to increase the range of growth parameters that enable persistence, resulting in increased richness and diversity in the modeled community. In laboratory experiments, six sequencing batch reactors treating domestic wastewater were operated in parallel at MRTs between 1 and 15 days. The communities were characterized using both 16S ribosomal RNA and non-target messenger RNA sequencing (metatranscriptomic analysis), and model-predicted monotonic increases in richness were confirmed in both profiles. Accordingly, taxonomic Shannon diversity also increased with MRT. In contrast, the diversity in enzyme class annotations resulting from the metatranscriptomic analysis displayed a non-monotonic trend over the MRT gradient. Disproportionately high abundances of transcripts encoding for rarer enzymes occur at longer MRTs and lead to the disconnect between taxonomic and functional diversity profiles.

Activated sludge bacterial communities of typical wastewater treatment plants: distinct genera identification and metabolic potential differential analysis

To investigate the differences in activated sludge microbial communities of different wastewater treatment plants (WWTPs) and understand their metabolic potentials, we sampled sludge from every biological treatment unit of 5 full-scale waste water treatment systems in 3 typical Chinese municipal WWTPs. The microbial communities and overall metabolic patterns were not only affected by influent characteristics but also varied between different biological treatment units. Distinct genera in different wastewater treatment systems were identified. The important microorganisms in domestic sewage treatment systems were unclassified SHA-20, Caldilinea, Dechloromonas, and unclassified genera from Rhodospirilaceae and Caldilineaceae. The important microorganisms in dyeing wastewater treatment systems were Nitrospira, Sphingobacteriales, Thiobacillus, Sinobacteraceae and Comamonadaceae. Compared with the obvious differences in microbial community composition, the metabolic potential showed no significant differences.

Elucidating the impact of microbial community biodiversity on pharmaceutical biotransformation during wastewater treatment

In addition to removing organics and other nutrients, the microorganisms in wastewater treatment plants (WWTPs) biotransform many pharmaceuticals present in wastewater. The objective of this study was to examine the relationship between pharmaceutical biotransformation and biodiversity in WWTP bioreactor microbial communities and identify taxa and functional genes that were strongly associated with biotransformation. Dilution-to-extinction of an activated sludge microbial community was performed to establish cultures with a gradient of microbial biodiversity. Batch experiments were performed using the dilution cultures to determine biotransformation extents of several environmentally relevant pharmaceuticals. With this approach, because the communities were all established from the same original community, and using sequencing of the 16S rRNA and metatranscriptome, we identified candidate taxa and genes whose activity and transcript abundances associated with the extent of individual pharmaceutical biotransformation and were lost across the biodiversity gradient. Metabolic genes such as dehydrogenases, amidases and monooxygenases were significantly associated with pharmaceutical biotransformation, and five genera were identified whose activity significantly associated with pharmaceutical biotransformation. Understanding how biotransformation relates to biodiversity will inform the design of biological WWTPs for enhanced removal of chemicals that negatively impact environmental health.

Insights into the variability of microbial community composition and micropollutant degradation in diverse biological wastewater treatment systems

The biological potential of conventional wastewater treatment plants to remove micropollutants mainly depends on process conditions and the predominant microbial community. To explore this dependence and to connect the occurrence of genera with operating conditions, five pilot-scale reactors with different process conditions were combined into two reactor cascades and fed with the effluent of the primary clarifier of a municipal WWTP. All reactors and the WWTP were analyzed for the removal of 33 micropollutants by LC-MS/MS and the presence of the microbial community using 16S rRNA gene sequencing. The overall removal of the micropollutants was slightly improved (ca. 20%) by the reactor cascades in comparison to the WWTP while certain compounds such as diatrizoate, venlafaxine or diclofenac showed an enhanced removal (ca. 70% in one or both cascades). To explore the diverse bacteria in more detail, the general community was divided into a core and a specialized community. Despite their profoundly different operating parameters (especially redox conditions), the different treatments share a core community consisted of 143 genera (9% of the overall community). Furthermore, the alpha- and beta-biodiversity as well as the occurrence of several genera belonging to the specialized microbial community could be linked to the prevalent process conditions of the individual treatments. Members of the specialized community also correlated with the removal of certain groups of micropollutants. Hence, the comparison of the specialized community with micropollutant removal and operating conditions via correlation analysis is a valuable tool for an extended evaluation of prevalent process conditions. Based on an extended data set this approach could also be used to identify organisms as indicators for operating conditions which are beneficial for an improved removal of specific micropollutants.

Reactor staging influences microbial community composition and diversity of denitrifying MBBRs- Implications on pharmaceutical removal

The subdivision of biofilm reactor in two or more stages (i.e., reactor staging) represents an option for process optimisation of biological treatment. In our previous work, we showed that the gradient of influent organic substrate availability (induced by the staging) can influence the microbial activity (i.e., denitrification and pharmaceutical biotransformation kinetics) of a denitrifying three-stage Moving Bed Biofilm Reactor (MBBR) system. However, it is unclear whether staging and thus the long-term exposure to varying organic carbon type and loading influences the microbial community structure and diversity. In this study, we investigated biofilm structure and diversity in the three-stage MBBR system (S) compared to a single-stage configuration (U) and their relationship with microbial functions. Results from 16S rRNA amplicon libraries revealed a significantly higher microbial richness in the staged MBBR (at 99% sequence similarity) compared to single-stage MBBR. A more even and diverse microbial community was selected in the last stage of S (S3), likely due to exposure to carbon limitation during continuous-flow operation. A core of OTUs was shared in both systems, consisting of Burkholderiales, Xanthomonadales, Flavobacteriales and Sphingobacteriales, while MBBR staging selected for specific taxa (i.e., Candidate division WS6 and Deinococcales). Results from quantitative PCR (qPCR) showed that S3 exhibited the lowest abundance of 16S rRNA but the highest abundance of atypical nosZ, suggesting a selection of microbes with more diverse N-metabolism (i.e., incomplete denitrifiers) in the stage exposed to the lowest carbon availability. A positive correlation (p < 0.05) was observed between removal rate constants of several pharmaceuticals with abundance of relevant denitrifying genes, but not with biodiversity. Despite the previously suggested positive relationship between microbial diversity and functionality in macrobial and microbial ecosystems, this was not observed in the current study, indicating a need to further investigate structure-function relationships for denitrifying systems.

Seasonal bacterial community succession in four typical wastewater treatment plants: correlations between core microbes and process performance

To understand the seasonal variation of the activated sludge (AS) bacterial community and identify core microbes in different wastewater processing systems, seasonal AS samples were taken from every biological treatment unit within 4 full-scale wastewater treatment plants. These plants adopted A2/O, A/O and oxidation ditch processes and were active in the treatment of different types and sources of wastewater, some domestic and others industrial. The bacterial community composition was analyzed using high-throughput sequencing technology. The correlations among microbial community structure, dominant microbes and process performance were investigated. Seasonal variation had a stronger impact on the AS bacterial community than any variation within different wastewater treatment system. Facing seasonal variation, the bacterial community within the oxidation ditch process remained more stable those in either the A2/O or A/O processes. The core genera in domestic wastewater treatment systems were Nitrospira, Caldilineaceae, Pseudomonas and Lactococcus. The core genera in the textile dyeing and fine chemical industrial wastewater treatment systems were Nitrospira, Thauera and Thiobacillus.

Organic Carbon Amendments for Enhanced Biological Attenuation of Trace Organic Contaminants in Biochar-Amended Stormwater Biofilters

This study sought to evaluate how dissolved organic carbon (DOC) affects attenuation of trace organic contaminants (TOrCs) in biochar-amended stormwater biofilters. It was hypothesized that (1) DOC-augmented runoff would demonstrate enhanced TOrC biodegradation and (2) biochar-amended sand bearing DOC-cultivated biofilms would achieve enhanced TOrC attenuation due to sorptive retention and biodegradation. Microcosm and column experiments were conducted utilizing actual runoff, DOC from straw and compost, and a suite of TOrCs. Biodegradation of TOrCs in runoff was more enhanced by compost DOC than straw DOC (particularly for atrazine, prometon, benzotriazole, and fipronil). 16S rRNA gene quantification and sequencing revealed that growth-induced microbial community changes were, among replicates, most consistent for compost-augmented microcosms and least consistent for raw runoff microcosms. Compost DOC most robustly enhanced utilization of TOrCs as carbon substrates, possibly due to higher residual nutrient levels upon TOrC exposure. Sand columns containing just 0.5 wt % biochar maintained sorptive TOrC retention in the presence of compost-DOC-cultivated biofilms, and TOrC removal was further enhanced by biological activity. Overall, these results suggest that coamendment with biochar and compost may robustly enhance TOrC attenuation in stormwater biofilters, a finding of significance for efforts to mitigate the impacts of runoff on water quality.

Anaerobic biodegradation of (emerging) organic contaminants in the aquatic environment

Although strictly anaerobic conditions prevail in several environmental compartments, up to now, biodegradation studies with emerging organic contaminants (EOCs), such as pharmaceuticals and personal care products, have mainly focused on aerobic conditions. One of the reasons probably is the assumption that the aerobic degradation is more energetically favorable than degradation under strictly anaerobic conditions. Certain aerobically recalcitrant contaminants, however, are biodegraded under strictly anaerobic conditions and little is known about the organisms and enzymatic processes involved in their degradation. This review provides a comprehensive survey of characteristic anaerobic biotransformation reactions for a variety of well-studied, structurally rather simple contaminants (SMOCs) bearing one or a few different functional groups/structural moieties. Furthermore it summarizes anaerobic degradation studies of more complex contaminants with several functional groups (CMCs), in soil, sediment and wastewater treatment. While strictly anaerobic conditions are able to promote the transformation of several aerobically persistent contaminants, the variety of observed reactions is limited, with reductive dehalogenations and the cleavage of ether bonds being the most prevalent. Thus, it becomes clear that the transferability of degradation mechanisms deduced from culture studies of SMOCs to predict the degradation of CMCs, such as EOCs, in environmental matrices is hampered due the more complex chemical structure bearing different functional groups, different environmental conditions (e.g. matrix, redox, pH), the microbial community (e.g. adaptation, competition) and the low concentrations typical for EOCs.

Nitrogen transforming bacteria within a full-scale partially saturated vertical subsurface flow constructed wetland treating urban wastewater

The aim of this study was to characterize the nitrogen transforming bacterial communities within a partially saturated vertical subsurface flow constructed wetland (VF) treating urban wastewater in southern Brazil. The VF had a surface area of 3144m², and was divided into four wetland cells, out of which two were operated while the other two rested, alternating cycles of 30days. The nitrifying and denitrifying bacterial communities were characterized in wetland cell 3 (764m² surface area) over a period of 12months by using the FISH technique. Samples were collected monthly (from Feb 2014 to Feb 2015) from different layers within the vertical profile, during operation and rest periods, comprising a total of 6 sampling campaigns while the cell was in operation and another 6 when the cell was at rest. This wetland cell operated with an average organic loading rate (OLR) of 4gCODm^-2d^-1 and a hydraulic loading rate of 24.5mmd^-1. The rest periods of the wetland cell presented influences on the abundance of ammonia-oxidizing bacteria (AOB) (8% and 3% for feed and rest periods, respectively), and nitrite-oxidizing bacteria (NOB) (5% and 2% for feed and rest periods, respectively). However, there was no influence of the rest periods on the denitrifying bacteria. AOB were only identified in the top layer (AOB β-proteobacteria) in both operational and rest periods. On the other hand, the NOB (Nistrospirae and Nitrospina gracilis) were identified in feed periods just in the top layer and during rest periods just in the intermediate layer. The denitrifying bacteria (Pseudomonas spp. and Thiobacillus denitrificans) were identified from the intermediate layer downwards, and remained stable in both periods. Based on the identified bacterial dynamics, the partially saturated VF wetland operated under low OLR enabled favorable conditions for simultaneous nitrification and denitrification.

Insights in Waste Management Bioprocesses Using Genomic Tools

Microbial capacities drive waste stabilization and resource recovery in environmental friendly processes. Depending on the composition of waste, a stress-mediated selection process ensures a scenario that generates a specific enrichment of microbial community. These communities dynamically change over a period of time while keeping the performance through the required utilization capacities. Depending on the environmental conditions, these communities select the appropriate partners so as to maintain the desired functional capacities. However, the complexities of these organizations are difficult to study. Individual member ratios and sharing of genetic intelligence collectively decide the enrichment and survival of these communities. The next-generation sequencing options with the depth of structure and function analysis have emerged as a tool that could provide the finer details of the underlying bioprocesses associated and shared in environmental niches. These tools can help in identification of the key biochemical events and monitoring of expression of associated phenotypes that will support the operation and maintenance of waste management systems. In this chapter, we link genomic tools with process optimization and/or management, which could be applied for decision making and/or upscaling. This review describes both, the aerobic and anaerobic, options of waste utilization process with the microbial community functioning as flocs, granules, or biofilms. There are a number of challenges involved in harnessing the microbial community intelligence with associated functional plasticity for efficient extension of microbial capacities for resource recycling and waste management. Mismanaged wastes could lead to undesired genotypes such as antibiotic/multidrug-resistant microbes.

Shotgun Metagenomic Profiles Have a High Capacity To Discriminate Samples of Activated Sludge According to Wastewater Type

This study was conducted to investigate whether functions encoded in the metagenome could improve our ability to understand the link between microbial community structures and functions in activated sludge. By analyzing data sets from six industrial and six municipal wastewater treatment plants (WWTPs), covering different configurations, operational conditions, and geographic regions, we found that wastewater influent composition was an overriding factor shaping the metagenomic composition of the activated sludge samples. Community GC content profiles were conserved within treatment plants on a time scale of years and between treatment plants with similar influent wastewater types. Interestingly, GC contents of the represented phyla covaried with the average GC contents of the corresponding WWTP metagenome. This suggests that the factors influencing nucleotide composition act similarly across taxa and thus the variation in nucleotide contents is driven by environmental differences between WWTPs. While taxonomic richness and functional richness were correlated, shotgun metagenomics complemented taxon-based analyses in the task of classifying microbial communities involved in wastewater treatment systems. The observed taxonomic dissimilarity between full-scale WWTPs receiving influent types with varied compositions, as well as the inferred taxonomic and functional assignment of recovered genomes from each metagenome, were consistent with underlying differences in the abundance of distinctive sets of functional categories. These conclusions were robust with respect to plant configuration, operational and environmental conditions, and even differences in laboratory protocols.

IMPORTANCE

This work contributes to the elucidation of drivers of microbial community assembly in wastewater treatment systems. Our results are significant because they provide clear evidence that bacterial communities in WWTPs assemble mainly according to influent wastewater characteristics. Differences in bacterial community structures between WWTPs were consistent with differences in the abundance of distinctive sets of functional categories, which were related to the metabolic potential that would be expected according to the source of the wastewater.

rRNA Gene Expression of Abundant and Rare Activated-Sludge Microorganisms and Growth Rate Induced Micropollutant Removal

The role of abundant and rare taxa in modulating the performance of wastewater-treatment systems is a critical component of making better predictions for enhanced functions such as micropollutant biotransformation. In this study, we compared 16S rRNA genes (rDNA) and rRNA gene expression of taxa in an activated-sludge-treatment plant (sequencing batch membrane bioreactor) at two solids retention times (SRTs): 20 and 5 days. These two SRTs were used to influence the rates of micropollutant biotransformation and nutrient removal. Our results show that rare taxa (<1%) have disproportionally high ratios of rRNA to rDNA, an indication of higher protein synthesis, compared to abundant taxa (≥1%) and suggests that rare taxa likely play an unrecognized role in bioreactor performance. There were also significant differences in community-wide rRNA expression signatures at 20-day SRT: anaerobic-oxic-anoxic periods were the primary driver of rRNA similarity. These results indicate differential expression of rRNA at high SRTs, which may further explain why high SRTs promote higher rates of micropollutant biotransformation. An analysis of micropollutant-associated degradation genes via metagenomics and direct measurements of a suite of micropollutants and nutrients further corroborates the loss of enhanced functions at 5-day SRT operation. This work advances our knowledge of the underlying ecosystem properties and dynamics of abundant and rare organisms associated with enhanced functions in engineered systems.

Tracing the limits of organic micropollutant removal in biological wastewater treatment

Removal of organic micropollutants was investigated in 15 diverse biological reactors through short and long-term experiments. Short-term batch experiments were performed with activated sludge from three parallel sequencing batch reactors (25, 40, and 80 d solid retention time, SRT) fed with synthetic wastewater without micropollutants for one year. Despite the minimal micropollutant exposure, the synthetic wastewater sludges were able to degrade several micropollutants present in municipal wastewater. The degradation occurred immediately after spiking (1-5 μg/L), showed no strong or systematic correlation to the sludge age, and proceeded at rates comparable to those of municipal wastewater sludges. Thus, the results from the batch experiments indicate that degradation of organic micropollutants in biological wastewater treatment is quite insensitive to SRT increases from 25 to 80 days, and not necessarily induced by exposure to micropollutants. Long-term experiments with municipal wastewater were performed to assess the potential for extended biological micropollutant removal under different redox conditions and substrate concentrations (carbon and nitrogen). A total of 31 organic micropollutants were monitored through influent-effluent sampling of twelve municipal wastewater reactors. In accordance with the results from the sludges grown on synthetic wastewater, several compounds such as bezafibrate, atenolol and acyclovir were significantly removed in the activated sludge processes fed with municipal wastewater. Complementary removal of two compounds, diuron and diclofenac, was achieved in an oxic biofilm treatment. A few aerobically persistent micropollutants such as venlafaxine, diatrizoate and tramadol were removed under anaerobic conditions, but a large number of micropollutants persisted in all biological treatments. Collectively, these results indicate that certain improvements in biological micropollutant removal can be achieved by combining different aerobic and anaerobic treatments, but that these improvements are restricted to a limited number of compounds.

Microbial community modeling using reliability theory

Linking microbial community composition with the corresponding ecosystem functions remains challenging. Because microbial communities can differ in their functional responses, this knowledge gap limits ecosystem assessment, design and management. To develop models that explicitly incorporate microbial populations and guide efforts to characterize their functional differences, we propose a novel approach derived from reliability engineering. This reliability modeling approach is illustrated here using a microbial ecology dataset from denitrifying bioreactors. Reliability modeling is well-suited for analyzing the stability of complex networks composed of many microbial populations. It could also be applied to evaluate the redundancy within a particular biochemical pathway in a microbial community. Reliability modeling allows characterization of the system's resilience and identification of failure-prone functional groups or biochemical steps, which can then be targeted for monitoring or enhancement. The reliability engineering approach provides a new perspective for unraveling the interactions between microbial community diversity, functional redundancy and ecosystem services, as well as practical tools for the design and management of engineered ecosystems.

Metagenomic Analysis of Chicken Gut Microbiota for Improving Metabolism and Health of Chickens - A Review

Chicken is a major food source for humans, hence it is important to understand the mechanisms involved in nutrient absorption in chicken. In the gastrointestinal tract (GIT), the microbiota plays a central role in enhancing nutrient absorption and strengthening the immune system, thereby affecting both growth and health of chicken. There is little information on the diversity and functions of chicken GIT microbiota, its impact on the host, and the interactions between the microbiota and host. Here, we review the recent metagenomic strategies to analyze the chicken GIT microbiota composition and its functions related to improving metabolism and health. We summarize methodology of metagenomics in order to obtain bacterial taxonomy and functional inferences of the GIT microbiota and suggest a set of indicator genes for monitoring and manipulating the microbiota to promote host health in future.

Understanding the Linkage between Elevation and the Activated-Sludge Bacterial Community along a 3,600-Meter Elevation Gradient in China

To understand the relationship between elevation and bacterial communities in wastewater treatment plants (WWTPs), bacterial communities in 21 municipal WWTPs across China, located 9 to 3,660 m above sea level (masl), were investigated by 454 pyrosequencing. A threshold for the association of elevation with bacterial community richness and evenness was observed at approximately 1,200 masl. At lower elevations, both richness and evenness were not significantly associated with elevation. At higher elevations, significant declines with increased elevations were observed for community richness and evenness. The declining evenness trend at the phylum level was reflected by distinct trends in relative abundance for individual bacterial phyla. Betaproteobacteria, Bacteroidetes, and Firmicutes displayed significant increases, while most other phyla showed declines. Spearman correlation analysis indicated that the community richness and evenness at high elevations were more correlated with elevation than with any other single environmental variable. Redundancy analysis indicated that the contribution of elevation to community composition variances increased from 3% at lower elevations to 11% at higher elevations whereas the community composition variance at higher elevations remained much more explained by operational variables (39.2%) than by elevation. The influent total phosphorus concentration, food/microorganism ratio, and treatment process were the three shared dominant contributors to the community composition variance across the whole elevation gradient, followed by effluent ammonia nitrogen and temperature at higher elevations.

Can meta-omics help to establish causality between contaminant biotransformations and genes or gene products?

There is increasing interest in using meta-omics association studies to investigate contaminant biotransformations. The general strategy is to characterize the complete set of genes, transcripts, or enzymes from in situ environmental communities and use the abundances of particular genes, transcripts, or enzymes to establish associations with the communities' potential to biotransform one or more contaminants. The associations can then be used to generate hypotheses about the underlying biological causes of particular biotransformations. While meta-omics association studies are undoubtedly powerful, they have a tendency to generate large numbers of non-causal associations, making it potentially difficult to identify the genes, transcripts, or enzymes that cause or promote a particular biotransformation. In this perspective, we describe general scenarios that could lead to pervasive non-causal associations or conceal causal associations. We next explore our own published data for evidence of pervasive non-causal associations. Finally, we evaluate whether causal associations could be identified despite the discussed limitations. Analysis of our own published data suggests that, despite their limitations, meta-omics association studies might still be useful for improving our understanding and predicting the contaminant biotransformation capacities of microbial communities.

Association of biodiversity with the rates of micropollutant biotransformations among full-scale wastewater treatment plant communities

Biodiversities can differ substantially among different wastewater treatment plant (WWTP) communities. Whether differences in biodiversity translate into differences in the provision of particular ecosystem services, however, is under active debate. Theoretical considerations predict that WWTP communities with more biodiversity are more likely to contain strains that have positive effects on the rates of particular ecosystem functions, thus resulting in positive associations between those two variables. However, if WWTP communities were sufficiently biodiverse to nearly saturate the set of possible positive effects, then positive associations would not occur between biodiversity and the rates of particular ecosystem functions. To test these expectations, we measured the taxonomic biodiversity, functional biodiversity, and rates of 10 different micropollutant biotransformations for 10 full-scale WWTP communities. We have demonstrated that biodiversity is positively associated with the rates of specific, but not all, micropollutant biotransformations. Thus, one cannot assume whether or how biodiversity will associate with the rate of any particular micropollutant biotransformation. We have further demonstrated that the strongest positive association is between biodiversity and the collective rate of multiple micropollutant biotransformations. Thus, more biodiversity is likely required to maximize the collective rates of multiple micropollutant biotransformations than is required to maximize the rate of any individual micropollutant biotransformation. We finally provide evidence that the positive associations are stronger for rare micropollutant biotransformations than for common micropollutant biotransformations. Together, our results are consistent with the hypothesis that differences in biodiversity can indeed translate into differences in the provision of particular ecosystem services by full-scale WWTP communities.