Metagenomes reveal microbial structures, functional potentials, and biofouling-related genes in a membrane bioreactor

Alterations in microbial communities and antibiotic resistance genes pre- and post-sludge bulking in a wastewater treatment plant

Sludge bulking is a common issue in wastewater treatment plants (WWTPs) that can disrupt microbial communities and potentially impact the abundance and spread of antibiotic resistance genes (ARGs) within treatment systems. This study employed high-throughput 16S rRNA gene sequencing and metagenomic sequencing to examine the changes in microbial communities and ARGs in a WWTP during non-bulking and bulking periods. The results indicated that bacterial diversity decreased in bulking sludge while maintaining a high removal efficiency of conventional pollutants. Significant differences were detected at the bacterial genus level between non-bulking and bulking sludge (p < 0.05). The proliferation of Candidatus_Microthrix contributed to sludge bulking, while Micropruina improved sludge settleability. When treating wastewater with the same water quality and quantity, anaerobic/anoxic/oxic (A2/O) exhibited the highest resistance to sludge bulking, followed by Bardenpho and the Carrousel oxidation ditch. The abundance of ARGs in bulking sludge (28.15-43.63 ppm) was lower than that in non-bulking sludge (51.72-59.01 ppm). The ARGs removal efficiency reached 96.24 % and 94.34 % during bulking and non-bulking periods, respectively. Network analysis revealed that Candidatus_Microthrix was positively correlated with aadS and tetX, and norank_f_Saprospiraceae exhibited positive correlations with vanRO and ANT(3″)-Iia. These findings provide valuable insights into the impacts of sludge bulking on WWTP performance and ARGs dynamics, informing evidence-based policies for sustainable wastewater treatment.

Novel Stepped Combined Constructed Wetland For Surface Water Removal: Enhancing the Performance and Responses of Microbial Communities

Micro-polluted surface waters (MPSWs) draw increased concern for environmental protection. However, traditional treatment methods such as activated sludge, ozone activated carbon, and membrane filtration suffer from high cost and susceptibility to secondary pollution and are rarely used to address MPSWs. Herein, a new stepped combined constructed wetland planted with Eichhornia crassipes without additional inputs was developed. In a 60-day experiment conducted in a drainage canal, we evaluated contaminant removal and bacterial communities using laboratory analysis and amplicon sequencing. Our results showed that the stepped combined constructed wetland achieved impressive removal rates for various contaminants. It was able to remove 70% of suspended solids, 51% of total nitrogen, 55% of total phosphorus, 70% of ammonia nitrogen, and 64% of the chemical oxygen demand. The dominant bacterial phyla found in stepped combined constructed wetland was Proteobacteria and Actinobacteria, with average relative abundances of 43.4 and 19.9%, respectively. We also observed clear differences in bacterial genera between the influent and effluent water samples. Specifically, we found that the stepped combined constructed wetland significantly reduced the abundance of bacteria such as hgcl clade, Rhizorhapis, and Cyanobacteria, while increasing the abundance of bacteria like Flavobacterium, Limnohabitans, Alpinimonas, Erwinia, and Saccharibacteria. The dominant bacterial community comprised nitrifying bacteria (Azoarcus and Nitrospira), denitrifying bacteria (e.g., Mycobacterium, Paracoccus, Ralstonia, Rhodobacter, Escherichia Shigella), and nitrogen-fixing bacteria (Rhizobium, Bradyrhizobium, Azospirillum). Notably, the abundance of nitrogen-fixing bacteria, nitrite-oxidizing bacteria, and denitrifying bacteria increased with the stepped combined constructed wetland presence. The stepped combined constructed wetland technology is highly cost-effective, with a total investment of only 259.83 USD. The majority of this investment is used for construction, with minimal expenditure required for operation and maintenance. Therefore, the stepped combined constructed wetland presents an economical and environmentally friendly solution for pollutant removal in slow flow and still water areas. It offers numerous benefits, including improved pollutant removal efficiency, low cost, ecological advantages, and extensive development potential, in various fields.

Microbial community structure of an anaerobic side-stream coupled anoxic-aerobic membrane bioreactor (AOMBR-ASSR) for an in-situ sludge reduction process

With the anoxic-aerobic membrane bioreactor (AO-MBR, CP) as a reference, high-throughput sequencing technology was used to reveal the characteristics of the microbial community structure in the anaerobic side-stream anoxic-aerobic membrane bioreactor sludge reduction process (AOMBR-ASSR, SRP). After the stable operation of two processes for 120 days, the average removal efficiencies of TN and TP in the effluent of SRP were increased by 5.6% and 29.8%, respectively. The observed sludge yields (Yobs) of the two processes were 0.14 and 0.17 gMLSS/(gCOD), respectively, and the sludge reduction rate of the SRP was 19.5%. Compared to the CP, the microbial richness and diversity index of SRP increased significantly. Chloroflexi, which is responsible for the degradation of organic substances under an anaerobic condition, seemed to be reduced in the SRP. Meanwhile, other phyla that involved in the nitrogen cycle, such as Nitrospirae and Planctomycetes, were found to be more abundant in the SRP than in the CP. A total of 21 identified classes were observed, and primarily hydrolyzed fermented bacteria (Sphingobacteriia, Betaproteobacteria, Actinobacteria and Deltaproteobacteria) and slow-growing microorganisms (Bacilli) were accumulated in the SRP. At the genus level, the inserted anaerobic side-stream reactor favored the hydrolyzed bacteria (Saprospiraceae, Rhodobacter and Candidatus_Competibacter), fermented bacteria (Lactococcus and Trichococcus), and slow-growing microorganisms (Dechloromonas and Haliangium), which play a crucial role in the sludge reduction. Furthermore, the enrichment of bacterial species related to nitrogen (Nitrospir and Azospira) provided the potential for nitrogen removal, while the anaerobic environment of the side-stream reactor promoted the enrichment of phosphorus-accumulating organisms.

Effects of Microbial Transfer during Food-Gut-Feces Circulation on the Health of Bombyx mori

Change in habitual diet may negatively affect health. The domestic silkworm (Bombyx mori) is an economically important oligophagous insect that feeds on mulberry leaves. The growth, development, and immune-disease resistance of silkworms have declined under artificial dietary conditions. In this study, we used B. mori as a model insect to explore the relationship between changes in diet and balance of intestinal microbes due to its simpler guts compared with those of mammals. We found that artificial diets reduced the intestinal bacterial diversity in silkworms and resulted in a simple intestinal microbial structure. By analyzing the correlations among food, gut, and fecal microbial diversity, we found that an artificial diet was more easily fermented and enriched the lactic acid bacteria in the gut of the silkworms. This diet caused intestinal acidification and microbial imbalance (dysbiosis). When combined with the artificial diet, Enterococcus mundtii, a colonizing opportunistic pathogen, caused dysbiosis and allowed the frequent outbreak of bacterial diseases in the silkworms. This study provides further systematic indicators and technical references for future investigations of the relationship between diet-based environmental changes and intestinal microbial balance. IMPORTANCE The body often appears unwell after habitual dietary changes. The domestic silkworm (Bombyx mori) raised on artificial diets is a good model to explore the relationship between dietary changes and the balance of intestinal microbes. In this study, the food-gut-feces microbial model was established, and some potential key genera that could regulate the balance of intestinal microbiota were screened out. Our findings will provide a reference for future research to further our understanding of healthy silkworm development and may even be useful for similar research on other animals.

Diversity and Functional Roles of the Gut Microbiota in Lepidopteran Insects

Lepidopteran insects are one of the most widespread and speciose lineages on Earth, with many common pests and beneficial insect species. The evolutionary success of their diversification depends on the essential functions of gut microorganisms. This diverse gut microbiota of lepidopteran insects provides benefits in nutrition and reproductive regulation and plays an important role in the defence against pathogens, enhancing host immune homeostasis. In addition, gut symbionts have shown promising applications in the development of novel tools for biological control, biodegradation of waste, and blocking the transmission of insect-borne diseases. Even though most microbial symbionts are unculturable, the rapidly expanding catalogue of microbial genomes and the application of modern genetic techniques offer a viable alternative for studying these microbes. Here, we discuss the gut structure and microbial diversity of lepidopteran insects, as well as advances in the understanding of symbiotic relationships and interactions between hosts and symbionts. Furthermore, we provide an overview of the function of the gut microbiota, including in host nutrition and metabolism, immune defence, and potential mechanisms of detoxification. Due to the relevance of lepidopteran pests in agricultural production, it can be expected that the research on the interactions between lepidopteran insects and their gut microbiota will be used for biological pest control and protection of beneficial insects in the future.

Analysis of Community Composition of Bacterioplankton in Changle Seawater in China by Illumina Sequencing Combined with Bacteria Culture

OBJECTIVES

To characterize the abundance and relative composition of seawater bacterioplankton communities in Changle city using Illumina MiSeq sequencing and bacterial culture techniques.

METHODS

Seawater samples and physicochemical factors were collected from the coastal zone of Changle city on 8 September 2019. Nineteen filter membranes were obtained after using a suction filtration system. We randomly selected eight samples for total seawater bacteria (SWDNA group) sequencing and three samples for active seawater bacteria (SWRNA group) sequencing by Illumina MiSeq. The remaining eight samples were used for bacterial culture and identification. Alpha diversity including species coverage (Coverage), species diversity (Shannon-Wiener and Simpson index), richness estimators (Chao1), and abundance-based richness estimation (ACE) were calculated to assess biodiversity of seawater bacterioplankton. Beta diversity was used to evaluate the differences between samples. The species abundance differences were determined using the Wilcoxon rank-sum test. Statistical analyses were performed in R environment.

RESULTS

The Alpha diversity in the SWDNA group in each index was ACE 3206.99, Chao1 2615.12, Shannon 4.64, Simpson 0.05, and coverage 0.97; the corresponding index was ACE 1199.55, Chao1 934.75, Shannon 3.49, Simpson 0.09, and coverage 0.99. The sequencing results of seawater bacterial genes in the coastal waters of Changle city showed that the phyla of high-abundance bacteria of both the SWDNA and SWRNA groups included Cyanobacteria, Proteobacteria, and Bacteroidetes. The main classes included Oxyphotobacteria, Alphaproteobacteria, and Gammaproteobacteria. The main genera included Synechococcus CC9902, Chloroplast, and Cyanobium_PCC-6307. Beta diversity analysis showed a significant difference between the SWDNA and SWRNA groups (P < 0.05). The species abundance differences between SWDNA and SWRNA groups after Wilcoxon rank-sum test showed that, at the phylum level, Actinomycetes was more abundant in SWDNA group (9.17 vs 1.02%, P < 0.05); at the class level, Actinomycetes (δ- Proteus) was more abundant in SWDNA group (9.47% vs 1.01%, P < 0.05); and at the genus level, Chloroplast was more abundant in SWRNA group (13.07% vs 44.57%, P < 0.05). Nine species and 53 colonies were found by bacterial culture: 20 strains of Vibrio (37.74%), 22 strains of Enterobacter (41.51%), and 11 strains of non-fermentative bacteria (20.75%).

CONCLUSION

Illumi MiSeq sequencing of seawater bacteria revealed that the total bacterial community groups and the active bacterial community groups mainly comprised Cyanobacteria, Proteobacteria, and Bacteroides at the phylum level; Oxyphotobacteria, α-Proteobacteria, and γ-Proteobacteria at the class level; with Synechococcus_CC9902, Chloroplast, and Cyanobium_PCC-6307 comprising the predominant genera. Exploring the composition and differences of seawater bacteria assists understanding regarding the biodiversity and the infections related to seawater bacteria along the coast of the Changle, provides information that will aid in the diagnosis and treatment of such infections.

Metagenomic insights into the "window" effect of static magnetic field on nitrous oxide emission from biological nitrogen removal process at low temperature

This study aimed to explore whether the "window" effect of static magnetic field (SMF) on nitrous oxide (N₂O) emission from the biological nitrogen removal process at low temperature existed and reveal its biological mechanism at the gene level. Four sequencing batch reactors (SBRs) with SMFs of 0, 10, 45, and 75 mT were operated continuously for 110 days at 10 °C and the lowest N₂O-Gas cumulative emission (5.50 mg N/day) and N₂O conversion rate (4.28 %) in 45 mT SMF-SBR verified the existence of the "window" effect. In 45 mT SMF-SBR, nearly all enzymatic activities related to N₂O reduction and corresponding functional gene abundances improved significantly. Metagenomic high-throughput sequencing analysis revealed that Alicycliphilus denitricans, Paracoccus denitrificans, Rhodopseudomonas palustris, Pseudomonas stutzeri, and Dechloromonas aromatica, as species related to N₂O reduction, could be separately enriched by applying suitable SMF intensity. Gene functions annotation based on KEGG and CAZy databases indicated that SMF not only accelerated the rate of free ammonia into ammonia-oxidizing bacteria and electrons delivered to the corresponding denitrification reductases, but also enhanced the degradation of complex organic matter into smaller molecules, and thus reducing the production of N₂O via nitrifier denitrification and incomplete denitrification pathways at 10 °C. These findings provided a guideline and presented a blueprint of ecophysiology for the future application of magnetic field to the reduction of N₂O emission in wastewater treatment plants in the cold region.

Assessment of seawater bacterial infection in rabbit tibia by Illumina MiSeq sequencing and bacterial culture

Objectives

We aimed to explore the bacterial community composition following ocean bacterial infection using an animal model.

Methods

This animal-based experiment was conducted from September 2019 to November 2019. Eighteen seawater filter membranes were collected from Changle City, Fujiian Province, China, on September 8, 2019. Ten filter membranes were used for implantation. Eight filter membranes that were used in the bacterial culture for the exploration of seawater bacteria were assigned to the seawater group (SG). Fourteen healthy adult New Zealand rabbits were randomly divided into the experimental group (EG) and control group (CG). Seawater filter membranes and asepsis membranes were implanted into the tibia in the EG and CG, respectively. One week after surgery, tibial bone pathology tissues were collected and assessed using light microscopy and scanning electron microscopy (SEM). Medullary cavity tissues were collected for the performance of Illumina MiSeq sequencing and bacterial culture. The differences between EG and CG were assessed by pathological observation under light microscopy and SEM, high-throughput bacterial sequencing, and bacterial culture.

Results

Compared with the CG, the infection rate was 100%, and the mortality value was 20% after the implantation of the filter membranes in the EG. Both light microscopy and SEM showed that a large number of bacteria were distributed in the bone marrow cavity after ocean bacterial infection. No bacterial growth was found in the CG. Illumina MiSeq sequencing found that Firmicutes, Proteobacteria, Thermotogae, Fusobacteria, Bacteroidetes, and Actinobacteria were the dominant bacteria at the phylum level and Clostridium_sensu_stricto_7, Haloimpatiens, Clostridium_sensu_stricto_15, Clostridiaceae_1, Clostridium_sensu_stricto_18, and Oceanotoga were the dominant bacteria in genus level among the EG. In the bacterial culture of the medullary cavity tissues, Klebsiella pneumoniae, Shewanella algae, Staphylococcus aureus, Escherichia coli, Enterobacter cloacae, and Vibrio vulnificus were the predominant infective species. Moreover, compared with the SG, the EG showed a higher detection rate of E. coli and S. aureus (P = 0.008 and P = 0.001, respectively). The detection rates of V. alginolyticus, V. parahaemolyticus, and V. fluvialis were higher in the SG than the EG (P = 0.007, P = 0.03, and P = 0.03, respectively).

Conclusions

Our model, which was comprehensively evaluated using four techniques: histopathology and SEM observation, gene detection, and bacteria culture, provides a scientific basis for the clinical diagnosis and treatment of patients in such settings.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13018-021-02553-9.

Realizing the role of N-acyl-homoserine lactone-mediated quorum sensing in nitrification and denitrification: A review

Nitrification and denitrification are crucial processes in the nitrogen cycle, a vital microbially driven biogeochemical cycle. N-acyl-homoserine lactone (AHL)-mediated quorum sensing (QS) is widespread in bacteria and plays a key role in their physiological status. Recently, there has been an increase in research into how the AHL-mediated QS system is involved in nitrification and denitrification. Consequentially, the AHL-mediated QS system has been considered a promising regulatory approach in nitrogen metabolism processes, with high potential for real-world applications. In this review, the universal presence of QS in nitrifiers and denitrifiers is summarized. Many microorganisms taking part in nitrification and denitrification harbor QS genes, and they may produce AHLs with different chain lengths. The phenotypes and processes affected by QS in real-world applications are also reviewed. In wastewater bioreactors, QS could affect nitrogen metabolism efficiency, granule aggregation, and biofilm formation. Furthermore, methods commonly used to identify the existence and functions of QS, including physiological tests, genetic manipulation and omics analyses are discussed.

Comparison of bacterial communities and antibiotic resistance genes in oxidation ditches and membrane bioreactors

Oxidation ditches (ODs) and membrane bioreactors (MBRs) are widely used in wastewater treatment plants (WWTPs) with bacteria and antibiotic resistance genes (ARGs) running through the whole system. In this study, metagenomic sequencing was used to compare the bacterial communities and ARGs in the OD and MBR systems, which received the same influent in a WWTP located in Xinjiang, China. The results showed that the removal efficiency of pollutants by the MBR process was better than that by the OD process. The composition and the relative abundance of bacteria in activated sludge were similar at the phylum and genus levels and were not affected by process type. Multidrug, fluoroquinolones and peptides were the main ARG types for the two processes, with macB being the main ARG subtype, and the relative abundance of ARG subtypes in MBR effluent was much higher than that in the OD effluent. The mobile genetic elements (MGEs) in the activated sludge were mainly transposons (tnpA) and insertion sequences (ISs; IS91). These results provide a theoretical basis for process selection and controlling the spread of ARGs.

Genomic studies on natural and engineered aquatic denitrifying eco-systems: A research update

Excess nitrogenous compounds in municipal or industrial wastewaters can stimulate growth of denitrifying bacteria, in return, to convert potentially hazardous nitrate to inorganic nitrogen gas. To explore the community structure, distributions and succession of functional strains, and their interactions with other microbial communities, contemporary studies were performed based on detailed genomic analysis. This mini-review updated contemporary genomic studies on denitrifying genes in natural and engineered aquatic systems, with the constructed wetlands being the demonstrative system for the latter. Prospects for the employment of genomic studies on denitrifying systems for process design, optimization and development of novel denitrifying processes were discussed.

Fermented Soybean Meal Replacement in the Diet of Lactating Holstein Dairy Cows: Modulated Rumen Fermentation and Ruminal Microflora

This study was conducted to examine the influences of replacing soybean meal (SBM) with fermented soybean meal (FSBM) in the diet of lactating Holstein cattle on rumen fermentation and ruminal bacterial microbiome. Twenty-four lactating Chinese Holstein dairy cattle were assigned to each of the two treatments in a completely randomized design: the SBM group [the basal total mixed ration (TMR) diet containing 5.77% SBM] and the FSBM group (the experimental TMR diet containing 5.55% FSBM). This trial lasted for 54 days (14 days for adjustment and 40 days for data and sample collection), and samples of rumen liquid were collected on 34 d and 54 d, respectively. The results showed that replacing SBM with FSBM significantly increased the molar percentages of propionate (P < 0.01) and valerate (P < 0.05), but reduced the total volatile fatty acid (TVFA) concentration (P < 0.05), butyrate molar proportion (P < 0.05), and the acetate to propionate ratio (P < 0.01). The copy numbers of total bacteria (P < 0.05), Fibrobacter succinogenes (P < 0.01), Selenomonas ruminantium (P < 0.01), and Prevotella spp. (P < 0.05) in the FSBM group were greater, while the density of Prevotella ruminicola (P < 0.05) was lower than those in the SBM treatment. Additionally, Succiniclasticum ruminis and Saccharofermentans acetigenes were significantly enriched (P < 0.05) in the rumen fluid of FSBM-fed cows, despite the fact that there was no remarkable difference in the Alpha diversity indexes, structure and KEGG pathway abundances of the bacterial community across the two treatments. It could hence be concluded that the substitution of FSBM for SBM modulated rumen fermentation and rumen bacterial microbiota in lactating Holstein dairy cows. Further research is required to elucidate the relevant mechanisms of FSBM, and provide more insights into the application of FSBM in dairy cattle.

Microbial community and function in nitrogen transformation of ectopic fermentation bed system for pig manure composting

In this work, agricultural wastes were treated by composting in an ectopic fermentation bed system (EFBS) with a continuous nitrogen addition technique. With decreasing of NH₄⁺-N concentration and increasing of NO₃^--N concentration were observed, and activities of protease, urease and nitrate reductase changed significantly during the fermentation process. To elucidate the key microbes and their function in nitrogen-transforming, microbial diversity and clusters of orthologous groups (COGs) in composting materials were evaluated using metagenomic technology. Comparing with ammonification, the COGs involved in nitrification and denitrification were predominant in the composts. The correlation heatmap revealed that Streptomyces predominant in ammonification was significantly affected by contents of N, NH₄⁺-N and NO₃^--N. Meanwhile, ammonia-oxidizing archaea (AOA) had a positive relationship with moisture. The most abundant genera in denitrification had positive relationships with N and NO₃^--N. The results indicated that EFBS had functionally diverse microbes and COGs for NH₃ removal.

Modulation of rumen fermentation and microbial community through increasing dietary cation-anion difference in Chinese Holstein dairy cows under heat stress conditions

AIMS

The effect of increasing dietary cation-anion difference (DCAD) on rumen fermentation and ruminal microbial community in dairy cows under heat stress (HS) conditions were evaluated.

METHODS AND RESULTS

This study was performed as a two-period cross-over design during the summer season, with eight lactating dairy cows randomly distributed to either a control DCAD diet (CON: 33·5 mEq/100 g DM) or high DCAD diet (HDCAD: 50·8 mEq/100 g DM). Throughout the present study, the temperature and humidity index (THI; 80·2 ± 4·29) was generally elevated above the threshold (THI = 72) that is reported to cause HS in lactating dairy cows. Rumen liquid samples were collected on 15 and 21 d during each 21 d-period. The absolute concentration of ruminal total volatile fatty acid (TVFA) in HDCAD treatment was significantly (P < 0·05) higher than those in the control, whilst the ruminal pH, NH₃ -N, and VFA molar percentages were unaffected through increasing DCAD. Furthermore, the copy numbers of the cellulolytic bacteria Ruminococcus albus and Ruminococcus flavefaciens in rumen fluid significantly (P < 0·05) rose along with the increment of DCAD. Although the Alpha diversity indexes and the bacterial microbiota structure were unaffected, increasing DCAD significantly (P < 0·05) enriched the phylum Fibrobacteres and genus Fibrobacter in the microflora of rumen fluid, whilst the genera Flexilinea and Dubosiella were the most differentially abundant taxa in the control.

CONCLUSIONS

Increasing DCAD under HS conditions resulted in a greater concentration of total VFA without affecting rumen bacteria diversity or structure, although the enrichment of some cellulolytic/hemicellulolytic bacteria was observed.

SIGNIFICANCE AND IMPACT OF THE STUDY

The present study provides information on the modulation of rumen fermentation and microbial community through the increment of DCAD in Holstein dairy cows under HS conditions.

Genome sequencing as a new window into the microbial community of membrane bioreactors - A critical review

Recent developed sequencing techniques have resulted in a new and unprecedented way to study biological wastewater treatment, in which most organisms are uncultivable. This review provides (i) an insight on state-of-the-art sequencing techniques and their limitations; (ii) a critical assessment of the microbial community in biological reactor and biofouling layer in a membrane bioreactor (MBR). The data from high-throughput sequencing has been used to infer microbial growth conditions and metabolisms of microorganisms present in MBRs at the time of sampling. These data shed new insight to two fundamental questions about a microbial community in the MBR process namely the microbial composition (who are they?) and the functions of each specific microbial assemblage (what are their function?). The results to date also highlight the complexity of the microbial community growing on MBRs. Environmental conditions are dynamic and diverse, and can influence the diversity and structural dynamics of any given microbial community for wastewater treatment. The benefits of understanding the structure of microbial communities on three major aspects of the MBR process (i.e. nutrient removal, biofouling control, and micropollutant removal) were symmetrically delineated. This review also indicates that the deployment of microbial community analysis for a practical engineering context, in terms of process design and system optimization, can be further realized.

Microbial community succession and its correlation with reactor performance in a sponge membrane bioreactor coupled with fiber-bundle anoxic bio-filter for treating saline mariculture wastewater

The application of MBR in high saline wastewater treatment is mainly constrained by poor nitrogen removal and severe membrane fouling caused by high salinity stress. A novel carriers-enhanced MBR system was successfully developed for treating saline mariculture wastewater, which showed efficient TN removal (93.2%) and fouling control. High-throughput sequencing revealed the enhancement mechanism of bio-carriers under high saline condition. Bio-carriers substantially improved the community structure, representatively, nitrifiers abundance (Nitrosomonas, Nitrospira) increased from 2.18% to 9.57%, abundance of denitrifiers (Sulfurimonas, Thermogutta, etc.) also rose from 3.81% to 14.82%. Thereby, the nitrogen removal process was enhanced. Noteworthy, ammonia oxidizer (Nitrosomonas, 8.26%) was the absolute dominant nitrifiers compared with nitrite oxidizer (Nitrospira, 1.13%). This supported the finding of shortcut nitrification-denitrification process in hybrid system. Moreover, a series of biomacromolecule degraders (Lutibacterium, Cycloclasticus, etc.) were detected in bio-carriers, which could account for the mitigation of membrane fouling as result of EPS and SMP degradation.

Research on Operation Efficiency and Membrane Fouling of A2/O-MBR in Reclaimed Water Treatment

Taking the public building domestic wastewater as an example, the combination of the MBR (membrane bioreactor) process and the traditional A²/O (anaerobic-anoxic-oxic) process was established and analyzed in terms of the removal effect of the pollutants, the impact of the microbial community changes on the process, the MBR membrane fouling, the cleaning methods, and the cleaning performance. The results indicated that the effluent water quality of the domestic wastewater treated with the A²/O-MBR process was stable and met the emission requirement to the natural water body. There was good microbial diversity in raw water, the anaerobic tank, the anoxic tank, the aerobic MBR tank and the disinfection tank, and the aerobic MBR tank has a wide variety of aerobic microorganisms, which elevates the removal of organics and the nitrification of ammonia nitrogen and ensures the qualification of nitrogen and phosphorus indexes of the system effluent water. For the fouled membrane, the surface of the contaminated membrane was covered by macromolecular contaminants, causing the membrane flux to drop, and after different cleaning methods to the membrane were compared, it was discovered that the combined use of cleaning agents had better effects than the single ones, and the cleaning method of sodium hydroxide followed by hydrochloric acid showed the best effect, achieving a membrane flux restoration ratio above 80% after cleaning.

Metagenomic Insights into the Effects of Seasonal Temperature Variation on the Activities of Activated Sludge

It is well acknowledged that the activities of activated sludge (AS) are influenced by seasonal temperature variation. However, the underlying mechanisms remain largely unknown. Here, the activities of activated sludge under three simulated temperature variation trends were compared in lab-scale. The TN, HN3-H, and COD removal activities of activated sludge were improved as temperature elevated from 20 °C to 35 °C. While, the TN, HN3-H, COD and total phosphorus removal activities of activated sludge were inhibited as temperature declined from 20 °C to 5 °C. Both the extracellular polymer substances (EPS) composition (e.g., total amount, PS, PN and DNA) and sludge index of activated sludge were altered by simulated seasonal temperature variation. The variation of microbial community structures and the functional potentials of activated sludge were further explored by metagenomics. Proteobacteria, Actinobacteria, Acidobacteria and Bacteroidetes were the dominant phyla for each activated sludge sample under different temperatures. However, the predominant genera of activated sludge were significantly modulated by simulated temperature variation. The functional genes encoding enzymes for nitrogen metabolism in microorganisms were analyzed. The enzyme genes related to ammonification had the highest abundance despite the changing temperature, especially for gene encoding glutamine synthetase. With the temperature raising from 20 °C to 35 °C. The abundance of amoCAB genes encoding ammonia monooxygenase (EC:1.14.99.39) increased by 305.8%. Meanwhile, all the enzyme genes associate with denitrification were reduced. As the temperature declined from 20 °C to 5 °C, the abundance of enzyme genes related to nitrogen metabolism were raised except for carbamate kinase (EC:2.7.2.2), glutamate dehydrogenase (EC:1.4.1.3), glutamine synthetase (EC:6.3.1.2). Metagenomic data indicate that succession of the dominant genera in microbial community structure is, to some extent, beneficial to maintain the functional stability of activated sludge under the temperature variation within a certain temperature range. This study provides novel insights into the effects of seasonal temperature variation on the activities of activated sludge.

Simultaneous decarburization, nitrification and denitrification (SDCND) in coking wastewater treatment using an integrated fluidized-bed reactor

There are two problems in biological treatment of coking wastewater (CWW): incapability of pre-anaerobic treatment to eliminate the toxicity in wastewater, and the lack of carbon source for subsequent denitrification in pre-aerobic treatment. To achieve simultaneous decarburization, nitrification and denitrification (SDCND) in CWW treatment, biological carrier materials was used to build an integrated fluidized-bed reactor (Reactor B, RB). A conventional fluidized-bed reactor (Reactor A, RA) was used as a control reactor under the same condition. The results showed that RB was more advantageous since its removal efficiencies of COD and TN were 90% and 87%, respectively, which were significantly higher than these in RA (82% and 45%), at a hydraulic retention time (HRT) of 60 h. Microelectrode measurement indicated that oxygen transfer was limited inside the carrier where the formation of a dissolved oxygen (DO) concentration gradient was observed. Microbial community analysis showed that the aerobic and anoxic microenvironments in RB promoted the co-existence of a wider variety of bacteria, thus achieving SDCND. These results indicated the integrated fluidized-bed reactor exhibited promising feasibility for simultaneous carbon and nitrogen removal in CWW treatment under the same aeration driven conditions. The SDCND process realized by fluidized-bed reactor provided a reference for the treatment of toxic industrial wastewater with high carbon to nitrogen ratio.

Floc-size effects of the pathogenic bacteria in a membrane bioreactor plant

The size nature of sludge flocs could affect the occurrence and distribution of bacterial pathogens in wastewater treatment plants (WWTPs). In this study, the floc-size dependence of bacterial pathogens in the activated sludge of a WWTP was investigated using high-throughput metagenomic sequencing approaches. The results showed that a total of 423 pathogenic species belonging to 123 genera were identified in the three size-fractionated flocs. Also, we found that all the pathogens on the WHO's global priority pathogens list were detected in the size-fractionated flocs, with relative abundance of 0.4%, 0.3% and 0.3% for large-size, medium-size and small-size flocs, respectively, indicating the severe human and environmental health risks of activated sludge. Importantly, our results revealed that the pathogenic species showed a clear floc-size dependent distribution manner, leading to significant differences (P < 0.05) of pathogenic communities among the size-fractionated flocs. Additionally, by partitioning pathogens based on the occurrence and significant difference in abundances, we suggested the following distribution features: 1) large flocs-associated pathogens, such as Borrelia recurrentis, Actinobacillus ureae and Campylobacter gracilis; 2) medium flocs-associated pathogens, such as Mycobacterium szulgai and Ureaplasma urealyticum; and 3) small flocs-associated pathogens, such as Rickettsia akari, Staphylococcus anginosus and Helicobacter cinaedi. Overall, this study provides a comprehensive understanding of pathogens in activated sludge, which is expected to aid in assessment and management of pathogen risks.

A novel approach for fouling mitigation in anaerobic-anoxic-oxic membrane bioreactor (A2O-MBR) by integrating worm predation

Membrane fouling is one of the biggest challenges in the widespread application of membrane bioreactors. In this study, a combined system of anaerobic-anoxic-oxic membrane bioreactor (A²O-MBR) and worm reactor (WR) was established for fouling control. In A²O-MBR-WR, the membrane filtration cycle was prolonged by 66.7% due to the confluence of microaerobic treatment and worm predation in WR with the interaction between WR and A²O-MBR. Compared with conventional A²O-MBR, membrane rejection of soluble and colloidal foulants (SCF) in the combined system was decreased by 26.0%, which could be attributed to the higher biodegradability of SCF and the higher bacterial activity in A²O-MBR. Although floc size in A²O-MBR was reduced due to sludge disintegration and worm predation in WR, changes of floc surface properties could counteract this negative effect on fouling. Complex effects of sludge flocs on membrane fouling were further analyzed by the interaction energy between sludge flocs and the clean/fouled membrane based on extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory. The energy barriers indicated that flocs in A²O-MBR-WR were difficult to adhere to the membrane and were more likely to detach. Moreover, high-throughput sequencing analysis revealed that the microbial community of the cake layer in the combined system was more even and had a higher proportion of foulants degradation related bacteria, which was beneficial for fouling mitigation. The combination of A²O-MBR and WR has shown significant advantages in membrane fouling mitigation.

Phthalic acid esters disturbed the genetic information processing and improved the carbon metabolism in black soils

Phthalic acid esters (PAEs), such as dimethyl phthalate (DMP) and dibutyl phthalate (DBP), are widely distributed as environmental pollutants. In this study, the effects of these chemicals were investigated in black soils using a metagenomics approach. The results clearly showed that DMP or DBP increased the abundance of genes involved in transcription, replication and repair in black soils. In addition, the abundances of genes associated with metabolic functions was improved following treatment with DMP or DBP, including those involved in lipid transport and metabolism, carbohydrate transport and metabolism, and energy production and conversion. There could be many reasons for these observed changes. First, the DMP or DBP treatments increased the abundances of genes associated with the LuxR family, the UvrABC repair system, DNA replication pathways, the RNA polymerase complex and base excision repair. Second, the abundances of genes associated with isocitrate lyase regulator (IclR) family transcriptional regulators, lipid metabolism and carbohydrate active enzymes (CAZys) were altered by the DMP or DBP treatments. Finally, the DMP or DBP treatments also increased the emission load of CO₂ and altered the fluorescence intensity of humic acid. Therefore, the results of this study suggested that DMP and DBP contamination altered the abundances of genes associated with genetic information processing and improved the carbon metabolism in black soils.

Applications of membrane bioreactors for water reclamation: Micropollutant removal, mechanisms and perspectives

Membrane bioreactors (MBRs) have attracted attention in water reclamation as a result of the recent technical advances and cost reduction in membranes. However, the increasing occurrence of micropollutants in wastewaters has posed new challenges. Therefore, we reviewed the current state of research to identify the outstanding needs in this field. In general, the fate of micropollutants in MBRs relates to sorption, biodegradation and membrane separation processes. Hydrophobic, nonionized micropollutants are favorable in sorption, and the biological degradation shows higher efficiency at relatively long SRTs (30-40 days) and HRTs (20-30 h), as a result of co-metabolism, metabolism and/or ion trapping. Although the membrane rejection rates for micropollutants are generally minor, final water quality can be improved via combination with other technologies. This review highlights the challenges and perspectives that should be addressed to facilitate the extended use of MBRs for the removal of micropollutants in water reclamation.

Variations of Bacterial Community Composition and Functions in an Estuary Reservoir during Spring and Summer Alternation

In this study, we focused on the dynamics of bacterial community composition in a large reservoir in the Yangtze estuary during spring and summer seasons, especially the variations of functional mechanisms of microbial community during the seasonal alternation between spring and summer. Both 16S rRNA gene sequencing and shotgun metagenomic sequencing technology were used for these purposes. The results indicated that obvious variations of bacterial community structures were found at different sites. Particle-associated bacterial taxa exhibited higher abundance at the inlet site, which was closer to the Yangtze River with a high level of turbidity. In other sites, Synechococcus, as the most dominant cyanobacterial species, revealed high abundance driven by increased temperature. Moreover, some heterotrophic bacterial taxa revealed high abundance following the increased Synechococcus in summer, which indicated potential correlations about carbon source utilization between these microorganisms. In addition, the shotgun metagenomic data indicated during the period of seasonal alternation between spring and summer, the carbohydrate transport and metabolism, energy production and conversion, translation/ribosomal biogenesis, and cell wall/membrane/envelope biogenesis were significantly enhanced at the exit site. However, the course of cell cycle control/division was more active at the internal site.

Potential roles of acyl homoserine lactone based quorum sensing in sequencing batch nitrifying biofilm reactors with or without the addition of organic carbon

Two lab-scale nitrifying sequencing batch biofilm reactors, with (SBBR_CN) or without the addition of organics (SBBR_N), were operated to investigate potential roles of acyl homoserine lactone (AHL) based quorum sensing. AHLs of N-[(RS)-3-Hydroxybutyryl]-L-homoserine lactone, N-hexanoyl-L-homoserine lactone (C₆-HSL) and N-octanoyl-L-homoserine lactone (C₈-HSL) were detected in both reactors. C₆-HSL and C₈-HSL were also detected in batch experiments, especially with stimulated nitrite oxidizing bacteria activities. Quorum sensing affected biofilm formation mainly through the regulation of extracellular protein production. By the metagenomics analysis, many identified genera and species could participate in quorum sensing, quorum quenching and extracellular polymeric substances (EPS) production. A high quorum quenching activity was obtained in SBBR_CN, whereas a high quorum sensing activity in SBBR_N. Nitrosomonas-like ammonia oxidizing bacteria, Nitrospira-like nitrite oxidizing bacteria and Comammox harbored genes for AHL synthesis and EPS production. Possible relationships among AHLs synthesis, biofilm formation and nitrifiers activity were proposed.

Nitrogen loading effects on nitrification and denitrification with functional gene quantity/transcription analysis in biochar packed reactors at 5 °C

This study investigated the nitrogen transformation rates of different nitrogen-loading (20, 30, and 50 mg TN/L) biochar packed reactors (C:N:P = 100:5:1) within 125 days at 5 °C. The results showed that high nitrogen loading resulted in an NH4+ (TN) removal efficiency decline from 98% (57%) to 83% (29%), with biochar yielding a higher NH4+, TN and DON removal rate than conventional activated sludge. Moreover, all biochar packed reactors realized a quick start-up by dropping in temperature stage by stage, and the effluent dissolved organic nitrogen (DON) concentrations of R20, R30, and R50 were 0.44 ± 0.18, 0.85 ± 0.35, and 0.66 ± 0.26 mg/L, respectively. The nirS/amoA, nxrA/amoA, and amoA/(narG + napA) were deemed to be the markers of ammonium oxidation rate (SAOR), specific nitrite oxidation rate (SNOR), and specific nitrate reduction rate (SNRR), respectively. Compared with functional gene quantity data, transcription data (mRNA) introduced into stepwise regression analyses agreed well with nitrogen transformation rates. High nitrogen loading also resulted in the cell viability decreased in R50. Nitrogen loadings and operation time both led to a significant variation in cell membrane composition, and unsaturated fatty acids (UFAs) significantly increased in R30 (46.49%) and R50 (36.34%). High-throughput sequencing revealed that nitrogen loadings increased the abundance of nitrifying bacteria (e.g., Nitrospira) and reduced the abundance of denitrifying bacteria (e.g., Nakamurella, Thermomonas, and Zoogloea) through linear discriminant analysis (LDA).

Disentangling the Drivers of Diversity and Distribution of Fungal Community Composition in Wastewater Treatment Plants Across Spatial Scales

Activated sludge microbial community composition is a key bio-indicator of the sustainability of wastewater treatment systems. Therefore, a thorough understanding of the activated sludge microbial community dynamics is critical for environmental engineers to effectively manage the wastewater treatment plants (WWTPs). However, fungal communities associated with activated sludge have been poorly elucidated. Here, the activated sludge fungal community in 18 geographically distributed WWTPs was determined by using Illumina sequencing. The results showed that differences in activated sludge fungal community composition were observed among all WWTPs and also between oxidation ditch and anaerobic-anoxic-aerobic (A/A/O) systems. Ascomycota was the largest phyla, followed by Basidiomycota in all samples. Sporidiobolales and Pezizales were the most abundant order in oxidation ditch and A/A/O systems, respectively. The network analysis indicated cooperative and co-occurrence interactions between fungal taxa in order to accomplish the wastewater treatment process. Hygrocybe sp., Sporobolomyces sp., Rhodotorula sp., Stemphylium sp., Parascedosporium sp., and Cylindrocarpon sp., were found to have statistically significant interactions. Redundancy analysis revealed that temperature, total phosphorus, pH, and ammonia nitrogen were significantly affected the fungal community. This study sheds light on providing the ecological characteristics of activated sludge fungal communities and useful guidance for improving wastewater treatment performance efficiency.

Gut bacterial and fungal communities of the domesticated silkworm (Bombyx mori) and wild mulberry-feeding relatives

Bombyx mori, the domesticated silkworm, is of great importance as a silk producer and as a powerful experimental model for the basic and applied research. Similar to other animals, abundant microorganisms live inside the silkworm gut; however, surprisingly, the microbiota of this model insect has not been well characterized to date. Here, we comprehensively characterized the gut microbiota of the domesticated silkworm and its wild relatives. Comparative analyses with the mulberry-feeding moths Acronicta major and Diaphania pyloalis revealed a highly diverse but distinctive silkworm gut microbiota despite thousands of years of domestication, and stage-specific signatures in both total (DNA-based) and active (RNA-based) bacterial populations, dominated by the phyla Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Most fungal sequences were assigned to the phyla Ascomycota and Basidiomycota. Environmental factors, including diet and human manipulation (egg production), likely influence the silkworm gut composition. Despite a lack of spatial variation along the gut, microbial community shifts were apparent between early instars and late instars, in concert with host developmental changes. Our results demonstrate that the gut microbiota of silkworms assembles into increasingly identical community throughout development, which differs greatly from those of other mulberry-feeding lepidopterans from the same niche, highlighting host-specific effects on microbial associations and the potential roles these communities play in host biology.

Metagenomic analysis of microbial community and function involved in cd-contaminated soil

Background

Soil contaminated with the heavy metal Cadmium (Cd) is a widespread problem in many parts of the world. Based on metagenomic analysis, we investigated the functional potential and structural diversity of the microbial community in Cd-contaminated and non-contaminated soil samples and we explored the associated metabolic pathway network in cluster of orthologous groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG).

Results

The results showed that microorganisms in these soils were quite abundant, and many of them possessed numerous physiological functions. However, Cd-contamination has the potential to reduce the microbial diversity and further alter the community structure in the soil. Notably, function analysis of the crucial microorganisms (e. g. Proteobacteria, Sulfuricella and Thiobacillus) indicated that these bacteria and their corresponding physiological functions were important for the community to cope with Cd pollution. The COG annotation demonstrated that the predominant category was the microbial metabolism cluster in both soil samples, while the relative abundance of metabolic genes was increased in the Cd-contaminated soil. The KEGG annotation results exhibited that the non-contaminated soil had more genes, pathways, modules, orthologies and enzymes involved in metabolic pathways of microbial communities than the Cd-contaminated soil. The relative abundance of some dominant KEGG pathways increased in the Cd contaminated soil, and they were mostly enriched to the metabolism, biosynthesis and degradation of amino acids, fatty acids and nucleotides, which was related to Cd tolerance of the microorganisms.

Conclusions

Cd-contamination can decrease the taxonomic species of microbes in soil and change the soil microbial composition. The functional pathways involved in the soil change with microbial structure variation, many of which are related to the heavy metal tolerance of soil microbes. The Cd-contaminated soil microbes is a potential resource for exploring cadmium resistant or tolerant bacteria.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1152-5) contains supplementary material, which is available to authorized users.

Dibutyl phthalate alters the metabolic pathways of microbes in black soils

Dibutyl phthalate (DBP) is well known as a high-priority pollutant. This study explored the impacts of DBP on the metabolic pathways of microbes in black soils in the short term (20 days). The results showed that the microbial communities were changed in black soils with DBP. In nitrogen cycling, the abundances of the genes were elevated by DBP. DBP contamination facilitated 3'-phosphoadenosine-5'-phosphosulfate (PAPS) formation, and the gene flux of sulfate metabolism was increased. The total abundances of ABC transporters and the gene abundances of the monosaccharide-transporting ATPases MalK and MsmK were increased by DBP. The total abundance of two-component system (TCS) genes and the gene abundances of malate dehydrogenase, histidine kinase and citryl-CoA lyase were increased after DBP contamination. The total abundance of phosphotransferase system (PTS) genes and the gene abundances of phosphotransferase, Crr and BglF were raised by DBP. The increased gene abundances of ABC transporters, TCS and PTS could be the reasons for the acceleration of nitrogen, carbon and sulfate metabolism. The degrading-genes of DBP were increased markedly in soil exposed to DBP. In summary, DBP contamination altered the microbial community and enhanced the gene abundances of the carbon, nitrogen and sulfur metabolism in black soils in the short term.

Comparative study of activated sludge with different individual nitrogen sources at a low temperature: Effluent dissolved organic nitrogen compositions, metagenomic and microbial community

The objective of this study was to explore nitrogen removal, especially effluent dissolved organic nitrogen (DON) composition, relative genes and microbial community structures with four individual nitrogen sources at 5°C. Results show that effluent DON did not have dependent relationship with the TN removal rate (urea>ammonia chloride>L-Alanine>D-Alanine). With the same influent TN, the highest effluent DON was formed with urea; the lowest DON was fed with ammonia chloride. The main DON composition was the product of cell metabolism excluding urea, rather than the original substrate. Glutamic acid synthesizing process was of great importance to DON accumulation at 5°C. The nitrogen source type was important to the diversity and heterogeneity of the nitrogen removal genes. Bacterial population structure using redundancy analysis (RDA) showed Simplicispira occupied a higher abundance remarkably in the reactors feeding with urea, and Dyadobacter occupied higher feeding with l-Alanine.

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.