Multistability and Reversibility of Aerobic Granular Sludge Microbial Communities Upon Changes From Simple to Complex Synthetic Wastewater and Back

Microbial genome collection of aerobic granular sludge cultivated in sequencing batch reactors using different carbon source mixtures

Aerobic granular sludge (AGS) consists of a microbial consortium that has an important role in wastewater treatment. This study investigates AGS microorganisms cultivated in a laboratory-scale sequencing batch reactor. Metagenomic sequencing was conducted using PacBio and Illumina, resulting in 759 metagenome-assembled genomes, 331 of which remained after dereplication.

Resistance of aerobic granular sludge microbiomes to periodic loss of biomass

Granular sludge is a biofilm process used for wastewater treatment which is currently being implemented worldwide. It is important to understand how disturbances affect the microbial community and performance of reactors. Here, two acetate-fed replicate reactors were inoculated with acclimatized sludge and the reactor performance, and the granular sludge microbial community succession were studied for 149 days. During this time, the microbial community was challenged by periodically removing half of the reactor biomass, subsequently increasing the food-to-microorganism (F/M) ratio. Diversity analysis together with null models show that overall, the microbial communities were resistant to the disturbances, observing some minor effects on polyphosphate-accumulating and denitrifying microbial communities and their associated reactor functions. Community turnover was driven by drift and random granule loss, and stochasticity was the governing ecological process for community assembly. These results evidence the aerobic granular sludge process as a robust system for wastewater treatment.

Insight into the effect of particulate organic matter on sludge granulation at the low organic load: Sludge characteristics, extracellular polymeric substances and microbial communities response

This paper investigated the effect of particulate organic matter (POM) on sludge granulation under low organic load. The results showed that POM promoted the formation of aerobic granular sludge (AGS) with a chemical oxygen demand (COD) fraction of 25%, and POM also enhanced the sludge settleability and biomass retention. However, when the COD fraction of POM increased to 50% and 75%, the AGS performance deteriorated. The analysis of extracellular polymeric substances revealed that the POM (accounted for ≤ 50% of COD in the influent) suppressed the secretion of extracellular protein. Analysis of the microbial community showed that species diversity was lower in the POM-fed system, with Rhodocyclaceae being the predominant bacteria responsible for carbon source degradation. Additionally, molecular ecological network analysis demonstrated that when the COD fraction of the POM exceeded 50%, the connectivity and modularity between microbial species decreased, which may explain the sludge performance deterioration.

Positive effects of lignocellulose on the formation and stability of aerobic granular sludge

Introduction

Lignocellulose is one of the major components of particulate organic matter in sewage, which has a significant influence on biological wastewater treatment process. However, the effect of lignocellulose on aerobic granular sludge (AGS) system is still unknown.

Methods

In this study, two reactors were operated over 5 months to investigate the effect of lignocellulose on granulation process, structure stability and pollutants removal of AGS.

Results and discussion

The results indicated that lignocellulose not only promoted the secretion of tightly bound polysaccharide in extracellular polymeric substances, but also acted as skeletons within granules, thereby facilitating AGS formation, and enhancing structural strength. Lignocellulose imposed little effect on the removal efficiency of pollutants, with more than 95, 99, and 92% of COD, NH4+-N, and PO43--P were removed in both reactors. However, it did exhibit a noticeable influence on pollutants conversion processes. This might be due to that the presence of lignocellulose promoted the enrichment of functional microorganisms, including Candidatus_Accumulibacter, Candidatus_Competibacter, Nitrosomonas, and Nitrospira, etc. These findings might provide valuable insights into the control strategy of lignocellulose in practical AGS systems.

CRISPR-Cas phage defense systems and prophages in Candidatus Accumulibacter

Candidatus Accumulibacter plays a major role in enhanced biological phosphorus removal (EBPR) from wastewater. Although bacteriophages have been shown to represent fatal threats to Ca. Accumulibacter organisms and thus interfere with the stability of the EBPR process, little is known about the ability of different Ca. Accumulibacter strains to resist phage infections. We conducted a systematic analysis of the occurrence and characteristics of clustered regularly interspaced short palindromic repeats and associated proteins (CRISPR-Cas) systems and prophages in Ca. Accumulibacter lineage members (43 in total, including 10 newly recovered genomes). Results indicate that 28 Ca. Accumulibacter genomes encode CRISPR-Cas systems. They were likely acquired via horizontal gene transfer, conveying a distinct adaptivity to phage predation to different Ca. Accumulibacter members. Major differences in the number of spacers show the unique phage resistance of these members. A comparison of the spacers in closely related Ca. Accumulibacter members from distinct geographical locations indicates that habitat isolation may have resulted in the acquisition of resistance to different phages by different Ca. Accumulibacter. Long-term operation of three laboratory-scale EBPR bioreactors revealed high relative abundances of Ca. Accumulibacter with CRISPSR-Cas systems. Their specific resistance to phages in these reactors was indicated by spacer analysis. Metatranscriptomic analyses showed the activation of the CRISPR-Cas system under both anaerobic and aerobic conditions. Additionally, 133 prophage regions were identified in 43 Ca. Accumulibacter genomes. Twenty-seven of them (in 19 genomes) were potentially active. Major differences in the occurrence of CRISPR-Cas systems and prophages in Ca. Accumulibacter will lead to distinct responses to phage predation. This study represents the first systematic analysis of CRISPR-Cas systems and prophages in the Ca. Accumulibacter lineage, providing new perspectives on the potential impacts of phages on Ca. Accumulibacter and EBPR systems.

Removal of organic micropollutants from municipal wastewater by aerobic granular sludge and conventional activated sludge

Removal performances of organic micropollutants by conventional activated sludge (CAS) and aerobic granular sludge (AGS) were investigated at a full-scale wastewater treatment plant. Lab-scale kinetic experiments were performed to assess the micropollutant transformation rates under oxic and anoxic conditions. Transformation rates were used to model the micropollutant removal in the full-scale processes. Metagenomic sequencing was used to compare the microbial communities and antimicrobial resistance genes of the CAS and AGS systems. Higher transformation ability was observed for CAS compared to AGS for most compounds, both at the full-scale plant and in the complementary batch experiments. Oxic conditions supported the transformation of several micropollutants with faster and/or comparable rates compared to anoxic conditions. The estimated transformation rates from batch experiments adequately predicted the removal for most micropollutants in the full-scale processes. While the compositions in microbial communities differed between AGS and CAS, the full-scale biological reactors shared similar resistome profiles. Even though granular biomass showed lower potential for micropollutant transformation, AGS systems had somewhat higher gene cluster diversity compared to CAS, which could be related to a higher functional diversity. Micropollutant exposure to biomass or mass transfer limitations, therefore played more important roles in the observed differences in OMP removal.

Phosphorus Removal from Aerobic Granular Sludge: Proliferation of Polyphosphate-Accumulating Organisms (PAOs) under Different Feeding Strategies

Aerobic granular sludge (AGS) is known for high phosphorus removal from wastewaters, and phosphorus can be recovered from high phosphorus-containing waste sludge granules. This study aimed at determining the feeding strategy that provides the best performance in terms of the proliferation of polyphosphate-accumulating organisms (PAOs) and phosphorus removal. Using three AGS bioreactors, this study compared phosphorus removal and the proliferation dynamics of PAOs under three different feeding strategies: anaerobic slow feeding (R1), pulse feeding + anaerobic mixing (R2), and pulse feeding (R3). Results indicate that R1 and R2 achieved significantly higher phosphorus removal (97.6 ± 3% for R1 and 98.3 ± 1% for R2) than R3 (55 ± 11%). The anaerobic slow feeding procedure (R1) achieved the highest specific phosphorus release rate (SPRR) and specific phosphorus uptake rate (SPUR) as compared to the other two feeding conditions. 16S ribosomal ribonucleic acid (rRNA) gene sequencing assay of the microbial community for the three feeding strategies indicated that although the feeding strategy impacted reactor performance, it did not significantly alter the microbial community. The bacteria community composition maintained a similar degree of diversity. Proteobacteria, Bacteroidetes, and Verrucomicrobia were the dominant bacterial phyla in the system. Dominant PAOs were from the class Betaproteobacteria and the genera Paracoccus and Thauera. Glycogen-accumulating organisms were significantly inhibited while other less-known bacteria such as Wandonia and Hyphomonas were observed in all three reactors.

Disentangle genus microdiversity within a complex microbial community by using a multi-distance long-read binning method: example of Candidatus Accumulibacter

Complete genomes can be recovered from metagenomes by assembling and binning DNA sequences into metagenome assembled genomes (MAGs). Yet, the presence of microdiversity can hamper the assembly and binning processes, possibly yielding chimeric, highly fragmented and incomplete genomes. Here, the metagenomes of four samples of aerobic granular sludge bioreactors containing Candidatus (Ca.) Accumulibacter, a phosphate-accumulating organism of interest for wastewater treatment, were sequenced with both PacBio and Illumina. Different strategies of genome assembly and binning were investigated, including published protocols and a binning procedure adapted to the binning of long contigs (MuLoBiSC). Multiple criteria were considered to select the best strategy for Ca. Accumulibacter, whose multiple strains in every sample represent a challenging microdiversity. In this case, the best strategy relies on long-read only assembly and a custom binning procedure including MuLoBiSC in metaWRAP. Several high-quality Ca. Accumulibacter MAGs, including a novel species, were obtained independently from different samples. Comparative genomic analysis showed that MAGs retrieved in different samples harbour genomic rearrangements in addition to accumulation of point mutations. The microdiversity of Ca. Accumulibacter, likely driven by mobile genetic elements, causes major difficulties in recovering MAGs, but it is also a hallmark of the panmictic lifestyle of these bacteria.

Nitrous oxide formation during simultaneous phosphorus and nitrogen removal in aerobic granular sludge treating different carbon substrates

The impact of different substrates on N₂O dynamics and gene expression of marker enzymes (nirS, nirK and nosZ) involved in denitrifying enhanced biological phosphorus removal (d-EBPR) was investigated. Aerobic granular sludge fed with VFAs led to an anoxic P-uptake (27.7 ± 1.2 mg PO₄^3--P.gVSS^-1) and N₂O emissions up to 80.7 ± 3.4% N₂O-N. A decisive role of Accumulibacter in N₂O formation was observed. Dosage of amino acids (12.0 ± 1.2 mg PO₄^3--P.gVSS^-1) and glucose (1.5 ± 0.9 mg PO₄^3--P.gVSS^-1) as sole substrate did not support d-EBPR activity. Presence of NO₂^- resulted in higher N₂O formation in comparison to nitrate and a nosZ/(nirS + nirK) ratio lower than 0.3. A linear correlation (R² > 0.95) between the nosZ/(nirS + nirK) ratio and the N₂O reductase rate was found only when dosing the same type of substrate. This suggests an interplay between the microbial community composition and different polyhydroxyalkanoates derivatives, when dosing different substrates.

The role of growth media on composition, bioconversion and susceptibility for mild thermal pre-treatment of waste activated sludge

The highly variable characteristics of waste activated sludge (WAS) hinder the comparison of experimental results on WAS bioconversion between the different studies that use excess sludge from different origin. Sludge grown under laboratory conditions with synthetic wastewater as feed showed high resistance to commonly applied pre-treatment techniques, such as thermal pre-treatment. However, a distinctly higher bioconversion of this sludge was recorded compared to WAS from a full-scale wastewater treatment plant (WWTP). The observed results casted concern on the suitability of the experimental laboratory-based data for practice. The physicochemical and biochemical characteristics of both WAS and lab-grown sludge are dependent on the wastewater characteristics or growth media on which the sludges were grown. The objective of this study was to formulate a growth medium that results into a lab-grown sludge which shows high similarity to the WAS coming from a specific full-scale WWTP in response to a pre-treatment technique. More specifically, in this study we targeted the formation of slowly-biodegradable lab-grown sludge that is similarly responsive to mild thermal pre-treatment with H₂O₂ addition. By comparing real and synthetic wastewaters, we discussed the various wastewater constituents that may lead to a higher degree of recalcitrance of the produced sludge. We then formulated a growth medium, which was fed to a lab-scale activated sludge reactor and evaluated the nutrient removal capacity, as well as the characteristics of the cultivated sludge before and after pre-treatment. Finally, the growth medium was modified to provoke a change in both the bioconversion and in the response to mild thermal pre-treatment. The growth medium proposed in this study resulted in a slowly-biodegradable sludge (195 ± 3.7 NLCH₄/kgVS_added) that after thermal pre-treatment resulted in an increase in methane production of 9 %, which was similar to the WAS coming from the full-scale WWTP. It was concluded that not only the bioconversion but also the response to mild thermal pre-treatment of lab-grown sludge was determined by the composition of the growth media.

Impact of the substrate composition on enhanced biological phosphorus removal during formation of aerobic granular sludge

Performance of enhanced biological phosphorus removal (EBPR) is often investigated with simple synthetic wastewater containing volatile fatty acids (VFAs). In this study, various (fermentable) substrates, individually and in mixtures, were examined during the application of a granulation strategy. In addition, the microbial community and N₂O formation were monitored. Sludge densification was observed in all systems. Stable EBPR, associated with the presence of Accumulibacter and an anaerobic P-release up to 21.9 mgPO₄^3--P.gVSS^-1, was only obtained when VFAs were present as sole substrate or in mixture. Systems fed with VFAs were strongly related to the formation of N₂O (maximum of 6.25% relative to the total available nitrogen). A moderate anaerobic dissolved organic carbon (DOC) uptake was observed when amino acids (64.27 ± 3.08%) and glucose (75.39 ± 5.79%) as sole carbon source were applied. The substrate/species-specific enrichment of Burkholderiaceae and Saccharimonadaceae respectively, resulted in unstable EBPR in those systems.

How environmental stress leads to alternative microbiota states in a river ecosystem: A new insight into river restoration

Catastrophic shifts in river ecosystems can abruptly degrade their structures and functions, often reducing the efficacy of traditional remediation targeting physicochemical properties. Alternative stable states theory can not only explain this phenomenon but also provide a new insight into river restoration; however, little is known about the existence and implications of alternative stable states in a river. Considering the important role of benthic microbiota in sustaining river ecosystem structures and functions, ecological theory and high-throughput sequencing were combined to firstly investigate multi-stability in microbial communities and its relationship with environmental factors in river sediments. The Nanjing reach of the Yangtze River was selected as the study area because of its huge spatial heterogeneity and varying degrees of pollution. Bimodal distributions combined with temporal variations of microbiota status provided direct evidence of bistability by showing the instability at the intermediate. In addition, environmental stress, particularly concentrations of NH₄⁺-N and NO₃^--N, was identified as an important driver of alternative microbiota states from the perspectives of the behavior of bistable ecosystems. Comparison of α-diversity indices and network properties between two alternative microbiota states revealed that the diversity and co-occurrence pattern of microbial communities will be high if they are settled in favorable environments (i.e., comprehensive sediment quality identification index > 3.7). Key taxa, including Clostridiales, Nitrospirales and Myxococcales, were discerned by combining LEfSe and network analysis, and their strong interspecies interactions were believed to be an important factor in triggering alternative microbiota states. This study suggests alternative stable states theory should be considered in river remediation to better understand the response of river ecosystems to environmental stress and the effect of hysteresis, benefiting the implementation of effective monitoring and restoration strategies in a river of urban area.