Candidatus Microthrix Research Articles

Alterations in the gut microbiota community are associated with childhood obesity and precocious puberty

ObjectiveTo explore the distribution and differences in the intestinal microbiota in girls with obesity-related precocious puberty and the relationship between intestinal microbiota and obesity-related precocious puberty.Methods16 S rRNA gene amplicons from fecal samples from girls with precocious puberty and obesity-complicated precocious puberty and healthy children were sequenced to define microbial taxa.ResultsThe α- and β-diversity indices of the microbiome significantly differed among the three groups. At the phylum level, the proportions of Firmicutes, Actinobacteriota, Bacteroidota, Bacteria, Campylobacterota, and Acidobacteriota were different. At the genus level, there were differences in Bifidobacterium, Bacteroides, Anaerostipes, Fusicatenibacter, Klebsiella, Lachnospiraceae, ErysipelotrichaceaeUCG-003, Prevotella9, Ruminococcus gnavus group, and Lachnoclostridium. Additionally, Bifidobacterium, Anaerostipes, Bacteroides, Candidatus Microthrix, Eubacterium hallii group, Klebsiella, and Erysipelotrichaceae UCG-003 were identified as bacterial biomarkers by LEfSe. Furthermore, Sellimonas, Intestinibacter, Anaerostipes, Ruminococcus gnavus group, and Oscillibacter were identified as the differential biomarkers by random forest. A receiver operating characteristic (ROC) curve was used to evaluate the biomarkers with high predictive value for obesity-related precocious puberty. Spearman correlation analysis confirmed that Anaerostipes levels were negatively correlated with body weight, body mass index (BMI), bone age, luteinizing hormone, follicle-stimulating hormone, and estradiol.ConclusionsThere was a significant correlation between obesity-associated precocious puberty and gut microbiota, especially the functional characteristics of the microbiome and its interactions, which can provide a theoretical basis for the clinical intervention of obesity and precocious puberty through the microbiome.

Thermal and alkaline pre‐treatments of inoculum halt methanogenesis and enable cheese whey valorization by batch acidogenic fermentation

AbstractBACKGROUNDCarboxylates such as volatile fatty acids (VFA) can be produced by acidogenic fermentation (AF) of dairy wastes including cheese whey, a massive residue produced at 160.67 million m3 of which 42% are not valorized and impact the environment. In mixed‐culture fermentations, selection pressures can favor AF and halt methanogenesis. In this study, inoculum pre‐treatment was evaluated as a selective pressure for AF demineralized cheese whey in batches. Alkaline (NaOH, pH 8.0, 6 h) and thermal (90 °C for 5 min, ice‐bath until 23 °C) pre‐treatments were tested with batch operations runs at initial pH 7.0 and 9.0, food‐to‐microorganism (F/M) ratios of 0.5 to 4.0 g COD g−1 VS, and under pressurized (P) and nonpressurized (NP) headspace, in experiments duplicated in two different research institutes.RESULTSAcetic acid was highly produced on both Unicamp and TU Delft samples (1.36 and 1.40 g CODAcOH L−1, respectively), at the expense of methanogenesis by combining a thermal pre‐treatment of inoculum with a NP batch operation started at pH 9.0. Microbial communities comprising VFA and alcohol producers, such as Clostridium, Fonticella and Intestinimonas, and fermenters such as Longilinea and Leptolinea. The lipid‐accumulating Candidatus microthrix was observed in both bulk material and foam. Despite the absence of methane production, Methanosaeta were detected within the microbial community. An F/M ratio of 0.5 g COD g−1 VS led to the best VFA production of 1769.4 mg L−1.CONCLUSIONOverall, inoculum thermal pre‐treatment, initial pH 9.0 and NP headspace acted as a selective pressure for halting methanogenesis and producing VFAs, valorizing cheese whey via batch acidogenic fermentation. © 2024 Society of Chemical Industry (SCI).

Dynamic calibration of a new secondary settler model using Cand. Microthrix as a predictor of settling velocity

Climate change is projected to increase the frequency of hydraulic shocks on urban water systems, affecting water resource recovery facilities (WRRFs). In these facilities, the settleability of activated sludge is a critical hydraulic bottleneck. However, to date, the dynamic prediction of hindered settling velocity (v0/rH) has remained unresolved. To address this significant knowledge gap, this study presents an assessment of microbial community predictors of hindered settling velocity. Through a regression analysis of independent laboratory and full-scale experimental data, we identified a close association between the relative abundance of Candidatus Microthrix filamentous bacteria and hindered settling velocity parameter values. While no direct association was observed between filamentous abundance and compression settling parameters, we propose linking the dynamic calibration of the compressive solid stress function to v0/rH. Notably, our results demonstrate, for the first time, the efficacy of dynamic calibration of SST models using the relative abundance of filamentous microbial predictors in a simulation model of the Kloten-Opfikon full-scale WRRF. Furthermore, besides Cand. Microthrix, Thiothrix is found to be a putative predictor for biomolecular SST calibration. These findings shed light on the potential of microbial communities to predict hindered settling velocity in WRRFs and offer valuable insights for improving wastewater treatment processes in the face of climate change challenges.

Mobilome-driven segregation of the resistome in biological wastewater treatment.

Biological wastewater treatment plants (BWWTP) are considered to be hotspots for the evolution and subsequent spread of antimicrobial resistance (AMR). Mobile genetic elements (MGEs) promote the mobilization and dissemination of antimicrobial resistance genes (ARGs) and are thereby critical mediators of AMR within the BWWTP microbial community. At present, it is unclear whether specific AMR categories are differentially disseminated via bacteriophages (phages) or plasmids. To understand the segregation of AMR in relation to MGEs, we analyzed meta-omic (metagenomic, metatranscriptomic and metaproteomic) data systematically collected over 1.5 years from a BWWTP. Our results showed a core group of 15 AMR categories which were found across all timepoints. Some of these AMR categories were disseminated exclusively (bacitracin) or primarily (aminoglycoside, MLS and sulfonamide) via plasmids or phages (fosfomycin and peptide), whereas others were disseminated equally by both. Combined and timepoint-specific analyses of gene, transcript and protein abundances further demonstrated that aminoglycoside, bacitracin and sulfonamide resistance genes were expressed more by plasmids, in contrast to fosfomycin and peptide AMR expression by phages, thereby validating our genomic findings. In the analyzed communities, the dominant taxon Candidatus Microthrix parvicella was a major contributor to several AMR categories whereby its plasmids primarily mediated aminoglycoside resistance. Importantly, we also found AMR associated with ESKAPEE pathogens within the BWWTP, and here MGEs also contributed differentially to the dissemination of the corresponding ARGs. Collectively our findings pave the way toward understanding the segmentation of AMR within MGEs, thereby shedding new light on resistome populations and their mediators, essential elements that are of immediate relevance to human health.

Chiral Inversion of 2-Arylpropionic Acid Enantiomers under Anaerobic Conditions.

This work examined the chiral inversion of 2-arylpropionic acids (2-APAs) under anaerobic conditions and the associated microbial community. The anaerobic condition was simulated by two identical anaerobic digesters. Each digester was fed with the substrate containing 11 either pure (R)- or pure (S)-2-APA enantiomers. Chiral inversion was evidenced by the concentration increase of the other enantiomer in the digestate and the changes in the enantiomeric fraction between the two enantiomers. Both digesters showed similar and poor removal of 2-APAs (≤30%, except for naproxen) and diverse chiral inversion behaviors under anaerobic conditions. Four compounds exhibited (S → R) unidirectional inversion [flurbiprofen, ketoprofen, naproxen, and 2-(4-tert-butylphenyl)propionic acid], and the remaining seven compounds showed bidirectional inversion. Several aerobic and facultative anaerobic bacterial genera (Candidatus Microthrix, Rhodococcus, Mycobacterium, Gordonia, and Sphingobium) were identified in both digesters and predicted to harbor the 2-arylpropionyl-CoA epimerase (enzyme involved in chiral inversion) encoding gene. These genera presented at low abundances, <0.5% in the digester dosed with (R)-2-APAs and <0.2% in the digester dosed with (S)-2-APAs. The low abundances of these genera explain the limited extent of chiral inversion observed in this study.

Novel application of aerobic granular biofilm systems for treating nitrate-polluted groundwater at low temperature: Microbial community and performance

An aerobic granular biofilm process was operated in a sequential batch reactor for treating nitrate-pollute groundwater at 6 ºC, which was fed with a progressively reduced carbon concentration to understand the nitrate removal efficacy in cold regions by denitrifying microorganisms. The evaluation of the performance reflected a quick granulation promoted by hydraulic stress and a high organic loading rate (OLR). The granules were dense and compact and kept stable conformation until the end of operation, despite the low temperature. Nitrate removal in the stage with high OLR was close to 100%, while the stage with the lowest OLR reached efficiencies higher than 87% in steady-state, suppose a successful advantage against other biological processes for treating drinking water. The bacterial community in the mature granules were colonized by cold-adapted microorganisms such as Holophagaceae and Candidatus Microthrix. Methanospirillum and Bathyarchaeota were the most abundant archaeal phylotypes, which showed a more stable consortium and Nectriaceae and Trichosporonaceae were the most dominant fungal phylotypes for all stages. The qPCR revealed that the crucial role was played by Fungi and Bacteria, while Archaea lost abundance in granular biomass, despite extreme conditions. Aerobic granular sludge is a robust biological technology able to remove nitrate in oligotrophic waters bodies.

Seasonal microbial community dynamics complicates the evaluation of filamentous bulking mitigation strategies in full-scale WRRFs

The activated sludge wastewater treatment process has been thoroughly researched in more than 100 years, yet there are still operational challenges that have not been fully resolved. Such a challenge is the control of filamentous bulking caused by the overgrowth of certain filamentous bacteria. In this study, we tested different mitigation strategies to reduce filamentous bulking, caused by two common filamentous genera found in full-scale water resource recovery facilities (WRRF), Candidatus Microthrix and Candidatus Amarolinea. PAX dosing, ozone addition, hydrocyclone implementation, and the addition of nano-coagulants were tested as mitigation strategies in four parallel treatment lines in a full-scale WRRF over three consecutive years. Unexpectedly, the activated sludge settleability was not affected by any of the mitigation strategies. Some of the strategies appeared to have a strong mitigating effect on the two filamentous species. However, detailed analyses of the microbial communities revealed strong recurrent seasonal variations in all four lines, including the control line which masked the real effect. After removing the effect of the seasonal variation by using a time-series decomposition approach, it was clear that the filamentous bacteria were mostly unaffected by the mitigation strategies. Only PAX dosing had some effect on Ca. Microthrix, but only on one species, Ca. Microthrix subdominans, and not on the most common Ca. Microthrix parvicella. Overall, our study shows the importance of long-term monitoring of microbial communities at species level to understand the normal seasonal pattern to effectively plan and execute full-scale experiments. Moreover, the results highlight the importance of using parallel reference treatment lines when evaluating the effect of mitigation strategies in full-scale treatment plants.

Comprehensive evaluation of starter culture impact on the bioreactor performance and microbial kinetics

The present study investigated the disregarded impact of microbial community composition, diversity and abundance of the starter biomass on lab-scale bioreactor performance, steady-state long time operation, biodegradation outcome and microbial kinetics. Standard lab-scale experiments are usually initiated with inoculum taken from wastewater treatment plants (WWTPs) without considering microbial community composition. Two identical sequencing batch bioreactors (SBR-1, SBR-2) were operated with inocula obtained from two domestic WWTPs to assess the role of inoculum composition on reactor performance and treatment efficacy. Filamentous microorganisms were dominated in SBR-1 (SVI: 265 mL/g), whereas their supremacy was diminished in SBR-2 (SVI: 160 mL/g). Next generation sequencing analyses verified high abundance of Candidatus Microthrix (14%) and Kouleothrix spp. (3%) in SBR-1. Although Chloroflexi C10-SB1A metagenome accounted for 16% of WWTP-2 community, SBR-2 was operated at steady-state for longer period without deterioration. Statistical indicators based on molecular studies showed that WWTP-2 has higher diversity than WWTP-1. Higher biodiversity in WWTP-2 community supported the stable process performance. Modelling studies denoted an increase in half saturation coefficients (Ks) in filamentous microorganisms dominated reactor. The results of this study provide insight on how the filamentous organisms typically found in WWTPs become a fundamental constituent during the bioreactor operation.

Revealing the dissimilar structure of microbial communities in different WWTPs that treat fish-canning wastewater with different NaCl content

Studies that characterize the microbial communities in wastewater treatment plants (WWTPs) are numerous, yet similar studies in industrial WWTPs treating fish-canning effluents are limited. The microbial communities in samples of 4 fish-canning WWTPs that operated under different NaCl concentrations were investigated by qPCR and partial 16S rRNA gene Illumina sequencing. The absolute abundances of key microbial populations (Total Bacteria, Archaea and Fungi, ammonium oxidizing bacteria (AOB), Mycolata, Candidatus Microthrix, Ca. Accumulibacter and Ca. Competibacter) presented statistical differences among the WWTPs. The NaCl concentration negatively affected the absolute abundance of Bacteria and Fungi, filamentous, and phosphate (PAO) and glycogen (GAO) accumulating bacteria, while AOB and Ca. Microthrix populations were statistically higher in the WWTP with higher NaCl contents. On the other hand, the main bacterial operational taxonomic units (OTUs) were classified as members of Kouleothrix (Chloroflexia, Chloroflexi) and Tetrasphaera (Actinomycetia, Actinobacteria), family Beijerinckiaceae (Alphaproteobacteria, Proteobacteria), order Betaproteobacteriales (Gammaproteobacteria, Proteobacteria), Sphingobacteriales (Sphingobacteriia, Bacteroidetes) and Frankiales (Actinobacteria, Actinobacteria), class Anaerolineae (Chloroflexi), phylum Chloroflexi and Bacteria_unclassified. The structure of the bacterial community was highly dissimilar among the 4 WWTPs, as the identities of the dominant OTUs differed significantly among them. Therefore, the individual characteristics of the different WWTPs, mainly NaCl concentration, were responsible for the narrow assemblage of the bacterial communities. Different OTUs belonging to the phyla Actinobacteria, Bacteroidetes, Chloroflexi, Gemmatimonadetes and Proteobacteria were revealed as salt-tolerant. Taking into account these results, NaCl content was an important driver of the abundance of microbial populations and the bacterial community structure in the analysed industrial facilities.

Coconut shell ash enhances short-chain fatty acids production from anaerobic algae fermentation

This study proposed a novel method to enhance short-chain fatty acids (SCFAs) production from anaerobic algae fermentation by using coconut shell ash. The maximum SCFAs production was 683.0 mg COD/g VS at the ash dosage of 1.2 g/g TS, which was about 1.4-folds that of the control, and the enhancement of acetate production was the main path for the promotion of SCFAs. Coconut shell ash increased the pH and alkalinity of digestate, thereby reducing the use of alkaline reagents and being more resistant to acidic environments. Coconut shell ash promoted the processes of solubilization, hydrolysis and acetogenesis, and enriched hydrolytic microorganisms (e.g., Candidatus Microthrix) and acidifying microorganisms with acetate as substrate (e.g., Caldilinea and Proteiniphilum). Anaerobic fermentation residue with ash containing inorganic elements has the potential to be used as fertilizer, making this waste-control-waste strategy with more economic and environmental benefits for potential practical applications.

Low Global Diversity of Candidatus Microthrix, a Troublesome Filamentous Organism in Full-Scale WWTPs.

Candidatus Microthrix is one of the most common bulking filamentous microorganisms found in activated sludge wastewater treatment plants (WWTPs) across the globe. One species, Ca. M. parvicella, is frequently observed, but global genus diversity, as well as important aspects of its ecology and physiology, are still unknown. Here, we use the MiDAS ecosystem-specific 16S rRNA gene database in combination with amplicon sequencing of Danish and global WWTPs to investigate Ca. Microthrix spp. diversity, distribution, and factors affecting their global presence. Only two species were abundant across the world confirming low diversity of the genus: the dominant Ca. M. parvicella and an unknown species typically present along with Ca. M. parvicella, although usually in lower abundances. Both species were mostly found in Europe at low-to-moderate temperatures and their growth was favored in municipal WWTPs with advanced process designs. As no isolate is available for the novel species, we propose the name “Candidatus Microthrix subdominans.” Ten high-quality metagenome-assembled genomes recovered from Danish WWTPs, including 6 representing the novel Ca. M. subdominans, demonstrated high genetic similarity between the two species with a likely preference for lipids, a putative capability to reduce nitrate and nitrite, and the potential to store lipids and poly-P. Ca. M. subdominans had a potentially more versatile metabolism including additional sugar transporters, higher oxygen tolerance, and the potential to use carbon monoxide as energy source. Newly designed fluorescence in situ hybridization probes revealed similar filamentous morphology for both species. Raman microspectroscopy was used to quantify the in situ levels of intracellular poly-P. Despite the observed similarities in their physiology (both by genomes and in situ), the two species showed different seasonal dynamics in Danish WWTPs through a 13-years survey, possibly indicating occupation of slightly different niches. The genomic information provides the basis for future research into in situ gene expression and regulation, while the new FISH probes provide a useful tool for further characterization in situ. This study is an important step toward understanding the ecology of Ca. Microthrix in WWTPs, which may eventually lead to optimization of control strategies for its growth in this ecosystem.

Demodex Infection Changes Ocular Surface Microbial Communities, in Which Meibomian Gland Dysfunction May Play a Role.

IntroductionDemodex and bacteria are both components of the ocular surface micro-ecology, constituting a complex interaction. This study aims to explore how ocular surface Demodex infestation (DI) affects ocular surface microbial communities and diversity. MethodsWe recruited 255 subjects, and examined the correlation between ocular surface mite infestation and clinical indicators such as age, blood glucose level, dry eye symptoms, and blood pressure. 16S rRNA sequencing was performed on the conjunctival swab samples of 14 patients with ocular DI (P group) and 17 healthy people (N group). For further analysis, the subjects were divided into four subgroups, i.e. N-NMGD (n = 11), N-MGD (n = 6), P-NMGD (n = 6), and P-MGD (n = 8), according to meibomian gland dysfunction (MGD) or no MGD (NMGD).ResultsThere was no difference in the α-diversity of ocular surface microbial communities between the DI and healthy control groups. In linear discriminant analysis effect size (LEfSe), there were more Acinetobacter, Novosphingobium, and Anoxybacillus in the DI group and fewer Novosphingobium, Lactobacillus, and Candidatus Microthrix in the healthy control group. P-NMGD had more Thermaceae and fewer Pseudomonas than P-MGD. There were more Bacteroidetes in N-NMGD than in N-MGD. The α-diversity of P-NMGD was lower than that of N-NMGD (Shannon index, P = 0.027). At the same time, the α-diversity of N-MGD was lower than that of N-NMGD (Shannon, Simpson, and dominance index, P = 0.048). There was no significant difference in β-diversity or in the primary flora at the phylum and genus levels between groups and subgroups.ConclusionDI had no significant effect on the diversity of ocular surface microbial communities. DI primarily changed the dominant flora and relative abundance of ocular surface microbial communities. MGD may play an important role in this process.

Achieving stable mainstream nitrogen and phosphorus removal assisted by hydroxylamine addition in a continuous partial nitritation/anammox process from real sewage

Hydroxylamine (NH2OH) as the putative intermediate for anammox ensures the robustness of partial nitritation/anammox (PN/A) process; however, the feasible for NH2OH addition to improve the stability of PN/A process under low-strength ammonia (NH4+-N) condition need to be further investigated. In this study, the restoration and steady operation of mainstream PN/A process were investigated to treat real sewage with in situ NH2OH added in a continuous alternating anoxic/aerobic with integrated fixed-film activated sludge (A3-IFAS) reactor. Results showed that the deteriorated PN/A process caused by nitrate (NO3−-N) built-up was rapidly restored with a distinct decrease of the NO3−-Nproduced/NH4+-Nconsumed ratio from 28.7% to <10.0% within 20 days, after 5 mg N/L of NH2OH was added daily into the aerobic zone of A3-IFAS reactor. After 230 days of operation, the average total nitrogen (TN) and phosphate (PO43−–P) removal efficiencies of 80.8% and 91.5%, respectively were stably achieved, with average effluent sCOD, NH4+-N, TN and PO43−–P concentrations reaching 23.1, 2.3, 7.7 and 0.4 mg/L, respectively. Microbial community characterization revealed Candidatus Brocadia (3.60% and 2.92%) and Ignavibacteriae (1.56% and 2.66%) as the dominant anammox bacteria and denitrifying bacteria, respectively, jointly attached in the biofilm_1 and biofilm_2, while Candidatus Microthrix (5.17%) dominant in floc sludge was main responsible for phosphorus removal. This study confirmed that NH2OH addition is an effective strategy for nitrite-oxidizing bacteria suppression, contributing to the in situ restoration of PN/A process and high stable mainstream nitrogen and phosphorus removal in a continuous PN/A process from real sewage.

Structural and functional changes in bacterial communities during sludge foaming in the sub-plateau MSTPs

Sludge foaming has been a persistent ailment in worldwide municipal sewage treatment plants (MSTPs). In particular, this problem frequently occurs and lasts throughout the winter and spring season in the sub-plateau MSTPs. Aims to explore the causes of sludge foaming under sub-plateau circumstance, the correlation between the structural and functional changes in bacterial communities and sewage properties was conducted using Illumina high-throughput sequencing technology. The results from 16S rRNA gene sequencing shown that the relative abundances of Actinobacteria (39.5 % ± 4.8 %) and Firmicutes (10.5 % ± 1.0 %) in the foaming sludge were remarkably higher than that in the non-foaming sludge. The abundances of Candidatus Microthrix parvicella (29.8 % ± 6.9 %), Trichococcus (6.5 % ± 1.0 %), and Ornithinibacter (3.5 % ± 0.6 %) were increased after sludge foaming, and which are considered as the dominated foaming-causative bacterial assemblages by the linear discriminant analysis (LDA). Spearman’s correlation analysis and redundancy analysis (RDA) also agreed that lower temperature and dissolved oxygen (DO) levels, higher lipid and protein contents were significantly correlated with sludge foaming. In addition, the predictive functional profiling indicated that the enzymes and their coding genes of the bacterial communities are mainly involved in the fast proliferation and lipid metabolism, and which abundance are highly upregulated during foaming period. These results suggested that the sludge foaming was strongly linked to the Actinobacteria and Firmicutes communities and higher lipid and protein content in the sewage under sub-plateau circumstance. The findings might be important for developing operating strategies to maintain the desired microbial community pattern and improve the performance of MSTPs.

Identification of microorganisms responsible for foam formation in mesophilic anaerobic digesters treating surplus activated sludge

Foaming is a common operational problem in anaerobic digestion (AD) systems, where hydrophobic filamentous microorganisms are usually considered to be the major cause. However, little is known about the identity of foam-stabilising microorganisms in AD systems, and control measures are lacking. This study identified putative foam forming microorganisms in 13 full-scale mesophilic digesters located at 11 wastewater treatment plants in Denmark, using 16S rRNA gene amplicon sequencing with species-level resolution and fluorescence in situ hybridization (FISH) for visualization. A foaming potential aeration test was applied to classify the digester sludges according to their foaming propensity. A high foaming potential for sludges was linked to the abundance of species from the genus Candidatus Microthrix, immigrating with the feed stream (surplus activated sludge), but also to several novel phylotypes potentially growing in the digester. These species were classified to the genera Ca. Brevefilum (Ca. B. fermentans) and Tetrasphaera (midas_s_5), the families ST-12K33 (midas_s_22), and Rikenellaceae (midas_s_141), and the archaeal genus Methanospirillum (midas_s_2576). Application of FISH showed that these potential foam-forming organisms all had a filamentous morphology. Additionally, it was shown that concentrations of ammonium and total nitrogen correlated strongly to the presence of foam-formers. This study provided new insight into the identity of putative foam-forming microorganisms in mesophilic AD systems, allowing for the subsequent surveillance of their abundances and studies of their ecology. Such information will importantly inform the development of control measures for these problematic microorganisms.

Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics

Viruses and plasmids (invasive mobile genetic elements (iMGEs)) have important roles in shaping microbial communities, but their dynamic interactions with CRISPR-based immunity remain unresolved. We analysed generation-resolved iMGE–host dynamics spanning one and a half years in a microbial consortium from a biological wastewater treatment plant using integrated meta-omics. We identified 31 bacterial metagenome-assembled genomes encoding complete CRISPR–Cas systems and their corresponding iMGEs. CRISPR-targeted plasmids outnumbered their bacteriophage counterparts by at least fivefold, highlighting the importance of CRISPR-mediated defence against plasmids. Linear modelling of our time-series data revealed that the variation in plasmid abundance over time explained more of the observed community dynamics than phages. Community-scale CRISPR-based plasmid–host and phage–host interaction networks revealed an increase in CRISPR-mediated interactions coinciding with a decrease in the dominant ‘Candidatus Microthrix parvicella’ population. Protospacers were enriched in sequences targeting genes involved in the transmission of iMGEs. Understanding the factors shaping the fitness of specific populations is necessary to devise control strategies for undesirable species and to predict or explain community-wide phenotypes.

Candidatus Amarolinea and Candidatus Microthrix Are Mainly Responsible for Filamentous Bulking in Danish Municipal Wastewater Treatment Plants.

Filamentous bulking is a common serious operational problem leading to deteriorated sludge settling that has long been observed in activated sludge biological wastewater treatment systems. A number of bacterial genera found therein possess filamentous morphology, where some have been shown to be implicated in bulking episodes (e.g., Ca. Microthrix), the impact of many others is still not clear. In this study we performed a survey of 17 Danish municipal wastewater treatment plants (WWTPs) with nutrient removal using 16S rRNA amplicon sequencing over a period of 13 years, where all known filamentous bacteria from 30 genera were analyzed. The filamentous community constituted on average 13 ± 6%, and up to 43% of total read abundance with the same genera common to all plants. Ca. Microthrix and several genera belonging to phylum Chloroflexi were among the most abundant filamentous bacteria. The effect of filamentous bacteria on sludge settling properties was analyzed using measurements of the diluted sludge volume index (DSVI). Strong positive correlations with DSVI were observed only for Ca. Microthrix and Ca. Amarolinea, the latter being a novel, recently characterized genus belonging to the phylum Chloroflexi. The bulking potential of other filamentous bacteria was not significant despite their presence in many plants. Low phylogenetic diversity was observed for both Ca. Microthrix and Ca. Amarolinea, making physiological characterization of individual species and potential development of control strategies more feasible. In this study we show that, despite the high diversity of filamentous phylotypes in Danish WWTPs, only few of them were responsible for severe bulking episodes.

Disentangling Community Structure of Ecological System in Activated Sludge: Core Communities, Functionality, and Functional Redundancy.

The microbial ecosystems of the sludge were characterized in terms of the core community structure, functional pathways, and functional redundancy through Illumina MiSeq sequencing and PICRUSt analysis on the activated sludge (AS) samples from an extended activated aeration process. Based on the identified OTU distribution, we identified 125 core community genera, including 3 abundant core genera and 21 intermittent abundant core genera. Putative genera Nitrosomonas, Nitrotoga, Zoogloea, Novosphingobium, Thermomonas, Amaricoccus, Tetrasphaera, Candidatus Microthrix, and Haliscomenobacter, which are associated with functions of nitrifying, denitrifying, phosphorus accumulating, and bulking and foaming, were found to present as the core community organisms in the AS sampled from the conventional extended aeration AS processes. The high-abundant nitrogen metabolic pathways were associated with nitrate reduction to ammonium (DNRA and ANRA), denitrification, and nitrogen fixation, while the ammonia oxidation-related genes (amo) were rarely annotated in the AS samples. Strict functional redundancy was not found with the AS ecosystem as it showed a high correlation between the community composition similarity and function similarity. In addition, the classified dominant core genera community was found to be sufficient to characterize the functionality of AS, which could invigorate applications of 16S rDNA MiSeq sequencing and PICRUSt for the prediction of functions of AS ecosystems.

Metagenomic analysis reveals enhanced nutrients removal from low C/N municipal wastewater in a pilot-scale modified AAO system coupling electrolysis

The conventional biological nutrients removal process is challenged by insufficient organic carbon in influent. To cross such an organic-dependent barrier, a pilot-scale electrolysis-integrated anaerobic/anoxic/oxic (AAO) process was developed for enhanced removal of nitrogen (N) and phosphorus (P) from low carbon/nitrogen (C/N) municipal wastewater. Average removal efficiencies of total nitrogen (TN) and total phosphorus (TP) in the electrolysis-AAO reached to 77.24% and 95.08% respectively, showing increases of 13.88% and 21.87%, as compared to the control reactor. Spatial variations of N and P showed that NH4+-N removal rate was promoted in aerobic zone of electrolysis-AAO. The intensified TN elimination, which was mostly reflected by abatement of NO3−-N with the concomitant slight accumulation of NH4+-N and NO2−-N, mainly occurred in anoxic2 compartment as the electrons supplied by electrolysis. Furthermore, minor P contents were measured and remained almost unchanged along the reaction units, indicating that chemical precipitation should be the dominant mechanism of P-removal in electrolysis-AAO. From the metagenomic-based taxonomy, phylum Actinobacteria was dramatically inhibited, and phylum Proteobacteria dominated the electrolysis-AAO. Particularly, nitrifying bacteria and multifarious autotrophic denitrifiers were enriched, meanwhile, a significant evolution of heterotrophic denitrifiers was found in electrolysis-AAO compared to control, which was mostly reflected by the inhibition of genus Candidatus Microthrix. Batch tests further confirmed that autotrophic denitrifiers using H2 and Fe2+ as essential electron sinks were mainly responsible for the electrolysis-induced denitrification. Differential metabolic capacities were revealed from the perspectives of functional enzymes and genes, and network analysis allowed insight of microbial taxa-functional genes associations and shed light on stronger relevance between autotrophic denitrifiers and denitrification-associated genes in the electrolysis-AAO system.

Factors influencing Candidatus Microthrix parvicella growth and specific filamentous bulking control: A review.

Candidatus Microthrix parvicella has been frequently detected as the dominant filamentous bacteria in bulking sludge and thus seriously affects the stable operation of activated sludge processes. The extremely low growth rate of Ca. M. parvicella and its sensitivity to environmental variations greatly limit the development of effective techniques to control filamentous bulking. Based on previous investigations, a variety of restrictive substrates, operating and culture conditions, environmental factors and other potential inhibitors have varying degrees of impact on the growth of this microorganism. This review systematically summarizes the key factors affecting Ca. M. parvicella growth with a focus on the influencing mechanism. Recent filamentous bulking control strategies are also critically reviewed and discussed. Additionally, research needs for the next few years are proposed with the aim of establishing effective and specific control strategies for filamentous sludge bulking.