Effects of solids retention time on the performance of bioreactors bioaugmented with a 17β-estradiol-utilizing bacterium, Sphingomonas strain KC8

Influence of solids and hydraulic retention times on microbial diversity and removal of estrogens and nonylphenols in a pilot-scale activated sludge plant

The removal of EDCs in activated sludge processes can be enhanced by increasing solid and hydraulic retention times (SRT and HRT); it has been suggested that the improvement in removal is due to changes in microbial community structure (MCS). Though the influence of SRT and HRT on chemical removal and MCS has been studied in isolation, their synergistic impact on MCS and the removal of estrogens and nonylphenols in activated sludge remains unknown. Hence, we investigated how both parameters influence MCS in activated sludge processes and their ulterior effect on EDC removal. In our study, an activated sludge pilot-plant was fed with domestic sewage fortified with 100 and 1000 ng/L nonylphenols or 2 and 15 ng/L estrogens and operated at 3, 10 and 27 d SRT (constant HRT) and at 8, 16 and 24 h HRT (constant SRT). The MCS was assessed by phospholipid fatty acids (PLFA) analysis, and the archaeal and bacterial diversities were determined by 16S rRNA analysis. From the PLFA, the microbial abundance ranked as follows: Gram-negative > fungi > Gram-positive > actinomycetes whilst 16S rRNA analysis revealed Proteobacteria > Bacteroidetes > Others. Both PLFA and 16S rRNA analysis detected changes in MCS as SRT and HRT were increased. An SRT increment from 3 to 10 d resulted in higher estrone (E1) removal from 19 to 93% and nonylphenol-4-exthoxylate (NP4EO) from 44 to 73%. These findings demonstrate that EDC-removal in activated sludge plants can be optimised where longer SRT (>10 d) and HRT (>8 h) are suitable. We have also demonstrated that PLFA can be used for routine monitoring of changes in MCS in activated sludge plants.

Dissecting the microbial community structure of internal organs during the early postmortem period in a murine corpse model

BACKGROUND

Microorganisms distribute and proliferate both inside and outside the body, which are the main mediators of decomposition after death. However, limited information is available on the postmortem microbiota changes of extraintestinal body sites in the early decomposition stage of mammalian corpses.

RESULTS

This study investigated microbial composition variations among different organs and the relationship between microbial communities and time since death over 1 day of decomposition in male C57BL/6 J mice by 16S rRNA sequencing. During 1 day of decomposition, Agrobacterium, Prevotella, Bacillus, and Turicibacter were regarded as time-relevant genera in internal organs at different timepoints. Pathways associated with lipid, amino acid, carbohydrate and terpenoid and polyketide metabolism were significantly enriched at 8 h than that at 0.5 or 4 h. The microbiome compositions and postmortem metabolic pathways differed by time since death, and more importantly, these alterations were organ specific.

CONCLUSION

The dominant microbes differed by organ, while they tended toward similarity as decomposition progressed. The observed thanatomicrobiome variation by body site provides new knowledge into decomposition ecology and forensic microbiology. Additionally, the microbes detected at 0.5 h in internal organs may inform a new direction for organ transplantation.

Heterogeneity of the Tissue-specific Mucosal Microbiome of Normal Grass Carp (Ctenopharyngodon idella)

Microbiome plays key roles in the digestion, metabolism, and immunity of the grass carp (Ctenopharyngodon idella). Here, we characterized the normal microbiome of the intestinal contents (IC), skin mucus (SM), oral mucosa (OM), and gill mucosa (GM) of the grass carp, as well as the microbiome of the sidewall (SW) of the raising pool, using full-length 16S rRNA sequencing based on the PacBio platform in this specie for the first time. Twenty phyla, 38 classes, 130 families, 219 genera, and 291 species were classified. One hundred four common classified species might be core microbiota of grass carp. Proteobacteria, Bacteroides, and Cyanobacteria were the dominant phyla in the niche of grass carp. Proteobacteria and Bacteroides dominated the taxonomic composition in the SM, GM, and OM, while Proteobacteria, Planctomycetota, and Cyanobacteria preponderated in the IC and SW groups. Microbiota of IC exhibited higher alpha diversity indices. The microbial communities clustered either in SW or the niche from grass carp, significantly tighter in the SW, based on Bray-Curtis distances (P < 0.05). SM, GM, and OM were similar in microbial composition but were significantly different from IC and SW, while IC had similarity with SW due to their common Cyanobacteria (P < 0.05). Differences were also reflected by niche-specific and differentially abundant microorganisms such as Noviherbaspirillum in the SM and Rhodopseudomonas palustris, Mycobacterium fortuitum, and Acinetobacter schindleri in GM. Significantly raised gene expression was found in IC and SM associated with cell cycle control, cell division, chromosome, coenzyme transport and metabolism, replication, recombination and repair, cell motility, post-translational modification, signal transduction mechanisms, intracellular trafficking, secretion, and vesicles by PICRUSt. This work may be of great value for understanding of fish-microbial co-workshops, especially in different niche of grass carp.

Genomic analysis of Gordonia polyisoprenivorans strain R9, a highly effective 17 beta-estradiol- and steroid-degrading bacterium

The increasing levels of estrogens and pollution by other steroids pose considerable challenges to the environment. In this study, the genome of Gordonia polyisoprenivorans strain R9, one of the most effective 17 beta-estradiol- and steroid-degrading bacteria, was sequenced and annotated. The circular chromosome of G. polyisoprenivorans R9 was 6,033,879 bp in size, with an average GC content of 66.91%. More so, 5213 putative protein-coding sequences, 9 rRNA, 49 tRNA, and 3 sRNA genes were predicted. The core-pan gene evolutionary tree for the genus Gordonia showed that G. polyisoprenivorans R9 is clustered with G. polyisoprenivorans VH2 and G. polyisoprenivorans C, with 93.75% and 93.8% similarity to these two strains, respectively. Altogether, the three G. polyisoprenivorans strains contained 3890 core gene clusters. Strain R9 contained 785 specific gene clusters, while 501 and 474 specific gene clusters were identified in strains VH2 and C, respectively. Furthermore, whole genome analysis revealed the existence of the steroids and estrogens degradation pathway in the core genome of all three G. polyisoprenivorans strains, although the G. polyisoprenivorans R9 genome contained more specific estrogen and steroid degradation genes. In strain R9, 207 ABC transporters, 95 short-chain dehydrogenases (SDRs), 26 monooxygenases, 21 dioxygenases, 7 aromatic ring-hydroxylating dioxygenases, and 3 CoA esters were identified, and these are very important for estrogen and steroid transport, and degradation. The results of this study could enhance our understanding of the role of G. polyisoprenivorans R9 in estradiol and steroid degradation as well as evolution within the G. polyisoprenivorans species.

Machine Learning Approach Reveals the Assembly of Activated Sludge Microbiome with Different Carbon Sources during Microcosm Startup

Activated sludge (AS) microcosm experiments usually begin with inoculating a bioreactor with an AS mixed culture. During the bioreactor startup, AS communities undergo, to some extent, a distortion in their characteristics (e.g., loss of diversity). This work aimed to provide a predictive understanding of the dynamic changes in the community structure and diversity occurring during aerobic AS microcosm startups. AS microcosms were developed using three frequently used carbon sources: acetate (A), glucose (G), and starch (S), respectively. A mathematical modeling approach quantitatively determined that 1.7–2.4 times the solid retention time (SRT) was minimally required for the microcosm startups, during which substantial divergences in the community biomass and diversity (33–45% reduction in species richness and diversity) were observed. A machine learning modeling application using AS microbiome data could successfully (>95% accuracy) predict the assembly pattern of aerobic AS microcosm communities responsive to each carbon source. A feature importance analysis pinpointed specific taxa that were highly indicative of a microcosm feed source (A, G, or S) and significantly contributed for the ML-based predictive classification. The results of this study have important implications on the interpretation and validity of microcosm experiments using AS.

Extended local similarity analysis (eLSA) reveals unique associations between bacterial community structure and odor emission during pig carcasses decomposition

Soil burial and composting methods have been widely used for the disposal of pig carcasses. The relationship between bacterial community structure and odor emission was examined using extended local similarity analysis (eLSA) during the degradation of pig carcasses in soil and compost. In soil, Hyphomicrobium, Niastella, Rhodanobacter, Polaromonas, Dokdonella and Mesorhizobium were associated with the emission of sulfur-containing odors such as hydrogen sulfide, methyl mercaptan and dimethyl disulfide. Sphingomonas, Rhodanobacter, Mesorhizobium, Dokdonella, Leucobacter and Truepera were associated with the emission of nitrogen-containing odors including ammonia and trimetylamine. In compost, however, Carnobacteriaceae, Lachnospiaceae and Clostridiales were highly correlated with the emission of sulfur-containing odors, while Rumincoccaceae was associated with the emission of nitrogen-containing odors. The emission of organic acids was closely related to Massilia, Sphaerobacter and Bradyrhizobiaceae in soil, but to Actinobacteria, Sporacetigenium, Micromonosporaceae and Solirubrobacteriales in compost. This study suggests that network analysis using eLSA is a useful strategy for exploring the mechanisms of odor emission during biodegradation of pig carcasses.

Model-based assessment of estrogen removal by nitrifying activated sludge

Complete removal of estrogens such as estrone (E1), estradiol (E2), estriol (E3) and ethinylestradiol (EE2) in wastewater treatment is essential since their release and accumulation in natural water bodies are giving rise to environment and health issues. To improve our understanding towards the estrogen bioremediation process, a mathematical model was proposed for describing estrogen removal by nitrifying activated sludge. Four pathways were involved in the developed model: i) biosorption by activated sludge flocs; ii) cometabolic biodegradation linked to ammonia oxidizing bacteria (AOB) growth; iii) non-growth biodegradation by AOB; and iv) biodegradation by heterotrophic bacteria (HB). The degradation kinetics was implemented into activated sludge model (ASM) framework with consideration of interactions between substrate update and microorganism growth as well as endogenous respiration. The model was calibrated and validated by fitting model predictions against two sets of batch experimental data under different conditions. The model could satisfactorily capture all the dynamics of nitrogen, organic matters (COD), and estrogens. Modeling results suggest that for E1, E2 and EE2, AOB-linked biodegradation is dominant over biodegradation by HB at all investigated COD dosing levels. However, for E3, the increase of COD dosage triggers a shift of dominant pathway from AOB biodegradation to HB biodegradation. Adsorption becomes the main contributor to estrogen removal at high biomass concentrations.

Removal of pharmaceuticals and personal care products (PPCPs) from wastewater: A review

The pharmaceutical and personal care products (PPCPs) are emerging pollutants which might pose potential hazards to environment and health. These pollutants are becoming ubiquitous in the environments because they cannot be effectively removed by the conventional wastewater treatment plants due to their toxic and recalcitrant performance. The presence of PPCPs has received increasing attention in recent years, resulting in great concern on their occurrence, transformation, fate and risk in the environments. A variety of technologies, including physical, biological and chemical processes have been extensively investigated for the removal of PPCPs from wastewater. In this paper, the classes, functions and the representatives of the frequently detected PPCPs in aquatic environments were summarized. The analytic methods for PPCPs were briefly introduced. The removal efficiency of PPCPs by wastewater treatment plants was analyzed and discussed. The removal of PPCPs from wastewater by physical, chemical and biological processes was analyzed, compared and summarized. Finally, suggestions are made for future study of PPCPs. This review can provide an overview for the removal of PPCPs from wastewater.

Enhanced Biological Trace Organic Contaminant Removal: A Lab-Scale Demonstration with Bisphenol A-Degrading Bacteria Sphingobium sp. BiD32

Discharge of trace organic contaminants (TOrCs) from wastewater treatment plants (WWTPs) may contribute to deleterious effects on aquatic life. Release to the environment occurs both through WWTP effluent discharge and runoff following land applications of biosolids. This study introduces Enhanced Biological TOrC Removal (EBTCR), which involves continuous bioaugmentation of TOrC-degrading bacteria for improved removal in WWTPs. Influence of bioaugmentation on enhanced degradation was investigated in two lab-scale sequencing batch reactors (SBRs), using bisphenol A (BPA) as the TOrC. The reactors were operated with 8 cycles per day and at two solids retention times (SRTs). Once each day, the test reactor was bioaugmented with Sphingobium sp. BiD32, a documented BPA-degrading culture. After bioaugmentation, BPA degradation (including both the dissolved and sorbed fractions) was 2-4 times higher in the test reactor than in a control reactor. Improved removal persisted for >5 cycles following bioaugmentation. By the last cycle of the day, enhanced BPA removal was lost, although it returned with the next bioaugmentation. A net loss of Sphingobium sp. BiD32 was observed in the reactors, supporting the original hypothesis that continuous bioaugmentation (rather than single-dose bioaugmentation) would be required to improve TOrCs removal during wastewater treatment. This study represents a first demonstration of a biologically based approach for enhanced TOrCs removal that both reduces concentrations in wastewater effluent and prevents transfer to biosolids.

Bioaugmentation Mitigates the Impact of Estrogen on Coliform-Grazing Protozoa in Slow Sand Filters

Exposure to endocrine-disrupting chemicals (EDCs), such as estrogens, is a growing issue for human and animal health as they have been shown to cause reproductive and developmental abnormalities in wildlife and plants and have been linked to male infertility disorders in humans. Intensive farming and weather events, such as storms, flash flooding, and landslides, contribute estrogen to waterways used to supply drinking water. This paper explores the impact of estrogen exposure on the performance of slow sand filters (SSFs) used for water treatment. The feasibility and efficacy of SSF bioaugmentation with estrogen-degrading bacteria was also investigated, to determine whether removal of natural estrogens (estrone, estradiol, and estriol) and overall SSF performance for drinking water treatment could be improved. Strains for SSF augmentation were isolated from full-scale, municipal SSFs so as to optimize survival in the laboratory-scale SSFs used. Concentrations of the natural estrogens, determined by gas chromatography coupled with mass spectrometry (GC-MS), revealed augmented SSFs reduced the overall estrogenic potency of the supplied water by 25% on average and removed significantly more estrone and estradiol than nonaugmented filters. A negative correlation was found between coliform removal and estrogen concentration in nonaugmented filters. This was due to the toxic inhibition of protozoa, indicating that high estrogen concentrations can have functional implications for SSFs (such as impairing coliform removal). Consequently, we suggest that high estrogen concentrations could impact significantly on water quality production and, in particular, on pathogen removal in biological water filters.

Removal of environmental estrogens by bacterial cell immobilization technique

Contamination of steroidal estrogens in the environment has raised a great public concern, and therefore, developing an effective method for removal of trace amount of environmental estrogens is necessary. In this study, two estrogen-degrading bacteria were isolated from activated sludge and were identified as strain Sphingomonas sp. AHC-F and strain Sphingobium sp. AX-B. They were capable of utilizing estrone (E1) and 17ß-estradiol (E2) as sole carbon and energy source. Cell immobilization technique was applied to these two estrogen-degrading bacteria. Confocal laser-scanning microscopy images with live and dead staining of entrapped bacterial cells showed that most bacteria were present inside the porous structure and were mostly viable after immobilization procedures. Batch estrogen degradation study showed that immobilized strains AHC-F and AX-B could effectively degrade 2 mg/L of E2 and its metabolite E1. Immobilized bacteria column reactors using pure culture of strain AHC-F were set up for continuous-flow removal of 850 ng/L of E2 in the influent. The removal efficiency of E2 and equivalent estrogenic quantity of E2 (EEQ) could achieve 94 and 87% under 12 h hydraulic retention time (HRT), respectively. Increasing HRT could further improve the removal efficiency of EEQ. When the HRT increased to 72 h, the effluent concentrations of E2 and E1 were not detectable by gas chromatography-mass spectrometry. Our results also proved that most of the estrogen removal was due to biodegradation. This study has demonstrated the potential use of immobilized bacteria technique for the removal of environmental estrogens.

Removal of triclosan in nitrifying activated sludge: effects of ammonia amendment and bioaugmentation

This study investigated two possible strategies, increasing ammonia oxidation activity and bioaugmenting with triclosan-degrader Sphingopyxis strain KCY1, to enhance triclosan removal in nitrifying activated sludge (NAS). Triclosan (2 mg L(-1)) was removed within 96-h in NAS bioreactors amended with 5, 25 and 75 mg L(-1) of ammonium (NH4-N). The fastest triclosan removal was observed in 25 mg NH4-NL(-1) amended-bioreactors where high ammonia oxidation occurred. Inhibition of ammonia oxidation and slower triclosan removal were observed in 75 mg NH4-NL(-1) amended-bioreactors. Triclosan removal was correlated to the molar ratio of the amount of nitrate produced to the amount of ammonium removed. Bioaugmentation with strain KCY1 did not enhance triclosan removal in the bioreactors with active ammonia oxidation. Approximately 36-42% and 59% of triclosan added were removed within 24-h by ammonia-oxidizing bacteria and unknown triclosan-degrading heterotrophs, respectively. The results suggested that increasing ammonia oxidation activity can be an effective strategy to enhance triclosan removal in NAS.

Kinetics modeling predicts bioaugmentation with Sphingomonad cultures as a viable technology for enhanced pharmaceutical and personal care products removal during wastewater treatment

Pharmaceutical and personal care products (PPCPs) discharged with wastewater treatment effluents are a surface water quality concern. PPCPs are partially removed during wastewater treatment and biological transformation is an important removal mechanism. To investigate the potential for enhanced PPCP removal using bioaugmentation, bacteria were previously isolated from activated sludge capable of degrading PPCPs to ng/L concentrations. This study examined the degradation kinetics of triclosan and bisphenol A by five of these bacteria, both in pure culture and when augmented to activated sludge. Sorption coefficients were determined to account for the influence of partitioning during bioremoval. When the bacteria were added to activated sludge, degradation increased. Experimentally determined kinetic parameters were used to model a full-scale continuous treatment process, showing that low biomass could achieve reduced effluent PPCP concentrations. These results demonstrated that bioaugmentation may improve PPCP removal using established wastewater infrastructure under conditions of high solids partitioning.

Support vector regression model of wastewater bioreactor performance using microbial community diversity indices: effect of stress and bioaugmentation

The relationship between microbial community structure and function has been examined in detail in natural and engineered environments, but little work has been done on using microbial community information to predict function. We processed microbial community and operational data from controlled experiments with bench-scale bioreactor systems to predict reactor process performance. Four membrane-operated sequencing batch reactors treating synthetic wastewater were operated in two experiments to test the effects of (i) the toxic compound 3-chloroaniline (3-CA) and (ii) bioaugmentation targeting 3-CA degradation, on the sludge microbial community in the reactors. In the first experiment, two reactors were treated with 3-CA and two reactors were operated as controls without 3-CA input. In the second experiment, all four reactors were additionally bioaugmented with a Pseudomonas putida strain carrying a plasmid with a portion of the pathway for 3-CA degradation. Molecular data were generated from terminal restriction fragment length polymorphism (T-RFLP) analysis targeting the 16S rRNA and amoA genes from the sludge community. The electropherograms resulting from these T-RFs were used to calculate diversity indices - community richness, dynamics and evenness - for the domain Bacteria as well as for ammonia-oxidizing bacteria in each reactor over time. These diversity indices were then used to train and test a support vector regression (SVR) model to predict reactor performance based on input microbial community indices and operational data. Considering the diversity indices over time and across replicate reactors as discrete values, it was found that, although bioaugmentation with a bacterial strain harboring a subset of genes involved in the degradation of 3-CA did not bring about 3-CA degradation, it significantly affected the community as measured through all three diversity indices in both the general bacterial community and the ammonia-oxidizer community (α = 0.5). The impact of bioaugmentation was also seen qualitatively in the variation of community richness and evenness over time in each reactor, with overall community richness falling in the case of bioaugmented reactors subjected to 3-CA and community evenness remaining lower and more stable in the bioaugmented reactors as opposed to the unbioaugmented reactors. Using diversity indices, 3-CA input, bioaugmentation and time as input variables, the SVR model successfully predicted reactor performance in terms of the removal of broad-range contaminants like COD, ammonia and nitrate as well as specific contaminants like 3-CA. This work was the first to demonstrate that (i) bioaugmentation, even when unsuccessful, can produce a change in community structure and (ii) microbial community information can be used to reliably predict process performance. However, T-RFLP may not result in the most accurate representation of the microbial community itself, and a much more powerful prediction tool can potentially be developed using more sophisticated molecular methods.

Impact of organic carbon on the biodegradation of estrone in mixed culture systems

The effects of organic carbon concentrations and loading on the degradation of estrone (E1) were examined under various conditions in batch reactors and membrane-coupled bioreactors (MBRs). Experiments examined effects on individual microorganisms (substrate competition and growth) and on the whole community (selection). Substrate competition with organic carbon (competitive inhibition and catabolic repression) was not a factor in E1 degradation (P = 0.19 and 0.29 for two different analyses). Conversely, addition of organic carbon increased E1 degradation rates, attributable to biomass growth in feast-famine reactors over a five-day period (P = 0.016). Subsequently, however, community dynamics controlled E1 degradation rates, with other organisms outcompeting E1 degraders. More moderate but sustained increases in E1 degradation rates were observed under starvation conditions. Low influent organic carbon strength was detrimental to E1 degradation in MBRs, where organic carbon concentration and loading were decoupled (P = 0.018). These results point to the importance of multiple substrate utilizers in E1 degradation. They also suggest that while initial growth of biomass depends on the presence of sufficient organic carbon, further enrichment under starvation conditions may improve E1 degradation capability via the growth and/or stimulation of multiple substrate utilizers rather than heterotrophs characterized by an r-strategist growth regime.

Application of (13)C-stable isotope probing to identify RDX-degrading microorganisms in groundwater

We employed stable isotope probing (SIP) with (13)C-labeled hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) to identify active microorganisms responsible for RDX biodegradation in groundwater microcosms. Sixteen different 16S rRNA gene sequences were derived from microcosms receiving (13)C-labeled RDX, suggesting the presence of microorganisms able to incorporate carbon from RDX or its breakdown products. The clones, residing in Bacteroidia, Clostridia, α-, β- and δ-Proteobacteria, and Spirochaetes, were different from previously described RDX degraders. A parallel set of microcosms was amended with cheese whey and RDX to evaluate the influence of this co-substrate on the RDX-degrading microbial community. Cheese whey stimulated RDX biotransformation, altered the types of RDX-degrading bacteria, and decreased microbial community diversity. Results of this study suggest that RDX-degrading microorganisms in groundwater are more phylogenetically diverse than what has been inferred from studies with RDX-degrading isolates.

Microbial degradation of steroidal estrogens

Steroidal estrogens, widespread in the environment, are contaminants of potential concern because exposure to these compounds can cause adverse impacts on aquatic life. Intensive research efforts have been undertaken in order to better understand the environmental occurrence of these compounds. In addition to physical/chemical reactions, biological processes - microbial biodegradation of steroidal estrogens - play a vital role in determining the fate and transport of these compounds in built and natural environments. This review summarizes the current state of knowledge on the microbiology of estrogen biodegradation. Aerobic and anaerobic estrogen-degrading microorganisms are phylogenetically diverse; they are mainly isolated from soils, activated sludge, dental plaque and intestines. Estrogens can be degraded via growth-linked and non-growth-linked reactions, as well as through abiotic degradation in the presence of selective microorganisms. Current knowledge on estrogen biodegradation kinetics and pathways is limited. Molecular methods are useful in deciphering estrogen-degrading microbial community and tracking the quantity of known degraders in bioreactors with different operating conditions. Future research efforts aimed at bridging knowledge gaps on estrogen biodegradation are also proposed.