In situ profiling of microbial communities in full-scale aerobic sequencing batch reactors treating winery waste in australia

Bacterial community and filamentous population of industrial wastewater treatment plants in Belgium

The discharge of industrial water requires the removal of its pollutants, where biological wastewater treatment plants (WWTPs) are the most used systems. Biological WWTPs make use of activated sludge (AS), where bacteria are responsible for the removal of pollutants. However, our knowledge of the microbial communities of industrial plants is limited. Understanding the microbial population is essential to provide solutions to industrial problems such as bulking. The aim of this study was to identify at a high taxonomic resolution the bacterial population of 29 industrial WWTPs using 16S rRNA amplicon sequencing. Our results revealed that the main functional groups were dominated by Thauera and Zoogloea within denitrifiers, Dechloromonas in phosphate-accumulating organisms, and Defluviicoccus in glycogen-accumulating organisms. The activated sludge characterization indicated that 59% of the industrial plants suffered from bulking sludge, with DSVI values of up to 448 mL g-1. From the bulking cases, 72% corresponded to filamentous bulking with Thiothrix as the most abundant filament; meanwhile, the other 28% corresponded to viscous bulking sludge in which Zoogloea was the most abundant genus. Furthermore, the bacterial population did not share a core of taxa across all industrial plants. However, 20 genera were present in at least 50% of the plants comprising the general core, including Thauera, Ca. Competibacter, and several undescribed microorganisms. Moreover, statistical analysis revealed that wastewater salinity strongly affected the microbial richness of the industrial plants. The bacterial population across industrial plants differed considerably from each other, resulting in unique microbial communities that are attributed to the specificity of their wastewaters. KEY POINTS: • The general core taxa of industrial plants were mostly made up of undescribed bacterial genera. • Filamentous bacteria constituted on average 4.1% read abundance of the industrial WWTPs. • Viscous bulking remains a significant type of bulking within industrial WWTPs.

Insight into the evolution of microbial communities and resistance genes induced by sucralose in partial nitrification system with triclosan pre-exposure

Sucralose (SUC), an artificial sweetener widely used in food, beverages and pharmaceuticals, is frequently detected in various environmental matrices. Triclosan (TCS) is commonly used as a disinfectant and often co-exists with SUC in sewage environments. This study investigated the effects of SUC (0.1-10 mg/L) on the transmission of intracellular and extracellular antibiotic resistance genes (ARGs) in the partial nitrification systems with and without TCS pre-exposure. The reactors operated for 150 days, and SUC did not affect ammonia oxidation performance, while TCS led to the maintenance of partial nitrification. The types and abundances of extracellular ARGs in sludge and free ARGs in water increased significantly after TCS pre-exposure when faced SUC stress, which might be caused by a decrease in α-Helix/(β-Sheet + Random coil). SUC was more easily to enrich ARGs in partial nitrification systems with TCS pre-exposure, exacerbating the risk of ARGs transmission. The microbial community showed stronger relationships to cope with the direct stress of SUC, and the functional bacteria (Thauera and Nitrosomonas) in TCS pre-exposure system might be potential hosts of ARGs. This study might provide insights for better understanding the fates of SUC in partial nitrification systems and the ecological risks in wastewater containing TCS and SUC. ENVIRONMENTAL IMPLICATION: Sucralose (SUC) is often detected in the environment and considered as an emerging contaminant due to its soaring consumption and environmental persistence. Triclosan (TCS) is an antibacterial agent that often co-exists with SUC in personal care products and sewage environments. During 150 d, two partial nitrification reactors with and without TCS pre-exposure were established to study the effects of SUC on nitrification performance, antibiotic resistance genes (ARGs) and microbial communities. This study showed the refractory nature of SUC, and SUC led to the transmission of extracellular ARGs in partial nitrification system with TCS pre-exposure, exacerbating the risk of ARGs dissemination.

Optimizing the hydrolysis-acidification stage in municipal wastewater treatment: comparison of immobilized fillers and granular sludge

The decomposition of organic macromolecules in sewage currently benefits substantially from hydrolysis-acidification. The full use of its qualities can help domestic sewage to biodegrade more quickly, which promotes the subsequent aerobic reactions. This study evaluated the hydrolysis-acidification performance of granular sludge and filler in residential sewage. Both forms were highly effective at producing volatile fatty acids (VFAs) at the beginning of the reaction, but the granular sludge gradually disintegrated over time, particularly at low temperatures. The production of VFAs decreased (68.08 mg/L), and the effluent dissolved organic nitrogen (DON) increased (6.23 mg/L). However, the effluent of fillers remained at a lower level (1.3 mg/L) and produced more VFAs (74.13 mg/L). High-throughput sequencing revealed that the filler included a greater quantity of hydrolytic-acidifying bacteria than the granular sludge, which resulted in higher performance. In this study, the optimal form of utilizing hydrolytic acidifying bacteria was discussed to provide a theoretical basis to improve the full utilization of organic matter in domestic sewage and the removal of as much total nitrogen as possible.

Unravelling roles of the intermediate settler in a microaerobic hydrolysis sludge in situ reduction process

The roles of the intermediate settler in the sludge process reduction activated sludge process (SPRAS), and the influences of its hydraulic retention time (HRT_ST) on pollutant removal and sludge reduction were investigated. Prolonging HRT_ST from 3.0 to 4.5 and 6.0 h resulted in sludge reduction efficiencies increased from 46.8% to 61.5% and 62.7%. The sludge accumulation in the intermediate settler formed an anaerobic zone but inhibited methane production, and the alternating microaerobic and anaerobic environment in the sludge process reduction (SPR) module increased the microbial diversity and enriched the hydrolytic and fermentative bacteria. Prolonging HRT_ST accelerated dissolved organic matter release and elevated the degradation of refractory fraction, and improved the sludge properties of the SPRAS. Metagenomic analysis showed that the SPR module enhanced the glycolysis pathway and decoupling metabolism for sludge reduction. The results revealed that the intermediate settler plays dual roles in solid-liquid separation and sludge reduction metabolism.

Biotreatment Potential and Microbial Communities in Aerobic Bioreactor Systems Treating Agro-Industrial Wastewaters

The thriving agro-industry sector accounts for an essential part of the global gross domestic product, as the need for food and feed production is rising. However, the industrial processing of agricultural products requires the use of water at all stages, which consequently leads to the production of vast amounts of effluents with diverse characteristics, which contain a significantly elevated organic content. This fact reinforces the need for action to control and minimize the environmental impact of the produced wastewater, and activated sludge systems constitute a highly reliable solution for its treatment. The current review offers novel insights on the efficiency of aerobic biosystems in the treatment of agro-industrial wastewaters and their ecology, with an additional focus on the biotechnological potential of the activated sludge of such wastewater treatment plants.

The phylogeny, ecology and ecophysiology of the glycogen accumulating organism (GAO) Defluviicoccus in wastewater treatment plants

This comprehensive review looks critically what is known about members of the genus Defluviicoccus, an example of a glycogen accumulating organism (GAO), in wastewater treatment plants, but found also in other habitats. It considers the operating conditions thought to affect its performance in activated sludge plants designed to remove phosphorus microbiologically, including the still controversial view that it competes with the polyphosphate accumulating bacterium Ca. Accumulibacter for readily biodegradable substrates in the anaerobic zone receiving the influent raw sewage. It looks at its present phylogeny and what is known about it's physiology and biochemistry under the highly selective conditions of these plants, where the biomass is recycled continuously through alternative anaerobic (feed); aerobic (famine) conditions encountered there. The impact of whole genome sequence data, which have revealed considerable intra- and interclade genotypic diversity, on our understanding of its in situ behaviour is also addressed. Particular attention is paid to the problems in much of the literature data based on clone library and next generation DNA sequencing data, where Defluviicoccus identification is restricted to genus level only. Equally problematic, in many publications no attempt has been made to distinguish between Defluviicoccus and the other known GAO, especially Ca. Competibacter, which, as shown here, has a very different ecophysiology. The impact this has had and continues to have on our understanding of members of this genus is discussed, as is the present controversy over its taxonomy. It also suggests where research should be directed to answer some of the important research questions raised in this review.

Comparative Genomics of Members of the Genus Defluviicoccus With Insights Into Their Ecophysiological Importance

Members of the genus Defluviicoccus occur often at high abundances in activated sludge wastewater treatment plants designed to remove phosphorus, where biomass is subjected to alternating anaerobic feed/aerobic famine conditions, believed to favor the proliferation of organisms like Ca. Accumulibacter and other phosphate-accumulating organisms (PAO), and Defluviicoccus. All have a capacity to assimilate readily metabolizable substrates and store them intracellularly during the anaerobic feed stage so that under the subsequent famine aerobic stage, these can be used to synthesize polyphosphate reserves by the PAO and glycogen by Defluviicoccus. Consequently, Defluviicoccus is described as a glycogen-accumulating organism or GAO. Because they share a similar anaerobic phenotype, it has been proposed that at high Defluviicoccus abundance, the PAO are out-competed for assimilable metabolites anaerobically, and hence aerobic P removal capacity is reduced. Several Defluviicoccus whole genome sequences have been published (Ca. Defluviicoccus tetraformis, Defluviicoccus GAO-HK, and Ca. Defluviicoccus seviourii). The available genomic data of these suggest marked metabolic differences between them, some of which have ecophysiological implications. Here, we describe the whole genome sequence of the type strain Defluviicoccus vanus^T, the only cultured member of this genus, and a detailed comparative re-examination of all extant Defluviicoccus genomes. Each, with one exception, which appears not to be a member of this genus, contains the genes expected of GAO members, in possessing multiple copies of those for glycogen biosynthesis and catabolism, and anaerobic polyhydroxyalkanoate (PHA) synthesis. Both 16S rRNA and genome sequence data suggest that the current recognition of four clades is insufficient to embrace their phylogenetic biodiversity, but do not support the view that they should be re-classified into families other than their existing location in the Rhodospirillaceae. As expected, considerable variations were seen in the presence and numbers of genes encoding properties associated with key substrate assimilation and metabolic pathways. Two genomes also carried the pit gene for synthesis of the low-affinity phosphate transport protein, pit, considered by many to distinguish all PAO from GAO. The data re-emphasize the risks associated with extrapolating the data generated from a single Defluviicoccus population to embrace all members of that genus.

Impacts of earthworm introduction and cadmium on microbial communities composition and function in soil

Heavy metal contamination of soil has become a public concern. Earthworms are key players in the functioning and service of soil ecosystems, with comprehension of their introduction in the polluted soil offering new insights into the protection of soil resources. In the present study, we evaluated the effects of earthworm (Eisenia fetida) introduction and Cd (0, 10, 30, and 60 mg kg^-1 of Cd) exposure upon soil microbial community using 16S rRNA gene amplicon sequencing. Our research demonstrated that Gemmatimonadetes and Deinococcus-Thermus upregulated significantly, while Chryseolinea showed an obvious decreasing trend after earthworm introduction. In Cd contaminated soil, many genera exhibited a greater presence of Cd-dependent bacteria, namely Cd-tolerant bacteria such as Altererythrobacter and Luteimonas, and a decrease of sensitive bacteria, such as Amaricoccus and Haliangium. Moreover, functional prediction analysis of soil microbiota indicated that earthworm introduction and Cd exposure changed functional pathways of soil microorganisms. The results obtained in this study are beneficial for understanding soil microbial community impacted by earthworm, and for exploring Cd resistant or tolerant bacteria, with potentially significant findings for soil biodiversity and Cd bioremediation.

Understanding mechanisms of sludge in situ reduction in anaerobic side-stream reactor coupled membrane bioreactors packed with carriers at different filling fractions

An anoxic/oxic membrane bioreactor (AO) and three pilot-scale anaerobic side stream reactors (ASSR) coupled MBRs (ASSR-MBRs), packed with 0%, 25% and 50% carriers in ASSRs, were continuously operated to study the mechanisms for sludge reduction. Four systems showed efficient COD and NH₄⁺-N removal, while packing carriers significantly enhanced nitrogen removal. 25% filling fraction (AP₂₅) achieved the highest sludge reduction efficiency of 50.5% compared to 0% (21.7%) and 50% (39.7%). Compared to ASSR-MBR, carriers enhanced the release of dissolved organic matters, and accelerated the secretion of enzyme for cell lysis and hydrolysis. In AP₂₅, the presence of carriers prompted the formation of environment propitious to sludge reduction in bulk sludge. AP₂₅ tended to enrich hydrolytic, fermentative and denitrifying bacteria to accelerate hydrolysis process, while excessive carriers had negative effect on biomass stability and movement of carriers.

Effect of transient pH variation on microbial activity and physical characteristics of aerobic granules treating 4-chlorophenol

Chlorophenols are inhibitory compounds that can be biodegraded by aerobic granules in discontinuous processes. Many industrial wastewaters are characterized by transient pH variation over time. These pH changes could affect the overall granule structure and microbial activity during the chlorophenol biodegradation. The objective of this research was to evaluate the effects of transient pH variation on the specific degradation rate (q), granule integrity coefficient (IC), and size in sequencing batch reactors treating 4-chlorophenol (4-CP). First, aerobic granules were acclimated for efficient 4-CP degradation (>99%). The acclimated granules consisted of 55.7% of the phyla Proteobacteria and 40.6% of Bacteroidetes. The main bacteria belong to the order Sphingobacteriales (24%), as well as Amaricoccus, Acidovorax, Shinella, Rhizobium, and Flavobacterium, some of which are new genera reported in acclimated granules degrading 4-CP. Then, pH changes were applied to the acclimated aerobic granules, observing that acid pHs decreased to a greater extent the specific degradation rate (67% to 99%) than basic pHs (34% to 80%). These pH changes caused the granule disaggregation but with lower effects on the IC. The effects of pH change were mainly on the microbial activity more than the physical characteristics of aerobic granules degrading 4-CP.

Effects of urbanization on the foraging ecology and microbiota of the generalist seabird Larus argentatus

Larus gull species have proven adaptable to urbanization and due to their generalist feeding behaviors, they provide useful opportunities to study how urban environments impact foraging behavior and host-associated microbiota. We evaluated how urbanization influenced the foraging behavior and microbiome characteristics of breeding herring gulls (Larus argentatus) at three different colonies on the east coast of the United States. Study colonies represented high, medium and low degrees of urbanization, respectively. At all colonies, gulls frequently foraged at landfills and in other urban environments, but both the use of urban environments and gull foraging metrics differed with the degree of urbanization. Gulls at the more urban colonies used urban environments more frequently, showed higher rates of site fidelity and took shorter trips. Gulls at less urban colonies used a greater diversity of habitat types and foraged offshore. We observed high microbial diversity at all colonies, though microbial diversity was highest at the least urban colony where gulls used a wider variety of foraging habitats. This suggests that gulls may acquire a wider range of bacteria when visiting a higher variety of foraging sites. Our findings highlight the influence of urban habitats on gull movements and microbiome composition and diversity during the breeding season and represent the first application of amplicon sequence variants, an objective and repeatable method of bacterial classification, to study the microbiota of a seabird species.

Correlation of microbial community structure with pollutants removal, sludge reduction and sludge characteristics in micro-aerobic side-stream reactor coupled membrane bioreactors under different hydraulic retention times

A micro-aerobic side-stream reactor (MSSR) was inserted in returned sludge line of a membrane bioreactor (MBR) for sludge reduction. Three MSSR coupled MBRs (M-MBRs) and an anoxic/oxic MBR (AO-MBR) were operated in parallel to investigate effects of micro-aerobic condition and hydraulic retention time (HRT) of MSSR (HRT_M) on process performance. M-MBRs and AO-MBR were equally effective in COD and NH₄-N removal. Rising HRT_M from 3.3 to 6.7 h increased sludge reduction from 10.8% to 47.5%, and promoted dissolved organic matters release and utilization by enriching hydrolytic, fermentative and predatory bacteria. M-MBR at HRT_M of 3.3 h obtained the highest nitrogen removal, and enriched denitrifiers (Thauera and Hyphomicrobium) in the MSSR. The highest relative abundance of polyphosphate-accumulating organisms was observed in M-MBR at HRT_M of 5.0 h, which achieved the highest phosphorus removal. Prolonging HRT_M to 6.7 h improved sludge dewaterability by enriching floc-formation bacteria (Nannocystis) and inhibiting filamentous bacteria (Candidatus_Alysiosphaera).

The microbial community of a biofilm contact reactor for the treatment of winery wastewater

AIMS

To utilize a three-tiered approach to provide insight into the microbial community structure, the spatial distribution and the metabolic capabilities of organisms of a biofilm in the two towers of a high-rate biological contact reactor treating winery wastewater.

METHODS AND RESULTS

Next-generation sequencing indicated that bacteria primarily responsible for the removal of carbohydrates, sugars and alcohol were more abundant in tower 1 than tower 2 while nitrifying and denitrifying bacteria were more abundant in tower 2. Yeast populations differed in each tower. Fluorescent in situ hybridization coupled with confocal microscopy showed distribution of organisms confirming an oxygen gradient across the biofilm depth. The Biolog system (ECO plates) specified the different carbon-metabolizing profiles of the two biofilms.

CONCLUSIONS

The three-tiered approach confirmed that the addition of a second subunit to the bioreactor, expanded the treatment capacity by augmenting the microbial and metabolic diversity of the system, improving the treatment scope of the system.

SIGNIFICANCE AND IMPACT OF THE STUDY

A three-tiered biofilm analysis provided data required to optimize the design of a bioreactor to provide favourable conditions for the development of a microbial consortium, which has optimal waste removal properties for the treatment requirements at hand.

High quality draft genome sequence of Meganema perideroedes str. Gr1(T) and a proposal for its reclassification to the family Meganemaceae fam. nov

Meganema perideroedes Gr1(T) is a filamentous bacterium isolated from an activated sludge wastewater treatment plant where it is implicated in poor sludge settleability (bulking). M. perideroedes is the sole described species of the genus Meganema and of the proposed novel family "Meganemaceae". Here we describe the features of the type strain Gr1(T) along with its annotated genome sequence. The 3,409,949 bp long draft genome consists of 22 scaffolds with 3,033 protein-coding and 59 RNA genes and is a part of Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes KMG project. Notably, genome annotation indicated the potential for facultative methylotrophy. However, the ability to utilize methanol as a carbon source could not be empirically demonstrated for the type strain or for in situ Meganema spp. strains.

Winery wastewater treatment by combination of Cryptococcus laurentii and Fenton's reagent

Winery wastewaters (WW) have high levels of organic matter, resulting in high COD and BOD and suspended solids. This paper studies the combination of biological and chemical processes in WW treatment. Among 10 yeast isolates, Filobasidium sp. (AGG 577) and Cryptococcus laurentii (AGG 726) were selected due to their superior performance in COD removal. During WW degradation, COD and total polyphenols (TPP) content removal of 89-90% for Filobasidium sp. and 90-93% for C. laurentii were obtained. However, despite similar degradation efficiency for both yeasts, COD kinetics and pH evolution during treatment reveals that C. laurentii presents a faster response than Filobasidium sp. The toxicity (inhibition of Vibrio fischeri luminescence) of C. laurentii treated WW decreases to an inhibition value below 2.5%. However, treated WW exceeds the legal limits, making necessary an additional treatment. In this case, the selection of Fenton's reagent as a chemical final polish step process is a good compromise between efficiency and lower practical complexity. The best results for both COD and TPP removal were obtained with H2O2 initial concentration of 39.2mM and a H2O2:Fe(2+) molar ratio of 15:1. The combined C. laurentii - Fenton's reagent treatment of WW achieved a total reduction of 98% and 96%, for COD and TPP, respectively.

Fluorescence in situ hybridization probes targeting members of the phylum Candidatus Saccharibacteria falsely target Eikelboom type 1851 filaments and other Chloroflexi members

The FISH probe TM7-305 is thought to target the filamentous Eikelboom morphotype 0041 as a member of the Candidatus ‘Saccharibacteria’ (formerly TM7) phylum. However, with activated sludge samples in both Japan and Australia, this probe hybridized consistently with filamentous bacteria fitting the description of the morphotype 1851, which also responded positively to the CHL1851 FISH probe designed to target Chloroflexi members of this morphotype. 16S rRNA clone libraries from samples containing type 1851 TM7-305-positive filaments yielded Chloroflexi clones with high sequence similarity to Kouleothrix aurantiaca. These contained a variant TM7-305 probe target site possessing weakly destabilizing mismatches insufficient to prevent probe hybridization. Furthermore, the TM7-905 FISH probe, designed to target members of the entire Candidatus ‘Saccharibacteria’ phylum, also hybridized with the filament morphotypes 0041/0675, which responded also to the phylum level Chloroflexi probes. Many Chloroflexi sequences have only a single base mismatch to the TM7-905 probe target sequence. When competitor probes for both the TM7-305 and TM7-905 Chloroflexi non-target sites were applied, no fluorescent signal was seen in any of the filamentous organisms also hybridizing with the aforementioned Chloroflexi probes. These data indicate that these competitor probes must be included in hybridizations when both the TM7-905 and TM7-305 FISH probes are applied, to minimize potential false positive FISH results.

Biodiversity and succession of microbial community in a multi-habitat membrane bioreactor

The present study focused on establishing a multi-habitat membrane bioreactor, as well as exploring its biodiversity and succession of microbial communities. In a long-term operational period (100 days), the dissolved oxygen level of a local zone within the bioreactor decreased consistently from the original oxic state to the final anaerobic state, which led to a continuous succession of the microbial community in the bioreactor. The results revealed that the biodiversity of the microbial community in different zones simultaneously increased, with a similar microbial composition in their final successional stage. The results also indicated that the dominant species during the whole operation were distributed among 6 major phyla. At the initial operational stages, the dominant species in the anoxic-anaerobic and the oxic zones exhibited distinguished difference, whereas at the final operational stage, both zones presented nearly the same dominant microbial species and a rather similar structure in their microbial communities.