High and stable substrate specificities of microorganisms in enhanced biological phosphorus removal plants

Effects of microplastics on microbial community structure and wheatgrass traits in Pb-contaminated riparian sediments under flood-drainage-planting conditions

The coexistence of microplastics (MPs) and heavy metals in sediments has caused a potential threat to sediment biota. However, differences in the effects of MPs and heavy metals on microbes and plants in sediments under different sediment conditions remain unclear. Hence, we investigated the influence of polyethylene (PE) and polylactic acid (PLA) MPs on microbial community structure, Pb bioavailability, and wheatgrass traits under sequential incubation of sediments (i.e., flood, drainage, and planting stages). Results showed that the sediment enzyme activities presented a dose-dependent effect of MPs. Besides, 10 % PLA MPs significantly increased the F1 fractions in three stages by 11.13 %, 30.10 %, and 17.26 %, respectively, thus resulting in higher Pb mobility and biotoxicity. MPs altered sediment bacterial composition and structures, and bacterial community differences were evident in different incubation stages. Moreover, the co-exposure of PLA MPs and Pb significantly decreased the shoot length and total biomass of wheatgrass and correspondingly activated the antioxidant enzyme activity. Further correlation analysis demonstrated that community structure induced by MPs was mainly driven by sediment enzyme activity. This study contributes to elucidating the combined effects of MPs and heavy metals on sediment ecosystems under different sediment conditions.

A comprehensive overview of the Chloroflexota community in wastewater treatment plants worldwide

IMPORTANCE

Chloroflexota are often abundant members of the biomass in wastewater treatment plants (WWTPs) worldwide, typically with a filamentous morphology, forming the backbones of the activated sludge floc. However, their overgrowth can often cause operational issues connected to poor settling or foaming, impairing effluent quality and increasing operational costs. Despite their importance, few Chloroflexota genera have been characterized so far. Here, we present a comprehensive overview of Chloroflexota abundant in WWTPs worldwide and an in-depth characterization of their morphology, phylogeny, and ecophysiology, obtaining a broad understanding of their ecological role in activated sludge.

Enhancement strategies of aerobic denitrification for efficient nitrogen removal from low carbon-to-nitrogen ratio shale oil wastewater

The strategy of high reflux ratio and long solids retention time was adopted to realize efficient nitrogen removal from real shale oil wastewater. This was undertaken with a low chemical oxygen demand to total nitrogen (COD/TN) ratio by strengthening aerobic denitrification in an anoxic/aerobic membrane bioreactor (A/O-MBR). The TN removal load climbed from 22 to 25 g N/(kg MLSS·d) as the COD/TN ratio declined from 8 to 3. The abundance of heterotrophic nitrifying and aerobic denitrifying (HNAD) bacteria increased by 13.8 times to 42.5%, displacing anoxic denitrifying bacteria as the predominant bacteria. The abundance of genes involved in denitrification (napAB, narGHI, norBC, nosZ) increased, however the genes related to assimilatory nitrate reduction (nirA, narB, nasC) decreased. The capacity of the dominant HNAD bacteria in an A/O-MBR to efficiently utilize a carbon source is the key to efficient nitrogen removal from shale oil wastewater with a low COD/TN ratio.

Wastewater microorganisms impact microbial diversity and important ecological functions of stream periphyton

Effluents of wastewater treatment plants can impact microbial communities in the receiving streams. However, little is known about the role of microorganisms in wastewater as opposed to other wastewater constituents, such as nutrients and micropollutants. We aimed therefore at determining the impact of wastewater microorganisms on the microbial diversity and function of periphyton, key microbial communities in streams. We used a flow-through channel system to grow periphyton upon exposure to a mixture of stream water and unfiltered or ultra-filtered wastewater. Impacts were assessed on periphyton biomass, activities and tolerance to micropollutants, as well as on microbial diversity. Our results showed that wastewater microorganisms colonized periphyton and modified its community composition, resulting for instance in an increased abundance of Chloroflexi and a decreased abundance of diatoms and green algae. This led to shifts towards heterotrophy, as suggested by the changes in nutrient stoichiometry and the increased mineralization potential of carbon substrates. An increased tolerance towards micropollutants was only found for periphyton exposed to unfiltered wastewater but not to ultra-filtered wastewater, suggesting that wastewater microorganisms were responsible for this increased tolerance. Overall, our results highlight the need to consider the role of wastewater microorganisms when studying potential impacts of wastewater on the receiving water body.

Metabolic Potential of the Superphylum Patescibacteria Reconstructed from Activated Sludge Samples from a Municipal Wastewater Treatment Plant

Patescibacteria are widely distributed in various environments and often detected in activated sludge. However, limited information is currently available on their phylogeny, morphology, and ecophysiological role in activated sludge or interactions with other microorganisms. In the present study, we identified microorganisms that interacted with Patescibacteria in activated sludge via a correlation ana-lysis using the 16S rRNA gene, and predicted the metabolic potential of Patescibacteria using a metagenomic ana-lysis. The metagenome-assembled genomes of Patescibacteria consisted of three Saccharimonadia, three Parcubacteria, and one Gracilibacteria, and showed a strong positive correlation of relative abundance with Chitinophagales. Metabolic predictions from ten recovered patescibacterial and five Chitinophagales metagenome-assembled genomes supported mutualistic interactions between a member of Saccharimonadia and Chitinophagales via N-acetylglucosamine, between a member of Parcubacteria and Chitinophagales via nitrogen compounds related to denitrification, and between Gracilibacteria and Chitinophagales via phospholipids in activated sludge. The present results indicate that various interactions between Patescibacteria and Chitinophagales are important for the survival of Patescibacteria in activated sludge ecosystems.

Temporal Variation of Nitrogen and Sulfur Species of Food Waste and Sludge during Anaerobic Co-Digestion

Anaerobic co-digestion (AcoD) has been a widely accepted method to treat food waste (FW) and sewage sludge (SS). However, there is a knowledge gap regarding the key speciation transformation of nitrogen and sulfur in AcoD. Here, we explored the changes of nitrogen (N) and sulfur (S) compounds in liquid digestion and biogas, as well as the composition of microbial community structure and related metabolic functions. The results showed that H2S in the biogas was the main form of S in the early stage, and then, it was converted into SO42− and SO32−, while NH3 and NH4+ were the main forms of N during the AcoD. In addition, bacterial diversity was associated with N and S compounds; Syntrophomonas and Aminobacterium were positively correlated to H2S, NH3, NH4+ and SO32−, and Saccharibacteria_genera_incertae_sedis, Candidatus_Cloacamonas and Thermomonas were positively correlated to SO42− and NO2−. Additionally, the FAPROTAX prediction showed that the functional composition related to N and S metabolism was different from SS and inoculum after the AcoD. This study provides detailed information of conversion of N and S of the AcoD, which could lay a foundation for the subsequent regulation of the mechanism of nitrogen and sulfur compounds in the methanogenic process.

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.

Simultaneous nitrogen and phosphorus removal by interactions between phosphate accumulating organisms (PAOs) and denitrifying phosphate accumulating organisms (DPAOs) in a sequencing batch reactor

The identification of phosphate-accumulating organisms (PAOs), denitrifying phosphate-accumulating organisms (DPAOs) and their relationship is a key pathway for optimizing nitrate and phosphate removal efficiency in activated sludge. In this study, the acclimatization of microorganisms in sequencing batch reactor were performed with anaerobic/aerobic (A/O) and anaerobic/anoxic (A/A) cycles, the biomass changes of PAOs and DPAOs and the correlations were then discussed. The results indicated that after acclimatization, the nutrient removal efficiencies reached to 85.34% (COD), 93.64% (PO₄^3--P) and 92.34% (NO₃^--N), respectively, with NO₃^--N:PO₄³-P of 1.5:1. The successful enrichment of PAOs and DPAOs (reached 97.9%) was verified by the change of relative metabolic activities, which was further proved by the change of bacterial diversity. The number of Candidatus Accumulibacter, Zoogloea, and Dechloromonas all increased at A/O and A/A stages while the number of Acinetobacter only increased at A/O stage. So Accumulibacter sp. was DPAO while Acinetobacter sp. was only PAO in this process, and genera Accumulibacter, Dechloromonas and Zoogloea greatly coordinated in denitrification and accumulating phosphorous though RDA and chord plot. This was worthy of attention and development to explore enhanced biological phosphorus removal (EBPR) in practical wastewater treatment via improving identification of bacterial species and symbiosis of bacteria community.

Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance

The development of reliable, mixed-culture biotechnological processes hinges on understanding how microbial ecosystems respond to disturbances. Here we reveal extensive phenotypic plasticity and niche complementarity in oleaginous microbial populations from a biological wastewater treatment plant. We perform meta-omics analyses (metagenomics, metatranscriptomics, metaproteomics and metabolomics) on in situ samples over 14 months at weekly intervals. Based on 1,364 de novo metagenome-assembled genomes, we uncover four distinct fundamental niche types. Throughout the time-series, we observe a major, transient shift in community structure, coinciding with substrate availability changes. Functional omics data reveals extensive variation in gene expression and substrate usage amongst community members. Ex situ bioreactor experiments confirm that responses occur within five hours of a pulse disturbance, demonstrating rapid adaptation by specific populations. Our results show that community resistance and resilience are a function of phenotypic plasticity and niche complementarity, and set the foundation for future ecological engineering efforts.

Herold et al. present an integrated meta-omics framework to investigate how mixed microbial communities, such as oleaginous bacterial populations in biological wastewater treatment plants, respond with distinct adaptation strategies to disturbances. They show that community resistance and resilience are a function of phenotypic plasticity and niche complementarity.

Power generation and microbial community analysis in microbial fuel cells: A promising system to treat organic acid fermentation wastewater

To explore a sustainable and efficient treatment approach for organic acid fermentation wastewater, two microbial fuel cells (MFCs) systems inoculated with wastewater or domesticated microbial community were constructed in this study. Compared with the MFC inoculated with domesticated microbial community, the MFC inoculated with wastewater not only showed higher power density (543.75 mW m^-2) and coulomb efficiency (22.10%), but also exhibited higher removal rates of chemical oxygen demand (75.59%), total nitrogen (76.15%), and ammonia nitrogen (83.23%), meeting the demand of wastewater discharge standard of China. Sequencing analysis revealed that the MFC inoculated with wastewater were richer in microbial community, and some bacteria such as Saprospiraceae and Caldilineaceae were beneficial for its good performance. In contrast, the microbial community of the MFC inoculated with domesticated microbial community was relatively simple. These results indicated that MFCs may be a sustainable method for organic acid fermentation wastewater treatment without any preprocessing.

Heterotrophic substrate specificity in the aquatic environment: The role of microscale patchiness investigated using modelling

Recent observations of natural bacterial communities show high genetic diversity in organic carbon uptake systems (microdiversity) and specificity in substrate species taken up. This seemingly contradicts a large body of literature from laboratory experiments under nutrient-limiting conditions, where mixed substrate use is the rule. This apparent discrepancy can be resolved by realizing that bacteria in the natural aquatic environment encounter nutrients as high-concentration patches. They may live in an ecologically nutrient-limiting environment, but they are rarely in a biologically nutrient-limited state. Rather they switch between non-growing and nutrient-replete states. During nutrient-replete growth the metabolism is saturated and assimilating additional substrates does not increase the growth rate, but carrying the assimilation system constitutes a cost. Consequently, the specialist strategy is beneficial, which is consistent with observations from laboratory experiments. When the bacteria are not growing, the added cost also reduces the fitness of the generalist species. A simple mathematical model encompassing the relevant mechanisms is developed and parameterized realistically based on the literature. The model predicts that, under pulsed conditions, specialization is beneficial when the metabolic cost of an additional uptake system is more than ~0.5% of the total metabolic cost, which is a reasonable estimate and illustrates that this is a plausible hypothesis.

Specificities and Efficiencies of Primers Targeting Candidatus Phylum Saccharibacteria in Activated Sludge

Candidatus Saccharibacteria is a well-described candidate phylum that has not been successfully isolated. Nevertheless, its presence was suggested by 16S rRNA gene sequencing data, and it is frequently detected in natural environments and activated sludge. Because pure culture representatives of Candidatus Saccharibacteria are lacking, the specificity of primers for the determination of their abundance and diversity should be carefully evaluated. In this study, eight Candidatus Saccharibacteria-specific primers were selected from previous studies and evaluated for their coverage against a public database, annealing temperature of the combined primer sets, as well as their utilization to determine the detection frequencies and phylogenetic diversity by cloning analysis, and in quantification by quantitative polymerase chain reaction (PCR). Among the eight primers, four primers (TM7314F, TM7580F, TM7-910R, and TM7-1177R) showed high coverage. Cloning analysis showed that four primer sets (TM7314F and TM7-910R, TM7314F and TM7-1177R, TM7580F and TM7-910R, and TM7580F and TM7-1177R) yielded high detection frequencies for Candidatus Saccharibacteria in activated sludge from a wastewater treatment plant in Higashihiroshima City, Japan. Quantitative PCR results indicated that the primer set containing TM7314F and TM7-910R was superior for the specific detection of Candidatus Saccharibacteria in activated sludge.

Genomic and in Situ Analyses Reveal the Micropruina spp. as Abundant Fermentative Glycogen Accumulating Organisms in Enhanced Biological Phosphorus Removal Systems

Enhanced biological phosphorus removal (EBPR) involves the cycling of biomass through carbon-rich (feast) and carbon-deficient (famine) conditions, promoting the activity of polyphosphate accumulating organisms (PAOs). However, several alternate metabolic strategies, without polyphosphate storage, are possessed by other organisms, which can compete with the PAO for carbon at the potential expense of EBPR efficiency. The most studied are the glycogen accumulating organisms (GAOs), which utilize aerobically stored glycogen to energize anaerobic substrate uptake and storage. In full-scale systems the Micropruina spp. are among the most abundant of the proposed GAO, yet little is known about their ecophysiology. In the current study, genomic and metabolomic studies were performed on Micropruina glycogenica str. Lg2^T and compared to the in situ physiology of members of the genus in EBPR plants using state-of-the-art single cell techniques. The Micropruina spp. were observed to take up carbon, including sugars and amino acids, under anaerobic conditions, which were partly fermented to lactic acid, acetate, propionate, and ethanol, and partly stored as glycogen for potential aerobic use. Fermentation was not directly demonstrated for the abundant members of the genus in situ, but was strongly supported by the confirmation of anaerobic uptake of carbon and glycogen storage in the absence of detectable polyhydroxyalkanoates or polyphosphate reserves. This physiology is markedly different from the classical GAO model. The amount of carbon stored by fermentative organisms has potentially important implications for phosphorus removal – as they compete for substrates with the Tetrasphaera PAO and stored carbon is not made available to the “Candidatus Accumulibacter” PAO under anaerobic conditions. This study shows that the current models of the competition between PAO and GAO are too simplistic and may need to be revised to take into account the impact of potential carbon storage by fermentative organisms.

Seasonal bacterial community succession in four typical wastewater treatment plants: correlations between core microbes and process performance

To understand the seasonal variation of the activated sludge (AS) bacterial community and identify core microbes in different wastewater processing systems, seasonal AS samples were taken from every biological treatment unit within 4 full-scale wastewater treatment plants. These plants adopted A2/O, A/O and oxidation ditch processes and were active in the treatment of different types and sources of wastewater, some domestic and others industrial. The bacterial community composition was analyzed using high-throughput sequencing technology. The correlations among microbial community structure, dominant microbes and process performance were investigated. Seasonal variation had a stronger impact on the AS bacterial community than any variation within different wastewater treatment system. Facing seasonal variation, the bacterial community within the oxidation ditch process remained more stable those in either the A2/O or A/O processes. The core genera in domestic wastewater treatment systems were Nitrospira, Caldilineaceae, Pseudomonas and Lactococcus. The core genera in the textile dyeing and fine chemical industrial wastewater treatment systems were Nitrospira, Thauera and Thiobacillus.

Structure and function of the microbial consortia of activated sludge in typical municipal wastewater treatment plants in winter

To better understand the relationship between the environmental variables and microbial communities of activated sludge, we took winter samples from different biological treatment units (anaerobic, oxic, etc) from the WWTP's of a number of Chinese cities. Differences in influent organic components and activated sludge microbial communities were identified by gas chromatography-mass spectrometry and high-throughput sequencing technology, respectively. Liquid nitrogen grinding pretreatment of samples was found to aid in the obtaining of a more bio-diversified sample. Influent type and dissolved oxygen concentration influenced the activated sludge microbial community structure. Nitrospira, Caldilineaceae and Anaerolineaceae were highly related to domestic wastewater treatment systems, whereas Thauera was the most abundant putative refractory aromatic hydrocarbon decomposer found in industrial wastewater treatment systems. Within the influent composition, we speculate that Thauera, Macellibacteroides and Desulfomicrobium are the key functional genera of the anaerobic environment of the textile dyeing industry wastewater treatment systems, whilst Thauera and Thiobacillus are key functional microbes in fine chemical wastewater treatment systems.

From Genes to Ecosystems in Microbiology: Modeling Approaches and the Importance of Individuality

Models are important tools in microbial ecology. They can be used to advance understanding by helping to interpret observations and test hypotheses, and to predict the effects of ecosystem management actions or a different climate. Over the past decades, biological knowledge and ecosystem observations have advanced to the molecular and in particular gene level. However, microbial ecology models have changed less and a current challenge is to make them utilize the knowledge and observations at the genetic level. We review published models that explicitly consider genes and make predictions at the population or ecosystem level. The models can be grouped into three general approaches, i.e., metabolic flux, gene-centric and agent-based. We describe and contrast these approaches by applying them to a hypothetical ecosystem and discuss their strengths and weaknesses. An important distinguishing feature is how variation between individual cells (individuality) is handled. In microbial ecosystems, individual heterogeneity is generated by a number of mechanisms including stochastic interactions of molecules (e.g., gene expression), stochastic and deterministic cell division asymmetry, small-scale environmental heterogeneity, and differential transport in a heterogeneous environment. This heterogeneity can then be amplified and transferred to other cell properties by several mechanisms, including nutrient uptake, metabolism and growth, cell cycle asynchronicity and the effects of age and damage. For example, stochastic gene expression may lead to heterogeneity in nutrient uptake enzyme levels, which in turn results in heterogeneity in intracellular nutrient levels. Individuality can have important ecological consequences, including division of labor, bet hedging, aging and sub-optimality. Understanding the importance of individuality and the mechanism(s) underlying it for the specific microbial system and question investigated is essential for selecting the optimal modeling strategy.

Bacterial and Fungal Community Structures in Loess Plateau Grasslands with Different Grazing Intensities

The Loess Plateau of China is one of the most fragile ecosystems worldwide; thus, human production activities need to be conducted very cautiously. In this study, MiSeq high-throughput sequencing was applied to assess the relationship between bacterial and fungal community structures and changes in vegetation and soil physical and chemical properties induced by grazing, in four grasslands with different levels of grazing intensity (0, 2.67, 5.33, and 8.67 sheep/ha) in the semiarid region of the Loess Plateau. The relative abundances of the bacterial community in the grasslands with 2.67 and 5.33 sheep/ha were significantly higher than those in grasslands with 0 and 8.67 sheep/ha, and the fungal diversity was significantly lower for grasslands with 2.67 sheep/ha than for the other grasslands. Redundancy analysis (RDA) showed that plant biomass, nitrate, and total nitrogen have significant effects on bacterial community structure, whereas nitrate and total nitrogen also significantly affect fungal community structure. Variation partitioning showed that soil and plant characteristics influence the bacterial and fungal community structures; these characteristics explained 51.9 and 52.9% of the variation, respectively. Thus, bacterial and fungal community structures are very sensitive to grazing activity and change to different extents with different grazing intensities. Based on our findings, a grazing intensity of about 2.67 sheep/ha is considered the most appropriate in semiarid grassland of the Loess Plateau.

Unraveling characteristics of nutrient removal and microbial community in a novel aerated landscape - Activated sludge ecological system

In this study, a novel landscape-activated sludge ecological system (LASeM) was constructed with the advantages of promising treatment, less land need and significant landscape services. Compared to literature, this study provided promising integrated wastewater treatment and landscape for wastewater treatment. This first-attempt study clearly deciphered interactive effect of aeration rate (AR) on nutrient removal and microbial community structure in LASeM. When AR was 0.016m(3)h(-1), the most appropriate removal of COD, NH4(+)-N and TP were 96%, 97% and 74% with the effluent of 14.3, 1.7 and 0.7mgL(-1), respectively, which showed satisfactory capabilities for rural domestic wastewater treatment. According to clone library analysis, Proteobacteria (71%), Bacteroidetes (17%) were found to be the dominant bacterial phylums present in LASeM for biodegradation. In particular, the incorporation of plants altered the microbial community and strengthened capability for the nutrients removal likely due to synergistic interactions among species in the ecosystem.

Genomic and in situ investigations of the novel uncultured Chloroflexi associated with 0092 morphotype filamentous bulking in activated sludge

Overgrowth of filamentous bacteria in activated sludge wastewater treatment plants (WWTPs) leads to impaired sludge settleability, a condition known as bulking, which is a common operational problem worldwide. Filaments with the Eikelboom 0092 morphotype are commonly associated with such bulking episodes. Members of the uncultured B45 phylotype, which is embraced within the phylum Chloroflexi, were recently shown to exhibit this morphology. Although these organisms are among the most abundant populations recorded in activated sludge processes, nothing is known about their metabolic characteristics. In this study, a genome sequence, representing the B45 phylotype, was retrieved from a metagenome generated from an activated sludge WWTP. The genome consisted of two chromosomes and one plasmid, which were 4.0, 1.0 and 0.04 Mbps in size, respectively. A metabolic model was constructed for this organism, based on annotation of its genome, showing its ability to generate energy by respiration, utilizing oxygen, nitrite or nitrous oxide as electron acceptors, or by fermentation of sugars. The ability of B45 members to ferment sugars under anaerobic conditions was validated in situ with microautoradiography-fluorescence in situ hybridization. The provisional name of 'Candidatus Promineofilum breve' is proposed for this species. This study represents the first detailed information on an uncultured genus of filamentous organisms from activated sludge.

Efficiency and bacterial populations related to pollutant removal in an upflow microaerobic sludge reactor treating manure-free piggery wastewater with low COD/TN ratio

A novel upflow microaerobic sludge reactor (UMSR) had proved excellent in nitrogen removal from manure-free piggery wastewater characterized by high concentration of ammonium (NH4(+)-N) and low chemical oxygen demand (COD) to total nitrogen (TN) ratio, but the biological mechanism in the UMSR was still indeterminate. With a constant nitrogen loading rate of 1.10kg/(m(3)d) at hydraulic retention time 8h, the UMSR was kept performing for 67days in the present research and the average load removal of COD, NH4(+)-N and TN was as high as 0.72, 0.76 and 0.94kg/(m(3)d), respectively. Compared with the inoculated sludge, the acclimated sludge was richer in genera responsible for the biological removal of carbon, nitrogen and phosphorus. Ammonium oxidation bacteria, heterotrophic denitrifiers, autotrophic denitrifiers and phosphate accumulating organisms coexisted perfectly in the microaerobic system, and their synergistic action made the UMSR perform well in COD, NH4(+)-N, TN and phosphate removal.

In situ phenotypic heterogeneity among single cells of the filamentous bacterium Candidatus Microthrix parvicella

Microorganisms in biological wastewater treatment plants require adaptive strategies to deal with rapidly fluctuating environmental conditions. At the population level, the filamentous bacterium Candidatus Microthrix parvicella (Ca. M. parvicella) has been found to fine-tune its gene expression for optimized substrate assimilation. Here we investigated in situ substrate assimilation by single cells of Ca. M. parvicella using nano-scale secondary-ion mass spectrometry (nanoSIMS). NanoSIMS imaging highlighted phenotypic heterogeneity among Ca. M. parvicella cells of the same filament, whereby ¹³C-oleic acid and ¹³C-glycerol-3-phosphate assimilation occurred in ≈21–55% of cells, despite non-assimilating cells being intact and alive. In response to alternating aerobic–anoxic regimes, ¹³C-oleic acid assimilation occurred among subpopulations of Ca. M. parvicella cells (≈3–28% of cells). Furthermore, Ca. M. parvicella cells exhibited two temperature optima for ¹³C-oleic acid assimilation and associated growth rates. These results suggest that phenotypic heterogeneity among Ca. M. parvicella cells allows the population to adapt rapidly to fluctuating environmental conditions facilitating its widespread occurrence in biological wastewater treatment plants.

Characterization of the In Situ Ecophysiology of Novel Phylotypes in Nutrient Removal Activated Sludge Treatment Plants

An in depth understanding of the ecology of activated sludge nutrient removal wastewater treatment systems requires detailed knowledge of the community composition and metabolic activities of individual members. Recent 16S rRNA gene amplicon surveys of activated sludge wastewater treatment plants with nutrient removal indicate the presence of a core set of bacterial genera. These organisms are likely responsible for the bulk of nutrient transformations underpinning the functions of these plants. While the basic activities of some of these genera in situ are known, there is little to no information for the majority. This study applied microautoradiography coupled with fluorescence in situ hybridization (MAR-FISH) for the in situ characterization of selected genus-level-phylotypes for which limited physiological information is available. These included Sulfuritalea and A21b, both within the class Betaproteobacteria, as well as Kaga01, within sub-group 10 of the phylum Acidobacteria. While the Sulfuritalea spp. were observed to be metabolically versatile, the A21b and Kaga01 phylotypes appeared to be highly specialized.

The activated sludge ecosystem contains a core community of abundant organisms

Understanding the microbial ecology of a system requires that the observed population dynamics can be linked to their metabolic functions. However, functional characterization is laborious and the choice of organisms should be prioritized to those that are frequently abundant (core) or transiently abundant, which are therefore putatively make the greatest contribution to carbon turnover in the system. We analyzed the microbial communities in 13 Danish wastewater treatment plants with nutrient removal in consecutive years and a single plant periodically over 6 years, using Illumina sequencing of 16S ribosomal RNA amplicons of the V4 region. The plants contained a core community of 63 abundant genus-level operational taxonomic units (OTUs) that made up 68% of the total reads. A core community consisting of abundant OTUs was also observed within the incoming wastewater to three plants. The net growth rate for individual OTUs was quantified using mass balance, and it was found that 10% of the total reads in the activated sludge were from slow or non-growing OTUs, and that their measured abundance was primarily because of immigration with the wastewater. Transiently abundant organisms were also identified. Among them the genus Nitrotoga (class Betaproteobacteria) was the most abundant putative nitrite oxidizer in a number of activated sludge plants, which challenges previous assumptions that Nitrospira (phylum Nitrospirae) are the primary nitrite-oxidizers in activated sludge systems with nutrient removal.

MiDAS: the field guide to the microbes of activated sludge

The Microbial Database for Activated Sludge (MiDAS) field guide is a freely available online resource linking the identity of abundant and process critical microorganisms in activated sludge wastewater treatment systems to available data related to their functional importance. Phenotypic properties of some of these genera are described, but most are known only from sequence data. The MiDAS taxonomy is a manual curation of the SILVA taxonomy that proposes a name for all genus-level taxa observed to be abundant by large-scale 16 S rRNA gene amplicon sequencing of full-scale activated sludge communities. The taxonomy can be used to classify unknown sequences, and the online MiDAS field guide links the identity to the available information about their morphology, diversity, physiology and distribution. The use of a common taxonomy across the field will provide a solid foundation for the study of microbial ecology of the activated sludge process and related treatment processes. The online MiDAS field guide is a collaborative workspace intended to facilitate a better understanding of the ecology of activated sludge and related treatment processes—knowledge that will be an invaluable resource for the optimal design and operation of these systems.

Database URL:http://www.midasfieldguide.org

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.

Metabolic model for the filamentous 'Candidatus Microthrix parvicella' based on genomic and metagenomic analyses

'Candidatus Microthrix parvicella' is a lipid-accumulating, filamentous bacterium so far found only in activated sludge wastewater treatment plants, where it is a common causative agent of sludge separation problems. Despite attracting considerable interest, its detailed physiology is still unclear. In this study, the genome of the RN1 strain was sequenced and annotated, which facilitated the construction of a theoretical metabolic model based on available in situ and axenic experimental data. This model proposes that under anaerobic conditions, this organism accumulates preferentially long-chain fatty acids as triacylglycerols. Utilisation of trehalose and/or polyphosphate stores or partial oxidation of long-chain fatty acids may supply the energy required for anaerobic lipid uptake and storage. Comparing the genome sequence of this isolate with metagenomes from two full-scale wastewater treatment plants with enhanced biological phosphorus removal reveals high similarity, with few metabolic differences between the axenic and the dominant community 'Ca. M. parvicella' strains. Hence, the metabolic model presented in this paper could be considered generally applicable to strains in full-scale treatment systems. The genomic information obtained here will provide the basis for future research into in situ gene expression and regulation. Such information will give substantial insight into the ecophysiology of this unusual and biotechnologically important filamentous bacterium.