Quantification of Biologically and Chemically Bound Phosphorus in Activated Sludge from Full-Scale Plants with Biological P-Removal

Phosphorus removal from fermented dairy manure concurrent with polyhydroxybutyrate-co-valerate synthesis under aerobic conditions

Wastewater phosphorus removal achieved biologically is associated with the process known as enhanced biological phosphorus removal (EBPR). In contrast with canonical EBPR operations that employ alternating anaerobic-aerobic conditions and achieve asynchronous carbon and phosphorus storage, research herein focused on phosphorus removal achieved under aerobic conditions synchronously with volatile fatty acid (VFA) storage as polyhydroxybutyrate-co-valerate (PHBV). 90.3 ± 3.4 % soluble phosphorus removal was achieved from dairy manure fermenter liquor; influent and effluent concentrations were 38.6 ± 9.5 and 3.7 ± 0.8 mgP/L, respectively. Concurrently, PHBV yield ranged from 0.17 to 0.64 mgCOD/mgCOD, yielding 147-535 mgCODPHBV/L. No evidence of EBPR mechanisms was observed, nor were canonical phosphorus accumulating organisms present; additionally, the polyphosphate kinase gene was not present in the microbial biomass. Phosphorus removal was primarily associated with biomass growth and secondarily with biomass complexation. Results demonstrate that concurrent PHBV synthesis and phosphorus recovery can be achieved microbially under aerobic dynamic feeding conditions when fed nutrient rich wastewater.

Revisiting the role of Acinetobacter spp. in side-stream enhanced biological phosphorus removal (S2EBPR) systems

We piloted the incorporation of side-stream enhanced biological phosphorus removal (S2EBPR) with A/B stage short-cut nitrogen removal processes to enable simultaneous carbon-energy-efficient nutrients removal. This unique configuration and system conditions exerted selective force on microbial populations distinct from those in conventional EBPR. Interestingly, effective P removal was achieved with the predominance of Acinetobacter (21.5 ± 0.1 %) with nearly negligible level of known conical PAOs (Ca. Accumulibacter and Tetrasphaera were 0.04 ± 0.10 % and 0.47 ± 0.32 %, respectively). Using a combination of techniques, such as fluorescence in situ hybridization (FISH) coupled with single cell Raman spectroscopy (SCRS), the metabolic tracing of Acinetobacter-like cells exerted PAO-like phenotypic profiling. In addition, comparative metagenomics analysis of the closely related Acinetobacter spp. revealed the EBPR relevant metabolic pathways. Further oligotyping analysis of 16s rRNA V4 region revealed sub-clusters (microdiversity) of the Acinetobacter and revealed that the sub-group (oligo type 1, identical (100 % alignment identity) hits from Acinetobacter_midas_s_49494, and Acinetobacter_midas_s_55652) correlated with EBPR activities parameters, provided strong evidence that the identified Acinetobacter most likely contributed to the overall P removal in our A/B-shortcut N-S2EBPR system. To the best of our knowledge, this is the first study to confirm the in situ EBPR activity of Acinetobacter using combined genomics and SCRS Raman techniques. Further research is needed to identify the specific taxon, and phenotype of the Acinetobacter that are responsible for the P-removal.

Reevaluating the accuracy and specificity of EDTA-based polyphosphate quantification method

Feng et al. (2020) developed a simple, nondestructive, and cost-effective method to quantify polyphosphate (poly-P) in poly-P-accumulating organism (PAO)-enriched sludge samples through 30-h anaerobic exposure to 1 % (w/v) ethylenediaminetetraacetic acid (EDTA). This study optimized the N/P ratio (∼2) of the PAO culture medium in order to provide excess P for poly-P formation in PAO cells. Subsequently, the fluorescence microscopic observation of stained cells confirmed that Corynebacterium glutamicum was a PAO species capable of heterotrophic nitrification. Finally, this study reevaluated the accuracy and specificity of the EDTA-based quantification method, using two confirmed PAO biomass, three confirmed non-PAO biomass, and two sludge samples. The 1 % (w/v) EDTA treatment appears destructive to non-PAO cells, causes the release of other P forms, and is not effective for all PAO species. Under the conditions, the actual P release amount should be calculated by subtracting approximately 8 mg P g-1 total suspended solids from the determination. The amounts of P released from sludge samples was determined not only by the PAO fractions described by Feng et al. but also by PAO community structure and sludge P content.

Blind spots of universal primers and specific FISH probes for functional microbe and community characterization in EBPR systems

Fluorescence in situ hybridization (FISH) and 16S rRNA gene amplicon sequencing are commonly used for microbial ecological analyses in biological enhanced phosphorus removal (EBPR) systems, the successful application of which was governed by the oligonucleotides used. We performed a systemic evaluation of commonly used probes/primers for known polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs). Most FISH probes showed blind spots and covered nontarget bacterial groups. Ca. Competibacter probes showed promising coverage and specificity. Those for Ca. Accumulibacter are desirable in coverage but targeted out-group bacteria, including Ca. Competibacter, Thauera, Dechlorosoma, and some polyphosphate-accumulating Cyanobacteria. Defluviicoccus probes are good in specificity but poor in coverage. Probes targeting Tetrasphaera or Dechloromonas showed low coverage and specificity. Specifically, DEMEF455, Bet135, and Dech453 for Dechloromonas covered Ca. Accumulibacter. Special attentions are needed when using these probes to resolve the PAO/GAO phenotype of Dechloromonas. Most species-specific probes for Ca. Accumulibacter, Ca. Lutibacillus, Ca. Phosphoribacter, and Tetrasphaera are highly specific. Overall, 1.4% Ca. Accumulibacter, 9.6% Ca. Competibacter, 43.3% Defluviicoccus, and 54.0% Dechloromonas in the MiDAS database were not covered by existing FISH probes. Different 16S rRNA amplicon primer sets showed distinct coverage of known PAOs and GAOs. None of them covered all members. Overall, 520F-802R and 515F-926R showed the most balanced coverage. All primers showed extremely low coverage of Microlunatus (<36.0%), implying their probably overlooked roles in EBPR systems. A clear understanding of the strength and weaknesses of each probe and primer set is a premise for rational evaluation and interpretation of obtained community results.

Synchronously construction of hierarchical porous channels and cationic surface charge on lanthanum-hydrogel for rapid phosphorus removal

Phosphorus (P) removal from wastewater is critical for ecosystem operation and resource recovery. To facilitate the recycling of the used absorbents through balancing their adsorption and desorption performance on P, in this work, a novel porous magnetic La(OH)3-loaded MAPTAC/chitosan (CTS)/polyethyleneimine (PEI) ternary composite hydrogel (p-MTCH-La(OH)3) with enhanced bifunctional adsorption sites was synthesized by simultaneous dissolution of pre-embedded CaCO3 and CTS powder, followed by grafting PEI and loading La. Hierarchical porous channels promoted good dispersion of La(OH)3, bringing an excellent P adsorption capacity of 107.23 ± 4.96 mg P/g at neutral condition. PEI grafted with CTS increased the surface charge and enhanced the electrostatic attraction, which facilitated the desorption of P. The porous structure and abundant active sites also facilitated rapid adsorption with an adsorption rate constant of 0.1 g mg-1 h-1. p-MTCH-La(OH)3 maintained effective P adsorption despite co-existence with competing substances and after 5 cycles. Further mechanistic analysis indicated that La-P inner sphere complexation and LaPO4 crystalline transformation were the main pathways for P removal. However, electrostatic interactions contributed 17.5%-46.7% of the adsorption amount during the first 30 min of rapid adsorption, enabling 92.8% of the adsorbed P at this stage to be desorbed by alkaline solution. Based on the variations of adsorption and desorption capacity with adsorption time, a rapid unsaturated adsorption of 1-2 h was proposed to facilitate the recycling of the adsorbent. This study proposed a method to promote P adsorption and desorption by enhancing bifunctional adsorption sites, and proved that p-MTCH-La(OH)3 is a promising phosphate adsorbent.

Effect of thermal hydrolyzed sludge filtrate as an external carbon source on biological nutrient removal performance of A2/O system

Thermal hydrolyzed sludge filtrate (THSF) rich in biodegradable organics could be a promising external carbon source for biological nutrient removal (BNR). The use of THSF can effectively reduce wastewater treatment plants operating costs and recover bioresources and bioenergy from the waste activated sludge. In this study, the effect of THSF on the BNR process was investigated using a lab-scale anaerobic/anoxic/oxic (A²/O) system. Total nitrogen (TN) and total phosphorus (TP) removal efficiencies of 74.26 ± 3.36% and 92.20 ± 3.13% at a 0.3% dosing ratio were achieved, respectively. Moreover, 20.42% of the chemical oxygen demand (COD) contained in THSF contributed to denitrification, enhancing nitrogen removal efficiency from 55.30 to 74.26%. However, the effluent COD increased by approximately 36.80%, due to 18.39% of the COD contained in THSF discharged with effluent. In addition, the maximum denitrification rate was approximately 16.01 mg N g VSS^-1 h^-1, while the nitrification rate was not significantly affected by THSF. Nitrosomonas, a common chemoautotrophic nitrifier, was not detected after the introduction of THSF. The aerobic denitrifier Rubellimicrobium was stimulated, and its relative abundance increased from 0.16 to 3.03%. Moreover, the relative abundance of Dechloromonas was 3.93%, indicating that the denitrifying phosphorus removal process was enhanced. This study proposes an engineering application route of THSF, and the chemical phosphate removal pretreatment might be a means to suppress the phosphate recirculation.

Overlooked pathways of endogenous simultaneous nitrification and denitrification in anaerobic/aerobic/anoxic sequencing batch reactors with organic supplementation

The anaerobic/aerobic/anoxic (A/O/A) process is a promising biotechnology to intensify denitrification in low carbon/nitrogen (C/N) wastewater treatment, but the neglected typical rate-limiting step-nitrification-would hinder its wider application. Heterotrophic nitrification driven by intracellular carbon (PHAs) could enhance nitrification and achieve endogenous simultaneous nitrification and denitrification (ESND) in the A/O/A process, but its feasibility remains unexamined. Here we established four A/O/A-SBRs at different C/N ratios (3, 7.5, 12, and 16.5) to address the above-mentioned knowledge gaps. The results showed that organic supplementation promoted both nitrification and denitrification (performance and relevant enzymatic activities) until organic overdose (C/N = 16.5) exacerbated niche competitions from other non-functional heterotrophs. qPCR and batch tests indicated that high C/N ratios inhibited autotrophic nitrifiers, and heterotrophic nitrifiers (HNB) dominated in the enhanced nitrification. Given the high HNB contribution (43.7%) and low COD variation (< 10 mg L^-1) in the SND (76.4%) of CN12, we proposed a potential SND pathway based on heterotrophic nitrification and denitrification driven by PHAs and verified it with batch tests. Microbial and functional analyses suggested that CN12 favored the intracellular carbon transformation and harbored the minimum autotrophic nitrifiers, supporting the dominance of ESND in the enhanced SND. Our findings expand the understanding of the relationships between intracellular carbon transformation and SND and provide a novel nitrogen removal pathway for the practical application of the A/O/A process.

TbasCO: trait-based comparative 'omics identifies ecosystem-level and niche-differentiating adaptations of an engineered microbiome

A grand challenge in microbial ecology is disentangling the traits of individual populations within complex communities. Various cultivation-independent approaches have been used to infer traits based on the presence of marker genes. However, marker genes are not linked to traits with complete fidelity, nor do they capture important attributes, such as the timing of gene expression or coordination among traits. To address this, we present an approach for assessing the trait landscape of microbial communities by statistically defining a trait attribute as a shared transcriptional pattern across multiple organisms. Leveraging the KEGG pathway database as a trait library and the Enhanced Biological Phosphorus Removal (EBPR) model microbial ecosystem, we demonstrate that a majority (65%) of traits present in 10 or more genomes have niche-differentiating expression attributes. For example, while many genomes containing high-affinity phosphorus transporter pstABCS display a canonical attribute (e.g. up-regulation under phosphorus starvation), we identified another attribute shared by many genomes where transcription was highest under high phosphorus conditions. Taken together, we provide a novel framework for unravelling the functional dynamics of uncultivated microorganisms by assigning trait-attributes through genome-resolved time-series metatranscriptomics.

Reevaluation of the Phylogenetic Diversity and Global Distribution of the Genus "Candidatus Accumulibacter"

“Candidatus Accumulibacter” was the first microorganism identified as a polyphosphate-accumulating organism (PAO) important for phosphorus removal from wastewater. Members of this genus are diverse, and the current phylogeny and taxonomic framework appear complicated, with most publicly available genomes classified as “Candidatus Accumulibacter phosphatis,” despite notable phylogenetic divergence. The ppk1 marker gene allows for a finer-scale differentiation into different “types” and “clades”; nevertheless, taxonomic assignments remain inconsistent across studies. Therefore, a comprehensive reevaluation is needed to establish a common understanding of this genus, in terms of both naming and basic conserved physiological traits. Here, we provide this reassessment using a comparison of genome, ppk1, and 16S rRNA gene-based approaches from comprehensive data sets. We identified 15 novel species, along with “Candidatus Accumulibacter phosphatis,” “Candidatus Accumulibacter delftensis,” and “Candidatus Accumulibacter aalborgensis.” To compare the species in situ, we designed new species-specific fluorescence in situ hybridization (FISH) probes and revealed their morphology and arrangement in activated sludge. Based on the MiDAS global survey, “Ca. Accumulibacter” species were widespread in wastewater treatment plants (WWTPs) with phosphorus removal, indicating process design as a major driver for their abundance. Genome mining for PAO-related pathways and FISH-Raman microspectroscopy confirmed the potential for PAO metabolism in all “Ca. Accumulibacter” species, with detection in situ of the typical PAO storage polymers. Genome annotation further revealed differences in the nitrate/nitrite reduction pathways. This provides insights into the niche differentiation of these lineages, potentially explaining their coexistence in the same ecosystem while contributing to overall phosphorus and nitrogen removal.

IMPORTANCE “Candidatus Accumulibacter” is the most studied PAO, with a primary role in biological nutrient removal. However, the species-level taxonomy of this lineage is convoluted due to the use of different phylogenetic markers or genome sequencing approaches. Here, we redefined the phylogeny of these organisms, proposing a comprehensive approach which could be used to address the classification of other diverse and uncultivated lineages. Using genome-resolved phylogeny, compared to phylogeny based on the 16S rRNA gene and other phylogenetic markers, we obtained a higher-resolution taxonomy and established a common understanding of this genus. Furthermore, genome mining of genes and pathways of interest, validated in situ by application of a new set of FISH probes and Raman microspectroscopy, provided additional high-resolution metabolic insights into these organisms.

MiDAS 4: A global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants

Microbial communities are responsible for biological wastewater treatment, but our knowledge of their diversity and function is still poor. Here, we sequence more than 5 million high-quality, full-length 16S rRNA gene sequences from 740 wastewater treatment plants (WWTPs) across the world and use the sequences to construct the ‘MiDAS 4’ database. MiDAS 4 is an amplicon sequence variant resolved, full-length 16S rRNA gene reference database with a comprehensive taxonomy from domain to species level for all sequences. We use an independent dataset (269 WWTPs) to show that MiDAS 4, compared to commonly used universal reference databases, provides a better coverage for WWTP bacteria and an improved rate of genus and species level classification. Taking advantage of MiDAS 4, we carry out an amplicon-based, global-scale microbial community profiling of activated sludge plants using two common sets of primers targeting regions of the 16S rRNA gene, revealing how environmental conditions and biogeography shape the activated sludge microbiota. We also identify core and conditionally rare or abundant taxa, encompassing 966 genera and 1530 species that represent approximately 80% and 50% of the accumulated read abundance, respectively. Finally, we show that for well-studied functional guilds, such as nitrifiers or polyphosphate-accumulating organisms, the same genera are prevalent worldwide, with only a few abundant species in each genus.

Microbial communities are responsible for biological wastewater treatment. Here, Dueholm et al. generate more than 5 million high-quality, full-length 16S rRNA gene sequences from wastewater treatment plants across the world to construct a database with a comprehensive taxonomy, providing insights into diversity and function of these microbial communities.