Identification and quantification of microbial populations in activated sludge and anaerobic digestion processes

Linking the shifts in the metabolically active microbiota in a UASB and hybrid anaerobic-aerobic bioreactor for swine wastewater treatment

Due to the high concentration of pollutants, swine wastewater needs to be treated prior to disposal. The combination of anaerobic and aerobic technologies in one hybrid system allows to obtain higher removal efficiencies compared to those achieved via conventional biological treatment, and the performance of a hybrid system depends on the microbial community in the bioreactor. Here, we evaluated the community assembly of an anaerobic-aerobic hybrid reactor for swine wastewater treatment. Sequencing of partial 16S rRNA coding genes was performed using Illumina from DNA and retrotranscribed RNA templates (cDNA) extracted from samples from both sections of the hybrid system and from a UASB bioreactor fed with the same swine wastewater influent. Proteobacteria and Firmicutes were the dominant phyla and play a key role in anaerobic fermentation, followed by Methanosaeta and Methanobacterium. Several differences were found in the relative abundances of some genera between the DNA and cDNA samples, indicating an increase in the diversity of the metabolically active community, highlighting Chlorobaculum, Cladimonas, Turicibacter and Clostridium senso stricto. Nitrifying bacteria were more abundant in the hybrid bioreactor. Beta diversity analysis revealed that the microbial community structure significantly differed among the samples (p < 0.05) and between both anaerobic treatments. The main predicted metabolic pathways were the biosynthesis of amino acids and the formation of antibiotics. Also, the metabolism of C5-branched dibasic acid, Vit B5 and CoA, exhibited an important relationship with the main nitrogen-removing microorganisms. The anaerobic-aerobic hybrid bioreactor showed a higher ammonia removal rate compared to the conventional UASB system. However, further research and adjustments are needed to completely remove nitrogen from wastewater.

Matrix-associated microbial communities in a nitrogen-removing on-site wastewater treatment system are largely structured by niche processes

On-site wastewater treatment systems (OWTSs) can be designed to promote microbial communities with naturally occurring metabolic functions desirable to wastewater treatment. Among such OWTSs are nitrogen-removing biofilters (NRBs), comprising a sand layer overlying a sand-lignocellulose (sand-lc) layer and intended to promote sequential nitrification and denitrification. The design of NRBs is based on the hypothesis that niche processes like environmental selection strongly structure the microbial communities, which predicts that immigrating wastewater communities and matrix-associated communities will be distinct and that the matrix communities in the two layers will be distinct. We characterized NRB microbial communities by 16S ribosomal RNA amplicon sequencing. Selection of the matrix-associated communities was indicated by clear differences from the immigrating community. For matrix-associated communities, alpha and beta diversity differed between the matrix layers, as did the relative abundances of many functional groups and genera. Functional groups with strict metabolisms were nearly exclusively detected in either the sand (ammonia and nitrite oxidizers) or sand-lc layer (methanogens), consistent with the niche hypothesis. Contrary to expectations, denitrifiers as a functional group were not present at greater relative abundance in the sand-lc than sand matrix because of a portfolio effect: some denitrifying genera were more abundant in the sand layer, whereas others were more abundant in the sand-lc layer. This study reveals niche processes acting at different levels of community organization for different biogeochemical functions, a crucial consideration in designing effective and reliable OWTSs to mitigate nitrogen pollution.

Phosphate, Microbiota and CKD

Phosphate is a key uremic toxin associated with adverse outcomes. As chronic kidney disease (CKD) progresses, the kidney capacity to excrete excess dietary phosphate decreases, triggering compensatory endocrine responses that drive CKD-mineral and bone disorder (CKD-MBD). Eventually, hyperphosphatemia develops, and low phosphate diet and phosphate binders are prescribed. Recent data have identified a potential role of the gut microbiota in mineral bone disorders. Thus, parathyroid hormone (PTH) only caused bone loss in mice whose microbiota was enriched in the Th17 cell-inducing taxa segmented filamentous bacteria. Furthermore, the microbiota was required for PTH to stimulate bone formation and increase bone mass, and this was dependent on bacterial production of the short-chain fatty acid butyrate. We review current knowledge on the relationship between phosphate, microbiota and CKD-MBD. Topics include microbial bioactive compounds of special interest in CKD, the impact of dietary phosphate and phosphate binders on the gut microbiota, the modulation of CKD-MBD by the microbiota and the potential therapeutic use of microbiota to treat CKD-MBD through the clinical translation of concepts from other fields of science such as the optimization of phosphorus utilization and the use of phosphate-accumulating organisms.

Determination of microbial numbers in anaerobically digested biofertilisers

This study aimed to quantity total numbers of bacteria, fungi and archaea in different types of commercial liquid anaerobic digestates, and to identify common patterns in their microbial numbers post-digestion and possible implications of their use as biofertiliser. Relationships between microbial numbers and physical-chemical traits of the digestates were also investigated. Quantification was performed using culturable and molecular (quantitative PCR) approaches. Bacterial and fungal CFUs ranged up to five orders of magnitude (10⁵-10¹⁰; 0-10⁵ g^-1 DW, respectively) between different types of anaerobic digestates. Bacterial, archaeal and fungal gene copy numbers (GCN) varied by two orders of magnitude (10⁸-10¹⁰; 10⁷-10⁹; 10⁴-10⁶ g^-1 DW, respectively) between digestates. All microbial variables analysed showed significant differences between the different types of anaerobic digestate investigated (p < 0.05). Culturable microbial numbers for fungi (6.43 × 10⁴ CFU g^-1 DW) were much lower than for bacteria (2.23 × 10⁹ CFU g^-1 DW). Gene copy numbers were highest for bacteria (16S) (1.09 × 10¹⁰ g^-1 DW), followed by archaea (16S) (5.87 × 10⁸ g^-1 DW), and fungi (18S) (1.77 × 10⁶ g^-1 DW). Liquid anaerobic digestates were predominantly dominated by bacteria, followed by archaeal and fungal populations. At 50% similarity level, the microbial profiles of the eleven anaerobic digestates tested separated into just two groups, indicating a broad relative degree of similarity in terms of microbial numbers. Higher bacterial (16S) GCN was associated with low OM and C/N ratio in digestates.

A Putative Type V Pilus Contributes to Bacteroides thetaiotaomicron Biofilm Formation Capacity

Bacteroides thetaiotaomicron is a prominent anaerobic member of the healthy human gut microbiota. While the majority of functional studies on B. thetaiotaomicron addressed its impact on the immune system and the utilization of diet polysaccharides, B. thetaiotaomicron biofilm capacity and its contribution to intestinal colonization are still poorly characterized. We tested the natural adhesion of 34 B. thetaiotaomicron isolates and showed that although biofilm capacity is widespread among B. thetaiotaomicron strains, this phenotype is masked or repressed in the widely used reference strain VPI 5482. Using transposon mutagenesis followed by a biofilm positive-selection procedure, we identified VPI 5482 mutants with increased biofilm capacity corresponding to an alteration in the C-terminal region of BT3147, encoded by the BT3148-BT3147 locus, which displays homology with Mfa-like type V pili found in many Bacteroidetes We show that BT3147 is exposed on the B. thetaiotaomicron surface and that BT3147-dependent adhesion also requires BT3148, suggesting that BT3148 and BT3147 correspond to the anchor and stalk subunits of a new type V pilus involved in B. thetaiotaomicron adhesion. This study therefore introduces B. thetaiotaomicron as a model to study proteinaceous adhesins and biofilm-related phenotypes in this important intestinal symbiont.IMPORTANCE Although the gut anaerobe Bacteroides thetaiotaomicron is a prominent member of the healthy human gut microbiota, little is known about its capacity to adhere to surfaces and form biofilms. Here, we identify that alteration of a surface-exposed protein corresponding to a type of pili found in many Bacteroidetes increases B. thetaiotaomicron biofilm formation. This study lays the ground for establishing this bacterium as a model organism for in vitro and in vivo studies of biofilm-related phenotypes in gut anaerobes.

Multivariate and Multiscale Approaches for Interpreting the Mechanisms of Nitrous Oxide Emission during Pig Manure-Wheat Straw Aerobic Composting

Nitrous oxide (N₂O) emission during composting causes nitrogen loss and air pollution. The interpretation of N₂O emission mechanisms will help to customize composting strategies that mitigate climate change. At pile and particle scales, this study characterized N₂O emission-related variables (gases, ions, and microbes) and their correlations during pig manure-wheat straw aerobic composting. Pile-scale results showed that N₂O emission mainly occurred in mesophilic, thermophilic, and cooling phases; the nitrification by ammonia-oxidizing bacteria ( AOB) and nitrite-oxidizing bacteria ( NOB) coexisted with the denitrification by denitrificans ( DEN); the major NOB and DEN were Nitrobacter ( NOB_Nba) and Thiobacillus denitrificans ( DEN_Tb), respectively. The mechanisms of nitrification, nitrifier denitrification, and anaerobic denitrification in composting particles were initially visualized by confocal laser scanning microscopy: Betaproteobacteria ( AOB_ Beta) sporadically distributed on the outer area of the particles, NOB_Nba internally attached to AOB_ Beta, and Nitrosomonas europea/ Nitrosomonas eutropha ( AOB_eu) and DEN_Tb concentrated in the interior. Correlation analysis of the variables showed that the distribution area of AOB_eu was proportional to N₂O emission ( R² = 0.84); AOB not only participated in nitrification but also nitrifier denitrification, and N₂O formation was mainly from nitrifier denitrification by AOB_eu during the mesophilic-thermophilic phase and from denitrification by AOB_eu and DEN during the cooling phase.

Gypsum in animal slurry systems enhances generation of hydrogen sulphide and increases occupational exposure hazard

Hydrogen sulphide gas (H₂S) produced by sulphate reducing bacteria (SRB) in stored animal slurry is highly toxic and, if emitted into poorly ventilated confined spaces, can build up to concentrations capable of causing asphyxiation. Therefore it is important to understand factors influencing H₂S emission from slurry. Powdered gypsum (hydrated calcium sulphate) may be used as animal bedding and, if it enters slurry systems, could be metabolised by SRB and further increase H₂S generation. Cattle slurry and cattle bedding collected from farms was used in laboratory-scale experiments sealed in 20litre vessels fitted with mechanical stirrers. H₂S was monitored in head space above the slurry using real-time gas detectors before and after stirring, and before and after adding 1% of two sources of gypsum powder. In one set of experiments, gypsum was already present in the slurry having been used in bedding on the farm. H₂S monitoring continued daily for up to 25days. Before stirring, H₂S levels in head spaces were minimal. After stirring, even without gypsum, maximum head space H₂S levels with slurry or bedding ranged from 330 to 1190ppm. By comparison, the UK short-term (15min) Workplace Exposure Limit is 10ppm. Statistically significant increases in H₂S levels were associated with gypsum addition, as high as 1772ppm with slurry and 3940ppm with bedding. Emissions peaked at around day 15 with slurry and bedding to which gypsum was freshly added, but within 5days when added to slurry already containing farm-added gypsum. Levels of H₂S produced from stirred slurry would constitute a hazard to anyone exposed to it, and adding gypsum further increased emission levels. Therefore, if gypsum residues enter slurry it could increase the risk of H₂S accumulation in confined spaces associated with slurry systems. It is important therefore to take this into account in managing risk.

Community dynamics of denitrifying bacteria in full-scale wastewater treatment plants

Effective and stable nitrogen removal from wastewater requires abundant and active denitrifying populations. In this study, a one-year investigation of the population dynamics of phylogenetic groups known to harbor nitrate reducers was conducted in three municipal wastewater treatment plants (WWTPs). The bacterial community composition was determined by amplicon sequencing of the 16S rRNA gene, and putative nitrate reducers were identified by sequencing narG and napA genes. Fluorescence in situ hybridization with oligonucleotide probes targeting known nitrate reducers in wastewater revealed that certain bacteria predominated in the WWTPs: Curvibacter-related bacteria, Comamonadaceae, Azoarcus, Thauera, Dechloromonas, and Candidatus Accumulibacter within Rhodocyclaceae. The data showed high diversity in the nitrate-reducing community and a large degree of redundancy, with a relatively stable core group of bacteria in each plant that ensured small yearly variation in nitrate reduction rates.

Abundance and diversity of bacterial nitrifiers and denitrifiers and their functional genes in tannery wastewater treatment plants revealed by high-throughput sequencing

Biological nitrification/denitrification is frequently used to remove nitrogen from tannery wastewater containing high concentrations of ammonia. However, information is limited about the bacterial nitrifiers and denitrifiers and their functional genes in tannery wastewater treatment plants (WWTPs) due to the low-throughput of the previously used methods. In this study, 454 pyrosequencing and Illumina high-throughput sequencing, combined with molecular methods, were used to comprehensively characterize structures and functions of nitrification and denitrification bacterial communities in aerobic and anaerobic sludge of two full-scale tannery WWTPs. Pyrosequencing of 16S rRNA genes showed that Proteobacteria and Synergistetes dominated in the aerobic and anaerobic sludge, respectively. Ammonia-oxidizing bacteria (AOB) amoA gene cloning revealed that Nitrosomonas europaea dominated the ammonia-oxidizing community in the WWTPs. Metagenomic analysis showed that the denitrifiers mainly included the genera of Thauera, Paracoccus, Hyphomicrobium, Comamonas and Azoarcus, which may greatly contribute to the nitrogen removal in the two WWTPs. It is interesting that AOB and ammonia-oxidizing archaea had low abundance although both WWTPs demonstrated high ammonium removal efficiency. Good correlation between the qPCR and metagenomic analysis is observed for the quantification of functional genes amoA, nirK, nirS and nosZ, indicating that the metagenomic approach may be a promising method used to comprehensively investigate the abundance of functional genes of nitrifiers and denitrifiers in the environment.