CRISPR-Cas phage defense systems and prophages in Candidatus Accumulibacter

Candidatus Accumulibacter plays a major role in enhanced biological phosphorus removal (EBPR) from wastewater. Although bacteriophages have been shown to represent fatal threats to Ca. Accumulibacter organisms and thus interfere with the stability of the EBPR process, little is known about the ability of different Ca. Accumulibacter strains to resist phage infections. We conducted a systematic analysis of the occurrence and characteristics of clustered regularly interspaced short palindromic repeats and associated proteins (CRISPR-Cas) systems and prophages in Ca. Accumulibacter lineage members (43 in total, including 10 newly recovered genomes). Results indicate that 28 Ca. Accumulibacter genomes encode CRISPR-Cas systems. They were likely acquired via horizontal gene transfer, conveying a distinct adaptivity to phage predation to different Ca. Accumulibacter members. Major differences in the number of spacers show the unique phage resistance of these members. A comparison of the spacers in closely related Ca. Accumulibacter members from distinct geographical locations indicates that habitat isolation may have resulted in the acquisition of resistance to different phages by different Ca. Accumulibacter. Long-term operation of three laboratory-scale EBPR bioreactors revealed high relative abundances of Ca. Accumulibacter with CRISPSR-Cas systems. Their specific resistance to phages in these reactors was indicated by spacer analysis. Metatranscriptomic analyses showed the activation of the CRISPR-Cas system under both anaerobic and aerobic conditions. Additionally, 133 prophage regions were identified in 43 Ca. Accumulibacter genomes. Twenty-seven of them (in 19 genomes) were potentially active. Major differences in the occurrence of CRISPR-Cas systems and prophages in Ca. Accumulibacter will lead to distinct responses to phage predation. This study represents the first systematic analysis of CRISPR-Cas systems and prophages in the Ca. Accumulibacter lineage, providing new perspectives on the potential impacts of phages on Ca. Accumulibacter and EBPR systems.

Performance of a Tower-Shaped Integrated Ecological Purification Device for Pollutants Removal from Domestic Sewage in Rural Areas

With the continuous development of China's modern economy and agricultural society, the discharge of rural sewage has been recognized as a major threat to the safety of the rural ecological environment. This study discussed the purification efficiency of a tower-shaped integrated ecological purification device (TIEPD)-consisting of a measuring tank, detention tank and three-stage purification unit-towards various common pollutants in rural areas during operation and tested the stability and efficiency of the TIEPD under different rural life events (fair activity days and nonfair activity days) and different precipitation intensities (light rain, moderate rain and heavy rain). The results showed that the average removal efficiencies of the TIEPD towards chemical oxygen demand, ammonia nitrogen, total nitrogen and total phosphorus were 69%, 67%, 54% and 73%, respectively. The average effluent concentration of each pollutant can meet the standard of the discharge of pollutants in China. The system exhibited good stability in removing pollutants and good ecological and economic benefits. This study provides the treatment of domestic sewage in the upper reaches of the Yangtze River and in mountainous areas of China and strengthens the prevention and control of rural nonpoint source pollution.

Diversified metabolism makes novel Thauera strain highly competitive in low carbon wastewater treatment

Thauera, as one of the core members of wastewater biological treatment systems, plays an important role in the process of nitrogen and phosphorus removal from low-carbon source sewage. However, there is a lack of systematic understanding of Thauera's metabolic pathway and genomics. Here we report on the newly isolated Thauera sp. RT1901, which is capable of denitrification using variety carbon sources including aromatic compounds. By comparing the denitrification processes under the conditions of insufficient, adequate and surplus carbon sources, it was found that strain RT1901 could simultaneously use soluble microbial products (SMP) and extracellular polymeric substances (EPS) as electron donors for denitrification. Strain RT1901 was also found to be a denitrifying phosphate accumulating bacterium, able to use nitrate, nitrite, or oxygen as electron acceptors during poly-β-hydroxybutyrate (PHB) catabolism. The annotated genome was used to reconstruct the complete nitrogen and phosphorus metabolism pathways of RT1901. In the process of denitrifying phosphorus accumulation, glycolysis was the only pathway for glycogen metabolism, and the glyoxylic acid cycle replaced the tricarboxylic acid cycle (TCA) to supplement the reduced energy. In addition, the abundance of conventional phosphorus accumulating bacteria decreased significantly and the removal rates of total nitrogen (TN) and chemical oxygen demand (COD) increased after the addition of RT1901 in the low carbon/nitrogen (C/N) ratio of anaerobic aerobic anoxic-sequencing batch reactor (AOA-SBR). This research indicated that the diverse metabolic capabilities of Thauera made it more competitive than other bacteria in the wastewater treatment system.

Interaction between β-lactam antibiotic and phosphorus-accumulating organisms

β-Lactam antibiotics have been widely used in clinic due to strong antibacterial activity with mild adverse side effects and have been detected in the environment. In the enhanced biological phosphorus removal (EBPR) process, phosphorus-accumulating organisms (PAOs) play a major role. In this study, amoxicillin, aztreonam, and cefoperazone are the selected antibiotics that applied in investigating the interaction mechanism of β-lactam antibiotics and PAO. The effects of β-lactam antibiotics on PAOs were analyzed comprehensively from the aspects of antibiotic impacts on phosphorus removal rate, intracellular polymer, their toxicity to PAOs, and PAO impacts on the fate of β-lactam antibiotics. It was found that the phosphorus removal rate of PAO increased by 19.21% and 15.75%, respectively at 10 mg/L amoxicillin and aztreonam, while cefoperazone had certain inhibition effect on phosphorus removal efficiency. Quantitative analysis shows that in the aerobic stage, three kinds of β-lactam antibiotics could promote the synthesis of polyphosphates (poly-P). The degradation rates of three antibiotics were as follows: amoxicillin > aztreonam > cefoperazone. The fate characteristics of antibiotics provide a theoretical basis for environmental risk assessment. The toxic effects of three antibiotics were as follows: cefoperazone > aztreonam > amoxicillin according to the bacteriostatic test. It provided a scientific theoretical basis for systematically evaluating the biological toxicity of antibiotic pollutants.

Genomic and Metabolic Insights into Two Novel Thiothrix Species from Enhanced Biological Phosphorus Removal Systems

Two metagenome-assembled genomes (MAGs), obtained from laboratory-scale enhanced biological phosphorus removal bioreactors, were analyzed. The values of 16S rRNA gene sequence identity, average nucleotide identity, and average amino acid identity indicated that these genomes, designated as RT and SSD2, represented two novel species within the genus Thiothrix, 'Candidatus Thiothrix moscowensis' and 'Candidatus Thiothrix singaporensis'. A complete set of genes for the tricarboxylic acid cycle and electron transport chain indicates a respiratory type of metabolism. A notable feature of RT and SSD2, as well as other Thiothrix species, is the presence of a flavin adenine dinucleotide (FAD)-dependent malate:quinone oxidoreductase instead of nicotinamide adenine dinucleotide (NAD)-dependent malate dehydrogenase. Both MAGs contained genes for CO₂ assimilation through the Calvin-Benson-Bassam cycle; sulfide oxidation (sqr, fccAB), sulfur oxidation (rDsr complex), direct (soeABC) and indirect (aprBA, sat) sulfite oxidation, and the branched Sox pathway (SoxAXBYZ) of thiosulfate oxidation to sulfur and sulfate. All these features indicate a chemoorganoheterotrophic, chemolithoautotrophic, and chemolithoheterotrophic lifestyle. Both MAGs comprise genes for nitrate reductase and NO-reductase, while SSD2 also contains genes for nitrite reductase. The presence of polyphosphate kinase and exopolyphosphatase suggests that RT and SSD2 could accumulate and degrade polyhosphates during the oxic-anoxic growth cycle in the bioreactors, such as typical phosphate-accumulating microorganisms.