Niche Differentiation among Three Closely RelatedCompetibacteraceaeClades at a Full-Scale Activated Sludge Wastewater Treatment Plant and Putative Linkages to Process Performance

Abstract

Multiple clades within a microbial taxon often coexist within natural and engineered environments. Because closely related clades have similar metabolic potential, it is unclear how diversity is sustained and what factors drive niche differentiation. In this study, we retrieved three near-complete Competibacter lineage genomes from activated sludge metagenomes at a full-scale pure oxygen activated sludge wastewater treatment plant. The three genomes represent unique taxa within theCompetibacteraceae. A comparison of the genomes revealed differences in capacity for exopolysaccharide (EPS) biosynthesis, glucose fermentation to lactate, and motility. Using quantitative PCR (qPCR), we monitored these clades over a 2-year period. The clade possessing genes for motility and lacking genes for EPS biosynthesis (CPB_P15) was dominant during periods of suspended solids in the effluent. Further analysis of operational parameters indicate that the dominance of the CPB_P15 clade is associated with low-return activated sludge recycle rates and low wasting rates, conditions that maintain relatively high levels of biomass within the system.IMPORTANCEMembers of the Competibacter lineage are relevant in biotechnology as glycogen-accumulating organisms (GAOs). Here, we document the presence of threeCompetibacteraceaeclades in a full-scale activated sludge wastewater treatment plant and their linkage to specific operational conditions. We find evidence for niche differentiation among the three clades with temporal variability in clade dominance that correlates with operational changes at the treatment plant. Specifically, we observe episodic dominance of a likely motile clade during periods of elevated effluent turbidity, as well as episodic dominance of closely related nonmotile clades that likely enhance floc formation during periods of low effluent turbidity.

Integrated omics analyses reveal differential gene expression and potential for cooperation between denitrifying polyphosphate and glycogen accumulating organisms

“…As illustrated in Fig. S2, GAO1 affiliates with the Competibacter lineage in the family Competibacteraceae , and taxa within the Competibacter lineage are expected to be GAOs (McIlroy et al ., 2014; 2015; Brand et al ., 2019). The putative assignment of this MAG as a GAO is also supported by the high observed transcriptional activity of genes encoding NAD‐dependent glyceraldehyde‐3‐phosphate dehydrogenase (involved in glycogen hydrolysis) and phosphoenolpyruvate carboxykinase and pyruvate phosphate dikinase (involved in glycogen synthesis) respectively (Table S3).…”

“…As illustrated in Fig. S2, GAO1 affiliates with the Competibacter lineage in the family Competibacteraceae, and taxa within the Competibacter lineage are expected to be GAOs (McIlroy et al, 2014;Brand et al, 2019). The putative assignment of this MAG as a GAO is also supported by the high observed transcriptional activity of genes encoding NAD-dependent glyceraldehyde-3-phosphate dehydrogenase (involved in glycogen hydrolysis) and phosphoenolpyruvate carboxykinase and pyruvate phosphate dikinase (involved in glycogen synthesis) respectively The tree includes ppk1 genes extracted from four available Type 1 genomes and three draft genomes from this reactor (sequence names in red; Acc-IF obtained in the study, Acc-IC and Acc-IA from our previous work (Gao et al, 2019)), ppk1 gene sequences obtained via cloning and sequencing (labelled in dark violet), ppk1 gene sequences identified in metagenomic contigs assembled in this study (labelled in pink), and ppk1 reference gene sequences from NCBI (labelled in black).…”

The effect of circular soil biosolarization treatment on the physiology, metabolomics, and microbiome of tomato plants under certain abiotic stresses

“…Tertiaricarbonis species negative correlation in this study with fruit weights and number, total brix and plant weight is interesting as it is not known to be related to soil stress or as a negative indication for soil conditions or for plant growth. Tertiaricarbonis is usually coming from aquatic systems ( Chen et al., 2018 ; Brand et al., 2019 ) and is worth an additional study to see if it has a role in SBS systems. The result of the correlation between the microbiome and the plant characteristics in this study suggest that the soil microbiome has a significant impact on the plant growth performance in tomato CSBS treatments.…”

Bacterial communities in sediments of an urban wetland in Bogota, Colombia

“…The dominant nosZ-type sequence in SML wetland sediments was Candidatus Competibacter denitrificans, obtained previously from laboratory-scale enrichment reactors through metagenomics [57]. Competibacter members present varying capabilities to assimilate thymidine, ferment glucose, produce exopolysaccharide, accumulate glycogen, and metabolize PHA and volatile fatty acids [57,58]. However, a genomic analysis of the species Candidatus C. denitrificans indicates its potential for full denitrification to nitrogen [57].…”