Abstract
Rhodocyclales is an abundant bacterial order in wastewater treatment systems and putatively plays key roles in multiple functions. Its phylogenomics, prevalence of denitrifying genes in sub-lineages and distribution in wastewater treatment plants (WWTPs) worldwide have not been well characterized. In the present study, we collected 78 Rhodocyclales genomes, including 17 from type strains, non-type strains and genome bins contributed by this study. Phylogenomics indicated that the order could be divided into five family-level lineages. With only a few exceptions (mostly in Rhodocyclaceae), nirS-containing genomes in this order usually contained the downstream genes of norB and nosZ. Multicopy of denitrifying genes occurred frequently and events of within-order horizontal transfer of denitrifying genes were phylogenetically deduced. The distribution of Rhodocyclaceae, Zoogloeaceae and Azonexaceae in global WWTPs were significantly governed by temperature, mixed liquor suspended solids, etc. Metagenomic survey showed that the order generally ranked at the top or second for different denitrifying genes in wastewater treatment systems. Our results provided comprehensive genomic insights into the phylogeny and features of denitrifying genes of Rhodocyclales. Its contribution to the denitrifying gene pool in WWTPs was proved.
Highlights
Rhodocyclales is an abundant bacterial order in wastewater treatment systems and putatively plays key roles in multiple functions
Consistent with the existing classification result only based on type strains[14], phylogenetic analysis on the basis of 16S rRNA gene sequences supported that the order consisted of four family-level lineages, namely, Rhodocyclaceae, Azonexaceae, Zoogloeaceae and Azovibrio_f (Figs. 1 and S2)
The genus-level phylogeny was consistent with the current taxonomic system in most cases, except for several sequences that were previously defined as Dechloromonas and Azospira
Summary
Rhodocyclales is an abundant bacterial order in wastewater treatment systems and putatively plays key roles in multiple functions. A key functional microbial taxon in wastewater treatment systems is Rhodocyclales, which is dominant in activated sludge samples according to the relative abundance of 16S rRNA genes and hybridization approach[4,5]. Diverse genera in Rhodocyclales can perform special treating functions, such as Candidatus Accumulibacter (Accumulibacter hereinafter) in enhanced biological phosphorus removal (EBPR) bioreactor in which the process of removing phosphorus is enhanced under the alternating appearance of anaerobic and aerobic conditions[6], Zoogloea in formation of bioflocs[7] and Azoarcus and Thauera in the degradation of polycyclic aromatic hydrocarbon[8,9] Many species in this order contributed to denitrification, as depicted by stable isotope probing and fluorescence in situ hybridization coupled with microautoradiography studies[10,11,12]. Our study aimed to reveal the phylogenomics of Rhodocyclales and the distribution and potential weight of denitrification of the order in wastewater treatment
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