Phylogenomics of Rhodocyclales and its distribution in wastewater treatment systems

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), nirScontaining 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.

Nitrogeniibacter aestuarii sp. nov., a Novel Nitrogen-Fixing Bacterium Affiliated to the Family Zoogloeaceae and Phylogeny of the Family Zoogloeaceae Revisited

“…Thus, the members should be considered to belong to the family Zoogloeaceae . Our analysis did not support the proposal of Uliginosibacterium as an independent family ( Wang et al, 2020 ). Compared to POCP values, AAI values demonstrated certain advantages to delineate the genus boundary of the members of the Zoogloeaceae ( Figure 4 ).…”

“…A total of 277 genomes affiliated to the order Rhodocyclales that meet the above standards were used in the phylogenomic analysis. Compared to the 78 and 92 genomes analyzed in phylogenomic studies of the order Rhodocyclales by Wang et al (2020) and Liao et al (2021) , respectively, our study further expanded the known phylogenetic groups within the order Rhodocyclales . The described species account for a minor part of the phylogenomic tree, indicating that majority of the members of Rhodocyclales are still waiting to be cultivated ( Figure 2 ).…”

“…2 With the advance of next-generation sequencing (NGS) and methods of constructing metagenomic-centric genomes and single-cell genomes used for uncultivated bacteria ( Rinke et al, 2013 ; Parks et al, 2018 ; Lapidus and Korobeynikov, 2021 ), a large number of genomes affiliated to the family Zoogloeaceae and the order Rhodocyclales were obtained and released publically in the Genome portal of GenBank. These genomes were obtained from various habitats including wastewater, soil, sediment, and freshwater ( Wang et al, 2020 ). The genomes of uncultivated Zoogloeaceae members expanded our knowledge on their ecological niches and phylogenetic diversity.…”

Nitrogeniibacter mangrovi gen. nov., sp. nov., a novel anaerobic and aerobic denitrifying betaproteobacterium and reclassification of Azoarcus pumilus as Aromatoleum pumilum comb. nov.

“…Denitrifying bacteria can reduce nitrate to nitrogen through a four-step reaction, facilitating the global nitrogen cycle [8]. Through analysis of metagenomes and 16S rRNA gene amplicons [9, 10], an increasing body of research has revealed that the order Rhodocyclales is distributed in global wastewater treatment plants (WWTPs), of which Zoogloeaceae is the major denitrifier used for reducing the risk of nitrate contamination in WWTPs [11, 12]. Additionally, most of the Zoogloeaceae , such as the species Aromatoleum evansii and Aromatoleum aromaticum [2], can degrade aromatic compounds in anaerobic environments using nitrate as the electron acceptor.…”

Bacterial Community Structure and Dynamic Changes in Different Functional Areas of a Piggery Wastewater Treatment System

“…The increase in Comamonadaceae levels in the aerobic zone of the piggery's wastewater treatment system observed in this study confirmed this conclusion. Wang et al and Xin et al used metagenomic studies to show that Rhodophyta plays a leading role in denitrification in wastewater treatment systems [40,41]; different genera of Rhodocyclaceae have special treatment functions. For example, the studies of McIlroy et al and Li et al showed that Rhodocyclaceae appears alternately in the enhanced biological phosphorus removal (EBPR) bioreactor under anaerobic and aerobic conditions to enhance the phosphorus removal effect [42,43].…”