Genome-resolved metagenomic analysis reveals different functional potentials of multiple <i>Candidatus</i> Brocadia species in a full-scale swine wastewater treatment system

doi:10.1007/s11783-023-1602-7

Front. Environ. Sci. Eng.

2023, Vol. 17

Issue (1) : 2 https://doi.org/10.1007/s11783-023-1602-7

RESEARCH ARTICLE

Genome-resolved metagenomic analysis reveals different functional potentials of multiple Candidatus Brocadia species in a full-scale swine wastewater treatment system

Yabing Meng^1,^2,³, Depeng Wang^1,^2,³(

), Zhong Yu^1,^2,³, Qingyun Yan^1,^2,³, Zhili He^1,^2,⁴, Fangang Meng^1,^2,³(

)

¹. School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
². Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China
³. National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha 410125, China
⁴. Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China

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Abstract

● Four Ca. Brocadia species were observed during the spontaneously enrichment.

● Novel anammox species SW510 and SW773 dominated the full-scale ecosystem.

● Urease and cyanase genes were detected in the new anammox genomes.

● Functional differentiation potentially facilitated co-occurrence of anammox species.

The increasing application of anammox processes suggests their enormous potential for nitrogen removal in wastewater treatment facilities. However, the functional potentials and ecological differentiation of cooccurring anammox species in complex ecosystems have not been well elucidated. Herein, by utilizing functional reconstruction and comparative genome analysis, we deciphered the cooccurring mechanisms of four Candidatus Brocadia species that were spontaneously enriched in a full-scale swine wastewater treatment system. Phylogenetic analysis indicated that species SW172 and SW745 were closely related to Ca. Brocadia caroliniensis and Ca. Brocadia sapporoensis, respectively, whereas the dominant species SW510 and SW773, with a total average abundance of 34.1%, were classified as novel species of the genus Ca. Brocadia. Functional reconstruction revealed that the novel species SW510 can encode both cytochrome cd₁-type nitrite reductase and hydroxylamine oxidase for nitrite reduction. In contrast, the detected respiratory pentaheme cytochrome c nitrite reductase and acetate kinase genes suggested that SW773 likely reduced nitrite to ammonium with acetate as a carbon source. Intriguingly, the presence of genes encoding urease and cyanase indicated that both novel species can use diverse organic nitrogen compounds in addition to ammonia and nitrite as substrates. Taken together, the recovery and comparative analysis of these anammox genomes expand our understanding of the functional differentiation and cooccurrence of the genus Ca. Brocadia in wastewater treatment systems.

Keywords Anammox Candidatus Brocadia Functional potential Cooccurring mechanisms Swine wastewater treatment facilities

Corresponding Author(s): Depeng Wang,Fangang Meng

Issue Date: 14 July 2022

Cite this article:

Yabing Meng,Depeng Wang,Zhong Yu, et al. Genome-resolved metagenomic analysis reveals different functional potentials of multiple Candidatus Brocadia species in a full-scale swine wastewater treatment system[J]. Front. Environ. Sci. Eng., 2023, 17(1): 2.

URL:

https://academic.hep.com.cn/fese/EN/10.1007/s11783-023-1602-7
https://academic.hep.com.cn/fese/EN/Y2023/V17/I1/2

Fig.1 Phylogeny and similarity between recovered anammox genomes and their closely associated genomes. Phylogenetic tree of anammox bacteria was inferred from the concatenated alignments of 400 most universal makers. The tree was constructed using RAxML, with PROTCATLG as the evolutionary model. The right panel showed the pairwise average nucleotide identities (ANI) (%) between anammox genomes.

Tab.1 Genome characteristics of four Ca. Brocadia genomes obtained in this study

Fig.2 Profile of the nitrogen-cycle genes in these anammox genomes. Point size represents the copy number of functional genes in each Ca. Brocadia genome. The detailed results in the reference genome were collected from the GenBank database and/or references reported.

Fig.3 Phylogenetic analysis and gene loci diagram of cytochrome cd₁-type nitrite reductase (NirS) protein sequences. The nirS gene was only annotated in SW510. The bootstrap values are indicated at the nodes. Color in the gene loci diagram represents the homologous genes. The genes without functional information are identified as hypothetical protein. Genes and noncoding regions are drawn to scale.

Fig.4 Phylogenetic analysis of hydroxylamine oxidase protein sequences in the four anammox genomes. The maximum likelihood phylogenetic tree was constructed using the hydroxylamine oxidase protein sequences identified in the four anammox species and the references collected from the NCBI-NR database. The bootstrap values are indicated at the nodes.

Fig.5 Phylogenetic analysis and gene loci diagram of urease alpha subunit (a, b) and cyanase (c, d) protein sequences. The maximum likelihood phylogenetic tree was constructed using the protein sequences identified in this study with reference sequences collected from the NCBI-NR database. The bootstrap values are indicated at the nodes. Color in the gene loci diagram represents the homologous genes. The genes without functional information are identified as hypothetical protein. Genes and noncoding regions are drawn to scale. The right and left arrows represent the orientation (1) and (–1), respectively.

Fig.6 Overview of functional potentials in the novel anammox bacteria Ca. Brocadia sp. SW510 (a) and Ca. Brocadia sp. SW773 (b). Solid lines indicate genes and pathways detected in the two genomes. The red dotted lines represent genes missing.

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