Genomic Characteristics of a Novel Species of Ammonia-Oxidizing Archaea from the Jiulong River Estuary

Abstract

<jats:p>Ammonia-oxidizing archaea (AOA) are ubiquitous in diverse ecosystems, and play a pivotal role in global nitrogen and carbon cycling. Although AOA diversity and distribution are widely studied mainly based on the <jats:italic>amoA</jats:italic> (alpha subunit of ammonia monooxygenase) genotypes, only limited investigations addressed the relationship between AOA genetic adaptation, metabolic features, and ecological niches, especially in estuaries. Here, we have described the AOA communities along the Jiulong River Estuary in Southern China. Nine high-quality AOA metagenome-assembled genomes (MAGs) were obtained by metagenomics. Five of the MAGs are proposed to constitute a new species, <jats:italic>Ca</jats:italic>. Nitrosopumilus aestuariumsis sp. nov., based on the phylogenies of the 16S–23S rRNA genes and concatenated ribosomal proteins, as well as the average amino acid identity. Comparative genomic analysis revealed unique features of the new species, including a high number of genes related to diverse carbohydrate-active enzymes, phosphatases, heavy metal transport systems, flagellation, and chemotaxis. These genes may be crucial for AOA adaptation to the eutrophic and heavy metal-contaminated Jiulong River Estuary. The uncovered detailed genomic characteristics of the new estuarine AOA species highlights AOA contribution to ammonia oxidation in the Jiulong River Estuary.</jats:p> <jats:p><jats:bold>IMPORTANCE</jats:bold> In this study, AOA communities along a river of Southern China were characterized and metagenome-assembled genomes (MAGs) of a novel AOA clade were also obtained. Based on the characterization of AOA genomes, this study suggested adaptation of the novel AOAs to estuarine environments, providing new information for ecology of estuarine AOA and nitrogen cycle in contaminated estuarine environments.</jats:p>

Comparative genomic analysis reveals metabolic flexibility of Woesearchaeota

“…DNA extraction was performed with PowerMax soil kit (Qiagen) as per the manufacturer’s instructions. The DNA fragments were purified, end-repaired, poly(A) tailed, and ligated with Illumina-compatible adapters prior to sequencing as described in Zou et al 46 . Shotgun sequencing was performed using the Illumina HiSeq 2000 (San Diego, California, U.S.) PE150.…”

Community, Distribution, and Ecological Roles of Estuarine Archaea

“…Accordingly, estuarine AOA reportedly have many genes related to phosphate transport and regulation systems related to phosphate acquisition ( Mosier et al, 2012b ; Zou et al, 2019 ). Alternatively, they may utilize diverse types of phosphorus sources by using polyphosphate enzymes and phosphatases ( Qin et al, 2020 ; Zou et al, 2020a ). In eutrophic estuaries, such as the Pearl River Estuary and the Jiulong River Estuary, AOA genomes encode extra genes involved in heavy metal transport and regulation systems, and carbohydrate metabolisms, which may be important strategies to adapt the eutrophication and heavy metal pollution in these estuaries ( Zou et al, 2019 , 2020a ).…”

Meta-Ribosomalomics: RNA Sequencing Is an Unbiased Method for Parasite Detection of Different Sample Types

“…In the above-mentioned examples, the generic meta-ribosomalomics approach was promising for diagnostics of typical but also neglected parasites and gut protists (e.g., Wylezich et al, 2019a , b , 2020 ). In addition, ribosomal gene sequences can be retrieved from DNA-based metagenomics datasets as shown for a novel species of ammonia-oxidizing Archaea ( Zou et al, 2020 ). Regarding parasite characterization, missing well-curated reference genomes hamper correct read assignments and often deliver false-positive hits (e.g., Wylezich et al, 2019a ).…”

“…• The possibility of quantification of detected taxa via found reads needs to be evaluated DNA-based metagenomics was used to investigate archaeal communities in a river estuary (Zou et al, 2020). Several genomes of ammonia-oxidizing Archaea were assembled from shotgun metagenomics datasets.…”