Genomic sequence data of Thiohalocapsa marina: a sulfur-oxidizing bacterium prevalent in treated municipal wastewater and commercial shrimp hatchery effluents

Abstract

Objectives

This study highlighted the gap in the genetic characterization of marine bacteria, specifically within the genus Thiohalocapsa. This genus thrives in contaminated environments with high concentrations of sulfide, such as treated municipal wastewater. Thc. marina is a phototrophic purple bacterium known for its role in sulfur oxidation and bioremediation in marine aquaculture systems. To date, only one Thc. marina genome has been published in the GenBank database. This study enhances the understanding of the ecological adaptation and bioremediation capabilities of Thc. marina in treated municipal wastewater effluents.

Data description

We present a draft genome of Thc. marina LNA26 recovered from treated municipal wastewater effluents using shotgun metagenomic sequencing. The genome of Thc. marina LNA26 harbors 4,356,720 bp and contains 4,032 genes (3,936 CDSs, 50 RNA genes, and 46 pseudogenes), some of them involved in sporulation, siderophores biosynthesis, arsenate bioremediation, sulfide metabolism, capacity for nitrogen fixation, the biosynthesis of PHA, and NHPL bacteriocins. Thc. marina LNA26 exhibits 3 CRISPR Arrays and a high abundance of COGs in signal transduction, energy production, and cell wall biogenesis, indicating advanced environmental responsiveness, energy efficiency, and cellular robustness.

Objective

Phototrophic purple bacteria play a critical role in maintaining ecosystem health, particularly in those environments contaminated with high concentrations of sulfide, such as treated municipal wastewater effluents [1]. Despite their importance, there has been limited genetic characterization of marine bacteria from these environments, particularly within the Thiohalocapsa genus [2].

Thc. marina is a phototrophic purple bacterium first isolated from anoxic sediment and water [3], where it plays an important role in carbon and nitrogen cycling, contributing to efficient bioremediation in shrimp culture ponds [4]. Unpublished data from our ongoing research indicates that Thc. marina is also prevalent in P. vannamei postlarvae and hatchery effluents. This fact suggests that Thc. marina could be playing a crucial role in improving water quality and nutrient management in aquaculture environments.

In addition, Thc. marina is a promising candidate for energy capture and resource recovery in the biological oxidation of sulfur in wastewater treatments, particularly due to the production of PHA [1]. These biological characteristics make it of great interest to search for genes with a wide range of biotechnological applications. However, to date, only one Thc. marina bacterial genome has been published [5]. We present herein the draft genome sequence of Thc. marina LNA26, which is the first genomic report of Thc. marina recovered from treated municipal wastewater using shotgun metagenomics. The data collected from the Thc. marina LNA26 genome enhances the understanding of the ecological adaptation, evolution, phylogenetics, and biological mechanisms for wastewater bioremediation.

Data description

A water microbiome study along a channel where effluents from treated municipal wastewater and commercial P. vannamei hatcheries converge was conducted. Approximately 500 mL of each effluent and the channel was filtered through 0.45-micron and 0.22-micron membranes, and an additional 500 mL was used for water quality analysis. Thc. marina LNA26 was identified in the treated municipal wastewater, prompting the measurement of key parameters, including salinity (5.00 g/L), dissolved oxygen concentration (0.26 mg·L⁻¹), and pH (7.92) were measured using a portable multi-meter (Hach HQ Series, Hach, Germany). In addition, the concentrations of nitrate (NO₃⁻—N = 0.1 mg·L⁻¹), nitrite (NO₂⁻—N = 0.3 mg·L⁻¹), and ammonia (NH₄⁺—N = 2.2 mg·L⁻¹) were determined according to a published protocol [6]. The membranes were pulverized in liquid nitrogen for subsequent DNA extraction. The gDNA was extracted using a Quick-DNA Fecal/Soil Microbe Miniprep Kit (Zymo Research, USA), and the quality and concentration were evaluated using a Denovix DS-11 spectrophotometer (Denovix Inc., USA). Shotgun library preparation and sequencing were performed by Novogene Inc. (Sacramento, USA) using the Illumina NovaSeq PE150 platform. The generated data (raw sequence reads) have been deposited at SRA-NCBI under accession number SRR30726425 (Table 1, Data set 1).

Table 1 Overview of data files/data sets

Metagenome analysis was conducted using the SqueezeMeta pipeline v1.6.4 [7] in coassembly mode with Megahit v1.2.9 [8]. After binning with DAS tool [9], the genome of Thc. marina LNA26 was reconstructed from the municipal wastewater samples. In addition, LNA26 was identified as one of the most abundant MAGs in the microbiome of treated wastewater effluent compared to hatchery effluent and channel. The quality assessment genome was performed using CheckM v1.1.6 [10] and annotation with the NCBI PGAP [11]. A circular genomic map (Data file 1, Fig. 1a) was constructed using Genovi [12]. The bacterium was identified as Thc. marina based on the taxonomic classification system of Kraken v2.0 [13] and 16S rRNA gene sequence homology using BLAST [14]. Thc. marina LNA26 showed an average nucleotide identity of 99.62% with the reference genome of Thc. marina DSM 19078 (Genbank GCA_008632335.1) using fastANI v1.3.3 [15].

Fig. 1

Genome representation of Thiohalocapsa marina LNA26. a) Genome map: circles from inside to outside: GC skew, GC content, rRNA, tRNA, negative CDS, and positive CDS. Genes are colored according to their function. b) Distribution of clusters of orthologous groups of proteins (COGs) of Thc. marina LNA26. Each COG, grouping the coding sequences (CDSs), was involved in a category from A to Z

The Thc. marina LNA26 genome possesses 4,356,720 bp in 139 contigs (Data file 1, Fig. 1a), with a completeness of 96.92%, a GC content of 66.38%, and an average read coverage of 139 x (Data set 2). Homology-based gene prediction identified a total of 4,032 genes, with 3,936 CDSs (3 CRISPR Arrays), 50 RNA genes (45 tRNA; 1 rRNA; 4 ncRNA), and 46 pseudogenes. Several genes encoding enzymes involved in sporulation, siderophores biosynthesis, arsenate bioremediation, sulfide metabolism, capacity for nitrogen fixation, and the biosynthesis of NHPL bacteriocins were detected. Thc. marina LNA26 shows high COG abundance in signal transduction, energy production, and cell wall biogenesis (Data file 1, Fig. 1b).

A genome-based phylogenomic analysis was performed (Data file 2, Fig. 2) using TYGS [16]. Nomenclature information was obtained from LPSN (available at https://lpsn.dsmz.de) [17]. The Thc. marina LNA26 genome was matched to all type strain genomes available in the TYGS database using the MASH algorithm [18], and the ten strains with the smallest MASH distances were chosen and calculated using the GBDP method.

Fig. 2

Phylogenetic tree of Thiohalocapsa marina genomes, including the Thc. marina LNA26 and related species

Limitations

The genomic data of Thiohalocapsa marina LNA26 was obtained through metagenomic shotgun sequencing from municipal wastewater samples, which are inherently complex and contaminated environments. These conditions may introduce challenges in accurately delineating the genomic characteristics and ecological roles of bacterium due to potential contamination and the presence of diverse microbial communities. Additionally, the complexity of the wastewater environment could complicate the functional annotation and interpretation of the genomic data, requiring cautious analysis and validation of inferred metabolic pathways and interactions.