Abstract
In this study, three metagenome-assembled genomes of a sediment sample were constructed. A Bin1 (JB001) genome was identified as a photo-litho-auto/heterotroph (purple sulfur bacteria) bacterium with the ability to fix nitrogen, tolerate salt, and to produce bacteriochlorophyll a. It has a genome length of 4.1 Mb and a G + C content of 64.9%. Phylogenetic studies based on concatenated 92 core genes and photosynthetic genes (pufLM and bchY) showed that Bin JB001 is related to Thiococcus pfennigii, “Thioflavicoccus mobilis” and to the Lamprocystis purpurea lineage. Bin JB001 and its closely related members were subjected to the genome-based study of phenotypic and phylogenomic analysis. Genomic similarity indices (dDDH and ANI) showed that Bin JB001 could be defined as a novel species. The average amino acid identity (AAI) and percentage of conserved proteins (POCP) values were below 60 and 50%, respectively. The pan-genome analysis indicated that the pan-genome was an open type wherein Bin JB001 had 855 core genes. This study shows that the binned genome, Bin JB001 could represent a novel species of a new genus under the family Chromatiaceae, for which the name “Candidatus Thioaporhodococcus sediminis” gen. nov. sp. nov. is proposed.
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Abbreviations
- APB:
-
Anoxygenic phototrophic bacteria
- MAG:
-
Metagenome assemble genome
- CTAB:
-
Cetyl trimethyl ammonium bromide
- MG-RAST:
-
Metagenomic Rapid Annotations using Subsystems Technology
- RAST:
-
Rapid Annotation using Subsystem Technology
- KEGG:
-
Kyoto Encyclopaedia of Genes and Genomes
- KAAS:
-
KEGG Automatic Annotation Server
- GTDB:
-
Genome Taxonomy Database
- AAI:
-
Average Amino Acid Identity
- cAAI:
-
Core Average Amino Acid Identity
- BPGA:
-
Bacterial Pan-genome Pipeline
- POCP:
-
Percentage of Conserved Proteins
- CAM:
-
Crassulacean Acid Metabolism
- TCA:
-
Tricarboxylic Acid Cycle
- WL:
-
Wood–Ljundahl
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Acknowledgements
We are grateful to Bernhard Schink, University of Konstanz, Germany, and Prof. Aharon Oren (The Hebrew University of Jerusalem) for correcting the protologues.
Funding
Amulya thanks IOE-UoH project for the JRF fellowship, and Anusha thanks DST, Government of India for the award of INSPIRE SRF. Ramana thanks the Department of Biotechnology, Government of India, for the award of Tata Innovation Fellowship and IoE-UoH for the project grant. Financial support received from CSIR is acknowledged. Sasikala thanks UGC for the award of the mid-career grant. Infrastructural facilities funded by DST-FIST (UoH and JNTUH), UGC-SAP (DRS; UoH), TEQIP, and AICTE (from JNTUH) are acknowledged.
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AS designed and planned the studies under the supervision of CS and CVR. AR and AS performed the genomic and phylogenetic analysis and tabulated the data. AR and AR wrote the manuscript. CVR and CS supervised the study and contributed to text preparation and revised the manuscript. All authors read and approved the final version of the manuscript.
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Amulyasai, B., Anusha, R., Sasikala, C. et al. Phylogenomic analysis of a metagenome-assembled genome indicates a new taxon of an anoxygenic phototroph bacterium in the family Chromatiaceae and the proposal of “Candidatus Thioaporhodococcus” gen. nov. Arch Microbiol 204, 688 (2022). https://doi.org/10.1007/s00203-022-03298-7
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DOI: https://doi.org/10.1007/s00203-022-03298-7