Dataset: Subsurface Nitrospirota and Nitrospinota Origins

Name: Subsurface Nitrospirota Origins
Published: 2024-07-22
Keywords: deep biosphere, nitrospirota, nitrospinota, subsurface life, oceans

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Spatial Extent: N:81.82 E:179.06 S:-77.01 W:-176.57

Temporal Extent: 2013-12 - 2024-04

Project:

Microbial activity in the crustal deep biosphere (Slow Life in Crust)

Principal Investigator:

Beth N. Orcutt (Bigelow Laboratory for Ocean Sciences)

Scientist:

Timothy D'Angelo (Bigelow Laboratory for Ocean Sciences)

BCO-DMO Data Manager:

Lynne M. Merchant (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2024-07-22

Restricted:

Validated:

Current State:

Preliminary and in progress

Subsurface Nitrospirota Origins

Abstract:

The phyla Nitrospirota and Nitrospinota have received significant research attention due to their unique mitrogen metabolisms important to biogeochemical and industrial processes. These phyla are common inhabitants of marine and terrestrial subsurface environments and contain members capable of diverse physiologies in addition to nitrite oxidation and complete ammonia oxidation. We used phylogenomics and gene-based analysis with ancestral state reconstruction and gene-tree-species tree reconciliation methods to investigate the life histories of these two phyla. This dataset includes list of previously-published sequence datasets that were used for the analysis. The data and interpretations are published at DOI 10.1038/s41396-023-01397-x.

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Methods & Sampling

Genomic dataset collection, curation and quality control: This study used publicly available genome assemblies. Existing publicly available genome assemblies were downloaded from the National Center for Biotechnology Investigation (NCBI) and the Integrated Microbial Genomes (IMG) database of the U.S. Department of Energy’s Joint Genome Institute in June 2021. The Genome Taxonomy Database (GTDB) website (release 202) was used to access lists of NCBI assembly accession numbers for the following GTDB-assigned phyla: Nitrospinota, Nitrospinota_A (now called Tectomicrobia), Nitrospinota_B, Nitrospirota, Nitrospirota_A (Leptospirilla). The IMG assemblies were found using the same GTDB taxonomy classifier using the search function on the IMG website. IMG metagenome assemblies that were designated as “public” and “published” were also downloaded for these phyla. Duplicate entries between IMG and NCBI were manually removed.

Data Processing Description

Quality control of the assemblies was performed using the CheckM qa workflow (v 1.07) to remove genomes with <50% genome completion and >10% sequence contamination, leaving genomes that fall within the MIMAG categories “medium” (>50% completion, <10% contamination) and “high” (>90% completion, <5% contamination). These resulting genomes were dereplicated with dRep, using default parameters, to remove nearly-identical assemblies. All genomes were then classified using the GTDB-tk classifier tool (v1.5.0, r202). Polyphyletic groups that were once considered a part of Nitrospirota and Nitrospinota (i.e., Nitrospirota_A (Leptospirilla), Nitrospinota_A (Tectomicrobia) and Nitrospinota_B) were included only in the phylogenomic trees. These groups were not included in the gene cluster based functional analyses. All code to recreate these processes are available at https://github.com/ts-dangelo/bioinformatic_scripts_python.

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Funding Sources