Complete Genome Sequence of Bacillus safensis Strain 3A, a Heavy Metal-Resistant Bacterium Isolated from Contaminated Estuarine Sediment in Brazil

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Abstract

Bacillus safensis 3A was isolated from a contaminated estuarine sediment sample with mine tailing from the Samarco dam disaster, which occurred in 2015 in Minas Gerais State, Brazil. We report here a draft genome sequence (3.6 Mb) of this bacterial strain. B. safensis exhibited strong resistance to heavy metals.

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Most cited references 13

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Basic local alignment search tool.

Stephen F Altschul, Warren Gish, Webb Miller … (1990)

A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.

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fastp: an ultra-fast all-in-one FASTQ preprocessor

Shifu Chen, Yanqing Zhou, Yaru Chen … (2018)

Abstract Motivation Quality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a different tool is used for each operation, such as quality control, adapter trimming and quality filtering. These tools are often insufficiently fast as most are developed using high-level programming languages (e.g. Python and Java) and provide limited multi-threading support. Reading and loading data multiple times also renders preprocessing slow and I/O inefficient. Results We developed fastp as an ultra-fast FASTQ preprocessor with useful quality control and data-filtering features. It can perform quality control, adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of the FASTQ data. This tool is developed in C++ and has multi-threading support. Based on our evaluation, fastp is 2–5 times faster than other FASTQ preprocessing tools such as Trimmomatic or Cutadapt despite performing far more operations than similar tools. Availability and implementation The open-source code and corresponding instructions are available at https://github.com/OpenGene/fastp.

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CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

Donovan Parks, Michael Imelfort, Connor Skennerton … (2015)

Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. Although this increasing breadth of draft genomes is providing key information regarding the evolutionary and functional diversity of microbial life, it has become impractical to finish all available reference genomes. Making robust biological inferences from draft genomes requires accurate estimates of their completeness and contamination. Current methods for assessing genome quality are ad hoc and generally make use of a limited number of “marker” genes conserved across all bacterial or archaeal genomes. Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. We demonstrate the effectiveness of CheckM using synthetic data and a wide range of isolate-, single-cell-, and metagenome-derived genomes. CheckM is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches. Using CheckM, we identify a diverse range of errors currently impacting publicly available isolate genomes and demonstrate that genomes obtained from single cells and metagenomic data vary substantially in quality. In order to facilitate the use of draft genomes, we propose an objective measure of genome quality that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities.

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Author and article information

Contributors

John J. Dennehy: Role: Editor

Journal

Journal ID (nlm-ta): Microbiol Resour Announc

Journal ID (iso-abbrev): Microbiol Resour Announc

Journal ID (hwp): ga

Journal ID (pmc): mra

Journal ID (publisher-id): MRA

Title: Microbiology Resource Announcements

Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )

ISSN (Electronic): 2576-098X

Publication date (Electronic): 22 April 2021

Publication date Collection: April 2021

Volume: 10

Issue: 16

Electronic Location Identifier: e00268-21

Affiliations

[a ]Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, São Paulo, Brazil

[b ]Laboratorio de Biologia Molecular Aplicada, Centro de Excelencia en Medicina Traslacional, Universidad de La Frontera, Temuco, Chile

[c ]Universidade Federal do Espírito Santo, Vitória, Brazil

[d ]Centro de Investigación en Biotecnologia, Instituto Tecnológico de Costa Rica, Cartago, Costa Rica

Queens College CUNY

Author notes

Address correspondence to Kattia Núñez-Montero, knunez@ 123456itcr.ac.cr .

Citation Defalco T, Vasconcelos ALS, Dias ACF, Barrientos L, Bernardino ÂF, Andreote FD, Núñez-Montero K. 2021. Complete genome sequence of Bacillus safensis strain 3A, a heavy metal-resistant bacterium isolated from contaminated estuarine sediment in Brazil. Microbiol Resour Announc 10:e00268-21. https://doi.org/10.1128/MRA.00268-21.

Author information

Kattia Núñez-Montero https://orcid.org/0000-0002-8629-5107

Article

Publisher ID: MRA00268-21

DOI: 10.1128/MRA.00268-21

PMC ID: 8063649

PubMed ID: 33888506

SO-VID: 17989eb0-fa21-44f5-b3d4-22975d20bbae

License:

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

History

Date received : 10 March 2021

Date accepted : 30 March 2021

Page count

Figures: 0, Tables: 0, Equations: 0, References: 13, Pages: 2, Words: 1335

Funding

Funded by: Institut chilien de l'Antarctique (INACH), https://doi.org/10.13039/501100015634;

Award ID: INACH DG_01-19

Award Recipient : Kattia Núñez-Montero

Funded by: Universidad de La Frontera (UFRO), https://doi.org/10.13039/501100005916;

Award ID: DI20-2018

Award Recipient : Leticia Barrientos

Funded by: Network for Extreme Environment Research (NEXER);

Award ID: NXR17-0003

Award Recipient : Leticia Barrientos

Funded by: Agencia Nacional de Investigacion y Desarrollo, Chile (ANID);

Award ID: CONICYT-PFCHA/Doctorado Nacional/2017‒21170263

Award Recipient : Kattia Núñez-Montero

Funded by: Fundação de Amparo à Pesquisa e Inovação do Espírito Santo;

Award ID: FAPES/CNPq/CAPES Rio Doce 77683544/2017

Award Recipient : Angelo F. Bernardino

Funded by: Coordenação de Aperfeiçoamento de Pessoal de Nível Superior;

Award ID: CAPES/PRINT 88887.370137/2019-00

Award Recipient : Ana Luisa Soares Vasconcelos

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cover-date April 2021

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Complete Genome Sequence of Bacillus safensis Strain 3A, a Heavy Metal-Resistant Bacterium Isolated from Contaminated Estuarine Sediment in Brazil

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SciELO Brazil

Most cited references 13

Basic local alignment search tool.

fastp: an ultra-fast all-in-one FASTQ preprocessor

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

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Affiliations

Author notes

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