Metagenome Assembled Genomes (MAG) Facilitate a Better Understanding of Microbially-mediated Heavy Metal Resistance in Soils from a Former Nuclear Materials Production Facility DOI Open Access

Navya Kommu,

Paul Stothard,

Christian Chukwujindu

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Oct. 23, 2023

Abstract Shotgun metagenomes is a repository of all the genes present in an environmental sample. With recent advancements bioinformatic techniques, it now possible to in-silico retrieve sequences that belong specific taxa, followed by assembly and annotation obtained are called as metagenome-assembled genome (MAG), which facilitates better understanding metabolic other traits without having culture microorganism. We applied MAG technique using nf-core/mag pipeline on shotgun metagenome from soil ecosystem has long-term co-contamination with radionuclides (mainly uranium), heavy metals (mercury, nickel etc.) organic compounds. Annotation MAGs was performed SPAdes MEGAHIT genomes were binned taxonomically classified GTDBTk CAT toolkits within nf-core/mag. Additional annotations done Prokka Prodigal dRep program used choose for further analysis. Initial analysis resulted total 254 met high-quality standard completeness > 95% contamination < 5%, accounting 26.67% (Fig SI-1). After bin refinement de-replication, 27 (18 Winter season 9 Summer season) reconstructed. These span across 6 bacterial phyla most predominant ones Proteobacteria, Bacteroidetes, Cyanobacteria regardless season. Overall, Arthrobacter found be one robust Over 1749 putatively involved crucial metabolism elements viz. nitrogen, phosphorous, sulfur 598 encoding enzymes resistance cadmium, zinc, chromium, arsenic copper. In summary, this project enhances our conferring uranium contaminated soils.

Language: Английский

Copper and cadmium co-contamination increases the risk of nitrogen loss in red paddy soils DOI
Yifan Guo, Shulan Cheng, Huajun Fang

et al.

Journal of Hazardous Materials, Journal Year: 2024, Volume and Issue: 479, P. 135626 - 135626

Published: Aug. 24, 2024

Language: Английский

Citations

6
Internal Transcribed Spacers Enable Species-Level Metataxonomic Analysis of Ciliated Protozoa DOI Creative Commons
Sripoorna Somasundaram, Zhongtang Yu

ISME Communications, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 11, 2025

Traditional morphology-based ciliate classification is often time-consuming and inaccurate, necessitating molecular approaches. Although 18S rRNA gene sequencing widely used for taxonomic analyses of ciliates, its high degree conservation makes it challenging to achieve species-level resolution. This study explores the potential internal transcribed spacers (ITS1 ITS2) 28S improve resolution beyond that offered by in free-living host-associated ciliates. A comparative analysis ITS, 18S, sequences retrieved from public databases indicated ITS regions exhibit greater inter- intra-specific sequence dissimilarity compared gene, supporting existing literature. We then designed universal primers targeting freshwater rumen These were rigorously evaluated their inclusiveness, specificity, amplification efficiency using in-silico PCR, experimental followed metataxonomic communities. In-silico revealed inclusiveness exceeding 80%, while validated specificity. Metataxonomic ciliates demonstrated captured significantly diversity than gene. Also, ITS1 superior detecting most species went unnoticed findings underscore superiority ITS1, a lesser extent ITS2, as markers enhancing recommend an alternative marker overcome limitations gene-based approaches taxonomy.

Language: Английский

Citations

0
Arsenic and its associated metabolism genes in Chinese soils: a comprehensive investigation of mine and paddy soils DOI
Yuting Lin,

Ruilian Yu,

Gongren Hu

et al.

Journal of Soils and Sediments, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 14, 2025

Language: Английский

Citations

0
Shotgun and Hi-C Sequencing Datasets for Binning Wheat Rhizosphere Microbiome DOI Creative Commons
Roshan Regmi, Jonathan P. Anderson,

Lauren Burgess

et al.

Scientific Data, Journal Year: 2025, Volume and Issue: 12(1)

Published: March 1, 2025

Abstract Binning is a crucial process in metagenomics studies, where sequenced reads are combined to form longer contigs and assigned individual genomes. Conventional methods, such as shotgun binning, rely on similarity measurements abundance profiles across multiple samples. However, cost constraints for sequencing limited sample collection capacity hinder their effectiveness. High-throughput chromosome conformation capture (Hi-C), DNA proximity ligation technique, has been adapted accurately bin metagenome-assembled genomes (MAGs) from single sample, addressing challenges like chimeric MAGs. In this study, we generated over 190 Gb of metagenomic data wheat rhizospheres grown two highly calcareous soils South Australian region compared conventional Hi-C binning methods. Two metagenomes libraries were generated, assembling 1089 MAGs 39 bacterial one archaeal taxon, including 94 based bins. performed using only short read sequences was prone high contamination, while the addition improved MAG quality identified mobile element-host-infection interaction. This dataset provides important tools studying microbial communities rhizosphere soils.

Language: Английский

Citations

0
Metagenomic Insights into the Bacterial Community Dynamics in Metal-Contaminated Rhizosphere DOI Open Access
Naresh Kaushik, Ranganathaswamy Madihalli Kenchappa, A Geetha Bhavani

et al.

Natural and Engineering Sciences, Journal Year: 2025, Volume and Issue: 10(1), P. 507 - 518

Published: April 1, 2025

Soil contamination with heavy metals, particularly in rhizosphere regions, presents significant environmental and ecological challenges. Diverse bacterial communities found the rhizosphere, small area of soil that is impacted by plant roots, are critical for metal detoxification, organic matter breakdown, nutrient cycling. This research investigates community dynamics Cu (copper)-contaminated Elsholtzia splendens. Using metagenomic analysis, 28 phyla were identified, 7 dominant contaminated soils. The composition diversity to be most significantly influenced pH out all parameters examined, including concentration, Total Organic Carbon (TOC), total nitrogen, pH, moisture content, temperature, texture. Changes microbial those can efficiently evaluated using Bray-Curtis dissimilarity, which used quantify differences between based on species abundance. findings reveal taxonomic composition; Proteobacteria was abundant phylum, constituting 45.2% Furthermore, Firmicutes increased from 18.3% 22.1% soils, while Pseudomonas abundance rose 11.5% 18.3%. Metagenomic profiling also revealed functional gene pathways associated tolerance related copper efflux oxidative stress responses, more prevalent highlights functions metal-contaminated rhizospheres, enhancing understanding adaptation bioremediation potential.

Language: Английский

Citations

0
Keystone taxa enhance the stability of soil bacterial communities and multifunctionality under steelworks disturbance DOI

Huizhen Chao,

Anjuan Cai,

Bastian Heimburger

et al.

Journal of Environmental Management, Journal Year: 2024, Volume and Issue: 356, P. 120664 - 120664

Published: March 20, 2024

Language: Английский

Citations

3
Internal Transcribed Spacers as Phylogenetic Markers Enable Species-level Metataxonomic Analysis of Ciliated Protozoa DOI Open Access
Sripoorna Somasundaram, Zhongtang Yu

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 7, 2024

Abstract Background The conventional morphology-based classification of ciliates is often inaccurate and time-consuming. To address this issue, sequencing, analysis the 18S rRNA gene have been used as an alternative. However, method has limitations because highly conserved nature makes it challenging to achieve species-level resolution. This study assesses capability two internal transcribed spacers, ITS1 ITS2, along with 28S gene, enhance taxonomic resolution beyond that offered by in free-living host-associated ciliates. Results We compared sequences ITSI, genes downloaded from public databases found ITS2 are more divergent at both inter- intra-specific levels than gene. designed universal primers specific ITS regions for rumen then systematically evaluated these using - silico analysis, PCR assays, metataxonomic or metabarcoding them primers. new inclusive, inclusiveness rate over 80% based on confirmed their specificity evaluation. validated metagenomic DNA freshwater samples samples. Our demonstrated could reveal greater ciliate diversity environments. In particular, detected highest number species, including species genera were not Conclusions regions, particularly ITS1, offer superior resolution, NCBI RefSeq database allows be classified. Therefore, a lesser extent recommended enhancing communities

Language: Английский

Citations

1
Utilizing a Metagenome Assembled Genome Approach Revealed Further Insights into Microbially Mediated Heavy-Metal Resistance in Soils from a Former Nuclear Materials Production Facility DOI Creative Commons

Navya Kommu,

Paul Stothard,

Christian Chukwujindu

et al.

Applied Microbiology, Journal Year: 2024, Volume and Issue: 4(1), P. 376 - 389

Published: Feb. 13, 2024

Soils and sediments from the Savannah River Site (SRS), located in USA are known to have a long history of co-contamination with radionuclides (mainly uranium) heavy metals. To better understand bacterial taxonomic genomic characteristic SRS soil habitat, shotgun metagenomes were obtained three different levels contaminated soil—high, medium, low. Sequences then assembled annotated generate metagenome-assembled genomes (MAGs) using toolkits within nf-core/mag. The initial analysis resulted total 254 MAGs. After bin refinement de-replication, 55 MAGs which met quality standard completeness > 75% contamination < 25%, accounting for 21.67% all MAGs, reconstructed. Further 90% 10% yielded 24 (18 winter season 6 summer season) spanning phyla, predominantly Actinomycetota, Proteobacteriota, Bacteroidota, Cyanobacteria. Overall, Arthrobacter MAG was found be robust further analysis, over 1749 genes putatively involved crucial metabolism elements viz. nitrogen, phosphorous, sulfur, 598 encoding enzymes resistance metals including cadmium, zinc, chromium, arsenic, copper. In summary, this project enhances our understanding conferring uranium-contaminated soils.

Language: Английский

Citations

1
Recent Advances Towards Improved Microbial Bioremediation of Heavy Metal Pollution DOI

Farzaneh Dianatdar,

Zahra Etemadifar

Earth and environmental sciences library, Journal Year: 2024, Volume and Issue: unknown, P. 115 - 138

Published: Jan. 1, 2024

Language: Английский

Citations

1
Distribution, characterization, and evolution of heavy metal resistance genes and Tn7-like associated heavy metal resistance Gene Island of Burkholderia DOI Creative Commons

Yanhong Lan,

Meijia Liu,

Yao Song

et al.

Frontiers in Microbiology, Journal Year: 2023, Volume and Issue: 14

Published: Nov. 23, 2023

Burkholderia is a rod-shaped aerobic Gram-negative bacteria with considerable genetic and metabolic diversity, which can beused for bioremediation production applications, has great biotechnology potential. However, there are few studies on the heavy metal resistance of genus.In this paper, distribution, characteristics evolution genes in gene island Tn7-like transposable element associated were studied by comparative genomic method based resistance.The classification status some species genus was improved, it found that dabaoshanensis novacaledonica do not belong to genus.Secondly, genomics pan-genome analysis core genome alarger proportion greater variety metalresistance than subsidiary strain specific genes. Heavy mostly distributed form various clusters (for example, mer clusters, ars czc/cusABC clusters). At same time, transposase, recombinase, integrase other foundupstream downstream indicating may beobtained through horizontal transfer. The natural selection pressure showed experienced strong purification under genome.The Tn7 like island, large number insertion events genomes. BGI islands related found, these only cepacia, polyvora, contaminant.

Language: Английский

Citations

3