Identifying local associations in biological time series: algorithms, statistical significance, and applications DOI
Dongmei Ai, Lulu Chen,

Jiemin Xie

et al.

Briefings in Bioinformatics, Journal Year: 2023, Volume and Issue: 24(6)

Published: Sept. 22, 2023

Abstract Local associations refer to spatial–temporal correlations that emerge from the biological realm, such as time-dependent gene co-expression or seasonal interactions between microbes. One can reveal intricate dynamics and inherent of systems by examining time series data for these associations. To accomplish this goal, local similarity analysis algorithms statistical methods facilitate alignment assess significance resulting alignments have been developed. Although were initially devised expression microarrays, they adapted accelerated multi-omics next generation sequencing datasets, achieving high scientific impact. In review, we present an overview historical developments recent advances algorithms, their properties, real applications in analyzing data. The benchmark scripts used review are freely available at http://github.com/labxscut/lsareview.

Language: Английский

Comprehensive analysis of heavy metal soil contamination in mining Environments: Impacts, monitoring Techniques, and remediation strategies DOI Creative Commons
Atoosa Haghighizadeh,

Omid Rajabi,

Arman Nezarat

et al.

Arabian Journal of Chemistry, Journal Year: 2024, Volume and Issue: 17(6), P. 105777 - 105777

Published: April 5, 2024

Soil contamination by lead, zinc, iron, manganese, and copper is a widespread environmental issue associated with the mining industry. Primary sources include activities, production processing operations, waste disposal management practices, atmospheric sediments. degradation, water pollution impacting aquatic ecosystems, plant absorption leading to agricultural product contamination, health risks exposure copper, along effects on fauna biodiversity, constitute primary impacts of contamination. In this study, diverse sampling analysis methods, geographic information systems, remote sensing techniques are investigated for monitoring assessing soil these metals. modification techniques, phytoremediation, other strategies reduction considered among most crucial, alongside protection risk strategies. Finally, article explores innovative methods solutions mineral remediation, application green chemistry sustainable practices in industry, utilization artificial intelligence controlling heavy metal ion pollution.

Language: Английский

Citations

63
Phytoremediaton Strategies for Co-Contaminated Soils: Overcoming Challenges, Enhancing Efficiency, and Exploring Future Advancements and Innovations DOI Open Access
Yun-Yeong Lee, Kyung‐Suk Cho, Jung-Mann Yun

et al.

Processes, Journal Year: 2025, Volume and Issue: 13(1), P. 132 - 132

Published: Jan. 6, 2025

Soils co-contaminated with petroleum hydrocarbons (PHs) and heavy metals pose significant challenges, such as reduced bioavailability of pollutants, toxic effects on soil microorganisms, unpredictable chemical interactions. These complex interactions hinder effective remediation. Phytoremediation, which utilizes plant microbial processes, offers a sustainable eco-friendly approach. However, its effectiveness is often constrained by the intricate interplay among PHs, metals, components, complicates pollutant degradation activity. This review explores between enhancement strategies, including amendments, growth-promoting bacteria (PGPB), genetic engineering, can synergistically enhance remediation efficiency. Key challenges include competition for adsorption sites contaminants, community disruptions, environmental variability. Moreover, limitations these their reliance specific species, sensitivity to variability, necessity long-term monitoring, are discussed. The proposed solutions focus integrating emerging technologies interdisciplinary approaches overcome improve removal Future advancements in approaches, biological techniques technological innovations, highlighted key addressing complexities environments improving

Language: Английский

Citations

1
Rhizosphere microbiome of plants used in phytoremediation of mine tailing dams DOI
Emmanuel Tetteh Doku, Augustina Angelina Sylverken, Ebenezer J. D. Belford

et al.

International Journal of Phytoremediation, Journal Year: 2024, Volume and Issue: 26(8), P. 1212 - 1220

Published: Jan. 12, 2024

Rhizospheric microbial communities improve the effectiveness of hyperaccumulators in phytoremediation heavy metals. However, limited access to tailing dams and inadequate assessment plants' potential limit characterization native accumulators, hindering local remediation efforts. This study evaluates metal sequestration potentials Pennisetum purpureum, Leucaena leucocephala, Pteris vittata their associated rhizospheric at Marlu Pompora Ghana. The results indicate shoot hyperaccumulation Cd (334.5 ± 6.3 mg/kg) Fe (10,647.0 12.6 P. purpureum L. respectively. Analysis bacterial revealed impact contamination on community composition, associating with Bacillus, Arthrobacter, Sphingomonas species. reports leucocephala enhanced by rhizosphere communities, suggesting application as an environmentally friendly process metals contaminated lands.

Language: Английский

Citations

5
Unraveling the shift in bacterial communities profile grown in sediments co-contaminated with chlorolignin waste of pulp-paper mill by metagenomics approach DOI Creative Commons
Vineet Kumar,

Fuád Ameén,

Pradeep Verma

et al.

Frontiers in Microbiology, Journal Year: 2024, Volume and Issue: 15

Published: March 11, 2024

Pulp-paper mills (PPMs) are known for consistently generating a wide variety of pollutants, that often unidentified and highly resistant to environmental degradation. The current study aims investigate the changes in indigenous bacterial communities profile grown sediment co-contaminated with organic inorganic pollutants discharged from PPMs. two samples, designated PPS-1 PPS-2, were collected different sites. Physico-chemical characterization PPS-2 revealed presence heavy metals (mg kg −1 ) like Cu (0.009–0.01), Ni (0.005–0.002), Mn (0.078–0.056), Cr (0.015–0.009), Pb (0.008–0.006), Zn (0.225–0.086), Fe (2.124–0.764), Al (3.477–22.277), Ti (99.792–45.012) along high content chlorophenol, lignin. comparative analysis samples using gas chromatography–mass spectrometry (GC–MS) major refractory compounds, such as stigmasterol, β-sitosterol, hexadecanoic acid, octadecanoic acid; 2,4-di-tert-butylphenol; heptacosane; dimethyl phthalate; hexachlorobenzene; 1-decanol,2-hexyl; furane 2,5-dimethyl, etc which reported potential toxic compounds. Simultaneously, high-throughput sequencing targeting V3–V4 hypervariable region 16S rRNA genes, resulted identification 1,249 1,345 operational taxonomic units (OTUs) derived total 115,665 119,386 sequences read, respectively. Analysis rarefaction curves indicated diversity OTU abundance between (1,249 OTUs) (1,345 OTUs). Furthermore, assignment metagenomics sequence data showed Proteobacteria (55.40%; 56.30%), Bacteoidetes (11.30%; 12.20%), Planctomycetes (5.40%; 4.70%) most abundant phyla; Alphproteobacteria (20.50%; 23.50%), Betaproteobacteria (16.00%; 12.30%), Gammaproteobacteria recorded classes At genus level, Thiobacillus (7.60%; 4.50%) was genera samples. results indicate significant differences both relative taxa associated when compared PPS-1. This unveils key insights into contaminant characteristics shifts within contaminated environments. It highlights developing efficient bioremediation techniques restore ecological balance pulp-paper mill waste-polluted areas, stressing importance identifying percentage unclassified species explore novel genes.

Language: Английский

Citations

4
Amide- COF material for soil remediation: Selective stabilization of lead in soil DOI
Shiyu Chen,

Hui Jin,

Zheng Liang

et al.

Journal of environmental chemical engineering, Journal Year: 2025, Volume and Issue: 13(1), P. 115331 - 115331

Published: Jan. 5, 2025

Language: Английский

Citations

0
Periphyton biofilms formulation and application for the removal of trace pollutants from water DOI
Khurram Shahzad, Shahid Mahmood, Azeem Khalid

et al.

International Biodeterioration & Biodegradation, Journal Year: 2025, Volume and Issue: 198, P. 106003 - 106003

Published: Jan. 10, 2025

Language: Английский

Citations

0
Variation of Soil Bacterial Communities in Forest Soil Contaminated with Chainsaw Lubricants DOI Creative Commons
Ikhyun Kim, Nguyen Manh Ha, Sang-Gon Lee

et al.

Microorganisms, Journal Year: 2024, Volume and Issue: 12(3), P. 508 - 508

Published: March 1, 2024

Pollutants can exist in the soil for a long time and alter bacterial community. Using lubricants to prevent wear of chainsaw blades is necessary thinning activities wood harvesting. We investigated influences contamination with on communities. Bio-oil, mineral oil, recycled oil were scattered each treatment investigate variations structure during treated periods using Illumina MiSeq sequencing platform. The results obtained 5943 ASVs, 5112 6136 ASVs after at one month, six months, twelve respectively. There was significant difference Shannon Simpson indices between treatments controls. A total 46 genera an average relative abundance more than 1.0% detected all samples. Massilia most common genus control 14.99%, while Chthoniobacter abundant bio-oil, 13.39%, 14.32%, 10.47%, Among three lubricants, bio-oil had fewer impacts oil. abundances several functional bacteria groups higher other Our indicated that different their application affected community composition.

Language: Английский

Citations

2
Artificially obtained humic-like substances from chicken manure and symbionts in in vitro and in situ improvement of oil degradation in soil DOI

Olga Senko,

Nikolay Stepanov, Olga Maslova

et al.

Arabian Journal of Geosciences, Journal Year: 2024, Volume and Issue: 17(11)

Published: Oct. 18, 2024

Language: Английский

Citations

0
Waste mitigation through synergistic solutions with plants and microbes DOI
Kavita Nanda, Varsha Singh, Shivam Kumar

et al.

Elsevier eBooks, Journal Year: 2024, Volume and Issue: unknown, P. 163 - 193

Published: Nov. 15, 2024

Language: Английский

Citations

0
Current Situation and Control Measures of Heavy Metal Pollution in Farmland Soil DOI Creative Commons

Xinyi Xiao

Academic Journal of Science and Technology, Journal Year: 2023, Volume and Issue: 6(3), P. 70 - 72

Published: July 27, 2023

With the acceleration of urbanization and industrialization, soil heavy metal pollution has become a widespread environmental issue concern both domestically internationally, seriously threatened stability Earth's ecosystem safety human life. Therefore, it is urgent to address pollution. Based on reality in China, this paper analyzes main sources farmland soil, proposes targeted remediation measures for pollutants through physical, chemical, Bioremediation technologies, with view providing reference alleviation problems China.

Language: Английский

Citations

1