Nanopore-based metagenomic analysis of the impact of nanoparticles on soil microbial communities

Chavan, Sangeeta; Sarangdhar, Vishwas; Vigneshwaran, N.

doi:10.1016/j.heliyon.2022.e09693

Cited by 5 publications

(4 citation statements)

References 54 publications

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“…Recently, third-generation sequencing systems have become available on the market, which provide longer and more informative DNA sequences than ‘second-generation’ sequencers and are increasingly being adopted by small and non-specialized laboratories. In particular, Oxford Nanopore Technologies (ONT) provides a miniaturized sequencer (MinION) supported by easy-to-use kits and online bespoken bioinformatics platforms that are used for targeted sequencing and shotgun protocols and have been successfully applied to the study of microbial communities of soils subjected to different treatments [ 105 ].…”

Section: Methods For Evaluating the Effect On The Soil Microbiome To ...mentioning

confidence: 99%

Microbial-Based Products to Control Soil-Borne Pathogens: Methods to Improve Efficacy and to Assess Impacts on Microbiome

Ptaszek

Canfora²,

Pugliese

et al. 2023

Microorganisms

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Microbial-based products (either as biopesticide or biofertilizers) have a long history of application, though their use is still limited, mainly due to a perceived low and inconsistent efficacy under field conditions. However, their efficacy has always been compared to chemical products, which have a completely different mechanism of action and production process, following the chemical paradigm of agricultural production. This paradigm has also been applied to regulatory processes, particularly for biopesticides, making the marketing of microbial-based formulations difficult. Increased knowledge about bioinocula behavior after application to the soil and their impact on soil microbiome should foster better exploitation of microbial-based products in a complex environment such as the soil. Moreover, the multifunctional capacity of microbial strains with regard to plant growth promotion and protection should also be considered in this respect. Therefore, the methods utilized for these studies are key to improving the knowledge and understanding of microbial-based product activity and improving their efficacy, which, from farmers’ point of view, is the parameter to assess the usefulness of a treatment. In this review, we are thus addressing aspects related to the production and formulation process, highlighting the methods that can be used to evaluate the functioning and impact of microbial-based products on soil microbiome, as tools supporting their use and marketing.

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Section: Methods For Evaluating the Effect On The Soil Microbiome To ...mentioning

confidence: 99%

Microbial-Based Products to Control Soil-Borne Pathogens: Methods to Improve Efficacy and to Assess Impacts on Microbiome

Ptaszek

Canfora²,

Pugliese

et al. 2023

Microorganisms

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“…All statistical analysis were performed using R version 4.3.1 (Larry 2012). The total number of reads per sample were variable; hence, normalization by log transformation was carried out prior to the analysis to make microbiome abundances comparable (Chavan et al 2022).…”

Section: Metagenomic Dna Isolation and Purificationmentioning

confidence: 99%

1 Effects of Phosphate-rock Mining Wastewater Fertigation on Chickpea (Cicer arietinum) Cultivation and Soil Microbial Diversity

Hammami,

Ferchichi,

Toukebri

et al. 2024

Preprint

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The conventional intensive use of chemical fertilizers poses significant threats to agro-ecosystem sustainability, leading to soil deterioration and environmental pollution. This study explores the potential of utilizing phosphate-rock mining wastewater (MWw) as a sustainable alternative for fertigation in chickpea cultivation. The investigation, conducted under both greenhouse and field conditions, evaluates the impact of raw and diluted MWw on chickpea growth, yield, and soil microbial diversity. In greenhouse experiments, chickpea plants subjected to MWw fertigation exhibited enhanced root and shoot growth, increased seed and pod production, and improved chlorophyll content. The inclusion of the Mesorhizobium mediterraneum strain "C11" further augmented these positive effects. Principal component analysis revealed a clear positive influence of MWw and inoculation on chickpea yield. Field trials conducted in a semi-arid region demonstrated that MWw fertigation significantly increased shoot dry weight, with variations observed between chickpea cultivars. Meta-genomic analysis of soil microbial communities indicated a substantial impact of fertigation on bacterial phyla composition, particularly an increase in Proteobacteria abundance. The induced and inhibited bacterial spectra highlighted the influence of MWw on specific bacterial families, including Rhodanobacteraceae and Dongiaceae. The MWw used in the study exhibited slightly alkaline pH and contained essential micronutrients. The study emphasizes the potential of MWw, combined with microbial inoculation, as a sustainable source of water and nutrients for chickpea cultivation. The positive effects on plant growth and soil microbial diversity suggest that MWw fertigation could contribute to more environmentally friendly agricultural practices. Overall, this research provides valuable insights into utilizing phosphate-rich wastewater for sustainable agriculture, particularly in regions facing water scarcity and environmental challenges.

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“…In addition, it is a small portable device, allowing the processing of samples on site without the need of elaborate laboratory infrastructure. Consequently, there is growing interest in using Nanopore for 16S rRNA gene amplicon sequencing, and recent publications have demonstrated its success with a variety of samples, for example freshwater [ 5 ], seawater and algal surfaces [ 6 ], soil [ 7 , 8 ], surfaces in the international space station [ 9 ], animal feces [ 10 ], urine [ 11 ], buccal and rectal swabs [ 12 ], ophthalmic samples [ 13 ], bronchoalveolar lavage fluid, blood, pleural and ascitic fluid, cerebrospinal fluid, and wound secretions [ 14 ].…”

Section: Introductionmentioning

confidence: 99%

Nanopore Is Preferable over Illumina for 16S Amplicon Sequencing of the Gut Microbiota When Species-Level Taxonomic Classification, Accurate Estimation of Richness, or Focus on Rare Taxa Is Required

Szoboszlay¹,

Schramm²,

Pinzauti³

et al. 2023

Microorganisms

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Nanopore sequencing is a promising technology used for 16S rRNA gene amplicon sequencing as it can provide full-length 16S reads and has a low up-front cost that allows research groups to set up their own sequencing workflows. To assess whether Nanopore with the improved error rate of the Kit 12 chemistry should be adopted as the preferred sequencing technology instead of Illumina for 16S amplicon sequencing of the gut microbiota, we used a mock community and human faecal samples to compare diversity, richness, and species-level community structure, as well as the replicability of the results. Nanopore had less noise, better accuracy with the mock community, a higher proportion of reads from the faecal samples classified to species, and better replicability. The difference between the Nanopore and Illumina results of the faecal bacterial community structure was significant but small compared to the variation between samples. The results show that Nanopore is a better choice for 16S rRNA gene amplicon sequencing when the focus is on species-level taxonomic resolution, the investigation of rare taxa, or an accurate estimation of richness. Illumina 16S sequencing should be reserved for communities with many unknown species, and for studies that require the resolution of amplicon sequence variants.

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Nanopore-based metagenomic analysis of the impact of nanoparticles on soil microbial communities

Cited by 5 publications

References 54 publications

Microbial-Based Products to Control Soil-Borne Pathogens: Methods to Improve Efficacy and to Assess Impacts on Microbiome

Microbial-Based Products to Control Soil-Borne Pathogens: Methods to Improve Efficacy and to Assess Impacts on Microbiome

1 Effects of Phosphate-rock Mining Wastewater Fertigation on Chickpea (Cicer arietinum) Cultivation and Soil Microbial Diversity

Nanopore Is Preferable over Illumina for 16S Amplicon Sequencing of the Gut Microbiota When Species-Level Taxonomic Classification, Accurate Estimation of Richness, or Focus on Rare Taxa Is Required

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