Profiling soil microbial communities with next-generation sequencing: the influence of DNA kit selection and technician technical expertise

Soliman, Taha; Yang, Sung‐Yin; Yamazaki, Tomoko; Jenke‐Kodama, Holger

doi:10.7717/peerj.4178

Cited by 52 publications

(31 citation statements)

References 37 publications

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“…Below order level, most OTUs remained unclassified without any taxonomic predictions. Our findings regarding the assignment success rate of OTUs agree with previous metagenomics studies carried out in a different environment (Schmidt et al, 2013;Soliman, Yang, Yamazaki, & Jenke-Kodama, 2017;Sun et al, 2015;Yuan et al, 2017).…”

Section: Mycobiome Of Eucalypt Tree Hollowssupporting

confidence: 91%

The mycobiome of Australian tree hollows in relation to the Cryptococcus gattii and C. neoformans species complexes

Irinyi

Malík

Powell

et al. 2019

Ecology and Evolution

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Cryptococcosis is a fungal infection caused by members of the Cryptococcus gattii and C. neoformans species complexes. The C. gattii species complex has a strong environmental association with eucalypt hollows (particularly Eucalyptus camaldulensis), which may present a source of infection. It remains unclear whether a specific mycobiome is required to support its environmental survival and growth. Conventional detection of environmental Cryptococcus spp. involves culture on differential media, such as Guizotia abyssinica seed agar. Next‐generation sequencing (NGS)‐based culture‐independent identification aids in contextualising these species in the environmental mycobiome. Samples from 23 Australian tree hollows were subjected to both culture‐ and amplicon‐based metagenomic analysis to characterize the mycobiome and assess relationships between Cryptococcus spp. and other fungal taxa. The most abundant genera detected were Coniochaeta, Aspergillus, and Penicillium, all being commonly isolated from decaying wood. There was no correlation between the presence of Cryptococcus spp. in a tree hollow and the presence of any other fungal genus. Some differences in the abundance of numerous taxa were noted in a differential heat tree comparing samples with or without Cryptococcus‐NGS reads. The study expanded the known environmental niche of the C. gattii and C. neoformans species complexes in Australia with detections from a further five tree species. Discrepancies between the detection of Cryptococcus spp. using culture or NGS suggest that neither is superior per se and that, rather, these methodologies are complementary. The inherent biases of amplicon‐based metagenomics require cautious interpretation of data through consideration of its biological relevance.

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Section: Mycobiome Of Eucalypt Tree Hollowssupporting

confidence: 91%

The mycobiome of Australian tree hollows in relation to the Cryptococcus gattii and C. neoformans species complexes

Irinyi

Malík

Powell

et al. 2019

Ecology and Evolution

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“…For a more detailed metataxonomic characterization of the soil microbial communities, next generation sequencing (NGS) was performed to identify representatives of different taxa present in soil amended with biofertilizers. The implementation of NGS in the field of environmental microbiology is very appealing for the exploration of soil microbial diversity due to the fact that it allows for an accurate and extensive analysis of multiple samples at the same time [81]. The metagenomic approach simplifies not only the study of phylogenetic relationships between microorganisms but it also determines their functionality in the soil environment [82].…”

Section: Discussionmentioning

confidence: 99%

The Status of Soil Microbiome as Affected by the Application of Phosphorus Biofertilizer: Fertilizer Enriched with Beneficial Bacterial Strains

Mącik

Gryta

Sas-Paszt

et al. 2020

IJMS

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Regarding the unfavourable changes in agroecosystems resulting from the excessive application of mineral fertilizers, biopreparations containing live microorganisms are gaining increasing attention. We assumed that the application of phosphorus mineral fertilizer enriched with strains of beneficial microorganisms contribute to favourable changes in enzymatic activity and in the genetic and functional diversity of microbial populations inhabiting degraded soils. Therefore, in field experiments conditions, the effects of phosphorus fertilizer enriched with bacterial strains on the status of soil microbiome in two chemically degraded soil types (Brunic Arenosol – BA and Abruptic Luvisol – AL) were investigated. The field experiments included treatments with an optimal dose of phosphorus fertilizer (without microorganisms – FC), optimal dose of phosphorus fertilizer enriched with microorganisms including Paenibacillus polymyxa strain CHT114AB, Bacillus amyloliquefaciens strain AF75BB and Bacillus sp. strain CZP4/4 (FA100) and a dose of phosphorus fertilizer reduced by 40% and enriched with the above-mentioned bacteria (FA60). The analyzes performed included: the determination of the activity of the soil enzymes (protease, urease, acid phosphomonoesterase, β-glucosidase), the assessment of the functional diversity of microorganisms with the application of BIOLOGTM plates and the characterization of the genetic diversity of bacteria, archaea and fungi with multiplex terminal restriction fragment length polymorphism and next generation sequencing. The obtained results indicated that the application of phosphorus fertilizer enriched with microorganisms improved enzymatic activity, and the genetic and functional diversity of the soil microbial communities, however these effects were dependent on the soil type.

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“…Another important factor which determines soil health, and thus, soil quality and productivity, is the structure of microbial communities [73], because these communities affect the stability of the soil ecosystem [7,11,74]. There is a strong correlation between the soil microbiome and the plant microbiome [75,76].…”

Section: Counts and Diversity Of Bacteriamentioning

confidence: 99%

Soil Bacterial Community and Soil Enzyme Activity Depending on the Cultivation of Triticum aestivum, Brassica napus, and Pisum sativum ssp. arvense

et al. 2019

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This study aims to determine the effects of crops and their cultivation regimes on changes in the soil microbiome. Three plant species were selected for the study: Triticum aestivum, Brassica napus, and Pisum sativum ssp. arvense, that were cultivated in soils with a similar particle size fraction. Field experiments were performed on the area of the Iławski Lake District (north-eastern Poland) at the Production and Experimental Station ‘Bałcyny’ (53°35′49″ N, 19°51′20″ E). In soil samples counts, organotrophic bacteria and actinobacteria were quantified, and the colony development index (CD) and ecophysiological diversity index (EP) were computed. In addition, a 16S amplicon sequencing encoding gene was conducted based on the hypervariable region V3–V4. Further analyses included an evaluation of the basic physiochemical properties of the soil and the activities of dehydrogenases, catalase, urease, acid phosphatase, alkaline phosphatase, arylsulfatase, and β-glucosidase. Analyses carried out in the study demonstrated that the rhizosphere of Triticum aestivum had a more beneficial effect on bacteria development than those of Brassica napus and Pisum sativum ssp. arvense, as indicated by the values of the ecophysiological diversity index (EP) and OTU abundance calculated for individual taxa in the soils in which the studied crops were grown. More OTUs of the taxa Alphaproteobacteria, Gammaproteobacteria, Clostridia, Sphingomonadales, Rhodospirillales, Xanthomonadales, Streptomycetaceae, Pseudonocardiaceae, Acetobacteraceae, Solibacteraceae, Kaistobacter, Cohnella, Azospirillum, Cryptosporangium, Rhodoplanes, and Saccharopolyspora were determined in the bacteriome structure of the soil from Triticum aestivum cultivation than in the soils from the cultivation of Brassica napus and Pisum sativum ssp. arvense. Also, the activities of most of the analyzed enzymes, including urease, catalase, alkaline phosphatase, β-glucosidase, and arylsulfatase, were the higher in the soil sown with Triticum aestivum than in those with the other two plant species.

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Profiling soil microbial communities with next-generation sequencing: the influence of DNA kit selection and technician technical expertise

Cited by 52 publications

References 37 publications

The mycobiome of Australian tree hollows in relation to the Cryptococcus gattii and C. neoformans species complexes

The mycobiome of Australian tree hollows in relation to the Cryptococcus gattii and C. neoformans species complexes

The Status of Soil Microbiome as Affected by the Application of Phosphorus Biofertilizer: Fertilizer Enriched with Beneficial Bacterial Strains

Soil Bacterial Community and Soil Enzyme Activity Depending on the Cultivation of Triticum aestivum, Brassica napus, and Pisum sativum ssp. arvense

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