Publisher Correction: The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology

Jeong, Jin-Uk; Yun, Kyeongeui; Mun, Seyoung; Chung, Won‐Hyong; Choi, Song‐Yi; Nam, Young-Do; Lim, Mi Young; Hong, Chang Pyo; Park, Chanhyeok; Ahn, Yong Ju; Han, Kyudong

doi:10.1038/s41598-021-90067-z

Cited by 25 publications

(7 citation statements)

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“…Amplicon-based sequencing of marker genes [16S rDNA, 18S rDNA, or ITS regions] have always been plagued by insufficient taxonomic resolutions due to inability of the present sequencing to sequence the whole gene. New long-read sequencing technologies like PacBio circular consensus sequencing and loop genomics synthetic long-read sequencing technology [sFL16S] can sequence the entire marker gene such as 16S rRNA gene [ 14 , 65 ]. These techniques could overcome the microbial misidentification caused by previous approach’s inability to sequence the whole marker gene and could correctly classified to the sub-species clades [ 14 , 65 ].…”

Section: Challenges and Prospects In Unboxing The Black Box Of Soil M...mentioning

confidence: 99%

“…New long-read sequencing technologies like PacBio circular consensus sequencing and loop genomics synthetic long-read sequencing technology [sFL16S] can sequence the entire marker gene such as 16S rRNA gene [ 14 , 65 ]. These techniques could overcome the microbial misidentification caused by previous approach’s inability to sequence the whole marker gene and could correctly classified to the sub-species clades [ 14 , 65 ]. These techniques could in turn generate high quality sequences from the unculturable environmental organisms, which can then help in developing robust databases including such environmental sequences.…”

Section: Challenges and Prospects In Unboxing The Black Box Of Soil M...mentioning

confidence: 99%

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Unboxing the black box—one step forward to understand the soil microbiome: A systematic review

Mishra

Singh

2022

Microb Ecol

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Soil is one of the most important assets of the planet Earth, responsible for maintaining the biodiversity and managing the ecosystem services for both managed and natural ecosystems. It encompasses large proportion of microscopic biodiversity, including prokaryotes and the microscopic eukaryotes. Soil microbiome is critical in managing the soil functions, but their activities have diminutive recognition in few systems like desert land and forest ecosystems. Soil microbiome is highly dependent on abiotic and biotic factors like pH, carbon content, soil structure, texture, and vegetation, but it can notably vary with ecosystems and the respective inhabitants. Thus, unboxing this black box is essential to comprehend the basic components adding to the soil systems and supported ecosystem services. Recent advancements in the field of molecular microbial ecology have delivered commanding tools to examine this genetic trove of soil biodiversity. Objective of this review is to provide a critical evaluation of the work on the soil microbiome, especially since the advent of the NGS techniques. The review also focuses on advances in our understanding of soil communities, their interactions, and functional capabilities along with understanding their role in maneuvering the biogeochemical cycle while underlining and tapping the unprecedented metagenomics data to infer the ecological attributes of yet undiscovered soil microbiome. This review focuses key research directions that could shape the future of basic and applied research into the soil microbiome. This review has led us to understand that it is difficult to generalize that soil microbiome plays a substantiated role in shaping the soil networks and it is indeed a vital resource for sustaining the ecosystem functioning. Exploring soil microbiome will help in unlocking their roles in various soil network. It could be resourceful in exploring and forecasting its impacts on soil systems and for dealing with alleviating problems like rapid climate change.

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Section: Challenges and Prospects In Unboxing The Black Box Of Soil M...mentioning

confidence: 99%

Section: Challenges and Prospects In Unboxing The Black Box Of Soil M...mentioning

confidence: 99%

Unboxing the black box—one step forward to understand the soil microbiome: A systematic review

Mishra

Singh

2022

Microb Ecol

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“…A previous study also reported that the Rubellimicrobium genus completely disappeared once plants grew on the soil (Köberl et al, 2013), despite Kocuria species being known to tolerate salinity, promote plant growth, and increase their ability to resist disease (Goswami et al, 2014). Recent studies recommended accurate species classification in other regions such as V2-V3 (Bukin et al, 2019) or other newer methods such as sFL16S (Jeong et al, 2021). However, some of the observed unidentified species could be due to the novelty of the species, as many belonged to relatively new genera and families.…”

Section: Discussionmentioning

confidence: 99%

The Microbiome of Suaeda monoica and Dipterygium glaucum From Southern Corniche (Saudi Arabia) Reveals Different Recruitment Patterns of Bacteria and Archaea

Jalal

Sheikh²,

Alotaibi³

et al. 2022

Front. Mar. Sci.

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Soil and plant interact differently in response to the same stress (e.g., salinity) and recruit certain bacteria. The southern corniche (Saudi Arabia) has limited plant growth, which could be due to the high temperature and salinity. The study aimed to determine the soil microbiome of selected plants and the interactions between soil and these plants. Suaeda monoica and Dipterygium glaucum soil samples were collected from the crust (surface) and rhizosphere, while soil with no plant growth from the nearby area was used as control. High-throughput hypervariable V3–V4 region of the 16S rRNA gene was used to evaluate the shifts in soil microbiome due to growth of plant growth. The analysis detected up to 16% archaeal strains in S. monoica-associated samples, while D. glaucum and control samples contained 100% bacterial strains. The top 10 phyla composition of the soil samples were Proteobacteria, Actinobacteria, Firmicutes, Gemmatimonadota, Bacteroidota, Halobacterota, Cyanobacteria, Cloroflexi, Planctomycetota, and Myxococcota. The V3–V4 region analysis successfully clustered the 5 samples into 3 clusters (control, D. glaucum, and S. monoica) at higher-order classification but not at the species level due to unidentified bacteria. The main differences between soil samples were due to halophyte S. monoica samples containing high amounts of halophilic archaea and halophilic bacteria. This showed that selected plants interacted differently with the soil. EC- and KO-based analyses of functional genes and pathways showed that 5 pathways were specific to control, 11 pathways were observed only in D. glaucum samples, 12 pathways were expressed in S. monoica samples only, and 9 pathways were common in all samples. The study also detected numerous relatively novel genera in high abundance such as Aliifodinibius, Pontibacter, and Lacunisphaera. This showed that the soil in the sampling area is not well explored and that novel species could be isolated from the soil samples and used for future research.

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“…Despite the increasing interest and development of protocols for full-length 16S rRNA gene sequencing (Callahan et al, 2019 ; Jeong et al, 2021 ; Matsuo et al, 2021 ) and metagenomic methods (Milanese et al, 2019 ; Ye et al, 2019 ; Lu and Salzberg, 2020 ), short-read amplicon analysis remains popular for studying microbial communities due to the comparative low-sequencing costs and high accuracy. Drawbacks of the short-read approach are the lower phylogenetic signal provided by short reads and the amplification efficiency bias that primer pairs can exhibit toward certain taxa (Albertsen et al, 2015 ).…”

Section: Resultsmentioning

confidence: 99%

Application of ecosystem-specific reference databases for increased taxonomic resolution in soil microbial profiling

et al. 2022

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Intensive agriculture systems have paved the way for a growing human population. However, the abundant use of mineral fertilizers and pesticides may negatively impact nutrient cycles and biodiversity. One potential alternative is to harness beneficial relationships between plants and plant-associated rhizobacteria to increase nutrient-use efficiency and provide pathogen resistance. Plant-associated microbiota profiling can be achieved using high-throughput 16S rRNA gene amplicon sequencing. However, interrogation of these data is limited by confident taxonomic classifications at high taxonomic resolution (genus- or species level) with the commonly applied universal reference databases. High-throughput full-length 16S rRNA gene sequencing combined with automated taxonomy assignment (AutoTax) can be used to create amplicon sequence variant resolved ecosystems-specific reference databases that are superior to the traditional universal reference databases. This approach was used here to create a custom reference database for bacteria and archaea based on 987,353 full-length 16S rRNA genes from Askov and Cologne soils. We evaluated the performance of the database using short-read amplicon data and found that it resulted in the increased genus- and species-level classification compared to commonly use universal reference databases. The custom database was utilized to evaluate the ecosystem-specific primer bias and taxonomic resolution of amplicon primers targeting the V5–V7 region of the 16S rRNA gene commonly used within the plant microbiome field. Finally, we demonstrate the benefits of custom ecosystem-specific databases through the analysis of V5–V7 amplicon data to identify new plant-associated microbes for two legumes and two cereal species.

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Publisher Correction: The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology

Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Cited by 25 publications

References 0 publications

Unboxing the black box—one step forward to understand the soil microbiome: A systematic review

Unboxing the black box—one step forward to understand the soil microbiome: A systematic review

The Microbiome of Suaeda monoica and Dipterygium glaucum From Southern Corniche (Saudi Arabia) Reveals Different Recruitment Patterns of Bacteria and Archaea

Application of ecosystem-specific reference databases for increased taxonomic resolution in soil microbial profiling

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