Large-Scale Characterization of the Soil Microbiome in Ancient Tea Plantations Using High-Throughput 16S rRNA and Internal Transcribed Spacer Amplicon Sequencing

Kui, Ling; Xiang, Guisheng; Ya, Wang; Wang, Zijun; Li, Guorong; Li, Dawei; Jian, Yan; Ye, Shuang; Wang, Chunping; Yang, Ling; Zhang, Shiyu; Zhang, Shuangyan; Zhou, Liqing; Gui, Heng; Xu, Jiawei; Chen, Wei; Zhang, Jun; Huang, Tuo; Majeed, Aasim; Sheng, Jun; Dong, Yang

doi:10.3389/fmicb.2021.745225

Cited by 20 publications

(17 citation statements)

References 70 publications

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“…Microbial community α-diversity showed an overall decreasing trend during the degradation of alpine meadows. This is because that during degradation, above-and below-ground biomass is reduced (Boddey et al 2004 Bacterial community diversity was more sensitive to changes in environmental factors during meadow degradation than fungal communities (Kui et al 2021). This may be explained by the fact that bacteria dominate the initial stages of apoplastic decomposition, i.e.…”

Section: Discussionmentioning

confidence: 99%

Microbial communities’ response along degradation gradient in alpine meadows of the Qilian Mountains

Yang²,

Li³

et al. 2023

Preprint

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Aims Degradation of alpine meadows on the Qinghai-Tibet Plateau is a major issue affecting both ecology and economy. Microorganisms play an important role in soil nutrient cycling and regulation of ecosystem function. This study aimed to investigate the species composition and diversity of microbial communities, and understand the response of microbial communities to changes in physicochemical properties resulting from meadow degradation. Methods In this study, the soil bacterial and fungal communities and diversity of alpine meadows of degradation gradient were sequenced by high-throughput sequencing. The function of microbial communities was predicted with Picrust2 and FUNGuild. Results As meadow degradation increased, there were 36 bacterial taxa and 28 fungal taxa showing significant differences. The relative abundance of meadow pathogenic fungi increased significantly (P < 0.05). Bacterial and fungal α- diversity mostly tended to decrease. Picrust2 analysis showed a decrease in synthesis-related functional gene abundance and an increase in metabolism-related functional gene abundance. FUNGuild analysis showed that symbiotic and saprophytic symbiotic nutrient fungi decreased significantly (P < 0.05). The pH and available nutrients were identified as the main drivers of changes in the structure, of microbial communities. Conclusion The degradation of meadows directly affects soil nutrient content, which in turn affects the diversity and function of soil microbial composition. The combined effect of soil nutrient reduction and microbial community changes reduces the stability of meadows. This work reveals the response and main environmental drivers of alpine meadow degradation in microbial communities, which provides theoretical support for the conservation and sustainable development of alpine meadows.

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Section: Discussionmentioning

confidence: 99%

Microbial communities’ response along degradation gradient in alpine meadows of the Qilian Mountains

Yang²,

Li³

et al. 2023

Preprint

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“…Although individual regions sequenced on Illumina such as V3V4, V4, internal transcribed spacer (ITS), and 23S capture the sequence divergence of many bacterial species (Pei et al, 2009;Snyder et al, 2011;Yarza et al, 2014;Russell et al, 2019;Kui et al, 2021), taxonomic classification and relative abundance calculations can differ greatly based on the hypervariable region sequenced or the primer-set selection, which may misrepresent and also completely omit taxa (Graspeuntner et al, 2018;Darwish et al, 2021). With the recent FDA approval of ONT for clinical diagnostics and an increased interest in a deeper understanding of environmental microbiomes as technologies become more accessible, it is timely that long-read pipelines be established with improved accuracy and confidence in classification compared to short-read sequencing (Yarza et al, 2014;Martínez-Porchas et al, 2016;PRWeb, 2020;De Coster et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

RESCUE: a validated Nanopore pipeline to classify bacteria through long-read, 16S-ITS-23S rRNA sequencing

et al. 2023

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Despite the advent of third-generation sequencing technologies, modern bacterial ecology studies still use Illumina to sequence small (~400 bp) hypervariable regions of the 16S rRNA SSU for phylogenetic classification. By sequencing a larger region of the rRNA gene operons, the limitations and biases of sequencing small portions can be removed, allowing for more accurate classification with deeper taxonomic resolution. With Nanopore sequencing now providing raw simplex reads with quality scores above Q20 using the kit 12 chemistry, the ease, cost, and portability of Nanopore play a leading role in performing differential bacterial abundance analysis. Sequencing the near-entire rrn operon of bacteria and archaea enables the use of the universally conserved operon holding evolutionary polymorphisms for taxonomic resolution. Here, a reproducible and validated pipeline was developed, RRN-operon Enabled Species-level Classification Using EMU (RESCUE), to facilitate the sequencing of bacterial rrn operons and to support import into phyloseq. Benchmarking RESCUE showed that fully processed reads are now parallel or exceed the quality of Sanger, with median quality scores of approximately Q20+, using the R10.4 and Guppy SUP basecalling. The pipeline was validated through two complex mock samples, the use of multiple sample types, with actual Illumina data, and across four databases. RESCUE sequencing is shown to drastically improve classification to the species level for most taxa and resolves erroneous taxa caused by using short reads such as Illumina.

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“…Soil microbiome play a crucial role in formation and retaining of soil fertility and quality (De Mandal et al 2019, Abakumov et al 2020, Chen et al 2020, Kui et al 2021, Nikitin et al 2022, which is especially important for severe conditions of agriculture in cryolithozone. The majority of agricultural lands in Russia is concentrated in the European part of the country ( [1] Stolbovoy 2002).…”

Section: Introductionmentioning

confidence: 99%

Microbiome of abandoned soils of former agricultural cryogenic ecosystems of central part of Yamal region

Abakumov¹,

Kimeklis²,

Gladkov³

et al. 2023

Czech Polar Rep.

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Microbial activity plays a crucial role in the development and formation of soil properties. The active and abandoned agricultural soils in the Arctic zone represent a valuable resource that can play a crucial role in providing food security in the northern regions. The reuse of abandoned land for agriculture will reduce environmental risks in the context of a changing climate. Therefore, there is a need for monitoring studies to assess changes in soil parameters after long-term abandonment (taxonomic diversity, agrochemical and physico-chemical qualities). In the study, we evaluated the taxonomic diversity of the microbiome in abandoned (postagrogenic) and pristine soils of the Central part of the Yamal region. In the process of taxonomic analysis, more than 30 different bacterial and archaeal phyla were identified. The formation of a specific microbiome associated with anthropogenic influence in post-agrogenic sites has been shown. Most common types of soil microorganisms in samples collected from pristine and postagrogenic soils were Firmicutes (average 26.86%), Proteobacteria (average 23.41%), and Actinobacteria (average 15.45%). Firmicutes phylum was found mainly in the agrocenoses soils, Proteobacteria were mainly described in the mature tundra soils, Actinobacteria in humid conditions. An increase in diversity indices in postagrogenic soils was shown.

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Large-Scale Characterization of the Soil Microbiome in Ancient Tea Plantations Using High-Throughput 16S rRNA and Internal Transcribed Spacer Amplicon Sequencing

Cited by 20 publications

References 70 publications

Microbial communities’ response along degradation gradient in alpine meadows of the Qilian Mountains

Microbial communities’ response along degradation gradient in alpine meadows of the Qilian Mountains

RESCUE: a validated Nanopore pipeline to classify bacteria through long-read, 16S-ITS-23S rRNA sequencing

Microbiome of abandoned soils of former agricultural cryogenic ecosystems of central part of Yamal region

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