A practical guide to amplicon and metagenomic analysis of microbiome data

Protein & Cell, Journal Year: 2020, Volume and Issue: 12(5), P. 315 - 330

Published: May 11, 2020

Abstract Advances in high-throughput sequencing (HTS) have fostered rapid developments the field of microbiome research, and massive datasets are now being generated. However, diversity software tools complexity analysis pipelines make it difficult to access this field. Here, we systematically summarize advantages limitations methods. Then, recommend specific for amplicon metagenomic analyses, describe commonly-used databases, help researchers select appropriate tools. Furthermore, introduce statistical visualization methods suitable analysis, including alpha- beta-diversity, taxonomic composition, difference comparisons, correlation, networks, machine learning, evolution, source tracing, common styles informed choices. Finally, a step-by-step reproducible guide is introduced. We hope review will allow carry out data more effectively quickly order efficiently mine biological significance behind data.

Language: Английский

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Erosion reduces soil microbial diversity, network complexity and multifunctionality

The ISME Journal, Journal Year: 2021, Volume and Issue: 15(8), P. 2474 - 2489

Published: March 12, 2021

Abstract While soil erosion drives land degradation, the impact of on microbial communities and multiple functions remains unclear. This hinders our ability to assess true ecosystem services restore eroded environments. Here we examined effect at two sites with contrasting texture climates. Eroded plots had lower network complexity, fewer taxa, associations among relative non-eroded plots. Soil also shifted community composition, decreased abundances dominant phyla such as Proteobacteria, Bacteroidetes, Gemmatimonadetes. In contrast, led an increase in some bacterial families involved N cycling, Acetobacteraceae Beijerinckiaceae. Changes microbiota characteristics were strongly related erosion-induced changes multifunctionality. Together, these results demonstrate that has a significant negative diversity functionality.

Language: Английский

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Biodiversity of key-stone phylotypes determines crop production in a 4-decade fertilization experiment

The ISME Journal, Journal Year: 2020, Volume and Issue: 15(2), P. 550 - 561

Published: Oct. 7, 2020

Language: Английский

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Plastic wastes biodegradation: Mechanisms, challenges and future prospects

The Science of The Total Environment, Journal Year: 2021, Volume and Issue: 780, P. 146590 - 146590

Published: March 19, 2021

Language: Английский

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Microbial diversity and the abundance of keystone species drive the response of soil multifunctionality to organic substitution and biochar amendment in a tea plantation

GCB Bioenergy, Journal Year: 2022, Volume and Issue: 14(4), P. 481 - 495

Published: Feb. 3, 2022

Abstract High nitrogen (N) fertilizer inputs accelerate soil acidification and degradation in tea plantations, thus posing a threat to microbial diversity, species composition, ecosystem service functions. The effects of organic biochar applications on improving fertility have been extensively studied cropland; however, little is known about their effectiveness promoting multifunctionality rapidly expanding acidic soils plantations. In this study, we conducted two‐year field experiment subtropical plantation investigate the substitution amendment communities multifunctionality. results showed that was enhanced plots amended with biochar. Soil significantly positively correlated alpha‐diversity bacteria but not fungi. We also found improved by altering abundance keystone species. classified as module hubs bacterial co‐occurrence network contributed contrast, categorized fungal negatively affected pH key driver community indicating increase under had crucial role biological processes. These suggest are beneficial preventing maintaining

Language: Английский

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Core phylotypes enhance the resistance of soil microbiome to environmental changes to maintain multifunctionality in agricultural ecosystems

Global Change Biology, Journal Year: 2022, Volume and Issue: 28(22), P. 6653 - 6664

Published: Aug. 13, 2022

Agricultural ecosystems are facing increasing environmental changes. Revealing ecological stability of belowground organisms is key to developing management strategies that maintain agricultural ecosystem services in a changing world. Here, we collected soils from adjacent pairs maize and rice fields along large spatial scale across Eastern Southeast China investigate the importance core microbiota as predictor resistance soil microbiome (e.g. bacteria, fungi protist) climate changes nutrient fertilization, their effect on multiple functions, representing for crop growth health agro-ecosystems. Soil exhibited stronger than soils, by considering aspects index, example, community, phylogenetic conservation network complexity. Community showed geographic pattern, with higher at lower latitudes, suggesting warmer regions. Particularly, highlighted role phylotypes enhancing community microbiome, which was essential maintenance multifunctionality ecosystems. Our results represent significant advance linking therefore forecasting agro-ecosystems dynamics response ongoing These suggest should be considered factor sustainability productivity under global change scenarios.

Language: Английский

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Microbial community succession in soil is mainly driven by carbon and nitrogen contents rather than phosphorus and sulphur contents

Soil Biology and Biochemistry, Journal Year: 2023, Volume and Issue: 180, P. 109019 - 109019

Published: March 20, 2023

Language: Английский

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Microbial interactions for nutrient acquisition in soil: Miners, scavengers, and carriers

Soil Biology and Biochemistry, Journal Year: 2023, Volume and Issue: 188, P. 109215 - 109215

Published: Oct. 24, 2023

Language: Английский

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Gut microbiota facilitate adaptation of invasive moths to new host plants

The ISME Journal, Journal Year: 2024, Volume and Issue: 18(1)

Published: Jan. 1, 2024

Abstract Gut microbiota are important in the adaptation of phytophagous insects to their plant hosts. However, interaction between gut microbiomes and pioneering populations invasive during new hosts, particularly initial phases invasion, has been less studied. We studied contribution microbiome host globally recognized pest, Hyphantria cunea, as it expands its range into southern China. The population H. cunea shows effective Metasequoia glyptostroboides exhibits greater larval survival on than original population. Genome resequencing revealed no significant differences functions related two populations. compatibility M. a correlation abundance several bacteria genera (Bacteroides, Blautia, Coprococcus) survival. Transplanting from northern enhanced adaptability latter previously unsuitable glyptostroboides. This research provides evidence that can enhance pests hosts enable more rapid habitats.

Language: Английский

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Intercropping enhances maize growth and nutrient uptake by driving the link between rhizosphere metabolites and microbiomes

New Phytologist, Journal Year: 2024, Volume and Issue: 243(4), P. 1506 - 1521

Published: June 14, 2024

Intercropping leads to different plant roots directly influencing belowground processes and has gained interest for its promotion of increased crop yields resource utilization. However, the precise mechanisms through which interactions between rhizosphere metabolites microbiome contribute production remain ambiguous, thus impeding understanding yield-enhancing advantages intercropping. This study conducted field experiments (initiated in 2013) pot experiments, coupled with multi-omics analysis, investigate plant-metabolite-microbiome maize. Field-based data revealed significant differences metabolite profiles soils maize monoculture In particular, intercropping exhibited higher microbial diversity chemodiversity. The chemodiversity composition were significantly related diversity, community composition, network complexity soil microbiomes, this relationship further impacted nutrient uptake. Pot-based findings demonstrated that exogenous application a metabolic mixture comprising key components enriched by (soyasapogenol B, 6-hydroxynicotinic acid, lycorine, shikimic phosphocreatine) enhanced root activity, content, biomass natural soil, but not sterilized soil. Overall, emphasized significance metabolite-microbe enhancing systems. It can provide new insights into controls within intensive agroecosystems, aiming enhance ecosystem services.

Language: Английский

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