Keystone taxa as drivers of microbiome structure and functioning

Nature Reviews Microbiology, Journal Year: 2018, Volume and Issue: 16(9), P. 567 - 576

Published: May 22, 2018

Language: Английский

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Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning

Nature Communications, Journal Year: 2019, Volume and Issue: 10(1)

Published: Oct. 24, 2019

Abstract The soil microbiome is highly diverse and comprises up to one quarter of Earth’s diversity. Yet, how such a functionally complex influences ecosystem functioning remains unclear. Here we manipulated the in experimental grassland ecosystems observed that diversity microbial network complexity positively influenced multiple functions related nutrient cycling (e.g. multifunctionality). Grassland microcosms with poorly developed networks reduced richness had lowest multifunctionality due fewer taxa present support same function (redundancy) lower different (reduced functional uniqueness). Moreover, explained pointing significance communities. These findings indicate importance interactions within among fungal bacterial communities for enhancing performance demonstrate extinction ecological associations belowground can impair functioning.

Language: Английский

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Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots

The ISME Journal, Journal Year: 2019, Volume and Issue: 13(7), P. 1722 - 1736

Published: March 8, 2019

Root-associated microbes play a key role in plant performance and productivity, making them important players agroecosystems. So far, very few studies have assessed the impact of different farming systems on root microbiota it is still unclear whether agricultural intensification influences structure complexity microbial communities. We investigated conventional, no-till, organic wheat fungal communities using PacBio SMRT sequencing samples collected from 60 farmlands Switzerland. Organic harbored much more complex network with significantly higher connectivity than conventional no-till systems. The abundance keystone taxa was highest under where lowest. also found strong negative association (R2 = 0.366; P < 0.0001) between connectivity. occurrence best explained by soil phosphorus levels, bulk density, pH, mycorrhizal colonization. majority are known to form arbuscular associations plants belong orders Glomerales, Paraglomerales, Diversisporales. Supporting this, fungi roots soils farming. To our knowledge, this first study report for agroecosystems, we demonstrate that reduces microbiome.

Language: Английский

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Balance between community assembly processes mediates species coexistence in agricultural soil microbiomes across eastern China

The ISME Journal, Journal Year: 2019, Volume and Issue: 14(1), P. 202 - 216

Published: Oct. 14, 2019

Language: Английский

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Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming

Microbiome, Journal Year: 2018, Volume and Issue: 6(1)

Published: Jan. 16, 2018

Harnessing beneficial microbes presents a promising strategy to optimize plant growth and agricultural sustainability. Little is known which extent how specifically soil microbiomes can be manipulated through different cropping practices. Here, we investigated wheat root microbial communities in system experiment consisting of conventional organic managements, both with tillage intensities. While richness was marginally affected, found pronounced effects on community composition, were specific for the respective microbiomes. Soil bacterial primarily structured by tillage, whereas fungal responded mainly management type additional tillage. In roots, also driving factor bacteria but not fungi, generally determined changes intensity. To quantify an "effect size" microbiota manipulation, that about 10% variation explained tested Cropping sensitive taxonomically diverse, they guilds taxa These included frequent members or co-occurring many other community, suggesting practices may allow manipulation influential members. Understanding abundance patterns basis towards developing strategies smart farming. For future targeted management—e.g., foster certain practices—a next step will identify functional traits microbes.

Language: Английский

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Bacterial–fungal interactions: ecology, mechanisms and challenges

FEMS Microbiology Reviews, Journal Year: 2018, Volume and Issue: 42(3), P. 335 - 352

Published: Feb. 16, 2018

Fungi and bacteria are found living together in a wide variety of environments. Their interactions significant drivers many ecosystem functions important for the health plants animals. A large number fungal bacterial families engage complex that lead to critical behavioural shifts microorganisms ranging from mutualism antagonism. The importance bacterial-fungal (BFI) environmental science, medicine biotechnology has led emergence dynamic multidisciplinary research field combines highly diverse approaches including molecular biology, genomics, geochemistry, chemical microbial ecology, biophysics ecological modelling. In this review, we discuss recent advances underscore roles BFI across relevant habitats ecosystems. particular focus is placed on understanding within communities regard metaorganism concept. We also discoveries clarify (molecular) mechanisms involved relationships, contribution new technologies decipher generic principles terms physical associations dialogues. Finally, future directions order stimulate synergy area resolve outstanding questions.

Language: Английский

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Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems

Microbiome, Journal Year: 2018, Volume and Issue: 6(1)

Published: Aug. 21, 2018

Soil microbiomes play an important role in the services and functioning of terrestrial ecosystems. However, little is known their vertical responses to restoration process contributions soil nutrient cycling subsurface profiles. Here, we investigated community assembly bacteria, archaea, fungi along (i.e., depths 0–300 cm) horizontal distance from trees 30–90 profiles a chronosequence reforestation sites that represent over 30 years restoration. In superficial layers (0–80 cm), bacterial fungal diversity decreased, whereas archaeal increased with increasing depth. As proceeded time, spatial variation communities while increased. Vertical distributions were more related properties, may be driven by gradient effect roots extending tree. Bacterial beta-diversity strongly multi-nutrient soil, respectively, playing major roles deep layers. Taken together, these results reveal new perspective on at fine scale single trees. Distinct response patterns underpinned as function during ex-arable land.

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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Distinct patterns and processes of abundant and rare eukaryotic plankton communities following a reservoir cyanobacterial bloom

The ISME Journal, Journal Year: 2018, Volume and Issue: 12(9), P. 2263 - 2277

Published: June 13, 2018

Abstract Plankton communities normally consist of few abundant and many rare species, yet little is known about the ecological role planktonic eukaryotes. Here we used a 18S ribosomal DNA sequencing approach to investigate dynamics eukaryotes, explore co-occurrence patterns eukaryotic plankton in subtropical reservoir following cyanobacterial bloom event. Our results showed that event significantly altered community composition diversity without affecting plankton. The similarities both subcommunities declined with increase time-lag, but stronger temporal turnover was observed taxa. Further, species explained higher percentage variation than richness. Both deterministic stochastic processes influenced assembly, pattern (e.g., drift) particularly pronounced for Co-occurrence network analysis revealed keystone taxa mainly belonged which may play fundamental roles persistence. Importantly, covariations between non-rare were predominantly positive, implying multispecies cooperation might contribute stability resilience microbial community. Overall, these findings expand current understanding mechanisms interactions underlying changing aquatic ecosystems.

Language: Английский

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Specialized metabolic functions of keystone taxa sustain soil microbiome stability

Microbiome, Journal Year: 2021, Volume and Issue: 9(1)

Published: Jan. 31, 2021

The relationship between biodiversity and soil microbiome stability remains poorly understood. Here, we investigated the impacts of bacterial phylogenetic diversity on functional traits microbiome. Communities differing in were generated by inoculating serially diluted suspensions into sterilized soil, was assessed detecting community variations under various pH levels. taxonomic features potential detected DNA sequencing.We found that communities with higher tended to be more stable, implying microbiomes are resistant perturbation. Functional gene co-occurrence network machine learning classification analyses identified specialized metabolic functions, especially "nitrogen metabolism" "phosphonate phosphinate metabolism," as keystone functions. Further annotation functions carried out specific taxa, including Nitrospira Gemmatimonas, among others.This study provides new insights our understanding relationships ecosystem highlights embedded taxa may essential for stability. Video abstract.

Language: Английский

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