Keystone taxa as drivers of microbiome structure and functioning

Banerjee, Samiran; Schlaeppi, Klaus; Heijden, Marcel G. A. van der

doi:10.1038/s41579-018-0024-1

Cited by 1,747 publications

(1,209 citation statements)

References 105 publications

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“…OTUs that provide complementary nutrients to the host are retained by the immune system: de Medina, Ortega‐González, González‐Pérez, Capitán‐Cañadas, & Martínez‐Augustin, ). Clostridia OTUs are also hubs for associations in the human gut community (Banerjee, Schlaeppi, & van der Heijden, ; Faust et al, ), but the importance of Mollicutes has not been, to our knowledge, reported elsewhere. Moreover, we detected no negative associations between Bacteroidetes and Firmicutes even though Bacteroidetes was common in our samples; this group may not play a dominant role in structuring moose gut microbial communities as they do in humans (Banerjee et al, ; Faust et al, ).…”

Section: Discussionmentioning

confidence: 99%

“…Clostridia OTUs are also hubs for associations in the human gut community (Banerjee, Schlaeppi, & van der Heijden, ; Faust et al, ), but the importance of Mollicutes has not been, to our knowledge, reported elsewhere. Moreover, we detected no negative associations between Bacteroidetes and Firmicutes even though Bacteroidetes was common in our samples; this group may not play a dominant role in structuring moose gut microbial communities as they do in humans (Banerjee et al, ; Faust et al, ). Whether the same relationships apply in herbivore populations where Bacteroidetes is dominant, as was the case in an Alaskan and Swedish moose (Ishaq & Wright, ; Svartström et al, ), remains an open question.…”

Section: Discussionmentioning

confidence: 99%

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Microbial associations and spatial proximity predict North American moose (Alces alces) gastrointestinal community composition

Fountain-Jones

Clark

Kinsley

et al. 2020

Journal of Animal Ecology

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Microbial communities are increasingly recognized as crucial for animal health. However, our understanding of how microbial communities are structured across wildlife populations is poor. Mechanisms such as interspecific associations are important in structuring free‐living communities, but we still lack an understanding of how important interspecific associations are in structuring gut microbial communities in comparison with other factors such as host characteristics or spatial proximity of hosts. Here, we ask how gut microbial communities are structured in a population of North American moose Alces alces. We identify key microbial interspecific associations within the moose gut and quantify how important they are relative to key host characteristics, such as body condition, for predicting microbial community composition. We sampled gut microbial communities from 55 moose in a population experiencing decline due to a myriad of factors, including pathogens and malnutrition. We examined microbial community dynamics in this population utilizing novel graphical network models that can explicitly incorporate spatial information. We found that interspecific associations were the most important mechanism structuring gut microbial communities in moose and detected both positive and negative associations. Models only accounting for associations between microbes had higher predictive value compared to models including moose sex, evidence of previous pathogen exposure or body condition. Adding spatial information on moose location further strengthened our model and allowed us to predict microbe occurrences with ~90% accuracy. Collectively, our results suggest that microbial interspecific associations coupled with host spatial proximity are vital in shaping gut microbial communities in a large herbivore. In this case, previous pathogen exposure and moose body condition were not as important in predicting gut microbial community composition. The approach applied here can be used to quantify interspecific associations and gain a more nuanced understanding of the spatial and host factors shaping microbial communities in non‐model hosts.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Microbial associations and spatial proximity predict North American moose (Alces alces) gastrointestinal community composition

Fountain-Jones

Clark

Kinsley

et al. 2020

Journal of Animal Ecology

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“…In return, the plant supplies the fungus with lipids and sugars, at a cost of up to 20% of the carbon (C) fixed by photosynthesis (Smith & Read, ; Bravo et al ., ; Jiang et al ., ). It is known that AM fungi play a key role in ecosystems and they have been recognized as keystone taxa in microbial communities (Van der Heijden et al ., ; Keymer et al ., ; Luginbuehl et al ., ; Powell & Rillig, ; Banerjee et al ., ).…”

Section: Introductionmentioning

confidence: 97%

Molecular dialogue between arbuscular mycorrhizal fungi and the nonhost plant Arabidopsis thaliana switches from initial detection to antagonism

et al. 2019

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Summary Approximately 29% of all vascular plant species are unable to establish an arbuscular mycorrhizal (AM) symbiosis. Despite this, AM fungi (Rhizophagus spp.) are enriched in the root microbiome of the nonhost Arabidopsis thaliana, and Arabidopsis roots become colonized when AM networks nurtured by host plants are available. Here, we investigated the nonhost–AM fungus interaction by analyzing transcriptional changes in Rhizophagus, Arabidopsis and the host plant Medicago truncatula while growing in the same mycorrhizal network. In early interaction stages, Rhizophagus activated the Arabidopsis strigolactone biosynthesis genes CCD7 and CCD8, suggesting that detection of AM fungi is not completely impaired. However, in colonized Arabidopsis roots, fungal nutrient transporter genes GintPT, GintAMT2, GintMST2 and GintMST4, essential for AM symbiosis, were not activated. RNA‐seq transcriptome analysis pointed to activation of costly defenses in colonized Arabidopsis roots. Moreover, Rhizophagus colonization caused a 50% reduction in shoot biomass, but also led to enhanced systemic immunity against Botrytis cinerea. This suggests that early signaling between AM fungi and Arabidopsis is not completely impaired and that incompatibility appears at later interaction stages. Moreover, Rhizophagus‐mediated defenses coincide with reduced Arabidopsis growth, but also with systemic disease resistance, highlighting the multifunctional role of AM fungi in host and nonhost interactions.

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“…Interestingly, the relative abundance of keystone species in our study was low (Table S3). Previous network studies reported that relative low abundance or even rare species are likely to be the keystone species in the soil networks (Banerjee, Schlaeppi, & van der Heijden, ; Shi et al, ). Less abundant species can be equally or more functionally important than abundant species in maintaining microbial networks (Lyons & Schwartz, ; Pester, Bittner, Deevong, Wagner, & Loy, ).…”

Section: Discussionmentioning

confidence: 99%

Seed mucilage interacts with soil microbial community and physiochemical processes to affect seedling emergence on desert sand dunes

Zhang

Baskin

et al. 2018

Plant Cell & Environment

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Seedling emergence is a critical stage in the establishment of desert plants. Soil microbes participate in plant growth and development, but information is lacking with regard to the role of microbes on seedling emergence. We applied the biocides (captan and streptomycin) to assess how seed mucilage interacts with soil microbial community and physiochemical processes to affect seedling emergence of Artemisia sphaerocephala on the desert sand dune. Fungal and bacterial community composition and diversity and fungal-bacterial interactions were changed by both captan and streptomycin. Mucilage increased soil enzyme activities and fungal-bacterial interactions. Highest seedling emergence occurred under streptomycin and mucilage treatment. Members of the phyla Firmicutes and Glomeromycota were the keystone species that improved A. sphaerocephala seedling emergence, by increasing resistance of young seedlings to drought and pathogen. Seed mucilage directly improved seedling emergence and indirectly interacted with the soil microbial community through strengthening fungal-bacterial interactions and providing favourable environment for soil enzymes to affect seedling emergence. Our study provides a comprehensive understanding of the regulatory mechanisms by which soil microbial community and seed mucilage interactively promote successful establishment of populations of desert plants on the barren and stressful sand dune.

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Keystone taxa as drivers of microbiome structure and functioning

Cited by 1,747 publications

References 105 publications

Microbial associations and spatial proximity predict North American moose (Alces alces) gastrointestinal community composition

Microbial associations and spatial proximity predict North American moose (Alces alces) gastrointestinal community composition

Molecular dialogue between arbuscular mycorrhizal fungi and the nonhost plant Arabidopsis thaliana switches from initial detection to antagonism

Seed mucilage interacts with soil microbial community and physiochemical processes to affect seedling emergence on desert sand dunes

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