Stochastic Community Assembly: Does It Matter in Microbial Ecology?

Microbiology and Molecular Biology Reviews, Journal Year: 2017, Volume and Issue: 81(4)

Published: Oct. 12, 2017

Understanding the mechanisms controlling community diversity, functions, succession, and biogeography is a central, but poorly understood, topic in ecology, particularly microbial ecology. Although stochastic processes are believed to play nonnegligible roles shaping structure, their importance relative deterministic hotly debated. The of ecological stochasticity structure far less appreciated. Some main reasons for such heavy debates difficulty defining diverse methods used delineating stochasticity. Here, we provide critical review synthesis data from most recent studies on assembly We then describe both components embedded various processes, including selection, dispersal, diversification, drift. also different approaches inferring observational diversity patterns highlight experimental communities. In addition, research challenges, gaps, future directions research.

Language: Английский

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Microbial interactions within the plant holobiont

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

Published: March 27, 2018

Since the colonization of land by ancestral plant lineages 450 million years ago, plants and their associated microbes have been interacting with each other, forming an assemblage species that is often referred to as a "holobiont." Selective pressure acting on holobiont components has likely shaped plant-associated microbial communities selected for host-adapted microorganisms impact fitness. However, high densities detected tissues, together fast generation time more ancient origin compared host, suggest microbe-microbe interactions are also important selective forces sculpting complex assemblages in phyllosphere, rhizosphere, endosphere compartments. Reductionist approaches conducted under laboratory conditions critical decipher strategies used specific cooperate compete within or outside tissues. Nonetheless, our understanding these shaping communities, along relevance host health natural context, remains sparse. Using examples obtained from reductionist community-level approaches, we discuss fundamental role (prokaryotes micro-eukaryotes) community structure health. We provide conceptual framework illustrating among microbiota members establishment maintenance host-microbial homeostasis.

Language: Английский

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Mycobiome diversity: high-throughput sequencing and identification of fungi

Nature Reviews Microbiology, Journal Year: 2018, Volume and Issue: 17(2), P. 95 - 109

Published: Nov. 15, 2018

Language: Английский

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FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles

Fungal Diversity, Journal Year: 2020, Volume and Issue: 105(1), P. 1 - 16

Published: Nov. 1, 2020

Language: Английский

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Ancestral alliances: Plant mutualistic symbioses with fungi and bacteria

Science, Journal Year: 2017, Volume and Issue: 356(6340)

Published: May 25, 2017

Within the plant microbiota, mutualistic fungal and bacterial symbionts are striking examples of microorganisms playing crucial roles in nutrient acquisition. They have coevolved with their hosts since initial adaptation to land. Despite evolutionary distances that separate mycorrhizal nitrogen-fixing symbioses, these associations share a number highly conserved features, including specific symbiotic signaling pathways, root colonization strategies circumvent immune responses, functional host-microbe interface formation, central role phytohormones symbiosis-associated developmental pathways. We highlight recent emerging areas investigation relating evolutionarily mechanisms, an emphasis on more ancestral associations, consider what extent this knowledge can contribute understanding plant-microbiota as whole.

Language: Английский

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Biophysical processes supporting the diversity of microbial life in soil

FEMS Microbiology Reviews, Journal Year: 2017, Volume and Issue: 41(5), P. 599 - 623

Published: July 10, 2017

Soil, the living terrestrial skin of Earth, plays a central role in supporting life and is home to an unimaginable diversity microorganisms. This review explores key drivers for microbial soils under different climates land-use practices at scales ranging from soil pores landscapes. We delineate special features as habitat (focusing on bacteria) consequences communities. covers recent modeling advances that link physical processes with (termed biophysical processes). Readers are introduced concepts governing water organization associated transport properties dispersion ranges often determined by spatial highly dynamic aqueous phase. The narrow hydrological windows wetting phase connectedness crucial resource distribution longer range Feedbacks between activity their immediate environment responsible emergence stabilization structure-the scaffolding ecological functioning. synthesize insights historical contemporary studies provide outlook challenges opportunities developing quantitative framework predict component

Language: Английский

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Threats Posed by the Fungal Kingdom to Humans, Wildlife, and Agriculture

mBio, Journal Year: 2020, Volume and Issue: 11(3)

Published: May 4, 2020

The fungal kingdom includes at least 6 million eukaryotic species and is remarkable with respect to its profound impact on global health, biodiversity, ecology, agriculture, manufacturing, biomedical research. Approximately 625 have been reported infect vertebrates, 200 of which can be human associated, either as commensals members our microbiome or pathogens that cause infectious diseases. These organisms pose a growing threat health the increase in incidence invasive infections, prevalence allergy, evolution resistant some all current classes antifungals. More broadly, there has an unprecedented worldwide emergence affecting animal plant biodiversity. 8,000 fungi Oomycetes are associated disease. Indeed, across such diseases plants include new devastating epidemics trees jeopardize food security by causing staple commodity crops feed billions. Further, ingestion mycotoxins contributes ill causes cancer. Coordinated international research efforts, enhanced technology translation, greater policy outreach scientists needed more fully understand biology drivers underlie mitigate against their impacts. Here, we focus poignant examples emerging threats each three areas: wildlife security.

Language: Английский

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Abundant fungi adapt to broader environmental gradients than rare fungi in agricultural fields

Global Change Biology, Journal Year: 2020, Volume and Issue: 26(8), P. 4506 - 4520

Published: April 23, 2020

Abstract Soil communities are intricately linked to ecosystem functioning, and a predictive understanding of how assemble in response environmental change is great ecological importance. Little known about the assembly processes governing abundant rare fungal across agro‐ecosystems, particularly with regard their adaptation. By considering taxa, we tested thresholds phylogenetic signals for preferences complex gradients reflect adaptation, explored factors influencing based on large‐scale soil survey agricultural fields eastern China. We found that taxa exhibited remarkably broader stronger compared taxa. Neutral played key role shaping subcommunity subcommunity. Null model analysis revealed was less clustered phylogenetically governed primarily by dispersal limitation, while homogeneous selection major process available sulfur factor mediating balance between stochastic deterministic both subcommunities, as indicated an increase stochasticity higher concentration. Based macroecological spatial scale datasets, our study potential adaptation identified distinct community fields. These results contribute mechanisms underlying generation maintenance diversity global change.

Language: Английский

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Fungi in aquatic ecosystems

Nature Reviews Microbiology, Journal Year: 2019, Volume and Issue: 17(6), P. 339 - 354

Published: March 12, 2019

Language: Английский

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The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome

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

Published: Feb. 12, 2018

Microorganisms serve important functions within numerous eukaryotic host organisms. An understanding of the variation in plant niche-level microbiome, from rhizosphere soils to canopies, is imperative gain a better how both structural and functional processes microbiomes impact health overall holobiome. Using Populus trees as model ecosystem, we characterized archaeal/bacterial fungal microbiome across 30 different tissue-level niches replicated deltoides hybrid trichocarpa × individuals using 16S ITS2 rRNA gene analyses. Our analyses indicate that varied primarily broader habitat classes (leaves, stems, roots, soils) regardless genotype, except for communities leaf niches, which were greatly impacted by genotype. Differences between tree genotypes are evident elevated presence two potential pathogens, Marssonina brunnea Septoria sp., on P. may turn be contributing divergence composition. Archaeal/bacterial diversity increased leaves, stem, root, soil habitats, whereas was greatest stems soils. This study provides holistic structure bioenergy relevant host, one most complete any plant. As such, it constitutes detailed atlas or map further hypothesis testing significance individual microbial taxa specific habitats baseline comparisons other species.

Language: Английский

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