Plant–microbiome interactions: from community assembly to plant health

Nature Reviews Microbiology, Journal Year: 2020, Volume and Issue: 18(11), P. 607 - 621

Published: Aug. 12, 2020

Language: Английский

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Microbiome definition re-visited: old concepts and new challenges

Microbiome, Journal Year: 2020, Volume and Issue: 8(1)

Published: June 30, 2020

The field of microbiome research has evolved rapidly over the past few decades and become a topic great scientific public interest. As result this rapid growth in interest covering different fields, we are lacking clear commonly agreed definition term "microbiome." Moreover, consensus on best practices is missing. Recently, panel international experts discussed current gaps frame European-funded MicrobiomeSupport project. meeting brought together about 40 leaders from diverse areas, while more than hundred all world took part an online survey accompanying workshop. This article excerpts outcomes workshop corresponding embedded short historical introduction future outlook. We propose based compact, clear, comprehensive description provided by Whipps et al. 1988, amended with set novel recommendations considering latest technological developments findings. clearly separate terms microbiota provide discussion composition microbiota, heterogeneity dynamics microbiomes time space, stability resilience microbial networks, core microbiomes, functionally relevant keystone species as well co-evolutionary principles microbe-host inter-species interactions within microbiome. These broad definitions suggested unifying concepts will help to improve standardization studies future, could be starting point for integrated assessment data resulting transfer knowledge basic science into practice. Furthermore, standards important solving new challenges associated anthropogenic-driven changes planetary health, which understanding might play key role. Video Abstract.

Language: Английский

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The sponge holobiont in a changing ocean: from microbes to ecosystems

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

Published: March 9, 2018

The recognition that all macroorganisms live in symbiotic association with microbial communities has opened up a new field biology. Animals, plants, and algae are now considered holobionts, complex ecosystems consisting of the host, microbiota, interactions among them. Accordingly, ecological concepts can be applied to understand host-derived processes govern dynamics interactive networks within holobiont. In marine systems, holobionts further integrated into larger more ecosystems, concept referred as "nested ecosystems." this review, we discuss dynamic interact at multiple scales respond environmental change. We focus on symbiosis sponges their communities—a resulted one most diverse environment. recent years, sponge microbiology remarkably advanced terms curated databases, standardized protocols, information functions microbiota. Like Russian doll, these translated holobiont impact surrounding ecosystem. For example, sponge-associated metabolisms, fueled by high filtering capacity substantially affect biogeochemical cycling key nutrients like carbon, nitrogen, phosphorous. Since increasingly threatened anthropogenic stressors jeopardize stability ecosystem, link between perturbations, dysbiosis, diseases. Experimental studies suggest community composition is tightly linked health, but whether dysbiosis cause or consequence collapse remains unresolved. Moreover, potential role microbiome mediating for acclimate adapt change unknown. Future should aim identify mechanisms underlying scales, from develop management strategies preserve provided our present future oceans.

Language: Английский

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Composition and Variation of the Human Milk Microbiota Are Influenced by Maternal and Early-Life Factors

Cell Host & Microbe, Journal Year: 2019, Volume and Issue: 25(2), P. 324 - 335.e4

Published: Feb. 1, 2019

Language: Английский

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Defining and quantifying the core microbiome: Challenges and prospects

Proceedings of the National Academy of Sciences, Journal Year: 2021, Volume and Issue: 118(51)

Published: Dec. 3, 2021

The term "core microbiome" has become widely used in microbial ecology over the last decade. Broadly, core microbiome refers to any set of taxa, or genomic and functional attributes associated with those that are characteristic a host environment interest. Most commonly, microbiomes measured as taxa shared among two more samples from particular environment. Despite popularity this its growing use, there is little consensus about how should be quantified practice. Here, we present brief history concept use representative sample literature review different metrics commonly for quantifying core. Empirical analyses have wide range microbiome, including arbitrary occurrence abundance cutoff values, focal taxonomic level ranging phyla amplicon sequence variants. However, many these susceptible sampling other biases. Developing standardized accounts such biases necessary testing specific hypotheses ecological roles microbiomes.

Language: Английский

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Field study reveals core plant microbiota and relative importance of their drivers

Environmental Microbiology, Journal Year: 2017, Volume and Issue: 20(1), P. 124 - 140

Published: Dec. 21, 2017

Harnessing plant microbiota can assist in sustainably increasing primary productivity to meet growing global demands for food and biofuel. However, development of rational microbiome-based approaches improving crop yield is currently hindered by a lack understanding the major biotic abiotic factors shaping microbiome under relevant field conditions. We examined bacterial fungal communities associated with both aerial (leaves, stalks) belowground (roots, soil) compartments four commercial sugarcane varieties (Saccharum spp.) grown several regions Australia. identified drivers conditions evaluated whether plants shared core microbiome. Sugarcane-associated microbial assemblages were primarily determined compartment, followed region, age, variety Yellow Canopy Syndrome (YCS). detected set members that influenced YCS incidence. Our study revealed key hub microorganisms networks leaves, stalks, roots rhizosphere soil despite location time-associated shifts community assemblages. Elucidating their functional roles identification keystone sustain health could provide technological breakthrough sustainable increase productivity.

Language: Английский

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MiDAS 4: A global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: April 7, 2022

Abstract Microbial communities are responsible for biological wastewater treatment, but our knowledge of their diversity and function is still poor. Here, we sequence more than 5 million high-quality, full-length 16S rRNA gene sequences from 740 treatment plants (WWTPs) across the world use to construct ‘MiDAS 4’ database. MiDAS 4 an amplicon variant resolved, reference database with a comprehensive taxonomy domain species level all sequences. We independent dataset (269 WWTPs) show that 4, compared commonly used universal databases, provides better coverage WWTP bacteria improved rate genus classification. Taking advantage carry out amplicon-based, global-scale microbial community profiling activated sludge using two common sets primers targeting regions gene, revealing how environmental conditions biogeography shape microbiota. also identify core conditionally rare or abundant taxa, encompassing 966 genera 1530 represent approximately 80% 50% accumulated read abundance, respectively. Finally, well-studied functional guilds, such as nitrifiers polyphosphate-accumulating organisms, same prevalent worldwide, only few in each genus.

Language: Английский

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The microbiome in threatened species conservation

Biological Conservation, Journal Year: 2018, Volume and Issue: 229, P. 85 - 98

Published: Nov. 24, 2018

Language: Английский

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The mosquito holobiont: fresh insight into mosquito-microbiota interactions

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

Published: March 20, 2018

The holobiont concept was first developed for coral ecosystems but has been extended to multiple organisms, including plants and other animals. Studies on insect-associated microbial communities have produced strong evidence that symbiotic bacteria play a major role in host biology. However, the understanding of these relationships mainly limited phytophagous insects, while host-associated microbiota haematophagous insect vectors remains largely unexplored. Mosquitoes are global public health concern, with concomitant increase people at risk infection. emergence re-emergence mosquito-borne diseases led many researchers study both mosquito its associated microbiota. Although most studies descriptive, they broad description bacterial hosted by populations. This review describes key advances progress field research also encompassing microbes environmental factors driving their composition diversity. discussion includes recent findings functional roles underlines interactions biology pathogen transmission. Insight into ecology multipartite interactions, we consider conferring term is useful get comprehensive vector pathosystem functioning so as be able develop innovative efficient novel control strategies.

Language: Английский

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Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops

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

Published: Sept. 12, 2019

Perennial grasses are promising feedstocks for biofuel production, with potential leveraging their native microbiomes to increase productivity and resilience environmental stress. Here, we characterize the 16S rRNA gene diversity seasonal assembly of bacterial archaeal two perennial cellulosic feedstocks, switchgrass (Panicum virgatum L.) miscanthus (Miscanthus x giganteus). We sample leaves soil every three weeks from pre-emergence through senescence consecutive growing seasons one season, identify core leaf taxa based on occupancy. Virtually all also detected in soil; source-sink modeling shows non-random, ecological filtering by leaf, suggesting that is an important reservoir phyllosphere diversity. Core include early, mid, late season groups were consistent across years crops. This consistency microbiome dynamics members manipulation or management support crop production.

Language: Английский

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