Plant developmental stage drives the differentiation in ecological role of the maize microbiome DOI Creative Commons
Chao Xiong, Brajesh K. Singh, Ji‐Zheng He

et al.

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

Published: Aug. 13, 2021

Abstract Background Plants live with diverse microbial communities which profoundly affect multiple facets of host performance, but if and how development impacts the assembly, functions interactions crop microbiomes are poorly understood. Here we examined both bacterial fungal across soils, epiphytic endophytic niches leaf root, plastic fake plant (representing environment-originating microbes) at three developmental stages maize two contrasting sites, further explored potential function phylloplane based on metagenomics. Results Our results suggested that stage had a much stronger influence diversity, composition interkingdom networks in compartments than strongest effect phylloplane. Phylloplane were co-shaped by growth seasonal environmental factors, air (represented plants) as its important source. Further, found more strongly driven deterministic processes early similar pattern was for late stage. Moreover, taxa played role network yield prediction stage, while did so Metagenomic analyses indicated possessed higher functional diversity genes related to nutrient provision enriched N assimilation C degradation Coincidently, abundant beneficial like Actinobacteria, Burkholderiaceae Rhizobiaceae observed saprophytic fungi Conclusions suggest influences microbiome assembly functions, take differentiated ecological different development. This study provides empirical evidence exerting strong selection during These findings have implications future tools manipulate sustainable increase primary productivity.

Language: Английский

Microbiome definition re-visited: old concepts and new challenges DOI Creative Commons
Gabriele Berg, Daria Rybakova, Doreen Fischer

et al.

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

Citations

1621
The Role of Soil Microorganisms in Plant Mineral Nutrition—Current Knowledge and Future Directions DOI Creative Commons
Richard P. Jacoby, Manuela Peukert, A. Succurro

et al.

Frontiers in Plant Science, Journal Year: 2017, Volume and Issue: 8

Published: Sept. 19, 2017

In their natural environment plants are part of a rich ecosystem including numerous and diverse microorganisms in the soil. It has been long recognized that some these microbes, such as mycorrhizal fungi or nitrogen fixing symbiotic bacteria, play important roles plant performance by improving mineral nutrition. However, full range microbes associated with potential to replace synthetic agricultural inputs only recently started be uncovered. last few years great progress made knowledge on composition rhizospheric microbiomes dynamics. There is clear evidence shape microbiome structures, most probably root exudates, also bacteria have developed various adaptations thrive niche. The mechanisms interactions processes driving alterations however largely unknown. this review we focus interaction enhancing nutrition, summarizing current several research fields can converge improve our understanding molecular underpinning phenomenon.

Language: Английский

Citations

1197
Genetic strategies for improving crop yields DOI Open Access
Julia Bailey‐Serres, Jane E. Parker, Elizabeth A. Ainsworth

et al.

Nature, Journal Year: 2019, Volume and Issue: 575(7781), P. 109 - 118

Published: Nov. 6, 2019

Language: Английский

Citations

1134
Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots DOI Creative Commons
Samiran Banerjee, Florian Walder, Lucie Büchi

et al.

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

Citations

942
Core microbiomes for sustainable agroecosystems DOI
Hirokazu Toju, Kabir Peay, Masato Yamamichi

et al.

Nature Plants, Journal Year: 2018, Volume and Issue: 4(5), P. 247 - 257

Published: April 24, 2018

Language: Английский

Citations

794
Plant–Pathogen Warfare under Changing Climate Conditions DOI Creative Commons
André C. Velásquez, Christian Danve M. Castroverde, Sheng Yang He

et al.

Current Biology, Journal Year: 2018, Volume and Issue: 28(10), P. R619 - R634

Published: May 1, 2018

Language: Английский

Citations

737
Rhizosphere microbiome structure alters to enable wilt resistance in tomato DOI

Min-Jung Kwak,

Hyun Gi Kong, Kihyuck Choi

et al.

Nature Biotechnology, Journal Year: 2018, Volume and Issue: 36(11), P. 1100 - 1109

Published: Oct. 8, 2018

Language: Английский

Citations

686
Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming DOI Creative Commons
Kyle Hartman, Marcel G. A. van der Heijden, Raphaël Wittwer

et al.

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

Citations

606
Rhizosphere bacteriome structure and functions DOI Creative Commons
Ning Ling, Tingting Wang, Yakov Kuzyakov

et al.

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

Published: Feb. 11, 2022

Abstract Microbial composition and functions in the rhizosphere—an important microbial hotspot—are among most fascinating yet elusive topics ecology. We used 557 pairs of published 16S rDNA amplicon sequences from bulk soils rhizosphere different ecosystems around world to generalize bacterial characteristics with respect community diversity, composition, functions. The selects microorganisms soil function as a seed bank, reducing diversity. is enriched Bacteroidetes, Proteobacteria, other copiotrophs. Highly modular but unstable networks (common for r -strategists) reflect interactions adaptations dynamic conditions. Dormancy strategies are dominated by toxin–antitoxin systems, while sporulation common soils. Functional predictions showed that genes involved organic compound conversion, nitrogen fixation, denitrification were strongly (11–182%), nitrification depleted.

Language: Английский

Citations

605
Drought and Salinity Stress Responses and Microbe-Induced Tolerance in Plants DOI Creative Commons
Ying Ma, Maria Celeste Dias, Helena Freitas

et al.

Frontiers in Plant Science, Journal Year: 2020, Volume and Issue: 11

Published: Nov. 13, 2020

Drought and salinity are among the most important environmental factors that hampered agricultural productivity worldwide. Both stresses can induce several morphological, physiological, biochemical, metabolic alterations through various mechanisms, eventually influencing plant growth, development, productivity. The responses of plants to these stress conditions highly complex depend on other factors, such as species genotype, age size, rate progression well intensity duration stresses. These have a strong effect response define whether mitigation processes related acclimation will occur or not. In this review, we summarize how drought extensively affect growth in agriculture ecosystems. particular, focus Moreover, discuss mechanisms underlying plant-microbe interactions confer abiotic tolerance.

Language: Английский

Citations

533