Current, faltering, and future strategies for advancing microbiome-assisted sustainable agriculture and environmental resilience DOI Creative Commons
Ahmad Humayan Kabir,

Md Zakaria Ibne Baki,

Bulbul Ahmed

et al.

New Crops, Journal Year: 2024, Volume and Issue: 1, P. 100013 - 100013

Published: Jan. 29, 2024

Establishing global sustainable agriculture emerges as the primary, indispensable strategy to meet escalating food demands and address environmental preservation amidst challenges posed by severe climate change. The intricate communities of microorganisms associated with plants, collectively termed plant microbiome, wield significant influence over vitality productivity species. Unleashing potential microbiome stands a pivotal approach safeguard rejuvenate our planet. However, complex nature interactions, coupled their limited persistence in settings due gaps understanding or technological limitations, has impeded substantial progress this field. This review explores innovative revitalized strategies for harnessing microbiome-based enhancements crop fitness. Additionally, we illuminate encountered deciphering interplay between its host, particularly context mitigating adverse influences change on resilience. To navigate these complexities, advocate comprehensive that considers both host microbiome-oriented perspectives. dual-focused aims overcome current limitations pave way toward future where intervention forms bedrock protection.

Language: Английский

Plant–microbiome interactions: from community assembly to plant health DOI
Pankaj Trivedi, Jan E. Leach, Susannah G. Tringe

et al.

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

Published: Aug. 12, 2020

Language: Английский

Citations

2325
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
Climate change impacts on plant pathogens, food security and paths forward DOI Open Access
Brajesh K. Singh, Manuel Delgado‐Baquerizo, Eleonora Egidi

et al.

Nature Reviews Microbiology, Journal Year: 2023, Volume and Issue: 21(10), P. 640 - 656

Published: May 2, 2023

Language: Английский

Citations

561
Host selection shapes crop microbiome assembly and network complexity DOI Creative Commons
Chao Xiong, Yong‐Guan Zhu, Juntao Wang

et al.

New Phytologist, Journal Year: 2020, Volume and Issue: 229(2), P. 1091 - 1104

Published: Aug. 27, 2020

Plant microbiomes are essential to host health and productivity but the ecological processes that govern crop microbiome assembly not fully known. Here we examined bacterial communities across 684 samples from soils (rhizosphere bulk soil) multiple compartment niches (rhizoplane, root endosphere, phylloplane, leaf endosphere) in maize (Zea mays)-wheat (Triticum aestivum)/barley (Hordeum vulgare) rotation system under different fertilization practices at two contrasting sites. Our results demonstrate along soil-plant continuum is shaped predominantly by niche species rather than site or practice. From epiphytes endophytes, selection pressure sequentially increased diversity network complexity consequently reduced, with strongest effect endosphere. Source tracking indicates mainly derived gradually enriched filtered plant niches. Moreover, were dominated a few dominant taxa (c. 0.5% of phylotypes), bacilli identified as important biomarker for wheat barley Methylobacteriaceae maize. work provides comprehensive empirical evidence on selection, potential sources enrichment assembly, has implications future management manipulation sustainable agriculture.

Language: Английский

Citations

495
The structure and function of the global citrus rhizosphere microbiome DOI Creative Commons
Jin Xu, Yunzeng Zhang, Pengfan Zhang

et al.

Nature Communications, Journal Year: 2018, Volume and Issue: 9(1)

Published: Nov. 14, 2018

Citrus is a globally important, perennial fruit crop whose rhizosphere microbiome thought to play an important role in promoting citrus growth and health. Here, we report comprehensive analysis of the structural functional composition microbiome. We use both amplicon deep shotgun metagenomic sequencing bulk soil samples collected across distinct biogeographical regions from six continents. Predominant taxa include Proteobacteria, Actinobacteria, Acidobacteria Bacteroidetes. The core comprises Pseudomonas, Agrobacterium, Cupriavidus, Bradyrhizobium, Rhizobium, Mesorhizobium, Burkholderia, Cellvibrio, Sphingomonas, Variovorax Paraburkholderia, some which are potential plant beneficial microbes. also identify over-represented microbial traits mediating plant-microbe microbe-microbe interactions, nutrition acquisition promotion rhizosphere. results provide valuable information guide isolation culturing and, potentially, harness power improve production

Language: Английский

Citations

424
Transfer of antibiotic resistance from manure-amended soils to vegetable microbiomes DOI Creative Commons
Yu Jing Zhang, Hang‐Wei Hu, Qing‐Lin Chen

et al.

Environment International, Journal Year: 2019, Volume and Issue: 130, P. 104912 - 104912

Published: June 17, 2019

The increasing antimicrobial resistance in manure-amended soil can potentially enter food chain, representing an important vehicle for antibiotic genes (ARGs) transmission into human microbiome. However, the pathways of ARGs from to plant remain unclear. Here, we explored impacts poultry and cattle manure application on patterns resistome lettuce microbiome including rhizosphere, root endosphere, leaf endosphere phyllosphere, identify potential routes soil-plant system. After 90 days cultivation, a total 144 were detected all samples using high-throughput quantitative PCR. Rhizosphere harbored most diverse compared with other components lettuce. Cattle increased abundance endophyte, while endophyte suggesting that may have stronger impact resistomes. ARG profiles significantly correlated bacterial community, enrichment resistomes was strongly affected by taxa Solibacteres, Chloroflexi, Acidobacteria, Gemm-1 Gemmatimonadetes, as revealed network analyses. Moreover, overlaps between tissues identified, which indicated environmental are interconnected. Our findings provide insights manured vegetables, highlight risks migration chain.

Language: Английский

Citations

382
Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling DOI Creative Commons
Jennifer E. Schmidt, Angela D. Kent, Vanessa Brisson

et al.

Microbiome, Journal Year: 2019, Volume and Issue: 7(1)

Published: Nov. 7, 2019

Abstract Background Rhizosphere microbial communities are key regulators of plant performance, yet few studies have assessed the impact different management approaches on rhizosphere microbiomes major crops. shaped by interactions between agricultural and host selection processes, but often consider these factors individually rather than in combination. We tested impacts (M) effects (R) community structure co-occurrence networks maize roots collected from long-term conventionally organically managed maize-tomato agroecosystems. also explored interaction (M × R) how it diversity composition, differential abundance, indicator taxa, network structure, nitrogen-cycling processes. Results Host processes moderate influence communities, although bacteria fungi respond differently to management. found that plants recruit management-system-specific taxa shift N-cycling pathways rhizosphere, distinguishing this soil compartment bulk soil. conventional organic systems were more similar their respective soils, composition was affected both M R effects. In contrast, fungal only management, selection. Quantification six genes ( nifH , amoA [bacterial archaeal], nirK nrfA nosZ ) revealed abundance higher system. Conclusions Plant interacts with practices shape patterns, at least one process. Reframing research priorities better understand adaptive plant-microbe feedbacks include as a significant moderating outcomes could help guide plant-oriented strategies improve productivity agroecosystem sustainability.

Language: Английский

Citations

288
Root microbiota shift in rice correlates with resident time in the field and developmental stage DOI
Jingying Zhang, Na Zhang, Yongxin Liu

et al.

Science China Life Sciences, Journal Year: 2018, Volume and Issue: 61(6), P. 613 - 621

Published: March 23, 2018

Language: Английский

Citations

280
New frontiers in agriculture productivity: Optimised microbial inoculants and in situ microbiome engineering DOI
Zhiguang Qiu, Eleonora Egidi, Hongwei Liu

et al.

Biotechnology Advances, Journal Year: 2019, Volume and Issue: 37(6), P. 107371 - 107371

Published: March 16, 2019

Language: Английский

Citations

267
Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops DOI Creative Commons
Keara L. Grady, Jackson W. Sorensen, Nejc Stopnišek

et al.

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

Citations

219