Assessment of soil quality for guided fertilization in 7 barley agro-ecological areas of China

Zhou, Yuan; Fan, Yingcheng; Lu, Guang; Zhang, Anyong; Zhao, Ting; Sun, Genlou; Sun, Dongqing; Yu, Qi; Ren, Xifeng

doi:10.1371/journal.pone.0261638

Cited by 4 publications

(4 citation statements)

References 61 publications

(75 reference statements)

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“…Environmental pH perturbation is a significant factor affecting both plants and their associated microbiota, as it can disrupt cellular homeostasis and physiology ( Zhou et al., 2022 ). The southwestern regions of China have experienced high levels of acid rain, which may have had an impact on foliar ecology ( Zhang et al., 2021 ).…”

Section: Resultsmentioning

confidence: 99%

Pan-metagenome reveals the abiotic stress resistome of cigar tobacco phyllosphere microbiome

Wang,

Peng,

et al. 2023

Front. Plant Sci.

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The important role of microbial associations in mediating plant protection and responses to abiotic stresses has been widely recognized. However, there have been limited studies on the functional profile of the phyllosphere microbiota from tobacco (Nicotiana tabacum), hindering our understanding of the mechanisms underlying stress resilience in this representative and easy-to-cultivate model species from the solanaceous family. To address this knowledge gap, our study employed shotgun metagenomic sequencing for the first time to analyze the genetic catalog and identify putative plant growth promoting bacteria (PGPB) candidates that confer abiotic stress resilience throughout the growth period of cigar tobacco in the phyllosphere. We identified abundant genes from specific bacterial lineages, particularly Pseudomonas, within the cigar tobacco phyllospheric microbiome. These genes were found to confer resilience against a wide range of stressors, including osmotic and drought stress, heavy metal toxicity, temperature perturbation, organic pollutants, oxidative stress, and UV light damage. In addition, we conducted a virome mining analysis on the metagenome to explore the potential roles of viruses in driving microbial adaptation to environmental stresses. Our results identified a total of 3,320 scaffolds predicted to be viral from the cigar tobacco phyllosphere metagenome, with various phages infecting Pseudomonas, Burkholderia, Enterobacteria, Ralstonia, and related viruses. Within the virome, we also annotated genes associated with abiotic stress resilience, such as alkaline phosphatase D (phoD) for nutrient solubilization and glutamate-5-semialdehyde dehydrogenase (proA) for osmolyte synthesis. These findings shed light on the unexplored roles of viruses in facilitating and transferring abiotic stress resilience in the phyllospheric microbiome through beneficial interactions with their hosts. The findings from this study have important implications for agricultural practices, as they offer potential strategies for harnessing the capabilities of the phyllosphere microbiome to enhance stress tolerance in crop plants.

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Section: Resultsmentioning

confidence: 99%

Pan-metagenome reveals the abiotic stress resistome of cigar tobacco phyllosphere microbiome

Wang,

Peng,

et al. 2023

Front. Plant Sci.

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“…Environmental pH is considered as an important factor for plants since it influences soil physical, chemical properties and nutrient availability and thereby affects plant inner homeostasis and growth ( Zhou et al., 2022 ). Interestingly, we have excavated seven microbe-derived gene entries linking with pH homeostasis maintenance and acid stress resistance in five tested plant genomes ( Table 2 ): two basic amino acid/spermidine/putrescine transporter and a proton extrusion protein (PcxA) encoding genes acquired from Bacteria, and genes within the arginine deiminase pathway (argininosuccinate synthase, argininosuccinate lyase, carbamate kinase and arginine deiminase) derived from Bacteria and Amoeba, which might conduct pH regulation by neutralization of proton with base substrates like ammonia, arginine and polyamine.…”

Section: Resultsmentioning

confidence: 99%

Genome mining reveals abiotic stress resistance genes in plant genomes acquired from microbes via HGT

Peng²,

Wang

et al. 2022

Front. Plant Sci.

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Colonization by beneficial microbes can enhance plant tolerance to abiotic stresses. However, there are still many unknown fields regarding the beneficial plant-microbe interactions. In this study, we have assessed the amount or impact of horizontal gene transfer (HGT)-derived genes in plants that have potentials to confer abiotic stress resistance. We have identified a total of 235 gene entries in fourteen high-quality plant genomes belonging to phyla Chlorophyta and Streptophyta that confer resistance against a wide range of abiotic pressures acquired from microbes through independent HGTs. These genes encode proteins contributed to toxic metal resistance (e.g., ChrA, CopA, CorA), osmotic and drought stress resistance (e.g., Na+/proline symporter, potassium/proton antiporter), acid resistance (e.g., PcxA, ArcA, YhdG), heat and cold stress resistance (e.g., DnaJ, Hsp20, CspA), oxidative stress resistance (e.g., GST, PoxA, glutaredoxin), DNA damage resistance (e.g., Rad25, Rad51, UvrD), and organic pollutant resistance (e.g., CytP450, laccase, CbbY). Phylogenetic analyses have supported the HGT inferences as the plant lineages are all clustering closely with distant microbial lineages. Deep-learning-based protein structure prediction and analyses, in combination with expression assessment based on codon adaption index (CAI) further corroborated the functionality and expressivity of the HGT genes in plant genomes. A case-study applying fold comparison and molecular dynamics (MD) of the HGT-driven CytP450 gave a more detailed illustration on the resemblance and evolutionary linkage between the plant recipient and microbial donor sequences. Together, the microbe-originated HGT genes identified in plant genomes and their participation in abiotic pressures resistance indicate a more profound impact of HGT on the adaptive evolution of plants.

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“…Barley has more than 5000 years of cultivation history in China [7]. It is mainly used as feed and beer industrial raw materials, and it is also the most important rotation crop and functional health food for Tibetan compatriots [8]. In recent years, with the improvement of people's living standards and the rapid development of the processing industry, the beer and feeding value of barley has been further improved [9].…”

Section: Introductionmentioning

confidence: 99%

“…Meanwhile, barley has the characteristics of wide adaptability, strong resistance to stress, and short growth period [10]. It is widely cultivated in northeast China, northwest China, south China, Huanghuai, Yunnan-Guizhou, and the Qinghai-Tibet Plateau [8]. Therefore, whether barley has a wide range of adaptability, salt and alkali resistance, barren resistance, and other stress resistance is related to its rhizosphere microecological environment, and determining the characteristics of the composition of these microbial communities is an urgent matter in terms of barley's wide adaptability and stress resistance [11,12].…”

Section: Introductionmentioning

confidence: 99%

Bacterial Community Structure in Rhizosphere of Barley at Maturity Stage

Zhang,

An,

Zhou

et al. 2023

Agronomy

Self Cite

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The crop rhizosphere is the main site of soil microbial activities. Understanding the structure and diversity of microbial communities in the crop rhizosphere will help us reveal interactions between rhizosphere microorganisms and plant growth. In this study, the rhizosphere soil was collected from 35 cultivated barley varieties at the mature stage. To investigate the structure and diversity of bacterial communities in the rhizosphere of different barley varieties, the 16S rDNA gene of microorganisms from the soil was sequenced using Illumina MiSeq next-generation high-throughput sequencing technology. The results showed that 13, 25, 49, and 59 bacterial flora with relative abundance >1% were detected from 35 barley rhizosphere samples at the phylum, class, order, and family levels, respectively. The abundance of bacteria among varieties differed relatively little, but the abundance of the same bacteria in rhizospheres of different varieties was different. In addition, both the cluster analysis and principal component analysis (PCA) divided the 35 samples into three clusters at the phylum level. Groups III and IV showed significantly higher abundance than group II in Proteobacteria, while group II exhibited significantly higher abundance of Chloroflexi than groups III and IV. This finding provides a realistic basis for further using the relationship between barley rhizosphere microorganisms and barley growth to improve the resistance and quality of barley.

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Assessment of soil quality for guided fertilization in 7 barley agro-ecological areas of China

Cited by 4 publications

References 61 publications

Pan-metagenome reveals the abiotic stress resistome of cigar tobacco phyllosphere microbiome

Pan-metagenome reveals the abiotic stress resistome of cigar tobacco phyllosphere microbiome

Genome mining reveals abiotic stress resistance genes in plant genomes acquired from microbes via HGT

Bacterial Community Structure in Rhizosphere of Barley at Maturity Stage

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