Salinity altered root distribution and increased diversity of bacterial communities in the rhizosphere soil of Jerusalem artichoke

Bacterial communities associated with roots influence the health and nutrition of the host plant. However, the microbiome discrepancy are not well understood under different healthy conditions. Here, we tested the hypothesis that rhizosphere soil microbial diversity and function varies along a degeneration gradient of poplar, with a focus on plant growth promoting bacteria (PGPB) and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG (antibiotics resistance genes) annotation revealed that available potassium (AK) was correlated with microbial diversity and function. We proposed several microbes, Bradyrhizobium, Sphingomonas, Mesorhizobium, Nocardioides, Variovorax, Gemmatimonadetes, Rhizobacter, Pedosphaera, Candidatus Solibacter, Acidobacterium, and Phenylobacterium, as candidates to reflect the soil fertility and the plant health. The highest abundance of multidrug resistance genes and the four mainly microbial resistance mechanisms (antibiotic efflux, antibiotic target protection, antibiotic target alteration, and antibiotic target replacement) in healthy poplar rhizosphere, corroborated the relationship between soil fertility and microbial activity. This result suggested that healthy rhizosphere soil harbored microbes with a higher capacity and had more complex microbial interaction network to promote plant growing and reduce intracellular levels of antibiotics. Our findings suggested a correlation between the plant degeneration gradient and bacterial communities, and provided insight into the role of high-turnover microbial communities as well as potential PGPB as real-time indicators of forestry soil quality, and demonstrated the inner interaction contributed by the bacterial communities.

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Bacterial Composition and Diversity Associated with Rhizosphere of the Chinese Medicinal Herb Dendrobium

10.21203/rs.3.rs-58638/v1 ◽

2020 ◽

Author(s):

Yingdan Yuan ◽

Mengting Zu ◽

Lei Liu ◽

Xiaomei Song

Keyword(s):

Microbial Community ◽

Environmental Factor ◽

Bacterial Communities ◽

Soil Microorganisms ◽

Rhizosphere Soil ◽

Available Phosphorus ◽

Maturity Stage ◽

Bacterial Phyla ◽

Rhizosphere Microorganisms ◽

Rhizosphere Microbial Community

Abstract Background: Dendrobium is a precious herbal belongs to Orchid and widely used as health care traditional Chinese medicine in Asia. Although orchids are mycorrhizal plants, most researches still focus on endophytes, and there is still large unknown in rhizosphere microorganisms. In order to investigate the rhizosphere microbial community of different Dendrobium species during the maturity stage, we used high-throughput sequencing to analyze microbial community in rhizosphere soil during maturity stage of three kinds of Dendrobium species.Results: In our study, a total of 240,320 sequences and 11,179 OTUs were obtained from these three Dendrobium species. According to the analysis of OTU annotation results, different Dendrobium rhizosphere soil bacteria include 2 kingdoms, 63 phyla, 72 classes, 159 orders, 309 families, 850 genera and 663 species. Among all sequences, the dominant bacterial phyla (relative abundance > 1%) were Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, Firmicutes, Verrucomicrobia, Planctomycetes, Chloroflexi, Gemmatimonadetes. We analyzed the environmental factors of the growth of Dendrobium and found that the environmental factor that affects the rhizosphere soil microorganisms of Dendrobium is the soil factor. Among them, soil factors most closely related to the influence of Dendrobium rhizosphere soil microorganisms include total nitrogen, available phosphorus, ammonium nitrogen and pH value.Conclusions: We found that the rhizosphere bacterial communities of the three kinds of Dendrobium have significant differences, and the main species of rhizosphere microorganisms of Dendrobium are concentrated in the Proteobacteria, Actinobacteria, Bacteroidetes. Moreover, the smaller the level of bacterial, the greater the difference among Dendrobium species. Soil is the most important environmental factor affecting the bacterial communities in the rhizosphere soil of Dendrobium. These results fill the gap in the rhizosphere microbial community of Dendrobium and provide a theoretical basis for the subsequent mining of microbial functions and the study of biological fertilizers.

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Effects of shade stress on turfgrasses morphophysiology and rhizosphere soil bacterial communities

BMC Plant Biology ◽

10.1186/s12870-020-2300-2 ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Juanjuan Fu ◽

Yilan Luo ◽

Pengyue Sun ◽

Jinzhu Gao ◽

Donghao Zhao ◽

...

Keyword(s):

Bacterial Communities ◽

Rhizosphere Soil ◽

Soil Bacterial Communities ◽

Soil Bacterial

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Analysis of bacterial communities in rhizosphere soil of healthy and diseased cotton (Gossypium sp.) at different plant growth stages

Plant and Soil ◽

10.1007/s11104-010-0600-2 ◽

2010 ◽

Vol 339 (1-2) ◽

pp. 447-455 ◽

Cited By ~ 35

Author(s):

Yan Zhang ◽

Bing-Hai Du ◽

Zhi-gang Jin ◽

Zheng-hua Li ◽

Hong-ning Song ◽

...

Keyword(s):

Plant Growth ◽

Bacterial Communities ◽

Rhizosphere Soil ◽

Growth Stages ◽

Plant Growth Stages

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Molecular characterization and in situ detection of bacterial communities associated with rhizosphere soil of high altitude native Poaceae from the Andean Puna region

Journal of Arid Environments ◽

10.1016/j.jaridenv.2010.04.008 ◽

2010 ◽

Vol 74 (10) ◽

pp. 1177-1185 ◽

Cited By ~ 9

Author(s):

Marcela A. Ferrero ◽

Eugenia Menoyo ◽

Mónica A. Lugo ◽

María A. Negritto ◽

María E. Farías ◽

...

Keyword(s):

High Altitude ◽

Molecular Characterization ◽

Bacterial Communities ◽

Rhizosphere Soil ◽

In Situ Detection

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Analysis of bacterial communities in rhizosphere soil of continuously cropped healthy and diseased konjac

World Journal of Microbiology and Biotechnology ◽

10.1007/s11274-017-2287-5 ◽

2017 ◽

Vol 33 (7) ◽

Cited By ~ 7

Author(s):

Jinping Wu ◽

Zhenbiao Jiao ◽

Jie Zhou ◽

Fengling Guo ◽

Zili Ding ◽

...

Keyword(s):

Bacterial Communities ◽

Rhizosphere Soil

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Differential response of archaeal and bacterial communities to nitrogen inputs and pH changes in upland pasture rhizosphere soil

Environmental Microbiology ◽

10.1111/j.1462-2920.2004.00627.x ◽

2004 ◽

Vol 6 (8) ◽

pp. 861-867 ◽

Cited By ~ 42

Author(s):

Graeme W. Nicol ◽

Gordon Webster ◽

L. Anne Glover ◽

James I. Prosser

Keyword(s):

Bacterial Communities ◽

Rhizosphere Soil ◽

Differential Response ◽

Ph Changes ◽

Nitrogen Inputs ◽

Upland Pasture

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Effects of shade stress on morphophysiology and rhizosphere soil bacterial communities of two contrasting shade-tolerant turfgrasses

10.21203/rs.2.16025/v1 ◽

2019 ◽

Author(s):

Juanjuan Fu ◽

Yilan Luo ◽

Pengyue Sun ◽

Jinzhu Gao ◽

Donghao Zhao ◽

...

Keyword(s):

Bacterial Community ◽

Plant Growth ◽

Bacterial Communities ◽

Shade Tolerance ◽

Rhizosphere Soil ◽

Photosynthetic Capacity ◽

Bacterial Community Composition ◽

Soil Microbial Communities ◽

Soil Bacterial ◽

The Impact

Abstract Background: Shade presents one of the major abiotic limitations for turfgrass growth. Shade influences plant growth and alters plant metabolism, yet little is known about how shade affects the structure of rhizosphere soil microbial communities and the role of soil microorganisms in plant shade responses. In this study, a glasshouse experiment was conducted to examine the impact of shade stress on the growth and photosynthetic capacity of two contrasting shade-tolerant turfgrasses, shade-tolerant dwarf lilyturf (Ophiopogon japonicus, OJ) and shade-intolerant perennial turf-type ryegrass (Lolium perenne, LP). We also examined soil-plant feedback effects on shade tolerance in the two turfgrass genotypes. Bacterial community composition was assayed using high-throughput sequencing. Results: Our physiochemical data showed that under shade stress, OJ maintained higher photosynthetic capacity and root growth, thus OJ was found to be more shade-tolerant than LP. Shade-intolerant LP responded better to both shade and soil microbes than shade-tolerant OJ. Shade and live soil decreased LP growth but increased biomass allocation to shoots in the live soil. The plant shade response index of LP is higher in the live soil than sterile soil, driven by weakened soil-plant feedback under shade stress. In contrast, there was no difference in these values for OJ under similar shade and soil treatments. Illumina sequencing data revealed that shade stress had little impact on the diversity of the OJ and LP’s bacterial communities, but instead impacted the composition of bacterial communities. The bacterial communities were mostly composed of Proteobacteria and Acidobacteria in OJ soil. Further pairwise fitting analysis showed that a positive correlation of shade-tolerance in two turfgrasses and their bacterial community compositions. Several soil properties (NO3--N, NH4+-N, AK) showed a tight coupling with several major bacterial communities under shade stress, indicating that they are important drivers determining bacterial community structures. Moreover, OJ shared core bacterial taxa known to promote plant growth and confer tolerance to shade stress, which suggests common principles underpinning OJ-microbe interactions. Conclusion: Plant shade tolerance is mediated by soil-plant feedback and shade-induced changes in rhizosphere soil bacterial community structure in OJ and LP plants.

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Activation of the SA-Associated Plant Defense Pathway Alters the Composition of Soil Bacterial Communities

10.21203/rs.3.rs-159617/v1 ◽

2021 ◽

Author(s):

Jing Zhang ◽

Peter G.L. Klinkhamer ◽

Klaas Vrieling ◽

T. Martijn Bezemer

Keyword(s):

Plant Growth ◽

Microbial Communities ◽

Signaling Pathway ◽

Bacterial Communities ◽

Rhizosphere Soil ◽

Soil Microbial Communities ◽

Core Microbiome ◽

Soil Microbial ◽

Soil Bacterial ◽

Sa Signaling

Abstract Background and aimsMany plant species grow better in sterilized than in live soil. Foliar application of SA mitigates this negative effect of live soil on the growth of the plant Jacobaea vulgaris. To examine what causes the positive effect of SA application on plant growth in live soils, we analyzed the effects of SA application on the composition of active rhizosphere bacteria in the live soil. Methods We studied this over four consecutive plant cycles (generations), using mRNA sequencing of the microbial communities in the rhizosphere of J. vulgaris. ResultsOur study shows that the composition of the rhizosphere bacterial communities of J. vulgaris greatly differed among generations. Application of SA resulted in both increases and decreases in a number of active bacterial genera in the rhizosphere soil, but the genera that were affected by the treatment differed among generations. In the first generation, there were no genera that were significantly affected by the SA treatment, indicating that induction of the SA defense pathway in plants does not lead to immediate changes in the soil microbial community. 89 species out of the total 270 (32.4%) were present in all generations in all soils of SA-treated and control plants suggesting that these make up the “core” microbiome. On average in each generation, 72.9% of all genera were present in both soils. Application of SA to plants significantly up-regulated genera of Caballeronia, unclassified Cytophagaceae, Crinalium and Candidatus Thermofonsia Clade 2, and down-regulated genera of Thermomicrobiales, unclassified Rhodobacterales, Paracoccus and Flavihumibacter. While the functions of many of these bacteria are poorly understood, bacteria of the genus Caballeronia play an important role in fixing nitrogen and promoting plant growth, and hence this suggests that activation of the SA signaling pathway in J. vulgaris plants may select for bacterial genera that are beneficial to the plant. ConclusionsOverall, our study shows that aboveground activation of defenses in the plant affects soil microbial communities and, as soil microbes can greatly influence plant performance, this implies that induction of plant defenses can lead to complex above-belowground feedbacks. Further studies should examine how activation of the SA signaling pathway in the plant changes the functional genes of the rhizosphere soil bacterial community.

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Difference in Rhizosphere Soil Bacterial Community was among Six Cinnamomum camphora Chemotypes

10.20944/preprints202111.0158.v1 ◽

2021 ◽

Author(s):

Zufei Xiao ◽

Beihong Zhang ◽

Yangbao Wang ◽

Zhinong Jin ◽

Feng Li ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Rhizosphere Soil ◽

Soil Nutrient ◽

Soil Bacterial Community ◽

Cinnamomum Camphora ◽

Close Relationship ◽

Soil Bacterial

Abstract: Plant types and soil bacterial communities had a close relationship, understanding the profound association between them contributes to better learn bacterial ecological function for plant growth. In this study, rhizosphere soil of six different chemotype Cinnamomum camphora trees were collected, including C. bodinieri var. citralifera, [C. camphora (Linn.) Presl], camphora-type, cineole-type, linalool-type and isoborneol-type. Soil properties content and bacterial communities were analyzed. Two chemotype C. camphora, including [C. camphora (Linn.) Presl] and linalool-type, shaped similar bacterial community structure, decreased Firmcutes relative abundance. richness estimators (Chao1 index and Ace index) of [C. camphora (Linn.) Presl] were decreased compared with the others. Furthermore, soil bacterial community structure was also similar among bodinieri var. citralifera, camphora-type, cineole-type and isoborneol-type. Hence, different chemotype C. camphora altered soil nutrient and shaped rhizosphere bacterial communities.

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