Spatial soil heterogeneity rather than the invasion of Spartina alterniflora drives soil bacterial community assembly in an Eastern Chinese intertidal zone along an estuary coastline

Zhang, Yukai; Li, Mo; zhang, Jiao; Cui, Jun; Wang, Xinyi; Song, Miaomiao; Qiao, Qicheng; Long, Xi-En

doi:10.1016/j.catena.2023.107784

Cited by 8 publications

(4 citation statements)

References 51 publications

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“…The cultivation duration predominantly impacts the microbial diversity within the fibrous roots compartment of ginseng. Our team’s prior research, along with studies by other scholars, has consistently shown a decrease in fungal diversity in ginseng soil with increasing cultivation years ( Xiao, 2015 ; Xiao et al, 2016 ; Jin et al, 2022 ; Shi et al, 2024 ; Zhang et al, 2024 ). Furthermore, our recent investigations revealed that cultivation years exerted a more pronounced effect on the microbiome diversity within the fibrous root compartment.…”

Section: Discussionmentioning

confidence: 72%

Temporal patterns of endophytic microbial heterogeneity across distinct ecological compartments within the Panax ginseng root system following deforestation for cultivation

Shi,

Yang,

Yang

et al. 2024

Front. Microbiol.

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Alterations in the microbial community significantly impact the yield and quality of ginseng. Yet, the dynamics of microbial community shifts within the root endophytes of ginseng across varying cultivation periods remain inadequately understood. This study zeroes in on the microbial community variations within the xylem (M), phloem (R), and fibrous roots (X) of ginseng during the fourth (F4) and fifth (F5) years of cultivation, aiming to bridge this research gap. We assessed soil physicochemical properties, enzyme activities, and nine individual saponins, complemented by high-throughput sequencing techniques (16S rDNA and ITS) to determine their profiles. The results showed that cultivation years mainly affected the microbial diversity of endophytic bacteria in ginseng fibrous roots compartment: the ASVs number and α-diversity Chao1 index of bacteria and fungi in F5X compartment with higher cultivation years were significantly higher than those in F4X compartment with lower cultivation years. It is speculated that the changes of fibrous roots bacterial groups may be related to the regulation of amino acid metabolic pathway. Such as D-glutamine and D-glutamate metabolism D-glutamine, cysteine and methionine metabolism regulation. The dominant bacteria in ginseng root are Proteobacteria (relative abundance 52.07–80.35%), Cyanobacteria (1.97–42.52%) and Bacteroidota (1.11–5.08%). Firmicutes (1.28–3.76%). There were two dominant phyla: Ascomycota (60.10–93.71%) and Basidiomycota (2.25–30.57%). Endophytic fungi were more closely related to soil physicochemical properties and enzyme activities. AN, TK, OP, SWC and EC were the main driving factors of endophytic flora of ginseng root. Tetracladium decreased with the increase of cultivation years, and the decrease was more significant in phloem (F4R: 33.36%, F5R: 16.48%). The relative abundance of Bradyrhizobium, Agrobacterium and Bacillus in each ecological niche increased with the increase of cultivation years. The relative abundance of Bradyrhizobium and Agrobacterium in F5X increased by 8.35 and 9.29 times, respectively, and Bacillus in F5M increased by 5.57 times. We found a variety of potential beneficial bacteria and pathogen antagonists related to ginseng biomass and saponins, such as Bradyrhizobium, Agrobacterium, Bacillus and Exophiala, which have good potential for practical application and development.

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Section: Discussionmentioning

confidence: 72%

Temporal patterns of endophytic microbial heterogeneity across distinct ecological compartments within the Panax ginseng root system following deforestation for cultivation

Shi,

Yang,

Yang

et al. 2024

Front. Microbiol.

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“…Some studies have proposed a multi-step selection model for rhizosphere microbial communities. This suggests that microorganisms are gradually selected across different environments, namely bulk soil, rhizosphere soil, and root, ultimately forming a rhizosphere-specific microbial community ( Tian et al, 2020 ; Zhang et al, 2024 ). However, most existing studies have considered microbial communities in the root soil as a single entity ( Ren et al, 2020 ; Song et al, 2020 ; Kui et al, 2021 ; Shi Y. H. et al, 2022 ; Wei et al, 2022 ; Zhang G. Z. et al, 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Temporal heterogeneity of the root microbiome in Panax ginseng soils across ecological compartments under mild soil disturbance

Shi,

Yang,

Yang

et al. 2024

Front. Microbiol.

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IntroductionKnowledge on spatiotemporal heterogeneity of plant root microbiomes is lacking. The diversity of the root microbiome must be revealed for understanding plant–microbe interactions and the regulation of functionally crucial microbial taxa.MethodsWe here investigated the dynamics of microbial group characteristics within each soil ecological compartment [rhizoplane (B), rhizosphere (J), and bulk soil (T)] across different cultivation years (year 4: F4 and year 5: F5) by using high-throughput sequencing (16S and ITS).ResultsAccording to the species diversity, microbiome diversity and the ASV (amplified sequence variant) number in the rhizoplane ecotone increased significantly with an increase in the planting years. By contrast, the microbiome diversity of the rhizosphere soil remained relatively stable. PCoA and PERMANOVA analyses revealed that microbial taxa among different planting years and ecological compartments varied significantly. Planting years exerted the least effect on the rhizosphere microbiome, but their impact on fungi in the rhizoplane and bacteria in the bulk soil was the most significant.DiscussionPlanting years influenced the microbial community composition in various ecological compartments of ginseng root soil. Potentially harmful fungi such as Cryptococcus (2.83%), Neonectria (0.89%), llyonectria (0.56%), Gibberella (0.41%), Piloderma (4.44%), and Plectosphaerella (3.88%) were enriched in F5B with an increase in planting years, whereas the abundance of potentially beneficial Mortierella increased. Correlation analysis indicated associations between bacterial taxa and soil pH/S-CAT, and between fungal taxa and soil moisture content/total potassium. Our study highlights the significance of changes in rhizoplane fungi and the stability of the rhizosphere microbial community in comprehending plant ecological sustainability.

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“…Furthermore, SOM played a signi cant role in altering the microbiological community in alfalfa rhizosphere soil in this study. Zhang's study also indicated that other soil organic fractions have a lesser impact on the distribution of the bacterial community compared to SOM(Zhang et al 2024). Other important variables that could in uence the changes in the microbial community composition in the rhizosphere soil of awnless brome include AK, SA, and SMBN, indicating that alterations in soil physico-chemical properties could cause changes in soil microbiomes either directly or indirectly(Win et al 2020).…”

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confidence: 96%

Effects of fertilization on the composition of bacterial populations in the rhizosphere soil of Legume-Gramineae mixtures in the Hexi Corridor region

Chen,

Nan,

Chen

et al. 2024

Preprint

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Background and aims Fertilization is a critical management practice for improving soil fertility and increasing agricultural production. We still don't fully understand how biotic and abiotic variables interact with soil multifunctionality in the rhizosphere soil of legume-Gramineae mixtures following fertilization. Studies on the effects of fertilization on the bacterial composition of legume-Gramineae mixtures in particular geographical areas are scarce. Methods To tackle this matter, we set up five treatments: no fertilizer zone (CK, N0P0K0), nitrogen-phosphorus-potassium zone (NPK, N2P2K2), nitrogen-less zone (PK, N0P2K2), phosphorus-less zone (NK, N2P0K2), and potassium-less zone (NP, N2P2K0). The soil data were measured to assess the response mechanism of legume-Gramineae mixtures to fertilization management. Results The fertilization treatment resulted in a beneficial impact on the rhizosphere soil nutrients, enzyme activity, and biological characteristics, reaching the maximum under N2P2K2 treatment. The analysis of the bacterial community revealed that the oligotrophic taxa decreased primarily due to fertilizer addition, including Acidobacteria, and enhancing the copiotrophic taxa, such as Bacteroidetes and Proteobacteria, in the soil. Furthermore, according to FAPROTAX analysis, the results indicated variations in the function of the bacterial community in the rhizosphere soil of legumes and gramineae. Fertilization indirectly affected soil versatility by changing the diversity and composition of bacterial communities. Conclusions The bacterial community can be reshaped and the properties of the rhizosphere soil can be modified by different fertilization treatments, thus impacting the potential function of the bacterial community. This study has the potential to offer scientific guidance for the rational management of fertilization in legume-Gramineae mixtures.

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Spatial soil heterogeneity rather than the invasion of Spartina alterniflora drives soil bacterial community assembly in an Eastern Chinese intertidal zone along an estuary coastline

Cited by 8 publications

References 51 publications

Temporal patterns of endophytic microbial heterogeneity across distinct ecological compartments within the Panax ginseng root system following deforestation for cultivation

Temporal patterns of endophytic microbial heterogeneity across distinct ecological compartments within the Panax ginseng root system following deforestation for cultivation

Temporal heterogeneity of the root microbiome in Panax ginseng soils across ecological compartments under mild soil disturbance

Effects of fertilization on the composition of bacterial populations in the rhizosphere soil of Legume-Gramineae mixtures in the Hexi Corridor region

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