Statistical procedures for agricultural research

Verdooren, L.R.

doi:10.1016/0378-4290(86)90076-6

Cited by 6 publications

(6 citation statements)

References 1 publication

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“…All data were analyzed using R (version 4.0.5) (Shake & Throw, 2021). The “vegan” package (Oksanen et al, 2010) was used for NMDS, PCA and RDA; the “lavaan” package (Rosseel, 2012) was used for SEM; “agricolae” package (Verdooren, 2021) was used for multiple comparisons, and the “ggplot2” package (Wickham, 2009) and software Origin 2018 was used for plotting figures.…”

Section: Methodsmentioning

confidence: 99%

Long‐term Spartina alterniflora invasion simplified soil seed bank and regenerated community in a coastal marsh wetland

Jia

et al. 2022

Ecological Applications

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The coastal wetland is easily invaded by alien species due to locating in the land and sea transitional area. As a potential driving regeneration force, the soil seed bank is vital to the community restoration and species diversity protection. To reveal the long‐term Spartina alterniflora invasion impact on the soil seed banks and regenerated communities, we investigated the seed banks under the different vegetation types (S. alterniflora, Phragmites australis, Scirpus mariqueter, ruderal and unvegetated site) and soil depths (0–5 and 5–10 cm) in the coastal salt marsh wetland, Chongming island, eastern China. The results showed that the soil seed bank richness and species density under different vegetation types were higher than the aboveground vegetation, and those of 0–5 cm seed banks were higher than 5–10 cm, except for the unvegetated site. The species richness and S. alterniflora seed proportion in the seed banks under S. alterniflora communities (S.AS) were lower and larger respectively than those of other sites. The species composition between S.AS and the aboveground communities showed high similarity with aggregation phylogenetic structures in two soil depths. The seed bank variations at 0–5 and 5–10 cm depths were interpreted 3.03% and 2.25% by the aboveground communities, while 4.92% and 5.55% were interpreted by the soil microbial biomass. The SEM model explained 98.1% and 91.8% of the seed banks richness at the 0–5 cm depth and 5–10 cm depth, respectively, and explained 98.8% and 46.1% of the seed banks species density at the 0–5 cm depth and 5–10 cm depth, respectively. The aboveground vegetation biomass and abundance directly affected the 0–5 cm seed banks richness and species density, while its height and biomass only affected the 5–10 cm seed banks species density. The 0–10 cm soil depth microbial biomass indirectly affected the 0–5 cm seed banks richness and species density, while affected the 5–10 cm seed banks richness. Soil physical and chemical properties only indirectly affected the 0–5 cm seed banks species density. The results provided a reference for the ecological evaluation of the impacts of S. alterniflora invasion into the coastal salt marsh wetland of eastern China, and guidance for the protection and restoration of the native plant communities.

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Section: Methodsmentioning

confidence: 99%

Long‐term Spartina alterniflora invasion simplified soil seed bank and regenerated community in a coastal marsh wetland

Jia

et al. 2022

Ecological Applications

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“…Tukey's honestly signi cant difference (HSD) test was used to compare the mean values that differed at P > 0.05. Microbial analysis was carried out using the vegan v2.6-4 [38], agricolae v1.3-7 [39], and indicspecies v1.7-14 [40] packages in R (version 4.3.2, https://www.r-project.org). The rarecurve function of the vegan package was employed to standardize the dataset by randomly subsampling read data from each sample to the lowest number of reads encountered for a sample.…”

Section: Statistical Analysesmentioning

confidence: 99%

The composition of the arbuscular mycorrhizal fungal bacteriome is species dependent

Lahrache,

Legeay,

Ahmed

et al. 2024

Preprint

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Background In addition to their role as endosymbionts for plant roots, arbuscular mycorrhizal fungi (AMF) engage in complex interactions with various soil microorganisms, the rhizosphere, and the root endosphere of host plants. They also host diverse prokaryotic groups within their mycelia, contributing to what is termed multipartite symbiosis. In this study, we examined the impact of three AMF species—Rhizophagus irregularis, R. clarus, and R. cerebriforme—combined with microbial bioaugmentation on the diversity and composition of bacterial communities in the mycelia and hyphosphere. Using a microcosm design to separate the influence of host plant roots from AMF mycelia, we employed Illumina MiSeq amplicon sequencing. Results Our results revealed that, while AMF identity and microbial bioaugmentation did not affect the structure of bacterial communities in the hyphosphere soil, they significantly altered the communities associated with their mycelia. Although all three AMF species belong to the same genus, with R. irregularis and R. clarus being closely related compared to R. cerebriforme, we observed variations in the bacterial communities associated with their mycelia. Interestingly, the mycelial bacterial community of R. cerebriforme contained 60 bacteriome core taxa exclusive to it, while R. clarum and R. irregularis had 25 and 9 exclusive taxa, respectively. Conclusion This study suggests that organismal phylogeny influences the bacterial communities associated with AMF mycelia. These findings provide new insights into AMF and bacterial interactions, which are crucial for the successful deployment of AMF inoculants. The taxonomic diversity of AMF inoculants is important for engineering the plant microbiome and enhancing ecosystem services.

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“…All data were analyzed using R (version 4.0.5) (Shake, Throw 2021). The 'lme4' package was used for mixed linear model (Bates et al 2021); the 'lavaan' package (Rosseel 2012) was used for SEM; 'agricolae' package (Verdooren 2021) was used for multiple comparisons, and the 'ggplot2' package (Wickham 2009) and software Origin 2018 was used for plotting figures.…”

Section: R=s…………………………………………………………………………………(3)mentioning

confidence: 99%

The spatial overlapping regulated by nitrogen promotes the Spartina alterniflora potential regenerated invasion in coastal wetlands

Jia,

Qu,

Jia

et al. 2023

Preprint

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The mechanisms that link the aboveground plant community structure with soil seed bank is crucial for predicting the potential regeneration direction. However, the spatial structure of invasive clonal plants should be reasonably quantified. We assume that the selection effect of Spartina alterniflora community spatial structure on soil seed bank composition would affect the seed reproduction invasion intensity. We set the native species of Phragmites australis in Dongtan wetland as a reference object, to explore the nitrogen regulation on the soil seed bank formation processes after S. alterniflora became the dominant species. The results showed that the S. alterniflora growth tended to be stable in summer and autumn, and its height change trend and peak height under different coverage was relatively consistent. The seasonal variation trend of P. australis height is opposite to that of S. alterniflora. In the autumn community structure at mature stage, the dominance index of S. alterniflora and P. australis showed a downward trend from low to high aboveground coverage after the soil seed bank germination, and the dominance index of S. alterniflora was higher than that of P. australis. The overlapping resistance structure of S. alterniflora community was synergistically affected by soil ammonium nitrogen, leaf total nitrogen and soil microbial biomass nitrogen, and the effect of this structure on the soil seed bank formation under different soil depth showed an opposite trend. Our results suggest that the overlapping complementarity between S. alterniflora plays a positive regulatory role between functional trait plasticity and sexual reproduction advantage.

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Statistical procedures for agricultural research

Cited by 6 publications

References 1 publication

Long‐term Spartina alterniflora invasion simplified soil seed bank and regenerated community in a coastal marsh wetland

Long‐term Spartina alterniflora invasion simplified soil seed bank and regenerated community in a coastal marsh wetland

The composition of the arbuscular mycorrhizal fungal bacteriome is species dependent

The spatial overlapping regulated by nitrogen promotes the Spartina alterniflora potential regenerated invasion in coastal wetlands

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