Visualizing Community Centric Network Layouts

Fagnan, Justin; Zaı̈ane, Osmar R.; Goebel, Randy

doi:10.1109/iv.2012.61

Cited by 9 publications

(6 citation statements)

References 13 publications

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“…A Kamada-Kawai plot based on the relative OTU abundances in the samples was constructed to reveal the interaction mode of co-occurring community members, and to infer possible cooperation between different microbial groups [ 36 ]. Based on distribution of the relative abundance of the obtained OTUs for each taxon in different samples, we identified microbial groups that co-occurred with each other, and then constructed the co-occurrence network of dominant microbial groups to explore their ecological significance.…”

Section: Resultsmentioning

confidence: 99%

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Wild rice harbors more root endophytic fungi than cultivated rice in the F1 offspring after crossbreeding

et al. 2021

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Background Rice, which serves as a staple food for more than half of the world’s population, is grown worldwide. The hybridization of wild and cultivated rice has enabled the incorporation of resistance to varying environmental conditions. Endophytic microbiota are known to be transferred with their host plants. Although some studies have reported on the endophytic microbiota of wild and cultivated rice, the inheritance from wild and cultivated rice accessions in next generations, in terms of endophytic microbiota, has not been examined. Results In the present study, the endophytic microbial community structures of Asian and African wild and cultivated rice species were compared with those of their F1 offspring. High-throughput sequencing data of bacterial 16S rDNA and fungal internal transcribed spacer regions were used to classify the endophytic microbiota of collected samples of rice. Results indicated that when either African or Asian wild rice species were crossed with cultivated rice accessions, the first generation harbored a greater number of root endophytic fungi than the cultivated parent used to make the crosses. Network analysis of the bacterial and fungal operational taxonomic units revealed that Asian and African wild rice species clustered together and exhibited a greater number of significant correlations between fungal taxa than cultivated rice. The core bacterial genus Acidovorax and the core fungal order Pleosporales, and genera Myrothecium and Bullera connected African and Asian wild rice accessions together, and both the wild rice accessions with their F1 offspring. On the other hand, the core bacterial genus Bradyrhizobium and the core fungal genera Dendroclathra linked the African and Asian cultivated rice accessions together. Conclusions This study has theoretical significance for understanding the effect of breeding on the inheritance of endophytic microbiota of rice and identifying beneficial endophytic bacteria and fungi among wild and cultivated rice species, and their F1 offspring.

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Section: Resultsmentioning

confidence: 99%

“…Euclidean distances were calculated and used in the PCA analysis. The network analysis to determine the correlations among the taxa in bacterial and fungal communities was performed using the dominant OTUs in each sample [ 36 ].…”

Section: Methodsmentioning

confidence: 99%

Wild rice harbors more root endophytic fungi than cultivated rice in the F1 offspring after crossbreeding

et al. 2021

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“…We can think of this algorithm as making the links between nodes behave like springs, i.e., nodes are attracted or pushed apart according to the strength of connections they have with the other nodes (Fagnan et al. , Decker et al. ).…”

Section: Methodsmentioning

confidence: 99%

Linking changes in species–trait relationships and ecosystem function using a network analysis of traits

Siwicka

Thrush

Hewitt

2019

Ecological Applications

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A major challenge in ecology and environmental management is linking changes in community composition to ecosystem functions. We developed the network analysis of traits (NAT) to show changes in community network structure based on the changes in the composition and connectivity between clusters of species that share traits that imply shifts in functional diversity. We tested the application of NAT on a 113 species found on an intertidal sandflat that was subject to experimental nitrogen addition (control [0 g N/m2], medium [150 g N/m2], and high [600 g N/m2]). This allowed us to directly link mechanistic changes in community composition and function with the trait‐space network patterns revealed by NAT. We demonstrate that under medium (150 g N/m2) N treatment, functional diversity remained consistent, whereas increasing disturbance to high (600 g N/m2) N treatment affected the species–trait network structure and caused merging of functional clusters implying a loss of functional trait diversity.

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“…Differences in the diversity across samples were determined by SPSS 19.0 software using a one-way ANOVA followed by a least signi cant difference (LSD) test. The network analysis for the connection between bacterial and fungal communities was performed by dominated OTUs in each sample (Fagnan et al 2012).…”

Section: Discussionmentioning

confidence: 99%

“…To determine the interaction mode of co-occurring community members and to infer the possible "cooperation" between different microbial groups, a Kamada-Kawai layout based on the relative OTU abundance of the samples for network analysis was performed (Fagnan et al 2012). According to the relative abundance distribution of OTUs or each taxon in different samples, we can identify the microbial groups that are co-occurring with each other, and then construct the co-occurrence network of dominant microbial groups to explore their ecological signi cance based on the Kamada-Kawai layout based on the OTUs.…”

Section: Network Analysis Based On Bacterial and Fungal Otusmentioning

confidence: 99%

Wild rice controls more root endophytic fungi than cultivated rice in the F1 offsprings after the crossbreeding

Tian

Lin

et al. 2020

Preprint

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Background: Rice, which serves as a staple food for more than half of the world's population, has been planted all over the world. The hybridization of wild and cultivated rice has helped rice gain resistance to variable environmental conditions. Endophytic microbiomes have been known to be transferred along with the plants. However, the endophytic bacteria or fungi for the wild and cultivated rice, and their first crossbred generation have not been illustrated until now.Results: In this study, we systematically compared the endophytic microbial community structures of Asian and African wild and cultivated rice species with their F1 offsprings. Results showed that both African and Asian wild rice controls more root endophytic fungi than cultivated rice in their first generation after crossbreeding. Furthermore, network analysis of the bacterial and fungal operational taxonomic units showed that Asian and African wild rice species can cluster and have more significant correlations than cultivated rice fungal species. The core bacterial species that connected wild rice with its F1 offsprings was Acidovorax, wherea the core bacterial species that linked cultivated rice to its F1 offsprings was Bradyrhizobium; and the core fungal species that can connect in wild rice and the F1 offsprings were Pleosporales, Myrothecium and Bullera, while the core fungal species that can connect in cultivated rice was those belonging to the Dendroclathra genus.Conclusions: This study may provide the theoretical significance of the endophytic bacteria and fungi for wild and cultivated rice along with their F1 offsprings.

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Visualizing Community Centric Network Layouts

Cited by 9 publications

References 13 publications

Wild rice harbors more root endophytic fungi than cultivated rice in the F1 offspring after crossbreeding

Wild rice harbors more root endophytic fungi than cultivated rice in the F1 offspring after crossbreeding

Linking changes in species–trait relationships and ecosystem function using a network analysis of traits

Wild rice controls more root endophytic fungi than cultivated rice in the F1 offsprings after the crossbreeding

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