Higher Sensitivity of Soil Microbial Network Than Community Structure under Acid Rain

Liu, Ziqiang; Wei, Hui; Zhang, Jiaen; Saleem, Muhammad; He, Yuxia; Zhong, Jiawen; Ma, Rui

doi:10.3390/microorganisms9010118

Cited by 17 publications

(3 citation statements)

References 72 publications

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“…They always interact with other microorganisms such as mutualism, parasitism, antagonism. Co-culture is often used to study the interaction between microorganisms [24], but due to the inculcability of most microorganisms, co-culture has shown great limitations. Therefore, it is necessary to find other reliable ways to study the interaction between microbial communities.…”

Section: Introductionmentioning

confidence: 99%

Composition and diversity of bacterial communities in the rhizosphere of the Chinese medicinal herb Dendrobium

Zuo

Liu

et al. 2021

BMC Plant Biol

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Background Dendrobium is a precious herbal that belongs to Orchidaceae and is widely used as health care traditional Chinese medicine in Asia. Although orchids are mycorrhizal plants, most research still focuses on endophytes, and there is still large amount unknown about rhizosphere microorganisms. 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 the 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, and Gemmatimonadetes. And through WGCNA analysis, we found the hub flora was also belong to Acidobacteria, Actinobacteria and Proteobacteria. Conclusions We found that the rhizosphere bacterial communities of the three kinds of Dendrobium have significant differences, and that the main species of rhizosphere microorganisms of Dendrobium are concentrated in the Proteobacteria, Actinobacteria, and Bacteroidetes. Moreover, the smaller the bacterial level, the greater the difference among Dendrobium species. These results fill knowledge gaps 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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Section: Introductionmentioning

confidence: 99%

Composition and diversity of bacterial communities in the rhizosphere of the Chinese medicinal herb Dendrobium

Zuo

Liu

et al. 2021

BMC Plant Biol

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“…It is a measure of broadcaster nodes, that is, nodes that can influence the network fastest Keystone taxa; taxa that, if perturbed, influence the network the fastest. [27,43,44] Betweenness centrality Centrality of a node based on how often a node is situated on paths between other nodes. It is a measurement of bridge nodes Keystone taxa; taxa more important in communication in the network.…”

Section: Referencesmentioning

confidence: 99%

“…It is a measurement of bridge nodes Keystone taxa; taxa more important in communication in the network. [4,27,41,44] PageRank Centrality measure that computes a ranking of the nodes based on the structure of the incoming links. It identifies hub nodes.…”

Section: Referencesmentioning

confidence: 99%

MicNet toolbox: Visualizing and unraveling a microbial network

Favila¹,

Madrigal-Trejo

Legorreta³

et al. 2022

PLoS ONE

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Applications of network theory to microbial ecology are an emerging and promising approach to understanding both global and local patterns in the structure and interplay of these microbial communities. In this paper, we present an open-source python toolbox which consists of two modules: on one hand, we introduce a visualization module that incorporates the use of UMAP, a dimensionality reduction technique that focuses on local patterns, and HDBSCAN, a clustering technique based on density; on the other hand, we have included a module that runs an enhanced version of the SparCC code, sustaining larger datasets than before, and we couple the resulting networks with network theory analyses to describe the resulting co-occurrence networks, including several novel analyses, such as structural balance metrics and a proposal to discover the underlying topology of a co-occurrence network. We validated the proposed toolbox on 1) a simple and well described biological network of kombucha, consisting of 48 ASVs, and 2) we validate the improvements of our new version of SparCC. Finally, we showcase the use of the MicNet toolbox on a large dataset from Archean Domes, consisting of more than 2,000 ASVs. Our toolbox is freely available as a github repository (https://github.com/Labevo/MicNetToolbox), and it is accompanied by a web dashboard (http://micnetapplb-1212130533.us-east-1.elb.amazonaws.com) that can be used in a simple and straightforward manner with relative abundance data. This easy-to-use implementation is aimed to microbial ecologists with little to no experience in programming, while the most experienced bioinformatics will also be able to manipulate the source code’s functions with ease.

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Thermostable Keystone Bacteria Maintain the Functional Diversity of the Ixodes scapularis Microbiome Under Heat Stress

et al. 2021

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Variations in the composition and diversity of tick microbiome due to high temperatures may influence the hierarchy of community members as a response to environmental change. Modifications in the community structure are hypothesized to drive alterations in the presence and/or abundance of functional pathways in the bacterial metagenome. In this study, this hypothesis was tested by using published 16S rRNA datasets of Ixodes scapularis males incubated at different temperatures (i.e., 4, 20, 30, and 37 °C) in a laboratory setting. Changes in community structure and functional profiles in response to temperature shifts were measured using co-occurrence networks and metagenome inference. Results from laboratory-reared ticks were then compared with those of field-collected ticks. The results from laboratory-reared ticks showed that high temperature altered the structure of the microbial community and decreased the number of keystone taxa. Notably, four taxa were identified as keystone in all the temperatures, and the functional diversity of the tick microbiome was contained in the four thermostable keystone their associated bacterial taxa. Three of the thermostable keystone taxa were also found in free-living ticks collected in Massachusetts. Moreover, the comparison of functional profiles of laboratory-reared and field-collected ticks revealed the existence of an important set of metabolic pathways that were common among the different datasets. Similar to the laboratory-reared ticks, the keystone taxa identified in field-collected ticks alongside their consortia (co-occurring taxa) were sufficient to retain the majority of the metabolic pathways in the functional profile. These results suggest that keystone taxa are essential in the stability and the functional resiliency of the tick microbiome under heat stress.

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Higher Sensitivity of Soil Microbial Network Than Community Structure under Acid Rain

Cited by 17 publications

References 72 publications

Composition and diversity of bacterial communities in the rhizosphere of the Chinese medicinal herb Dendrobium

Composition and diversity of bacterial communities in the rhizosphere of the Chinese medicinal herb Dendrobium

MicNet toolbox: Visualizing and unraveling a microbial network

Thermostable Keystone Bacteria Maintain the Functional Diversity of the Ixodes scapularis Microbiome Under Heat Stress

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