scholarly journals Using network analysis to explore co-occurrence patterns in soil microbial communities

2011 ◽  
Vol 6 (2) ◽  
pp. 343-351 ◽  
Author(s):  
Albert Barberán ◽  
Scott T Bates ◽  
Emilio O Casamayor ◽  
Noah Fierer
Keyword(s):  
Network Analysis ◽  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Soil Microbial ◽  
Occurrence Patterns

scholarly journals Erratum: Using network analysis to explore co-occurrence patterns in soil microbial communities

2014 ◽  
Vol 8 (4) ◽  
pp. 952-952 ◽  
Author(s):  
Albert Barberán ◽  
Scott T Bates ◽  
Emilio O Casamayor ◽  
Noah Fierer
Keyword(s):  
Network Analysis ◽  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Soil Microbial ◽  
Occurrence Patterns

scholarly journals From Diversity to Complexity: Microbial Networks in Soils

2021 ◽  
Author(s):  
Ksenia Guseva ◽  
Sean Darcy ◽  
Eva Simon ◽  
Lauren V. Alteio ◽  
Alicia Montesinos-Navarro ◽  
...  
Keyword(s):  
Network Analysis ◽  
Microbial Communities ◽  
Microbial Ecology ◽  
Soil Microbial Communities ◽  
Small Scale ◽  
Soil Microbial Ecology ◽  
Test Dataset ◽  
Soil Microbial ◽  
Network Properties ◽  
Plant Animal Interactions

Network analysis has been used for many years in ecological research to analyze organismal associations, for example in food webs, plant-plant or plant-animal interactions. Although network analysis is widely applied in microbial ecology, only recently has it entered the realms of soil microbial ecology, shown by a rapid rise in studies applying co-occurrence analysis to soil microbial communities. While this application offers great potential for deeper insights into the ecological structure of soil microbial ecosystems, it also brings new challenges related to the specific characteristics of soil datasets and the type of ecological questions that can be addressed. In this Perspectives Paper we assess the challenges of applying network analysis to soil microbial ecology due to the small-scale heterogeneity of the soil environment and the nature of soil microbial datasets. We review the different approaches of network construction that are commonly applied to soil microbial datasets and discuss their features and limitations. Using a test dataset of microbial communities from two depths of a forest soil, we demonstrate how different experimental designs and network constructing algorithms affect the structure of the resulting networks, and how this in turn may influence ecological conclusions. We will also reveal how assumptions of the construction method, methods of preparing the dataset, an definitions of thresholds affect the network structure. Finally, we discuss the particular questions in soil microbial ecology that can be approached by analyzing and interpreting specific network properties. Targeting these network properties in a meaningful way will allow applying this technique not in merely descriptive, but in hypothesis-driven research.

Alkaline soil pH affects bulk soil, rhizosphere and root endosphere microbiomes of plants growing in a Sandhills ecosystem

2021 ◽  
Vol 97 (4) ◽  
Author(s):  
Lucas Dantas Lopes ◽  
Jingjie Hao ◽  
Daniel P Schachtman
Keyword(s):  
Microbial Communities ◽  
Plant Species ◽  
Soil Ph ◽  
Soil Microbial Communities ◽  
Bulk Soil ◽  
Strong Impact ◽  
Alkaline Soil ◽  
Alkaline Soils ◽  
Soil Microbial ◽  
Soil Rhizosphere

ABSTRACT Soil pH is a major factor shaping bulk soil microbial communities. However, it is unclear whether the belowground microbial habitats shaped by plants (e.g. rhizosphere and root endosphere) are also affected by soil pH. We investigated this question by comparing the microbial communities associated with plants growing in neutral and strongly alkaline soils in the Sandhills, which is the largest sand dune complex in the northern hemisphere. Bulk soil, rhizosphere and root endosphere DNA were extracted from multiple plant species and analyzed using 16S rRNA amplicon sequencing. Results showed that rhizosphere, root endosphere and bulk soil microbiomes were different in the contrasting soil pH ranges. The strongest impact of plant species on the belowground microbiomes was in alkaline soils, suggesting a greater selective effect under alkali stress. Evaluation of soil chemical components showed that in addition to soil pH, cation exchange capacity also had a strong impact on shaping bulk soil microbial communities. This study extends our knowledge regarding the importance of pH to microbial ecology showing that root endosphere and rhizosphere microbial communities were also influenced by this soil component, and highlights the important role that plants play particularly in shaping the belowground microbiomes in alkaline soils.

LDPE microplastics affect soil microbial communities and nitrogen cycling

2021 ◽  
Vol 773 ◽  
pp. 145640
Author(s):  
Lili Rong ◽  
Longfei Zhao ◽  
Leicheng Zhao ◽  
Zhipeng Cheng ◽  
Yiming Yao ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Nitrogen Cycling ◽  
Soil Microbial Communities ◽  
Soil Microbial

Azorella Cushion Plants and Aridity are Important Drivers of Soil Microbial Communities in Andean Ecosystems

Ecosystems ◽  
2021 ◽  
Author(s):  
Susana Rodríguez-Echeverría ◽  
Manuel Delgado-Baquerizo ◽  
José A. Morillo ◽  
Aurora Gaxiola ◽  
Marlene Manzano ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Soil Microbial ◽  
Cushion Plants
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