Disentangling Large- and Small-Scale Abiotic and Biotic Factors Shaping Soil Microbial Communities in an Alpine Cushion Plant System

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.

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Small-scale soil microbial community heterogeneity linked to landforms on King George Island, maritime Antarctica

10.1101/310490 ◽

2018 ◽

Cited By ~ 2

Author(s):

Yumin Zhang ◽

Lu Lu ◽

Xulu xChang ◽

Fan Jiang ◽

Xiangdong Gao ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Soil Microbial Communities ◽

Small Scale ◽

King George Island ◽

Maritime Antarctica ◽

Volcanic Stratigraphy ◽

Elemental Compositions ◽

Soil Microbial ◽

Environmental Attributes

ABSTRACTWe analysed soil-borne microbial (bacterial, archaeal, and fungal) communities around the Fildes Region of King George Island, maritime Antarctica, which were divided into two groups according to soil elemental compositions and environmental attributes (soil chemical parameters and vegetation conditions) located in Holocene raised beach and Tertiary volcanic stratigraphy. Prokaryotic communities of the two groups were well separated; they predominantly correlated with soil elemental compositions, and were secondly correlated with environmental attributes (e.g., soil pH, total organic carbon, , and vegetation coverage; Pearson test, r = 0.59 vs. 0.52, both P < 0.01). The relatively high abundance of P, S, Cl, and Br in Group 1 was likely due to landform uplift. Lithophile-elements (Si, Al, Ca, Sr, Ti, V, and Fe) correlated with prokaryotic communities in Group 2 may originate from weathering of Tertiary volcanic rock. The elements and nutrients accumulated during formation of different landforms influenced the development of soils, plant growth, and microbial communities, and resulted in small-scale spatially heterogeneous biological distributions. We propose that the geological evolution of the Fildes Region was crucial to its microbial community development.IMPORTANCEThis current study analyzed soil-borne microbial communities around the Fildes Region of King George Island, maritime Antarctica, which were divided into two groups according to soil elemental compositions and environmental attributes. We provide new evidence for the crucial influence of landforms on small-scale structures and spatial heterogeneity of soil microbial communities.

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1041 - Molecular hydrogen interferes with the structure and functions of soil microbial communities

10.26226/morressier.5b5199c1b1b87b000ecee813 ◽

2018 ◽

Author(s):

Sarah Piché-Choquette

Keyword(s):

Microbial Communities ◽

Molecular Hydrogen ◽

Soil Microbial Communities ◽

Soil Microbial ◽

Structure And Functions

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0924 - The role of petrichor in desert soil microbial communities resuscitation during a rain event

10.26226/morressier.5b5199c1b1b87b000ecee737 ◽

2018 ◽

Author(s):

Capucine Baubin

Keyword(s):

Microbial Communities ◽

Soil Microbial Communities ◽

Desert Soil ◽

Rain Event ◽

Soil Microbial

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Faculty Opinions recommendation of Ant colonies promote the diversity of soil microbial communities.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.734763716.793559498 ◽

2019 ◽

Author(s):

Hang-Wei Hu

Keyword(s):

Microbial Communities ◽

Soil Microbial Communities ◽

Ant Colonies ◽

Soil Microbial

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Decision letter for "Preparing for the worst: Utilizing stress‐tolerant soil microbial communities to aid ecological restoration in the Anthropocene"

10.1002/2688-8319.12027/v1/decision1 ◽

2020 ◽

Keyword(s):

Microbial Communities ◽

Ecological Restoration ◽

Soil Microbial Communities ◽

Soil Microbial

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

FEMS Microbiology Ecology ◽

10.1093/femsec/fiab028 ◽

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.

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