Network topology reveals high connectance levels and few key microbial genera within soils

By M. Lupatini, A. K. Suleiman, R. Jacques, Z. Antoniolli, A. S. Ferreira, E. Kuramae, L. Roesch. Frontiers in Environmental Science, 2014

262 citations recorded by the source corpus.

Microbes have a central role in soil global biogeochemical process, yet specific microbe-microbe relationships are largely unknown. Analytical approaches as network analysis may shed new lights in understanding of microbial ecology and environmental microbiology. We investigated the soil bacterial community interactions through cultivation-independent methods in several land uses common in two Brazilian biomes. Using correlation network analysis we identified bacterial genera that presented important microbial associations within the soil community. The associations revealed nonrandomly structured microbial communities and clusters of operational taxonomic units (OTUs) that reflected relevant bacterial relationships. Possible keystone genera were found in each soil. Irrespective of the biome or land use studied only a small portion of OTUs showed positive or negative interaction with other members of the soil bacterial community. The more interactive genera were also more abundant however, within those genera, the abundance was not related to taxon importance as measured by the Betweenness Centrality. Most of the soil bacterial genera were important to the overall connectance of the network, whereas only few genera play a key role as connectors, mainly belonged to phyla Proteobacteria and Actinobacteria. Finally it was observed that each land use presented a different set of keystone genera and that no keystone genus presented a generalized distribution. Taking into account that species interactions could be more important to soil processes than species richness and abundance, especially in complex ecosystems, this approach might represent a step forward in microbial ecology beyond the conventional studies of microbial richness and abundance.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/7d3e238b29ca97f72a61608f32f0580c60d3132d

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Citations in the corpus

Specialized metabolic functions of keystone taxa sustain soil microbiome stability (2021, background): “In addition, Gemmatimonas, affiliated with the Gemmatimonadetes, was the most abundant genus involved in phosphonate and phosphinate metabolism, followed by Solirubrobacter within Actinobacteria, and Brevundimonas and Rhizomicrobium within Proteobacteria.”
Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China (2016, background): “Topology-based analysis of large networks has proven powerful for studying the characteristics of co-occurrence patterns at various taxonomic levels, and identifying keystone microbial groups in different soils (Lupatini et al., 2014).”
Continuous‐cropping tobacco caused variance of chemical properties and structure of bacterial network in soils (2018, background): “Interactions among different microbial species are very important for ecosystem community's function in the complex soil ecosystem (Barberán et al., 2012; Lupatini et al., 2014).”
Biogeographic patterns of microbial association networks in paddy soil within Eastern China (2020, result): “Our finding is in alignment with a previous observation that putative keystone species change with conditions (Lu et al., 2013; Lupatini et al., 2014).”
Microbial diversity and ecological networks as indicators of environmental quality (2017, background): “…sensitive to atmospheric pollutions at the level of plant mats (Karimi et al. 2016), to metallic contaminants in the soil (Zappelini et al. 2015), to the type of land use (Lupatini et al. 2014; Zappelini et al. 2015) and more particularly to specific agricultural practices (Sauvadet et al. 2016).”