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

By A. Barberán, S. Bates, E. Casamayor, Noah Fierer. The ISME Journal, 2011

2,585 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/5e1f5263b0fa4eb99401d37f2fd1bb1457c7b385

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In Ecology

In Molecular Biology

Citations in the corpus

Describe, understand and predict: why do we need networks in ecology? (2016, background): “…and quantification their complexity (Bascompte 2009) and could contribute to finally unlocking key questions such as community assembly (Montoya & Sole 2003; Barber an et al. 2012), coexistence (Allesina & Levine 2011; Ulrich et al. 2014) and the concept of trophic niches (Dehling et al. 2016).”
Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes? (2016, background): “…R 2 0.59) and microbial predictors (average adjusted R 2 0.38) relative to other systems, and metrics of community diversity were more strongly correlated with the environment ( n = 7, average adjusted R 2 0.24) and had lower added value (average adjusted R 2 0.06) than in other ecosystem types.”
Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming (2018, background): “applied in soil microbial ecology to explore patterns of community assembly [35], visualize response patterns of different taxonomic groups to agronomic practices [36], and to identify individual microbiome members that”
Comparative analysis of diversity and environmental niches of soil bacterial, archaeal, fungal and protist communities reveal niche divergences along environmental gradients in the Alps (2021, background): “For example, Ktedonobacteria (Chloroflexi) were identified in higher proportions as specialists, possibly reflecting their habitat preference for oligotrophic and extreme environments (Barberán et al., 2012; Lynch et al., 2012; Tebo et al., 2015), including high elevation alpine soils (Adamczyk et a”
Biogeographic patterns of microbial association networks in paddy soil within Eastern China (2020, background): “Although the network hub is missing in many network studies (Barber�an et al., 2012; Faust et al., 2012; Deng et al., 2016; Ma et al., 2016; Shi et al., 2016), a number of network hubs in the fungal and diazotrophic networks, as well as the bacteria-fungi network, were identified (Tables 2 and S6).”
Soil networks become more connected and take up more carbon as nature restoration progresses (2017, positive): “Tightening of the networks reflects stronger co-occurring patterns of variation in soil biota 26 .”
Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes (2015, background): “, 2003), proteins in metabolic pathways (Guimerà and Amaral, 2005), coexisting patterns among microbial taxa in soils (Barberán et al., 2012), activated sludge (Ju et al.”