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Table 1 Relevant properties of co-occurrence networks

From: Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling

 Bacterial networksFungal networks
CategoryMetricDefinitionEcological relevanceCBCROBORCBCROBOR
SizeNodesEach node represents a bacterial/archaeal or fungal OTU.Larger networks contain a greater number of interacting (co-occurring or co-excluding) OTUs.332335335335139142144144
SizeEdgesEdges indicate significant co-occurrence or co-exclusion relationships.Co-occurrence could represent a number of ecological interactions, from predator-prey relationships to commensalism to shared ecological niches [12]. Co-exclusion may represent competition or inhibition.3698299520882261616457669349
DegreeMean degreeDegree refers to the number of edges a given node has. Mean degree is the average degree across all nodes in a network [10].Higher mean degree indicates more co-occurrence or co-exclusion relationships per OTU.22.2817.8812.4713.508.866.449.294.85
CohesionDensityDensity is defined as the ratio of the number of edges in a given network to the number of edges possible for that many nodes.High-density networks contain a large proportion of interacting OTUs.0.0670.0540.0370.0400.0640.0460.0650.034
CentralityCentralization indexThe degree of organization of a network around specific (central) nodes.High scores indicate that networks are centralized around one or a few focal nodes; low scores indicate decentralized structure [103].
ModularityModularity indexEdges belonging to a module minus those that would be expected from a random network with the same number of edges [104].High modularity indicates more structured communities within a network [104].0.440.490.660.630.450.720.390.77
 Number of modulesModules are groups of OTUs that interact more closely with one another than with other OTUs.Can represent overlapping ecological niches or phylogenetic groups [19].149191318131613