plant_fungus_japan — Japanese plant-root fungal associations (2018)

Description

Bipartite networks of associations between plants and root-associated fungi in eight forests across the Japanese Archipelago (four cool-temperate, one warm-temperate and three subtropical forests, from 45.0 to 24.4 °N), from Toju et al. In each forest, 2 cm segments of terminal roots were sampled at 1 m intervals (240 samples per forest), irrespective of their morphology or mycorrhizal type. The plant of each sample was identified by DNA barcoding (rbcL and ITS1 regions; not all could be identified to species level), and its fungi by Illumina sequencing of the fungal ITS1 region, with reads clustered into operational taxonomic units (OTUs) at 97% sequence similarity (94% for Glomeromycota), with taxonomic assignment based on the NCBI nt database and functional groups inferred with FUNGuild. Associations that represented less than 0.1% of the reads of a sample were removed. The data include arbuscular mycorrhizal, ectomycorrhizal, endophytic, saprotrophic and pathogenic fungi, among others. In each network, an edge connects a plant to a fungal OTU found in its root samples, weighted by the number of root samples in which the association was observed.

metacommunity: the metacommunity-scale network of all eight forests, in which each plant node is a local population of a plant species/taxon in one forest (227 populations of 150 plant species/taxa) and each fungal node an OTU (8080 OTUs). The paper also analyzes the networks of the four northern (cool-temperate) and four southern forests, which are subnetworks of this one.
site1 to site8: the local networks of each forest, with plant species/taxa and fungal OTUs as nodes. Sites 1 to 4 are cool-temperate forests (codes TES, TOMA, YKS and SGD), site 5 a warm-temperate forest (YSD), and sites 6 to 8 subtropical forests (YAKU, YONA and IRI).

The networks have the following properties:

Nodes: name, the plant species/taxon (e.g. "Acer", "Poaceae_1"; in metacommunity with the code of the forest appended, e.g. "Acer_TES") or the OTU identifier (e.g. "F_0001"); is_fungus, whether the node is a fungal OTU (otherwise a plant).
Plant nodes in metacommunity: site, the code of the forest.
Fungal nodes: otu_code, the sequence identifier of the OTU; phylum, class, order, family, genus and species, the taxonomic assignment (empty if not resolved at that level); guild and trophic_mode, the functional guild and trophic mode inferred with FUNGuild (empty if not assigned); category, the functional category used in the paper (e.g. "Arbuscular_Mycorrhizal", "Ectomycorrhizal", "Saprotroph", "Plant_Pathogen", "Others_Unknown").
Edges: weight, the number of root samples in which the association was observed.

Tags

Biological Weighted Metadata

Citation

H. Toju, H. Tanabe, H. S. Ishii, "Network hubs in root-associated fungal metacommunities." Microbiome 6, 116 (2018) 10.1186/s40168-018-0497-1 Sci-Hub

Upstream URL OK

https://doi.org/10.1186/s40168-018-0497-1

Upstream license

Creative Commons Attribution 4.0 International (CC BY 4.0), https://creativecommons.org/licenses/by/4.0/

Networks

Tip: click on a column header to sort the list, or hover over it for a description.

Column legend

$\left<k\right>$: Mean degree
$\sigma_k$: Standard deviation of the degrees
$\lambda_h$: Largest eigenvalue of the Hashimoto (non-backtracking) matrix
$\tau$: Random walk mixing time
$r$: Degree assortativity
$c$: Global clustering coefficient
$\oslash$: (Pseudo-) diameter
$S$: Relative size of the largest component
NPs: Node properties
EPs: Edge properties

Name	Nodes	Edges	$\left<k\right>$	$\sigma_k$	$\lambda_h$	$\tau$	$r$	$\oslash$	$S$	Kind	Mode	NPs	EPs	gt	GraphML	GML	csv
metacommunity	8,307	30,610	7.37	33.23	57.70	8.38	-0.50	7	1.00	Undirected	Bipartite	name is_fungus site otu_code phylum class order family genus species guild trophic_mode category	weight	167 KiB	256 KiB	248 KiB	265 KiB
site1	1,479	3,594	4.86	27.08	31.20	3.32	-0.62	6	1.00	Undirected	Bipartite	name is_fungus otu_code phylum class order family genus species guild trophic_mode category	weight	29 KiB	40 KiB	39 KiB	41 KiB
site2	1,170	2,671	4.57	26.15	26.99	2.81	-0.50	6	1.00	Undirected	Bipartite	name is_fungus otu_code phylum class order family genus species guild trophic_mode category	weight	24 KiB	32 KiB	32 KiB	33 KiB
site3	1,415	2,369	3.35	29.67	21.70	4.16	-0.52	6	1.00	Undirected	Bipartite	name is_fungus otu_code phylum class order family genus species guild trophic_mode category	weight	27 KiB	35 KiB	34 KiB	36 KiB
site4	1,252	2,605	4.16	19.57	19.96	5.41	-0.47	6	1.00	Undirected	Bipartite	name is_fungus otu_code phylum class order family genus species guild trophic_mode category	weight	25 KiB	34 KiB	33 KiB	34 KiB
site5	1,623	3,714	4.58	28.83	32.07	4.67	-0.68	6	1.00	Undirected	Bipartite	name is_fungus otu_code phylum class order family genus species guild trophic_mode category	weight	31 KiB	42 KiB	41 KiB	44 KiB
site6	1,799	4,351	4.84	27.17	30.67	3.56	-0.52	6	1.00	Undirected	Bipartite	name is_fungus otu_code phylum class order family genus species guild trophic_mode category	weight	33 KiB	46 KiB	45 KiB	48 KiB
site7	1,495	4,778	6.39	30.53	40.96	2.23	-0.67	6	1.00	Undirected	Bipartite	name is_fungus otu_code phylum class order family genus species guild trophic_mode category	weight	29 KiB	43 KiB	42 KiB	43 KiB
site8	1,852	6,528	7.05	26.91	40.88	2.92	-0.54	6	1.00	Undirected	Bipartite	name is_fungus otu_code phylum class order family genus species guild trophic_mode category	weight	36 KiB	53 KiB	53 KiB	54 KiB