Figure Caption
Fig. 1 . The relative abundances of gene modules. The letters a,
b, and c indicate statistically significant differences between groups
(p < 0.05). Functional modules correspond to the following
designations: A-energy production and conversion, B-amino acid transport
and metabolism, C-nucleotide transport and metabolism, D-carbohydrate
transport and metabolism, E-intracellular trafficking, secretion, and
vesicular transport, F-lipid transport and metabolism, G-transcription,
H-cell wall or membrane or envelope biogenesis, I-extracellular
structures, J-signal transduction mechanisms, K-coenzyme transport and
metabolism, L-inorganic ion transport and metabolism, M-RNA processing
and modification, N-secondary metabolite biosynthesis, transport, and
catabolism, O-cell motility, P-defense mechanisms, Q-general function
prediction only, R-function unknown, S-cell cycle control, cell
division, chromosome partitioning, T-post-translational modification,
protein turnover, and chaperones, U-replication, recombination and
repair, V-chromatin structure and dynamics, and W-translation, ribosomal
structure, and biogenesis. Gene modules with very low RAs were amplified
10–1000 times to better visualize their relative ratios across groups
(M, I and V). The modules can be characterized into six general groups
including basic metabolism-related (dark yellow), interaction-related
(gray), cofactor metabolite-related (yellow), environmental
resistance-related (brown), other (blue), and reproduction-related
(green) functions.
Fig. 2 . Important nodes and modules within the soil microbial
networks. Fig.2A shows the identity of the module hubs and connectors
for the three soil types. The nodes with Zi > 2.5 were
considered module hubs, and nodes with Pi > 0.625 were
considered connectors, while nodes with both Zi > 2.5 and
Pi > 0.625 were considered network hubs. The module hub and
connector node identities at the phylum level are shown on the right
side of the panels. Fig.2B shows the modularity of soil networks and the
location of T.matsutake within the networks. Blue circles show
T.matsutake, yellow circles show bacterial OTUs, and green circles show
fungal OTUs. Yellow and green lines show positive and negative
interactions, respectively. Several smaller modules that were highly
marginalized are not included in the figure to allow for better
visualization of each stage’s network.
Fig. 3 . The interactions and interactive OTUs associated with
T.matsutake. Fig.3A shows the ratio of positive to negative
interactions. Fig.3B shows the relative abundances of different
interaction types across the T.matsutake habitat degradation gradient. +
and - indicate positive and negative interactions, respectively. B and F
indicate bacterial and fungal nodes, respectively, wherein B+F indicates
inferred positive interactions between bacterial OTUs and fungal OTUs.
Fig.3C shows variation in the relative abundances of OTUs that
originally interacted with T.matsutake, *** indicates statistically
significant differences among groups (p < 0.001).
Fig. 4. The linear relationships between T.matsutake RAs
and soil properties, community diversity, community structure, and
community network structures. Upward arrows indicate components that
were positively related to extraction. BE, BR, and BS indicate bacterial
equitability, richness, and Shannon index values, respectively, while
FE, FR, and FS indicate the respective fungal counterparts. Community
structure was extracted from PC1 of the bacterial and fungal PCoAs,
while network structure was comprised of the values from the network
indices avgK, avgCC, and Tran. Shaded areas show 95% confidence
intervals.