Food web construction
Trophic groups and classes: We assigned the retrieved
taxonomically annotated MOTUs to 10 trophic classes including
autotrophs, decomposers, detritivores, phytophages or phytoparasites,
plant mutualists, bacterivores, fungivores, omnivores, predators and
zooparasites. We then refined those trophic classes by subdividing them
into 55 trophic groups in total. These were defined by separating
phylogenetic distant groups that could have a different set of
prey/predators (e.g., bacterivorous mites vs. bacterivorous nematodes)
and groups differing in their resources acquisition strategy (e.g.,
different types of mycorrhiza and saprotrophs). The taxonomic rank used
to delimitate phylogenetic distant groups comprised Bacteria, Fungi,
Protista, the different phyla within Metazoa, and the different classes
or orders within Arthropoda and Annelida. (Appendix 2).
To facilitate the assignment of the taxonomically annotated MOTUs to
trophic classes, we first built a knowledge graph integrating
information about the trophic interactions and feeding habits of
soil-associated consumers from multiple data sources using the
ontology-based data integration pipeline described in Le Guillarme &
Thuiller (2023). This trophic knowledge graph uses the NCBITaxon
ontology and the Soil Food Web Ontology (SFWO)(Le Guillarme et
al. 2023) as global schemas for reconciling taxonomic and semantic
heterogeneities between the data sources. It provides a unified access
to multisource trophic information across taxonomic groups and trophic
levels. The list of data sources and details on the assignment criteria
can be found in Appendix 2.
Building the metaweb: A metaweb is a potential network containing
all trophic groups and their potential interactions (Dunne 2006). We
added three basal resources to construct our metaweb: light (or chemical
energy), plants, and organic matter. Trophic links were then added
between groups based on their main feeding preferences. Therefore, plant
mutualists and phytoparasites were linked with the plant resource,
detritivores and decomposers were linked with the organic matter
resource and autotrophs were associated with the light resource.
Bacterivores were linked with all trophic groups containing bacteria,
and fungivores with all trophic groups containing fungi. The trophic
interactions of omnivores, predators and zooparasites, were determined
through a literature review of dietary preferences of taxa representing
over 90% of the read abundance of the group (Appendix 2).
Local food webs: From the metaweb, the composition and structure
of the local soil food webs were deduced based on locally present
trophic groups, i.e., local webs are subgraphs of the metaweb. This
assumes that co-occurring groups interact locally as defined in the
metaweb. We approximated local relative abundance of each trophic group
using a double-transformation, where first, total read counts were
transformed into proportions within the sample, and second, the
resulting proportions were standardised by the largest proportion
observed across samples for each trophic group (‘eDNA index’ in Kellyet al. 2019). The relative abundance of each trophic group varied
thus between 0 (absent) to 1 (largest observed proportion), allowing to
have a comparable measure across trophic groups. Abundance values of the
basal resources (light, plant, organic matter) were set to non-null
(0.001) to not affect diversity measurements. For trophic class
abundance estimates, we summed group relative abundances.