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Jennifer Grenz is currently a sessional lecturer at the University of British Columbia and owns a land healing company, Greener This Side. Her recently completed PhD dissertation explores the science of invasive species management and restoration through the lens of an ‘Indigenous ecology’, which she defines as “relationally guided healing of our lands, waters, and relations through intentional shaping of ecosystems by humans to bring a desired balance that meets the fluid needs of communities while respecting and honouring our mutual dependence through reciprocity.” Here we ask about her research and experiences as an Indigenous woman in ecology. More

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From SSN to PFCsWe analyzed the 1,914,171 proteins from 885 MAGs from marine plankton, recovered from 12 geographically bound assemblies of metagenomic sets corresponding to a total of 93 Tara Oceans samples from the 0.2 to 3 µm and 0.2 to 1.6 µm size fractions21. A flowchart of our bioinformatic pipeline is available in Supplementary Fig. 1. 39.6% of the MAGs’ proteins (757,457) were involved in our SSN, i.e., they had at least one similarity relationship with another protein that satisfied the chosen threshold of 80% similarity and 80% coverage (see “Methods”). In total, 51.1% of the network proteins could be annotated to 4922 unique molecular function IDs in the KEGG database37, associated with 327 distinct metabolic pathways (a full list of these pathways is available in Supplementary Data 1). In total, 85.2% of the network proteins were annotated to 17,009 eggNOG functional descriptions38,39.The SSN involved 233,756 connected components (CCs), i.e., groups of nodes (here proteins) connected together by at least one path and disconnected from the rest of the network. According to KEGG and eggNOG databases, 15.3% and 48.5% of the CCs remained without any functional annotation (i.e., all sequences from the CC were unmatched in the databases, or had a match but were not yet linked to any biological function, Table 1), and 14.8% were functionally unannotated for both databases. We ranked the functional homogeneity of CCs involving at least one functional annotation from 0 (all annotations in the CC are different) to 1 (all annotations in the CC are the same) and found mean homogeneity scores of 0.99 over 1 for KEGG annotations and 0.94 over 1 for eggNOG ones (see “Methods” for score calculation details). Only 88 (0.04%) CCs had a homogeneity score below 0.5 in both annotation databases, all with sizes below five proteins. 177 CCs (0.07%) had a score below 0.8 in both databases, all under 12 proteins in size. These CCs were kept in the analysis while tagged as poorly homogenous. We thereafter considered each CC as a PFC, numbered from #1 to #233,756.Table 1 Metrics computed on the 233,756 protein functional clusters (PFC) from the sequence similarity network of MAGs proteins.Full size tableTo check for the influence of taxonomic relationships between the MAGs on our PFCs, we computed different metrics based on MAGs taxonomic annotations provided by Delmont et al.21. (Table 1). This taxonomic annotation based on 43 single-copy core genes allowed to annotate 100% of the MAGs at the domain level, and 95% of the MAGs at the phylum level, the remaining 5% corresponding to Bacteria MAGs of unidentified phyla21. Only 1330 PFCs (0.6%) mixed proteins from the Archaea and Bacteria domains. PFCs were very homogeneous at the phylum level, then the homogeneity decreased at lower taxonomic rank, meaning that PFCs studied here were generally not specific from a single class, order, family, genus, or MAG (Table 1). In total, 7834 PFCs (3.4%) were only composed of proteins with no functional annotation in KEGG and eggNOG databases, and no taxonomic annotation under the phylum level. Their sizes ranged from 2 to 30 proteins (mean of 2.62). Their 20,552 proteins came from Euryarchaeota MAGs (12,458; 60.6%), Bacteria MAGs of unidentified phylum (2742; 13.3%), Candidatus Marinimicrobia MAGs (2451; 11.9%), Proteobacteria MAGs (1528; 7.4%), Acidobacteria MAGs (1031; 5%), Verrucomicrobia MAGs (103; 0.5%), Planctomycetes MAGs (89; 0.4%), Bacteroidetes MAGs (79; 0.4%), Chloroflexi MAGs (59; 0.3%) and Candidate Phyla Radiation MAGs (12; 0.05%). We hereafter considered these functionally and taxonomically unknown PFCs as “dark” PFCs40,41. Their nucleotidic sequences are available in separate supplementary files (see “Data availability”). The abundance of dark PFCs was significantly different from the abundance of other PFCs in 85 samples over 93 (two-sided Wilcoxon rank-sum test, p-value  More