PMC

Phylogenetic tree of NifH sequences from MAGs (a) and comparison of the nif operon from SZUA-77, the closest nif operon in NCBI, and the nif operons of representative Nitrospirae diazotrophs (b). The scale bar in the phylogenetic trees represents 0.1 amino acid substitutions per sequence position. The information of reference NifH sequences used in the phylogeny is in Table S6

A schema representation of cell type mapping between NeuroMorpho.Org and three relevant ontologies: NIF Standard (NIFSTD), Open Biomedical Ontologies (OBO), and Subcellular Anatomy Ontology (SAO). Each NeuroMorpho.Org cell type is represented as a tree node in the hierarchy. Rectangular nodes are mapped onto equivalent terms in NIFSTD (prefix “nif_cell”), OBO (prefix “CL”), or SAO (prefix “sao”). The nodes in oval shape are not mapped. Arrows represent “is-a” relationships (e.g. “Chandelier cells are interneurons”).

NifHDK chronogram from 189 taxa, with an overlay of aerobic/facultative anaerobic lineages in green. The outgroup lineage for the rooted tree is depicted by a dotted line. The terminals of lineages are depicted by a heat map indicating the complexity of the nif gene clusters. The presence (black boxes) or absence (white boxes) of individual nif gene cluster-associated loci as well as the phylum-level classification for each taxon are indicated. See Table S1 in the supplemental material for additional details of the nif gene contents and gene accession numbers for each taxon.

The interior node values of the tree are clade credibility values, values lower than 100% are indicated. Branches are colored blue (Mo-nitrogenase, Nif), green (V-nitrogenase, Vnf), purple (Fe-nitrogenase, Anf), light blue (uncharacterized homolog), dark yellow (uncharacterized nitrogenase). The text colored red was Paenibacillus.