Summary
The bacterial tree contains many deep‐rooting clades without any cultured representatives. One such clade is ‘
E
ndomicrobia’, a class‐level lineage in the phylum
E
lusimicrobia
represented so far only by intracellular symbionts of termite gut flagellates. Here, we report the isolation and characterization of the first free‐living member of this clade from sterile‐filtered gut homogenate of defaunated (starch‐fed)
R
eticulitermes santonensis
. Strain
R
sa215 is a strictly anaerobic ultramicrobacterium that grows exclusively on glucose, which is fermented to lactate, acetate, hydrogen and
CO
2
. Ultrastructural analysis revealed a
G
ram‐negative cell envelope and a peculiar cell cycle. The genome contains a single set of
nif
genes that encode homologues of
G
roup
IV
nitrogenases, which were so far considered to have functions other than nitrogen fixation. We documented nitrogenase activity and diazotrophic growth by measuring acetylene reduction activity and
15
N
2
incorporation into cell mass, and demonstrated that transcription of
nifH
and nitrogenase activity occur only in the absence of ammonium. Based on the ancestral relationship to ‘
C
andidatus
E
ndomicrobium trichonymphae’ and other obligate endosymbionts, we propose the name ‘
E
ndomicrobium proavitum
’ gen. nov., sp. nov. for the first isolate of this lineage and the name ‘
E
ndomicrobia
’ class. nov. for the entire clade.