ABSTRACT
The
Sphaerotilus-Leptothrix
group of bacteria includes one of the first described microorganisms,
Leptothrix ochracea
, an uncultured type strain, plus isolates of
Leptothrix
and
Sphaerotilus
. This group is unified by the ability to form sheaths and oxidize metals, although
L. ochracea
exhibits obvious ecological, morphological, and functional differences from the rest of
Sphaerotilus-Leptothrix
. Recently, there have been calls to combine the group into one genus,
Sphaerotilus
; however, these studies lacked adequate genomic representation of
L. ochracea
. Here, we present a comprehensive comparative genomic analysis of the
Sphaerotilus-Leptothrix
group, including expanded representation of
L. ochracea
, a closely related novel species,
Leptothrix toolikensis
, and two new isolates (
Leptothrix mechoopdaensis
). Analysis of 38 genomes resolves three phylogenetic and functional groups: the
ochracea
-type
Leptothrix
(Group 1), the
mobilis
-type
Leptothrix
(Group 2), and
Sphaerotilus
(Group 3). Group 1 genomes form a separate genus based on average nucleotide identity and alignment fraction. The genomes clearly diverge from the rest of
Sphaerotilus-Leptothrix
in phylogeny, size, and metabolic potential. Group 1 genomes are much smaller (2.59–3.04 Mb) than those of Groups 2 (4.55–6.06 Mb) and 3 (3.94–5.07 Mb), while encoding more metal oxidases and fewer carbohydrate-active enzymes. Group 2 clusters with Group 3 phylogenetically and is similar in organic carbon metabolisms but maintains more metal oxidation genes. Group 2 members lack homogeneity in phenotype and genotype, suggesting that additional isolates and genomes are needed for confident classification. However, Group 1 genomes (
L. ochracea
and
L. toolikensis
) show clear divergence, precluding their inclusion in
Sphaerotilus
and supporting the retention of the genus
Leptothrix
.
IMPORTANCE
Researchers have long noted differences in metal oxidation, morphology, and ecology among
Sphaerotilus-Leptothrix
, but longstanding confusion over phylogeny and genus boundaries led to inconsistent taxonomic classification between the two genera. This confusion stems from previous work that used isolates that are unavailable or lost distinguishing traits in culture, and from limited genomic data. Furthermore, the
Leptothrix
type strain
L. ochracea
has never been isolated. This study provides molecular evidence that substantiates calls to reassign some
Leptothrix
members to the genus
Sphaerotilus
but adds to an emerging body of evidence that Group 1
L. ochracea
and now
L. toolikensis
represent a functionally distinct lineage. While genomic similarity metrics left taxonomic divisions unclear, integrating metabolic potential with phylogeny resolved genus boundaries based on clear functional groupings. This polyphasic approach for delineating genera clarifies longstanding taxonomic confusion and refines our understanding of functional diversity both across and within
Sphaerotilus-Leptothrix
lineages.