Evolution of longitudinal division in multicellular bacteria of the Neisseriaceae family

Abstract

Rod-shaped bacteria typically elongate and divide by transverse fission. However, several bacterial species can form rod-shaped cells that divide longitudinally. Here, we study the evolution of cell shape and division mode within the family Neisseriaceae, which includes Gram-negative coccoid and rod-shaped species. In particular, bacteria of the genera Alysiella, Simonsiella and Conchiformibius, which can be found in the oral cavity of mammals, are multicellular and divide longitudinally. We use comparative genomics and ultrastructural microscopy to infer that longitudinal division within Neisseriaceae evolved from a rod-shaped ancestor. In multicellular longitudinally-dividing species, neighbouring cells within multicellular filaments are attached by their lateral peptidoglycan. In these bacteria, peptidoglycan insertion does not appear concentric, i.e. from the cell periphery to its centre, but as a medial sheet guillotining each cell. Finally, we identify genes and alleles associated with multicellularity and longitudinal division, including the acquisition of amidase-encoding gene amiC2, and amino acid changes in proteins including MreB and FtsA. Introduction of amiC2 and allelic substitution of mreB in a rod-shaped species that divides by transverse fission results in shorter cells with longer septa. Our work sheds light on the evolution of multicellularity and longitudinal division in bacteria, and suggests that members of the Neisseriaceae family may be good models to study these processes due to their morphological plasticity and genetic tractability.

Phylogenomic analysis of the understudiedNeisseriaceaespecies reveals a poly- and paraphyleticKingellagenus

“…All of these overall genome relatedness indices (OGRI) support the close relationship between these three genera, and the ANI falls above the proposed 73% genus cutoff score. Moreover, Nyongesa and co-workers [15] hypothesize that the MuLDi phenotype evolved twice in the Neisseriaceae , first in Conchiformibius species and then in the common ancestor of Simonsiella and Alysiella, a hypothesis that is strongly supported by our phylogenetic analyses.…”

“…Finally, another recent evolutionary study of these taxa has used less stringent similarity and gene presence cutoff to define the core genome for species in the Neisseriaceae for subsequent phylogenetic analyses [15]. We replicated this analysis by reanalyzing the data using a sequence similarity cut off of 50% for genes present in 99% or 80% of analyzed genomes.…”

“…Alysiella and Simonsiella are commensal genera associated with the oral microbiome of mammals [14, 33, 34]. These two genera, along with the genus Conchiformibius , are distinctive for being multicellular, longitudinally-dividing (MuLDi) species that comprise the only known animal multicellular bacterial symbionts [15]. Based on a whole genome approach, Alysiella and Simonsiella diverged from the rest of the Kingella species more recently than K. denitrificans or K. oralis diverged.…”

Previously uncharacterized rectangular bacterial structures in the dolphin mouth

“…The taxonomic identification of specific cell morphotypes from complex communities can be extremely difficult, to the point that it often remains unresolved 27, 52, 53 . Results collected here strongly suggest that the RBS-As are not affiliated with the multicellular longitudinally dividing Neisseriaceae genus Conchiformibius , whose members also form rectangularly shaped clusters of rod-like cells 54 . First, the marker gene amplicon sequencing workflow employed here did not detect any Neisseriaceae amplicons in 54 dolphin oral samples that underwent deep 16S rRNA gene amplicon sequencing, although this workflow did detect S. muelleri after cells from this taxon were intentionally spiked into aliquots of dolphin oral samples.…”

“…Fourth, visual comparisons of RBS-A images presented here with the TEM and fluorescence microscopy images of multicellular longitudinally dividing Neisseriaceae ( Alysiella , Simonsiella , and Conchiformibius ) in ref. 54 suggest that they are different taxa. For example, RBSs appear to contain segments (cells) that are embedded in a matrix-like material and fully encapsulated by an S-layer-like structure, whereas multicellular longitudinally dividing Neisseriaceae belonging to the same filament only appeared to share their outer membrane 54 .…”