Genomes of novel Myxococcota reveal severely curtailed machineries for predation and cellular differentiation

Abstract

Cultured Myxococcota are predominantly aerobic soil inhabitants, characterized by their highly coordinated predation and cellular differentiation capacities. Little is currently known regarding yet-uncultured Myxococcota from anaerobic, non-soil habitats. We analyzed genomes representing one novel order (o__JAFGXQ01) and one novel family (f__JAFGIB01) in the Myxococcota from an anoxic freshwater spring in Oklahoma, USA. Compared to their soil counterparts, anaerobic Myxococcota possess smaller genomes, and a smaller number of genes encoding biosynthetic gene clusters (BGCs), peptidases, one- and two-component signal transduction systems, and transcriptional regulators. Detailed analysis of thirteen distinct pathways/processes crucial to predation and cellular differentiation revealed severely curtailed machineries, with the notable absence of homologs for key transcription factors (e.g. FruA and MrpC), outer membrane exchange receptor (TraA), and the majority of sporulation-specific and A-motility-specific genes. Further, machine-learning approaches based on a set of 634 genes informative of social lifestyle predicted a non-social behavior for Zodletone Myxococcota. Metabolically, Zodletone Myxococcota genomes lacked aerobic respiratory capacities, but encoded genes suggestive of fermentation, dissimilatory nitrite reduction, and dissimilatory sulfate-reduction (in f_JAFGIB01) for energy acquisition. We propose that predation and cellular differentiation represent a niche adaptation strategy that evolved circa 500 Mya in response to the rise of soil as a distinct habitat on earth.

Microbial life in ancient permafrost along a salinity gradient illuminated by metagenomics

“…Contemporary descendants of the microorganisms, which were exclusively discovered in CH1_17, were found to be highly metabolically exible organisms that could adapt to resource variability by using different electron donors and acceptors or being involved in syntrophic interactions. For example, Myxococcota from anoxic aquatic environments being a strict anaerobe are capable of using fermentation, nitrate reduction, and dissimilarity sulfate reduction for energy acquisition [71]. The current discovery of MAGs for Desulfobacterota and MBNT15 in deeper MP_16.9 sample are in line with the previously obtained data that obligately anaerobic taxa such as sulfate reducers and candidate lineage MBNT15 thrive in more stable deeper marine sediments [72].…”

Diverse secondary metabolites are expressed in particle-associated and free-living microorganisms of the permanently anoxic Cariaco Basin

“…BGCs in the PA fraction were expressed predominantly from MAGs affiliated with the Omnitrophota, Desulfobacterota, Planctomycetota, Myxococcota, and Gammaproteobacteria. Planctomycetota genomes have recently been reported to contain diverse biosynthetic potential 37 , while the Gammaproteobacteria and Myxococcota are prolific producers of secondary metabolites 30,38 . The majority of expressed BGCs in the PA fraction encoded terpenes, RiPPs, and non-ribosomal peptides.…”

Greenhouse gas emissions and soil microbial activity for selected land use systems in floodplains

“…Myxococcota bacteria was found more abundant in the AF and RF systems relative to AG which could be attributed to the positive correlation of this phyla with increased N (Wu et al, 2021). Myxococcota have been detected in a wide range of environments in predominantly anaerobic habitats (Murphy et al, 2021), and we found the maximum abundance of this phyla under FD conditions. Bacteroidetes phyla have been reported to be living in the rhizosphere (Mhete et al, 2020) which might be the reason for their higher abundance in the RF and AF with extensive tree root systems as compared to AG.…”