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. 2021 Nov 10;87(23):e0170621.
doi: 10.1128/AEM.01706-21. Epub 2021 Sep 15.

Genomes of Novel Myxococcota Reveal Severely Curtailed Machineries for Predation and Cellular Differentiation

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Genomes of Novel Myxococcota Reveal Severely Curtailed Machineries for Predation and Cellular Differentiation

Chelsea L Murphy et al. Appl Environ Microbiol. .

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, nonsoil habitats. We analyzed genomes representing one novel order (o__JAFGXQ01) and one novel family (f__JAFGIB01) in the Myxococcota from an anoxic freshwater spring (Zodletone 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 13 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 nonsocial behavior for Zodletone Myxococcota. Metabolically, Zodletone Myxococcota genomes lacked aerobic respiratory capacities but carried 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 million years ago (Mya) in response to the rise of soil as a distinct habitat on Earth. IMPORTANCE The phylum Myxococcota is a phylogenetically coherent bacterial lineage that exhibits unique social traits. Cultured Myxococcota are predominantly aerobic soil-dwelling microorganisms that are capable of predation and fruiting body formation. However, multiple yet-uncultured lineages within the Myxococcota have been encountered in a wide range of nonsoil, predominantly anaerobic habitats, and the metabolic capabilities, physiological preferences, and capacity of social behavior of such lineages remain unclear. Here, we analyzed genomes recovered from a metagenomic analysis of an anoxic freshwater spring in Oklahoma, USA, that represent novel, yet-uncultured, orders and families in the Myxococcota. The genomes appear to lack the characteristic hallmarks for social behavior encountered in Myxococcota genomes and displayed a significantly smaller genome size and a smaller number of genes encoding biosynthetic gene clusters, peptidases, signal transduction systems, and transcriptional regulators. Such perceived lack of social capacity was confirmed through detailed comparative genomic analysis of 13 pathways associated with Myxococcota social behavior, as well as the implementation of machine learning approaches to predict social behavior based on genome composition. Metabolically, these novel Myxococcota are predicted to be strict anaerobes, utilizing fermentation, nitrate reduction, and dissimilarity sulfate reduction for energy acquisition. Our results highlight the broad patterns of metabolic diversity within the yet-uncultured Myxococcota and suggest that the evolution of predation and fruiting body formation in the Myxococcota has occurred in response to soil formation as a distinct habitat on Earth.

Keywords: Myxobacteria; fruiting body formation; genome resolved metagenomics; predation.

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Figures

FIG 1
FIG 1
Phylogenomics of the Myxococcota, including novel lineages from Zodletone Spring. The maximum likelihood trees were constructed in RAxML (79) using all Myxococcota genomes available from the GTDB r95 database based on the concatenated alignments of 120 housekeeping genes obtained from GTDB-Tk (78). The tree was rooted (root not shown) with the two Bdellovibrionota genomes Halobacteriovorax marinus (GenBank assembly accession number GCF_000210915.2) and Bdellovibrio bacteriovorus (GenBank assembly accession number GCF_000196175.1). The tree is wedged (shown as black circles at the end of branches) to represent genus level taxonomy (g__), unless the number of available genomes per genus is less than 5, in which case the family level (f__), or order level (o__) taxonomy is shown instead. The size of the wedge is proportional to the number of genomes. Bootstrap support values based on 100 replicates are shown as triangles for nodes with >70% support. Class-level taxonomy is color-coded as shown in the legend. The track around the tree represents the ecosystem classification of the habitat from which the genomes originated. Zodletone genomes are labeled in blue bold text with their GenBank assembly accession number.
FIG 2
FIG 2
Comparative genomics of Zodletone novel Myxococcota genomes to the genomes of 27 type species belonging to the classes Myxococcia, Polyangia, and Bradymonadia. The species and their GenBank assembly accession numbers are Anaeromyxobacter dehalogenans 2CP-1, GCF_000022145.1; Haliangium ochraceum DSM 14365, GCF_000024805.1; Plesiocystis pacifica SIR-1, GCF_000170895.1; Corallococcus coralloides DSM 2259, GCF_000255295.1; Cystobacter fuscus DSM 2262, GCF_000335475.2; Hyalangium minutum, GCF_000737315.1; Sandaracinus amylolyticus, GCF_000737325.1; Archangium gephyra, GCF_001027285.1; Chondromyces crocatus, GCF_001189295.1; Vulgatibacter incomptus, GCF_001263175.1; Labilithrix luteola, GCF_001263205.1; Minicystis rosea, GCF_001931535.1; Melittangium boletus DSM 14713, GCF_002305855.1; Nannocystis exedens, GCF_002343915.1; Bradymonas sediminis, GCF_003258315.1; Lujinxingia litoralis, GCF_003260125.1; Polyangium fumosum, GCF_005144585.1; Persicimonas caeni, GCF_006517175.1; Myxococcus fulvus, GCF_007991095.1; Pyxidicoccus fallax, GCF_012933655.1; Stigmatella aurantiaca, GCF_900109545.1; Vitiosangium, GCF_003044305.1; Aggregicoccus, GCA_009659535.1; Pajaroellobacter abortibovis, GCF_001931505.1; Byssovorax cruenta, GCA_001312805.1; Enhygromyxa salina, GCF_002994615.1; and Sorangium cellulosum B, GCF_000067165.1. Zodletone genomes are labeled in blue bold text with their GenBank assembly accession number. Class-level taxonomy is color-coded as shown in the legend. The tracks underneath the tree show the ecosystem classification of the habitat from which the genomes originated, the assembly genome size (gray bars), GC content (yellow bars), total number of genes in the genome (cyan bars), and coding density (pink bars). The number of biosynthetic gene clusters (BGCs, purple), proteases (yellow), CAZymes (green), and transcription factors (blue) encoded in each genome are shown as a heatmap with the color tones explained in the legend. Under the heatmaps, the two outermost tracks denote the presence (filled squares)/absence (empty squares) of the Myxococcota typical social lifestyle as evidenced by experimental pure culture work (blue), and/or the machine learning approach (green) we used for lifestyle prediction based on the informative set of KO numbers provided in Data Set S1. BGCs, biosynthetic gene clusters; GH, glycosyl hydrolases; PL, polysaccharide lyases; CE, carbohydrate esterase; OCSs, one-component systems; TFs, transcription factors; RR, response regulator; SF, sigma factor; TCSs, two-component systems; HK, histidine kinases; PP, phospho-relay proteins.
FIG 3
FIG 3
A cartoon depicting the 13 pathways associated with Myxococcota social lifestyle examined in detail in this study. Myxococcus cells are shown as blue rods, while prey cells are depicted as gray cocci and rods. Pathways active during nutrient availability are shown above the dotted line, while those induced by starvation are shown below the dotted line. Each of the pathways is shown in bold text within a color-coded outline. The same color code is used for the group of genes in each pathway and in Table S6. For each pathway, a pie chart for the number of gene homologues identified in Zodletone genomes as a percentage of the total number of genes in the pathway is shown in blue, while the percentage of gene homologues absent is shown in orange. The size of the pie chart is proportional to the number of genes in each pathway and ranges from 1 (FruA module) to 35 (the aggregation/sporulation/fruiting body formation module). Arrowheads depict the effect where activation is shown as triangular arrowheads, and inhibition is shown as horizontal line arrowheads. FruA* denotes the active form of FruA. EPS, exopolysaccharide; OME, outer membrane exchange.

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