Global Distribution Patterns and Pangenomic Diversity of the Candidate Phylum “Latescibacteria” (WS3)

Abstract

We investigated the global distribution patterns and pangenomic diversity of the candidate phylum "" (WS3) in 16S rRNA gene as well as metagenomic data sets. We document distinct distribution patterns for various "" orders in 16S rRNA gene data sets, with prevalence of orders sediment_1 in terrestrial, PBSIII_9 in groundwater and temperate freshwater, and GN03 in pelagic marine, saline-hypersaline, and wastewater habitats. Using a fragment recruitment approach, we identified 68.9 Mb of ""-affiliated contigs in publicly available metagenomic data sets comprising 73,079 proteins. Metabolic reconstruction suggests a prevalent saprophytic lifestyle in all "" orders, with marked capacities for the degradation of proteins, lipids, and polysaccharides predominant in plant, bacterial, fungal/crustacean, and eukaryotic algal cell walls. As well, extensive transport and central metabolic pathways for the metabolism of imported monomers were identified. Interestingly, genes and domains suggestive of the production of a cellulosome-e.g., protein-coding genes harboring dockerin I domains attached to a glycosyl hydrolase and scaffoldin-encoding genes harboring cohesin I and CBM37 domains-were identified in order PBSIII_9, GN03, and MSB-4E2 fragments recovered from four anoxic aquatic habitats; hence extending the cellulosomal production capabilities in beyond the Gram-positive In addition to fermentative pathways, a complete electron transport chain with terminal cytochrome oxidases Caa3 (for operation under high oxygen tension) and Cbb3 (for operation under low oxygen tension) were identified in PBSIII_9 and GN03 fragments recovered from oxygenated and partially/seasonally oxygenated aquatic habitats. Our metagenomic recruitment effort hence represents a comprehensive pangenomic view of this yet-uncultured phylum and provides insights broader than and complementary to those gained from genome recovery initiatives focusing on a single or few sampled environments. Our understanding of the phylogenetic diversity, metabolic capabilities, and ecological roles of yet-uncultured microorganisms is rapidly expanding. However, recent efforts mainly have been focused on recovering genomes of novel microbial lineages from a specific sampling site, rather than from a wide range of environmental habitats. To comprehensively evaluate the genomic landscape, putative metabolic capabilities, and ecological roles of yet-uncultured candidate phyla, efforts that focus on the recovery of genomic fragments from a wide range of habitats and that adequately sample the intraphylum diversity within a specific target lineage are needed. Here, we investigated the global distribution patterns and pangenomic diversity of the candidate phylum "" Our results document the preference of specific "" orders to specific habitats, the prevalence of plant polysaccharide degradation abilities within all "" orders, the occurrence of all genes/domains necessary for the production of cellulosomes within three "" orders (GN03, PBSIII_9, and MSB-4E2) in data sets recover...

Bacterial community composition under long‐term reduced tillage and no till management

“…Latescibacteria, a candidate phylum found to contain genes for degradation of plant polysaccharides (Farag et al . ) and believed to be involved in organic matter turnover (Youssef et al . ), was found in greater abundance in no till soils.…”

“…In addition, several of the taxa and OTUs found to be more abundant in no till soils are known to contain organic matter degraders. Latescibacteria, a candidate phylum found to contain genes for degradation of plant polysaccharides (Farag et al 2017) and believed to be involved in organic matter turnover (Youssef et al 2015), was found in greater abundance in no till soils. In addition, several of the OTUs in greater abundance in no till soil were classified as Actinobacteria and Verrucomicrobia, two phyla composed primarily of chemoheterotrophs that utilize complex polysaccharides (Hedlund 2010;Barka et al 2016).…”

The Pedological Context Modulates the Response of Soil Microbial Communities to Agroecological Management

“…These two groups belong to yet-uncultured microbial candidate phyla and therefore their metabolic capabilities and ecological roles are not yet well-understood. Recent studies have highlighted the prevalent saprophytic lifestyle in the Latescibacteria lineage (member of the Fibrobacteres-Chlorobi-Bacteroidetes (FCB) superphylum) suggesting their important role in soil organic detritus degradation (Farag et al, 2017). Patescibacteria belong to the candidate phyla radiation (CPR) (Brown et al, 2015), a phylogenetic super-clade that is characterized by limited metabolic capabilities, and small streamlined genomes that might point to symbiotic or syntrophic lifestyles (Wrighton et al, 2012;Nelson and Stegen, 2015).…”

The Wood–Ljungdahl pathway as a key component of metabolic versatility in candidate phylum Bipolaricaulota (Acetothermia, OP1)

“…The presence and functionality of the pathway outside the Firmicutes has been reported, e.g., in Treponema primitia, and anammox Planctomycetes bacteria (Graber and Breznak, 2004;Schouten et al, 2004;Strous et al, 2006). The recent availability of genomes from uncultured organisms allowed the documentation of its presence in a wide range of yet-uncultured bacterial phyla (Farag et al, 2017;Adam et al, 2018;Suzuki et al, 2018;Vavourakis et al, 2018).…”