Phylogenetic tree of life. (Eloe-Fadrosh)
Our view of microbial diversity has greatly expanded, primarily through the wide application of PCR-based surveys of the small-subunit ribosomal RNA (SSU rRNA) gene and shotgun metagenome sequencing. Advances in metagenomic sequencing, assembly, and binning for examining uncultivated microbes have begun yielding complete or near-complete genomes from many novel lineages. These approaches have already led to the discovery of new candidate phylogenetic lineages (phylogenetic groups without cultivated representatives) and are providing a more complete topology of the tree of life.
The DOE JGI is applying large-scale data mining efforts to uncover new microbial groups as part of the New Lineages of Life (NeLLi) project. As part of this effort, we revealed the extent of taxonomic ‘blind spots,’ those lineages that have eluded detection in environmental PCR surveys due to PCR primer mismatches and biases caused by intervening sequences in 16S rRNA genes, from a systematic survey of shotgun metagenomic data available through IMG/M. An example of one such ‘blind spot’ is Candidatus Kryptonia, a proposed candidate phylum identified through genome-resolved metagenomics and single-cell genomics. Additional work is currently underway to catalogue candidate phylogenetic lineages using genome-resolved metagenomics and identify metabolic and functional features associated with these uncultivated microbes.
References:
Castelle CJ, et al. (2013) Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nat Commun. 4:2120.
Castelle CJ, et al. (2015) Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling. Curr Biol. 25:690-701.
Luef B, et al. (2015) Diverse uncultivated ultra-small bacterial cells in groundwater. Nat Commun. 6:6372.
Eloe-Fadrosh EA, et al. (2016) Metagenomics uncovers gaps in amplicon-based detection of microbial diversity. Nat Microbiol. 15032.
Eloe-Fadrosh EA, et al. (2016) Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs. Nat Commun. 7:10476.