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Metagenomic Analysis Unearths Metabolic Teamwork of Bacteria in Biogeochemical Processes

NEW YORK (GenomeWeb) – Using a metagenomic approach, a team of US researchers has surveyed sediment and groundwater samples to uncover some 2,500 bacterial genomes and analyze their roles in biogeochemical cycles.

As the team, led by the University of California, Berkeley, and Lawrence Berkeley National Laboratory, reported in Nature Communications today, those bacterial genomes included representatives from nearly 80 percent of known phylum-level bacterial lineages and from 47 new lineages. Further, by analyzing the metabolic capabilities of these various bacteria, the researchers found that each one encodes only one or two steps of redox pathways, meaning that multiple bacteria types are needed to conduct key global biogeochemical processes.

"We didn't expect to find this incredible microbial diversity," senior author Jill Banfield from UC Berkeley and LBNL said in a statement. "But then again, we know little about the roles of subsurface microbes in biogeochemical processes, and more broadly, we don't really know what's down there."

Banfield and her colleagues studied sediment and groundwater samples collected from an aquifer near the Colorado River. All in all, they sequenced 33 samples to generate 4.58 billion paired-end Illumina reads. They then reconstructed bacterial genomes by binning them based on their GC content, tetranucleotide signature, and the taxonomic affiliation of encoded genes, among other features. From this, they generated 2,516 bacterial genomes — of which 21 were complete— and 24 archaeal genomes.

To examine the phylogeny of these bacteria, the researchers analyzed both genes encoding concatenated ribosomal proteins and 16S rRNA genes. Based on this analysis, they estimated that the bacteria they found at this site included representatives from about 78 percent of known phylum-level bacterial lineages and representatives from 47 putative new lineages, 46 of which hadn't been uncovered by 16S rRNA sequencing before. If confirmed, the researchers said, the addition of these lineages would boost the number of bacterial lineages by about half.

The team named a number of these new bacterial groups after researchers from UC Berkeley and LBNL. The new Candidatus Andersenbacteria is an homage to phylochip inventor Gary Andersen, while Candidatus Doudnabacteria honors CRISPR researcher Jennifer Doudna.

In total, these reconstructed genomes housed more than four million protein-coding genes. By matching these genes against those in various databases, the researchers gauged their metabolic potential. Between about a quarter and a third of the genomes analyzed could use carbon monoxide, hydrogen, or reduced sulfur species as electron donors, they reported. This suggests that the metabolism of these subsurface microbes is involved in the carbon, hydrogen, and sulfur biogeochemical cycles.

However, Banfield and her colleagues noted that only a few microbes could complete a full oxidation of sulfide to sulfate or denitrification of nitrate to nitrogen gas. Instead, the microbes they analyzed appeared to encode only one or two parts of the process. Rather than attributing this to incomplete genomes, they said this means that many bacteria types have to work in cahoots as the products of one type are handed off to another as starting ingredients.

"The combination of high microbial diversity and interconnections through metabolic handoffs likely results in high ecosystem resilience," Banfield added.