Earth and Planetary Science
EPS Planetary Science

Berkeley Scientists Find the Prevalence of Bacterial Methylotrophy and Archaeal Hetereotrophy below the Grass Root Zone

Tuesday, March 7, 2017

Susan Spaulding Brian Thomas, Andrea Singh, Alexander Probst, and Jillian Banfield (pictured) are co-authors of “Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone.” The article came out November 8 2016 in the peer-reviewed journal PeerJ.

Annually, half of all plant-derived carbon is added to soil where it is microbially respired to CO2. However, understanding of the microbiology of this process is limited because most culture-independent methods cannot link metabolic processes to the organisms present, and this link to causative agents is necessary to predict the results of perturbations on the system. The researchers collected soil samples at two sub-root depths (10–20 cm and 30–40 cm) before and after a rainfall-driven nutrient perturbation event in a Northern California grassland that experiences a Mediterranean climate. From ten samples, they reconstructed 198 metagenome-assembled genomes that represent all major phylotypes. They also quantified 6,835 proteins and 175 metabolites and showed that after the rain event the concentrations of many sugars and amino acids approach zero at the base of the soil profile. Unexpectedly, the genomes of novel members of the Gemmatimonadetes and Candidate Phylum Rokubacteria phyla encode pathways for methylotrophy. The researchers infer that these abundant organisms contribute substantially to carbon turnover in the soil, given that methylotrophy proteins were among the most abundant proteins in the proteome. Previously undescribed Bathyarchaeota and Thermoplasmatales archaea are abundant in deeper soil horizons and are inferred to contribute appreciably to aromatic amino acid degradation. Many of the other bacteria appear to breakdown other components of plant biomass, as evidenced by the prevalence of various sugar and amino acid transporters and corresponding hydrolyzing machinery in the proteome. Overall, their work provides organism-resolved insight into the spatial distribution of bacteria and archaea whose activities combine to degrade plant-derived organics, limiting the transport of methanol, amino acids and sugars into underlying weathered rock. The new insights into the soil carbon cycle during an intense period of carbon turnover, including biogeochemical roles to previously little known soil microbes, were made possible via the combination of metagenomics, proteomics, and metabolomics.

Susan Spaulding and Alexander Probst are postdoctoral researchers in the Banfield Lab. Brian Thomas and Andrea Singh are research staff members in the Banfield Lab. Prof. Banfield is a geomicrobiologist and biogeochemist whose work focuses on the fundamental relationship between microorganisms and their chemical environments. She is jointly appointed in the Berkeley Earth & Planetary Science and Environmental Science, Policy, and Management Departments and is a recipient of the MacArthur genius grant.

For the full-length article please click here (open access).