Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

BER-RENEW iSAVe: New Energy Sciences Workforce to Advance Innovations in Sustainable Arid Vegetation


Nathalie Delherbe* (, Courtney Cameron* (, Chynna Bowman, Elizabeth Waters, Marina G. Kalyuzhnaya


San Diego State University


(1) Uncovering the natural principles that control greenhouse gas–capturing capacities of native arid soils; (2) Defining key players of the C1B community and evaluating their impact on soil-atmosphere exchange fluxes, soil chemistry, and water retention; (3) Validating the applicability of C1B supplements to benefit crop growth in nutrient-limited arid environments; and (4) Evaluating impacts and constraints of the C1B-based technology implementation at midscale farm levels for energy crop production.


Sustainable use of arid soil will critically depend on the ability to foster natural principles that preserve soils and support the structure and functions of native ecosystem microbiomes in the long term. Native arid ecosystems represent an untapped reservoir of microbial functions essential for promoting plant growth and survival under water-limited and nutrient-poor conditions. The main goal of this study was to interrogate metagenomic data and functional capabilities of natural arid land microbiomes to design critical solutions for threatened agricultural land.

Here, the team presents a holistic study that started with thorough investigation of in situ methane (CH4) fluxes and microbial communities inhabiting soil in the Anza Borrego Desert, a model arid ecosystem. Researchers found that in situ CH4 fluxes indicate differences in the consumption of CH4 between vegetated and unvegetated soil patches, reaching their peak on vegetated sites at the highest daylight times around noon with up to 12 micromoles per square meter x h. The metagenomic and enrichment studies revealed a ubiquitous presence of methanotrophic bacteria in the Anza Borrego Desert soil. The network analysis highlights the co-occurrence of CH4-consuming bacteria (Methylocaldum, Methylobacter, and Methylomicrobium) and several members of Rhizobia and nitrifying bacteria. Sixty-one metagenome assembled genomes (MAGs) were generated, and eight MAGs were identified as methanotrophs, including four Methylocaldum spp. and Methylobacter luteus. Additional high-resolution sampling efforts revealed the co-occurrence of several methanotroph genera, of which the highest proportion corresponded to Methylocaldum, in both vegetated and unvegetated patches.

Several methanotrophic bacteria, most belonging to the genus Methylocaldum, were isolated and sequenced. Comparative genomic studies were carried out. The examination of the genome inventory of these strains found significant redundancy in primary metabolic pathways, including numerous copies of a key gene for methane oxidation and several genes for methanol oxidation, in addition to three pathways for one-carbon assimilation, and two strategies of carbon storage (glycogen and polyhydroxyalkanoates).

Furthermore, the interaction of native methanotrophic species with the California-native plant Boechera depauperata (Brassicaceae) were examined. When supplemented with methanotrophic traits, B. depauperata displays drought tolerance and increased growth as well as quantitative measures of plant resilience, including photosystem activity and increased leaf area. Metabolomic and transcriptomic analysis revealed promoting flavonoids in the plants and a decrease in various amino acids including tryptophan, followed by an upregulation in genes involved in the tryptophan mediated–indole-3-acetic acid (IAA) biosynthesis pathway.

These results suggest a mutualistic relationship between B. depauperata and Methylocaldum sp. leading to higher plant drought tolerance. Data suggest that in this arid ecosystem, methanotrophs are associated with vegetation and the association might enhance native plant drought tolerance. This work provides essential evidence that the association between plants and methanotrophs in (semi)arid ecosystems plays a major role in supporting the vegetation diversity of those ecosystems that subsequently might be key for methane cycling, having a significant impact on the global levels of this potent greenhouse gas and ultimately influencing the global climate.

Funding Information

Metagenomic and Methylocaldum spp. genome sequencing and assembly were carried out by the DOE Joint Genome Institute (JGI). This work was funded by the U.S. DOE under the DOE Office of Science Reaching a New Energy Sciences Workforce (RENEW) contract DE-SC0024289.