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Microbial Processes Mediating Biogeochemical Cycling and Trace Gas Emissions from Grassland, Wetland, and Agricultural Soils

Rice cultivation and its environmental implications, along with the exploration of varied microbiomes in distinct ecosystems, are pivotal in our understanding of greenhouse gas emissions and broader biogeochemical processes. Our research delves into the nuanced microbial interactions within these contexts, aiming to provide insights for sustainable practices and mitigation strategies.

Rice soil microbiomes and greenhouse gas emissions


Rice is an important staple food, accounting for 19% of global calories and 13% of global protein in 2009. As the world population continues to grow, rice production will need to expand to meet rising demands. Unfortunately, the cultivation of rice is also a major greenhouse gas contributor. It accounts for about 10% of anthropogenic methane emissions. Rice production emits methane because rice paddies are flooded. Flooding prevents the emergence of weeds but also creates an anoxic soil environment that forces carbon (e.g., rice straw and root exudates) to be broken down anaerobically, eventually leading to methane as an end product.
While significant strides have been made in understanding the microbiology responsible for methane production in rice fields, most in situ studies rely on marker genes to identify the key players. In a pilot experiment, we sampled a paddy at the Rice Experiment Station in Biggs, CA over the course of the 2021 growing season, pairing metagenomics and metatranscriptomics to gas fluxes over time. Our goal is to use genome-resolved metagenomics to elucidate the metabolic potential of the key players in the system and leverage metatranscriptomics to understand how environmental conditions drive methanogenesis and methanotrophy. The field-based experiments will continue for the next two years.

In 2022, we conducted an experiment in the Rice Experiment Station to understand the effect of a mid-growing season drying event (often referred to as alternative wetting and drying, AWD) on paddy soil microbiology and, consequently, methane emissions. The mitigating effect of AWD on methane emissions, up to 70%, has been well documented. Studies have thus far relied on specific biomarker genes to assess the shifts in methanogenesis and methanotrophy upon AWD treatment. However, these approaches lack community-level analysis and can introduce biases as a result of primer selection and design. We will leverage metagenomics and metatranscriptomics to show the mechanistic details that underlie decreases in methane emission from AWD treatment. Understanding the specific mechanisms can help explain the high variability in AWD effectiveness across different rice paddies and optimize AWD practices for best results.
In a second project in collaboration with Prof. Pam Ronald, UC Davis, we are probing how rice genetic variants differ from wild type rice in terms of their root-associated microbial communities and potential for greenhouse gas emissions. The initial phase is a greenhouse-based study, but experiments in the following two years will likely transition into field studies in rice paddies. Ultimately, we hope that this will yield insights that will inform the best practices for rice growing to mitigate methane emissions for a greener future.



Methane-oxidizing archaea and their extrachromosomal elements, including Borgs 

Working in wetland soils, we discovered surprisingly large, linear, peculiar genetic elements (named Borgs) that we infer to associate directly with the anaerobic, methane-oxidizing Methanoperedens archaea. Notably, these elements encode many genes that are directly implicated in methane oxidation metabolism. We will continue to explore Borgs and other types of extrachromosomal elements and investigate their distribution, evolution, and the potential biogeochemical importance of this association. We hope to learn how to harness this partnership to reduce methane emissions from anaerobic, carbon-rich environments such as rice paddies.


Probing soil and root-associated microbiomes in sorghum

In addition to rice, sorghum is a globally important cereal crop that is gaining interest for increased production by farmers in California. Sorghum is drought-tolerant, a source of biofuels, and is grown for human and animal food products. We are interested in understanding the extent of carbon sequestration by sorghum at various soil depths. Through metagenomic studies of the sorghum rhizosphere and surrounding soil, we will characterize the metabolic potential of the associated microbial communities. This initiative will inform ongoing efforts by others, including Prof. Peggy Lemaux, to increase sorghum’s ability to sequester carbon in the soil, ultimately reducing the levels of atmospheric carbon dioxide and the extent of climate change.

Biogeochemical processing in watershed ecosystem compartments

Our lab is part of a team studying biogeochemical processes at the watershed scale. The study is led out of LBNL, with research conducted in the headwaters catchment of East River, CO. Our part of this multidisciplinary project relates to the microbial underpinnings that, although they occur at the micron-scale, impact watershed function and ecosystem outputs at the tens of kilometers scale. Watershed functioning relies on complex interactions among vegetation, hydrology, topography, and geology that lead to distinct conditions, and our work aims to capture many of these effects using genome-resolved metagenomics and transcriptomics bioinformatics methods. We are studying multiple ecosystem compartments, ranging from the soils of the river corridor to soils along hillslopes to soils along moisture gradients.  We hypothesize that detailed analysis of specific and

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The hyporheic zone. Meanders were subdivided into the river channel, hyporheic zone (the region of sediment and porous space where river water and shallow groundwater mix), and the surface and subsurface vegetated soils and sediments, whose characteristics reflect past and present river flow dynamics. The objectives are to infer processes that contribute to C and N cycling based on the metabolic potential of the microbial communities and to identify hotspots and hot moments of microbial activity in the riparian zone and their impacts on nutrient cycling in the watershed. In collaboration with Dr. Michelle Newcomer (Lawrence Berkeley National Laboratory), we are studying microbial communities of the hyporheic zone to understand how the hydrology, geology, and water chemistry surrounding and within the hyporheic zone influence the microbial community and the metabolic capacities of the organisms present and, in turn, how microbial activity impacts nutrient exports via the river as well as trace gas emission.


Wetlands of the river corridor. Wetlands are the largest natural source of methane emissions, responsible for approximately 20% - 30% of global emissions. Many wetlands have formed along the East River, and we are interested in understanding how microbes drive methane metabolism in these wetlands. Specifically, we are interested in what metabolic capacity these microbes possess and how their in situ activity varies spatially and temporally in the wetlands with respect to methane emissions. As part of the SFA watershed team, we are collaborating with Dr. Markus Bill and Dr. Mark Conrad (Lawrence Berkeley National Laboratory) to quantify methane gas and methane isotopes to provide context for our microbiome research in the wetland ecosystem. 

representative ecosystem compartments can generate insights about key biogeochemical processes that can be used to approximate the function of the larger system. Specific projects are:

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Hillslope carbon cycling. Warming of mountainous watersheds, causing decreased snow cover and earlier snowmelt, is expected to reduce overland flow, increase early-season infiltration, and lead to deeper transport of solutes and increased production of CO2 within the vadose zone. As part of the SFA team led by Dr. Tetsu Tokunaga, we are studying the contribution of East River’s subsurface microbial communities to the carbon cycle. Temporal and spatial (along a hillslope gradient as well as depth-resolved) metagenomics and metatranscriptomic samples are interrogated to answer this question.

Hillslope vegetation. The vegetation of the Upper East River watershed is representative of the Western US, including upland meadows, stands of aspens and conifers, and patches of sagebrush. We hypothesize that there are differences in the soil metabolic potential between these vegetation types and along the longitudinal profile of the Upper East River watershed. By using genome-resolved metagenomics, we aim to link above-ground vegetation types to below-ground soil processes. This information should enable watershed-scale predictions of soil processes from the distribution of these vegetation types.

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Hillslope water gradients. Our newest project investigates how the droughts that are plaguing the Rocky Mountains and much of the Western US impact soil microbiome function by changing microbial diversity and metabolisms. We anticipate that drought will alter nutrient cycling in the ecosystem and threaten core watershed functions. By linking changes in microbial life strategies (traits) to in situ biogeochemical cycling in simulated drought conditions (dry down from snowmelt), we can test our hypothesis that drought is driving changes in microbial carbon and nitrogen cycling. Consequently, this research will help predict future forest health and greenhouse gas emissions in mountainous watersheds struggling with drought.  This project is in collaboration with Dr. Eoin Brodie.

Relevant Publications

Al-Shayeb, B., Schoelmerich, M.C., West-Roberts, J., Valentin-Alvarado, L.E., Sachdeva, R., Mullen, S., Crits-Christoph, A., Wilkins, M.J., Williams, K.H., Doudna, J.A. and Banfield, J.F., 2022. Borgs are giant genetic elements with potential to expand metabolic capacity. Nature, pp.1-6.

Schoelmerich, M.C., Sachdeva, R., West-Roberts, J., Waldburger, L. and Banfield, J.F., 2023. Tandem repeats in giant archaeal Borg elements undergo rapid evolution and create new intrinsically disordered regions in proteins. Plos Biology, 21(1), p.e3001980.

Schoelmerich, M.C., Ouboter, H.T., Sachdeva, R., Penev, P.I., Amano, Y., West-Roberts, J., Welte, C.U. and Banfield, J.F., 2022. A widespread group of large plasmids in methanotrophic Methanoperedens archaea. Nature Communications, 13(1), p.7085.

Lavy, A., Geller McGrath, D., Matheus Carnevali, P.B., Wan, J., Dong, W., Tokunaga, T.K., Thomas, B.C., Williams, K.H., Hubbard, S.S., and Banfield, J.F.  (2019) Microbial communities across a hillslope‐riparian transect shaped by proximity to the stream, groundwater table, and weathered bedrock. Ecology and Evolution, DOI: 10.1002/ece3.5254

Matheus Carnevali P., Lavy, A., Thomas, A.D. Crits-Christoph, A., Diamond, S., Méheust, R., Olm, M.R., Sharrar, A., Lei, S., Dong, W., Falco, M., Bouskill, N., Newcomer, M., Nico, P., Wainwright, H., Dwivedi, D., Williams, K.H., Hubbard, S., and Banfield, J.F. (2021) Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale. Microbiome, 9 (1), 1-23

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