The rhizosphere, the portion of soil directly influenced by plant roots, is an area of great biological activity and intense carbon (C) cycling. Interactions among the residents of the rhizosphere, such as bacteria, fungi, viruses, and fauna, result in transformation and transfer C from root exudates and root debris to biomass and developing soil organic matter. The primary object of this research project was to explore the complex interactions controlling C flow in the rhizosphere and the response of these interactions to soil water conditions. We used stable isotope techniques combined with molecular analyses to observe the flow of C as it is fixed by plants from the atmosphere, deposited into the soil through plant roots, and exchanged through multiple pathways of the soil food web. This technical report summarizes the achievements of this project from field, greenhouse, and lab experiments.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Rhizosphere Carbon Turnover from Cradle to Grave: The Role of Microbe–Plant Interactions

Plant roots are the primary source of organic materials that become stabilized in soil. While most root carbon is decomposed into carbon dioxide (CO 2 ), the remainder typically undergoes multiple microbial transformations before it forms longer-term associations with soil minerals. However, the mechanisms by which roots affect microbial utilization of organic materials and subsequent mineral stabilization processes are poorly understood. It is well known that living roots increase the biomass of nearby microbial communities, and shape their population dynamics, diversity, and interactions. Community assembly and metabolic potential of these rhizosphere-enriched microorganisms are strongly influenced by the chemical composition of the exudates released by the host plant. The root exudate pools of plants undergo compositional changes as they grow, reproduce, and senesce. In the well-studied annual grasses Avena barbata and Avena fatua, this changing rhizosphere substrate pool and the “bloom” of organisms that respond are phylogenetically coherent; Acidobacteria and Actinobacteria are consistently depleted, whereas Alpha and Betaproteobacteria and Bacteroidetes are reliably enriched. When compared to non-root-influenced bulk soils, the responsive community is predictably less taxon-rich, yet forms more complex networks. Finally, these rhizosphere dynamics have significant downstream effects on the colonization of nearby soil minerals, degradation of prior season’s root litters, and the balance of stabilized versus lost soil carbon.

Pett-Ridge, Jennifer↗

DOE OSTI2020

Untangling the sequence of events during the S 2 → S 3 transition in photosystem II and implications for the water oxidation mechanism

In oxygenic photosynthesis, light-driven oxidation of water to molecular oxygen is carried out by the oxygen-evolving complex (OEC) in photosystem II (PS II). Recently, we reported the room-temperature structures of PS II in the four (semi)stable S-states, S 1 , S 2 , S 3 , and S 0 , showing that a water molecule is inserted during the S 2 → S 3 transition, as a new bridging O(H)-ligand between Mn1 and Ca. To understand the sequence of events leading to the formation of this last stable intermediate state before O 2 formation, we recorded diffraction and Mn X-ray emission spectroscopy (XES) data at several time points during the S 2 → S 3 transition. At the electron acceptor site, changes due to the two-electron redox chemistry at the quinones, Q A and Q B , are observed. At the donor site, tyrosine Y Z and His190 H-bonded to it move by 50 µs after the second flash, and Glu189 moves away from Ca. This is followed by Mn1 and Mn4 moving apart, and the insertion of O X (H) at the open coordination site of Mn1. This water, possibly a ligand of Ca, could be supplied via a “water wheel”-like arrangement of five waters next to the OEC that is connected by a large channel to the bulk solvent. XES spectra show that Mn oxidation (τ of ∼350 µs) during the S 2 → S 3 transition mirrors the appearance of O X electron density. This indicates that the oxidation state change and the insertion of water as a bridging atom between Mn1 and Ca are highly correlated.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Fabricated ecosystem workshop: bridging laboratory to field science. Workshop report.

Lawrence Berkeley National Laboratory (Berkeley Lab) scientists held a workshop at the DOE BER Genomic Sciences PI meeting on the use of Fabricated Ecosystems in Washington D.C. on February 25th, 2020. Ecosystem fabrication is an approach to creating controlled microbial, soil and plant ecologies within a laboratory setting that enable discovery and dissection of environmental variables, activities, and interactions. At Berkeley Lab, we are developing two systems which span spatial and temporal scales — the EcoFAB and the EcoPOD. The participants of the workshop discussed the potential applications and challenges of using fabricated ecosystems as tools to tackle BER-relevant scientific questions. Specifically, they identified (1) research challenges that would benefit from ready access to this infrastructure (2) identified and prioritized technical challenges that currently limit these systems and (3) discussed how to use them to bridge the gap between lab and field research. To ensure that the fabricated ecosystems , in particular the larger-scale EcoPODs, are of use to as much of the BER community as possible, the workshop participants made the following recommendations: 1. Produce publicly available datasets for a set of control variables. Use for benchmarking, and assessing reproducibility between systems. 2. Implement data standards. 3. Develop/leverage nano/micro sensors and in situ root imaging. 4. Encourage the development of interdisciplinary teams to develop EcoPOD experiments. 5. Develop fabricated ecosystems with size and complexity that sits between the EcoFAB and EcoPOD to accelerate use and access.

42 ENGINEERING↗