BER Research Highlights

Search Date: October 21, 2020

5 Records match the search term(s):


July 06, 2020

The Traits of Microbes Matter in Microbial Carbon Cycling and Storage

Several microbial community traits influence the fate of carbon in soil.

The Science
Soils are rich in many types of microbes. Each species of microbe has a unique set of genes in its genome, but scientists do not know if this diversity affects how plant matter breaks down. Plant organic matter that is not broken down can be stored in soils, removing carbon from the atmosphere for long periods of time. Researchers wanted to know if different microbial communities (microbiomes) would be equally good at breaking down leaf litter. They sampled more than 200 soils and measured the products that the microbes in these soils produced from leaf litter. The researchers also measured the activity of microbial genes. These data helped to identify the microbial traits that might lead to carbon storage or loss. The data suggest that the makeup of a soil microbiome is critical to the fate of carbon in that soil.

The Impact
This study indicates that there is a strong connection between the makeup of a microbiome and the rate at which leaf litter can be decomposed to carbon dioxide (CO2) or other products. It also identifies microbial traits linked to increased storage of carbon in soil. The research suggests the possibility of harnessing, manipulating, or even adapting microbiomes to increase carbon storage in soil. This could have benefits for soil health, agriculture, sustainable biofuels production, and other applications.

Summary
Soil microbes can break down plant organic matter to CO2 or convert it to dissolved organic carbon (DOC) compounds. This leads either to long-term carbon storage, because DOC can bind to soil particles, or to the release of carbon back to the atmosphere as CO2. The relative contributions of these two processes have been hard to reconcile in global carbon models, in part because scientists do not fully understand the underlying microbial processes. This study conducted a large number of controlled trials on litter degradation with a diverse set of microbial communities. Using a combination of analytical and other biological research techniques (for example, genomics), the work aimed to identify “effect traits,” which are microbial properties that lead to changes in the environment. The researchers used a “common garden” research design to sample 206 different microbiomes under similar environmental conditions. The researchers then identified distinct groups of high- and low-performing communities. Next, they used machine-learning tools to identify community members and genetic traits that predict the rate of CO2 production and DOC release. Greater species richness and genetic diversity were found in samples that produced lower levels of DOC and higher levels of CO2 release. These communities also exhibited greater potential for complex organic matter degradation based on genomic data. On the contrary, microbial communities that produced higher levels of DOC appeared more attuned to the degradation of simpler carbon substrates. While these findings are contrary to the commonly held assumption that microbial populations are adapted to achieve maximal environmental efficiencies, they suggest microbiomes can potentially be engineered or manipulated toward desirable outcomes. A better understanding of the controls on microbially mediated carbon flow can also help to improve efforts to model the fate of carbon in the environment.

Contacts
Program Manager
Boris Wawrik
U.S. Department of Energy Office of Science, Office of Biological and Environmental Research
Biological Systems Science Division (SC-33.2)
Environmental Genomics
boris.wawrik@science.doe.gov

Principal Investigator
John Dunbar
Los Alamos National Laboratory
Los Alamos, NM 87545
dunbar@lanl.gov

Funding
This work was supported by the Office of Biological and Environmental Research, within the U.S. Department of Energy Office of Science, via a Scientific Focus Area award.

Publications
Albright, M. B. N. et al.Differences in substrate use linked to divergent carbon flow during litter decomposition.” FEMS Microbiology Ecology 96(8), fiaa135 (2020). [DOI:10.1093/femsec/fiaa135]

Topic Areas:

Division: SC-33.2 Biological Systems Science Division, BER


May 28, 2020

New Technique Helps Solve a Long-Standing Obstacle for Microbial Genetic Engineering

SEER, a new method to rapidly search for proteins involved in rearranging DNA molecules, increases genome-editing efficiency.

The Science
Using genetic engineering, scientists can alter genes and transfer them from one organism to another. To do this, genetic engineers use proteins that can move fragments of DNA between organisms. Once scientists find a gene that carries out a desired function, for example, in a wild microbe, they can take the DNA fragment that contains that gene or synthesize a copy and insert it into the genome of an industrially useful organism. Scientists can then modify the gene however they want. This process, called DNA recombination, refers to the natural or artificial way that DNA moves and changes. Now scientists have developed a fast method to find new proteins involved in DNA recombination that can improve the efficiency of genetic engineering.

The Impact
For decades, scientists have used a tool called recombination-mediated genetic engineering, or recombineering. This technique works well in Escherichia coli, a type of bacteria often used in laboratory experiments. However, it does not work well for a long list of microbes that are used in industry. A new technique called Serial Enrichment for Efficient Recombineering (SEER) should help. SEER allows biologists to apply recombineering to many different species of bacteria and will help speed up the engineering of microbes for biotechnology applications.

Summary
Recombineering  allows scientists to introduce genetic material from different species into bacterial genomes, as well as to make edits to existing DNA, conferring new functions to edited bacteria. For example, scientists can add genetic material for the synthesis of biofuels or other valuable compounds. Although they are useful and flexible, these recombineering approaches do not work well in other microbial species, including many industrially relevant microorganisms. To solve this problem, scientists have now developed the high-throughput SEER screening method. SEER allows researchers to identify new single-stranded DNA-annealing proteins (SSAPs) that promote efficient recombineering. SSAPs are often found in phages, which are viruses that infect bacteria. Using SEER, the investigators rapidly tested more than 200 SSAPs and found two promising recombineering proteins that greatly improve gene-editing efficiency in diverse bacterial species, including E. coli, Pseudomonas aeruginosa (a human pathogen), and Citrobacter freundii (an industrially relevant bacterium). SEER will facilitate the discovery of many recombineering proteins in new and different bacteria that will expand their use to other industrial microbes. Using these new proteins in combination with multiplex recombineering technologies, such as multiplex automated genome engineering (MAGE), will enable scientists to simultaneously edit multiple genes, for applications such as whole metabolic pathway optimization, in important bacterial species in a single experiment.

Contacts
BER Program Manager
Pablo Rabinowicz
U.S. Department of Energy Office of Science, Office of Biological and Environmental Research
Biological Systems Science Division (SC-33.2)
Foundational Genomics Research and Biosystems Design
pablo.rabinowicz@science.doe.gov

Principal Investigators
Timothy Wannier
Postdoctoral fellow
Department of Genetics, Harvard Medical School
timothy_wannier@hms.harvard.edu

George Church
Professor, Department of Genetics, Harvard Medical School
gchurch@genetics.med.harvard.edu

Funding
Funding for this research was provided by the Office of Biological and Environmental Research (BER), within the U.S. Department of Energy Office of Science. Funding for individual researchers was provided by the European Research Council, the Lendület (Momentum) Program of the Hungarian Academy of Sciences, a Ph.D. fellowship from the Boehringer Ingelheim Fonds, a European Molecular Biology Organization (EMBO) Long-Term Fellowship, the Szeged Scientists Academy under the sponsorship of the Hungarian Ministry of Human Capacities, the New National Excellence Program of the Hungarian Ministry of Human Capacities, and the New National Excellence Program of the Hungarian Ministry for Innovation and Technology.

Publications
Wannier, T. M. et al. “Improved bacterial recombineering by parallelized protein discovery.” Proceedings of the National Academy of Sciences USA 117(24), 13689–13698 (2020). [DOI:10.1073/pnas.2001588117]

Related Links

Topic Areas:

Division: SC-33.2 Biological Systems Science Division, BER


May 20, 2020

Breathing New Life into an Old Question: What Plants’ Emissions Reveal about Their Cell Walls

Detecting gaseous methanol and acetic acid released from plants sheds light on plant cell wall composition changes throughout leaf development.

The Science
Scientists know that plants emit large amounts of gases like methanol and acetic acid. These gases are not directly related to photosynthesis, but their origins are unknown. Now researchers have found a possible source. Plant cell walls consist mostly of cellulose. As plants develop and change over their lives, the cellulose in their cells can also change due to natural chemical modifications. As these changes occur, the metabolisms of plants cause their leaves to release certain gases into the atmosphere. By analyzing these gas emissions, along with the composition of the cell walls, scientists can identify the sources of those emissions and why they occur.

The Impact
Cellulose from plant cell walls can be used as a raw material to make biofuels and other products. One way to make these fuels is microbial-based fermentation, which involves bacteria and other tiny organisms breaking down plant material. However, chemical modifications in cellulose can dramatically affect the efficiency of fermentation. Current methods to quantify those modifications are time consuming and expensive. The new method allows scientists to quickly analyze cellulose modifications based on emissions from intact plants. This ability will help scientists better understand the cellulose composition of bioenergy crops and help them identify the best plants for biofuel production. Using this approach will also help scientists understand how the cell walls of plants affect their physiology and metabolism.

Summary
Plants emit methanol and, to a lesser extent, acetic acid at high rates. Scientists believed that methanol originated from methyl-esters that modify the cellulose in the plant cell walls. They did not have a widely accepted explanation for the source of acetic acid. This new study quantified foliar methanol and acetic acid emissions in parallel with leaf cell wall content of methyl-ester and another chemical modification of cellulose (O-acetyl-ester) in poplars, a tree species that is a potential bioenergy crop. By correlating volatile emissions from leaves with the chemical composition of cell walls, researchers confirmed that methanol originates from methyl-esters while O-acetyl-esters are the source of gaseous acetic acid. The study also found that acetic acid follows the same emission pattern throughout leaf development as methanol, suggesting that plant cell walls are a major source of both gases. Further supporting these findings, the investigators showed that the ratio between O-acetyl-esters and methyl-esters quantitatively reflected the observed acetic acid to methanol emission ratio. Using this analytic approach to monitor methanol and acetic acid emissions at different times and locations will help scientists develop more efficient bioenergy crops and understand the response of crops to stress at the ecosystem level.

Contacts
BER Program Manager
Pablo Rabinowicz
U.S. Department of Energy Office of Science, Office of Biological and Environmental Research
Biological Systems Science Division (SC-33.2)
Foundational Genomics Research and Biosystems Design
pablo.rabinowicz@science.doe.gov

Principal Investigator
Kolby Jardine
Lawrence Berkeley National Laboratory
Berkeley, CA  94720
kjjardine@lbl.gov

Funding
This material is based on work supported by the Biological Systems Science Division (BSSD) of the Office of Biological and Environmental Research (BER) within the U.S. Department of Energy (DOE) Office of Science. The research is part of a BSSD Early Career Research award on Plant Systems for the Production of Biofuels and Bioproducts (Award No. FP00007421) to Lawrence Berkeley National Laboratory (LBNL). The work is also supported through the DOE Joint BioEnergy Institute (JBEI; www.jbei.org), which is funded by BER through Contract No. DE-AC02-05CH11231 between LBNL and DOE. In addition, material is based on research supported by BER’s Next-Generation Ecosystem Experiments (NGEE)–Tropics project under Contract No. DE-AC02-05CH11231.

Publication
Dewhirst, R. A., et al., “Cell wall O-acetyl and methyl esterification patterns of leaves reflected in atmospheric emission signatures of acetic acid and methanol.” PLOS One 15(5), e0227591 (2020). [DOI:10.1371/journal.pone.0227591].

 

Topic Areas:

Division: SC-33.2 Biological Systems Science Division, BER


April 16, 2020

Digging into the Roots of Phosphorus Availability

New root-blotting technique will help scientists identify more efficient strategies for producing bioenergy crops and for agriculture in general.

The Science
Phosphorous is an important nutrient for plants. However, scientists do not fully understand the mechanisms that plants use to extract phosphorus from soil and incorporate it into their biomass. Now, researchers have developed a new technique to visualize the activity and distribution of enzymes that mobilize phosphate around plant roots. Enzymes are substances in plants and other organisms that cause chemical changes. Tracking the location of these enzymes can help researchers better understand the chemical dynamics between roots, microbes, and soil that influence how plants get nutrients. The technique could also be applied to other nutrient-cycling enzymes.

The Impact
Phosphorus is an essential nutrient for plants, and demand for phosphorus fertilizers is increasing as the world’s population grows. Most of these fertilizers are made from rock phosphorus, a nonrenewable resource. This research provides new insights into the complex dynamics of phosphorous exchange between soil, microbes, and plant roots. This new approach will help scientists identify strategies to use phosphorus more efficiently for producing bioenergy crops and for agriculture in general.

Summary
Soil bacteria, fungi, and plants produce enzymes called phosphatases, which convert organic sources of phosphorus into a form that plants can absorb. Researchers have studied the activity of bacteria and fungi in soil samples to learn about the overall functional potential of the environment. But to better understand the dynamics between soil, plants, and microbes, scientists need more detail. To accomplish that, a team of researchers developed a new technique based on root blotting to reveal phosphatase activity and distribution around plant roots. They grew switchgrass in flat pots or “rhizoboxes” containing soil with pellets of root matter as sources of organic phosphorus. They next applied a nitrocellulose membrane to capture proteins around the roots. Finally, the researchers stained the membrane with fluorescent indicators for phosphatase activity and protein concentration. This revealed the spatial distribution of phosphatase around the roots of plants and highlighted regions of increased phosphatase activity.

The new technique’s combination of membrane extraction with rapid analysis via fluorescent probes to reveal the location of phosphatase activity offers a new tool for environmental applications. This technique could be used to study phosphatase activity over time, as well as the activity of other nutrient-cycling enzymes. By expanding this technique, scientists could simultaneously visualize multiple enzyme types in soil systems.

Contacts
BER Program Manager
Pablo Rabinowicz
U.S. Department of Energy Office of Science, Office of Biological and Environmental Research
Biological Systems Science Division (SC-33.2)
Foundational Genomics Research and Biosystems Design
pablo.rabinowicz@science.doe.gov

Principal Investigator
Jim Moran
Pacific Northwest National Laboratory
Richland, WA  99352
James.Moran@pnnl.gov

Funding
Development of this method was funded by the Office of Biological and Environmental Research, within the U.S. Department of Energy (DOE) Office of Science, through the DOE Office of Science Early Career Research Program and Genomic Science program for principal investigator James Moran.

Publications
Lin, V. S. et al. “Non-destructive spatial analysis of phosphatase activity and total protein distribution in the rhizosphere using a root blotting method.” Soil Biology and Biochemistry 146, 107820 (2020). [DOI:10.1016/j.soilbio.2020.107820]

Related Links
The Inner Workings of the Root Microbiome, DOE Office of Science Environmental Molecular Sciences Laboratory user facility.

Topic Areas:

Division: SC-33.2 Biological Systems Science Division, BER


March 15, 2020

Stronger Membranes Help Yeast Tolerate Bioenergy Production Chemicals

Incorporating sterols in the outer membrane of Yarrowia lipolytica makes it significantly more tolerant of ionic liquids.

The Science
Creating biofuels and other products from plant material is a complex process. Breaking down plant cells requires chemicals, among other things. Organic solvents like ionic liquids (ILs) represent one example. Scientists also need microbes such as yeast to convert the resulting plant material into biofuels and biochemicals. However, ILs often keep microbes from growing. Now, scientists have learned how one strain of yeast, Yarrowia lipolytica, strengthens its membranes. With stronger membranes, this yeast can better withstand ILs.

The Impact
This study produced the microorganism most tolerant to ILs. “Exceptional solvent tolerance in Yarrowia lipolytica is enhanced by sterols.Metabolic Engineering 54(C), 83–95 (2019). [DOI:10.1016/j.ymben.2019.03.003]

Topic Areas:

Division: SC-33.2 Biological Systems Science Division, BER