In this study, we examined hypersaline microbial mat communities, which are known for their taxonomic and metabolic diversity and steep environmental gradients. Here, we illustrate how metagenome sequencing can be used to meaningfully assess microbial ecology and genetic partitioning in these complex communities, using binning to reconstruct organisms in silico to assess ecosystem partitioning. We were able to distinguish putative core and accessory genes for the dominant Cyanobacteria in the system, Coleofasciculus chthonoplastes, indicating highest differentiation in nutrient utilization and stress response, suggesting salinity, metals, and light may drive differentiation in this group. We also identified a distinct set of glycoside hydrolases in C.chthonoplastes, building on previous SFA research showing the importance of these polysaccharides in carbon cycling in the mats. The analysis also uncovered evidence of putative phototrophs within the Gemmatimonadetes and Gammaproteobacteria.
[Lee, JZ, Everroad, CR, Karaoz, U, Detweiler, AM, Pett-Ridge, J, Weber PK, Prufert-Bebout, L, Bebout, BM. Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat. PLoS ONE 13(9): e0202792. 2018]
The LLNL Biofuels SFA is collaborating with Dr. Christine Hawkes (NC State) to improve our understanding of sustainable bioenergy agriculture—studying plant symbionts and belowground processes such as water use efficiency and soil C storage. In a recent experiment, LLNL post-college appointee Max Li worked with the Hawkes lab to harvest Panicum virgatum plants from a study of how foliar fungal endophytes affect plant drought physiology. These endophytes range from antagonistic to beneficial, and are expected to affect the plant’s physiology, biomass, and root metabolites/gene expression.
We observed mutualistic interactions between heterotrophic bacteria and two species of biofuels-relevant microalgae, Nannochloropsis salina and Phaeodactylum tricornutum, mediated by physical association between individual cells. At the bulk scale, microalgae in these co-cultures exhibited enhanced growth and yield. At the microscale, we used the LLNL NanoSIMS to observe that both species exhibited enhanced carbon fixation in response to the presence of the microbiomes, but there were divergent responses by each species to bacterial attachment. We illustrate how P. tricornutum may be predisposed to interact mutualistically with bacteria via attachment, but N. salina does not share these traits. Attached bacteria benefit from these relationships by receiving more reduced carbon from their algal host compared to free living cells.
[Samo TJ, Kimbrel JA, Nilson DJ, Pett-Ridge J, Weber PK, Mayali X. Attachment between heterotrophic bacteria and microalgae influences symbiotic microscale interactions. Environmental Microbiology 2018, doi: 10.1111/1462‐2920.14357]
SFA team member Adam Chorazyczewski, a master’s student with Dr. Paul Zimba at Texas A&M successfully defended his master’s thesis entitled “Do phycosphere-associated bacteria affect the growth and lipid accumulation of Phaeodactylum tricornutum.” His SFA-funded research involved profiling and characterizing growth and lipid accumulation in co-cultures of P. tricornutum and 16 separate bacterial species provided by LLNL team members. He identified bacterial isolates with positive effects on both growth and single cell lipid content. SFA algae-bacterial lead Xavier Mayali served as a committee member.
SFA team members led by Ty Samo were awarded an EMSL grant entitled “Nano- to microscale characterization of metabolic cooperation facilitated by physical associations between phototrophic microalgae and heterotrophic bacterial symbionts.” Co-Investigators include R. Stuart, X. Mayali, C. Ward, P. Weber, T. Northen (LBL), and C. Buie (MIT).
SFA team members Carolyn Fisher (Sandia), Xavier Mayali (LLNL), and Chris Ward (LLNL) helped host a hands-on work station, called “Algae Invader Investigation,” on algae and algal predators. Students learned about bioenergy research on algae and the current cultivation obstacles, such as algal predators. They used both microscopes and household items such as beans and pasta to demonstrate how algae are studied in the lab. According to the Sandia summer intern Franny Carcellar: “I had one girl tell me after looking through the microscope that now she wants to be a scientist. If we just inspire one kid, then it’s all worth it!”
For more information on the event, see the article titled “STEM Day at the Lab gives underserved students a taste of the wonders of science” on the LLNL website.
We are developing high sensitivity, high spatial resolution methods to image essential metals in biological systems. Here, we collaborated with the C. Chang Lab at UC Berkeley to standardize our NanoSIMS copper measurements and apply the method to analysis of copper metabolism in zebrafish. Using this method, we were able to demonstrate that the fish metal distribution system prioritizes delivering copper to the eye, despite a severe copper deficit caused by a genetic mutation which mimics a human copper dysregulation disorder, Menkes disease.
[Ackerman CM, Weber PK, Xiao T, Thai B, Kuo TJ, Zhang E, Pett-Ridge J, Chang CJ. Multimodal LA-ICP-MS and nanoSIMS imaging enables copper mapping within photoreceptor megamitochondria in a zebrafish model of Menkes disease. Metallomics 2018 10(3):474-85.]
Our new greenhouse facility is now operational. It is a new IGC Arch Series 6500 greenhouse (1800 sf) with full temperature and light controls. It will eventually house an array of Coy isotope labeling chambers for plant 13CO2 isotope labeling and our Picarro portable Cavity Ring-Down Spectroscopy (CRDS) analyzer. We are currently setting up a series of plant-AMF inoculations.
SFA team member Ali Navid recently gave an invited seminar as part of the LLNL’s and nearby Las Positas College student science and engineering seminar series. His talk, given to a large audience of community college science students and faculty, was titled “Computational Systems Biology: Simulating life from microbes to humans.” He discussed the state of computational systems biology in general and particularly at LLNL and presented examples of different types of modeling (e.g., constraint-based genome-scale, dynamic pharmacology, and 3D microbial biophysics models) that span multiple time and spatial scales from his SFA and biosecurity-related research.
SFA team members Xavier Mayali and Peter Weber have a new publication, supported by the Biofuels SFA, on the use of the Chip-SIP method (NanoSIMS and microarrays) to quantify the taxon-specific incorporation of algal-derived organic components by bacteria and eukaryotes. They carried out simultaneous incubations with 14 different stable isotope labeled substrates to examine phylogenetic signal of resource utilization and mixotrophy. The unique aspect of examining such a high number of substrates enabled them to identify substrate partitioning, and the data showed that two thirds of the taxa exhibited unique incorporation patterns, with strategies ranging from generalists to specialists.
[X. Mayali and P.K. Weber, Quantitative isotope incorporation reveals substrate partitioning in a coastal microbial community, FEMS Micro Ecol 94 (5), fiy047 (2018), doi:10.1093/femsec/fiy047]
Five SFA team members presented at the 13th annual Department of Energy Joint Genome Institute (JGI) “Genomics of Energy and Environment” meeting in San Francisco, CA. Three posters were presented: Chris Ward, “Towards an integrative understanding of chytrid parasitism and its drivers in mass algal culture,” Jeff Kimbrel, “Combining multiple functional annotation tools increases completeness of metabolic annotation,” and Xavier Mayali, “Nanoscale Stable Isotope Tracing to Investigate Interactions between Bacteria and Biofuel-producing Algae.” Mayali’s poster won the “Outside the Box Poster Award.” The LLNL team also presented two invited talks: “Exploring Microbial Ecology with Isotopes and Imaging” by Jennifer Pett-Ridge and “Exploring Metabolite Production from Tryptophan Precursors in Two Algal Associated Bacteria, Algoriphagus sp. ARW1R1 and Marinobacter sp. 19DW” by Ty Samo.
Visit the JGI website for more information.
We have a position for a postdoc to examine host-microbe metabolic interactions and exchange in microalgae and perennial grasses using metabolomics, stable isotope probing, and proteogenomic approaches. For more information, see position 103155 at https://jobs.llnl.gov. If you have questions, feel free to contact Michael Thelen at firstname.lastname@example.org.
New research supported by the LLNL Biofuels Scientific Focus Area (SFA) shows the promise and challenge of studying the role of viruses in microbial systems. Viruses are known to be ubiquitous and infect all forms of life, including microbes. As such, they are thought to have major roles in carbon and nutrient cycling, but to date, these rates have been unexplored in most systems. With this research, SFA researchers Peter Weber and Ben Stewart and colleagues explored the potential to use high-spatial resolution secondary ion mass spectrometry (SIMS) with a NanoSIMS 50 to characterize nutrient transfer from host to virus using isotopically labeled DNA as a tracer. Their work showed the expected transfer of isotopic label, which is promising for future application of SIMS to virus ecology, but they also found that at the start of SIMS analysis, these tiny structures eroded 100 times faster than previously expected. For the relatively large Vaccinia virus in this study, this was not a major problem, but for bacterial phage, which are as small as 20 nm in diameter, new methods may be necessary to ensure quality measurements of nutrient uptake and cycling.
[S. Gates, R.C. Condit, N. Moussatche, B.J. Stewart, A.J. Malkin, and P.K. Weber, High Initial Sputter Rate Found for Vaccinia Virions Using Isotopic Labeling, NanoSIMS, and AFM, Anal. Chem. 90 (3), 1613 (2018), doi: 10.1021/acs.analchem.7b02786]
SFA members Xavier Mayali and Ty Samo attended the 2018 Ocean Sciences meeting in Portland, Oregon in February to present some of their work on algal-bacterial interactions using stable isotope probing and NanoSIMS. Ty presented a talk entitled “Stable Isotope Probing and NanoSIMS Reveals Effects of Physical Association on Mutualisms Between Individual Bacterial Cells and Two Species of Phytoplankton” in the session “Bridging Microbial, Stable Isotope, and Micronutrient Approaches to Marine Carbon and Nitrogen Recycling.” Xavier presented a talk entitled “Investigating C transfer between diatoms and phycosphere-associated bacteria with stable isotopes and NanoSIMS” in the session “Phytoplankton-Bacteria Interactions: From Microscales to Ocean Scales.”
Learn more about the conference on the 2018 Ocean Sciences Meeting site.
In this video, SFA scientists help explain what algae are and what they can do for us.