Experimental and Computational Facilities

Our team takes advantage of LBNL’s extensive experimental and computational facilities to answer research questions. Particularly important for our current research activities are experimental facilities for terrestrial biogeochemistry, microbiology and genomics, isotope geochemistry, synchrotron science, electron microscopy, and molecular signatures. In addition, we have easy access to the demanding computational capability required for climate modeling and for large-scale ecosystem data storage systems. (We describe our field research sites separately.)

Terrestrial Biogeochemistry Laboratory

This laboratory routinely prepares and analyzes plant, soil, and air samples for elemental and isotopic (13C,14C, 15N) composition. It is equipped with a vacuum line designed for the separation of complex gas mixtures (e.g., whole air samples) and extraction of water from plant and soil material for isotopic analyses. The laboratory is equipped with a Shimadzu 2014 Gas Chromatograph for analysis of CH4 and CO2 and a PICARRO G2131-I Cavity Ring Down Spectroscopic Analyzer equipped with Small Sample Isotope Module for analysis of 13C stable isotopic content in CO2. The analyzer can be used in the lab or in the field. A muffle furnace is available for combustion of solid phase samples, a roller mill and SPEX-Certiprep 8000M mixer mill for homogenizing solid phase sample material, a Leica stereo-microscope, three drying ovens, a freeze dryer, refrigerators and freezers, and a Sartorius SE2 supermicrobalance. We have a LICOR LI-6400 portable infra-red gas analyzer for photosynthesis and soil respiration measurements. Our lab has a vacuum manifold for cryogenic purification of CO2 from combusted solid environmental samples as well as soil and atmospheric gas samples in preparation for 14C or 13C analysis.

Facilities are available for density fractionation and chemical analysis of whole soils. Available laboratory equipment includes analytical balances, DI water dispenser, pH meter, shaker table, wrist action shaker, sonifier, bench top mixer, a floor-mounted centrifuge with four-place swinging bucket rotor, and a high-precision centrifuge with temperature control equipped with a four-place swinging bucket rotor and a 24-place fixed angle (25º) rotor, chemical fume hoods, magnetic stirrer/hotplates, and chemical storage and sample preparation areas.

Lab manager: Rachel Porras. Under Margaret Torn’s direction.

Microbial, Ecology and Genomics Laboratories

The Microbial ecology and genomics laboratories consist of three main units occupying a total area of 2,500 square feet. The laboratories are set up for class II, type A/B3 molecular- and microbiology work.  The laboratories are equipped for advanced molecular, functional and physiological characterization of microbial isolates and communities.

The laboratories include general equipment such as autoclave, DI-water, refrigerators, freezers for low temperature storage of temperature sensitive materials, balance, ice-maker, shakers, incubators, magnetic stirrer, hotplates, microcentrifuges, different electrophoresis boxes and power supplies, and chemical fume hoods. Work-specific equipment and instruments available in the laboratories:

  • Five SterilGARD II 6-foot vertical laminar-flow, biological safety cabinet (Baker)
  • Three BioRad MyiQ RT-PCR systems
  • Nanodrop model ND 1000 Spectrophotometer
  • Nanodrop model ND 3300 Fluorospectrophotometer
  • FastPrep 120 Bead mill homogenizer (QBiogene)
  • Dual 96-well tissue homogenizer (Qiagen)
  • Two Coy double wide anaerobic chambers with incubators (Coy)
  • GeneAmp PCR system 9600 (Perkin-Elmer)
  • Columbus Instruments Microrespirometer (H2, H2S, CO2, CH4, O2)
  • Illumina GAIIx DNA sequencer (Illumina)
  • Qiacube automated sample processing system (Qiagen)
  • BioRobot Universal automated liquid handling device (Qiagen)
  • SpectraMax fluorometric plate reader (Molecular Devices)
  • Unisense microelectrode microprofiling system with micromanipulator (x2)
  • Picarro G2508 gas analyzer
  • LKB Bromma 2112 Redirac fraction collector

These labs use an allocation on the newest NERSC supercomputer, Cori (see “Computing Resources” below for details). This system is used for large scale analytics, simulation and metagenome assembly jobs, for example, using the parallelized RayMeta or MetaHipMer algorithms. Moderate assembly jobs can be run on the Genepool system, which is a heterogeneous collection of nodes to serve the diverse workload of the Joint Genome Institute users.

Under Eoin Brodie’s direction.

Center for Isotope Geochemistry

The Center for Isotope Geochemistry (CIG) is a joint UC Berkeley-LBNL facility for research on the use of isotopic variations in natural materials to understand biogeochemical and geochemical processes. It comprises a number of analytical laboratories: stable isotope; soil carbon and biogeochemistry; analytical chemistry; inductively coupled plasma multi-collector magnetic sector mass spectrometry (MC-ICPMS), and thermal-ionization mass spectrometry (TIMS).

The Stable Isotope Laboratory instrumentation includes a Micromass JA Series Isoprime mass spectrometer and a Thermo Delta V Plus mass spectrometer. The Isoprime is fitted with a trace gas pre-concentration system designed for analyses of the isotopic compositions of atmospheric gases (CO2, CH4 and N2O) with a Gilson auto-sampler and an automated large volume (1-liter) flask sampling system designed for measurements of low abundance atmospheric trace gases. The system has an automated headspace sampler used for analysis of soil gas CO2, groundwater-dissolved inorganic carbon, and groundwater nitrate. The Isoprime is interfaced to a GC-combustion system designed for compound-specific carbon isotope analyses of organic compounds down to concentrations of 10 ppb in water and cell extracts (e.g., phospholipid fatty acids). The system has been modified for measurements of chlorine isotopes (as methyl chloride). The Delta V Plus includes a Costech ECS 4010 elemental analyzer for measuring carbon, nitrogen, and sulfur abundances and isotopic compositions of carbon, nitrogen, and sulfur (this system is capable of operating in stand-alone mode), a high temperature TC/EA for hydrogen and oxygen isotope analyses, and a GC Isolink for high-temperature, compound-specific analyses of nitrogen and hydrogen in organic compounds. In addition to the isotope mass spectrometers, this laboratory includes a GC-MS for gas abundance measurements and a vacuum line for doing off-line preparation of samples for isotopic analyses.

The IsoProbe (MC-ICPMS) Laboratory consists of two laboratory spaces, one housing a multiple collector inductively coupled plasma multi-collector magnetic sector mass spectrometer, (the IsoProbe, manufactured by the former Micromass Ltd, now GV Instruments) and the other containing a clean sample preparation area. Isotopic analyses are routinely conducted for Li, K, Cr, Sr, Nd, Pb, U and Th.

The Radiogenic Isotope Laboratory is a facility with capabilities for high-precision isotopic and elemental abundance measurements of K, Ca, Fe, Cr, Sr, Nd, Pb, U, and Th, using conventional thermal ionization mass spectrometry.

Synchrotron Science

The Advanced Light Source (ALS) is a national user facility that generates ultraviolet and soft x-rays with wavelengths ranging from 0.0001 to 0.1 m, which enable detailed structural analysis of materials at the atomic and molecular scale. Of the U.S. synchrotron light sources, only the ALS is optimized for “soft x-ray” production, which is the spectral range necessary for spectroscopy of light elements such as C, N, and O, and is therefore ideal for investigation of C dynamics. We have used Scanning Transmission X-ray Microscopy at ALS to visualize the spatial patterns of carbon and nitrogen atoms in relation to reactive iron on a mineral surface. The ALS offers unmatched capabilities for carbon cycle research within LBNL’s Terrestrial Ecosystem Science SFAs. The four core environmental beamlines for our applications are (1) Beamline 1.4.3, a synchrotron FT Infrared spectroscopy line with a beam size of ~2-10 m, (2) Beamline 8.3.2, a microtomography beamline that allows for 3D imaging of samples with spatial resolution of a few microns, (3) Beamline 10.3.2, a hard x-ray microprobe that can be used for 2D mapping of transition metal elements as well as for micro-x-ray absorption spectroscopy and micro-XRD, and (4) Beamline 11.0.2, with two end stations, a Scanning Transmission X-ray Microscope with a spatial resolution of ~35 nm and an ambient pressure x-ray photoelectron spectrometer.

National Center for Electron Microscopy (NCEM)

NCEM offers cutting-edge instrumentation, along with accessible expertise and proven techniques, for exceptionally high-resolution imaging and electron-optical characterization of a broad array of materials. Its staff conducts fundamental research that relates microstructural and microchemical characteristics to properties of materials; develops advanced electron microscopy techniques, computer algorithms and instrumentation; and helps educate future scientists in theory and application of electron optical microcharacterization.

Computing Resources at LBNL

NERSC: Our team members have access to leading-edge computing platforms and services through the National Energy Research Scientific Computing Center (NERSC). NERSC is the primary scientific computing facility for the Office of Science of U.S. Department of Energy, and is managed by LBNL. NERSC supercomputers are available through a DOE allocation process. Systems at NERSC are:

  • Edison , a Cray XC30, consisting of 134,064 nodes with two 12-core Intel 2.4 GHz processors per node, 357 TB memory, and 2.57 Pflop/sec peak performance
  • Cori, a Cray XC40, consisting of Phase-I with 2,004 2.3 GHz 16-core Intel Xeon nodes and 203 TB memory; and Phase-II with 9688 1.4 Ghz 68-core Intel Phi nodes and 1PB. Cori Phase-I is capable of 83 TFlop/sec peak performance and expected Cori Phase-II is expected to have 29.1 PFlop/sec. Cori was listed the 5th fastest computer by the Top500 List in November 2016.
  • HPSS—or High-Performance Storage System, which is coupled with both Edison and Cori, with current capacities of 7.56 petabytes (Edison) and 30 petabytes (Cori).

Our researchers also have access to a wide variety of Linux clusters with modern software configurations. The team members use these for exploratory development of code and diagnostics. The largest such machine is a Linux cluster called Lawrencium, consisting of 172-nodes with Intel 2.6Ghz Xeon 8-core 64-bit Sandybridge and 11 TB aggregate memory.

Software: Our team members use commercial analytical software, such as Portland Group Fortran, C and C++ compilers, Tecplot, IDL, and MATLAB. Various teams at LBNL have developed their own specialized code for spatial and temporal analyses of land-surface and coupled model predictions, which is available to our researchers. In addition to these software resources, we have developed our own code for spatial and temporal analyses of land-surface and coupled model predictions.