Berkeley Lab

A New View of the Tree of life

Tree of Life

An artistic representation of the tree of life, with the many groups of bacteria on the left, the uncultivable bacteria at upper right (purple), and the Archaea and eukaryotes (green) – which includes humans – at the lower right. (Graphic by Zosia Rostomian, Lawrence Berkeley National Laboratory)

 

Supported primarily by the Watershed Function SFA, UC Berkeley researchers have reconfigured the tree of life to account for newly discovered microscopic life forms. The new tree, published online in the journal Nature Microbiology, reinforces once again that the life we see around us – plants, animals, humans and other so-called eukaryotes – represent a tiny percentage of the world’s biodiversity. The high-impact paper has generated a great deal of press coverage.

Read more about the research in this press release from UC Berkeley.

Functional metagenomic selection of ribulose 1,5-bisphosphate carboxylase/oxygenase from uncultivated bacteria

Operon structure alignments of the recovered metagenomic fragments from the Rifle groundwater aquifer, along with closest RubisCO hits and related sequences in NCBI. pcrf stands for peptide chain release factor.

Scientific Achievement

We report a functional metagenomic selection that recovers physiologically active RuBisCO molecules directly from uncultivated and largely unknown members of natural microbial communities.

Significance and Impact

Functional metagenomic selection leverages natural biological diversity and billions of years of evolution to provide a new window into the discovery of CO2‐fixing enzymes

Research Details
  • Selection based on CO2‐dependent growth in a strain expressing environmental DNA
  • RuBisCOs selected, purified and tested for CO2/O2specificity
  • X‐ray crystallography: one enzyme is a hexamer, the second form II multimer ever solved and the first structure from an uncultivated bacterium.
Citation

Varaljay, V. A.; Satagopan, S.; North, J. A.; Witte, B.; Dourado, M. N.; Anantharaman, K.; Arbing, M. A.; McCann, S. H.; Oremland, R. S.; Banfield, J. F.; Wrighton, K. C.; Tabita, F. R. (2016) Functional metagenomic selection of ribulose 1,5-bisphosphate carboxylase/oxygenase from uncultivated bacteria, Environmental Microbiology, 18, 1187-1199 DOI: 10.1111/1462-2920.13138.

iMatTOUGH: An Open-source Matlab-based Graphical User Interface for Pre- and Post-Processing of TOUGH2 and iTOUGH2 Models

Workflow of the iMatTOUGH for pre- and post-processing TOUGH2 and iTOUGH2 models

Scientific Achievement

TOUGH2 and iTOUGH2 are powerful models that simulate the heat and fluid flows in porous and fracture media, and perform parameter estimation. An open source Matlab-based tool is developed to support the generation of all necessary inputs and to visualize the model outputs

Significance and Impact

This study provides an GUI for TOUGH2 and iTOUGH2 models, which supports users to better process and visualize their model input and output.

Research Details
  • Developed GUI for both TOUGH2 and iTOUGH
  • Supports the generation of rectangular computational mesh
  • Allows the specification of initial and time-dependent boundary conditions
Citation

Tran, A. P.; Dafflon, B.; Hubbard, S. S. (2016), iMatTOUGH: An open-source Matlab-based graphical user interface for pre- and post-processing of TOUGH2 and iTOUGH2 models, Computers & Geosciences, 89, 132-143, DOI: 10.1016/j.cageo.2016.02.006.

Simulating Bioclogging Effects on Dynamic RiverbedPermeability and Infiltration

Scientific Achievement

Our research provides a numerical modeling approach predicting the impact of natural bioclogging processes in rivers, including an explanation for why variable connection and disconnection between rivers and aquifers occurs. Our study highlights that consideration of riverbed dynamic permeability coupled with the connection status of the river is required for accurate prediction of infiltration dynamics.

Significance and Impact

Bioclogging in rivers can detrimentally impact aquifer recharge. This is particularly so in dry regions, where losing rivers are common, and where disconnection between surface water and groundwater (leading to the development of an unsaturated zone) can occur. Reduction in riverbed permeability due to biomass growth is a time-variable parameter that is often neglected, yet permeability reduction from bioclogging can introduce order of magnitude changes in seepage fluxes.

Research Details
  • We developed numerical representations of bioclogging processes within a one-dimensional, variably-saturated flow model representing losing-connected and losing-disconnected rivers
  • We tested these formulations using a synthetic case study informed with biological data obtained from the Russian River, California, U.S.A.
  • Modeled biomass growth reduced seepage for losing-connected and losing-disconnected rivers
Citation

Newcomer, M. E., Hubbard, S. S., Fleckenstein, J. H., Maier, U., Schmidt, C., Thullner, M., et al. (2016). Simulating bioclogging effects on dynamic riverbed permeability and infiltration. Water Resources Research, 52(4), 2883–2900. DOI: 10.1002/2015WR018351

Using phenocams to monitor our changing Earth: toward a global phenocam network

Scientific Achievement

Phenocam and other near-surface sensing technologies provide an avenue to observe and characterize the timing of plant growth, becoming more powerful in combination with microclimate monitoring.

Significance and Impact

Standardizing approaches to manage data and improve design will further expand the use of these technologies.

Research Details
  • Automated digital time-lapse cameras (phenocams) are powerful tools for recording and understanding ecological responses to global environmental change.
  • Documenting such changes in the environment is critical for informed decision making and to reduce or counteract negative outcomes
  • Standardization of practices and metadata recording will improve the utility of phenocams and facilitate their integration with other monitoring methods
Citation

Citation: Brown, T. B.; Hultine, K. R.; Steltzer, H.; Denny, E. G.; Denslow, M. W.; Granados, J.; Henderson, S.; Moore, D.; Nagai, S.; SanClements, M.; Sanchez-Azofeifa, A.; Sonnentag, O.; Tazik, D.; Richardson, A. D. (2016), Using phenocams to monitor our changing Earth: toward a global phenocam network, Frontiers in Ecology and the Environment, 14(2), 84-93, DOI: 10.1002/fee.1222.

Estimating groundwater dynamics at a Colorado River floodplain site using historical hydrological data and climate information

Projected daily groundwater levels at the location of a borehole from year 2020 to year 2099, where the black, red, and green curves are the estimated median and lower and upper bounds of 95% predictive intervals.

Scientific Achievement

We developed a Bayesian model to combine small-scale historical hydrological data (i.e., 47 years of streamflow data from a gaging station approximately 27 miles upstream) with large-scale, long-term climate prediction on the Upper Colorado River Basin to estimate groundwater dynamics at a floodplain site in Rifle, Colorado.

Significance and Impact

Although future groundwater levels are expected to be similar to the current levels, the timing of the high groundwater levels is predicted to occur about one month earlier. The results can be used for a watershed reactive transport model to predict how climate-induced changes will influence future biogeochemical cycling

Research Details
  • Predict groundwater dynamics using historical streamflow and climate information
  • No significant trends found in future groundwater levels at the Rifle study site
  • Peak groundwater levels occur one month earlier towards the end of this century
Citation

Chen, J., Hubbard, S. S., Williams, K. H., and Ficklin, D. L. (2016), Estimating groundwater dynamics at a Colorado River floodplain site using historical hydrological data and climate information, Water Resources Research, 52(3), 1881-1898. DOI: 10.1002/2015WR017777

Hot Spots and Hot Moments of Carbon in the Rifle Floodplain

Schematic representation of the genome-informed geochemical reaction network included in model simulations.

Scientific Achievement

We use a genome-informed reactive transport modeling approach to analyze the cumulative impact of naturally reduced zones, water table fluctuations, and temperature gradients on subsurface carbon fluxes within a floodplain environment.

Significance and Impact
  • Model simulations considering only abiotic reactions underestimated atmospheric CO2 fluxes by up to 230% compared to simulations with genome-informed biotic pathways.
  • Ignoring annual water table fluctuations in model simulations led to an overestimation of groundwater carbon exports from the Rifle floodplain, while ignoring annual temperature gradient variations underestimated carbon exports by almost 150%.
Research Details
  • 2-D coupled variably-saturated, non-isothermal flow and biogeochemical reactive transport modeling was applied to improve our understanding of the abiotic and microbially mediated reactions controlling carbon dynamics at the Rifle floodplain site.
  • This study indicates that spatial microbial and redox zonation as well as temporal fluctuations of temperature and water table depth contribute significantly to subsurface carbon fluxes in floodplains and need to be represented appropriately in model simulations.
Citation

Arora, B., Spycher, N.F., Steefel, C.I., Molins, S., Bill, M., Conrad, M.E., Dong, W., Faybishenko, B., Tokunaga, T.K., Wan, J. and Williams, K.H., 2016. Influence of hydrological, biogeochemical and temperature transients on subsurface carbon fluxes in a flood plain environment. Biogeochemistry, 127(2-3), pp.367-396. DOI: 10.1007/s10533-016-0186-8

Preface to the Special Issue of Vadose Zone Journal on Soil as Complex Systems

170 scientists from 13 countries represented many scientific disciplines—ecology, hydrology, geophysics, agriculture, soil chemistry, physics, microbiology, and modeling of soil–climate interactions.
More than 120 abstracts were published in the Conference Proceedings.

Scientific Achievement

The conference presentations and publications revealed that soil systems are not simply complicated, but fall under the definition of a complex system, and there is no general theory in the field of complex soil systems. New experimental methods and models are critically needed to quantify the integrated effects of physical, chemical, and biological soil processes to predict soil behavior for a variety of scientific and practical applications.

Significance and Impact

The Conference’s provided a motivating framework towards improved understanding of complex soil systems, as well as outlined the paradigm shift in soil studies critically needed illuminate interactions and feedbacks within the soil systems needed for the development of sustainable agriculture, soil and groundwater remediation, and responses to climate change challenges.

Research Details

The Conference presentations addressed fundamental concepts and advances in soil characterization, experimentation and modeling of complex soil systems needed to understand how soil physical, chemical, and biological components and processes influence the soil–plant–atmosphere system at multiple spatial and temporal scales. This knowledge is central in addressing scientific and practical applications, including those from managed and unmanaged environmental systems.

Citation

Faybishenko, B.; Hubbard, S.; Brodie, E.; Nico, P.; Molz, F.; Hunt, A.; Pachepsky, Y. (2016), Preface to the Special Issue of Vadose Zone Journal on Soil as Complex Systems, Vadose Zone Journal, 15(2), DOI: 10.2136/vzj2016.01.0005

https://www.soils.org/files/about-soils/complex-soil-systems-flyer2014.pdf

Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum

Lifestyle and ecosystem impacts are predicted and rendered as a cell cartoon

Scientific Achievement

Complete genomes reconstructed for five closely related and highly novel groundwater-associated bacteria were used to predict their environmental impact. The genomes define a new Class in Peregrinibacteria, potentially a new phylum.

Significance and Impact

Complete genomes from complex metagenomes are essentially unprecedented. Having such high quality sequences is critical for accurate ecological and evolutionary analyses.

Research Details
  • Field samples were collected, DNA extracted and shotgun sequenced
  • Advanced bioinformatics approaches were used to recover draft genomes and curate them to completion
  • Phylogenetic analyses place the newly sampled organisms in the Candidate Phyla Radiation as a sibling lineage to Peregrinibacteria.
Citation

Anantharaman, K.; Brown, C. T.; Burstein, D.; Castelle, C. J.; Probst, A. J.; Thomas, B. C.; Williams, K. H.; Banfield, J. F. (2016), Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum, PeerJ, 4, e1607, DOI: 10.7717/peerj.1607

New Pathway for Decomposition of Dissolved Organic Matter

Schematic shows how Iron (Fe) can start a catalytic pathway that accelerates the oxidation of natural organic matter by oxygen (O2). The important reactive oxygen species intermediates are also show, hydrogen peroxide (H2O2) and superoxide (O2-●)

Scientific Achievement

We were able to experimentally demonstrate and numerically model a new pathway by which natural organic matter can be oxidized (decomposed) by oxygen. We showed that a type of organic matter that was not directly oxidized by oxygen rapidly oxidized with the addition of catalytic amounts of iron.

Significance and Impact

The pathways and rates of oxidation of natural organic matter is an important part of the global carbon cycle. If modeling of global carbon cycling is to be accurate it is important that we have a clear understanding of all the significant pathways. This work contributes to that need.

Research Details
  • We used a model organic compound to represent natural organic matter.
  • We measured the rate of oxidation of this compound in the presence and absence of iron.
  • We used a numerical kinetic model to show that iron initiates an important catalytic oxidation pathway that relies on important reactive oxygen species intermediates, hydrogen peroxide (H2O2) and superoxide (O2-●)
Citation

Yuan, X.; Davis, J. A.; Nico, P. S. (2016), Iron-Mediated Oxidation of Methoxyhydroquinone under Dark Conditions: Kinetic and Mechanistic Insights, Environmental Science & Technology, 50(4), 1731-1740 DOI: 10.1021/acs.est.5b03939.