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Title: Nutrient cycling for biomass: Interactive proteomic/transcriptomic networks for global carbon management processes within poplar-mycorrhizal interactions

Abstract

This project addresses the need to develop system-scale models at the symbiotic interface between ectomycorrhizal fungi (Laccaria bicolor) and tree species (Populus tremuloides) in response to environmental nutrient availability / biochemistry. Using our now well-established laboratory Laccaria x poplar system, we address the hypothesis that essential regulatory and metabolic mechanisms can be inferred from genomic, transcriptomic and proteomic-level changes that occur in response to environmental nutrient availability. The project addresses this hypothesis by applying state-of-the-art protein-level analytic approaches to fill the gap in our understanding of how mycorrhizal regulatory and metabolic processes at the transcript-level translate to nutrient uptake, carbon management and ultimate net primary productivity of plants. In most cases, these techniques were not previously optimized for poplar trees or Laccaria. Thus, one of the major contributions of this project has been to provide avenues for new research in these species by overcoming the pitfalls that had previously prevented the use of techniques such as ChIP-Seq and SWATH-proteomics. Since it is the proteins that sense and interact with the environment, participate in signal cascades, activate and regulate gene expression, perform the activities of metabolism and ultimately sequester carbon and generate biomass, an understanding of protein activities during symbiosis-linked nutrientmore » uptake is critical to any systems-level approach that links metabolic processes to the environment. This project uses a team of experts at The University of Alabama in Huntsville (UAH), The University of Alabama at Birmingham (UAB) and Argonne National Laboratory (ANL) to address the above hypothesis using a multiple "omics" approach that combines gene and protein expression as well as protein modifications, and biochemical analyses (performed at Brookhaven National Laboratory (BNL)) in poplar trees under mycorrhizal and free living conditions. Together, the assembled team of experts completed all of the planned milestones set forth in this project. In addition to the planned approaches, several lines of exciting new research have also evolved during the course of this project that involved FTIR Imaging using the National Synchrotron Light Source at BNL. A summary of the approaches used in this project and key highlights are as follows: Having the right combination of microbes associated with plants is largely responsible for the plant’s ability to mine nutrients from the soil and to develop a strong “immune system”. Our current chemically focused and intensive culture tends to forget that plants obtain nutrients in two ways: (1) via water soluble chemical nutrients and (2) via the activity of acquired microbial symbionts. In healthy natural ecosystems, chemical nutrients are always in low abundance because the organisms within that system have already locked such nutrients away within the biological system itself. Thus, in nature it is the biological sources of nutrients and the microbes that have the capacity to mine those nutrients for their plant hosts that actually control the terrestrial nutrient cycles on this planet. Thus, a new push in the future may very well be to use our skills at elucidating complex patterns to strategically guide soil microbe communities to do what we want, essentially allowing nature to do the work of figuring out what is most efficient and effective for human needs. However, the findings of this project and other work in our lab lead to the hypothesis that the specific soil community composition is less important than the emergent properties of those communities. So, additional research into what soil communities are effective and how they are established will be key in developing human understanding of how to manipulate biological systems to meet human needs without causing undue damage to our environment.« less

Authors:
 [1]
  1. Univ. of Alabama, Huntsville, AL (United States)
Publication Date:
Research Org.:
Univ. of Alabama, Huntsville, AL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1325004
Report Number(s):
DOE-UAH-SC0006652
26799
DOE Contract Number:
SC0006652
Resource Type:
Technical Report
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; SWATH Proteomics; ChIP-Seq; Biochemical Analysis; Populus tremuloides; Laccaria bicolor

Citation Formats

Cseke, Leland. Nutrient cycling for biomass: Interactive proteomic/transcriptomic networks for global carbon management processes within poplar-mycorrhizal interactions. United States: N. p., 2016. Web. doi:10.2172/1325004.
Cseke, Leland. Nutrient cycling for biomass: Interactive proteomic/transcriptomic networks for global carbon management processes within poplar-mycorrhizal interactions. United States. doi:10.2172/1325004.
Cseke, Leland. 2016. "Nutrient cycling for biomass: Interactive proteomic/transcriptomic networks for global carbon management processes within poplar-mycorrhizal interactions". United States. doi:10.2172/1325004. https://www.osti.gov/servlets/purl/1325004.
@article{osti_1325004,
title = {Nutrient cycling for biomass: Interactive proteomic/transcriptomic networks for global carbon management processes within poplar-mycorrhizal interactions},
author = {Cseke, Leland},
abstractNote = {This project addresses the need to develop system-scale models at the symbiotic interface between ectomycorrhizal fungi (Laccaria bicolor) and tree species (Populus tremuloides) in response to environmental nutrient availability / biochemistry. Using our now well-established laboratory Laccaria x poplar system, we address the hypothesis that essential regulatory and metabolic mechanisms can be inferred from genomic, transcriptomic and proteomic-level changes that occur in response to environmental nutrient availability. The project addresses this hypothesis by applying state-of-the-art protein-level analytic approaches to fill the gap in our understanding of how mycorrhizal regulatory and metabolic processes at the transcript-level translate to nutrient uptake, carbon management and ultimate net primary productivity of plants. In most cases, these techniques were not previously optimized for poplar trees or Laccaria. Thus, one of the major contributions of this project has been to provide avenues for new research in these species by overcoming the pitfalls that had previously prevented the use of techniques such as ChIP-Seq and SWATH-proteomics. Since it is the proteins that sense and interact with the environment, participate in signal cascades, activate and regulate gene expression, perform the activities of metabolism and ultimately sequester carbon and generate biomass, an understanding of protein activities during symbiosis-linked nutrient uptake is critical to any systems-level approach that links metabolic processes to the environment. This project uses a team of experts at The University of Alabama in Huntsville (UAH), The University of Alabama at Birmingham (UAB) and Argonne National Laboratory (ANL) to address the above hypothesis using a multiple "omics" approach that combines gene and protein expression as well as protein modifications, and biochemical analyses (performed at Brookhaven National Laboratory (BNL)) in poplar trees under mycorrhizal and free living conditions. Together, the assembled team of experts completed all of the planned milestones set forth in this project. In addition to the planned approaches, several lines of exciting new research have also evolved during the course of this project that involved FTIR Imaging using the National Synchrotron Light Source at BNL. A summary of the approaches used in this project and key highlights are as follows: Having the right combination of microbes associated with plants is largely responsible for the plant’s ability to mine nutrients from the soil and to develop a strong “immune system”. Our current chemically focused and intensive culture tends to forget that plants obtain nutrients in two ways: (1) via water soluble chemical nutrients and (2) via the activity of acquired microbial symbionts. In healthy natural ecosystems, chemical nutrients are always in low abundance because the organisms within that system have already locked such nutrients away within the biological system itself. Thus, in nature it is the biological sources of nutrients and the microbes that have the capacity to mine those nutrients for their plant hosts that actually control the terrestrial nutrient cycles on this planet. Thus, a new push in the future may very well be to use our skills at elucidating complex patterns to strategically guide soil microbe communities to do what we want, essentially allowing nature to do the work of figuring out what is most efficient and effective for human needs. However, the findings of this project and other work in our lab lead to the hypothesis that the specific soil community composition is less important than the emergent properties of those communities. So, additional research into what soil communities are effective and how they are established will be key in developing human understanding of how to manipulate biological systems to meet human needs without causing undue damage to our environment.},
doi = {10.2172/1325004},
journal = {},
number = ,
volume = ,
place = {United States},
year = 2016,
month = 8
}

Technical Report:

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  • This report summarizes progress in three years of field research designed to evaluate biological and chemical indicators of the current and future health of the Southern Appalachian spruce-fir ecosystem. The emphasis of this research has been on the identification and understanding of mechanisms through which current levels of acidic deposition are impacting ecosystem processes. The identification of these principal mechanisms and key biological indicators of change was designed to improve our capabilities to detect, monitor, and assess the effects of air quality regulations and attendant future air quality changes on ecosystem response. Individual research tasks focused on the following researchmore » areas: (1) the significance of foliar uptake of atmospheric sources of nitrogen in relationship to plant utilization of N from available soil reserves; (2) linkages between atmospheric inputs to the soil surface, solution chemistry, and decomposition in the upper organic soil horizons; (3) effects of soil solution chemistry on uptake of cations and aluminum by fine roots; and (4) the effects of varying rates of calcium supply on carbon metabolism of Fraser fir and red spruce, and the relationship between calcium levels in wood cells and integrity of wood formed in bole and branches. Each of the individual tasks was designed to focus upon a mechanism or process that we consider critical to understanding chemical and biological linkages. These linkages will be important determinants in understanding the basis of past and potential future responses of the high elevation Southern Appalachian Forest to acidic deposition and other co-occurring environmental stresses. This report contains (1) background and rationale for the research undertaken in 1992-94; (2) a summary of principal research findings; (3) publications from this research; and (4) characterization of data sets produced by this research which will be the basis of future research, analyses and/or publications.« less
  • Assessing the risk of toxic chemicals to soil nutrient cycling processes involves an understanding of the potential for chemical effects on the diversity and the activity of the microbial communities and higher life forms in the natural system. Substantial progress has been made in discerning how anthropogenic stressors affect the cycling of nutrients in soil. Most of the work has focused on individual assessments at specific sites using endpoints designed to measure ecosystem structure or process effects. This chapter summarizes much of the literature and seeks to integrate or suggest needed research activities to assure further progress in understanding themore » ecotoxicology of nutrient cycling.« less
  • This report documents the multispecies nutrient cycling model (MSNUCY) and reviews the range of questions in theoretical ecology to which it can be applied. MSNUCY is a hybrid of (1) resource utilization models, in which population growth rate is governed by resource uptake kinetics that reduce potential growth when resources are limiting and (2) models of population dynamics, which take into account interactions governing the rate of consumption of one population by another. The hybrid is then constrained to look like an ecosystem model having nutrient cycles and energy flows. MSNUCY is written in FORTRAN IV but has many ofmore » the features of structured programming and provides graphical outputs of the food webs, population biomass changes, and species turnover. Sample input and output are given. 25 refs., 13 figs., 15 tabs.« less
  • The paper presents a framework for studying responses of mycorrhizal roots to external stresses, including possible feedback effects, which are likely to occur. A conceptual model is presented to discuss how carbon may be involved in singular and multiple stress interactions of mycorrhizal seedlings. Recent literature linking carbon allocation and host/fungal response under natural and anthropogenic stresses is reviewed. Due to its integral role in metabolic processes, characterizing carbon and carbon allocation in controlled laboratory environments could be useful for understanding host/fungal responses to a variety of natural and anthropogenic stresses. Carbon allocation at the whole plant level reflects anmore » integrated response which links photosynthesis to growth and maintenance processes. A root-mycocosm system is described which permits spatial separation of a portion of extramatrical hyphae growing in association with seedling roots. The results are presented in a fashion to illustrate the nature of information which can be obtained using this system. Current projects using the mycocosms include characterizing the dynamics of carbon allocation under ozone stress, and following the fate of organic pollutants. The authors believe that the system could be used to differentiate fungal and host mediated responses to a large number of other stresses, and to study a variety of physiological processes in mycorrhizal plants.« less