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Published on: September 15, 2015
Environmental proteomics, biodiversity statistics and food-web structure.
Nicholas J Gotelli1, Aaron M Ellison, Bryan A Ballif
1Department of Biology, University of Vermont, 109 Carrigan Drive, Burlington, VT 05405, USA. ngotelli@uvm.edu
Trends in Ecology & Evolution
|March 31, 2012
Summary
Environmental proteomics links protein diversity to ecological function. Adapting biodiversity statistics and field manipulations is key to understanding protein significance in complex ecosystems.
Area of Science:
- Environmental proteomics
- Ecological systems biology
- Bioinformatics
Background:
- Environmental proteomics studies reveal protein diversity-ecological function links in simple communities like microbial biofilms.
- High-throughput proteomic methods are expanding to complex ecological systems involving microbe-macroorganism interactions.
- Biodiversity and protein survey data share structural similarities, suggesting statistical method transferability.
Purpose of the Study:
- To highlight the need for adapting ecological statistical methods for analyzing protein diversity data.
- To emphasize that large protein and bioinformatics datasets alone do not explain functional significance.
- To advocate for field manipulation experiments to determine the functional roles of protein cohorts.
Main Methods:
- Comparative analysis of data structures in biodiversity and proteomics.
- Adaptation of statistical methods from biodiversity analysis to quantitative protein surveys.
- Design of replicated field manipulation experiments (e.g., nutrient enrichment, predator removal).
Main Results:
- Protein and biodiversity data exhibit analogous structures, supporting the adaptation of ecological statistical techniques.
- Quantitative surveys of protein diversity can benefit from established ecological analytical frameworks.
- Field manipulations are crucial for linking changes in protein abundance to specific ecological functions.
Conclusions:
- Statistical methods used in biodiversity research are applicable and valuable for analyzing environmental proteomic data.
- Understanding the functional significance of proteins in complex ecosystems requires experimental validation through field manipulations.
- Future environmental proteomics research should integrate ecological field experiments with advanced statistical analyses to reveal protein functions.
Related Concept Videos
01:33Proteomics
A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
01:19Methods to Assess Microbial Communities
Microbial communities, comprising bacteria, archaea, and eukaryotic microorganisms, inhabit diverse ecosystems and play crucial roles in environmental and biological processes. Their diversity is defined by three main parameters: species richness (the number of distinct species), species abundance (the relative quantity of each species), and species evenness (how uniformly individual species are distributed in various locations). These factors together shape the structure and ecological balance...
02:26Protein Networks
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
02:26Protein Networks
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
02:31Habitat Fragmentation
Habitat fragmentation describes the division of a more extensive, continuous habitat into smaller, discontinuous areas. Human activities such as land conversion, as well as slower geological processes leading to changes in the physical environment, are the two leading causes of habitat fragmentation. The fragmentation process typically follows the same steps: perforation, dissection, fragmentation, shrinkage, and attrition.
01:19What is Biodiversity?
Biodiversity describes the variety of living things at multiple organizational levels: genetic, species and ecosystem diversity. Species diversity includes all branches of the evolutionary tree from single-celled prokaryotic organisms, bacteria, and archaea, to the eukaryotic kingdoms: plants; animals; fungi; and protists. To date, there have been about 1.75 million species identified, and new species are discovered every week.