A general framework for quantitatively assessing ecological stochasticity
Abstract
Understanding the community assembly mechanisms controlling biodiversity patterns is a central issue in ecology. Although it is generally accepted that both deterministic and stochastic processes play important roles in community assembly, quantifying their relative importance is challenging. Here we propose a general mathematical framework to quantify ecological stochasticity under different situations in which deterministic factors drive the communities more similar or dissimilar than null expectation. An index, normalized stochasticity ratio ( NST ), was developed with 50% as the boundary point between more deterministic (<50%) and more stochastic (>50%) assembly. NST was tested with simulated communities by considering abiotic filtering, competition, environmental noise, and spatial scales. All tested approaches showed limited performance at large spatial scales or under very high environmental noise. However, in all of the other simulated scenarios, NST showed high accuracy (0.90 to 1.00) and precision (0.91 to 0.99), with averages of 0.37 higher accuracy (0.1 to 0.7) and 0.33 higher precision (0.0 to 1.8) than previous approaches. NST was also applied to estimate stochasticity in the succession of a groundwater microbial community in response to organic carbon (vegetable oil) injection. Our results showed that community assembly was shifted from more deterministic ( NST = 21%) tomore »
- Authors:
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1547822
- Alternate Identifier(s):
- OSTI ID: 1580904
- Grant/Contract Number:
- AC02-05CH11231; SC0014079; SC0016247; SC0010715
- Resource Type:
- Published Article
- Journal Name:
- Proceedings of the National Academy of Sciences of the United States of America
- Additional Journal Information:
- Journal Name: Proceedings of the National Academy of Sciences of the United States of America Journal Volume: 116 Journal Issue: 34; Journal ID: ISSN 0027-8424
- Publisher:
- National Academy of Sciences
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 54 ENVIRONMENTAL SCIENCES; stochasticity; community assembly; microbial ecology
Citation Formats
Ning, Daliang, Deng, Ye, Tiedje, James M., and Zhou, Jizhong. A general framework for quantitatively assessing ecological stochasticity. United States: N. p., 2019.
Web. doi:10.1073/pnas.1904623116.
Ning, Daliang, Deng, Ye, Tiedje, James M., & Zhou, Jizhong. A general framework for quantitatively assessing ecological stochasticity. United States. https://doi.org/10.1073/pnas.1904623116
Ning, Daliang, Deng, Ye, Tiedje, James M., and Zhou, Jizhong. Wed .
"A general framework for quantitatively assessing ecological stochasticity". United States. https://doi.org/10.1073/pnas.1904623116.
@article{osti_1547822,
title = {A general framework for quantitatively assessing ecological stochasticity},
author = {Ning, Daliang and Deng, Ye and Tiedje, James M. and Zhou, Jizhong},
abstractNote = {Understanding the community assembly mechanisms controlling biodiversity patterns is a central issue in ecology. Although it is generally accepted that both deterministic and stochastic processes play important roles in community assembly, quantifying their relative importance is challenging. Here we propose a general mathematical framework to quantify ecological stochasticity under different situations in which deterministic factors drive the communities more similar or dissimilar than null expectation. An index, normalized stochasticity ratio ( NST ), was developed with 50% as the boundary point between more deterministic (<50%) and more stochastic (>50%) assembly. NST was tested with simulated communities by considering abiotic filtering, competition, environmental noise, and spatial scales. All tested approaches showed limited performance at large spatial scales or under very high environmental noise. However, in all of the other simulated scenarios, NST showed high accuracy (0.90 to 1.00) and precision (0.91 to 0.99), with averages of 0.37 higher accuracy (0.1 to 0.7) and 0.33 higher precision (0.0 to 1.8) than previous approaches. NST was also applied to estimate stochasticity in the succession of a groundwater microbial community in response to organic carbon (vegetable oil) injection. Our results showed that community assembly was shifted from more deterministic ( NST = 21%) to more stochastic ( NST = 70%) right after organic carbon input. As the vegetable oil was consumed, the community gradually returned to be more deterministic ( NST = 27%). In addition, our results demonstrated that null model algorithms and community similarity metrics had strong effects on quantifying ecological stochasticity.},
doi = {10.1073/pnas.1904623116},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 34,
volume = 116,
place = {United States},
year = {2019},
month = {8}
}
https://doi.org/10.1073/pnas.1904623116
Web of Science
Figures / Tables:

Works referenced in this record:
Stochastic Assembly Leads to Alternative Communities with Distinct Functions in a Bioreactor Microbial Community
journal, March 2013
- Zhou, Jizhong; Liu, Wenzong; Deng, Ye
- mBio, Vol. 4, Issue 2
Biodiversity and Ecosystem Functioning
journal, November 2014
- Tilman, David; Isbell, Forest; Cowles, Jane M.
- Annual Review of Ecology, Evolution, and Systematics, Vol. 45, Issue 1
Beyond biogeographic patterns: processes shaping the microbial landscape
journal, May 2012
- Hanson, China A.; Fuhrman, Jed A.; Horner-Devine, M. Claire
- Nature Reviews Microbiology, Vol. 10, Issue 7
Using null models to disentangle variation in community dissimilarity from variation in α-diversity
journal, February 2011
- Chase, Jonathan M.; Kraft, Nathan J. B.; Smith, Kevin G.
- Ecosphere, Vol. 2, Issue 2
Estimating and mapping ecological processes influencing microbial community assembly
journal, May 2015
- Stegen, James C.; Lin, Xueju; Fredrickson, Jim K.
- Frontiers in Microbiology, Vol. 6
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update
journal, May 2018
- Afgan, Enis; Baker, Dannon; Batut, Bérénice
- Nucleic Acids Research, Vol. 46, Issue W1
Random Sampling Process Leads to Overestimation of β-Diversity of Microbial Communities
journal, June 2013
- Zhou, Jizhong; Jiang, Yi-Huei; Deng, Ye
- mBio, Vol. 4, Issue 3
A niche for neutrality
journal, February 2007
- Adler, Peter B.; HilleRisLambers, Janneke; Levine, Jonathan M.
- Ecology Letters, Vol. 10, Issue 2
Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning
journal, February 2018
- He, Zhili; Zhang, Ping; Wu, Linwei
- mBio, Vol. 9, Issue 1
High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats
journal, January 2015
- Zhou, Jizhong; He, Zhili; Yang, Yunfeng
- mBio, Vol. 6, Issue 1
Statistical Methods in Assessing Agreement: Models, Issues, and Tools
journal, March 2002
- Lin, Lawrence; Hedayat, A. S.; Sinha, Bikas
- Journal of the American Statistical Association, Vol. 97, Issue 457
Assessing the effects of spatial contingency and environmental filtering on metacommunity phylogenetics
journal, August 2012
- Peres-Neto, Pedro R.; Leibold, Mathew A.; Dray, Stéphane
- Ecology, Vol. 93, Issue sp8
Opposing effects of competitive exclusion on the phylogenetic structure of communities: Phylogeny and coexistence
journal, June 2010
- Mayfield, Margaret M.; Levine, Jonathan M.
- Ecology Letters, Vol. 13, Issue 9
Stochastic Community Assembly: Does It Matter in Microbial Ecology?
journal, October 2017
- Zhou, Jizhong; Ning, Daliang
- Microbiology and Molecular Biology Reviews, Vol. 81, Issue 4
Reproducibility and quantitation of amplicon sequencing-based detection
journal, February 2011
- Zhou, Jizhong; Wu, Liyou; Deng, Ye
- The ISME Journal, Vol. 5, Issue 8
Stochastic and deterministic assembly processes in subsurface microbial communities
journal, March 2012
- Stegen, James C.; Lin, Xueju; Konopka, Allan E.
- The ISME Journal, Vol. 6, Issue 9
All-scale spatial analysis of ecological data by means of principal coordinates of neighbour matrices
journal, July 2002
- Borcard, Daniel; Legendre, Pierre
- Ecological Modelling, Vol. 153, Issue 1-2
Community trait overdispersion due to trophic interactions: concerns for assembly process inference
journal, October 2016
- Pontarp, Mikael; Petchey, Owen L.
- Proceedings of the Royal Society B: Biological Sciences, Vol. 283, Issue 1840
Phylogenies and Community Ecology
journal, November 2002
- Webb, Campbell O.; Ackerly, David D.; McPeek, Mark A.
- Annual Review of Ecology and Systematics, Vol. 33, Issue 1
Assessing the relative importance of neutral stochasticity in ecological communities
journal, September 2014
- Vellend, Mark; Srivastava, Diane S.; Anderson, Kathryn M.
- Oikos, Vol. 123, Issue 12
Conceptual Synthesis in Community Ecology
journal, June 2010
- Vellend, Mark
- The Quarterly Review of Biology, Vol. 85, Issue 2
Rethinking Community Assembly through the Lens of Coexistence Theory
journal, December 2012
- HilleRisLambers, J.; Adler, P. B.; Harpole, W. S.
- Annual Review of Ecology, Evolution, and Systematics, Vol. 43, Issue 1
Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession
journal, March 2015
- Dini-Andreote, Francisco; Stegen, James C.; van Elsas, Jan Dirk
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 11
Ectomycorrhizal fungi and interspecific competition: species interactions, community structure, coexistence mechanisms, and future research directions: Tansley review
journal, July 2010
- Kennedy, Peter
- New Phytologist, Vol. 187, Issue 4
Null Model Analysis of Species Co-Occurrence Patterns
journal, September 2000
- Gotelli, Nicholas J.
- Ecology, Vol. 81, Issue 9
Patterns and Processes of Microbial Community Assembly
journal, September 2013
- Nemergut, D. R.; Schmidt, S. K.; Fukami, T.
- Microbiology and Molecular Biology Reviews, Vol. 77, Issue 3
Disentangling the importance of ecological niches from stochastic processes across scales
journal, August 2011
- Chase, Jonathan M.; Myers, Jonathan A.
- Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 366, Issue 1576
Analyzing or Explaining beta Diversity? Comment
journal, November 2008
- Legendre, Pierre; Borcard, Daniel; Peres-Neto, Pedro R.
- Ecology, Vol. 89, Issue 11
Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development
journal, August 2015
- Burns, Adam R.; Stephens, W. Zac; Stagaman, Keaton
- The ISME Journal, Vol. 10, Issue 3
A Concordance Correlation Coefficient to Evaluate Reproducibility
journal, March 1989
- Lin, Lawrence I-Kuei
- Biometrics, Vol. 45, Issue 1
Drought mediates the importance of stochastic community assembly
journal, October 2007
- Chase, J. M.
- Proceedings of the National Academy of Sciences, Vol. 104, Issue 44
Beyond Neutrality—Ecology Finds Its Niche
journal, August 2006
- Gewin, Virginia
- PLoS Biology, Vol. 4, Issue 8
Sampling Hubbell's neutral theory of biodiversity: Sampling neutral theory
journal, August 2004
- Alonso, David; McKane, Alan J.
- Ecology Letters, Vol. 7, Issue 10
Stochasticity, succession, and environmental perturbations in a fluidic ecosystem
journal, February 2014
- Zhou, Jizhong; Deng, Ye; Zhang, Ping
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 9
Stochastic Community Assembly Causes Higher Biodiversity in More Productive Environments
journal, May 2010
- Chase, J. M.
- Science, Vol. 328, Issue 5984
Predators temper the relative importance of stochastic processes in the assembly of prey metacommunities
journal, November 2009
- Chase, Jonathan M.; Biro, Elizabeth G.; Ryberg, Wade A.
- Ecology Letters, Vol. 12, Issue 11
Comparing Classical Community Models: Theoretical Consequences for Patterns of Diversity
journal, January 2002
- Chave, Jérôme; Muller‐Landau, Helene C.; Levin, Simon A.
- The American Naturalist, Vol. 159, Issue 1
Dynamic Succession of Groundwater Sulfate-Reducing Communities during Prolonged Reduction of Uranium in a Contaminated Aquifer
journal, March 2017
- Zhang, Ping; He, Zhili; Van Nostrand, Joy D.
- Environmental Science & Technology, Vol. 51, Issue 7
Refining the stress-gradient hypothesis for competition and facilitation in plant communities
journal, March 2009
- Maestre, Fernando T.; Callaway, Ragan M.; Valladares, Fernando
- Journal of Ecology, Vol. 97, Issue 2
Changes in assembly rules along a stress gradient from open dry grasslands to wetlands
journal, January 2016
- Lhotsky, Barbara; Kovács, Bence; Ónodi, Gábor
- Journal of Ecology, Vol. 104, Issue 2
Exploring the Phylogenetic Structure of Ecological Communities: An Example for Rain Forest Trees
journal, August 2000
- Webb, Campbell O.
- The American Naturalist, Vol. 156, Issue 2
Quantifying the roles of immigration and chance in shaping prokaryote community structure
journal, April 2006
- Sloan, William T.; Lunn, Mary; Woodcock, Stephen
- Environmental Microbiology, Vol. 8, Issue 4
Diversity and the Coevolution of Competitors, or the Ghost of Competition Past
journal, October 1980
- Connell, Joseph H.
- Oikos, Vol. 35, Issue 2
Quantifying community assembly processes and identifying features that impose them
journal, June 2013
- Stegen, James C.; Lin, Xueju; Fredrickson, Jim K.
- The ISME Journal, Vol. 7, Issue 11
Abiotic stress tolerance and competition-related traits underlie phylogenetic clustering in soil bacterial communities
journal, August 2014
- Goberna, Marta; Navarro-Cano, Jose A.; Valiente-Banuet, Alfonso
- Ecology Letters, Vol. 17, Issue 10
Reconciling niche and neutrality: the continuum hypothesis: Reconciling niche and neutrality
journal, March 2006
- Gravel, Dominique; Canham, Charles D.; Beaudet, Marilou
- Ecology Letters, Vol. 9, Issue 4
Half-century evidence from western Canada shows forest dynamics are primarily driven by competition followed by climate
journal, March 2015
- Zhang, Jian; Huang, Shongming; He, Fangliang
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 13
Community Regulation: Variation in Disturbance, Competition, and Predation in Relation to Environmental Stress and Recruitment
journal, November 1987
- Menge, Bruce A.; Sutherland, John P.
- The American Naturalist, Vol. 130, Issue 5
Stochastic and deterministic drivers of spatial and temporal turnover in breeding bird communities: Drivers of spatial and temporal turnover
journal, August 2012
- Stegen, James C.; Freestone, Amy L.; Crist, Thomas O.
- Global Ecology and Biogeography, Vol. 22, Issue 2
The Problem of Pattern and Scale in Ecology: The Robert H. MacArthur Award Lecture
journal, December 1992
- Levin, Simon A.
- Ecology, Vol. 73, Issue 6
Experimentally assessing the relative importance of predation and competition as agents of selection
journal, May 2010
- Calsbeek, Ryan; Cox, Robert M.
- Nature, Vol. 465, Issue 7298
Network succession reveals the importance of competition in response to emulsified vegetable oil amendment for uranium bioremediation: Competition in bioremediation system
journal, August 2015
- Deng, Ye; Zhang, Ping; Qin, Yujia
- Environmental Microbiology, Vol. 18, Issue 1
Disentangling the Drivers of Diversity Along Latitudinal and Elevational Gradients
journal, September 2011
- Kraft, N. J. B.; Comita, L. S.; Chase, J. M.
- Science, Vol. 333, Issue 6050
The Ecology and Evolution of Microbial Competition
journal, October 2016
- Ghoul, Melanie; Mitri, Sara
- Trends in Microbiology, Vol. 24, Issue 10
Climate warming leads to divergent succession of grassland microbial communities
journal, August 2018
- Guo, Xue; Feng, Jiajie; Shi, Zhou
- Nature Climate Change, Vol. 8, Issue 9
Figures / Tables found in this record: