skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Tracking Replicate Divergence in Microbial Community Composition and Function in Experimental Microcosms

Abstract

The study of microbial community functions necessitates replicating microbial communities. Variation in community development over time renders this an imperfect process. Thus, anticipating the likely degree of variation among replicate communities may aid in experimental design. We examined divergence in replicate community composition and function among 128 naturally assembled starting communities obtained from soils, each replicated three times, following a 30-day microcosm incubation period. Bacterial and fungal communities diverged in both composition and function among replicates, but remained much more similar to each other than to communities from different starting inocula. Variation in bacterial community composition among replicates was, however, correlated with variation in dissolved organic carbon production. A smaller-scale experiment testing nine starting communities showed that divergence was similar whether replicates were incubated on sterile or non-sterile pine litter, suggesting the impact of a pre-existing community on replicate divergence is minor. However, replicates in this experiment which were incubated for 114 days diverged more than those incubated for 30 days, suggesting experiments that run over long time periods will likely see greater variation among replicate community composition. Here these results suggest that while replicates diverge at a community level, such divergence is unlikely to severely impede the study ofmore » community function.« less

Authors:
ORCiD logo [1]; ORCiD logo [1];  [1];  [1];  [1]; ORCiD logo [1]; ORCiD logo [1]
  1. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE Office of Science (SC). Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1511629
Report Number(s):
LA-UR-19-20283
Journal ID: ISSN 0095-3628
Grant/Contract Number:  
89233218CNA000001
Resource Type:
Accepted Manuscript
Journal Name:
Microbial Ecology
Additional Journal Information:
Journal Volume: 78; Journal Issue: 4; Journal ID: ISSN 0095-3628
Publisher:
Springer
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Biological Science; Community; Microbial community composition; Microcosm; Community replication

Citation Formats

Johansen, Renee, Albright, Michaeline Burr Nelson, Gallegos-Graves, La Verne, Lopez, Deanna Lynn, Runde, Andreas Christian, Yoshida, Thomas M., and Dunbar, John Martin. Tracking Replicate Divergence in Microbial Community Composition and Function in Experimental Microcosms. United States: N. p., 2019. Web. doi:10.1007/s00248-019-01368-w.
Johansen, Renee, Albright, Michaeline Burr Nelson, Gallegos-Graves, La Verne, Lopez, Deanna Lynn, Runde, Andreas Christian, Yoshida, Thomas M., & Dunbar, John Martin. Tracking Replicate Divergence in Microbial Community Composition and Function in Experimental Microcosms. United States. doi:10.1007/s00248-019-01368-w.
Johansen, Renee, Albright, Michaeline Burr Nelson, Gallegos-Graves, La Verne, Lopez, Deanna Lynn, Runde, Andreas Christian, Yoshida, Thomas M., and Dunbar, John Martin. Tue . "Tracking Replicate Divergence in Microbial Community Composition and Function in Experimental Microcosms". United States. doi:10.1007/s00248-019-01368-w. https://www.osti.gov/servlets/purl/1511629.
@article{osti_1511629,
title = {Tracking Replicate Divergence in Microbial Community Composition and Function in Experimental Microcosms},
author = {Johansen, Renee and Albright, Michaeline Burr Nelson and Gallegos-Graves, La Verne and Lopez, Deanna Lynn and Runde, Andreas Christian and Yoshida, Thomas M. and Dunbar, John Martin},
abstractNote = {The study of microbial community functions necessitates replicating microbial communities. Variation in community development over time renders this an imperfect process. Thus, anticipating the likely degree of variation among replicate communities may aid in experimental design. We examined divergence in replicate community composition and function among 128 naturally assembled starting communities obtained from soils, each replicated three times, following a 30-day microcosm incubation period. Bacterial and fungal communities diverged in both composition and function among replicates, but remained much more similar to each other than to communities from different starting inocula. Variation in bacterial community composition among replicates was, however, correlated with variation in dissolved organic carbon production. A smaller-scale experiment testing nine starting communities showed that divergence was similar whether replicates were incubated on sterile or non-sterile pine litter, suggesting the impact of a pre-existing community on replicate divergence is minor. However, replicates in this experiment which were incubated for 114 days diverged more than those incubated for 30 days, suggesting experiments that run over long time periods will likely see greater variation among replicate community composition. Here these results suggest that while replicates diverge at a community level, such divergence is unlikely to severely impede the study of community function.},
doi = {10.1007/s00248-019-01368-w},
journal = {Microbial Ecology},
number = 4,
volume = 78,
place = {United States},
year = {2019},
month = {4}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Save / Share:

Works referenced in this record:

Replicate or lie: The need for replication
journal, March 2010


Assembly of microbial communities in replicate nutrient‐cycling model ecosystems follows divergent trajectories, leading to alternate stable states
journal, July 2017

  • Pagaling, Eulyn; Vassileva, Kristin; Mills, Catherine G.
  • Environmental Microbiology, Vol. 19, Issue 8
  • DOI: 10.1111/1462-2920.13849

Bacterial succession on decomposing leaf litter exhibits a specific occurrence pattern of cellulolytic taxa and potential decomposers of fungal mycelia
journal, August 2016

  • Tláskal, Vojtěch; Voříšková, Jana; Baldrian, Petr
  • FEMS Microbiology Ecology, Vol. 92, Issue 11
  • DOI: 10.1093/femsec/fiw177

Deterministic processes vary during community assembly for ecologically dissimilar taxa
journal, October 2015

  • Powell, Jeff R.; Karunaratne, Senani; Campbell, Colin D.
  • Nature Communications, Vol. 6, Issue 1
  • DOI: 10.1038/ncomms9444

Fungal community on decomposing leaf litter undergoes rapid successional changes
journal, October 2012


Signature Wood Modifications Reveal Decomposer Community History
journal, March 2015


Small-scale spatial heterogeneity of ecosystem properties, microbial community composition and microbial activities in a temperate mountain forest soil
journal, September 2016

  • Štursová, Martina; Bárta, Jiří; Šantrůčková, Hana
  • FEMS Microbiology Ecology, Vol. 92, Issue 12
  • DOI: 10.1093/femsec/fiw185

Model Microbial Consortia as Tools for Understanding Complex Microbial Communities
journal, October 2018


Mycobiome diversity: high-throughput sequencing and identification of fungi
journal, November 2018

  • Nilsson, R. Henrik; Anslan, Sten; Bahram, Mohammad
  • Nature Reviews Microbiology, Vol. 17, Issue 2
  • DOI: 10.1038/s41579-018-0116-y

Replication
journal, August 2014

  • Blainey, Paul; Krzywinski, Martin; Altman, Naomi
  • Nature Methods, Vol. 11, Issue 9
  • DOI: 10.1038/nmeth.3091

Next-generation experiments linking community structure and ecosystem functioning: Crystal ball
journal, November 2018


Dead or Alive; or Does It Really Matter? Level of Congruency Between Trophic Modes in Total and Active Fungal Communities in High Arctic Soil
journal, January 2019


16S rRNA Gene Sequencing for Bacterial Identification in the Diagnostic Laboratory: Pluses, Perils, and Pitfalls
journal, July 2007

  • Janda, J. M.; Abbott, S. L.
  • Journal of Clinical Microbiology, Vol. 45, Issue 9
  • DOI: 10.1128/JCM.01228-07

Diversity begets diversity in competition for space
journal, May 2017

  • Maynard, Daniel S.; Bradford, Mark A.; Lindner, Daniel L.
  • Nature Ecology & Evolution, Vol. 1, Issue 6
  • DOI: 10.1038/s41559-017-0156

Divergent assemblage patterns and driving forces for bacterial and fungal communities along a glacier forefield chronosequence
journal, March 2018


Contrasting primary successional trajectories of fungi and bacteria in retreating glacier soils
journal, September 2013

  • Brown, Shawn P.; Jumpponen, Ari
  • Molecular Ecology, Vol. 23, Issue 2
  • DOI: 10.1111/mec.12487