Estimating taxon-specific population dynamics in diverse microbial communities

Benjamin J. Koch, Theresa A. McHugh, Michaela Hayer, Egbert Schwartz, Steven J. Blazewicz, Paul Dijkstra, Natasja V.A.N. Gestel, Jane C Marks, Rebecca L. Mau, Ember M. Morrissey, Jennifer Pett-Ridge, Bruce A Hungate

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Understanding how population-level dynamics contribute to ecosystem-level processes is a primary focus of ecological research and has led to important breakthroughs in the ecology of macroscopic organisms. However, the inability to measure population-specific rates, such as growth, for microbial taxa within natural assemblages has limited ecologists’ understanding of how microbial populations interact to regulate ecosystem processes. Here, we use isotope incorporation within DNA molecules to model taxon-specific population growth in the presence of 18O-labeled water. By applying this model to phylogenetic marker sequencing data collected from stable-isotope probing studies, we estimate rates of growth, mortality, and turnover for individual microbial populations within soil assemblages. When summed across the entire bacterial community, our taxon-specific estimates are within the range of other whole-assemblage measurements of bacterial turnover. Because it can be applied to environmental samples, the approach we present is broadly applicable to measuring population growth, mortality, and associated biogeochemical process rates of microbial taxa for a wide range of ecosystems and can help reveal how individual microbial populations drive biogeochemical fluxes.

Original languageEnglish (US)
Article numbere02090
JournalEcosphere
Volume9
Issue number1
DOIs
StatePublished - Jan 1 2018

Fingerprint

microbial communities
microbial community
population dynamics
ecosystem
population growth
turnover
mortality
ecosystems
stable isotope
isotope
ecology
phylogenetics
DNA
ecologists
bacterial communities
stable isotopes
microbial growth
isotopes
rate
soil

Keywords

  • Population growth rate
  • Population mortality rate
  • Quantitative stable-isotope probing (qSIP)
  • Rewetting
  • Soil bacteria
  • Turnover

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Ecology

Cite this

Estimating taxon-specific population dynamics in diverse microbial communities. / Koch, Benjamin J.; McHugh, Theresa A.; Hayer, Michaela; Schwartz, Egbert; Blazewicz, Steven J.; Dijkstra, Paul; Gestel, Natasja V.A.N.; Marks, Jane C; Mau, Rebecca L.; Morrissey, Ember M.; Pett-Ridge, Jennifer; Hungate, Bruce A.

In: Ecosphere, Vol. 9, No. 1, e02090, 01.01.2018.

Research output: Contribution to journalArticle

Koch, BJ, McHugh, TA, Hayer, M, Schwartz, E, Blazewicz, SJ, Dijkstra, P, Gestel, NVAN, Marks, JC, Mau, RL, Morrissey, EM, Pett-Ridge, J & Hungate, BA 2018, 'Estimating taxon-specific population dynamics in diverse microbial communities', Ecosphere, vol. 9, no. 1, e02090. https://doi.org/10.1002/ecs2.2090
Koch, Benjamin J. ; McHugh, Theresa A. ; Hayer, Michaela ; Schwartz, Egbert ; Blazewicz, Steven J. ; Dijkstra, Paul ; Gestel, Natasja V.A.N. ; Marks, Jane C ; Mau, Rebecca L. ; Morrissey, Ember M. ; Pett-Ridge, Jennifer ; Hungate, Bruce A. / Estimating taxon-specific population dynamics in diverse microbial communities. In: Ecosphere. 2018 ; Vol. 9, No. 1.
@article{0ee85cf207654f199ad7c6018720029d,
title = "Estimating taxon-specific population dynamics in diverse microbial communities",
abstract = "Understanding how population-level dynamics contribute to ecosystem-level processes is a primary focus of ecological research and has led to important breakthroughs in the ecology of macroscopic organisms. However, the inability to measure population-specific rates, such as growth, for microbial taxa within natural assemblages has limited ecologists’ understanding of how microbial populations interact to regulate ecosystem processes. Here, we use isotope incorporation within DNA molecules to model taxon-specific population growth in the presence of 18O-labeled water. By applying this model to phylogenetic marker sequencing data collected from stable-isotope probing studies, we estimate rates of growth, mortality, and turnover for individual microbial populations within soil assemblages. When summed across the entire bacterial community, our taxon-specific estimates are within the range of other whole-assemblage measurements of bacterial turnover. Because it can be applied to environmental samples, the approach we present is broadly applicable to measuring population growth, mortality, and associated biogeochemical process rates of microbial taxa for a wide range of ecosystems and can help reveal how individual microbial populations drive biogeochemical fluxes.",
keywords = "Population growth rate, Population mortality rate, Quantitative stable-isotope probing (qSIP), Rewetting, Soil bacteria, Turnover",
author = "Koch, {Benjamin J.} and McHugh, {Theresa A.} and Michaela Hayer and Egbert Schwartz and Blazewicz, {Steven J.} and Paul Dijkstra and Gestel, {Natasja V.A.N.} and Marks, {Jane C} and Mau, {Rebecca L.} and Morrissey, {Ember M.} and Jennifer Pett-Ridge and Hungate, {Bruce A}",
year = "2018",
month = "1",
day = "1",
doi = "10.1002/ecs2.2090",
language = "English (US)",
volume = "9",
journal = "Ecosphere",
issn = "2150-8925",
publisher = "Ecological Society of America",
number = "1",

}

TY - JOUR

T1 - Estimating taxon-specific population dynamics in diverse microbial communities

AU - Koch, Benjamin J.

AU - McHugh, Theresa A.

AU - Hayer, Michaela

AU - Schwartz, Egbert

AU - Blazewicz, Steven J.

AU - Dijkstra, Paul

AU - Gestel, Natasja V.A.N.

AU - Marks, Jane C

AU - Mau, Rebecca L.

AU - Morrissey, Ember M.

AU - Pett-Ridge, Jennifer

AU - Hungate, Bruce A

PY - 2018/1/1

Y1 - 2018/1/1

N2 - Understanding how population-level dynamics contribute to ecosystem-level processes is a primary focus of ecological research and has led to important breakthroughs in the ecology of macroscopic organisms. However, the inability to measure population-specific rates, such as growth, for microbial taxa within natural assemblages has limited ecologists’ understanding of how microbial populations interact to regulate ecosystem processes. Here, we use isotope incorporation within DNA molecules to model taxon-specific population growth in the presence of 18O-labeled water. By applying this model to phylogenetic marker sequencing data collected from stable-isotope probing studies, we estimate rates of growth, mortality, and turnover for individual microbial populations within soil assemblages. When summed across the entire bacterial community, our taxon-specific estimates are within the range of other whole-assemblage measurements of bacterial turnover. Because it can be applied to environmental samples, the approach we present is broadly applicable to measuring population growth, mortality, and associated biogeochemical process rates of microbial taxa for a wide range of ecosystems and can help reveal how individual microbial populations drive biogeochemical fluxes.

AB - Understanding how population-level dynamics contribute to ecosystem-level processes is a primary focus of ecological research and has led to important breakthroughs in the ecology of macroscopic organisms. However, the inability to measure population-specific rates, such as growth, for microbial taxa within natural assemblages has limited ecologists’ understanding of how microbial populations interact to regulate ecosystem processes. Here, we use isotope incorporation within DNA molecules to model taxon-specific population growth in the presence of 18O-labeled water. By applying this model to phylogenetic marker sequencing data collected from stable-isotope probing studies, we estimate rates of growth, mortality, and turnover for individual microbial populations within soil assemblages. When summed across the entire bacterial community, our taxon-specific estimates are within the range of other whole-assemblage measurements of bacterial turnover. Because it can be applied to environmental samples, the approach we present is broadly applicable to measuring population growth, mortality, and associated biogeochemical process rates of microbial taxa for a wide range of ecosystems and can help reveal how individual microbial populations drive biogeochemical fluxes.

KW - Population growth rate

KW - Population mortality rate

KW - Quantitative stable-isotope probing (qSIP)

KW - Rewetting

KW - Soil bacteria

KW - Turnover

UR - http://www.scopus.com/inward/record.url?scp=85041227380&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85041227380&partnerID=8YFLogxK

U2 - 10.1002/ecs2.2090

DO - 10.1002/ecs2.2090

M3 - Article

VL - 9

JO - Ecosphere

JF - Ecosphere

SN - 2150-8925

IS - 1

M1 - e02090

ER -