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.
N1 - Funding Information:
This work was supported in part by the National Science Foundation (DEB-1241094, DEB-1146449), the Department of Energy’s Biological Systems Science Division, Program in Genomic Science (DE-SC0016207), and the Technology Research Initiative Fund from the State of Arizona. Work at Lawrence Livermore National Laboratory (LLNL) was funded by the Department of Energy through the Genome Sciences Program under contracts SCW1024 and SCW1590 and performed under the auspices of LLNL under Contract DE-AC52-07NA27344. Comments from J. Cliff and two anonymous reviewers improved the manuscript.
Funding Information:
This work was supported in part by the National Science Foundation (DEB-1241094, DEB-1146449), the Department of Energy’s Biological Systems Science Division, Program in Genomic Science (DE- SC0016207), and the Technology Research Initiative Fund from the State of Arizona. Work at Lawrence Livermore National Laboratory (LLNL) was funded by the Department of Energy through the Genome Sciences Program under contracts SCW1024 and SCW1590 and performed under the auspices of LLNL under Contract DE- AC52-07NA27344. Comments from J. Cliff and two anonymous reviewers improved the manuscript.
Publisher Copyright:
© 2018 Koch et al.
PY - 2018/1
Y1 - 2018/1
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
U2 - 10.1002/ecs2.2090
DO - 10.1002/ecs2.2090
M3 - Article
AN - SCOPUS:85041227380
VL - 9
JO - Ecosphere
JF - Ecosphere
SN - 2150-8925
IS - 1
M1 - e02090
ER -