Online citations, reference lists, and bibliographies.
← Back to Search

A Comparison Of The Ability Of PLFA And 16S RRNA Gene Metabarcoding To Resolve Soil Community Change And Predict Ecosystem Functions

K. Orwin, I. Dickie, R. Holdaway, J. R. Wood
Published 2018 · Biology

Cite This
Download PDF
Analyze on Scholarcy
Share
Abstract Soil bacterial community structure has traditionally been measured using phospholipid fatty acid (PLFA) profiling. However, with the development of high-throughput sequencing technologies and metabarcoding techniques, more studies are now using 16S rRNA gene metabarcoding to measure bacterial community structure. Metabarcoding provides a much greater level of detail than PLFA profiling does, but it remains unclear whether or not the two techniques have a similar ability to answer many of the common questions asked by ecologists. We test the relative ability of the two techniques to quantify differences in bacterial community structure among five land uses (natural and planted forest, unimproved and improved grasslands, and vineyards), and to predict ecosystem functions. We also test whether PLFA- and metabarcoding-based metrics indicative of microbial growth strategies are correlated to each other. We show that both techniques showed broadly similar patterns of bacterial community composition change with land use and a remarkably similar ability to predict a wide range of ecosystem functions (carbon and nutrient cycling, and responses to drought). However, they were also complementary, as each showed different strengths in discriminating land uses and predicting ecosystem functions. PLFA metrics (i.e. the gram-positive:gram-negative ratio and fungal:bacterial ratio) were strongly correlated with the equivalent 16S rRNA gene metabarcoding metrics (i.e. the gram-positive:gram-negative and oligotrophic:copiotrophic ratios), although PLFA metrics were less well correlated with the Proteobacteria:Acidobacteria ratio. For many ecological questions the two techniques thus give broadly comparable results, providing confidence in the ability of both techniques to quantify meaningful changes in bacterial communities.
This paper references
10.1111/1365-2745.12616
Direct and indirect effects of native range expansion on soil microbial community structure and function
Courtney G. Collins (2016)
10.1128/AEM.67.5.2284-2291.2001
Diversity and Seasonal Fluctuations of the Dominant Members of the Bacterial Soil Community in a Wheat Field as Determined by Cultivation and Molecular Methods
E. Smit (2001)
10.1038/ismej.2011.159
Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients
N. Fierer (2012)
10.1016/J.SOILBIO.2010.11.021
Use and misuse of PLFA measurements in soils
Å. Frostegård (2011)
10.1016/J.SOILBIO.2016.02.012
Do shifts in life strategies explain microbial community responses to increasing nitrogen in tundra soil
M. Männistö (2016)
10.1038/nrmicro2367
The ecological coherence of high bacterial taxonomic ranks
L. Philippot (2010)
10.2307/2390215
Changes in the microbial biomass and metabolic quotient during leaf litter succession in some New Zealand forest and scrubland ecosystems
D. Wardle (1993)
10.1111/j.1574-6941.2003.tb01066.x
The impact of grassland management regime on the community structure of selected bacterial groups in soils.
C. D. Clegg (2003)
10.1016/J.SOILBIO.2004.04.036
New indices for quantifying the resistance and resilience of soil biota to exogenous disturbances
K. Orwin (2004)
10.1007/s003740050533
Fatty acid patterns of phospholipids and lipopolysaccharides in the characterisation of microbial communities in soil: a review
L. Zelles (1999)
10.1016/J.MIMET.2003.08.009
Review and re-analysis of domain-specific 16S primers.
G. C. Baker (2003)
10.1016/j.tim.2010.06.005
A phylum level perspective on bacterial cell envelope architecture.
I. Sutcliffe (2010)
10.1126/SCIENCE.1094875
Ecological Linkages Between Aboveground and Belowground Biota
D. Wardle (2004)
10.3389/fmicb.2013.00265
Controls on soil microbial community stability under climate change
F. T. de Vries (2013)
10.1038/nmicrobiol.2016.242
Relic DNA is abundant in soil and obscures estimates of soil microbial diversity
Paul R. Carini (2016)
10.1007/s10482-011-9616-8
Origin of diderm (Gram-negative) bacteria: antibiotic selection pressure rather than endosymbiosis likely led to the evolution of bacterial cells with two membranes
R. Gupta (2011)
10.1073/pnas.1508382112
Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe
J. W. Leff (2015)
10.1111/1365-2435.12610
Soil microbial community structure explains the resistance of respiration to a dry–rewet cycle, but not soil functioning under static conditions
K. Orwin (2016)
10.1139/O59-099
A rapid method of total lipid extraction and purification.
Bligh Eg (1959)
10.1038/ismej.2013.104
Responses of soil bacterial and fungal communities to extreme desiccation and rewetting
R. Barnard (2013)
10.1016/J.APSOIL.2014.06.003
Soil carbon quality and nitrogen fertilization structure bacterial communities with predictable responses of major bacterial phyla
H. Cederlund (2014)
10.1016/J.SOILBIO.2016.02.003
A method for simultaneous measurement of soil bacterial abundances and community composition via 16S rRNA gene sequencing
Wenke Smets (2016)
10.1371/journal.pcbi.1002743
Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance
S. Kembel (2012)
10.1111/jam.12902
Phospholipid fatty acid profiling of microbial communities–a review of interpretations and recent applications
C. Willers (2015)
10.1038/nmeth.2604
UPARSE: highly accurate OTU sequences from microbial amplicon reads
R. Edgar (2013)
10.1111/1365-2745.12247
Microbial community composition explains soil respiration responses to changing carbon inputs along an Andes-to-Amazon elevation gradient
J. Whitaker (2014)
10.1007/BF00382522
Changes in soil fungal:bacterial biomass ratios following reductions in the intensity of management of an upland grassland
R. Bardgett (2004)
10.1038/ismej.2013.34
Loss in microbial diversity affects nitrogen cycling in soil
L. Philippot (2013)
10.1111/j.1461-0248.2011.01650.x
Evolutionary trade-offs among decomposers determine responses to nitrogen enrichment.
K. Treseder (2011)
10.1111/j.1365-294X.2011.05317.x
Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies
P. Taberlet (2012)
10.1016/J.SOILBIO.2013.02.003
Roots from beech (Fagus sylvatica L.) and ash (Fraxinus excelsior L.) differentially affect soil microorganisms and carbon dynamics
S. Cesarz (2013)
10.1111/1365-2745.12014
Relative contributions of plant traits and soil microbial properties to mountain grassland ecosystem services
K. Grigulis (2013)
10.1111/j.1469-8137.2010.03473.x
Insidious effects of sequencing errors on perceived diversity in molecular surveys.
I. Dickie (2010)
10.1002/ECS2.1997
No single driver of biodiversity: divergent responses of multiple taxa across land use types
J. R. Wood (2017)
10.1111/1574-6941.12373
Functional diversification within bacterial lineages promotes wide functional overlapping between taxonomic groups in a Mediterranean forest soil.
J. Curiel Yuste (2014)
10.1371/journal.pone.0135352
Key Edaphic Properties Largely Explain Temporal and Geographic Variation in Soil Microbial Communities across Four Biomes
K. M. Docherty (2015)
10.1016/J.SOILBIO.2011.01.016
Nitrogen losses from two grassland soils with different fungal biomass
F. T. Vries (2011)
10.1007/s13213-014-1002-0
Soil chemical properties affect the reaction of forest soil bacteria to drought and rewetting stress
Marcin Chodak (2014)
10.1016/J.PEDOBI.2006.03.003
Choice of Methods for Soil Microbial Community Analysis: PLFA Maximizes Power Compared to CLPP and PCR-Based Approaches
Philip W. Ramsey (2006)
10.1016/J.APSOIL.2015.09.001
European scale analysis of phospholipid fatty acid composition of soils to establish operating ranges
R. Francisco (2016)
10.1111/ele.12206
Climate change alters ecological strategies of soil bacteria.
S. Evans (2014)
R: A language and environment for statistical computing.
R. Team (2014)
10.1111/J.1365-2486.2012.02639.X
Consistent effects of nitrogen amendments on soil microbial communities and processes across biomes
K. S. Ramirez (2012)
10.1007/s00442-003-1419-9
Microbial community utilization of recalcitrant and simple carbon compounds: impact of oak-woodland plant communities
M. Waldrop (2003)
10.1007/s003740050554
The measurement of soil fungal:bacterial biomass ratios as an indicator of ecosystem self-regulation in temperate meadow grasslands
R. Bardgett (1999)
10.1016/J.SOILBIO.2016.02.002
Detection of short-term cropping system-induced changes to soil bacterial communities differs among four molecular characterization methods
David S. Duncan (2016)
10.1016/J.APSOIL.2012.11.004
Diversity of microorganisms from forest soils differently polluted with heavy metals
Marcin Chodak (2013)
10.1890/05-1839
Toward an ecological classification of soil bacteria.
N. Fierer (2007)



This paper is referenced by
10.3390/agronomy10060771
Long-Term Fertilization with Potassium Modifies Soil Biological Quality in K-Rich Soils
Qiu-yu Chen (2020)
10.1007/s13157-020-01287-4
Peat Properties, Dominant Vegetation Type and Microbial Community Structure in a Tropical Peatland
N. T. Girkin (2020)
10.1007/s11104-020-04739-2
Afforestation of cropland fundamentally alters the soil fungal community
J. Liu (2020)
10.1007/978-3-319-54529-5_12-1
Phospholipids as Life Markers in Geological Habitats
K. Mangelsdorf (2019)
10.1016/J.ECOLENG.2019.08.004
Ecological restoration of heavy metal-contaminated soil using Na-bentonite and green compost coupled with the cultivation of the grass Festuca arundinacea
D. Wasilkowski (2019)
10.1016/j.soilbio.2019.107577
Reduced soil respiration beneath invasive Rhododendron ponticum persists after cutting and is related to substrate quality rather than microbial community
Gruffydd Lloyd Jones (2019)
10.1016/J.JCLEPRO.2019.06.050
Environmental risk of chlorine-controlled clogging in drip irrigation system using reclaimed water: the perspective of soil health
P. Song (2019)
10.3389/fmicb.2019.01488
Soil Microbial Biomass and Fungi Reduced With Canola Introduced Into Long-Term Monoculture Wheat Rotations
Jeremy C. Hansen (2019)
10.1016/j.scitotenv.2018.12.061
Shifts of soil microbial community composition along a short-term invasion chronosequence of Spartina alterniflora in a Chinese estuary.
G. Zhang (2019)
10.1080/26395940.2020.1770628
Soil microbial community structure, metabolic potentials and influencing factors in a subtropical mountain forest ecosystem of China
Rudong Zhao (2020)
10.1016/j.scitotenv.2020.138562
Soil microbiome-induced changes in the priming effects of 13C-labelled substrates from rice residues.
Yi-Min Wang (2020)
10.1007/s11104-020-04513-4
Interspecific difference in N:P stoichiometric homeostasis drives nutrient release and soil microbial community composition during decomposition
Hanxiong Song (2020)
10.1016/j.scitotenv.2020.140602
Low-dose biochar added to sediment improves water quality and promotes the growth of submerged macrophytes.
Wei Li (2020)
10.1007/s00253-018-9120-4
Extracellular DNA in natural environments: features, relevance and applications
Magdalena Nagler (2018)
Draft Exploratory Fact-Finding Scoping Study on “Digital Sequence Information” on Genetic Resources for Food and Agriculture
Heinemann Ja (2018)
10.1371/journal.pone.0214233
Deprivation of root-derived resources affects microbial biomass but not community structure in litter and soil
Sarah L Bluhm (2019)
10.1139/cjss-2019-0088
Microbial response to carbon and nutrient additions in boreal forest soils and coversoils used during post-mining reclamation
J. Lejoly (2019)
10.1016/j.apsoil.2019.103400
Short term effects of different green manure amendments on the composition of main microbial groups and microbial activity of a submerged rice cropping system
M. I. Khan (2020)
10.1016/J.EJSOBI.2018.07.003
Changes in soil microbial community structure in relation to plant succession and soil properties during 4000 years of pedogenesis
S. Shanmugam (2018)
10.1016/j.apsoil.2019.103481
Responses of nematode, bacterial, and fungal populations to high frequency applications and increasing rates of biosolids in an agricultural soil
A. Mills (2020)
10.1016/j.catena.2020.104607
Drought stress induced increase of fungi:bacteria ratio in a poplar plantation
Yu-An Sun (2020)
10.1016/j.envexpbot.2020.104049
Sex-related responses in rhizosphere processes of dioecious Populus cathayana exposed to drought and low phosphorus stress
Zhi-Chao Xia (2020)
10.7717/peerj.7501
Improvement of subsoil physicochemical and microbial properties by short-term fallow practices
Guangyu Li (2019)
Interactive comment on “Bacterial and fungal predator – prey interactions modulate soil aggregation” by Amandine Erktan et al
A. Erktan (2020)
10.1016/J.APSOIL.2018.08.004
Response of the rhizosphere microbial community to fine root and soil parameters following Robinia pseudoacacia L. afforestation
J. Liu (2018)
10.3390/f10100828
Effects of Thinning on Microbial Community Structure in the Organic Horizon of Chinese Pine Plantations in Badaling, Beijing, China
L. Wang (2019)
10.1016/J.GEODERMA.2018.04.027
Current knowledge and future research directions to link soil health and water conservation in the Ogallala Aquifer region
Amanda Cano (2018)
10.1016/j.scitotenv.2019.134233
Time in pasture rotation alters soil microbial community composition and function and increases carbon sequestration potential in a temperate agroecosystem.
D. Lin (2019)
10.1016/J.GEODERMA.2018.11.023
Soil C/N and pH together as a comprehensive indicator for evaluating the effects of organic substitution management in subtropical paddy fields after application of high-quality amendments
Xianglin Dai (2019)
10.1016/j.scitotenv.2020.140957
How do soil microbial communities respond to fire in the intermediate term? Investigating direct and indirect effects associated with fire occurrence and burn severity.
J. Adkins (2020)
10.1007/s00248-019-01430-7
Bacterial Succession in Salt Marsh Soils Along a Short-term Invasion Chronosequence of Spartina alterniflora in the Yellow River Estuary, China
G. Zhang (2019)
10.1016/j.ecoenv.2020.111083
Effects of co-contamination of heavy metals and total petroleum hydrocarbons on soil bacterial community and function network reconstitution.
Q. Li (2020)
See more
Semantic Scholar Logo Some data provided by SemanticScholar