Cautionary notes on the use of co-occurrence networks in soil ecology

被引:117
作者
Goberna, Marta [1 ]
Verdu, Miguel [2 ]
机构
[1] CSIC, Inst Nacl Invest & Tecnol Agr, Dept Environm & Agron, Carretera Coruna Km 7-5, Madrid 28040, Spain
[2] CSIC, Ctr Invest Desertificac CIDE, Dept Ecol, Carretera Moncada Naquera Km 4-5, Valencia 46113, Spain
关键词
Co-occurrence patterns; Ecological interactions; Keystone taxa; Microbial networks; Network analysis; Soil microbiome; MICROBIAL INTERACTIONS; ANTIBIOTIC-RESISTANCE; ANALYSIS REVEALS; BACTERIAL; COMMUNITIES; PATTERNS; DYNAMICS; ABUNDANCE; GENES;
D O I
10.1016/j.soilbio.2021.108534
中图分类号
S15 [土壤学];
学科分类号
0903 ; 090301 ;
摘要
Soil ecology is witnessing exponential growth in the number of studies using co-occurrence network analysis. Researchers reconstruct networks based on the co-occurrence of taxa or genes across soil samples at a wide range of geographic scales from single aggregates to the whole planet and taxonomic scopes, some studies targeting specific taxa or guilds to others surveying the whole microbiome as well as micro-and mesofauna. Co-occurrence networks can be very useful to extract simple patterns from complex datasets. Applications include the detection of abiotic and biotic factors that determine community structure, the identification of keystone taxa and their relationship to specific soil functions, and the inference of mechanisms of community assembly. However, networks are more and more often misused and serve as mere graphic tools with no attempt at hypothesis testing. In this perspectives article, we first review the main usage of co-occurrence network analysis in soil ecology during the last decade. We then discuss the applications and caveats of network analysis in soil ecology, leaving apart strictly methodological aspects of network reconstruction, which is beyond the focus of this article. Finally, we include recommendation guidelines - such as the possibility of informing networks with geographic, environmental and/or phylogenetic information - with the hope that this will facilitate network analysis to become a useful tool that helps elucidate meaningful patterns in soil ecology.
引用
收藏
页数:10
相关论文
共 90 条
[1]   The geographic scaling of biotic interactions [J].
Araujo, Miguel B. ;
Rozenfeld, Alejandro .
ECOGRAPHY, 2014, 37 (05) :406-415
[2]   How sample heterogeneity can obscure the signal of microbial interactions [J].
Armitage, David W. ;
Jones, Stuart E. .
ISME JOURNAL, 2019, 13 (11) :2639-2646
[3]   Keystone taxa as drivers of microbiome structure and functioning [J].
Banerjee, Samiran ;
Schlaeppi, Klaus ;
van der Heijden, Marcel G. A. .
NATURE REVIEWS MICROBIOLOGY, 2018, 16 (09) :567-576
[4]   Network analysis reveals functional redundancy and keystone taxa amongst bacterial and fungal communities during organic matter decomposition in an arable soil [J].
Banerjee, Samiran ;
Kirkby, Clive A. ;
Schmutter, Dione ;
Bissett, Andrew ;
Kirkegaard, John A. ;
Richardson, Alan E. .
SOIL BIOLOGY & BIOCHEMISTRY, 2016, 97 :188-198
[5]   Using network analysis to explore co-occurrence patterns in soil microbial communities [J].
Barberan, Albert ;
Bates, Scott T. ;
Casamayor, Emilio O. ;
Fierer, Noah .
ISME JOURNAL, 2012, 6 (02) :343-351
[6]   Fundamental contradictions among observational and experimental estimates of non-trophic species interactions [J].
Barner, Allison K. ;
Coblentz, Kyle E. ;
Hacker, Sally D. ;
Menge, Bruce A. .
ECOLOGY, 2018, 99 (03) :557-566
[7]   Microbial networks inferred from environmental DNA data for biomonitoring ecosystem change: Strengths and pitfalls [J].
Barroso-Bergada, Didac ;
Pauvert, Charlie ;
Vallance, Jessica ;
Deliere, Laurent ;
Bohan, David A. ;
Buee, Marc ;
Vacher, Corinne .
MOLECULAR ECOLOGY RESOURCES, 2021, 21 (03) :762-780
[8]   Deciphering microbial interactions and detecting keystone species with co-occurrence networks [J].
Berry, David ;
Widder, Stefanie .
FRONTIERS IN MICROBIOLOGY, 2014, 5
[9]   Co-occurrence is not evidence of ecological interactions [J].
Blanchet, F. Guillaume ;
Cazelles, Kevin ;
Gravel, Dominique .
ECOLOGY LETTERS, 2020, 23 (07) :1050-1063
[10]   A framework for evaluating the influence of climate, dispersal limitation, and biotic interactions using fossil pollen associations across the late Quaternary [J].
Blois, Jessica L. ;
Gotelli, Nicholas J. ;
Behrensmeyer, Anna K. ;
Faith, J. Tyler ;
Lyons, S. Kathleen ;
Williams, John W. ;
Amatangelo, Kathryn L. ;
Bercovici, Antoine ;
Du, Andrew ;
Eronen, Jussi T. ;
Graves, Gary R. ;
Jud, Nathan ;
Labandeira, Conrad ;
Looy, Cindy V. ;
McGill, Brian ;
Patterson, David ;
Potts, Richard ;
Riddle, Brett ;
Terry, Rebecca ;
Toth, Aniko ;
Villasenor, Amelia ;
Wing, Scott .
ECOGRAPHY, 2014, 37 (11) :1095-1108