Articles | Volume 8, issue 1
https://doi.org/10.5194/soil-8-297-2022
© Author(s) 2022. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/soil-8-297-2022
© Author(s) 2022. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Original research article
| 
08 Apr 2022
Original research article |
| 08 Apr 2022
Lower functional redundancy in “narrow” than “broad” functions in global soil metagenomics
State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen
University, Shenzhen, 518107, China
Kayan Ma
State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen
University, Shenzhen, 518107, China
Yu Huang
State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen
University, Shenzhen, 518107, China
Qi Fu
State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen
University, Shenzhen, 518107, China
Yingbo Qiu
State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen
University, Shenzhen, 518107, China
Jiajiang Lin
CORRESPONDING AUTHOR
Fujian Key Laboratory of Pollution Control and Resource Reuse, College
of Environmental Science and Engineering, Fujian Normal University, Fuzhou,
350007, China
Christopher W. Schadt
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN
37831, USA
Department of Microbiology, University of Tennessee, Knoxville, TN
37996, USA
Hao Chen
State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen
University, Shenzhen, 518107, China
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Cited articles
Allison, S. D. and Martiny, J. B.: Resistance, resilience, and redundancy
in microbial communities, P. Natl. Acad. Sci. USA,
105, 11512–11519, 2008.
Babicki, S., Arndt, D., Marcu, A., Liang, Y., Grant, J. R., Maciejewski, A.,
and Wishart, D. S.: Heatmapper: web-enabled heat mapping for all, Nucleic
Acids Res., 44, W147–W153, 2016.
Balser, T. C., Kinzig, A. P., and Firestone, M. K.: Linking soil microbial
communities and ecosystem functioning, in: The functional consequences of
biodiversity: empirical progress and theoretical extensions, edited by: Kinzig, A. P., Pacala, S., and Tilman, D., Princeton University Press, 265–293, https://doi.org/10.1515/9781400847303.265, 2002.
Banerjee, S., Kirkby, C. A., Schmutter, D., Bissett, A., Kirkegaard, J. A.,
and Richardson, A. E.: Network analysis reveals functional redundancy and
keystone taxa amongst bacterial and fungal communities during organic matter
decomposition in an arable soil, Soil Biol. Biochem., 97, 188–198,
2016.
Bastida, F., Torres, I. F., Moreno, J. L., Baldrian, P., Ondoño, S.,
Ruiz-Navarro, A., Hernández, T., Richnow, H. H., Starke, R., and
García, C.: The active microbial diversity drives ecosystem
multifunctionality and is physiologically related to carbon availability in
Mediterranean semi-arid soils, Mol. Ecol., 25, 4660–4673, 2016.
Beier, S., Shen, D., Schott, T., and Jürgens, K.: Metatranscriptomic
data reveal the effect of different community properties on multifunctional
redundancy, Mol. Ecol., 26, 6813–6826, 2017.
Bryant, C., Wheeler, N., Rubel, F., and French, R.: kgc: Koeppen–Geiger
climatic zones, R package version 1.0.0.2, https://cran.r-project.org/package=kgc (last access: 10 September 2019), 2017.
Clarke, K. and Gorley, R.: Getting started with PRIMER v7, PRIMER-E:
Plymouth, Plymouth Marine Laboratory, http://updates.primer-e.com/primer7/manuals/Getting_started_with_PRIMER_7.pdf (last access: 10 September 2019), 2015.
Cole, J. R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R. J.,
Kulam-Syed-Mohideen, A., McGarrell, D. M., Marsh, T., and Garrity, G. M.:
The Ribosomal Database Project: improved alignments and new tools for rRNA
analysis, Nucleic Acids Res., 37, D141–D145, 2008.
Crowther, T. W., Van den Hoogen, J., Wan, J., Mayes, M. A., Keiser, A., Mo,
L., Averill, C., and Maynard, D. S.: The global soil community and its
influence on biogeochemistry, Science, 365, eaav0550, https://doi.org/10.1126/science.aav0550, 2019.
Delgado-Baquerizo, M., Maestre, F. T., Reich, P. B., Jeffries, T. C.,
Gaitan, J. J., Encinar, D., Berdugo, M., Campbell, C. D., and Singh, B. K.:
Microbial diversity drives multifunctionality in terrestrial ecosystems,
Nat. Commun., 7, 10541, https://doi.org/10.1038/ncomms10541, 2016a.
Delgado-Baquerizo, M., Giaramida, L., Reich, P. B., Khachane, A. N.,
Hamonts, K., Edwards, C., Lawton, L. A., and Singh, B. K.: Lack of
functional redundancy in the relationship between microbial diversity and
ecosystem functioning, J. Ecol., 104, 936–946, 2016b.
Delgado-Baquerizo, M., Oliverio, A. M., Brewer, T. E.,
Benavent-González, A., Eldridge, D. J., Bardgett, R. D., Maestre, F. T.,
Singh, B. K., and Fierer, N.: A global atlas of the dominant bacteria found
in soil, Science, 359, 320–325, 2018.
Deng, Y., Jiang, Y.-H., Yang, Y., He, Z., Luo, F., and Zhou, J.: Molecular
ecological network analyses, BMC Bioinformatics, 13, 113, https://doi.org/10.1186/1471-2105-13-113, 2012.
Desantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L.,
Keller, K., Huber, T., Dalevi, D., Hu, P., and Andersen, G. L.: Greengenes,
a chimera-checked 16S rRNA gene database and workbench compatible with ARB,
Appl. Environ. Microbiol., 72, 5069–5072, 2006.
Faust, K. and Raes, J.: Microbial interactions: from networks to models,
Nat. Rev. Microbiol., 10, 538, https://doi.org/10.1038/ismej.2011.159, 2012.
Fick, S. E. and Hijmans, R. J.: WorldClim 2: new 1-km spatial resolution
climate surfaces for global land areas, Int. J.
Climatol., 37, 4302–4315, 2017.
Fierer, N., Lauber, C. L., Ramirez, K. S., Zaneveld, J., Bradford, M. A.,
and Knight, R.: Comparative metagenomic, phylogenetic and physiological
analyses of soil microbial communities across nitrogen gradients, ISME
J., 6, 1007, https://doi.org/10.1038/nrmicro2832, 2012.
Fierer, N., Ladau, J., Clemente, J. C., Leff, J. W., Owens, S. M., Pollard,
K. S., Knight, R., Gilbert, J. A., and McCulley, R. L.: Reconstructing the
microbial diversity and function of pre-agricultural tallgrass prairie soils
in the United States, Science, 342, 621–624, 2013.
Galand, P. E., Pereira, O., Hochart, C., Auguet, J. C., and Debroas, D.: A
strong link between marine microbial community composition and function
challenges the idea of functional redundancy, ISME J., 12,
2470–2478, https://doi.org/10.1038/s41396-018-0158-1, 2018.
Galperin, M. Y., Makarova, K. S., Wolf, Y. I., and Koonin, E. V.: Expanded
microbial genome coverage and improved protein family annotation in the COG
database, Nucleic Acids Res., 43, D261–D269, 2014.
Gamfeldt, L., Hillebrand, H., and Jonsson, P. R.: Multiple functions
increase the importance of biodiversity for overall ecosystem functioning,
Ecology, 89, 1223–1231, 2008.
Gans, J., Wolinsky, M., and Dunbar, J.: Computational improvements reveal
great bacterial diversity and high metal toxicity in soil, Science, 309,
1387–1390, 2005.
Gloor, G. B., Macklaim, J. M., Pawlowsky-Glahn, V., and Egozcue, J. J.:
Microbiome datasets are compositional: and this is not optional, Front.
Microbiol., 8, 2224, https://doi.org/10.3389/fmicb.2017.02224, 2017.
Guimerà, R. and Nunes Amaral, L. A.: Functional cartography of complex
metabolic networks, Nature, 433, 895–900, https://doi.org/10.1038/nature03288, 2005.
Guimerà, R., Sales-Pardo, M., and Amaral, L. A. N.: Classes of complex
networks defined by role-to-role connectivity profiles, Nat. Phys., 3,
63–69, https://doi.org/10.1038/nphys489, 2007.
Hall, E. K., Bernhardt, E. S., Bier, R. L., Bradford, M. A., Boot, C. M.,
Cotner, J. B., del Giorgio, P. A., Evans, S. E., Graham, E. B., and Jones,
S. E.: Understanding how microbiomes influence the systems they inhabit,
Nat. Microbiol., 3, 977–982, 2018.
Heberle, H., Meirelles, G. V., da Silva, F. R., Telles, G. P., and Minghim,
R.: InteractiVenn: a web-based tool for the analysis of sets through Venn
diagrams, BMC Bioinformatics, 16, 169, https://doi.org/10.1186/s12859-015-0611-3, 2015.
Hector, A. and Bagchi, R.: Biodiversity and ecosystem multifunctionality,
Nature, 448, 188–190, https://doi.org/10.1038/nature05947, 2007.
Hijmans, R. J., Van Etten, J., Cheng, J., Mattiuzzi, M., Sumner, M.,
Greenberg, J. A., Lamigueiro, O. P., Bevan, A., Racine, E. B., and
Shortridge, A.: Package “raster”, R package, 734, https://cran.r-project.org/package=raster (last access: 10 September 2019), 2015.
Huerta-Cepas, J., Szklarczyk, D., Forslund, K., Cook, H., Heller, D.,
Walter, M. C., Rattei, T., Mende, D. R., Sunagawa, S., and Kuhn, M.: eggNOG
4.5: a hierarchical orthology framework with improved functional annotations
for eukaryotic, prokaryotic and viral sequences, Nucleic Acids Res., 44,
D286–D293, 2015.
Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M., and Tanabe, M.: KEGG
as a reference resource for gene and protein annotation, Nucleic Acids
Res., 44, D457–D462, 2015.
Kottek, M., Grieser, J., Beck, C., Rudolf, B., and Rubel, F.: World map of
the Köppen-Geiger climate classification updated, Meteorol.
Z., 15, 259–263, 2006.
Leff, J. W., Jones, S. E., Prober, S. M., Barberán, A., Borer, E. T.,
Firn, J. L., Harpole, W. S., Hobbie, S. E., Hofmockel, K. S., and Knops, J.
M.: Consistent responses of soil microbial communities to elevated nutrient
inputs in grasslands across the globe, P. Natl. Acad.
Sci. USA, 112, 10967–10972, 2015.
Louca, S., Parfrey, L. W., and Doebeli, M.: Decoupling function and taxonomy
in the global ocean microbiome, Science, 353, 1272–1277, 2016.
Louca, S., Jacques, S. M., Pires, A. P., Leal, J. S., Srivastava, D. S.,
Parfrey, L. W., Farjalla, V. F., and Doebeli, M.: High taxonomic variability
despite stable functional structure across microbial communities, Nat.
Ecol. Evol., 1, 0015, https://doi.org/10.1038/s41559-016-0015, 2017.
Louca, S., Polz, M. F., Mazel, F., Albright, M. B., Huber, J. A., O'Connor,
M. I., Ackermann, M., Hahn, A. S., Srivastava, D. S., and Crowe, S. A.:
Function and functional redundancy in microbial systems, Nat. Ecol.
Evol., 2, 936–943, https://doi.org/10.1038/s41559-018-0519-1, 2018.
McGill, B. J., Enquist, B. J., Weiher, E., and Westoby, M.: Rebuilding
community ecology from functional traits, Trend. Ecol. Evol.,
21, 178–185, 2006.
Meyer, F., Paarmann, D., D'Souza, M., Olson, R., Glass, E. M., Kubal, M.,
Paczian, T., Rodriguez, A., Stevens, R., and Wilke, A.: The metagenomics
RAST server – a public resource for the automatic phylogenetic and functional
analysis of metagenomes, BMC Bioinformatics, 9, 386, https://doi.org/10.1186/1471-2105-9-386, 2008.
Moulin, L., Munive, A., Dreyfus, B., and Boivin-Masson, C.: Nodulation of
legumes by members of the β-subclass of Proteobacteria, Nature, 411,
948–950, https://doi.org/10.1038/35082070, 2001.
Olesen, J. M., Bascompte, J., Dupont, Y. L., and Jordano, P.: The smallest
of all worlds: Pollination networks, J. Theor. Biol., 240,
270–276, https://doi.org/10.1016/j.jtbi.2005.09.014, 2006.
Olesen, J. M., Bascompte, J., Dupont, Y. L., and Jordano, P.: The modularity
of pollination networks, P. Natl. Acad. Sci. USA,
104, 19891–19896, 2007.
Overbeek, R., Olson, R., Pusch, G. D., Olsen, G. J., Davis, J. J., Disz, T.,
Edwards, R. A., Gerdes, S., Parrello, B., and Shukla, M.: The SEED and the
Rapid Annotation of microbial genomes using Subsystems Technology (RAST),
Nucleic Acids Res., 42, D206–D214, 2013.
Pan, Y., Cassman, N., de Hollander, M., Mendes, L. W., Korevaar, H., Geerts,
R. H., van Veen, J. A., and Kuramae, E. E.: Impact of long-term N, P, K, and
NPK fertilization on the composition and potential functions of the
bacterial community in grassland soil, FEMS Microbiol. Ecol., 90,
195–205, 2014.
Peter, H., Beier, S., Bertilsson, S., Lindström, E. S., Langenheder, S.,
and Tranvik, L. J.: Function-specific response to depletion of microbial
diversity, ISME J., 5, 351–361, https://doi.org/10.1038/ismej.2010.119, 2011.
Philippot, L., Spor, A., Hénault, C., Bru, D., Bizouard, F., Jones, C.
M., Sarr, A., and Maron, P.-A.: Loss in microbial diversity affects nitrogen
cycling in soil, ISME J., 7, 1609–1619, https://doi.org/10.1038/ismej.2013.34, 2013.
Pruesse, E., Quast, C., Knittel, K., Fuchs, B. M., Ludwig, W., Peplies, J.,
and Glöckner, F. O.: SILVA: a comprehensive online resource for quality
checked and aligned ribosomal RNA sequence data compatible with ARB, Nucleic
Acids Res., 35, 7188–7196, 2007.
Ramírez-Flandes, S., González, B., and Ulloa, O.: Redox traits
characterize the organization of global microbial communities, P. Natl. Acad. Sci., 116, 3630–3635, 2019.
Rivett, D. W. and Bell, T.: Abundance determines the functional role of
bacterial phylotypes in complex communities, Nat. Microbiol., 3, 767–772, https://doi.org/10.1038/s41564-018-0180-0,
2018.
Rocca, J. D., Hall, E. K., Lennon, J. T., Evans, S. E., Waldrop, M. P.,
Cotner, J. B., Nemergut, D. R., Graham, E. B., and Wallenstein, M. D.:
Relationships between protein-encoding gene abundance and corresponding
process are commonly assumed yet rarely observed, ISME J., 9, 1693–1699, https://doi.org/10.1038/ismej.2014.252,
2015.
Rosenfeld, J. S.: Functional redundancy in ecology and conservation, Oikos,
98, 156–162, 2002.
Rousk, J., Brookes, P. C., and Bååth, E.: Contrasting soil pH
effects on fungal and bacterial growth suggest functional redundancy in
carbon mineralization, Appl. Environ. Microbiol., 75, 1589–1596, 2009.
Schimel, J.: Ecosystem consequences of microbial diversity and community
structure, in: Arctic and alpine biodiversity: patterns, causes and
ecosystem consequences, Springer, 239–254, https://doi.org/10.1007/978-3-642-78966-3_17, 1995.
Schimel, J. P. and Gulledge, J.: Microbial community structure and global
trace gases, Glob. Change Biol., 4, 745–758, 1998.
Segata, N., Izard, J., Waldron, L., Gevers, D., Miropolsky, L., Garrett, W.
S., and Huttenhower, C.: Metagenomic biomarker discovery and explanation,
Genome Biol., 12, R60, https://doi.org/10.1186/gb-2011-12-6-r60, 2011.
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D.,
Amin, N., Schwikowski, B., and Ideker, T.: Cytoscape: a software environment
for integrated models of biomolecular interaction networks, Genome Res.,
13, 2498–2504, 2003.
Souza, R. C., Hungria, M., Cantão, M. E., Vasconcelos, A. T. R.,
Nogueira, M. A., and Vicente, V. A.: Metagenomic analysis reveals microbial
functional redundancies and specificities in a soil under different tillage
and crop-management regimes, Appl. Soil Ecol., 86, 106–112, 2015.
Stephen, J. R., McCaig, A. E., Smith, Z., Prosser, J. I., and Embley, T. M.:
Molecular diversity of soil and marine 16S rRNA gene sequences related to
beta-subgroup ammonia-oxidizing bacteria, Appl. Environ. Microbiol., 62,
4147–4154, 1996.
Tatusova, T., Ciufo, S., Fedorov, B., O'Neill, K., and Tolstoy, I.: RefSeq
microbial genomes database: new representation and annotation strategy,
Nucleic Acids Res., 42, D553–D559, 2013.
Torsvik, V. and Øvreås, L.: Microbial diversity and function in soil:
from genes to ecosystems, Curr. Opin. Microbiol., 5, 240–245, 2002.
Tringe, S. G., Von Mering, C., Kobayashi, A., Salamov, A. A., Chen, K.,
Chang, H. W., Podar, M., Short, J. M., Mathur, E. J., and Detter, J. C.:
Comparative metagenomics of microbial communities, Science, 308, 554–557,
2005.
Wellington, E. M., Berry, A., and Krsek, M.: Resolving functional diversity
in relation to microbial community structure in soil: exploiting genomics
and stable isotope probing, Curr. Opin. Microbiol., 6, 295–301,
2003.
Wilke, A., Gerlach, W., Harrison, T., Paczian, T., Trimble, W. L., and
Meyer, F.: MG-RAST manual for version 4, revision 3, Lemont, IL, Argonne
National Laboratory, https://help.mg-rast.org/user_manual.html (last access: 10 September 2019), 2017.
Xu, X., Qiu, Y., Zhang, K., Yang, F., Chen, M., Luo, X., Yan, X., Wang, P.,
Zhang, Y., and Chen, H.: Climate warming promotes deterministic assembly of
arbuscular mycorrhizal fungal communities, Glob. Change Biol., 28, 1147–1161, 2021.
Yin, B., Crowley, D., Sparovek, G., De Melo, W. J., and Borneman, J.:
Bacterial functional redundancy along a soil reclamation gradient, Appl.
Environ. Microbiol., 66, 4361–4365, 2000.
Zhou, J., Deng, Y., Luo, F., He, Z., and Yang, Y.: Phylogenetic molecular
ecological network of soil microbial communities in response to elevated
CO2, MBio, 2, e00122–00111, 2011.
Short summary
By analyzing and generalizing microbial taxonomic and functional profiles, we provide strong evidence that the degree of soil microbial functional redundancy differs significantly between “broad” and “narrow” functions across the globe. Future sequencing efforts will likely increase our confidence in comparative metagenomes and provide time-series information to further identify to what extent microbial functional redundancy regulates dynamic ecological fluxes across space and time.
By analyzing and generalizing microbial taxonomic and functional profiles, we provide strong...
