CoChat
Sign Up
Cited by 60Soil Carbon and Nitrogen DynamicsMicrobial Community Ecology and PhysiologyMicrobial Fuel Cells and Bioremediation

The microbiomes and metagenomes of forest biochars

Open access
Noyce, Genevieve L., Winsborough, Carolyn, Fulthorpe, Roberta, Basiliko, Nathan·2016·Scientific Reports
DOI 10.1038/srep26425PMC PMC4876420
Open this paper in CoChat — free accountOpen PDF

Abstract

Biochar particles have been hypothesized to provide unique microhabitats for a portion of the soil microbial community, but few studies have systematically compared biochar communities to bulk soil communities. Here, we used a combination of sequencing techniques to assess the taxonomic and functional characteristics of microbial communities in four-year-old biochar particles and in adjacent soils across three forest environments. Though effects varied between sites, the microbial community living in and around the biochar particles had significantly lower prokaryotic diversity and higher eukaryotic diversity than the surrounding soil. In particular, the biochar bacterial community had proportionally lower abundance of Acidobacteria, Planctomycetes, and β-Proteobacteria taxa, compared to the soil, while the eukaryotic biochar community had an 11% higher contribution of protists belonging to the Aveolata superphylum. Additionally, we were unable to detect a consistent biochar effect on the genetic functional potential of these microbial communities for the subset of the genetic data for which we were able to assign functions through MG-RAST. Overall, these results show that while biochar particles did select for a unique subset of the biota found in adjacent soils, effects on the microbial genetic functional potential appeared to be specific to contrasting forest soil environments.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/srep26425

Cites

4 of 4 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 50

  1. Singh N.. Transformation and stabilization of pyrogenic organic matter in a temperate forest field experiment. Glob. Change Biol. 1629– 1642 doi: 10.1111/gcb.12459 (2013). 25544969 · DOI
  2. Sackett T. E.. Soil and greenhouse gas responses to biochar addition in a temperate hardwood forest. GCB Bioenergy doi: 10.1111/gcbb.12211 (2014). · DOI
  3. Thies J. E. & Rillig M. C. Chapter 6: Characteristics of biochar: Biological properties. Biochar for Environmental Management Lehmann J., Joseph S. (eds.) 85– 106 (Earthscan, 2009).
  4. Jin H. Characterization of microbial life colonizing biochar and biochar-amended soils. PhD thesis, Cornell University (2010).
  5. Noyce G. L., Basiliko N., Fulthorpe R., Sackett T. E. & Thomas S. C. Soil microbial responses over 2 years following biochar addition to a north temperate forest. Biol. Fertil. Soils doi: 10.1007/s00374-015-1010-7 1– 11 (2015). · DOI
  6. Taketani R. G.. Bacterial community composition of anthropogenic biochar and Amazonian anthrosols assessed by 16S rRNA gene 454 pyrosequencing. Antonie Van Leeuwenhoek 104, 233– 242 (2013). 23743632
  7. Xu H.-J.. Biochar impacts soil microbial community composition and nitrogen cycling in an acidic soil planted with rape. Environ. Sci. Technol. 48, 9391– 9399 (2014). 25054835
  8. Lima A. B., Muniz A. W. & Dumont M. G. Activity and abundance of methane-oxidizing bacteria in secondary forest and manioc plantations of Amazonian Dark Earth and their adjacent soils. Front. Microbiol. 5, 550 doi: 10.3389/fmicb.2014.00550 (2014). 25374565 PMC4205850 · DOI
  9. Lima A. B.. Amazonian dark earth and plant species from the Amazon region contribute to shape rhizosphere bacterial communities. Microb. Ecol. 69, 855– 866 (2014). 25103911
  10. Brossi M. J., de L., Mendes L. W., Germano M. G., Lima A. B. & Tsai S. M. Assessment of bacterial bph gene in Amazonian Dark Earth and their adjacent soils. PLos ONE 9, e99597 doi: 10.1371/journal.pone.0099597 (2014). 24927167 PMC4057261 · DOI
  11. Dinsdale E. A.. Functional metagenomic profiling of nine biomes. Nature 452, 629– 632 (2008). 18337718
  12. Fierer N.. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc. Natl. Acad. Sci. 109, 21390– 21395 (2012). 23236140 PMC3535587
  13. Fierer N.. Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J. 6, 1007– 1017 (2012). 22134642 PMC3329107
  14. Cayuela M. L.. Biochar and denitrification in soils: when, how much and why does biochar reduce N2O emissions? Sci. Rep. 3, 1732 doi: 10.1038/srep01732 (2013). 23615819 PMC3635057 · DOI · Paper page
  15. Roesch L. F. W.. Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J. 1, 283– 290 (2007). 18043639 PMC2970868
  16. Ameloot N., Graber E. R., Verheijen F. G. A. & De Neve S. Interactions between biochar stability and soil organisms: review and research needs. Eur. J. Soil Sci. 64, 379– 390 (2013).
  17. Fierer N., Bradford M. A. & Jackson R. B. Toward an ecological classification of soil bacteria. Ecology 88, 1354– 1364 (2007). 17601128
  18. DeBruyn J. M., Nixon L. T., Fawaz M. N., Johnson A. M. & Radosevich M. Global biogeography and quantitative seasonal dynamics of Gemmatimonadetes in soil. Appl. Environ. Microbiol. 77, 6295– 6300 (2011). 21764958 PMC3165389
  19. Lehmann J.. Biochar effects on soil biota: A review. Soil Biol. Biochem. 43, 1812– 1836 (2011).
  20. Dumbrell A. J., Nelson M., Helgason T., Dytham C. & Fitter A. H. Relative roles of niche and neutral processes in structuring a soil microbial community. ISME J. 4, 337– 345 (2009). 19924158
  21. De Wit R. & Bouvier T. ‘Everything is everywhere, but, the environment selects’; what did Baas Becking and Beijerinck really say? Environ. Microbiol. 8, 755– 758 (2006). 16584487
  22. Hubbell S. P. The Unified Neutral Theory of Biodiversity and Biogeography: Monographs in Population Biology. (Princeton University Press: NJ, USA, 2001).
  23. Leibold M. A. & McPeek M. A. Coexistence of the niche and neutral perspectives in community ecology. Ecology 87, 1399– 1410 (2006). 16869414
  24. Kuczynski J.. Microbial community resemblance methods differ in their ability to detect biologically relevant patterns. Nat. Methods 7, 813– 819 (2010). PMC2948603 20818378
  25. Delmont T. O.. Metagenomic mining for microbiologists. ISME J. 5, 1837– 1843 (2011). 21593798 PMC3223302
  26. Delmont T. O.. Structure, fluctuation and magnitude of a natural grassland soil metagenome. ISME J. 6, 1677– 1687 (2012). 22297556 PMC3498926
  27. Lozupone C. A., Hamady M., Kelley S. T. & Knight R. Quantitative and qualitative β diversity measures lead to different insights into factors that structure microbial communities. Appl. Environ. Microbiol. 73, 1576– 1585 (2007). 17220268 PMC1828774
  28. Loreau M.. Biodiversity and ecosystem functioning: current knowledge and future challenges. Science 294, 804– 808 (2001). 11679658
  29. Konopka A., Lindemann S. & Fredrickson J. Dynamics in microbial communities: unraveling mechanisms to identify principles. ISME J. doi: 10.1038/ismej.2014.251 (2014). PMC4478703 25526370 · DOI
  30. Philippot L.. The ecological coherence of high bacterial taxonomic ranks. Nat. Rev. Microbiol. 8, 523– 529 (2010). 20531276
  31. Reed H. E. & Martiny J. B. H. Testing the functional significance of microbial composition in natural communities. FEMS Microbiol. Ecol. 62, 161– 170 (2007). 17937673
  32. Choudoir M. J., Campbell A. N. & Buckley D. H. Grappling with Proteus: population level approaches to understanding microbial diversity. Front. Microbiol. 3, doi: 10.3389/fmicb.2012.00336 (2012). PMC3441200 23024645 · DOI
  33. Salles J. F., Le Roux X. & Poly F. Relating phylogenetic and functional diversity among denitrifiers and quantifying their capacity to predict community functioning. Front. Microbiol. 3, doi: 10.3389/fmicb.2012.00209 (2012). PMC3373147 22701450 · DOI
  34. Schimel J. P. & Schaeffer S. M. Microbial control over carbon cycling in soil. Front. Microbiol. 3, doi: 10.3389/fmicb.2012.00348 (2012). PMC3458434 23055998 · DOI
  35. de Menezes A., Clipson N. & Doyle E. Comparative metatranscriptomics reveals widespread community responses during phenanthrene degradation in soil. Environ. Microbiol. 14, 2577– 2588 (2012). 22625871
  36. Harter J.. Linking N2O emissions from biochar-amended soil to the structure and function of the N-cycling microbial community. ISME J. 8, 660– 674 (2014). 24067258 PMC3930306
  37. Fox A., Kwapinski W., Griffiths B. S. & Schmalenberger A. The role of sulfur- and phosphorus-mobilizing bacteria in biochar-induced growth promotion of Lolium perenne. FEMS Microbiol. Ecol. 90, 78– 91 (2014). 24965962
  38. He H., Qian T.-T., Liu W.-J., Jiang H. & Yu H.-Q. Biological and chemical phosphorus solubilization from pyrolytical biochar in aqueous solution. Chemosphere 113, 175– 181 (2014). 25065807
  39. DeLuca T. H., MacKenzie M. D. & Gundale M. J. Chapter 14: Biochar effects on soil nutrient transformations. Biochar for Environmental Management. Lehmann J., Joseph S. (eds.) 251– 270 (Earthscan, 2009).
  40. Lehmann J., Gaunt J. & Rondon M. Biochar sequestration in terrestrial ecosystems: A review. Mitig. Adapt. Strateg. Glob. Change 11, 395– 419 (2006).
  41. Ranjard L. & Richaume A. Quantitative and qualitative microscale distribution of bacteria in soil. Res. Microbiol. 152, 707– 716 (2001). 11686384
  42. Prosser J. I. Dispersing misconceptions and identifying opportunities for the use of ‘omics’ in soil microbial ecology. Nat. Rev. Microbiol. 13, 439– 446 (2015). 26052662
  43. Myrold D. D., Zeglin L. H. & Jansson J. K. The potential of metagenomic approaches for understanding soil microbial processes. Soil Sci. Soc. Am. J. 78, 3 doi: 10.2136/sssaj2013.07.0287dgs (2013). · DOI
  44. Gilbert J. A., Meyer F. & Bailey M. J. The future of microbial metagenomics (or is ignorance bliss?). ISME J. 5, 777– 779 (2011). 21107444 PMC3105764
  45. Pugliese S. C.. Wood ash as a forest soil amendment: the role of boiler and soil type on soil property response. Can. J. Soil Sci. doi: 10.4141/CJSS-2014-037 (2014). · DOI
  46. Caporaso J. G.. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl. Acad. Sci. 108, 4516– 4522 (2011). 20534432 PMC3063599
  47. Edgar R. C. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat. Methods 10, 996– 998 (2013). 23955772
  48. Pylro V. S.. Data analysis for 16S microbial profiling from different benchtop sequencing platforms. J. Microbiol. Methods 107, 30– 37 (2014). 25193439
  49. Lozupone C. & Knight R. UniFrac: A new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71, 8228– 8235 (2005). 16332807 PMC1317376
  50. Meyer F.. The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9, 386 doi: 10.1186/1471-2105-9-386 (2008). 18803844 PMC2563014 · DOI

Cited by

Sorted by citations

Authors
Noyce, G. L., Winsborough, C., Fulthorpe, R., & Basiliko, N.
Affiliations
University of Toronto (CA)
Corresponding author
Noyce, Genevieve L.
ORCID
Venue
Scientific Reports
Publisher
Springer Science and Business Media LLC
Published
2016-05-23
Volume
6
Issue
1
Pages
26425-26425
ISSN
2045-2322 (ISSN-L)
DOI
10.1038/srep26425
PMC
PMC4876420
OpenAlex
W2406163589
Cited by
60
References
4
Citations by year
2026: 3 · 2025: 4 · 2024: 5 · 2023: 11 · 2022: 5 · 2021: 6 · 2020: 7 · 2019: 2 · 2018: 8 · 2017: 6 · 2016: 3
FWCI
7.41
Type
journal article
Language
en
Open access
Licence
Locations
  • Scientific Reports (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
  • University of Toronto
  • Natural Sciences and Engineering Research Council of Canada
Topics
  • Life Sciences › Agricultural and Biological Sciences › Soil Science › Soil Carbon and Nitrogen Dynamics
  • Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
  • Physical Sciences › Environmental Science › Environmental Engineering › Microbial Fuel Cells and Bioremediation
Keywords
biochar, forest soils, soil microbial communities, microbial diversity, prokaryotic diversity, eukaryotic diversity, Acidobacteria, Planctomycetes, Betaproteobacteria, microbial functional potential, microhabitat
MeSH terms
Bacteria, Charcoal, Soil Microbiology, Sequence Analysis, DNA, Betaproteobacteria, Metagenome, Acidobacteria, Planctomycetales, Microbiota, Forests

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review