The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients
Open accessAbstract
Terrestrial ecosystems are receiving elevated inputs of nitrogen (N) from anthropogenic sources and understanding how these increases in N availability affect soil microbial communities is critical for predicting the associated effects on belowground ecosystems. We used a suite of approaches to analyze the structure and functional characteristics of soil microbial communities from replicated plots in two long-term N fertilization experiments located in contrasting systems. Pyrosequencing-based analyses of 16S rRNA genes revealed no significant effects of N fertilization on bacterial diversity, but significant effects on community composition at both sites; copiotrophic taxa (including members of the Proteobacteria and Bacteroidetes phyla) typically increased in relative abundance in the high N plots, with oligotrophic taxa (mainly Acidobacteria) exhibiting the opposite pattern. Consistent with the phylogenetic shifts under N fertilization, shotgun metagenomic sequencing revealed increases in the relative abundances of genes associated with DNA/RNA replication, electron transport and protein metabolism, increases that could be resolved even with the shallow shotgun metagenomic sequencing conducted here (average of 75 000 reads per sample). We also observed shifts in the catabolic capabilities of the communities across the N gradients that were significantly correlated with the phylogenetic and metagenomic responses, indicating possible linkages between the structure and functioning of soil microbial communities. Overall, our results suggest that N fertilization may, directly or indirectly, induce a shift in the predominant microbial life-history strategies, favoring a more active, copiotrophic microbial community, a pattern that parallels the often observed replacement of K-selected with r-selected plant species with elevated N.
Overview
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.
Integrity signals
Registry
Cites
Statistics
Verification
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.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
QIIME allows analysis of high-throughput community sequencing data
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887
Self-citationThe diversity and biogeography of soil bacterial communities
Fierer, N., & Jackson, R. B. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0507535103 · Cited by 5,711
Self-citationNitrogen cycles: Past, present, and future
Galloway, J. N., Dentener, F. J., Capone, D. G., Boyer, E. W., Howarth, R. W., Seitzinger, S. P., Asner, G. P., Cleveland, C. C., Green, P. A., Holland, E. A., et al. (2004) · Biogeochemistry · doi:10.1007/s10533-004-0370-0 · Cited by 5,315
Lauber, C. L., Hamady, M., Knight, R., & Fierer, N. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.00335-09 · Cited by 4,063
Self-citationDiet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans
Muegge, B. D., Kuczynski, J., Knights, D., Clemente, J. C., González, A., Fontana, L., Henrissat, B., Knight, R., & Gordon, J. I. (2011) · Science · doi:10.1126/science.1198719 · Cited by 1,988
Self-citationNitrogen additions and microbial biomass: a meta-analysis of ecosystem studies
Treseder, K. K. (2008) · Ecology Letters · doi:10.1111/j.1461-0248.2008.01230.x · Cited by 1,607
Functional- and abundance-based mechanisms explain diversity loss due to N fertilization
Suding, K. N., Collins, S. L., Gough, L., Clark, C., Cleland, E. E., Gross, K. L., Milchunas, D. G., & Pennings, S. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0408648102 · Cited by 1,053
Functional metagenomic profiling of nine biomes
Dinsdale, E. A., Edwards, R. A., Hall, D., Angly, F., Breitbart, M., Brulc, J. M., Furlan, M., Desnues, C., Haynes, M., Li, L., et al. (2008) · Nature · doi:10.1038/nature06810 · Cited by 980
Carbon input to soil may decrease soil carbon content.
Fontaine, S., Bardoux, G., Abbadie, L., & Mariotti, A. (2004) · Ecology Letters · doi:10.1111/j.1461-0248.2004.00579.x · Cited by 814
Cited by
Cross-biome metagenomic analyses of soil microbial communities and their functional attributes
Fierer, N., Leff, J. W., Adams, B. J., Nielsen, U. N., Bates, S. T., Lauber, C. L., Owens, S., Gilbert, J. A., Wall, D. H., & Caporaso, J. G. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1215210110 · Cited by 1,643
Self-citationScaling laws predict global microbial diversity
Locey, K. J., & Lennon, J. T. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1521291113 · Cited by 1,184
Global negative effects of nitrogen deposition on soil microbes
Zhang, T., Chen, H. Y. H., & Ruan, H. (2018) · The ISME Journal · doi:10.1038/s41396-018-0096-y · Cited by 707
Ramirez, K. S., Leff, J. W., Barberán, A., Bates, S. T., Betley, J., Crowther, T. W., Kelly, E. F., Oldfield, E. E., Shaw, E. A., Steenbock, C., et al. (2014) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2014.1988 · Cited by 423
Self-citationSpatial Ecology of Bacteria at the Microscale in Soil
Raynaud, X., & Nunan, N. (2014) · PLoS ONE · doi:10.1371/journal.pone.0087217 · Cited by 401
Metadata
- Authors
- Fierer, N., Lauber, C. L., Ramirez, K. S., Zaneveld, J., Bradford, M. A., & Knight, R.
- Venue
- The ISME Journal
- Publisher
- Oxford University Press (OUP)
- Published
- 2011-12-01
- Volume
- 6
- Issue
- 5
- Pages
- 1007-1017
- ISSN
- 1751-7362 (ISSN-L)
- 1751-7370
- OpenAlex
- W2131927212
- Cited by
- 1,866
- References
- 9
- FWCI
- 55.48
- Type
- journal article
- Language
- en
- Open access
- hybrid
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
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. https://app.cochat.ai/papers/10.1038/ismej.2011.159
- The paper
- Fierer, N., Lauber, C. L., Ramirez, K. S., Zaneveld, J., Bradford, M. A., & Knight, R. (2012). Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. The ISME Journal. https://doi.org/10.1038/ismej.2011.159
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
