Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients

By Noah Fierer, C. Lauber, Kelly S. Ramirez, Jesse R. Zaneveld, M. Bradford, Rob Knight. The ISME Journal, 2011

1,662 citations recorded by the source corpus.

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.

Subfields: Ecology, Molecular Biology, Soil Science

View Paper: https://www.semanticscholar.org/paper/7fc4f04509f1507b3285f082c3e838e2bb1c4539

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Citations in the corpus

Mineral vs. Organic Amendments: Microbial Community Structure, Activity and Abundance of Agriculturally Relevant Microbes Are Driven by Long-Term Fertilization Strategies (2016, background): “On the other hand, Acidobacteria were more abundant in the unfertilized soil compared to the fertilized ones and a negative correlation between this phylum and pH has been widely reported (Rousk et al., 2010; Fierer et al., 2012; Liu et al., 2015).”
Bacterial rather than fungal community composition is associated with microbial activities and nutrient-use efficiencies in a paddy soil with short-term organic amendments (2018, background): “An explanation for this result is that nitrogen is required simultaneously when microbes decompose organic material, and the nitrogen substrates subsequently affects the predominant microbial lifehistory strategies and community composition (Fierer et al. 2012; Li et al. 2017; Sun et al. 2015).”
Chronic nitrogen additions fundamentally restructure the soil fungal community in a temperate forest (2016, background): “This type of mechanism has been proposed to operate in the structuring of bacterial communities in N-enriched soils, with N enrichment favoring copiotrophs and disfavoring oligotrophs that degrade relatively recalcitrant organic matter (Fierer et al., 2012).”
Microbial regulation of terrestrial nitrous oxide formation: understanding the biological pathways for prediction of emission rates. (2015, background): “acterize and predict the response of microbes to environmental parameters (Fierer et al. 2011).”
Scaling laws predict global microbial diversity (2016, background): “Represented in this compilation were samples from arctic aquatic systems (130 sites; MG-RAST ID: mgp138), hydrothermal vents (123 sites; MG-RAST ID: mgp327) (48), freshwater lakes in China (187 sites; MG-RAST ID: mgp2758) (49), arctic soils (44 sites; MG-RAST ID: mgp69) (50), temperate soils (84 sit”
Soil pH Determines Microbial Diversity and Composition in the Park Grass Experiment (2014, background): “The microbial phyla determined at the PGE were found to be abundant in many other soils [5–7, 23–27].”
Consistent effects of nitrogen amendments on soil microbial communities and processes across biomes (2012, background): “A similar hypothesis, the copiotrophic hypothesis, suggests that N additions decrease microbial activities by directly shifting microbial community composition (Fontaine et al. , 2003; Fierer et al. , 2007, 2011; Ramirez et al. , 2010a,b).”
The Potential of Metagenomic Approaches for Understanding Soil Microbial Processes (2014, methodology): “A few studies have used the Illumina sequencing platform for generating shotgun metagenomes from soils (Fierer et al., 2012b; Mackelprang et al., 2011), and one has combined both sequencing platforms (Uroz et al., 2013).”
Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: Differentiation by vineyard management (2016, background): “…soil microbial community structure include soil texture, pH, water content, carbon (C) and nitrogen (N) content, and C:N ratio (e.g. Cookson et al., 2006; Drenovsky et al., 2004; Fierer and Jackson, 2006; Fierer et al., 2012a; Hogberg et al., 2007; Steenwerth et al., 2008; Lauber et al., 2009).”
Microbial control over carbon cycling in soil (2012, background): “We consider the phylogenetic level at which microbes form meaningful guilds, based on overall life history strategies, and suggest that these are associated with deep evolutionary divergences, while much of the species-level diversity probably reflects functional redundancy.”
The Role of Soil Microorganisms in Plant Mineral Nutrition—Current Knowledge and Future Directions (2017, background): “From metagenomic studies that compare the effects of different fertilizer inputs, it seems apparent that certain genes are more abundant in soils with lower fertilizer inputs, such as urea metabolism (Fierer et al., 2012) and unclassified metabolic genes (Leff et al., 2015).”