Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe

Abstract

Soil microorganisms are critical to ecosystem functioning and the maintenance of soil fertility. However, despite global increases in the inputs of nitrogen (N) and phosphorus (P) to ecosystems due to human activities, we lack a predictive understanding of how microbial communities respond to elevated nutrient inputs across environmental gradients. Here we used high-throughput sequencing of marker genes to elucidate the responses of soil fungal, archaeal, and bacterial communities using an N and P addition experiment replicated at 25 globally distributed grassland sites. We also sequenced metagenomes from a subset of the sites to determine how the functional attributes of bacterial communities change in response to elevated nutrients. Despite strong compositional differences across sites, microbial communities shifted in a consistent manner with N or P additions, and the magnitude of these shifts was related to the magnitude of plant community responses to nutrient inputs. Mycorrhizal fungi and methanogenic archaea decreased in relative abundance with nutrient additions, as did the relative abundances of oligotrophic bacterial taxa. The metagenomic data provided additional evidence for this shift in bacterial life history strategies because nutrient additions decreased the average genome sizes of the bacterial community members and elicited changes in the relative abundances of representative functional genes. Our results suggest that elevated N and P inputs lead to predictable shifts in the taxonomic and functional traits of soil microbial communities, including increases in the relative abundances of fastergrowing, copiotrophic bacterial taxa, with these shifts likely to impact belowground ecosystems worldwide.soil bacteria | soil fungi | shotgun metagenomics | soil ecology | fertilization

Plant community and soil conditions individually affect soil microbial community assembly in experimental mesocosms

“…Crenarchaeota include ammonia oxidizers and have been suggested to play important functional roles in carbon metabolism (Kemnitz, Kolb, & Conrad, 2007) and nitrogen cycling in soils (Gubry‐Rangin, Nicol, & Prosser, 2010; Schauss et al., 2009). They are known to respond positively to N addition (Leff et al., 2015), but here, we observed a negative correlation between their relative abundance and ammonia levels. Diversity within the Crenarchaeota has also been shown to increase during primary succession (Nicol, Tscherko, Embley, & Prosser, 2005).…”

“…The three bacterial phyla that responded to vegetation treatment were Actinobacteria, Firmicutes, and Planctomycetes. Actinobacteria are generally considered to be copiotrophic and typically increase in response to soil fertilization (Leff et al., 2015; Ramirez et al., 2010), but here, we observed they were negatively correlated with ammonia levels and positively correlated with soil C:N indicating they may do well in lower nitrogen environments. The plant treatment associated variation here—highest abundance in control pools and lowest abundance in Solidago pools—may be related to their life history strategy or other nonresource‐mediated mechanisms.…”

“…We might have expected Acidobacteria, a largely oligotrophic phylum, to decrease with increasing N content (i.e., increasing topsoil content; Leff et al., 2015; Ramirez et al., 2010) and Bacteroidetes, a copiotrophic phylum (Fierer et al., 2007), to increase, but we found the opposite. Acidobacteria were negatively correlated with nitrate levels and positively correlated with ammonia, while Bacteroidetes abundance was negatively correlated with ammonia.…”

“…Euryarchaeota decreased in abundance with increasing sand content and were positively correlated with ammonia levels. This result is contrary to what we might expect given that Euryarchaeota includes N‐fixing methanogens which are at a competitive advantage under low‐nitrogen conditions (Leff et al., 2015). Our results indicate that more complicated patterns than just total nitrogen variation between our soil treatments were likely driving compositional variation in response to soil treatment.…”

“…Little is known about archaea in soils and how they may or may not behave like bacteria (although see Leff et al. (2015) for discussion of archaeal responses to N fertilization).…”