Michael S. Strickland

Global patterns in belowground communities

Although belowground ecosystems have been studied extensively and soil biota play integral roles in biogeochemical processes, surprisingly we have a limited understanding of global patterns in belowground biomass and community structure. To address this critical gap, we conducted a meta-analysis of published data (> 1300 datapoints) to compare belowground plant, microbial and faunal biomass across seven of the major biomes on Earth. We also assembled data to assess biome-level patterns in belowground microbial community composition. Our analysis suggests that variation in microbial biomass is predictable across biomes, with microbial biomass carbon representing 0.6-1.1% of soil organic carbon (r(2) = 0.91) and 1-20% of total plant biomass carbon (r(2) = 0.42). Approximately 50% of total animal biomass can be found belowground and soil faunal biomass represents < 4% of microbial biomass across all biomes. The structure of belowground microbial communities is also predictable: bacterial community composition and fungal : bacterial gene ratios can be predicted reasonably well from soil pH and soil C : N ratios respectively. Together these results identify robust patterns in the structure of belowground microbial and faunal communities at broad scales which may be explained by universal mechanisms that regulate belowground biota across biomes.

Testing the functional significance of microbial community composition

A critical assumption underlying terrestrial ecosystem models is that soil microbial communities, when placed in a common environment, will function in an identical manner regardless of the composition of that community. Given high species diversity in microbial communities and the ability of microbes to adapt rapidly to new conditions, this assumption of functional redundancy seems plausible. We test the assumption by comparing litter decomposition rates in experimental microcosms inoculated with distinct microbial communities. We find that rates of carbon dioxide production from litter decomposition were dependent upon the microbial inoculum, with differences in the microbial community alone accounting for substantial (approximately 20%) variation in total carbon mineralized. Communities that shared a common history with a given foliar litter exhibited higher decomposition rates when compared to communities foreign to that habitat. Our results suggest that the implicit assumption in ecosystem models (i.e., microbial communities in the same environment are functionally equivalent) is incorrect. To predict accurately how biogeochemical processes will respond to global change may require consideration of the community composition and/or adaptation of microbial communities to past resource environments.

Fear of Predation Slows Plant-Litter Decomposition

Fear Itself A direct connection exists between aboveground communities and belowground soil microbiota: Soil microbes break down detrital inputs from above. Generally, it has been assumed that this relationship is largely driven by the soil community and the quality of the unconsumed plant-matter that makes up the majority of detritus in most ecosystems. However, Hawlena et al. (p. 1434) found that grasshoppers exposed to the threat of spider predation have an altered carbon to nitrogen ratio. When these grasshopper carcasses were subsequently integrated into the plant litter, they significantly slowed the decomposition rate, although there was no impact on the rate of decomposition of the grasshoppers themselves. Thus, the mere presence of predators, and the stress they impose, can have cascading trophic impacts and even influence the process of decomposition. The risk of being eaten by spiders changes the elemental composition of grasshoppers, which affects soil microbes. Aboveground consumers are believed to affect ecosystem functioning by regulating the quantity and quality of plant litter entering the soil. We uncovered a pathway whereby terrestrial predators regulate ecosystem processes via indirect control over soil community function. Grasshopper herbivores stressed by spider predators have a higher body carbon-to-nitrogen ratio than do grasshoppers raised without spiders. This change in elemental content does not slow grasshopper decomposition but perturbs belowground community function, decelerating the subsequent decomposition of plant litter. This legacy effect of predation on soil community function appears to be regulated by the amount of herbivore protein entering the soil.

Relic DNA is abundant in soil and obscures estimates of soil microbial diversity

Extracellular DNA from dead microorganisms can persist in soil for weeks to years1–3. Although it is implicitly assumed that the microbial DNA recovered from soil predominantly represents intact cells, it is unclear how extracellular DNA affects molecular analyses of microbial diversity. We examined a wide range of soils using viability PCR based on the photoreactive DNA-intercalating dye propidium monoazide4. We found that, on average, 40% of both prokaryotic and fungal DNA was extracellular or from cells that were no longer intact. Extracellular DNA inflated the observed prokaryotic and fungal richness by up to 55% and caused significant misestimation of taxon relative abundances, including the relative abundances of taxa integral to key ecosystem processes. Extracellular DNA was not found in measurable amounts in all soils; it was more likely to be present in soils with low exchangeable base cation concentrations, and the effect of its removal on microbial community structure was more profound in high-pH soils. Together, these findings imply that this ‘relic DNA’ remaining in soil after cell death can obscure treatment effects, spatiotemporal patterns and relationships between microbial taxa and environmental conditions.

Empirical evidence that soil carbon formation from plant inputs is positively related to microbial growth

Plant-carbon inputs to soils in the form of dissolved sugars, organic acids and amino acids fuel much of heterotrophic microbial activity belowground. Initial residence times of these compounds in the soil solution are on the order of hours, with microbial uptake a primary removal mechanism. Through microbial biosynthesis, the dissolved compounds become dominant precursors for formation of stable soil organic carbon. How the chemical class (e.g. sugar) of a dissolved compound influences stabilization in field soils is unknown and predictions from our understanding of microbial metabolism, turnover and identity are contradictory. We show that soil carbon formation, from chronic amendments of dissolved compounds to fertilized and unfertilized grasslands, is 2.4-times greater from a sugar than an amino acid. Formation rates are negatively correlated with respiration rates of the compounds, and positively correlated with their recovery in microbial biomass. These relationships suggest that the efficiency of microbial growth on a compound is positively related to formation rates of soil organic carbon. Fertilization does not alter these findings, but together nitrogen and phosphorus additions reduce soil carbon formation. Our results highlight the need to consider both nutrient enrichment and global-change induced shifts in the form of dissolved root inputs to soils to predict future soil carbon stocks and hence phenomena such as climate warming and food security to which these stock sizes are intimately tied.

Trophic cascade alters ecosystem carbon exchange

Trophic cascades—the indirect effects of carnivores on plants mediated by herbivores—are common across ecosystems, but their influence on biogeochemical cycles, particularly the terrestrial carbon cycle, are largely unexplored. Here, using a 13C pulse-chase experiment, we demonstrate how trophic structure influences ecosystem carbon dynamics in a meadow system. By manipulating the presence of herbivores and predators, we show that even without an initial change in total plant or herbivore biomass, the cascading effects of predators in this system begin to affect carbon cycling through enhanced carbon fixation by plants. Prolonged cascading effects on plant biomass lead to slowing of carbon loss via ecosystem respiration and reallocation of carbon among plant aboveground and belowground tissues. Consequently, up to 1.4-fold more carbon is retained in plant biomass when carnivores are present compared with when they are absent, owing primarily to greater carbon storage in grass and belowground plant biomass driven largely by predator nonconsumptive (fear) effects on herbivores. Our data highlight the influence that the mere presence of predators, as opposed to direct consumption of herbivores, can have on carbon uptake, allocation, and retention in terrestrial ecosystems.

Disentangling the mechanisms underlying functional differences among decomposer communities

Summary 1. Home-field advantage (HFA) is a commonly used sports analogy, which has seen recent growth within the ecosystem ecology literature. It is most often invoked in litter transplant studies, where local adaptation (HFA) explains higher decomposition rates of leaf litter on ‘home’ soil communities. 2. In exploring the mechanisms driving functional differences among soil decomposer communities, a consistent quantitative framework is lacking. 3. We review methods for calculating HFA, propose a consolidated regression approach and demonstrate why HFA must be calculated along with a new ‘ability’ metric if we are to test definitively the competing hypotheses that soil decomposer communities are functionally equivalent versus dissimilar. We demonstrate that qualitative interpretations of HFA differ when the ability of a decomposer community is calculated simultaneously with HFA. For example, communities may differ in their ability to degrade litter in the absence of HFA, or apparent HFA may instead be caused by differing abilities, changing our ecological interpretation of the factors generating functional differences among decomposer communities. 4. Synthesis: We propose a single, statistical approach to help evaluate how and why soil decomposer communities differ in functional abilities. Our approach should help formalize mechanistic interpretations of why soil community composition commonly influences litter decomposition rates.

Metagenomic Analysis of Antibiotic Resistance Genes in Dairy Cow Feces following Therapeutic Administration of Third Generation Cephalosporin

Although dairy manure is widely applied to land, it is relatively understudied compared to other livestock as a potential source of antibiotic resistance genes (ARGs) to the environment and ultimately to human pathogens. Ceftiofur, the most widely used antibiotic used in U.S. dairy cows, is a 3rd generation cephalosporin, a critically important class of antibiotics to human health. The objective of this study was to evaluate the effect of typical ceftiofur antibiotic treatment on the prevalence of ARGs in the fecal microbiome of dairy cows using a metagenomics approach. β-lactam ARGs were found to be elevated in feces from Holstein cows administered ceftiofur (n = 3) relative to control cows (n = 3). However, total numbers of ARGs across all classes were not measurably affected by ceftiofur treatment, likely because of dominance of unaffected tetracycline ARGs in the metagenomics libraries. Functional analysis via MG-RAST further revealed that ceftiofur treatment resulted in increases in gene sequences associated with “phages, prophages, transposable elements, and plasmids”, suggesting that this treatment also enriched the ability to horizontally transfer ARGs. Additional functional shifts were noted with ceftiofur treatment (e.g., increase in genes associated with stress, chemotaxis, and resistance to toxic compounds; decrease in genes associated with metabolism of aromatic compounds and cell division and cell cycle), along with measureable taxonomic shifts (increase in Bacterioidia and decrease in Actinobacteria). This study demonstrates that ceftiofur has a broad, measureable and immediate effect on the cow fecal metagenome. Given the importance of 3rd generation cephalospirins to human medicine, their continued use in dairy cattle should be carefully considered and waste treatment strategies to slow ARG dissemination from dairy cattle manure should be explored.

Native, insect herbivore communities derive a significant proportion of their carbon from a widespread invader of forest understories.

Research on natural enemies demonstrates the potential for exotic plants to be integrated into foodwebs through the activities of native herbivores. The quantitative importance of exotics as a food resource to herbivores is more difficult to ascertain. In addition, some widespread invaders appear to have minimal herbivore loads. Microstegium vimineum is one example. It is an annual, C4 grass that invades forest understories and is widespread across the eastern US. Its invasion alters the structure and composition of forests. We sampled invertebrates in a tree-canopy gap and under canopy area, and used the unique carbon isotope value of M. vimineum to estimate the quantitative importance of the invader as a food resource relative to native plants. Seven of the eight invertebrate species derived on average >35% of their biomass carbon from M. vimineum, and some individuals representing both ‘chewing’ and ‘sucking’ feeding guilds derived their biomass carbon exclusively from M. vimineum. Our results show that M. vimineum can be a significant food resource for a multi-species, multi-guild, assemblage of native, invertebrate herbivores. Future work is required to assess whether M. vimineum is acquiring herbivores in other parts of its introduced range, and if so what might be the ecological consequences.

Biofuel intercropping effects on soil carbon and microbial activity

Biofuels will help meet rising demands for energy and, ideally, limit climate change associated with carbon losses from the biosphere to atmosphere. Biofuel management must therefore maximize energy production and maintain ecosystem carbon stocks. Increasingly, there is interest in intercropping biofuels with other crops, partly because biofuel production on arable land might reduce availability and increase the price of food. One intercropping approach involves growing biofuel grasses in forest plantations. Grasses differ from trees in both their organic inputs to soils and microbial associations. These differences are associated with losses of soil carbon when grasses become abundant in forests. We investigated how intercropping switchgrass (Panicum virgalum), a major candidate for cellulosic biomass production, in loblolly pine (Pinus taeda) plantations affects soil carbon, nitrogen, and microbial dynamics. Our design involved four treatments: two pine management regimes where harvest residues (i.e., biomass) were left in place or removed, and two switchgrass regimes where the grass was grown with pine under the same two biomass scenarios (left or removed). Soil variables were measured in four 1-ha replicate plots in the first and second year following switchgrass planting. Under switchgrass intercropping, pools of mineralizable and particulate organic matter carbon were 42% and 33% lower, respectively. These declines translated into a 21% decrease in total soil carbon in the upper 15 cm of the soil profile, during early stand development. The switchgrass effect, however, was isolated to the interbed region where switchgrass is planted. In these regions, switchgrass-induced reductions in soil carbon pools with 29%, 43%, and 24% declines in mineralizable, particulate, and total soil carbon, respectively. Our results support the idea that grass inputs to forests can prime the activity of soil organic carbon degrading microbes, leading to net reductions in stocks of soil carbon. Active microbial biomass, however, is higher under switchgrass, and this microbial biomass is a dominant precursor of soil carbon formation. Future studies need to investigate soil carbon dynamics throughout the lifetime of intercropping rotations to evaluate whether increases in microbial biomass can offset initial declines in soil carbon, and hence, maintain ecosystem carbon stocks.