A keystone microbial enzyme for nitrogen control of soil carbon storage

Agricultural and industrial activities have increased atmospheric nitrogen (N) deposition to ecosystems worldwide. N deposition can stimulate plant growth and soil carbon (C) input, enhancing soil C storage. Changes in microbial decomposition could also influence soil C storage, yet this influence has been difficult to discern, partly because of the variable effects of added N on the microbial enzymes involved. We show, using meta-analysis, that added N reduced the activity of lignin-modifying enzymes (LMEs), and that this N-induced enzyme suppression was associated with increases in soil C. In contrast, N-induced changes in cellulase activity were unrelated to changes in soil C. Moreover, the effects of added soil N on LME activity accounted for more of the variation in responses of soil C than a wide range of other environmental and experimental factors. Our results suggest that, through responses of a single enzyme system to added N, soil microorganisms drive long-term changes in soil C accumulation. Incorporating this microbial influence on ecosystem biogeochemistry into Earth system models could improve predictions of ecosystem C dynamics.

Microbial rRNA Synthesis and Growth Compared through Quantitative Stable Isotope Probing with H218O

Growing bacteria have a high concentration of ribosomes to ensure sufficient protein synthesis, which is necessary for genome replication and cellular division. To elucidate whether metabolic activity of soil microorganisms is coupled with growth, we investigated the relationship between rRNA and DNA synthesis in a soil bacterial community using quantitative stable isotope probing (qSIP) with H218O. Most soil bacterial taxa were metabolically active and grew, and there was no significant difference between the isotopic composition of DNA and RNA extracted from soil incubated with H218O. The positive correlation between 18O content of DNA and rRNA of taxa, with a slope statistically indistinguishable from 1 (slope = 0.96; 95% confidence interval [CI], 0.90 to 1.02), indicated that few taxa made new rRNA without synthesizing new DNA. There was no correlation between rRNA-to-DNA ratios obtained from sequencing libraries and the atom percent excess (APE) 18O values of DNA or rRNA, suggesting that the ratio of rRNA to DNA is a poor indicator of microbial growth or rRNA synthesis. Our results support the notion that metabolic activity is strongly coupled to cellular division and suggest that nondividing taxa do not dominate soil metabolic activity.IMPORTANCE Using quantitative stable isotope probing of microbial RNA and DNA with H218O, we show that most soil taxa are metabolically active and grow because their nucleic acids are significantly labeled with 18O. A majority of the populations that make new rRNA also grow, which argues against the common paradigm that most soil taxa are dormant. Additionally, our results indicate that relative sequence abundance-based RNA-to-DNA ratios, which are frequently used for identifying active microbial populations in the environment, underestimate the number of metabolically active taxa within soil microbial communities.

Taxonomic patterns in the nitrogen assimilation of soil prokaryotes

Nitrogen (N) is frequently a limiting nutrient in soil; its availability can govern ecosystem functions such as primary production and decomposition. Assimilation of N by microorganisms impacts the availability of N in soil. Despite its established ecological significance, the contributions of microbial taxa to N assimilation are unknown. Here we measure N uptake and use by microbial phylotypes and taxonomic groups within a diverse assemblage of soil microbes through quantitative stable isotope probing (qSIP) with ¹⁵ N. Following incubation with ¹⁵ NH4+, distinct patterns of ¹⁵ N assimilation among taxonomic groups were observed. For instance, glucose addition stimulated ¹⁵ N assimilation in most members of Actinobacteria and Proteobacteria but generally decreased ¹⁵ N use by Firmicutes and Bacteriodetes. While NH4+ is considered a preferred and universal source of N to prokaryotes, the majority (> 80%) of N assimilation in our soils could be attributed to a handful of active orders. Characterizing N assimilation of taxonomic groups with ¹⁵ N qSIP may provide a basis for understanding how microbial community composition influences N availability in the environment.

Ecosystem responses to elevated CO2 governed by plant-soil interactions and the cost of nitrogen acquisition

Contents Summary 507 I. Introduction 507 II. The return on investment approach 508 III. CO₂ response spectrum 510 IV. Discussion 516 Acknowledgements 518 References 518 SUMMARY: Land ecosystems sequester on average about a quarter of anthropogenic CO₂ emissions. It has been proposed that nitrogen (N) availability will exert an increasingly limiting effect on plants' ability to store additional carbon (C) under rising CO₂ , but these mechanisms are not well understood. Here, we review findings from elevated CO₂ experiments using a plant economics framework, highlighting how ecosystem responses to elevated CO₂ may depend on the costs and benefits of plant interactions with mycorrhizal fungi and symbiotic N-fixing microbes. We found that N-acquisition efficiency is positively correlated with leaf-level photosynthetic capacity and plant growth, and negatively with soil C storage. Plants that associate with ectomycorrhizal fungi and N-fixers may acquire N at a lower cost than plants associated with arbuscular mycorrhizal fungi. However, the additional growth in ectomycorrhizal plants is partly offset by decreases in soil C pools via priming. Collectively, our results indicate that predictive models aimed at quantifying C cycle feedbacks to global change may be improved by treating N as a resource that can be acquired by plants in exchange for energy, with different costs depending on plant interactions with microbial symbionts.

Higher yields and lower methane emissions with new rice cultivars

Breeding high-yielding rice cultivars through increasing biomass is a key strategy to meet rising global food demands. Yet, increasing rice growth can stimulate methane (CH₄ ) emissions, exacerbating global climate change, as rice cultivation is a major source of this powerful greenhouse gas. Here, we show in a series of experiments that high-yielding rice cultivars actually reduce CH₄ emissions from typical paddy soils. Averaged across 33 rice cultivars, a biomass increase of 10% resulted in a 10.3% decrease in CH₄ emissions in a soil with a high carbon (C) content. Compared to a low-yielding cultivar, a high-yielding cultivar significantly increased root porosity and the abundance of methane-consuming microorganisms, suggesting that the larger and more porous root systems of high-yielding cultivars facilitated CH₄ oxidation by promoting O₂ transport to soils. Our results were further supported by a meta-analysis, showing that high-yielding rice cultivars strongly decrease CH₄ emissions from paddy soils with high organic C contents. Based on our results, increasing rice biomass by 10% could reduce annual CH₄ emissions from Chinese rice agriculture by 7.1%. Our findings suggest that modern rice breeding strategies for high-yielding cultivars can substantially mitigate paddy CH₄ emission in China and other rice growing regions.

Faster turnover of new soil carbon inputs under increased atmospheric CO2

Rising levels of atmospheric CO₂ frequently stimulate plant inputs to soil, but the consequences of these changes for soil carbon (C) dynamics are poorly understood. Plant-derived inputs can accumulate in the soil and become part of the soil C pool ("new soil C"), or accelerate losses of pre-existing ("old") soil C. The dynamics of the new and old pools will likely differ and alter the long-term fate of soil C, but these separate pools, which can be distinguished through isotopic labeling, have not been considered in past syntheses. Using meta-analysis, we found that while elevated CO₂ (ranging from 550 to 800 parts per million by volume) stimulates the accumulation of new soil C in the short term (<1 year), these effects do not persist in the longer term (1-4 years). Elevated CO₂ does not affect the decomposition or the size of the old soil C pool over either temporal scale. Our results are inconsistent with predictions of conventional soil C models and suggest that elevated CO₂ might increase turnover rates of new soil C. Because increased turnover rates of new soil C limit the potential for additional soil C sequestration, the capacity of land ecosystems to slow the rise in atmospheric CO₂ concentrations may be smaller than previously assumed.

Bacterial carbon use plasticity, phylogenetic diversity and the priming of soil organic matter

Microorganisms perform most decomposition on Earth, mediating carbon (C) loss from ecosystems, and thereby influencing climate. Yet, how variation in the identity and composition of microbial communities influences ecosystem C balance is far from clear. Using quantitative stable isotope probing of DNA, we show how individual bacterial taxa influence soil C cycling following the addition of labile C (glucose). Specifically, we show that increased decomposition of soil C in response to added glucose (positive priming) occurs as a phylogenetically diverse group of taxa, accounting for a large proportion of the bacterial community, shift toward additional soil C use for growth. Our findings suggest that many microbial taxa exhibit C use plasticity, as most taxa altered their use of glucose and soil organic matter depending upon environmental conditions. In contrast, bacteria that exhibit other responses to glucose (reduced growth or reliance on glucose for additional growth) clustered strongly by phylogeny. These results suggest that positive priming is likely the prototypical response of bacteria to sustained labile C addition, consistent with the widespread occurrence of the positive priming effect in nature.

The economic value of grassland species for carbon storage

Carbon storage by ecosystems is valuable for climate protection. Biodiversity conservation may help increase carbon storage, but the value of this influence has been difficult to assess. We use plant, soil, and ecosystem carbon storage data from two grassland biodiversity experiments to show that greater species richness increases economic value: Increasing species richness from 1 to 10 had twice the economic value of increasing species richness from 1 to 2. The marginal value of each additional species declined as species accumulated, reflecting the nonlinear relationship between species richness and plant biomass production. Our demonstration of the economic value of biodiversity for enhancing carbon storage provides a foundation for assessing the value of biodiversity for decisions about land management. Combining carbon storage with other ecosystem services affected by biodiversity may well enhance the economic arguments for conservation even further.

Identification of growing bacteria during litter decomposition in freshwater through H218O quantitative stable isotope probing

Identification of microorganisms that facilitate the cycling of nutrients in freshwater is paramount to understanding how these ecosystems function. Here, we identify growing aquatic bacteria using H218O quantitative stable isotope probing. During 8 day incubations in 97 atom % H218O, 54% of the taxa grew. The most abundant phyla among growing taxa were Proteobacteria (45%), Bacteroidetes (30%) and Firmicutes (10%). Taxa differed in isotopic enrichment, reflecting variation in DNA replication of bacterial populations. At the class level, the highest atom fraction excess was observed for OPB41 and δ-Proteobacteria. There was no linear relationship between ¹⁸ O incorporation and abundance of taxa. δ-Proteobacteria and OPB41 were not abundant, yet the DNA of both taxa was highly enriched in ¹⁸ O. Bacteriodetes, in contrast, were abundant but not highly enriched. Our study shows that a large proportion of the bacterial taxa found on decomposing leaf litter grew slowly, and several low abundance taxa were highly enriched. These findings indicating that rare organisms may be important for the decomposition of leaf litter in streams, and that quantitative stable isotope probing with H218O can be used to advance our understanding of microorganisms in freshwater by identifying species that are growing in complex communities.

Mycorrhizal association as a primary control of the CO2 fertilization effect

Plants buffer increasing atmospheric carbon dioxide (CO2) concentrations through enhanced growth, but the question whether nitrogen availability constrains the magnitude of this ecosystem service remains unresolved. Synthesizing experiments from around the world, we show that CO2 fertilization is best explained by a simple interaction between nitrogen availability and mycorrhizal association. Plant species that associate with ectomycorrhizal fungi show a strong biomass increase (30 ± 3%, P < 0.001) in response to elevated CO2 regardless of nitrogen availability, whereas low nitrogen availability limits CO2 fertilization (0 ± 5%, P = 0.946) in plants that associate with arbuscular mycorrhizal fungi. The incorporation of mycorrhizae in global carbon cycle models is feasible, and crucial if we are to accurately project ecosystem responses and feedbacks to climate change.

Predicting the Responses of Soil Nitrite-Oxidizers to Multi-Factorial Global Change: A Trait-Based Approach

Soil microbial diversity is huge and a few grams of soil contain more bacterial taxa than there are bird species on Earth. This high diversity often makes predicting the responses of soil bacteria to environmental change intractable and restricts our capacity to predict the responses of soil functions to global change. Here, using a long-term field experiment in a California grassland, we studied the main and interactive effects of three global change factors (increased atmospheric CO₂ concentration, precipitation and nitrogen addition, and all their factorial combinations, based on global change scenarios for central California) on the potential activity, abundance and dominant taxa of soil nitrite-oxidizing bacteria (NOB). Using a trait-based model, we then tested whether categorizing NOB into a few functional groups unified by physiological traits enables understanding and predicting how soil NOB respond to global environmental change. Contrasted responses to global change treatments were observed between three main NOB functional types. In particular, putatively mixotrophic Nitrobacter, rare under most treatments, became dominant under the ‘High CO₂+Nitrogen+Precipitation’ treatment. The mechanistic trait-based model, which simulated ecological niches of NOB types consistent with previous ecophysiological reports, helped predicting the observed effects of global change on NOB and elucidating the underlying biotic and abiotic controls. Our results are a starting point for representing the overwhelming diversity of soil bacteria by a few functional types that can be incorporated into models of terrestrial ecosystems and biogeochemical processes.

The Influence of Time and Plant Species on the Composition of the Decomposing Bacterial Community in a Stream Ecosystem

Foliar chemistry influences leaf decomposition, but little is known about how litter chemistry affects the assemblage of bacterial communities during decomposition. Here we examined relationships between initial litter chemistry and the composition of the bacterial community in a stream ecosystem. We incubated replicated genotypes of Populus fremontii and P. angustifolia leaf litter that differ in percent tannin and lignin, then followed changes in bacterial community composition during 28 days of decomposition using 16S rRNA gene-based pyrosequencing. Using a nested experimental design, the majority of variation in bacterial community composition was explained by time (i.e., harvest day) (R(2) = 0.50). Plant species, nested within harvest date, explained a significant but smaller proportion of the variation (R(2) = 0.03). Significant differences in community composition between leaf species were apparent at day 14, but no significant differences existed among genotypes. Foliar chemistry correlated significantly with community composition at day 14 (r = 0.46) indicating that leaf litter with more similar phytochemistry harbor bacterial communities that are alike. Bacteroidetes and β-proteobacteria dominated the bacterial assemblage on decomposing leaves, and Verrucomicrobia and α- and δ-proteobacteria became more abundant over time. After 14 days, bacterial diversity diverged significantly between leaf litter types with fast-decomposing P. fremontii hosting greater richness than slowly decomposing P. angustifolia; however, differences were no longer present after 28 days in the stream. Leaf litter tannin, lignin, and lignin: N ratios all correlated negatively with diversity. This work shows that the bacterial community on decomposing leaves in streams changes rapidly over time, influenced by leaf species via differences in genotype-level foliar chemistry.

Phylogenetic organization of bacterial activity

Phylogeny is an ecologically meaningful way to classify plants and animals, as closely related taxa frequently have similar ecological characteristics, functional traits and effects on ecosystem processes. For bacteria, however, phylogeny has been argued to be an unreliable indicator of an organism's ecology owing to evolutionary processes more common to microbes such as gene loss and lateral gene transfer, as well as convergent evolution. Here we use advanced stable isotope probing with ¹³C and ¹⁸O to show that evolutionary history has ecological significance for in situ bacterial activity. Phylogenetic organization in the activity of bacteria sets the stage for characterizing the functional attributes of bacterial taxonomic groups. Connecting identity with function in this way will allow scientists to begin building a mechanistic understanding of how bacterial community composition regulates critical ecosystem functions.