Microbial life-history strategies mediate microbial carbon pump efficacy in response to N management depending on stoichiometry of microbial demand.

The soil microbial carbon pump (MCP) is increasingly acknowledged as being directly linked to soil organic carbon (SOC) accumulation and stability. Given the close coupling of carbon (C) and nitrogen (N) cycles and the constraints imposed by their stoichiometry on microbial growth, N addition might affect microbial growth strategies with potential consequences for necromass formation and carbon stability. However, this topic remains largely unexplored. Based on two multi-level N fertilizer experiments over 10 years in two soils with contrasting soil fertility located in the North (Cambisol, carbon-poor) and Southwest (Luvisol, carbon-rich), we hypothesized that different resource demands of microorganism elicit a trade-off in microbial growth potential (Y-strategy) and resource-acquisition (A-strategy) in response to N addition, and consequently on necromass formation and soil carbon stability. We combined measurements of necromass metrics (MCP efficacy) and soil carbon stability (chemical composition and mineral associated organic carbon) with potential changes in microbial life history strategies (assessed via soil metagenomes and enzymatic activity analyses). The contribution of microbial necromass to SOC decreased with N addition in the Cambisol, but increased in the Luvisol. Soil microbial life strategies displayed two distinct responses in two soils after N amendment: shift toward A-strategy (Cambisol) or Y-strategy (Luvisol). These divergent responses are owing to the stoichiometric imbalance between microbial demands and resource availability for C and N, which presented very distinct patterns in the two soils. The partial correlation analysis further confirmed that high N addition aggravated stoichiometric carbon demand, shifting the microbial community strategy toward resource-acquisition which reduced carbon stability in Cambisol. In contrast, the microbial Y-strategy had the positive direct effect on MCP efficacy in Luvisol, which greatly enhanced carbon stability. Such findings provide mechanistic insights into the stoichiometric regulation of MCP efficacy, and how this is mediated by site-specific trade-offs in microbial life strategies, which contribute to improving our comprehension of soil microbial C sequestration and potential optimization of agricultural N management.

Metagenomic analysis of ecological niche overlap and community collapse in microbiome dynamics.

Species utilizing the same resources often fail to coexist for extended periods of time. Such competitive exclusion mechanisms potentially underly microbiome dynamics, causing breakdowns of communities composed of species with similar genetic backgrounds of resource utilization. Although genes responsible for competitive exclusion among a small number of species have been investigated in pioneering studies, it remains a major challenge to integrate genomics and ecology for understanding stable coexistence in species-rich communities. Here, we examine whether community-scale analyses of functional gene redundancy can provide a useful platform for interpreting and predicting collapse of bacterial communities. Through 110-day time-series of experimental microbiome dynamics, we analyzed the metagenome-assembled genomes of co-occurring bacterial species. We then inferred ecological niche space based on the multivariate analysis of the genome compositions. The analysis allowed us to evaluate potential shifts in the level of niche overlap between species through time. We hypothesized that community-scale pressure of competitive exclusion could be evaluated by quantifying overlap of genetically determined resource-use profiles (metabolic pathway profiles) among coexisting species. We found that the degree of community compositional changes observed in the experimental microbiome was correlated with the magnitude of gene-repertoire overlaps among bacterial species, although the causation between the two variables deserves future extensive research. The metagenome-based analysis of genetic potential for competitive exclusion will help us forecast major events in microbiome dynamics such as sudden community collapse (i.e., dysbiosis).

Microbial growth under drought is confined to distinct taxa and modified by potential future climate conditions.

Climate change increases the frequency and intensity of drought events, affecting soil functions including carbon sequestration and nutrient cycling, which are driven by growing microorganisms. Yet we know little about microbial responses to drought due to methodological limitations. Here, we estimate microbial growth rates in montane grassland soils exposed to ambient conditions, drought, and potential future climate conditions (i.e., soils exposed to 6 years of elevated temperatures and elevated CO2 levels). For this purpose, we combined 18O-water vapor equilibration with quantitative stable isotope probing (termed 'vapor-qSIP') to measure taxon-specific microbial growth in dry soils. In our experiments, drought caused >90% of bacterial and archaeal taxa to stop dividing and reduced the growth rates of persisting ones. Under drought, growing taxa accounted for only 4% of the total community as compared to 35% in the controls. Drought-tolerant communities were dominated by specialized members of the Actinobacteriota, particularly the genus Streptomyces. Six years of pre-exposure to future climate conditions (3 °C warming and + 300 ppm atmospheric CO2) alleviated drought effects on microbial growth, through more drought-tolerant taxa across major phyla, accounting for 9% of the total community. Our results provide insights into the response of active microbes to drought today and in a future climate, and highlight the importance of studying drought in combination with future climate conditions to capture interactive effects and improve predictions of future soil-climate feedbacks.

Facilitative interaction networks in experimental microbial community dynamics.

Facilitative interactions between microbial species are ubiquitous in various types of ecosystems on the Earth. Therefore, inferring how entangled webs of interspecific interactions shift through time in microbial ecosystems is an essential step for understanding ecological processes driving microbiome dynamics. By compiling shotgun metagenomic sequencing data of an experimental microbial community, we examined how the architectural features of facilitative interaction networks could change through time. A metabolic modeling approach for estimating dependence between microbial genomes (species) allowed us to infer the network structure of potential facilitative interactions at 13 time points through the 110-day monitoring of experimental microbiomes. We then found that positive feedback loops, which were theoretically predicted to promote cascade breakdown of ecological communities, existed within the inferred networks of metabolic interactions prior to the drastic community-compositional shift observed in the microbiome time-series. We further applied "directed-graph" analyses to pinpoint potential keystone species located at the "upper stream" positions of such feedback loops. These analyses on facilitative interactions will help us understand key mechanisms causing catastrophic shifts in microbial community structure.

Alternative stable states, nonlinear behavior, and predictability of microbiome dynamics.

BACKGROUND: Microbiome dynamics are both crucial indicators and potential drivers of human health, agricultural output, and industrial bio-applications. However, predicting microbiome dynamics is notoriously difficult because communities often show abrupt structural changes, such as "dysbiosis" in human microbiomes. METHODS: We integrated theoretical frameworks and empirical analyses with the aim of anticipating drastic shifts of microbial communities. We monitored 48 experimental microbiomes for 110 days and observed that various community-level events, including collapse and gradual compositional changes, occurred according to a defined set of environmental conditions. We analyzed the time-series data based on statistical physics and non-linear mechanics to describe the characteristics of the microbiome dynamics and to examine the predictability of major shifts in microbial community structure. RESULTS: We confirmed that the abrupt community changes observed through the time-series could be described as shifts between "alternative stable states" or dynamics around complex attractors. Furthermore, collapses of microbiome structure were successfully anticipated by means of the diagnostic threshold defined with the "energy landscape" analysis of statistical physics or that of a stability index of nonlinear mechanics. CONCLUSIONS: The results indicate that abrupt microbiome events in complex microbial communities can be forecasted by extending classic ecological concepts to the scale of species-rich microbial systems. Video Abstract.

Cropland intensification mediates the radiative balance of greenhouse gas emissions and soil carbon sequestration in maize systems of sub-Saharan Africa.

Sub-Saharan Africa (SSA) must undertake proper cropland intensification for higher crop yields while minimizing climate impacts. Unfortunately, no studies have simultaneously quantified greenhouse gas (GHG; CO2 , CH4 , and N2 O) emissions and soil organic carbon (SOC) change in SSA croplands, leaving it a blind spot in the accounting of global warming potential (GWP). Here, based on 2-year field monitoring of soil emissions of CO2 , CH4 , and N2 O, as well as SOC changes in two contrasting soil types (sandy vs. clayey), we provided the first, full accounting of GWP for maize systems in response to cropland intensifications (increasing nitrogen rates and in combination with crop residue return) in SSA. To corroborate our field observations on SOC change (i.e., 2-year, a short duration), we implemented a process-oriented model parameterized with field data to simulate SOC dynamic over time. We further tested the generality of our findings by including a literature synthesis of SOC change across maize-based systems in SSA. We found that nitrogen application reduced SOC loss, likely through increased biomass yield and consequently belowground carbon allocation. Residue return switched the direction of SOC change from loss to gain; such a benefit (SOC sequestration) was not compromised by CH4 emissions (negligible) nor outweighed by the amplified N2 O emissions, and contributed to negative net GWP. Overall, we show encouraging results that, combining residue and fertilizer-nitrogen input allowed for sequestering 82-284 kg of CO2 -eq per Mg of maize grain produced across two soils. All analyses pointed to an advantage of sandy over clayey soils in achieving higher SOC sequestration targets, and thus call for a re-evaluation on the potential of sandy soils in SOC sequestration across SSA croplands. Our findings carry important implications for developing viable intensification practices for SSA croplands in mitigating climate change while securing food production.

Contrasting drivers of belowground nitrogen cycling in a montane grassland exposed to a multifactorial global change experiment with elevated CO2 , warming, and drought.

Depolymerization of high-molecular weight organic nitrogen (N) represents the major bottleneck of soil N cycling and yet is poorly understood compared to the subsequent inorganic N processes. Given the importance of organic N cycling and the rise of global change, we investigated the responses of soil protein depolymerization and microbial amino acid consumption to increased temperature, elevated atmospheric CO2 , and drought. The study was conducted in a global change facility in a managed montane grassland in Austria, where elevated CO2 (eCO2 ) and elevated temperature (eT) were stimulated for 4 years, and were combined with a drought event. Gross protein depolymerization and microbial amino acid consumption rates (alongside with gross organic N mineralization and nitrification) were measured using 15 N isotope pool dilution techniques. Whereas eCO2  showed no individual effect, eT had distinct effects which were modulated by season, with a negative effect of eT on soil organic N process rates in spring, neutral effects in summer, and positive effects in fall. We attribute this to a combination of changes in substrate availability and seasonal temperature changes. Drought led to a doubling of organic N process rates, which returned to rates found under ambient conditions within 3 months after rewetting. Notably, we observed a shift in the control of soil protein depolymerization, from plant substrate controls under continuous environmental change drivers (eT and eCO2 ) to controls via microbial turnover and soil organic N availability under the pulse disturbance (drought). To the best of our knowledge, this is the first study which analyzed the individual versus combined effects of multiple global change factors and of seasonality on soil organic N processes and thereby strongly contributes to our understanding of terrestrial N cycling in a future world.

Ecological memory of recurrent drought modifies soil processes via changes in soil microbial community.

Climate change is altering the frequency and severity of drought events. Recent evidence indicates that drought may produce legacy effects on soil microbial communities. However, it is unclear whether precedent drought events lead to ecological memory formation, i.e., the capacity of past events to influence current ecosystem response trajectories. Here, we utilize a long-term field experiment in a mountain grassland in central Austria with an experimental layout comparing 10 years of recurrent drought events to a single drought event and ambient conditions. We show that recurrent droughts increase the dissimilarity of microbial communities compared to control and single drought events, and enhance soil multifunctionality during drought (calculated via measurements of potential enzymatic activities, soil nutrients, microbial biomass stoichiometry and belowground net primary productivity). Our results indicate that soil microbial community composition changes in concert with its functioning, with consequences for soil processes. The formation of ecological memory in soil under recurrent drought may enhance the resilience of ecosystem functioning against future drought events.

Warming and elevated CO2 intensify drought and recovery responses of grassland carbon allocation to soil respiration.

Photosynthesis and soil respiration represent the two largest fluxes of CO2 in terrestrial ecosystems and are tightly linked through belowground carbon (C) allocation. Drought has been suggested to impact the allocation of recently assimilated C to soil respiration; however, it is largely unknown how drought effects are altered by a future warmer climate under elevated atmospheric CO2 (eT_eCO2 ). In a multifactor experiment on managed C3 grassland, we studied the individual and interactive effects of drought and eT_eCO2 (drought, eT_eCO2 , drought × eT_eCO2 ) on ecosystem C dynamics. We performed two in situ 13 CO2 pulse-labeling campaigns to trace the fate of recent C during peak drought and recovery. eT_eCO2 increased soil respiration and the fraction of recently assimilated C in soil respiration. During drought, plant C uptake was reduced by c. 50% in both ambient and eT_eCO2 conditions. Soil respiration and the amount and proportion of 13 C respired from soil were reduced (by 32%, 70% and 30%, respectively), the effect being more pronounced under eT_eCO2 (50%, 84%, 70%). Under drought, the diel coupling of photosynthesis and SR persisted only in the eT_eCO2 scenario, likely caused by dynamic shifts in the use of freshly assimilated C between storage and respiration. Drought did not affect the fraction of recent C remaining in plant biomass under ambient and eT_eCO2 , but reduced the small fraction remaining in soil under eT_eCO2 . After rewetting, C uptake and the proportion of recent C in soil respiration recovered more rapidly under eT_eCO2 compared to ambient conditions. Overall, our findings suggest that in a warmer climate under elevated CO2 drought effects on the fate of recent C will be amplified and the coupling of photosynthesis and soil respiration will be sustained. To predict the future dynamics of terrestrial C cycling, such interactive effects of multiple global change factors should be considered.

Microbial growth and carbon use efficiency show seasonal responses in a multifactorial climate change experiment.

Microbial growth and carbon use efficiency (CUE) are central to the global carbon cycle, as microbial remains form soil organic matter. We investigated how future global changes may affect soil microbial growth, respiration, and CUE. We aimed to elucidate the soil microbial response to multiple climate change drivers across the growing season and whether effects of multiple global change drivers on soil microbial physiology are additive or interactive. We measured soil microbial growth, CUE, and respiration at three time points in a field experiment combining three levels of temperature and atmospheric CO2, and a summer drought. Here we show that climate change-driven effects on soil microbial physiology are interactive and season-specific, while the coupled response of growth and respiration lead to stable microbial CUE (average CUE = 0.39). These results suggest that future research should focus on microbial growth across different seasons to understand and predict effects of global changes on soil carbon dynamics.

Composition and activity of nitrifier communities in soil are unresponsive to elevated temperature and CO2, but strongly affected by drought.

Nitrification is a fundamental process in terrestrial nitrogen cycling. However, detailed information on how climate change affects the structure of nitrifier communities is lacking, specifically from experiments in which multiple climate change factors are manipulated simultaneously. Consequently, our ability to predict how soil nitrogen (N) cycling will change in a future climate is limited. We conducted a field experiment in a managed grassland and simultaneously tested the effects of elevated atmospheric CO2, temperature, and drought on the abundance of active ammonia-oxidizing bacteria (AOB) and archaea (AOA), comammox (CMX) Nitrospira, and nitrite-oxidizing bacteria (NOB), and on gross mineralization and nitrification rates. We found that N transformation processes, as well as gene and transcript abundances, and nitrifier community composition were remarkably resistant to individual and interactive effects of elevated CO2 and temperature. During drought however, process rates were increased or at least maintained. At the same time, the abundance of active AOB increased probably due to higher NH4+ availability. Both, AOA and comammox Nitrospira decreased in response to drought and the active community composition of AOA and NOB was also significantly affected. In summary, our findings suggest that warming and elevated CO2 have only minor effects on nitrifier communities and soil biogeochemical variables in managed grasslands, whereas drought favors AOB and increases nitrification rates. This highlights the overriding importance of drought as a global change driver impacting on soil microbial community structure and its consequences for N cycling.

Quantifying microbial growth and carbon use efficiency in dry soil environments via 18 O water vapor equilibration.

Soil microbial physiology controls large fluxes of C to the atmosphere, thus, improving our ability to accurately quantify microbial physiology in soil is essential. However, current methods to determine microbial C metabolism require liquid water addition, which makes it practically impossible to measure microbial physiology in dry soil samples without stimulating microbial growth and respiration (namely, the "Birch effect"). We developed a new method based on in vivo 18 O-water vapor equilibration to minimize soil rewetting effects. This method allows the isotopic labeling of soil water without direct liquid water addition. This was compared to the main current method (direct 18 O-liquid water addition) in moist and air-dry soils. We determined the time kinetics and calculated the average 18 O enrichment of soil water over incubation time, which is necessary to calculate microbial growth from 18 O incorporation in genomic DNA. We tested isotopic equilibration patterns in three natural and six artificially constructed soils covering a wide range of soil texture and soil organic matter content. We then measured microbial growth, respiration and carbon use efficiency (CUE) in three natural soils (either air-dry or moist). The proposed 18 O-vapor equilibration method provided similar results as the current method of liquid 18 O-water addition when used for moist soils. However, when applied to air-dry soils the liquid 18 O-water addition method overestimated growth by up to 250%, respiration by up to 500%, and underestimated CUE by up to 40%. We finally describe the new insights into biogeochemical cycling of C that the new method can help uncover, and we consider a range of questions regarding microbial physiology and its response to global change that can now be addressed.

Corrigendum: Root Exudation of Primary Metabolites: Mechanisms and Their Roles in Plant Responses to Environmental Stimuli.

[This corrects the article DOI: 10.3389/fpls.2019.00157.].

Root Exudation of Primary Metabolites: Mechanisms and Their Roles in Plant Responses to Environmental Stimuli.

Root exudation is an important process determining plant interactions with the soil environment. Many studies have linked this process to soil nutrient mobilization. Yet, it remains unresolved how exudation is controlled and how exactly and under what circumstances plants benefit from exudation. The majority of root exudates including primary metabolites (sugars, amino acids, and organic acids) are believed to be passively lost from the root and used by rhizosphere-dwelling microbes. In this review, we synthetize recent advances in ecology and plant biology to explain and propose mechanisms by which root exudation of primary metabolites is controlled, and what role their exudation plays in plant nutrient acquisition strategies. Specifically, we propose a novel conceptual framework for root exudates. This framework is built upon two main concepts: (1) root exudation of primary metabolites is driven by diffusion, with plants and microbes both modulating concentration gradients and therefore diffusion rates to soil depending on their nutritional status; (2) exuded metabolite concentrations can be sensed at the root tip and signals are translated to modify root architecture. The flux of primary metabolites through root exudation is mostly located at the root tip, where the lack of cell differentiation favors diffusion of metabolites to the soil. We show examples of how the root tip senses concentration changes of exuded metabolites and translates that into signals to modify root growth. Plants can modify the concentration of metabolites either by controlling source/sink processes or by expressing and regulating efflux carriers, therefore challenging the idea of root exudation as a purely unregulated passive process. Through root exudate flux, plants can locally enhance concentrations of many common metabolites, which can serve as sensors and integrators of the plant nutritional status and of the nutrient availability in the surrounding environment. Plant-associated micro-organisms also constitute a strong sink for plant carbon, thereby increasing concentration gradients of metabolites and affecting root exudation. Understanding the mechanisms of and the effects that environmental stimuli have on the magnitude and type of root exudation will ultimately improve our knowledge of processes determining soil CO2 emissions, ecosystem functioning, and how to improve the sustainability of agricultural production.

Mineral-Associated Soil Carbon is Resistant to Drought but Sensitive to Legumes and Microbial Biomass in an Australian Grassland.

Drought is predicted to increase in many areas of the world with consequences for soil carbon (C) dynamics. Plant litter, root exudates and microbial biomass can be used as C substrates to form organo-mineral complexes. Drought effects on plants and microbes could potentially compromise these relative stable soil C pools, by reducing plant C inputs and/or microbial activity. We conducted a 2-year drought experiment using rainout shelters in a semi-natural grassland. We measured aboveground biomass and C and nitrogen (N) in particulate organic matter (Pom), the organo-mineral fraction (Omin), and microbial biomass within the first 15 cm of soil. Aboveground plant biomass was reduced by 50% under drought in both years, but only the dominant C4 grasses were significantly affected. Soil C pools were not affected by drought, but were significantly higher in the relatively wet second year compared to the first year. Omin-C was positively related to microbial C during the first year, and positively related to clay and silt content in the second year. Increases in Omin-C in the second year were explained by increases in legume biomass and its effect on Pom-N and microbial biomass N (MBN) through structural equation modeling. In conclusion, soil C pools were unaffected by the drought treatment. Drought resistant legumes enhanced formation of organo-mineral complexes through increasing Pom-N and MBN. Our findings also indicate the importance of microbes for the formation of Omin-C as long as soil minerals have not reached their maximum capacity to bind with C (that is, saturation).

Photosynthesis and assimilate partitioning between carbohydrates and isoprenoid products in vegetatively active and dormant guayule: physiological and environmental constraints on rubber accumulation in a semiarid shrub.

The stems and roots of the semiarid shrub guayule, Parthenium argentatum, contain a significant amount of natural rubber. Rubber accumulates in guayule when plants are vegetatively and reproductively dormant, complicating the relationship between growth/reproduction and product synthesis. To evaluate the factors regulating the partitioning of carbon to rubber, carbon assimilation and partitioning were measured in guayule plants that were grown under simulated summer- and winter-like conditions and under winter-like conditions with CO(2) enrichment. These conditions were used to induce vegetatively active and dormant states and to increase the source strength of vegetatively dormant plants, respectively. Rates of CO(2) assimilation, measured under growth temperatures and CO(2) , were similar for plants grown under summer- and winter-like conditions, but were higher with elevated CO(2) . After 5 months, plants grown under summer-like conditions had the greatest aboveground biomass, but the lowest levels of non-structural carbohydrates and rubber. In contrast, the amount of resin in the stems was similar under all growth conditions. Emission of biogenic volatile compounds was more than three-fold higher in plants grown under summer- compared with winter-like conditions. Taken together, the results show that guayule plants maintain a high rate of photosynthesis and accumulate non-structural carbohydrates and rubber in the vegetatively dormant state, but emit volatile compounds at a lower rate when compared with more vegetatively active plants. Enrichment with CO(2) in the vegetatively dormant state increased carbohydrate content but not the amount of rubber, suggesting that partitioning of assimilate to rubber is limited by sink strength in guayule.