Linking microbial activity and soil organic matter transformations in forest soils under elevated CO2

Soil organic matter (SOM) dynamics ultimately govern the ability of soil to provide long‐term C sequestration and the nutrients required for ecosystem productivity. Predicting belowground responses to elevated CO₂ requires an integrated understanding of SOM transformations and the microbial activity that governs them. It remains unclear how the microorganisms upon which these transformations depend will function in an elevated CO₂ world. This study examines SOM transformations and microbial metabolism in soils from the Duke Free Air Carbon Enrichment site in North Carolina, USA. We assessed microbial respiration and net nitrogen (N) mineralization in soils with and without elevated CO₂ exposure during a 100‐day incubation. We also traced the depleted C isotopic signature of the supplemental CO₂ into SOM and the soils' phospholipid fatty acids (PLFA), which serve as biomarkers for living cells. Cumulative net N mineralization in elevated CO₂ soils was 50% that in control soils after a 100‐day incubation. Respiration was not altered with elevated CO₂. C : N ratios of bulk SOM did not change with elevated CO₂, but incubation data suggest that the C : N ratios of mineralized organic matter increased with elevated CO₂. Values of SOM δ¹³C were depleted with elevated CO₂ (?26.7±0.2 vs. ?30.2±0.3‰), reflecting the depleted signature of the supplemental CO₂. We compared δ¹³C of individual PLFA with the δ¹³C of SOM to discern incorporation of the depleted C isotopic signature into soil microbial groups in elevated CO₂ plots. PLFA i15:0, a15:0, and 10Met18:0 reflected significant incorporation of recently produced photosynthate, suggesting that the bacterial groups defined by these biomarkers are active metabolizers in elevated CO₂ soils. At least one of these groups (actinomycetes, 10Met18:0) specializes in metabolizing less labile substrates. Because control plots did not receive an equivalent ¹³C tracer, we cannot determine from these data whether this group of organisms was stimulated by elevated CO₂ compared with these organisms in control soils. Stimulation of this group, if it occurred in the elevated CO₂ plot, would be consistent with a decline in the availability of mineralizable organic matter with elevated CO₂, which incubation data suggest may be the case in these soils.     

Elevated CO2 increases microbial carbon substrate use and nitrogen cycling in Mojave Desert soils

Identifying soil microbial responses to anthropogenically driven environmental changes is critically important as concerns intensify over the potential degradation of ecosystem function. We assessed the effects of elevated atmospheric CO₂ on microbial carbon (C) and nitrogen (N) cycling in Mojave Desert soils using extracellular enzyme activities (EEAs), community‐level physiological profiles (CLPPs), and gross N transformation rates. Soils were collected from unvegetated interspaces between plants and under the dominant shrub (Larrea tridentata) during the 2004–2005 growing season, an above‐average rainfall year. Because most measured variables responded strongly to soil water availability, all significant effects of soil water content were used as covariates to remove potential confounding effects of water availability on microbial responses to experimental treatment effects of cover type, CO₂, and sampling date. Microbial C and N activities were lower in interspace soils compared with soils under Larrea, and responses to date and CO₂ treatments were cover specific. Over the growing season, EEAs involved in cellulose (cellobiohydrolase) and orthophosphate (alkaline phosphatase) degradation decreased under ambient CO₂, but increased under elevated CO₂. Microbial C use and substrate use diversity in CLPPs decreased over time, and elevated CO₂ positively affected both. Elevated CO₂ also altered microbial C use patterns, suggesting changes in the quantity and/or quality of soil C inputs. In contrast, microbial biomass N was higher in interspace soils than soils under Larrea, and was lower in soils exposed to elevated CO₂. Gross rates of NH₄⁺ transformations increased over the growing season, and late‐season NH₄⁺ fluxes were negatively affected by elevated CO₂. Gross NO₃⁻ fluxes decreased over time, with early season interspace soils positively affected by elevated CO₂. General increases in microbial activities under elevated CO₂ are likely attributable to greater microbial biomass in interspace soils, and to increased microbial turnover rates and/or metabolic levels rather than pool size in soils under Larrea. Because soil water content and plant cover type dominates microbial C and N responses to CO₂, the ability of desert landscapes to mitigate or intensify the impacts of global change will ultimately depend on how changes in precipitation and increasing atmospheric CO₂ shift the spatial distribution of Mojave Desert plant communities.     

Altered microbial community structure and organic matter composition under elevated CO2 and N fertilization in the duke forest

The dynamics and fate of terrestrial organic matter (OM) under elevated atmospheric CO₂ and nitrogen (N) fertilization are important aspects of long‐term carbon sequestration. Despite numerous studies, questions still remain as to whether the chemical composition of OM may alter with these environmental changes. In this study, we employed molecular‐level methods to investigate the composition and degradation of various OM components in the forest floor (O horizon) and mineral soil (0–15 cm) from the Duke forest free air CO₂ enrichment (FACE) experiment. We measured microbial responses to elevated CO₂ and N fertilization in the mineral soil using phospholipid fatty acid (PLFA) profiles. Increased fresh carbon inputs into the forest floor under elevated CO₂ were observed at the molecular‐level by two degradation parameters of plant‐derived steroids and cutin‐derived compounds. The ratios of fungal to bacterial PLFAs and Gram‐negative to Gram‐positive bacterial PLFAs decreased in the mineral soil with N fertilization, indicating an altered soil microbial community composition. Moreover, the acid to aldehyde ratios of lignin‐derived phenols increased with N fertilization, suggesting enhanced lignin degradation in the mineral soil. ¹H nuclear magnetic resonance (NMR) spectra of soil humic substances revealed an enrichment of leaf‐derived alkyl structures with both elevated CO₂ and N fertilization. We suggest that microbial decomposition of SOM constituents such as lignin and hydrolysable lipids was promoted under both elevated CO₂ and N fertilization, which led to the enrichment of plant‐derived recalcitrant structures (such as alkyl carbon) in the soil.     

Soil warming alters microbial substrate use in alpine soils

Will warming lead to an increased use of older soil organic carbon (SOC) by microbial communities, thereby inducing C losses from C‐rich alpine soils? We studied soil microbial community composition, activity, and substrate use after 3 and 4 years of soil warming (+4 °C, 2007–2010) at the alpine treeline in Switzerland. The warming experiment was nested in a free air CO₂ enrichment experiment using depleted ¹³CO₂ (δ¹³C = ?30‰, 2001–2009). We traced this depleted ¹³C label in phospholipid fatty acids (PLFA) of the organic layer (0–5 cm soil depth) and in C mineralized from root‐free soils to distinguish substrate ages used by soil microorganisms: fixed before 2001 (‘old’), from 2001 to 2009 (‘new’) or in 2010 (‘recent’). Warming induced a sustained stimulation of soil respiration (+38%) without decline in mineralizable SOC. PLFA concentrations did not reveal changes in microbial community composition due to soil warming, but soil microbial metabolic activity was stimulated (+66%). Warming decreased the amount of new and recent C in the fungal biomarker 18:2ω6,9 and the amount of new C mineralized from root‐free soils, implying a shift in microbial substrate use toward a greater use of old SOC. This shift in substrate use could indicate an imbalance between C inputs and outputs, which could eventually decrease SOC storage in this alpine ecosystem.     

Bacteria and Fungi Respond Differently to Multifactorial Climate Change in a Temperate Heathland,Traced with 13C-Glycine and FACE CO2

It is vital to understand responses of soil microorganisms to predicted climate changes, as these directly control soil carbon (C) dynamics. The rate of turnover of soil organic carbon is mediated by soil microorganisms whose activity may be affected by climate change. After one year of multifactorial climate change treatments, at an undisturbed temperate heathland, soil microbial community dynamics were investigated by injection of a very small concentration (5.12 µg C g⁻¹ soil) of ¹³C-labeled glycine (¹³C₂, 99 atom %) to soils in situ. Plots were treated with elevated temperature (+1°C, T), summer drought (D) and elevated atmospheric carbon dioxide (510 ppm [CO2]), as well as combined treatments (TD, TCO2, DCO2 and TDCO2). The ¹³C enrichment of respired CO₂ and of phospholipid fatty acids (PLFAs) was determined after 24 h. ¹³C-glycine incorporation into the biomarker PLFAs for specific microbial groups (Gram positive bacteria, Gram negative bacteria, actinobacteria and fungi) was quantified using gas chromatography-combustion-stable isotope ratio mass spectrometry (GC-C-IRMS).Gram positive bacteria opportunistically utilized the freshly added glycine substrate, i.e. incorporated ¹³C in all treatments, whereas fungi had minor or no glycine derived ¹³C-enrichment, hence slowly reacting to a new substrate. The effects of elevated CO₂ did suggest increased direct incorporation of glycine in microbial biomass, in particular in G⁺ bacteria, in an ecosystem subjected to elevated CO₂. Warming decreased the concentration of PLFAs in general. The FACE CO₂ was ¹³C-depleted (δ¹³C = 12.2‰) compared to ambient (δ¹³C = ∼−8‰), and this enabled observation of the integrated longer term responses of soil microorganisms to the FACE over one year. All together, the bacterial (and not fungal) utilization of glycine indicates substrate preference and resource partitioning in the microbial community, and therefore suggests a diversified response pattern to future changes in substrate availability and climatic factors.     

Altered patterns of soil carbon substrate usage and heterotrophic respiration in a pine forest with elevated CO2 and N fertilization

To assess how heterotrophic microorganisms may alter their activities and thus their CO₂‐C return to the atmosphere with elevated CO₂ and changing N availability, we examined soil organic matter (SOM) dynamics at the Duke Free Air Carbon Enrichment (FACE) site, after N fertilizer was applied. We measured heterotrophic respiration during early and late stages of SOM mineralization in soil incubations to capture activity on relatively labile and refractory SOM pools. We also measured δ¹³C of respired CO₂‐C and phospholipid fatty acids (PLFAs) during early mineralization stages to track the microbial groups involved in substrate use. We calculated , a measure of δ¹³C_PLFA normalized by respired δ¹³CO₂, to assess microbial function with C substrates formed with elevated CO₂ and altered N availability, via the distinct δ¹³C of the supplemental CO₂. We also quantified extracellular enzyme activity (EEA) during labile and recalcitrant SOM mineralization. Early in the incubations, increased N availability reduced heterotrophic CO₂‐C release. By the later stages of SOM mineralization, elevated CO₂ soils with fertilization had respired 72% of the CO₂‐C respired by all other soils. values suggest that fungi in elevated CO₂ plots took up C substrates possessing the δ¹³C signature of recently formed SOM, and added N promoted the activity of Gram‐negative bacteria and reduced that of Gram‐positive bacteria, particularly actinomycetes. Consistent with this, the enzyme responsible for the degradation of peptidoglycan and chitin, compounds produced by Gram‐positive bacteria and fungi, respectively, experienced a decline in activity with N fertilization. If patterns observed in this study with N additions are reversed with progressive N limitation at this site, actinomycetes and other Gram‐positive bacteria responsible for mineralizing relatively recalcitrant substrates may experience increases in their activity. Such shifts in microbial functioning may result in increased turnover of, and C release from, relatively decay‐resistant material.     

Microbial assimilation of new photosynthate is altered by plant species richness and nitrogen deposition

To determine how plant species richness impacts microbial assimilation of new photosynthate, and how this may be modified by atmospheric N deposition, we analyzed the microbial assimilation of recent photosynthate in a 6-year-long field experiment in which plant species richness, atmospheric N deposition, and atmospheric CO₂ concentration were manipulated in concert. The depleted δ¹³C of fumigation CO₂ enabled us to investigate the effect of plant species richness and atmospheric N deposition on the metabolism of soil microbial communities in the elevated CO₂ treatment. To accomplish this, we determined the δ¹³C of bacterial, actinobacterial, and fungal phospholipid fatty acids (PLFAs). In the elevated CO₂ conditions of this study, the δ¹³C of bacterial PLFAs (i15:0, i16:0, 16:1ω7c, 16:1ω9c, 10Me16:0, and 10Me18:0) and the fungal PLFA 18:1ω9c was significantly lower in species-rich plant communities than in species-poor plant communities, indicating that microbial incorporation of new C increased with plant species richness. Despite an increase in plant production, total PLFA decreased under N deposition. Moreover, N deposition also decreased fungal relative abundance in species-rich plant communities. In our study, plant species richness directly increased microbial incorporation of new photosynthate, providing a mechanistic link between greater plant detritus production in species-rich plant communities and larger and more active soil microbial community.     

Microbial community utilization of recalcitrant and simple carbon compounds: impact of oak-woodland plant communities

Little is known about how the structure of microbial communities impacts carbon cycling or how soil microbial community composition mediates plant effects on C-decomposition processes. We examined the degradation of four ¹³C-labeled compounds (starch, xylose, vanillin, and pine litter), quantified rates of associated enzyme activities, and identified microbial groups utilizing the ¹³C-labeled substrates in soils under oaks and in adjacent open grasslands. By quantifying increases in non-¹³C-labeled carbon in microbial biomarkers, we were also able to identify functional groups responsible for the metabolism of indigenous soil organic matter. Although microbial community composition differed between oak and grassland soils, the microbial groups responsible for starch, xylose, and vanillin degradation, as defined by ¹³C-PLFA, did not differ significantly between oak and grassland soils. Microbial groups responsible for pine litter and SOM-C degradation did differ between the two soils. Enhanced degradation of SOM resulting from substrate addition (priming) was greater in grassland soils, particularly in response to pine litter addition; under these conditions, fungal and Gram + biomarkers showed more incorporation of SOM-C than did Gram – biomarkers. In contrast, the oak soil microbial community primarily incorporated C from the added substrates. More ¹³C (from both simple and recalcitrant sources) was incorporated into the Gram – biomarkers than Gram + biomarkers despite the fact that the Gram + group generally comprised a greater portion of the bacterial biomass than did markers for the Gram – group. These experiments begin to identify components of the soil microbial community responsible for decomposition of different types of C-substrates. The results demonstrate that the presence of distinctly different plant communities did not alter the microbial community profile responsible for decomposition of relatively labile C-substrates but did alter the profiles of microbial communities responsible for decomposition of the more recalcitrant substrates, pine litter and indigenous soil organic matter.     

Dark microbial CO2 fixation in temperate forest soils increases with CO2 concentration

Dark, that is, nonphototrophic, microbial CO₂ fixation occurs in a large range of soils. However, it is still not known whether dark microbial CO₂ fixation substantially contributes to the C balance of soils and what factors control this process. Therefore, the objective of this study was to quantitate dark microbial CO₂ fixation in temperate forest soils, to determine the relationship between the soil CO₂ concentration and dark microbial CO₂ fixation, and to estimate the relative contribution of different microbial groups to dark CO₂ fixation. For this purpose, we conducted a ¹³C‐CO₂ labeling experiment. We found that the rates of dark microbial CO₂ fixation were positively correlated with the CO₂ concentration in all soils. Dark microbial CO₂ fixation amounted to up to 320 µg C kg^?1 soil day^?1 in the Ah horizon. The fixation rates were 2.8–8.9 times higher in the Ah horizon than in the Bw1 horizon. Although the rates of dark microbial fixation were small compared to the respiration rate (1.2%–3.9% of the respiration rate), our findings suggest that organic matter formed by microorganisms from CO₂ contributes to the soil organic matter pool, especially given that microbial detritus is more stable in soil than plant detritus. Phospholipid fatty acid analyses indicated that CO₂ was mostly fixed by gram‐positive bacteria, and not by fungi. In conclusion, our study shows that the dark microbial CO₂ fixation rate in temperate forest soils increases in periods of high CO₂ concentrations, that dark microbial CO₂ fixation is mostly accomplished by gram‐positive bacteria, and that dark microbial CO₂ fixation contributes to the formation of soil organic matter.     

Sequestration and turnover of bacterial- and fungal-derived carbon in a temperate grassland soil under long-term elevated atmospheric pCO2

Temperate grasslands contribute about 20% to the global C budget. Elevation of atmospheric CO₂ concentration (pCO₂) could lead to additional C sequestration into these ecosystems. Microbial‐derived C in the soil comprising about 1–5% of total soil organic carbon may be an important ‘pool’ for long‐term storage of C under future increased atmospheric CO₂ concentrations. In our study, the impact of elevated pCO₂ on bacterial‐ and fungal‐derived C in the soil of Lolium perenne pastures was investigated under free air carbon dioxide enrichment (FACE) conditions. For 7 years, L. perenne swards were exposed to ambient and elevated pCO₂ (36 and 60 Pa pCO₂, respectively). The additional CO₂ in the FACE plots was depleted in ¹³C compared with ambient plots, so that ‘new’ (<7 years) C inputs in the form of microbial‐derived residues could be determined by means of stable C isotope analysis. Amino sugars in soil are reliable organic biomarkers for indicating the presence of microbial‐derived residues, with particular amino sugars indicative of either bacterial or fungal origin. It is assumed that amino sugars are stabilized to a significant extent in soil, and so may play an important role in long‐term C storage. In our study, we were also able to discriminate between ‘old’ (> 7 years) and ‘new’ microbial‐derived C using compound‐specific δ¹³C analysis of individual amino sugars. This new tool was very useful in investigating the potential for C storage in microbial‐derived residues and the turnover of this C in soil under increased atmospheric pCO₂. The ¹³C signature of individual amino sugars varied between ?17.4‰ and ?39.6‰, and was up to 11.5% depleted in ¹³C in the FACE plots when compared with the bulk δ¹³C value of the native C3 L. perenne soil. New amino sugars in the bulk soil contributed up to 16% to the overall amino sugar pool after the first year and between 62% and 125% after 7 years of exposure to elevated pCO₂. Amounts of new glucosamine increased by the greatest amount (16–125%) during the experiment, followed by mannosamine (?9% to 107%), muramic acid (?11% to 97%), and galactosamine (15–62%). Proportions of new amino sugars in particle size fractions varied between 38% for muramic acid in the clay fraction and 100% for glucosamine and galactosamine in the coarse sand fraction. Summarizing, during the 7‐year period, amino sugars constituted only between 0.9% and 1.6% of the total SOC content. Therefore, their absolute significance for long‐term C sequestration is limited. Additionally new amino sugars were only sequestered in the silt fraction upon elevated pCO₂ exposure while amino sugar concentrations in the clay fraction decreased. Overall, amino sugar concentrations in bulk soil did not change significantly upon exposure to elevated pCO₂. The calculated mean residence time of amino sugars was surprisingly low varying between 6 and 90 years in the bulk soil, and between 3 and 30 years in the particle size fractions, representing soil organic matter pools with different but relatively low turnover times. Therefore, compound‐specific δ¹³C analysis of individual amino sugars clearly revealed a high amino sugar turnover despite more or less constant amino sugar concentrations over a 7 years period of exposure to elevated pCO₂.     

Nitrogen deposition promotes the production of new fungal residues but retards the decomposition of old residues in forest soil fractions

Atmospheric nitrogen (N) deposition has frequently been observed to increase soil carbon (C) storage in forests, but the underlying mechanisms still remain unclear. Changes in microbial community composition and substrate use are hypothesized to be one of the key mechanisms affected by N inputs. Here, we investigated the effects of N deposition on amino sugars, which are used as biomarkers for fungal‐ and bacterial‐derived microbial residues in soil. We made use of a 4‐year combined CO₂ enrichment and N deposition experiment in model forest ecosystems, providing a distinct ¹³C signal for ‘new’ and ‘old’ C in soil organic matter and microbial residues measured in density and particle‐size fractions of soils. Our hypothesis was that N deposition decreases the amount of fungal residues in soils, with the new microbial residues being more strongly affected than old residues. The soil fractionation showed that organic matter and microbial residues are mainly stabilized by association with soil minerals in the heavy and fine fractions. Moreover, the bacterial residues are relatively enriched at mineral surfaces compared to fungal residues. The ¹³C tracing indicated a greater formation of fungal residues compared to bacterial residues after 4 years of experiment. In contradiction to our hypotheses, N deposition significantly increased the amount of new fungal residues in bulk soil and decreased the decomposition of old microbial residues associated with soil minerals. The preservation of old microbial residues could be due to decreased N limitation of microorganisms and therefore a reduced dependence on organic N sources. This mechanism might be especially important in fine heavy fractions with low C/N ratios, where microbial residues are effectively protected from decomposition by association with soil minerals.     

No overall stimulation of soil respiration under mature deciduous forest trees after 7 years of CO2 enrichment

The anthropogenic rise in atmospheric CO₂ is expected to impact carbon (C) fluxes not only at ecosystem level but also at the global scale by altering C cycle processes in soils. At the Swiss Canopy Crane (SCC), we examined how 7 years of free air CO₂ enrichment (FACE) affected soil CO₂ dynamics in a ca. 100‐year‐old mixed deciduous forest. The use of ¹³C‐depleted CO₂ for canopy enrichment allowed us to trace the flow of recently fixed C. In the 7th year of growth at ～550 ppm CO₂, soil respiratory CO₂ consisted of 39% labelled C. During the growing season, soil air CO₂ concentration was significantly enhanced under CO₂‐exposed trees. However, elevated CO₂ failed to stimulate cumulative soil respiration (R_s) over the growing season. We found periodic reductions as well as increases in instantaneous rates of R_s in response to elevated CO₂, depending on soil temperature and soil volumetric water content (VWC; significant three‐way interaction). During wet periods, soil water savings under CO₂‐enriched trees led to excessive VWC (>45%) that suppressed R_s. Elevated CO₂ stimulated R_s only when VWC was ≤40% and concurrent soil temperature was high (>15 °C). Seasonal Q₁₀ estimates of R_s were significantly lower under elevated (Q₁₀=3.30) compared with ambient CO₂ (Q₁₀=3.97). However, this effect disappeared when three consecutive sampling dates of extremely high VWC were disregarded. This suggests that elevated CO₂ affected Q₁₀ mainly indirectly through changes in VWC. Fine root respiration did not differ significantly between treatments but soil microbial biomass (C_mic) increased by 14% under elevated CO₂ (marginally significant). Our findings do not indicate enhanced soil C emissions in such stands under future atmospheric CO₂. It remains to be shown whether C losses via leaching of dissolved organic or inorganic C (DOC, DIC) help to balance the C budget in this forest.     

Effects of long term CO2 enrichment on microbial community structure in calcareous grassland

Elevated CO₂ generally increases plant productivity, and has been found to alter plant community composition in many ecosystems. Because soil microbes depend on plant-derived C and are often associated with specific plant species, elevated CO₂ has the potential to alter structure and functioning of soil microbial communities. We investigated soil microbial community structure of a species-rich semi-natural calcareous grassland that had been exposed to elevated CO₂ (600 μL L^?1) for 6 growing seasons. We analysed microbial community structure using phospholipid fatty acid (PLFA) profiles and DNA fingerprints obtained by Denaturing Gradient Gel Electrophoresis (DGGE) of 16S rDNA fragments amplified by the Polymerase Chain Reaction (PCR). PLFA profiles were not affected by CO₂ enrichment and the ratio of fungal and bacterial PLFA did not change. Ordination analysis of DNA fingerprints revealed a significant relation between CO₂ enrichment and variation in DNA fingerprints in summer (P=0.01), but not in spring. This variation was due to changes in low-intensity bands, while dominant bands did not differ between CO₂ treatments. Diversity of the bacterial community, as assessed by number of bands in DNA fingerprints and calculation of Shannon diversity indices, was not affected by elevated CO₂. Overall, only minor effects on microbial community structure were detected, corroborating earlier findings that soil carbon inputs did probably change much less than suggested by plant photosynthetic responses.     

Translocation and turnover of rhizodeposit carbon within soil microbial communities of an extensive grassland ecosystem

Background and Aims

A substantial amount of photosynthesized plant-C is allocated belowground in grassland ecosystems where it influences the structure and function of the soil microbial community with potential implications for C cycling and storage. We applied stable isotope probing of microbial PLFAs and repeated soil sampling in a grassland over a period of 1 year to assess the role of microbial communities in the cycling of rhizodeposit-C.

Methods

Pulse-labeling with ¹³CO₂ was performed in a grassland site near Gent (Belgium). Soil samples were taken 24 h, 1 week, 1 month, 4 months, 9 months and 1 year following labeling and analyzed for ¹³C in soil, roots and microbial PLFAs.

Results

C enrichment of PLFAs occurred rapidly (within 24 h) but temporally varied across microbial groups. PLFAs indicative for fungi and gram-negative bacteria showed a faster ¹³C uptake compared to gram-positive bacteria and actinomycetes. However, the relative ¹³C concentrations of the latter communities increased after 1 week, while those of fungi decreased and those of gram-negative bacteria remained constant. PLFA ¹³C mean residence times were much shorter for fungi compared to bacteria and actinomycetes.

Conclusions

Our results indicate temporally varying rhizodeposit-C uptake by different microbial groups, and faster turnover rates of mycorrhizal versus saprotrophic fungi and fungi versus bacteria. Fungi appeared to play a major role in the initial processing and possible rapid channeling of rhizodeposit-C into the soil microbial community. Actinomycetes and gram-positive bacteria appeared to have a delayed utilization of rhizodeposit-C or to prefer other C sources upon rhizodeposition.     

Impacts of 3 years of elevated atmospheric CO2 on rhizosphere carbon flow and microbial community dynamics

Carbon (C) uptake by terrestrial ecosystems represents an important option for partially mitigating anthropogenic CO₂ emissions. Short‐term atmospheric elevated CO₂ exposure has been shown to create major shifts in C flow routes and diversity of the active soil‐borne microbial community. Long‐term increases in CO₂ have been hypothesized to have subtle effects due to the potential adaptation of soil microorganism to the increased flow of organic C. Here, we studied the effects of prolonged elevated atmospheric CO₂ exposure on microbial C flow and microbial communities in the rhizosphere. Carex arenaria (a nonmycorrhizal plant species) and Festuca rubra (a mycorrhizal plant species) were grown at defined atmospheric conditions differing in CO₂ concentration (350 and 700 ppm) for 3 years. During this period, C flow was assessed repeatedly (after 6 months, 1, 2, and 3 years) by ¹³C pulse‐chase experiments, and label was tracked through the rhizosphere bacterial, general fungal, and arbuscular mycorrhizal fungal (AMF) communities. Fatty acid biomarker analyses and RNA‐stable isotope probing (RNA‐SIP), in combination with real‐time PCR and PCR‐DGGE, were used to examine microbial community dynamics and abundance. Throughout the experiment the influence of elevated CO₂ was highly plant dependent, with the mycorrhizal plant exerting a greater influence on both bacterial and fungal communities. Biomarker data confirmed that rhizodeposited C was first processed by AMF and subsequently transferred to bacterial and fungal communities in the rhizosphere soil. Over the course of 3 years, elevated CO₂ caused a continuous increase in the ¹³C enrichment retained in AMF and an increasing delay in the transfer of C to the bacterial community. These results show that, not only do elevated atmospheric CO₂ conditions induce changes in rhizosphere C flow and dynamics but also continue to develop over multiple seasons, thereby affecting terrestrial ecosystems C utilization processes.     

南亚热带红椎和格木人工幼龄林土壤微生物群落结构特征

采用氯仿熏蒸浸提法和磷脂脂肪酸法(Phospholipids fatty acid,PLFA)研究了我国南亚热带地区非固氮树种红椎(Castanopsis hystrix)和固氮树种格木(Erythrophleum fordii)人工幼龄林土壤微生物生物量与微生物群落结构特征。结果表明,在旱季和雨季,红椎幼龄林土壤微生物总PLFAs量,细菌PLFAs量、放线菌PLFAs量及丛枝菌根真菌PLFAs量均大于格木幼龄林。红椎幼龄林土壤PLFA Shannon多样性指数(H_(PLFA))在旱季和雨季均大于格木幼龄林。主成分分析表明,土壤微生物群落结构组成受到林分类型和季节的双重影响。冗余分析表明,土壤硝态氮(NO_3~--N)含量、土壤含水量、p H及土壤微生物生物量氮(MBN)与特征磷脂脂肪酸之间呈显著相关关系。以上结果表明固氮树种格木与非固氮树种红椎人工幼龄林对土壤微生物生物量和群落结构的影响存在显著差异。     

A Microbial Link between Elevated CO2 and Methane Emissions that is Plant Species-Specific

Rising atmospheric CO₂ levels alter the physiology of many plant species, but little is known of changes to root dynamics that may impact soil microbial mediation of greenhouse gas emissions from wetlands. We grew co-occurring wetland plant species that included an invasive reed canary grass (Phalaris arundinacea L.) and a native woolgrass (Scirpus cyperinus L.) in a controlled greenhouse facility under ambient (380 ppm) and elevated atmospheric CO₂ (700 ppm). We hypothesized that elevated atmospheric CO₂ would increase the abundance of both archaeal methanogen and bacterial methanotroph populations through stimulation of plant root and shoot biomass. We found that methane levels emitted from S. cyperinus shoots increased 1.5-fold under elevated CO₂, while no changes in methane levels were detected from P. arundincea. The increase in methane emissions was not explained by enhanced root or shoot growth of S. cyperinus. Principal components analysis of the total phospholipid fatty acid (PLFA) recovered from microbial cell membranes revealed that elevated CO₂ levels shifted the composition of the microbial community under S. cyperinus, while no changes were detected under P. arundinacea. More detailed analysis of microbial abundance showed no impact of elevated CO₂ on a fatty acid indicative of methanotrophic bacteria (18:2ω6c), and no changes were detected in the terminal restriction fragment length polymorphism (T-RFLP) relative abundance profiles of acetate-utilizing archaeal methanogens. Plant carbon depleted in ¹³C was traced into the PLFAs of soil microorganisms as a measure of the plant contribution to microbial PLFA. The relative contribution of plant-derived carbon to PLFA carbon was larger in S. cyperinus compared with P. arundinacea in four PLFAs (i14:0, i15:0, a15:0, and 18:1ω9t). The δ¹³C isotopic values indicate that the contribution of plant-derived carbon to microbial lipids could differ in rhizospheres of CO₂-responsive plant species, such as S. cyperinus in this study. The results from this study show that the CO₂–methane link found in S. cyperinus can occur without a corresponding change in methanogen and methanotroph relative abundances, but PLFA analysis indicated shifts in the community profile of bacteria and fungi that were unique to rhizospheres under elevated CO₂.     

Carbon and nitrogen pools and mineralization in a grassland gley soil under elevated carbon dioxide at a natural CO2 spring

The growth and chemical composition of most plants are influenced by elevated CO₂, but accompanying effects on soil organic matter pools and mineralization are less clearly defined, partly because of the short‐term nature of most studies. Herein we describe soil properties from a naturally occurring cold CO₂ spring (Hakanoa) in Northland, New Zealand, at which the surrounding vegetation has been exposed to elevated CO₂ for at least several decades. The mean annual temperature at this site is ≈ 15.5 °C and rainfall ≈ 1550 mm. The site was unfertilized and ungrazed, with a vegetation of mainly C3 and C4 grasses, and had moderate levels of ‘available’ P. Two soils were present ? a gley soil and an organic soil – but only the gley soil is examined here. Average atmospheric CO₂ concentrations at 17 sampling locations in the gley soil area ranged from 372 to 670 ppmv. In samples at 0–5 cm depth, pH averaged 5.4; average values for organic C were 150 g, total N 11 g, microbial C 3.50 g, and microbial N 0.65 g kg^?1, respectively. Under standardized moisture conditions at 25 °C, average rates of CO₂‐C production (7–14 days) were 5.4 mg kg^?1 h^?1 and of net mineral‐N production (14 ?42 days) 0.40 mg kg^?1 h^?1. These properties were all correlated positively and significantly (P < 0.10) with atmospheric CO₂ concentrations, but not with soil moisture (except for CO₂‐C production) or with clay content; they were, however, correlated negatively and mainly significantly with soil pH. In spite of uncertainties associated with the uncontrolled environment of naturally occurring springs, we conclude that storage of C and N can increase under prolonged exposure to elevated CO₂, and may include an appreciable labile fraction in mineral soil with an adequate nutrient supply.     

Laboratory incubations reveal potential responses of soil nitrogen cycling to changes in soil C and N availability in Mojave Desert soils exposed to elevated atmospheric CO2

Elevated atmospheric carbon dioxide (CO₂) has the potential to alter soil carbon (C) and nitrogen (N) cycling in arid ecosystems through changes in net primary productivity. However, an associated feedback exists because any sustained increases in plant productivity will depend upon the continued availability of soil N. We took soils from under the canopies of major shrubs, grasses, and plant interspaces in a Mojave Desert ecosystem exposed to elevated atmospheric CO₂ and incubated them in the laboratory with amendments of labile C and N to determine if elevated CO₂ altered the mechanistic controls of soil C and N on microbial N cycling. Net ammonification increased under shrubs exposed to elevated CO₂, while net nitrification decreased. Elevated CO₂ treatments exhibited greater fluxes of N₂O–N under Lycium spp., but not other microsites. The proportion of microbial/extractable organic N increased under shrubs exposed to elevated CO₂. Heterotrophic N₂‐fixation and C mineralization increased with C addition, while denitrification enzyme activity and N₂O–N fluxes increased when C and N were added in combination. Laboratory results demonstrated the potential for elevated CO₂ to affect soil N cycling under shrubs and supports the hypothesis that energy limited microbes may increase net inorganic N cycling rates as the amount of soil‐available C increases under elevated CO₂. The effect of CO₂ enrichment on N‐cycling processes is mediated by its effect on the plants, particularly shrubs. The potential for elevated atmospheric CO₂ to lead to accumulation of NH₄⁺ under shrubs and the subsequent volatilization of NH₃ may result in greater losses of N from this system, leading to changes in the form and amount of plant‐available inorganic N. This introduces the potential for a negative feedback mechanism that could act to constrain the degree to which plants can increase productivity in the face of elevated atmospheric CO₂.     

Does deep soil N availability sustain long‐term ecosystem responses to elevated CO2?

A scrub‐oak woodland has maintained higher aboveground biomass accumulation after 11 years of atmospheric CO₂ enrichment (ambient +350 μmol CO₂ mol^?1), despite the expectation of strong nitrogen (N) limitation at the site. We hypothesized that changes in plant available N and exploitation of deep sources of inorganic N in soils have sustained greater growth at elevated CO₂. We employed a suite of assays performed in the sixth and 11th year of a CO₂ enrichment experiment designed to assess soil N dynamics and N availability in the entire soil profile. In the 11th year, we found no differences in gross N flux, but significantly greater microbial respiration (P≤0.01) at elevated CO₂. Elevated CO₂ lowered extractable inorganic N concentrations (P=0.096) considering the whole soil profile (0–190 cm). Conversely, potential net N mineralization, although not significant in considering the entire profile (P=0.460), tended to be greater at elevated CO₂. Ion‐exchange resins placed in the soil profile for approximately 1 year revealed that potential N availability at the water table was almost 3 × greater than found elsewhere in the profile, and we found direct evidence using a ¹⁵N tracer study that plants took up N from the water table. Increased microbial respiration and shorter mean residence times of inorganic N at shallower depths suggests that enhanced SOM decomposition may promote a sustained supply of inorganic N at elevated CO₂. Deep soil N availability at the water table is considerable, and provides a readily available source of N for plant uptake. Increased plant growth at elevated CO₂ in this ecosystem may be sustained through greater inorganic N supply from shallow soils and N uptake from deep soil.