Nitrogen Fertilization Has a Stronger Effect on Soil Nitrogen-Fixing Bacterial Communities than Elevated Atmospheric CO2

Biological nitrogen fixation is the primary supply of N to most ecosystems, yet there is considerable uncertainty about how N-fixing bacteria will respond to global change factors such as increasing atmospheric CO₂ and N deposition. Using the nifH gene as a molecular marker, we studied how the community structure of N-fixing soil bacteria from temperate pine, aspen, and sweet gum stands and a brackish tidal marsh responded to multiyear elevated CO₂ conditions. We also examined how N availability, specifically, N fertilization, interacted with elevated CO₂ to affect these communities in the temperate pine forest. Based on data from Sanger sequencing and quantitative PCR, the soil nifH composition in the three forest systems was dominated by species in the Geobacteraceae and, to a lesser extent, Alphaproteobacteria. The N-fixing-bacterial-community structure was subtly altered after 10 or more years of elevated atmospheric CO₂, and the observed shifts differed in each biome. In the pine forest, N fertilization had a stronger effect on nifH community structure than elevated CO₂ and suppressed the diversity and abundance of N-fixing bacteria under elevated atmospheric CO₂ conditions. These results indicate that N-fixing bacteria have complex, interacting responses that will be important for understanding ecosystem productivity in a changing climate.     

Elevated pCO2 alters marine heterotrophic bacterial community composition and metabolic potential in response to a pulse of phytoplankton organic matter

Factors that affect the respiration of organic carbon by marine bacteria can alter the extent to which the oceans act as a sink of atmospheric carbon dioxide. We designed seawater dilution experiments to assess the effect of pCO₂ enrichment on heterotrophic bacterial community composition and metabolic potential in response to a pulse of phytoplankton-derived organic carbon. Experiments included treatments of elevated (1000 p.p.m.) and low (250 p.p.m.) pCO₂ amended with 10 μmol L⁻¹ dissolved organic carbon from Emiliana huxleyi lysates, and were conducted using surface-seawater collected from the South Pacific Subtropical Gyre. To assess differences in community composition and metabolic potential, shotgun metagenomic libraries were sequenced from low and elevated pCO₂ treatments collected at the start of the experiment and following exponential growth. Our results indicate bacterial communities changed markedly in response to the organic matter pulse over time and were significantly affected by pCO₂ enrichment. Elevated pCO₂ also had disproportionate effects on the abundance of sequences related to proton pumps, carbohydrate metabolism, modifications of the phospholipid bilayer, resistance to toxic compounds and conjugative transfer. These results contribute to a growing understanding of the effects of elevated pCO₂ on bacteria-mediated carbon cycling during phytoplankton bloom conditions in the marine environment.     

Colloidal and Dissolved Organic Matter Excreted by a Mixotrophic Flagellate during Bacterivory and Autotrophy

Excretion of dissolved and colloidal organic carbon by a mixotrophic flagellate, the chrysophyte Poterioochromonas malhamensis, was studied. Flagellates were incubated either with ¹⁴C-labeled bacteria or with inorganic ¹⁴C, in order to compare organic exudates originating from primary production with exudates originating from ingested bacteria. Colloids of >0.02 μm constituted a larger fraction of the exudates originating from ingested bacteria, compared with exudates derived from primary production. Flagellate feeding on bacteria specifically labeled in different cell components was compared. Cell wall components gave rise to less colloidal organic carbon than did other cell constituents. To investigate the degradability of flagellate ¹⁴C-exudates, they were added to lake water and mineralization to ¹⁴CO₂ was monitored. Bacterially derived exudates were more recalcitrant than exudates originating from photosynthesis. The results support the hypothesis that bacterial utilization of labile organic compounds, followed by flagellate bacterivory and exudation, results in a transformation of labile organic matter into more recalcitrant forms.     

Algal Exudates and Stream Organic Matter Influence the Structure and Function of Denitrifying Bacterial Communities

Within aquatic ecosystems, periphytic biofilms can be hot spots of denitrification, and previous work has suggested that algal taxa within periphyton can influence the species composition and activity of resident denitrifying bacteria. This study tested the hypothesis that algal species composition within biofilms influences the structure and function of associated denitrifying bacterial communities through the composition of organic exudates. A mixed population of bacteria was incubated with organic carbon isolated from one of seven algal species or from one of two streams that differed in anthropogenic inputs. Pyrolysis-gas chromatography-mass spectrometry (Py-GC/MS) revealed differences in the organic composition of algal exudates and stream waters, which, in turn, selected for distinct bacterial communities. Organic carbon source had a significant effect on potential denitrification rates (DNP) of the communities, with organics isolated from a stream with high anthropogenic inputs resulting in a bacterial community with the highest DNP. There was no correlation between DNP and numbers of denitrifiers (based on nirS copy numbers), but there was a strong relationship between the species composition of denitrifier communities (as indicated by tag pyrosequencing of nosZ genes) and DNP. Specifically, the relative abundance of Pseudomonas stutzeri-like nosZ sequences across treatments correlated significantly with DNP, and bacterial communities incubated with organic carbon from the stream with high anthropogenic inputs had the highest relative abundance of P. stutzeri-like nosZ sequences. These results demonstrate a significant relationship between bacterial community composition and function and provide evidence of the potential impacts of anthropogenic inputs on the structure and function of stream microbial communities.     

Changes in microbial activity and composition in a pasture ecosystem exposed to elevated atmospheric carbon dioxide

Elevated atmospheric CO₂ increases aboveground plant growth and productivity. However, carbon dioxide-induced alterations in plant growth are also likely to affect belowground processes, including the composition of soil biota. We investigated the influence of increased atmospheric CO₂on bacterial numbers and activity, and on soil microbial community composition in a pasture ecosystem under Free-Air Carbon Dioxide Enrichment (FACE). Composition of the soil microbial communities, in rhizosphere and bulk soil, under two atmospheric CO₂ levels was evaluated by using phospholipid fatty acid analysis (PLFA), and total and respiring bacteria counts were determined by epifluorescence microscopy. While populations increased with elevated atmospheric CO₂ in bulk soil of white clover (Trifolium repens L.), a higher atmospheric CO₂ concentration did not affect total or metabolically active bacteria in bulk soil of perennial ryegrass (Lolium perenne L.). There was no effect of atmospheric CO₂ on total bacteria populations per gram of rhizosphere soil. The combined effect of elevated CO₂ on total root length of each species and the bacterial population in these rhizospheres, however, resulted in an 85% increase in total rhizosphere bacteria and a 170% increase in respiring rhizosphere bacteria for the two plant species, when assessed on a per unit land area basis. Differences in microbial community composition between rhizosphere and bulk soil were evident in samples from white clover, and these communities changed in response to CO₂ enrichment. Results of this study indicate that changes in soil microbial activity, numbers, and community composition are likely to occur under elevated atmospheric CO₂, but the extent of those changes depend on plant species and the distance that microbes are from the immediate vicinity of the plant root surface.     

Soil Fungi Respond More Strongly than Fine Roots to Elevated CO2 in a Model Regenerating Longleaf Pine-Wiregrass Ecosystem

Rising atmospheric CO₂ concentration will affect belowground processes and forest function. However, the direction and magnitude of change for many soil processes are unknown. We used minirhizotrons to observe fine root and fungal dynamics in response to elevated CO₂ in a model regenerating longleaf pine community in open-top chambers. The model community consisted of five plant species common to xeric sandhills longleaf pine stands: Pinus palustris, Quercus margaretta, Aristida stricta, Crotalaria rotundifolia, and Asclepias tuberosa. Elevated CO₂ significantly increased both fine root and mycorrhizal tip standing crop by more than 50% in the deeper soil horizon (17–34 cm). Rhizomorph standing crop was nearly doubled in both deep and shallow soil (P = 0.04). Survivorship results for fine roots and rhizomorphs varied between soil depths. Fine root survivorship was likely influenced more by changes in community composition and species interactions driven by elevated CO₂ rather than by direct effects of elevated CO₂ on the fine roots of individual species. In this system, it appears that elevated CO₂ led to a greater reliance on fungal symbionts to meet additional nutrient requirements rather than substantially increased root growth.     

Effects of elevated CO2 and Pb on the microbial community in the rhizosphere of Pinus densiflora

Rising levels of atmospheric CO₂ may stimulate forest productivity in the future, resulting in increased carbon storage in terrestrial ecosystems. However, heavy metal contamination may interfere with this, though the response is not yet known. In this study, we investigated the effect of elevated CO₂ and Pb contamination on microorganisms and decomposition in pine tree forest soil. Three-year old pine trees (Pinus densiflora) were planted in Pb contaminated soils (500 mg/kg-soil) and uncontaminated soils and cultivated for three months in a growth chamber where the CO₂ concentration was controlled at 380 or 760 mg/kg. Structures of the microbial community were comparatively analyzed in bulk and in rhizosphere soil samples using community-level physiological profiling (CLPP) and 16S rRNA gene PCR-DGGE (denaturing gradient gel electrophoresis). Additionally, microbial activity in rhizospheric soil, growth and the C/N ratio of the pine trees were measured. Elevated CO₂ significantly increased microbial activities and diversity in Pb contaminated soils due to the increase in carbon sources, and this increase was more distinctive in rhizospheric soil than in bulk soils. In addition, increased plant growth and C/N ratios of pine needles at elevated CO₂ resulted in an increase in cation exchange capacity (CEC) and dissolved organic carbon (DOC) of the rhizosphere in Pb contaminated soil. Taken together, these findings indicate that elevated CO₂ levels and heavy metals can affect the soil carbon cycle by changing the microbial community and plant metabolism.     

Responses of the Anaerobic Bacterial Community to Addition of Organic C in Chromium(VI)- and Iron(III)-Amended Microcosms

Chromium (VI) is toxic to microorganisms and can inhibit the biodegradation of organic pollutants in contaminated soils. We used microcosms amended with either glucose or protein (to drive bacterial community change) and Fe(III) (to stimulate iron-reducing bacteria) to study the effect of various concentrations of Cr(VI) on anaerobic bacterial communities. Microcosms were destructively sampled based on microbial activity (measured as evolution of CO₂) and analyzed for the following: (i) dominant bacterial community by PCR-denaturing gradient gel electrophoresis (DGGE) of the 16S rRNA gene; (ii) culturable Cr-resistant bacteria; and (iii) enrichment of iron-reducing bacteria of the Geobacteraceae family by real-time PCR. The addition of organic C stimulated the activities of anaerobic communities. Cr(VI) amendment resulted in lower rates of CO₂ production in glucose microcosms and a slow mineralization phase in protein-amended microcosms. Glucose and protein amendments selected for different bacterial communities. This selection was modified by the addition of Cr(VI), since some DGGE bands were intensified and new bands appeared in Cr(VI)-amended microcosms. A second dose of Cr(VI), added after the onset of activity, had a strong inhibitory effect when higher levels of Cr were added, indicating that the developing Cr-resistant communities had a relatively low tolerance threshold. Most of the isolated Cr-resistant bacteria were closely related to previously studied Cr-resistant anaerobes, such as Pantoea, Pseudomonas, and Enterobacter species. Geobacteraceae were not enriched during the incubation. The studied Cr(VI)-contaminated soil contained a viable anaerobic bacterial community; however, Cr(VI) altered its composition, which could affect the soil biodegradation potential.     

Interaction between Medicago truncatula and Pseudomonas fluorescens: Evaluation of Costs and Benefits across an Elevated Atmospheric CO2

Soil microorganisms play a key role in both plants nutrition and health. Their relation with plant varies from mutualism to parasitism, according to the balance of costs and benefits for the two partners of the interaction. These interactions involved the liberation of plant organic compounds via rhizodeposition. Modification of atmospheric CO₂ concentration may affect rhizodeposition and as a consequence trophic interactions that bind plants and microorganisms. Positive effect of elevated CO₂ on plants are rather well known but consequences for micoorganisms and their interactions with plants are still poorly understood. A gnotobiotic system has been developed to study the interaction between Medicago truncatula Jemalong J5 and the mutualistic bacteria Pseudomonas fluorescens strain C7R12 under two atmospheric CO₂ concentrations: ambient (365 ppm) versus enriched (750 ppm). Costs and benefits for each partner have been determined over time by measuring plant development and growth, the C and N contents of the various plant parts and the density of the bacteria in rhizosphere compartments. Following the increase in CO₂, there was a beneficial effect of P. fluorescens C7R12 on development, vegetative growth, and C/N content of M. truncatula. Concerning plant reproduction, an early seed production was noticed in presence of the bacterial strain combined with increased atmospheric CO₂ conditions. Paradoxically, this transient increase in seed production was correlated with a decrease in bacterial density in the rhizosphere soil, revealing a cost of increased CO₂ for the bacterial strain. This shift of costs-benefits ratio disappeared later during the plant growth. In conclusion, the increase in CO₂ concentration modifies transiently the cost-benefit balance in favor of the plant. These results may be explained either by a competition between the two partners or a change in bacterial physiology. The ecosystem functioning depends on the stability of many plant-microbe associations that abiotic factors can disrupt.     

Changes of bacterial communities in the rhizosphere of sugarcane under elevated concentration of atmospheric CO2

It is believed that climate change will influence most of interactions that sustain life on Earth. Among these, the recruitment exerted by plants in their roots vicinity can change, leading to differential assemblages of microbiomes in the rhizosphere. We approached this issue analyzing the variations in the composition of bacterial communities in the rhizosphere of sugarcane cultivated under two concentrations of atmospheric CO₂ (350 or 700 ppm). In addition to the analysis of bacterial community, the use of DNA‐SIP allowed the comparison of bacterial groups assimilating roots exudates (based on ¹³C‐labeled DNA) in both conditions, in a period of 8 days after the CO₂ pulse. The separation of ¹³C‐DNA indicated the low but increasing frequency of labeling in the rhizosphere, as averages of 0.6, 2.4 and 5.0% of total DNA were labeled after 2, 4, and 8 days after the ¹³CO₂ pulse, respectively. Based on large‐scale sequencing of the V6 region in the gene 16S rRNA, we found an increase in the bacterial diversity in the ¹³C‐DNA along the sampling period. We also describe the occurrence of distinct bacterial groups assimilating roots exudates from sugarcane cultivated under each CO₂ concentration. Bacilli, Gammaproteobacteria, and Clostridia showed high affinity for the C‐sources released by sugarcane under 350 ppm of CO₂, while under elevated concentration of CO₂, the assimilation of roots exudates was prevalently made by members of Bacilli and Betaproteobacteria. The communities became more similar along time (4 and 8 days after CO₂ pulse), in both concentrations of CO₂, electing Actinobacteria, Sphingobacteriia, and Alphaproteobacteria as the major cross‐feeders on sugarcane exudates. In summary, we described the bacterial groups with higher affinity to assimilate roots exudates in the rhizosphere of sugarcane, and also demonstrated that the rhizosphere community can be differentially assembled in a future scenario with increased contents of CO₂.     

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.     

Long-term field fertilization alters the diversity of autotrophic bacteria based on the ribulose-1,5-biphosphate carboxylase/oxygenase (RubisCO) large-subunit genes in paddy soil

Carbon dioxide (CO₂) assimilation by autotrophic bacteria is an important process in the soil carbon cycle with major environmental implications. The long-term impact of fertilizer on CO₂ assimilation in the bacterial community of paddy soils remains poorly understood. To narrow this knowledge gap, the composition and abundance of CO₂-assimilating bacteria were investigated using terminal restriction fragment length polymorphism and quantitative PCR of the cbbL gene [that encodes ribulose-1,5-biphosphate carboxylase/oxygenase (RubisCO)] in paddy soils. Soils from three stations in subtropical China were used. Each station is part of a long-term fertilization experiment with three treatments: no fertilizer (CK), chemical fertilizers (NPK), and NPK combined with rice straw (NPKM). At all of the stations, the cbbL-containing bacterial communities were dominated by facultative autotrophic bacteria such as Rhodopseudomonas palustris, Bradyrhizobium japonicum, and Ralstonia eutropha. The community composition in the fertilized soil (NPK and NPKM) was distinct from that in unfertilized soil (CK). The bacterial cbbL abundance (3–8?×?10⁸ copies g soil^?1) and RubisCO activity (0.40–1.76 nmol CO₂ g soil^?1 min^?1) in paddy soils were significantly positively correlated, and both increased with the addition of fertilizer. Among the measured soil parameters, soil organic carbon and pH were the most significant factors influencing the community composition, abundance, and activity of the cbbL-containing bacteria. These results suggest that long-term fertilization has a strong impact on the activity and community of cbbL-containing bacterial populations in paddy soils, especially when straw is combined with chemical fertilizers.     

Soil–Nitrogen Cycling in a Pine Forest Exposed to 5 Years of Elevated Carbon Dioxide

Empirical and modeling studies have shown that the magnitude and duration of the primary production response to elevated carbon dioxide (CO₂) can be constrained by limiting supplies of soil nitrogen (N). We have studied the response of a southern US pine forest to elevated CO₂ for 5 years (1997–2001). Net primary production has increased significantly under elevated CO₂. We hypothesized that the increase in carbon (C) fluxes to the microbial community under elevated CO₂ would increase the rate of N immobilization over mineralization. We tested this hypothesis by quantifying the pool sizes and fluxes of inorganic and organic N in the forest floor and top 30 cm of mineral soil during the first 5 years of CO₂ fumigation. We observed no statistically significant change in the gross or net rate of inorganic N mineralization and immobilization in any soil horizon under elevated CO₂. Similarly, elevated CO₂ had no statistically significant effect on the concentration or flux of organic N, including amino acids. Microbial biomass N was not significantly different between CO₂ treatments. Thus, we reject our hypothesis that elevated CO₂ increases the rate of N immobilization. The quantity and chemistry of the litter inputs to the forest floor and mineral soil horizons can explain the limited range of microbially mediated soil–N cycling responses observed in this ecosystem. Nevertheless a comparative analysis of ecosystem development at this site and other loblolly pine forests suggests that rapid stand development and C sequestration under elevated CO₂ may be possible only in the early stages of stand development, prior to the onset of acute N limitation.     

Elevated CO2 and nitrate levels increase wheat root-associated bacterial abundance and impact rhizosphere microbial community composition and function

Elevated CO₂ stimulates plant growth and affects quantity and composition of root exudates, followed by response of its microbiome. Three scenarios representing nitrate fertilization regimes: limited (30 ppm), moderate (70 ppm) and excess nitrate (100 ppm) were compared under ambient and elevated CO₂ (eCO₂, 850 ppm) to elucidate their combined effects on root-surface-associated bacterial community abundance, structure and function. Wheat root-surface-associated microbiome structure and function, as well as soil and plant properties, were highly influenced by interactions between CO₂ and nitrate levels. Relative abundance of total bacteria per plant increased at eCO₂ under excess nitrate. Elevated CO₂ significantly influenced the abundance of genes encoding enzymes, transporters and secretion systems. Proteobacteria, the largest taxonomic group in wheat roots (~ 75%), is the most influenced group by eCO₂ under all nitrate levels. Rhizobiales, Burkholderiales and Pseudomonadales are responsible for most of these functional changes. A correlation was observed among the five gene-groups whose abundance was significantly changed (secretion systems, particularly type VI secretion system, biofilm formation, pyruvate, fructose and mannose metabolism). These changes in bacterial abundance and gene functions may be the result of alteration in root exudation at eCO₂, leading to changes in bacteria colonization patterns and influencing their fitness and proliferation.Subject terms: Microbiome, Microbial ecology, Metagenomics, Microbial ecology     

Elevated CO2 affects porewater chemistry in a brackish marsh

As atmospheric CO₂ concentrations continue to rise and impact plant communities, concomitant shifts in belowground microbial processes are likely, but poorly understood. We measured monthly porewater concentrations of sulfate, sulfide, methane (CH₄), dissolved inorganic carbon and dissolved organic carbon over a 5-year period in a brackish marsh. Samples were collected using porewater wells (i.e., sippers) in a Schoenoplectus americanus-dominated (C₃ sedge) community, a Spartina patens-dominated (C₄ grass) community and a mixed (C₃ and C₄) community within the marsh. Plant communities were exposed to ambient and elevated (ambient + 340 ppm) CO₂ levels for 15 years prior to porewater sampling, and the treatments continued over the course of our sampling. Sulfate reduction was stimulated by elevated CO₂ in the C₃-dominated community, but not in the C₄-dominated community. Elevated CO₂ also resulted in higher porewater concentrations of CH₄ and dissolved organic carbon in the C₃-dominated system, though inhibition of CH₄ production by sulfate reduction appears to temper the porewater CH₄ response. These patterns mirror the typical divergent responses of C₃ and C₄ plants to elevated CO₂ seen in this ecosystem. Porewater concentrations of nitrogen (as ammonium) and phosphorus did not decrease despite increased plant biomass in the C₃-dominated community, suggesting nutrients do not strongly limit the sustained vegetation response to elevated CO₂. Overall, our data demonstrate that elevated CO₂ drives changes in porewater chemistry and suggest that increased plant productivity likely stimulates microbial decomposition through increases in dissolved organic carbon availability.     

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.     

Compositions isotopiques naturelles des bactéries hétérotrophes et détermination de l'origine du carbone organique dissous biodisponible

Several studies of salt marsh systems have attempted to quantify the flow of organic matter between the land and coastal waters. However, the techniques used could not identify sources of dissolved organic carbon (DOC) rapidly assimilated by heterothrophic bacteria. Recently, the assay of carbon isotope ratios has allowed characterization of the different sources of organic matter in salt marshes. In this study, we wanted to find out if the natural isotopic composition assayed in heterotrophic bacteria distinguished the origin of bioavailable DOC. We determined the δ¹³C values for 1) three bacterial strains and their nucleic acids cultured on glucose and tryptose substrates, respectively, and 2) naturally occurring bacteria recovered from seawater in which salt marsh vegetation had been immersed. First, we showed that the isotopic fractionation was the same for the three bacterial strains cultured on the same synthetic substrate, but could vary depending on the nature of DOC. There was no significant difference between the δ¹³ C values of bacteria and their nucleic acids. Second, natural bacteria were grown in a medium enriched in DOC from halophytic plants. The δ¹³C values of this community were close to those of dissolved organic carbon from plant leachates. The comparison between the isotopic ratios of natural bacteria in Vibrio alginolyticus showed that the heterogeneity of the bacterial community averaged the isotopic fractionation from the preferential assimilation of organic compounds in the medium by each bacterial strain. The δ¹³ C values recorded for the bacterial community in the field and their nucleic acids made it possible to identify the source of organic matter readily accessible to microorganisms in a coastal 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.     

Nematode Genera in Forest Soil Respond Differentially to Elevated CO2

Previous reports suggest that fungivorous nematodes are the only trophic group in forest soils affected by elevated CO₂. However, there can be ambiguity within trophic groups, and we examined data at a genus level to determine whether the conclusion remains similar. Nematodes were extracted from roots and soil of loblolly pine (Pinus taeda) and sweet gum (Liquidambar styraciflua) forests fumigated with either ambient air or CO₂-enriched air. Root length and nematode biomass were estimated using video image analysis. Most common genera included Acrobeloides, Aphelenchoides, Cephalobus, Ditylenchus, Ecphyadorphora, Filenchus, Plectus, Prismatolaimus, and Tylencholaimus. Maturity Index values and diversity increased with elevated CO₂ in loblolly pine but decreased with elevated CO₂ in sweet gum forests. Elevated CO₂ treatment affected the occurrence of more nematode genera in sweet gum than loblolly pine forests. Numbers were similar but size of Xiphinema decreased in elevated CO₂. Abundance, but not biomass, of Aphelenchoides was reduced by elevated CO₂. Treatment effects were apparent at the genus levels that were masked at the trophic level. For example, bacterivores were unaffected by elevated CO₂, but abundance of Cephalobus was affected by CO₂ treatment in both forests.