Enrichment of high-affinity CO oxidizers in Maine forest soil

Carboxydotrophic activity in forest soils was enriched by incubation in a flowthrough system with elevated concentrations of headspace CO (40 to 400 ppm). CO uptake increased substantially over time, while the apparent K(m) ((app)K(m)) for uptake remained similar to that of unenriched soils (<10 to 20 ppm). Carboxydotrophic activity was transferred to and further enriched in sterile sand and forest soil. The (app)K(m)s for secondary and tertiary enrichments remained similar to values for unenriched soils. CO uptake by enriched soil and freshly collected forest soil was inhibited at headspace CO concentrations greater than about 1%. A novel isolate, COX1, obtained from the enrichments was inhibited similarly. However, in contrast to extant carboxydotrophs, COX1 consumed CO with an (app)K(m) of about 15 ppm, a value comparable to that of fresh soils. Phylogenetic analysis based on approximately 1,200 bp of its 16S rRNA gene sequence suggested that the isolate is an alpha-proteobacterium most closely related to the genera Pseudaminobacter, Aminobacter, and Chelatobacter (98.1 to 98.3% sequence identity).     

Oxidation and Assimilation of Atmospheric Methane by Soil Methane Oxidizers

The metabolism of atmospheric methane in a forest soil was studied by radiotracer techniques. Maximum (sup14)CH(inf4) oxidation (163.5 pmol of C cm(sup-3) h(sup-1)) and (sup14)C assimilation (50.3 pmol of C cm(sup-3) h(sup-1)) occurred at the A(inf2) horizon located 15 to 18 cm below the soil surface. At this depth, 31 to 43% of the atmospheric methane oxidized was assimilated into microbial biomass; the remaining methane was recovered as (sup14)CO(inf2). Methane-derived carbon was incorporated into all major cell macromolecules by the soil microorganisms (50% as proteins, 19% as nucleic acids and polysaccharides, and 5% as lipids). The percentage of methane assimilated (carbon conversion efficiency) remained constant at temperatures between 5 and 20(deg)C, followed by a decrease at 30(deg)C. The carbon conversion efficiency did not increase at methane concentrations between 1.7 and 1,000 ppm. In contrast, the overall methane oxidation activity increased at elevated methane concentrations, with an apparent K(infm) of 21 ppm (31 nM CH(inf4)) and a V(infmax) of 188 pmol of CH(inf4) cm(sup-3) h(sup-1). Methane oxidizers from soil depths with maximum methanotrophic activity respired approximately 1 to 3% of the assimilated methane-derived carbon per day. This apparent endogenous respiration did not change significantly in the absence of methane. Similarly, the potential for oxidation of atmospheric methane was relatively insensitive to methane starvation. Soil samples from depths above and below the zone with maximum atmospheric methane oxidation activity showed a dramatic increase in the turnover of the methane assimilated (>20 times increase). Physical disturbance such as sieving or mixing of soil samples decreased methane oxidation and assimilation by 50 to 58% but did not alter the carbon conversion efficiency. Ammonia addition (0.1 or 1.0 (mu)mol g [fresh weight](sup-1)) decreased both methane oxidation and carbon conversion efficiency. This resulted in a dramatic decrease in methane assimilation (85 to 99%). In addition, ammonia-treated soil showed up to 10 times greater turnover of the assimilated methane-derived carbon (relative to untreated soil). The results suggest a potential for microbial growth on atmospheric methane. However, growth was regulated strongly by soil parameters other than the methane concentration. The pattern observed for metabolism of atmospheric methane in soils was not consistent with the physiology of known methanotrophic bacteria.     

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.     

Long-term Effects of Free Air CO2 Enrichment (FACE) on Soil Respiration

Emissions of CO₂ from soils make up one of the largest fluxes in the global C cycle, thus small changes in soil respiration may have large impacts on global C cycling. Anthropogenic additions of CO₂ to the atmosphere are expected to alter soil carbon cycling, an important component of the global carbon budget. As part of the Duke Forest Free-Air CO₂ Enrichment (FACE) experiment, we examined how forest growth at elevated (+200 ppmv) atmospheric CO₂ concentration affects soil CO₂ dynamics over 7 years of continuous enrichment. Soil respiration, soil CO₂ concentrations, and the isotopic signature of soil CO₂ were measured monthly throughout the 7 years of treatment. Estimated annual rates of soil CO₂ efflux have been significantly higher in the elevated plots in every year of the study, but over the last 5 years the magnitude of the CO₂ enrichment effect on soil CO₂ efflux has declined. Gas well samples indicate that over 7 years fumigation has led to sustained increases in soil CO₂ concentrations and depletion in the δ¹³C of soil CO₂ at all but the shallowest soil depths.     

Attributes of Atmospheric Carbon Monoxide Oxidation by Maine Forest Soils

CO, one of the most important trace gases, regulates tropospheric methane, hydroxyl radical, and ozone contents. Ten to 25% of the estimated global CO flux may be consumed by soils annually. Depth profiles for ¹⁴CO oxidation and CO concentration indicated that CO oxidation occurred primarily in surface soils and that photooxidation of soil organic matter did not necessarily contribute significantly to CO fluxes. Kinetic analyses revealed that the apparent K_m was about 18 nM (17 ppm) and the V_max was 6.9 μmol g (fresh weight)⁻¹ h⁻¹; the apparent K_m was similar to the apparent K_m for atmospheric methane consumption, but the V_max was more than 100 times higher. Atmospheric CO oxidation responded sensitively to soil water regimes; decreases in water content in initially saturated soils resulted in increased uptake, and optimum uptake occurred at water contents of 30 to 60%. However, extended drying led to decreased uptake and net CO production. Rewetting could restore CO uptake, albeit with a pronounced hysteresis. The responses to changing temperatures indicated that the optimum temperature for net uptake was between 20 and 25°C and that there was a transition to net production at temperatures above 30°C. The responses to methyl fluoride and acetylene indicated that populations other than ammonia oxidizers and methanotrophs must be involved in forest soils. The response to acetylene was notable, since the strong initial inhibition was reversed after 12 h of incubation; in contrast, methyl fluoride did not have an inhibitory effect. Ammonium did not inhibit CO uptake; the level of nitrite inhibition was initially substantial, but nitrite inhibition was reversible over time. Nitrite inhibition appeared to occur through indirect effects based on abiological formation of NO.     

Influence of Non-nitrogenous Soil Amendments on Soil CO2 Efflux and Fine Root Production in an N-Saturated Northern Hardwood Forest

Non-nitrogenous mineral nutrients may be an important constraint on forest productivity and belowground processes in many ecosystems. We measured responses of soil CO₂ efflux (FCO₂), fine root production, and root-free incubation soil respiration to experimental additions of non-nitrogenous mineral nutrients (phosphorus (P) + potassium (K) fertilizer, dolomitic lime, and P + K plus lime) over 2 years in a sugar-maple-dominated forest in central Ontario; this region receives some of the highest anthropogenic nitrogen (N) inputs in North America, and evidence exists for co-limitation by P, magnesium (Mg), and calcium (Ca) of the growth of dominant trees. Soil amendments, in particular P + K fertilization, reduced FCO₂, fine root production and microbial respiration, with decreases in FCO₂ of 28–51% in fertilized compared to control plots. Partial regression analyses indicated that soil available P had a negative effect on FCO₂, fine root production, and microbial respiration, but detected no significant effects of N, Ca, or Mg. Path analysis further suggested that available P reduced both fine root production and microbial respiration, and that these effects were largely responsible for reduced FCO₂. There was also a residual direct negative relationship between available P and FCO₂, which may represent reduced metabolic activity of roots. The study indicates that P is a critical nutrient dominating belowground processes in an N-saturated forest ecosystem, and suggests that additions of P may enhance C sink strength in managed forests in part through reductions in soil CO₂ efflux.     

Short-Term Response of Soil Bacteria to Carbon Enrichment in Different Soil Microsites

The response of bacteria in bulk soil and earthworm casts to carbon enrichment was studied by an RNA stable-isotope probing/terminal restriction fragment length polymorphism strategy with ¹³C-labeled glucose and acetate. Both the soil microsite status and the carbon enrichment selected rapidly for different active bacterial communities, which resulted in different degradation kinetics. Our study clearly illustrates the biases that are generated by adding C substrates to detect metabolically active bacteria in soil.     

Response of Atmospheric Methane Consumption by Maine Forest Soils to Exogenous Aluminum Salts

Atmospheric methane consumption by Maine forest soils was inhibited by additions of environmentally relevant levels of aluminum. Aluminum chloride was more inhibitory than nitrate or sulfate salts, but its effect was comparable to that of a chelated form of aluminum. Inhibition could be explained in part by the lower soil pH values which resulted from aluminum addition. However, significantly greater inhibition by aluminum than by mineral acids at equivalent soil pH values indicated that inhibition also resulted from direct effects of aluminum per se. The extent of inhibition by exogenous aluminum increased with increasing methane concentration for soils incubated in vitro. At methane concentrations of >10 ppm, inhibition could be observed when aluminum chloride was added at concentrations as low as 10 nmol g (fresh weight) of soil⁻¹. These results suggest that widespread acidification of soils and aluminum mobilization due to acid precipitation may exacerbate inhibition of atmospheric methane consumption due to changes in other parameters and increase the contribution of methane to global warming.     

Stable Isotope Probing Analysis of Interactions between Ammonia Oxidizers

The response of natural microbial communities to environmental change can be assessed by determining DNA- or RNA-targeted changes in relative abundance of 16S rRNA gene sequences by using fingerprinting techniques such as denaturing gradient gel electrophoresis (DNA-DGGE and RNA-DGGE, respectively) or by stable isotope probing (SIP) of 16S rRNA genes following incubation with a ¹³C-labeled substrate (DNA-SIP-DGGE). The sensitivities of these three approaches were compared during batch growth of communities containing two or three Nitrosospira pure or enriched cultures with different tolerances to a high ammonia concentration. Cultures were supplied with low, intermediate, or high initial ammonia concentrations and with ¹³C-labeled carbon dioxide. DNA-SIP-DGGE provided the most direct evidence for growth and was the most sensitive, with changes in DGGE profiles evident before changes in DNA- and RNA-DGGE profiles and before detectable increases in nitrite and nitrate production. RNA-DGGE provided intermediate sensitivity. In addition, the three molecular methods were used to follow growth of individual strains within communities. In general, changes in relative activities of individual strains within communities could be predicted from monoculture growth characteristics. Ammonia-tolerant Nitrosospira cluster 3b strains dominated mixed communities at all ammonia concentrations, and ammonia-sensitive strains were outcompeted at an intermediate ammonia concentration. However, coexistence of ammonia-tolerant and ammonia-sensitive strains occurred at the lowest ammonia concentration, and, under some conditions, strains inhibited at high ammonia in monoculture were active at high ammonia in mixed cultures, where they coexisted with ammonia-tolerant strains. The results therefore demonstrate the sensitivity of SIP for detection of activity of organisms with relatively low yield and low activity and its ability to follow changes in the structure of interacting microbial communities.Molecular characterization of natural microbial communities has demonstrated the existence of novel high-level taxonomic groups with no cultured representatives and with significant diversity within phylogenetic and functional groups already established through analysis of organisms in laboratory culture. Autotrophic ammonia-oxidizing bacteria (AOB) exemplify the latter situation. Their low growth rates and the limited number of readily measured phenotypic characteristics available for identification of these organisms necessitate the use of molecular techniques for characterization of their diversity in natural environments. Phylogenetic analysis of 16S rRNA gene sequences places the majority of cultivated autotrophic bacterial ammonia oxidizers in a monophyletic group within the Betaproteobacteria (8, 26). Amplification and phylogenetic analysis of 16S rRNA gene sequences from enrichment cultures of ammonia oxidizers and sequences of environmental clones (31) suggest the existence of novel groups with no cultivated representative and considerable diversity within those represented by pure cultures.Increased awareness of microbial diversity has raised questions regarding links between species diversity and functional diversity, functional redundancy, and the influence of environmental conditions on the activities of representatives of different phylotypes. For ammonia-oxidizing bacteria, relationships exist between broad phylogenetic groups and the environments from which laboratory isolates were obtained, which are linked, in some cases, to differences in physiological characteristics (11). There is also evidence of links between the relative abundance of different ammonia oxidizer groups and environmental conditions (1, 13, 14, 18, 21, 23, 34), suggesting selection for organisms with particular physiological characteristics. In one study (36), a combination of molecular and physiological studies has demonstrated links between species diversity, functional diversity, and soil nitrification kinetics. However, for ammonia oxidizers and other groups, there is little direct evidence about which strains within diverse communities are active under particular conditions or the extent of competition for substrates.Stable isotope probing (SIP) (24, 27) of nucleic acids provides direct evidence of which members of mixed communities are active. This involves addition of substrates labeled with a stable isotope (most commonly ¹³C), extraction of nucleic acids, separation of ¹²C- and ¹³C-labeled nucleic acids by density gradient centrifugation, and subsequent molecular analysis. Sequences amplified from ¹³C-labeled DNA or RNA are derived from organisms actively assimilating the substrate. This approach has been used to identify organisms that utilize methane or methanol (4, 19), organic compounds (15, 20), or CO₂ (6, 9) in microcosms and those that assimilate plant root exudates in the field (28). SIP therefore links phylogeny to ecosystem function and has identified established and novel groups by utilizing labeled compounds in complex soil communities. The technique also enables in situ physiological studies and investigation of interactions between organisms in mixed cultures belonging to the same functional group. For autotrophic betaproteobacterial ammonia oxidizers, amplification of 16S rRNA genes from ¹³C-labeled DNA during incubation with [¹³C]CO₂ has the potential for discriminating which strains are active under specific conditions. Assessment of the discriminatory ability of this approach in complex natural environments requires studies under controlled and well-characterized conditions. The first aim of this study was, therefore, to assess the ability of SIP to discriminate activities of different members of simple mixed communities in comparison with direct measurement of product concentration and DNA- and RNA-denaturing gradient gel electrophoresis (DGGE). The second was to determine whether the activities of members of mixed communities of ammonia-oxidizing bacteria, in particular, their ability to grow at high ammonia concentrations, could be predicted from their physiological characteristics in monoculture. Of particular interest was whether strains with low ammonia tolerance are competitive at low ammonia concentrations. Mixed cultures were assembled from pure culture representatives of Nitrosospira clusters 0, 3a, and 3b (26, 36), which are frequently found in soil environments, and from enrichment cultures containing representatives of these clusters with heterotrophic contaminants. Other criteria for choice of community members were similarities in specific growth rate and cultivation conditions to enable meaningful competition experiments.     

Growth and N Allocation in Rice Plants under CO2 Enrichment

The effects of CO2 enrichment on growth and N allocation of rice (Oryza sativa L.) were examined. The plants were grown hydroponically in growth chambers with a 14-h photoperiod (1000 [mu]mol quanta m-2 s-1) and a day/night temperature of 25/20[deg]C. From the 28th to 70th d after germination, the plants were exposed to two CO2 partial pressures, namely 36 and 100 Pa. The CO2 enrichment increased the final biomass, but this was caused by a stimulation of the growth rate during the first week of the exposure to elevated CO2 partial pressures. The disappearance of the initial stimulation of the growth rate was associated with a decreased leaf area ratio. Furthermore, CO2 enrichment decreased the investment of N in the leaf blades, whereas the N allocation into the leaf sheaths and roots increased. Thus, the decrease in leaf N content by CO2 enrichment was not due to dilution of N caused by a relative increase in the plant biomass but was due to the change in N allocation at the whole-plant level. We conclude that the growth responses of rice to CO2 enrichment are mainly controlled by leaf area expansion and N allocation into leaf blades at the whole-plant level.     

Photoautotrophic in vitro Multiplication of the Orchid Dendrobium under CO2 Enrichment

An attempt to reduce the production cost on tissue cultured plants, photoautotrophic culture of a high value orchid Dendrobium was established under CO2-enriched conditions. The shoot length and the number of leaves were almost equal in plantlets grown on medium with 2 % sucrose or without sucrose and under normal or enhanced (40 g m-3) CO2 concentration, whereas the fresh and dry masses were higher in cultures grown in sucrose containing media or under CO2 enrichment. Development of roots was observed only on media without sucrose, but CO2 enrichment did not have significant effects on in vitro rootings. This revised version was published online in July 2006 with corrections to the Cover Date.     

Heterotrophic Fixation of CO2 in Soil

The occurrence of heterotrophic CO₂ fixation by soil microorganisms was tested in several mineral soils differing in pH and two artificial soils (a mixture of silica sand, alfalfa powder, and nutrient medium inoculated with a soil suspension). Soils were incubated at ambient (∼0.05 vol%) and elevated (∼5 vol%) CO₂ concentrations under aerobic conditions for up to 21 days. CO₂ fixation was detected using either a technique for determining the natural abundance of ¹³C or by measuring the distribution of labeled ¹⁴C-CO₂ in soil and bacteria. The effects of elevated CO₂ on microbial biomass (direct counts, chloroform fumigation extraction method), composition of microbial community (phospholipid fatty acids), microbial activity (respiration, dehydrogenase activity), and turnover rate were also measured. Heterotrophic CO₂ fixation was proven in all soils under study, being higher in neutral soils. The main portion of the fixed CO₂ (98–99%) was found in extracellular metabolites while only ∼1% CO₂ was incorporated into microbial cells. High CO₂ concentration always induced an increase in microbial activity, changes in the composition of the microbial community, and a decrease in microbial turnover. The results suggest that heterotrophic CO₂ fixation could be a widespread process in soils.     

Cultivation of Mesophilic Soil Crenarchaeotes in Enrichment Cultures from Plant Roots

Because archaea are generally associated with extreme environments, detection of nonthermophilic members belonging to the archaeal division Crenarchaeota over the last decade was unexpected; they are surprisingly ubiquitous and abundant in nonextreme marine and terrestrial habitats. Metabolic characterization of these nonthermophilic crenarchaeotes has been impeded by their intractability toward isolation and growth in culture. From studies employing a combination of cultivation and molecular phylogenetic techniques (PCR-single-strand conformation polymorphism, sequence analysis of 16S rRNA genes, fluorescence in situ hybridization, and real-time PCR), we present evidence here that one of the two dominant phylotypes of Crenarchaeota that colonizes the roots of tomato plants grown in soil from a Wisconsin field is selectively enriched in mixed cultures amended with root extract. Clones recovered from enrichment cultures were found to group phylogenetically with sequences from clade C1b.A1. This work corroborates and extends our recent findings, indicating that the diversity of the crenarchaeal soil assemblage is influenced by the rhizosphere and that mesophilic soil crenarchaeotes are found associated with plant roots, and provides the first evidence for growth of nonthermophilic crenarchaeotes in culture.     

Effects of Forest Gaps on Soil Properties in Castanopsis kawakamii Nature Forest

The aim of this study is to analyze the effects of forest gaps on the variations of soil properties in Castanopsis kawakamii natural forest. Soil physical and chemical properties in various sizes and development stages were studied in C. kawakamii natural forest gaps. The results showed that forest gaps in various sizes and development stages could improve soil pore space structure and water characteristics, which may effectively promote the water absorbing capacity for plant root growth and play an important role in forest regeneration. Soil pore space structure and water characteristics in small gaps showed more obvious improvements, followed by the medium and large gaps. Soil pore space structure and water characteristics in the later development stage of forest gaps demonstrated more obvious improvements, followed by the early and medium development stages. The contents of hydrolysable N and available K in various sizes and development stages of forest gaps were higher than those of non-gaps, whereas the contents of total N, total P, available P, organic matter, and organic carbon were lower. The contents of total N, hydrolysable N, available K, organic matter, and organic carbon in medium gaps were higher than those of large and small gaps. The disturbance of forest gaps could improve the soils’ physical and chemical properties and increase the population species’ richness, which would provide an ecological basis for the species coexistence in C. kawakamii natural forest.     

Free Atmospheric CO2 Enrichment (FACE) Increased Labile and Total Carbon in the Mineral Soil of a Short Rotation Poplar Plantation

The global net terrestrial carbon sink was estimated to range between 0.5 and 0.7 Pg C y⁻¹ for the early 1990s. FACE (free atmospheric CO₂ enrichment) studies conducted at the whole-tree and community scale indicate that there is a marked increase of primary production, mainly allocated into below-ground biomass. The enhanced carbon transfer to the root system may result in enhanced rhizodeposition and subsequent transfer to soil C pools. During the first rotation of the POP/EuroFACE experiment in a short-rotation Poplar plantation, total soil C content increased more under ambient CO₂ treatment than under FACE, while under FACE more new C was incorporated than under ambient CO₂. These unexpected and opposite effects may have been caused by a priming effect, where priming effect is defined as the stimulation of SOM decomposition caused by the addition of labile substrates. In order to gain insight into these processes affecting SOM decomposition, we obtained the labile, refractory and stable pools of soil C and N by chemical fractionation (acid hydrolysis) and measured rates of N-mineralization. Results of the first 2 years of the second rotation show a larger increase of total soil C% under FACE than under ambient CO₂. In contrast to the first rotation, total C% is now increasing faster under FACE than under ambient CO₂. Based on these observations we infer that the priming effect ceased during the second rotation. FACE treatment increased the labile C fraction at 0–10 cm depth, which is in agreement with the larger input of plant litter and root exudates under FACE. N-mineralization rates were not affected by FACE. We infer that the system switched from a state where extra labile C and sufficient N-availability (due to the former agricultural use of the soil) caused a priming effect (first rotation), to a state where extra C input is accumulating due to limited N-availability (second rotation). Our results on N-mineralization (second rotation) are in agreement with observations made at three forest FACE sites (Duke Forest, Oak Ridge, and Rhinelander), but our finding of increasing mineral soil C content contrasted with results at the Duke Forest where no significant increase in C content of the mineral soil occurred. However, the FACE induced increase in total C content occurred within the fraction with the shortest turnover time, i.e. the labile fraction. The refractory and stable fractions were not affected. The question remains whether the currently observed larger increase of total soil C and the increase of labile C under FACE will eventually result in long-term C storage in refractory and stable organic matter fractions.     

Mechanisms for Success after Long-term Nutrient Enrichment in a Boreal Forest Understory

Global levels of reactive nitrogen are predicted to rise in the coming decades as a result of increased deposition from the burning of fossil fuels and the large-scale conversion of nitrogen into a useable form for agriculture. Many plant communities respond strongly to increases in soil nitrogen, particularly in northern ecosystems where nitrogen levels are naturally very low. An experiment in northern Canada that was initiated in 1990 has been investigating the effects of long-term nutrient enrichment (fertilizer added annually) on a boreal forest understory community. We used this experiment to investigate why some species increase in abundance under nutrient enrichment whereas others decline. We focused on four species that differed in their responses to fertilization: Mertensia paniculata and Epilobium angustifolium increased in abundance, Achillea millefolium remained relatively constant and Festuca altaica declined. We hypothesized that the two species that were successful in the new high-nutrient, light-limited environment would be taller, have higher specific leaf area, change phenology by growing earlier in the season and be more morphologically plastic than their less successful counterparts. We compared plant height, specific leaf area, growth spurt date and allocation to leaves in plants grown in control and fertilized plots. We demonstrated that each of the two species that came to dominate fertilized plots has a different combination of traits and responses that likely gave them a competitive advantage; M. paniculata has the highest specific leaf area of the four species whereas E. angustifolium is tallest and exhibits morphological plasticity when fertilized by increasing biomass allocation to leaves. These results indicate that rather than one strategy determining success when nutrients become available, a variety of traits and responses may contribute to a species'' ability to persist in a nutrient-enriched boreal forest understory.     

Microbial Community Responses to Atmospheric Carbon Dioxide Enrichment in a Warm-Temperate Forest

Forest productivity depends on nutrient supply, and sustained increases in forest productivity under elevated carbon dioxide (CO₂) may ultimately depend on the response of microbial communities to changes in the quantity and chemistry of plant-derived substrates, We investigated microbial responses to elevated CO₂ in a warm-temperate forest under free-air CO₂ enrichment for 5 years (1997–2001). The experiment was conducted on three 30 m diameter plots under ambient CO₂ and three plots under elevated CO₂ (200 ppm above ambient). To understand how microbial processes changed under elevated CO₂, we assayed the activity of nine extracellular enzymes responsible for the decomposition of labile and recalcitrant carbon (C) substrates and the release of nitrogen (N) and phosphorus (P) from soil organic matter. Enzyme activities were measured three times per year in a surface organic horizon and in the top 15 cm of mineral soil. Initially, we found significant increases in the decomposition of labile C substrates in the mineral soil horizon under elevated CO₂; this overall pattern was present but much weaker in the O horizon. Beginning in the 4th year of this study, enzyme activities in the O horizon declined under elevated CO₂, whereas they continued to be stimulated in the mineral soil horizon. By year 5, the degradation of recalcitrant C substrates in mineral soils was significantly higher under elevated CO₂. Although there was little direct effect of elevated CO₂ on the activity of N- and P-releasing enzymes, the activity of nutrient-releasing enzymes relative to those responsible for C metabolism suggest that nutrient limitation is increasingly regulating microbial activity in the O horizon. Our results show that the metabolism of microbial communities is significantly altered by the response of primary producers to elevated CO₂. We hypothesize that ecosystem responses to elevated CO₂ are shifting from primary production to decomposition as a result of increasing nutrient limitation.     

Response of Nitrosospira sp. Strain AF-Like Ammonia Oxidizers to Changes in Temperature, Soil Moisture Content, and Fertilizer Concentration

Very little is known regarding the ecology of Nitrosospira sp. strain AF-like bacteria, a unique group of ammonia oxidizers within the Betaproteobacteria. We studied the response of Nitrosospira sp. strain AF-like ammonia oxidizers to changing environmental conditions by applying molecular methods and physiological measurements to Californian grassland soil manipulated in the laboratory. This soil is naturally high in Nitrosospira sp. strain AF-like bacteria relative to the much-better-studied Nitrosospira multiformis-like ammonia-oxidizing bacteria. Increases in temperature, soil moisture, and fertilizer interacted to reduce the relative abundance of Nitrosospira sp. strain AF-like bacteria, although they remained numerically dominant. The overall abundance of ammonia-oxidizing bacteria increased with increasing soil moisture and decreased with increasing temperature. Potential nitrification activity was altered by interactions among temperature, soil moisture, and fertilizer, with activity tending to be higher when soil moisture and temperature were increased. The increase in potential nitrification activity with increased temperature was surprising, given that the overall abundance of ammonia-oxidizing bacteria decreased significantly under these conditions. This observation suggests that (i) Nitrosospira sp. strain AF-like bacteria may respond to increased temperature with an increase in activity, despite a decrease in abundance, or (ii) that potential nitrification activity in these soils may be due to organisms other than bacteria (e.g., archaeal ammonia oxidizers), at least under conditions of increased temperature.