Tropical tree species composition affects the oxidation of dissolved organic matter from litter

Plant species effects on soil nutrient availability are relatively well documented, but the effects of species differences in litter chemistry on soil carbon cycling are less well understood, especially in the species-rich tropics. In many wet tropical forest ecosystems, leaching of dissolved organic matter (DOM) from the litter layer accounts for a significant proportion of litter mass loss during decomposition. Here we investigated how tree species differences in soluble dissolved organic C (DOC) and nutrients affected soil CO₂ fluxes in laboratory incubations. We leached DOM from freshly fallen litter of six canopy tree species collected from a tropical rain forest in Costa Rica and measured C-mineralization. We found significant differences in litter solubility and nutrient availability. Following DOM additions to soil, rates of heterotrophic respiration varied by as much as an order of magnitude between species, and overall differences in total soil CO₂ efflux varied by more than four-fold. Variation in the carbon: phosphorus ratio accounted for 51% of the variation in total CO₂ flux between species. These results suggest that tropical tree species composition may influence soil C storage and mineralization via inter-specific variation in plant litter chemistry.     

Linking microbial community composition and soil processes in a California annual grassland and mixed-conifer forest

To investigate the potential role of microbial community composition in soil carbon and nitrogen cycling, we transplanted soil cores between a grassland and a conifer ecosystem in the Sierra Nevada California and measured soil process rates (N-mineralization, nitrous oxide and carbondioxide flux, nitrification potential), soil water and temperature, and microbial community parameters (PLFA and substrate utilization profiles) over a 2 year period. Our goal was to assess whether microbial community composition could be related to soil process rates independent of soil temperature and water content. We performed multiple regression analyses using microbial community parameters and soil water and temperature as X-variables and soil process rates and inorganic N concentrations as Y-variables. We found that field soil temperature had the strongest relationship with CO₂ production and soil NH₄⁺ concentration, while microbial community characteristics correlated with N₂O production, nitrification potential, gross N-mineralization, and soil NO₃^– concentration, independent of environmentalcontrollers. We observed a relationship between specific components of the microbial community (as determined by PLFA) and soil processes,particularly processes tightly linked to microbial phylogeny (e.g. nitrification). The most apparent change in microbial community composition in response to the 2 year transplant was a change in relative abundance of fungi (there was only one significant change in PLFA biomarkers for bacteria during 2 years). The relationship between microbial community composition and soil processes suggests that prediction of ecosystem response to environmental change may be improved by recognizing and accounting for changes in microbial community composition and physiological ecology.     

Dynamics of C, N, P and microbial community composition in particulate soil organic matter during residue decomposition

Decomposing residues can be an important source of nutrients for plants, especially of N and P, but the relationship between N and P release and microbial community dynamics have rarely been studied. Two pea (Pisum sativum L.) residues with contrasting chemical composition, shoots from flowering pea (Pea-Y) with 2.9 mg P and 36 mg N kg⁻¹ and from mature pea (Pea-M) with 0.3 mg P and 13 mg N kg⁻¹, were added at a rate of 20 g kg soil⁻¹ to a sandy soil low in nutrients. Particulate organic matter (POM) was isolated on days (d) 0, 5, 15, 28, 42 and 61 after residue addition and analysed for C, N, P and microbial community structure (fatty acid methyl ester analysis). The recovery of POM from residue-amended soils decreased over time to 30–40% of added amounts for both residues. Apart from d 0, the N concentration in POM was lower in residue-amended soil than in the control. Due to a rapid decrease in P concentration during the first 5 days in Pea-Y and a slow increase over the whole experiment in Pea-M, P concentrations in POM on d 61 were similar in all treatments. In Pea-Y, the dynamics of C, N and P were coupled, with amounts of C, N and P decreasing during the first 15 days and remaining stable thereafter. In Pea-M, a steady loss of C from POM was contrasted by a slight increase in P. As a result, the C/P ratio decreased from 1,330 on d 0 to 390 on d 61. The C/N ratio of Pea-M decreased only during the second phase of decomposition. The different nutrient dynamics in Pea-Y and Pea-M led to similar amounts of N and P in POM towards the end of the incubation. Microbial community composition in the POM in Pea-Y and Pea-M remained distinct from the control, even though it changed over time. POM was shown to be an important source of potentially available nutrients after addition of plant residues. In the unamended soil, stable nutrient amounts in POM suggested very low net nutrient release from native POM compared to POM after residue addition.     

Forest- and pasture-derived carbon contributions to carbon stocks and microbial respiration of tropical pasture soils

The clearing of tropical forest for pasture leads to important changes in soil organic carbon (C) stocks and cycling patterns. We used the naturally occurring distribution of¹³C in soil organic matter (SOM) to examine the roles of forest- and pasture-derived organic matter in the carbon balance in the soils of 3- to 81-year-old pastures created following deforestation in the western Brazilian Amazon Basin state of Rondônia. Different ¹³C values of C3 forest-derived C (-28) and C4 pasture-derived C (-13) allowed determination of the origin of total soil C and soil respiration. The ¹³C of total soil increased steadily across ecosystems from -27.8 in the forest to -15.8 in the 81-year-old pasture and indicated a replacement of forest-derived C with pasture-derived C. The ¹³C of respired CO₂ increased more rapidly from -26.5 in the forest to -17 in the 3- to 13-year-old pastures and indicated a faster shift in the origin of more labile SOM. In 3-year-old pasture, soil C derived from pasture grasses made up 69% of respired C but only 17% of total soil C in the top 10 cm. Soils of pastures 5 years old and older had higher total C stocks to 30 cm than the original forest. This occurred because pasture-derived C in soil organic matter increased more rapidly than forest-derived C was lost. The increase of pasture-derived C in soils of young pastures suggests that C inputs derived from pasture grasses play a critical role in development of soil C stocks in addition to fueling microbial respiration. Management practices that promote high grass production will likely result in greater inputs of grass-derived C to pasture soils and will be important for maintaining tropical pasture soil C stocks.     

The variability of soil microbial community composition of different types of tidal wetland in Chongming Dongtan and its effect on soil microbial respiration

Previous studies have shown that the soil enzyme activity and microbial respiration intensities varied in two different types of tidal wetland in Chongming Dongtan, the first a sandy soil in a scouring bank with Phragmites australis and the second a saline-alkali clay soil in silting bank with P. australis/Spartina alterniflora/Scirpus mariqueter, resulting in different organic carbon reservation capabilities; however, their microbial biomass did not differ significantly. To clarify the microbial mechanism that explains the variability of soil respiration among different wetland areas, the community structure and abundance of soil microorganisms in different types of wetland were investigated using denaturing gradient gel electrophoresis (DGGE) plus real-time quantitative polymerase chain reaction (PCR) technologies, and the relationship between soil environmental factors and the microbial community structure and the soil respiration intensity was elucidated. The results revealed that the soil microbial diversity and community structure differed between the two typical wetland areas. The common population was uncultured bacterium in both areas, and the most abundant community was α-, β-, γ-Proteobacteria, which play an important role in the cycling of carbon in soil. However, the abundance of α-Proteobacteria in Area A was 18.2% of that in Area B (P <0.05), while the β-Proteobacteria in Area A was 3.23 times higher than that in Area B (P <0.05). In addition, one cellulose-degrading bacteria, uncultured Bacilli, was detected in Area A. PCA (Principal component analysis) revealed that γ-Proteobacteria and β-Proteobacteria had the greatest impact on soil respiration intensity. Both soil water content and salinity depressed the propagation of β-Proteobacteria. Considering the similar microbial biomass and abundance of γ-Proteobacteria between the two areas, the lower level of β-Proteobacteria, uncultured Bacilli bacterium in Area B might be important factors involved in the lower soil respiration, and hence the higher soil organic carbon reservation capability in Area B.     

Root controls on soil microbial community structure in forest soils

We assessed microbial community composition as a function of altered above- and belowground inputs to soil in forest ecosystems of Oregon, Pennsylvania, and Hungary as part of a larger Detritus Input and Removal Treatment (DIRT) experiment. DIRT plots, which include root trenching, aboveground litter exclusion, and doubling of litter inputs, have been established in forested ecosystems in the US and Europe that vary with respect to dominant tree species, soil C content, N deposition rate, and soil type. This study used phospholipid fatty-acid (PLFA) analysis to examine changes in the soil microbial community size and composition in the mineral soil (0–10 cm) as a result of the DIRT treatments. At all sites, the PLFA profiles from the plots without roots were significantly different from all other treatments. PLFA analysis showed that the rootless plots generally contained larger quantities of actinomycete biomarkers and lower amounts of fungal biomarkers. At one of the sites in an old-growth coniferous forest, seasonal changes in PLFA profiles were also examined. Seasonal differences in soil microbial community composition were greater than treatment differences. Throughout the year, treatments without roots continued to have a different microbial community composition than the treatments with roots, although the specific PLFA biomarkers responsible for these differences varied by season. These data provide direct evidence that root C inputs exert a large control on microbial community composition in the three forested ecosystems studied.     

Response of compost maturity and microbial community composition to pentachlorophenol (PCP)-contaminated soil during composting

Two composting piles were prepared by adding to a mixture of rice straw, vegetables and bran: (i) raw soil free from pentachlorophenol (PCP) contamination (pile A) and (ii) PCP-contaminated soil (pile B). It was shown by the results that compost maturity characterized by water soluble carbon (WSC), TOC/TN ratio, germination index (GI) and dehydrogenase activity (DA) was significantly affected by PCP exposure, which resulted in an inferior degree of maturity for pile B. DGGE analysis revealed an inhibited effect of PCP on compost microbial abundance. The bacteria community shifts were mainly consistent with composting factors such as temperature, pH, moisture content and substrates. By contrast, the fungal communities were more sensitive to PCP contamination due to the significant correlation between fungal community shifts and PCP removal. Therefore, the different microbial community compositions for properly evaluating the degree of maturity and PCP contamination were suggested.     

The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide

One of the major factors associated with global change is the ever-increasing concentration of atmospheric CO₂. Although the stimulating effects of elevated CO₂ (eCO₂) on plant growth and primary productivity have been established, its impacts on the diversity and function of soil microbial communities are poorly understood. In this study, phylogenetic microarrays (PhyloChip) were used to comprehensively survey the richness, composition and structure of soil microbial communities in a grassland experiment subjected to two CO₂ conditions (ambient, 368 p.p.m., versus elevated, 560 p.p.m.) for 10 years. The richness based on the detected number of operational taxonomic units (OTUs) significantly decreased under eCO₂. PhyloChip detected 2269 OTUs derived from 45 phyla (including two from Archaea), 55 classes, 99 orders, 164 families and 190 subfamilies. Also, the signal intensity of five phyla (Crenarchaeota, Chloroflexi, OP10, OP9/JS1, Verrucomicrobia) significantly decreased at eCO₂, and such significant effects of eCO₂ on microbial composition were also observed at the class or lower taxonomic levels for most abundant phyla, such as Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Acidobacteria, suggesting a shift in microbial community composition at eCO₂. Additionally, statistical analyses showed that the overall taxonomic structure of soil microbial communities was altered at eCO₂. Mantel tests indicated that such changes in species richness, composition and structure of soil microbial communities were closely correlated with soil and plant properties. This study provides insights into our understanding of shifts in the richness, composition and structure of soil microbial communities under eCO₂ and environmental factors shaping the microbial community structure.     

The variation of soil microbial respiration with depth in relation to soil carbon composition

The vertical variation in soil microbial respiratory activity and its relationship to organic carbon pools is critical for modeling soil C stock and predicting impacts of climate change, but is not well understood. Mineral soil samples, taken from four Scottish soils at different depths (0–8, 8–16, 16–24, 24–32 cm), were analyzed and incubated in the laboratory under constant temperature and environmental conditions. The vegetation type/plant species showed significant effects on the absolute concentration of C components and microbial activity, but the relative distribution of C and respiration rate with soil depth are similar across sites. Soil C pools and microbial respiratory activity declined rapidly with soil depth, with about 30% of total organic carbon (TOC) and dissolved organic carbon (DOC), and about half microbial carbon (C_mic) and respired CO₂ observed in the top 8 cm. The ratio of CO₂:TOC generally decreased with soil depth, but CO₂:DOC was significantly higher in the top 8 cm of soil than in the subsoil (8–32 cm). No general pattern between qCO₂ (CO₂:C_mic) and soil depth was found. The vertical distributions of soil C pools and microbial respiratory activity were best fitted with a single exponential equation. Compared with TOC and DOC, C_mic appears to be an adequate predictor for the variation in microbial respiration rate with soil depth, with 95% of variation in normalized respiration rate accounted for by a linear relationship.     

水溶性有机质对土壤中镉吸附行为的影响

水溶性有机质 (DOM)是陆地生态系统和水生生态系统中的一种很活跃的组分 .本文以赤红壤、水稻土和褐土作为供试土壤 ,研究了来源于稻秆和底泥的DOM对土壤中Cd吸附行为的影响 .DOM对土壤中Cd的吸附行为具有明显的抑制作用 .这种抑制作用与土壤类型和DOM种类有关 .在 3种供试土壤中 ,无论添加稻秆DOM还是底泥DOM ,都会使Cd的最大吸附容量和吸附率明显降低 ,其下降幅度为17 3%～ 93 9%.在添加同一种DOM的前提下 ,DOM对Cd吸附的抑制作用均为 :赤红壤 >水稻土 >褐土 .如果不添加DOM ,则土壤对Cd的最大吸附容量主要取决于土壤固相的吸附特性 ,添加DOM后土壤对Cd的最大吸附容量则主要取决于液相中的DOM .由此推断 ,传统的看法 ,通过施用有机肥来固定土壤中的Cd并达到治理重金属污染土壤的观点值得商榷 .     

Effect of carbon dioxide concentration on microbial respiration in soil

In order to assess the validity of conventional methods for measuring CO₂ flux from soil, the relationship between soil microbial respiration and ambient CO₂ concentration was studied using an open-flow infra-red gas analyser (IRGA) method. Andosol from an upland field in central Japan was used as a soil sample. Soil microbial respiration activity was depressed with the increase of CO₂ concentration in ventilated air from 0 to 1000 ppmv. At 1000 ppmv, the respiration rate was less than half of that at 0 ppmv. Thus, it is likely that soil respiration rate is overestimated by the alkali absorption method, because CO₂ concentration in the absorption chamber is much lower than the normal level. Metabolic responses to CO₂ concentration were different among groups of soil microorganisms. The bacteria actinomycetes group cultivated on agar medium showed a more sensitive response to the CO₂ concentration than the filamentous fungi group.     

Plant community composition, not diversity, regulates soil respiration in grasslands

Soil respiration is responsible for recycling considerable quantities of carbon from terrestrial ecosystems to the atmosphere. There is a growing body of evidence that suggests that the richness of plants in a community can have significant impacts on ecosystem functioning, but the specific influences of plant species richness (SR), plant functional-type richness and plant community composition on soil respiration rates are unknown. Here we use 10-year-old model plant communities, comprising mature plants transplanted into natural non-sterile soil, to determine how the diversity and composition of plant communities influence soil respiration rates. Our analysis revealed that soil respiration was driven by plant community composition and that there was no significant effect of biodiversity at the three levels tested (SR, functional group and species per functional group). Above-ground plant biomass and root density were included in the analysis as covariates and found to have no effect on soil respiration. This finding is important, because it suggests that loss of particular species will have the greatest impact on soil respiration, rather than changes in biodiversity per se.     

Modelling the effect of active roots on soil organic matter turnover

The aim of this experiment was to study the effect of living roots on soil carbon metabolism at different decomposition stages during a long-term incubation. Plant material labelled with ¹⁴C and ¹⁵N was incubated in two contrasting soils under controlled laboratory conditions, over two years. Half the samples were cropped with wheat (Triticum aestivum) 11 times in succession. At earing time the wheat was harvested, the roots were extracted from the soil and a new crop was started. Thus the soils were continuously occupied by active root systems. The other half of the samples was maintained bare, without plants under the same conditions. Over the 2 years, pairs of cropped and bare soils were analysed at eight sampling occasions (total-, plant debris-, and microbial biomass-C and -¹⁴C). A five compartment (labile and recalcitrant plant residues, labile microbial metabolites, microbial biomass and stabilised humified compounds) decomposition model was fitted to the labelled and soil native organic matter data of the bare and cropped soils. Two different phases in the decomposition processes showed a different plant effect. (1) During the initial fast decomposition stage, labile ¹⁴C-material stimulated microbial activities and N immobilisation, increasing the ¹⁴C-microbial biomass. In the presence of living roots, competition between micro-organisms and plants for inorganic N weakly lowered the measured and predicted total-¹⁴C mineralisation and resulted in a lower plant productivity compared to subsequent growths. (2) In contrast, beyond 3–6 months, when the labile material was exhausted, during the slow decomposition stage, the presence of living roots stimulated the mineralisation of the recalcitrant plant residue-¹⁴C in the sandy soil and of the humified-¹⁴C in the clay soil. In the sandy soil, the presence of roots also substantially stimulated decomposition of old soil native humus compounds. During this slow decomposition stage, the measured and predicted plant induced decrease in total-¹⁴C and -C was essentially explained by the predicted decrease in humus-¹⁴C and -C. The ¹⁴C-microbial biomass (MB) partly decayed or became inactive in the bare soils, whereas in the rooted soils, the labelled MB turnover was accelerated: the MB-¹⁴C was replaced by unlabelled-C from C derived from living roots. At the end of experiment, the MB-C in the cropped soils was 2.5–3 times higher than in the bare soils. To sustain this biomass and activity, the model predicted a daily root derived C input (rhizodeposition), amounting to 5.4 and 3.2% of the plant biomass-C or estimated at 46 and 41% of the daily net assimilated C (shoot + root + rhizodeposition C) in the clay and sandy soil, respectively. This revised version was published online in June 2006 with corrections to the Cover Date.     

Soil plus root respiration and microbial biomass following water, nitrogen, and phosphorus application at a high arctic semi desert

In order to investigate the effects of anticipated increased precipitation and changing soil nutrient levels on soil CO₂ efflux from high arctic semi desert, a field experiment was carried out in Northeast Greenland. Water, phosphorus, and nitrogen were added to plots in a fully factorial design. Soil microbial biomass carbon was analysed after one year, and respiration from soil plus roots was measured in situ throughout the third growing season after initiation of the experiment. Soil plus root respiration was enhanced by up to 47%, and the microbial biomass by 24%, by the weekly water additions, but not by nutrient additions. The direct effect of increased soil moisture on CO₂ efflux suggests that future changes of precipitation levels and patterns may strongly affect below-ground respiration in arctic semi deserts, with direction of responses depending upon amounts and frequencies of precipitation events. Morover, low CO₂ emission at low light intensities regardless of treatment suggests that the major part of the below-ground respiration originated from turnover of recently fixed C. Hence, the more recalcitrant soil organic matter C pool may not change in proportion to changes in below-ground respiration rate.     

Altered utilization patterns of young and old soil C by microorganisms caused by temperature shifts and N additions

To determine if changes in microbial community composition and metabolic capacity alter decomposition patterns of young and old soil carbon pools, we incubated soils under conditions of varying temperature, N-availability, and water content. We used a soil from a pineapple plantation (CAM; ¹³C litter = –14.1) that had previously been under tropical forest (C3; ¹³C soil carbon = –26.5). Forest derived carbon represented 'old' carbon and plantation inputs represented 'new' carbon. In order to differentiate utilization of young (< 14 years) and old (> 14 years) soil carbon, we measured the ¹³C of respired CO₂ and microbial phospholipid fatty acids (PLFAs) during a 103 day laboratory incubation. We determined community composition (PLFA and bacterial intergenic transcribed spacer (ITS) analysis) in addition to carbon degrading and nutrient releasing enzyme activities. We observed that greater quantities of older carbon were respired at higher temperatures (20 and 35°C) compared to the lower temperature (5°C). This effect could be explained by changes in microbial community composition and accompanying changes in enzyme activities that affect C degradation. Nitrogen addition stimulated the utilization of older soil carbon, possibly due to greater peroxidase activity, but microbial community composition was unaffected by this treatment. Increasing soil moisture had no effect on the utilization of older SOM, but enzyme activity typically declined. Increased oxidative enzyme activities in response to elevated temperature and nitrogen additions point to a plausible mechanism for alterations in C resource utilization patterns.     

The imprint of coarse woody debris on soil chemistry in the Western Oregon Cascades

Coarse woody debris (CWD) may create a spatially discrete soil imprint through the release of carbon rich, acidic dissolved organic matter (DOM). DOM has been implicated in many soil processes such as humus formation, nutrient immobilization, podzolization, and the dissolution of soil minerals. We investigated a potential CWD imprint on soil chemistry by sampling leachates and soil solutions under CWD at different stages of decay and under the forest floor as controls. Solutions were analyzed for total dissolved organic carbon (DOC) and polyphenol concentrations. DOC was further separated by chemical fractionation. We also sampled soil from underneath CWD and from control areas without CWD. Samples were analyzed for pH, base saturation, exchangeable acidity, and several aluminum and iron fractions. The pH of CWD leachates was lower (p 0.001) and contained more polyphenols (p 0.0001) and DOC than control leachates, although chemical DOC fractions from CWD and the forest floor were similar. Surface mineral soils under CWD were lower in pH (p 0.005), had more exchangeable acidity (p 0.002) and more exchangeable aluminum (p 0.04) and iron (p 0.06) than forest floor soils. At depths greater than 5 cm, there were no differences between forest floor soils and soils under CWD. Our results suggest that CWD in the middle stages of decay acidifies the surface soil as it decomposes by decreasing exchangeable bases and increasing exchangeable acidity and aluminum. Soils under the most highly decayed CWD, or deeper soils were not affected by CWD. Although we hypothesized that well-decayed CWD would show a spatially explicit imprint on soils, the effect of CWD on soil chemistry was small and limited to surface mineral soils.     

Response of wetland soil carbon to groundwater conservation: Probabilistic outcomes from error propagation

Water loss compromises functions performed by wetland ecosystems. Efforts to rehabilitate wetland function typically begin with attempts to reestablish hydrology. These activities are often not monitored, so tools to extract information from them could partly offset the lost opportunity to learn from whole-ecosystem hydrological manipulation. In 2002, groundwater abstraction was lessened by 35% throughout 1700 km² of west-central Florida (USA). I assembled a pathway of correlations to project how this hydrological manipulation affected water levels and soil carbon (C) storage in overlying wetlands. Parameter values and residual error in these statistical models were resampled from known variances, thereby propagating uncertainty through the pathway of relationships, and expressing the response of soil C probabilistically. Projected soil C probability distributions were most distinguishable between full and moderate (30% less) abstraction. With more severe abstraction cutbacks, gains in projected soil C became more marginal and uncertain, suggesting that wetland soil C pools are not notably impacted by low-volume groundwater abstraction. Reducing uncertainty in projected soil C will require better understanding the dynamic response of soil C to increases in the amount of time that wetland soil is inundated. The step-by-step error propagation routine presented here is a platform for assimilating information from diverse sources in order to project probabilistic responses of ecosystem function to wetland restoration attempts, and it helps identify where further certainty is most wanted in a pathway of cause–effect relationships.     

Chemical and carbon isotopic evidence for the source and fate of dissolved organic matter in the northern Everglades

Surface waters in the Florida Everglades contain high levels ofdissolved organic carbon (DOC) compounds. ¹³C values of DOCsamples collected from the northern Everglades indicate that less than about23%of the DOC was derived from sugarcane (the dominant agricultural crop in thearea), and the amount of DOC from sugarcane was greater during the dry period.Most of the DOC (> 50%) in the northern Everglades was in the low molecularweight (< 1000 Dalton) fraction (LMW-DOC). The relative amount of highmolecular weight DOC (HMW-DOC) was higher in the wet period than in the dryperiod. Radiocarbon ages of the DOC ranged from > modern toabout 2400 years B.P., indicating that DOC was derived from both historic peatdeposits and modern vegetation. At each site, the HMW-DOC had older radiocarbonages than the LMW-DOC, and therefore contained a greater fraction of DOCderivedfrom the historic peat deposits. It appears that at least some of the old DOCcompounds from the historic peat deposits were decomposed during theirresidencein the surface water system in the northern Everglades, and the LMW-DOC wasmoremicrobially labile than the HMW-DOC. Our analysis suggests that accelerateddecomposition of organic matter in the historic peat deposits (due to land-usechange) could be a significant source of DOC and nutrients in the northernEverglades. Our data also suggest that the radiocarbon signature of DOC couldbeused as a sensitive indicator of the overall effectiveness of a wetlandrestoration project.