Linking soil process and microbial ecology in freshwater wetland ecosystems

Soil microorganisms mediate many processes such as nitrification, denitrification, and methanogenesis that regulate ecosystem functioning and also feed back to influence atmospheric chemistry. These processes are of particular interest in freshwater wetland ecosystems where nutrient cycling is highly responsive to fluctuating hydrology and nutrients and soil gas releases may be sensitive to climate warming. In this review we briefly summarize research from process and taxonomic approaches to the study of wetland biogeochemistry and microbial ecology, and highlight areas where further research is needed to increase our mechanistic understanding of wetland system functioning. Research in wetland biogeochemistry has most often been focused on processes (e.g., methanogenesis), and less often on microbial communities or on populations of specific microorganisms of interest. Research on process has focused on controls over, and rates of, denitrification, methanogenesis, and methanotrophy. There has been some work on sulfate and iron transformations and wetland enzyme activities. Work to date indicates an important process level role for hydrology and soil nutrient status. The impact of plant species composition on processes is potentially critical, but is as yet poorly understood. Research on microbial communities in wetland soils has primarily focused on bacteria responsible for methanogenesis, denitrification, and sulfate reduction. There has been less work on taxonomic groups such as those responsible for nitrogen fixation, or aerobic processes such as nitrification. Work on general community composition and on wetland mycorrhizal fungi is particularly sparse. The general goal of microbial research has been to understand how microbial groups respond to the environment. There has been relatively little work done on the interactions among environmental controls over process rates, environmental constraints on microbial activities and community composition, and changes in processes at the ecosystem level. Finding ways to link process-based and biochemical or gene-based assays is becoming increasingly important as we seek a mechanistic understanding of the response of wetland ecosystems to current and future anthropogenic perturbations. We discuss the potential of new approaches, and highlight areas for further research.     

The effects of salinity on aquatic plant germination and zooplankton hatching from two wetland sediments

1. The effect of increasing salinity on the emergence of zooplankton eggs and the germination of aquatic plant seeds from the sediment of two wetlands was examined. Salinity was found to cause reductions in species richness and abundance of aquatic plants and zooplankton at salinities between 1000 and 5000 mg L^?1. Aquatic plants also had an associated decrease in above ground biomass. 2. Individual taxa showed different responses to salinity, and four response patterns were identified: (i) increased number of organisms emerging at 1000 mg L^?1; (ii) decreased number of organisms emerging above 1000 mg L^?1; (iii) decreased number of organisms emerging between 300 and 1000 mg L^?1; (iv) no difference in number of organisms emerging across the range of salinities. Response patterns (iii) and (iv) were common to both plants and zooplankton, whereas response patterns (i) and (ii) were only identified for zooplankton. 3. Results indicate that there is potential for the increasing salinity in Australian rivers and wetlands to decrease the species richness of aquatic communities resulting in loss of wetland biodiversity.     

Simulation of the decomposition and nitrogen mineralization of aboveground plant material in two unfertilized grassland ecosystems

A simple model of the decomposition and nitrogen mineralization of plant material from two unfertilized grassland ecosystems has been developed, with only the proportion of leaves and stems in the original material, the initial nitrogen contents of these plant parts and temperature as input data. The model simulates carbon losses from stems and leaves, using a double exponential decay function, with the temperature sum as independent variable. Mineralization of nitrogen is not calculated via microbial growth rates, but simulated on the basis of the carbon utilization efficiency of the microorganisms and the critical C/N ratio, i.e. the C/N ratio of the litter at which the microbial demand for nitrogen is met exactly. The parameter values for leaching fractions of carbon and nitrogen, relative decay rates, microbial carbon utilization efficiencies and critical C/N ratios were derived from a litter bag experiment with 12 litter types (species) including both green and dead materials, carried out in two unfertilized grassland ecosystems differing in production level. The model was evaluated using a cross-validation method, in which one species was omitted from the parametrization procedure, and its decomposition and mineralization were predicted by the resulting model. In general there was good agreement between the observed and predicted amounts of carbon and nitrogen remaining for all green litter types/species, but carbon and nitrogen dynamics in the dead material of Festuca rubra were poorly predicted. This disparity has been attributed to the proportion of leaves in the material of Festuca rubra (95%) being far beyond the range of leaf proportions in the three litter types the calibration set consisted of (8–35%). When the data of all litter types were used to determine the model parameters, good agreement was obtained between measured and simulated values for the changes in nitrogen and carbon in all litter types of both the green and dead material series. Optimization yielded parameter values for microbial carbon utilization efficiencies of 0.30 for microorganisms associated with green litter and 0.35 for those associated with dead litter. The critical C/N ratios for green and dead material were found to be 29 and 36, respectively.     

The ndhF chloroplast gene detected in all vascular plant divisions

A 335-bp segment of the NADH dehydrogenase F (ndhF) gene from a representative of each nonflowering vascular plant division (Coniferophyta, Filicophyta, Ginkgophyta, Gnetophyta, Lycophyta, Psilophyta, Sphenophyta) has been sequenced and aligned with those of rice, tobacco, an orchid and a liverwort. Because ndhF is apparently absent in the genus Pinus L. (Coniferophyta), it has been speculated that this gene may be absent in the gymnosperms. However, this study suggests that the absence of the ndhF gene in Pinus may be unique and is not a general characteristic of the gymnosperms.Abbreviations ndhF NADH dehydrogenase F - PCR polymerase chain reactionThis research was supported by grants from NSF LASER/EPS-CoR 92-96-ADP-02, LEGSF RD-A-13 (1991–1994), and by the Department of Plant Biology, Louisiana State University.     

Anaerobic degradation of benzoate to methane by a microbial consortium

A stabilized consortium of microbes which anaerobically degraded benzoate and produced CH₄ was established by inoculation of a benzoate-mineral salts medium with sewage sludge; the consortium was routinely subcultured anaerobically in this medium for 3 years. Acetate, formate, H₂ and CO₂ were identified as intermediates in the overall conversion of benzoate to CH₄ by the culture. Radioactivity was equally divided between the CH₄ and CO₂ from the degradation of uniformly ring-labeled [¹⁴C]benzoate. The methyl group of acetate was stoichiometrically converted to CH₄. Acetate, cyclohexanecarboxylate, 2-hydroxycyclohexanecarboxylate, o-hydroxybenzoic acid and pimelic acid were converted to CH₄ without a lag suggesting that benzoate was degraded by a reductive pathway. Addition of o-chlorobenzoate inhibited benzoate degradation but not acetate degradation or methane formation. Two methanogenic organisms were isolated from the mixed culture, neither organism was able to degrade benzoate, showing that the methanogenic bacteria served as terminal organisms of a metabolic food chain composed of several organisms. Removal of intermediates by the methanogenic bacteria provided thermodynamically favorable conditions for benzoate degradation.     

Effect of lignocellulose degradation products on microbial biomass and lipid production by the oleaginous yeast Cryptococcus curvatus

This work investigated effects of lignocellulose degradation products on cell biomass and lipid production by Cryptococcus curvatus. Furfural was found to have the strongest inhibitory effect. For the three phenolic compounds tested, vanillin was the most toxic, while PHB and syringaldehyde showed comparable inhibitions in the concentration range of 0–1.0 g/L. Generally little significant differences on the relative cell biomass and lipid contents at the same concentrations of tested compounds were observed between glucose and xylose as a sole carbon source. At 1.0 g/L of furfural, the cell biomass and lipid content decreased by 78.4% and 61.0% for glucose as well as 72.0% and 59.3% for xylose, respectively. C. curvatus ceased to grow at concentrations of PHB over 1.0 g/L or vanillin over 1.5 g/L. The strain could survive in the presence of syringaldehyde up to 2.0 g/L for glucose or 1.5 g/L for xylose. The compounds’ negative impact was reduced by an increase in inoculum size and a 10% (v/v) seed was detected to be optimal for cell biomass and lipid production. The results demonstrated C. curvatus could effectively utilize most of the dominant monosaccharides and cellobiose existing in lignocellulosic biomass hydrolysate in the presence of toxic compounds.     

Occurrence of sucrose phosphatase in vascular and non-vascular plants

Green plants including representatives of angiosperms, gymnosperms, ferns, mosses, liverworts and green algae were shown to contain a specific sucrose phosphatase, the last enzyme in the pathway of sucrose synthesis. The enzyme from all species required Mg²⁺ for activity and it was partially inhibited by sucrose. It was not detected in a red alga, brown algae, or mushroom species which contain little or no sucrose.     

Kinetics of zinc uptake by two rice cultivars

Summary Rice (Oryzae sativa L.) cultivars differ widely in their susceptibility to zinc (Zn) dificiency. Excised root apices of cv IR26 actively absorbed Zn at a rate twice that of cv M101 roots. This difference in Zn uptake rates could not be attributed to greater root surface area in cv IR26 as compared to cv M101. The maximum rates of Zn uptake (Vmax) and the Km values also differed markedly between these two cultivars. Roots of cv M101 have a two-fold greater affinity for Zn than do those of cv IR26. Leaf blade tissues of IR26 and M101 rice absorbed Zn at similar rates. Rice cv IR26 readily develops Zn deficiency symptoms in hydroponic culture but cv M101 rarely does so.     

Tight coupling between leaf area index and foliage N content in arctic plant communities

The large spatial heterogeneity of arctic landscapes complicates efforts to quantify key processes of these ecosystems, for example productivity, at the landscape level. Robust relationships that help to simplify and explain observed patterns, are thus powerful tools for understanding and predicting vegetation distribution and dynamics. Here we present the same linear relationship between Leaf area index (LAI) and Total foliar nitrogen (TFN), the two factors determining the photosynthetic capacity of vegetation, across a wide range of tundra vegetation types in both northern Sweden and Alaska between leaf area indices of 0 and 1 m² m^–2, which is essentially the entire range of leaf area index values for the Arctic as a whole. Surprisingly, this simple relationship arises as an emergent property at the plant community level, whereas at the species level a large variability in leaf traits exists. As the relationship between LAI and TFN exists among such varied ecosystems, the arctic environment must impose tight constraints on vegetation canopy development. This relationship simplifies the quantification of vegetation productivity of arctic vegetation types as the two most important drivers of productivity can be estimated reliably from remotely sensed NDVI images.     

The distribution of flavonoids in chloroplasts of twenty five species of vascular plants

A survey was made of the major flavonoids in whole leaf extracts and in chloroplast preparations from twenty five species of vascular plants including Anthophyta (20), Coniferophyta (1), Ginkophyta (1), Pterophyta (2), and Arthrophyta (1). The chloroplasts variously contained derivatives of flavones, C-glycosylflavones, flavonols, flavanones, isoflavones, 3-deoxyanthocyanidins, and anthocyanins. Twenty three species contain one or more flavonoids in isolated chloroplast, usually in a pattern quite similar to that found in whole-leaf extracts but occasionally showing enrichment of one or more flavonoids in the chloroplasts. Flavonoids are apparently absent from chloroplasts of Phaseolus aureus and Morus alba although whole-leaf extracts of these species are rich in quercetin derivatives.     

Structure of herbaceous plant assemblages in a forested riparian landscape

We assessed patterns of herbaceous and woody species richness, plant-environment interactions, and correspondence between the herb and tree layer in a riparian landscape (the Ozark National Scenic Riverways, Missouri, USA). A total of 269 herb and 70 tree species were identified on 94 sample plots. Gradient analysis revealed that environmental variables and vegetation were influenced by a strong elevation gradient. However, high variability in environmental variables (pH, elevation, slope, sand, clay, organic matter) indicated a high level of substrate heterogeneity across the riparian landscape. We were unable to predict the composition of the herb understory from the canopy trees with any detailed accuracy and no clear characterization of herb species assemblages was found using cluster analysis or ecological land type (ELT) classifications. Canonical correspondence analysis (CCA) results for both tree and herb plots showed that elevation (height above river) and pH were the dominant environmental gradients influencing vegetation patterns on the first CCA axis while soil particle size exhibited the strongest correlation with the second CCA axis. Secondary gradients of importance included slope, soil container capacity, and organic matter. No significant linear or quadratic correlation was found between elevation and herb or woody species richness. Environmental variables alone or in combination, were weak predictors of herb and woody species richness, despite the patterns observed in the gradient analysis and the correlations observed in the CCA results. Ecotonal analysis showed that the herb layer exhibited a high species replacement rate at the lower elevations most susceptible to flooding (0–3 m). Above the flooding zone, there was more or less continuous species replacement, suggesting the presence of a gradual ecotone/ecocline. The tree layer exhibited much stronger discontinuities than the herb layer in the lower elevations along the height gradient (0–10 m). Recognizing the limitations of classification techniques for riparian herb assemblages and the importance of scale and heterogeneity in vegetation layers is especially important in light of mandates to preserve, protect, and manage for plant diversity.     

Kinetics of Cellobiohydrolase (Cel7A) Variants with Lowered Substrate Affinity

Cellobiohydrolases are exo-active glycosyl hydrolases that processively convert cellulose to soluble sugars, typically cellobiose. They effectively break down crystalline cellulose and make up a major component in industrial enzyme mixtures used for deconstruction of lignocellulosic biomass. Identification of the rate-limiting step for cellobiohydrolases remains controversial, and recent reports have alternately suggested either association (on-rate) or dissociation (off-rate) as the overall bottleneck. Obviously, this uncertainty hampers both fundamental mechanistic understanding and rational design of enzymes with improved industrial applicability. To elucidate the role of on- and off-rates, respectively, on the overall kinetics, we have expressed a variant in which a tryptophan residue (Trp-38) in the middle of the active tunnel has been replaced with an alanine. This mutation weakens complex formation, and the population of substrate-bound W38A was only about half of the wild type. Nevertheless, the maximal, steady-state rate was twice as high for the variant enzyme. It is argued that these opposite effects on binding and activity can be reconciled if the rate-limiting step is after the catalysis (i.e. in the dissociation process).     

Distribution trends of rare vascular plant species in Estonia

On the basis of quantitative analysis of the vascular plant distribution maps for Estonia, we specified the list of rare species which occur in less than 5% of grid quadrangles, and studied the possible correlations between their rarity and habitat preference, distribution, and sensitivity to human impact. Rare species occur statistically more often among species that are at the limit of their geographical range. The proportion of rare species was significantly higher among arctomontane and disjunct circumpolar taxa. Among apophytes, there were less rare taxa than would be expected according to the common native flora, but among hemerophobes, there were significantly more rare species than would be expected. The number of rare species was in strong positive correlation with the species richness of the region. Besides the western part of Estonia, where the greatest number of rare species occur, some small areas rich in rare species also lie in East and North Estonia.     

Kinetics of doubletime kinase-dependent degradation of the Drosophila period protein

Robust circadian oscillations of the proteins PERIOD (PER) and TIMELESS (TIM) are hallmarks of a functional clock in the fruit fly Drosophila melanogaster. Early morning phosphorylation of PER by the kinase Doubletime (DBT) and subsequent PER turnover is an essential step in the functioning of the Drosophila circadian clock. Here using time-lapse fluorescence microscopy we study PER stability in the presence of DBT and its short, long, arrhythmic, and inactive mutants in S2 cells. We observe robust PER degradation in a DBT allele-specific manner. With the exception of doubletime-short (DBT(S)), all mutants produce differential PER degradation profiles that show direct correspondence with their respective Drosophila behavioral phenotypes. The kinetics of PER degradation with DBT(S) in cell culture resembles that with wild-type DBT and posits that, in flies DBT(S) likely does not modulate the clock by simply affecting PER degradation kinetics. For all the other tested DBT alleles, the study provides a simple model in which the changes in Drosophila behavioral rhythms can be explained solely by changes in the rate of PER degradation.