Microbial Extracellular Enzyme Research Articles

The Influence of Vegetation on Microbial Enzyme Activity and Bacterial Community Structure in Freshwater Constructed Wetland Sediments

Microorganisms play important roles in wetland ecosystems, but little is known about the influence of wetland plants on microbial community structure and activity. A greenhouse experiment was conducted to study the short-term influence of wetland vegetation on the sediment microbial community. Mesocosms were either planted with Juncus effusus, Carex lurida, or Dichanthelium acuminatum var. acuminatum or remained unvegetated. After eight weeks, sediment samples were taken and assayed for the activity of five microbial extracellular enzymes associated with carbon, nitrogen, and phosphorus cycling. β-1,4-glucosidase, phosphatase, and N-acetylglucosaminidase exhibited similar activity for all vegetation treatments, while the activity of the phenolic-degrading enzymes phenol oxidase and peroxidase was higher in sediments with no vegetation. Denaturing gradient gel electrophoresis and sequencing of partial 16S rRNA genes indicate differences in the sediment bacterial community associated with each plant regime. Acidobacteria, Firmicutes and Proteobacteria were the dominant phyla, although unvegetated sediments contained proportionally fewer Firmicutes and Alphaproteobacteria. This study provides insights into the structure of wetland bacterial communities and suggests that vegetation can influence both bacterial community structure and specific enzyme activity in wetland sediments. Moreover, these influences can occur over a relatively short time and could occur within just a few months of vegetation changes.

Low Concentrations of Silver Nanoparticles in Biosolids Cause Adverse Ecosystem Responses under Realistic Field Scenario

A large fraction of engineered nanomaterials in consumer and commercial products will reach natural ecosystems. To date, research on the biological impacts of environmental nanomaterial exposures has largely focused on high-concentration exposures in mechanistic lab studies with single strains of model organisms. These results are difficult to extrapolate to ecosystems, where exposures will likely be at low-concentrations and which are inhabited by a diversity of organisms. Here we show adverse responses of plants and microorganisms in a replicated long-term terrestrial mesocosm field experiment following a single low dose of silver nanoparticles (0.14 mg Ag kg−1 soil) applied via a likely route of exposure, sewage biosolid application. While total aboveground plant biomass did not differ between treatments receiving biosolids, one plant species, Microstegium vimeneum, had 32 % less biomass in the Slurry+AgNP treatment relative to the Slurry only treatment. Microorganisms were also affected by AgNP treatment, which gave a significantly different community composition of bacteria in the Slurry+AgNPs as opposed to the Slurry treatment one day after addition as analyzed by T-RFLP analysis of 16S-rRNA genes. After eight days, N2O flux was 4.5 fold higher in the Slurry+AgNPs treatment than the Slurry treatment. After fifty days, community composition and N2O flux of the Slurry+AgNPs treatment converged with the Slurry. However, the soil microbial extracellular enzymes leucine amino peptidase and phosphatase had 52 and 27% lower activities, respectively, while microbial biomass was 35% lower than the Slurry. We also show that the magnitude of these responses was in all cases as large as or larger than the positive control, AgNO3, added at 4-fold the Ag concentration of the silver nanoparticles.

Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes.

Understanding the relationship between prokaryotic traits and phylogeny is important for predicting and modeling ecological processes. Microbial extracellular enzymes have a pivotal role in nutrient cycling and the decomposition of organic matter, yet little is known about the phylogenetic distribution of genes encoding these enzymes. In this study, we analyzed 3058 annotated prokaryotic genomes to determine which taxa have the genetic potential to produce alkaline phosphatase, chitinase and β-N-acetyl-glucosaminidase enzymes. We then evaluated the relationship between the genetic potential for enzyme production and 16S rRNA phylogeny using the consenTRAIT algorithm, which calculated the phylogenetic depth and corresponding 16S rRNA sequence identity of clades of potential enzyme producers. Nearly half (49.2%) of the genomes analyzed were found to be capable of extracellular enzyme production, and these were non-randomly distributed across most prokaryotic phyla. On average, clades of potential enzyme-producing organisms had a maximum phylogenetic depth of 0.008004-0.009780, though individual clades varied broadly in both size and depth. These values correspond to a minimum 16S rRNA sequence identity of 98.04-98.40%. The distribution pattern we found is an indication of microdiversity, the occurrence of ecologically or physiologically distinct populations within phylogenetically related groups. Additionally, we found positive correlations among the genes encoding different extracellular enzymes. Our results suggest that the capacity to produce extracellular enzymes varies at relatively fine-scale phylogenetic resolution. This variation is consistent with other traits that require a small number of genes and provides insight into the relationship between taxonomy and traits that may be useful for predicting ecological function.

Response of soil microbial activity to grazing, nitrogen deposition, and exotic cover in a serpentine grassland

Exotic species, nitrogen (N) deposition, and grazing are major drivers of change in grasslands. However little is known about the interactive effects of these factors on below-ground microbial communities. We simulated realistic N deposition increases with low-level fertilization and manipulated grazing with fencing in a split-plot experiment in California’s largest serpentine grassland. We also monitored grazing intensity using camera traps and measured total available N to assess grazing and nutrient enrichment effects on microbial extracellular enzyme activity (EEA), microbial N mineralization, and respiration rates in soil. Continuous measures of grazing intensity and N availability showed that increased grazing and N were correlated with increased microbial activity and were stronger predictors than the categorical grazing and fertilization measures. Exotic cover was also generally correlated with increased microbial activity resulting from exotic-driven nutrient cycling alterations. Seasonal effects, on abiotic factors and plant phenology, were also an important factor in EEA with lower activity occurring at peak plant biomass. In combination with previous studies from this serpentine grassland, our results suggest that grazing intensity and soil N availability may affect the soil microbial community indirectly via effects on exotic cover and associated changes in nutrient cycling while grazing directly impacts soil community function.

Labile and Recalcitrant Organic Matter Utilization by River Biofilm Under Increasing Water Temperature

Microbial biofilms in rivers contribute to the decomposition of the available organic matter which typically shows changes in composition and bioavailability due to their origin, seasonality, and watershed characteristics. In the context of global warming, enhanced biofilm organic matter decomposition would be expected but this effect could be specific when either a labile or a recalcitrant organic matter source would be available. A laboratory experiment was performed to mimic the effect of the predicted increase in river water temperature (+4°C above an ambient temperature) on the microbial biofilm under differential organic matter sources. The biofilm microbial community responded to higher water temperature by increasing bacterial cell number, respiratory activity (electron transport system) and microbial extracellular enzymes (extracellular enzyme activity). At higher temperature, the phenol oxidase enzyme explained a large fraction of respiratory activity variation suggesting an enhanced microbial use of degradation products from humic substances. The decomposition of hemicellulose (β-xylosidase activity) seemed to be also favored by warmer conditions. However, at ambient temperature, the enzymes highly responsible for respiration activity variation were β-glucosidase and leu-aminopeptidase, suggesting an enhanced microbial use of polysaccharides and peptides degradation products. The addition of labile dissolved organic carbon (DOC; dipeptide plus cellobiose) caused a further augmentation of heterotrophic biomass and respiratory activity. The changes in the fluorescence index and the ratio Abs(250)/total DOC indicated that higher temperature accelerated the rates of DOC degradation. The experiment showed that the more bioavailable organic matter was rapidly cycled irrespective of higher temperature while degradation of recalcitrant substances was enhanced by warming. Thus, pulses of carbon at higher water temperature might have consequences for DOC processing.

The role of endogenous and exogenous enzymes in chronic wounds: A focus on the implications of aberrant levels of both host and bacterial proteases in wound healing

Cutaneous wound healing is orchestrated by a number of physiological pathways that ultimately lead to reformation of skin integrity and the production of functional scar tissue. The remodeling of a wound is significantly affected by matrix metalloproteinases (MMPs), which act to control the degradation of the extracellular matrix (ECM). Regulation of MMPs is imperative for wound healing as excessive levels of MMPs can lead to disproportionate destruction of the wound ECM compared to ECM deposition. In addition to human MMPs, bacterial proteases have been found to be influential in tissue breakdown and, as such, have a role to play in the healing of infected wounds. For example, the zinc-metalloproteinase, elastase, produced by Pseudomonas aeruginosa, induces degradation of fibroblast proteins and proteoglycans in chronic wounds and has also been shown to degrade host immune cell mediators. Microbial extracellular enzymes have also been shown to degrade human wound fluid and inhibit fibroblast cell growth. It is now being acknowledged that host and bacterial MMPs may act synergistically to cause tissue breakdown within the wound bed. Several studies have suggested that bacterial-derived secreted proteases may act to up-regulate the levels of MMPs produced by the host cells. Together, these findings indicate that bacterial phenotype in terms of protease producing potential of bacteria should be taken into consideration during diagnostic and clinical intervention of infected wound management. Furthermore, both host MMPs and those derived from infecting bacteria need to be targeted in order to increase the healing capacity of the injured tissue. The aim of this review is to investigate the evidence suggestive of a relationship between unregulated levels of both host and bacterial proteases and delayed wound healing.

TheMichaelis–Menten kinetics of soil extracellular enzymes in response to temperature: a cross‐latitudinal study

AbstractDecomposition of soil organic matter (SOM) is mediated by microbial extracellular hydrolytic enzymes (EHEs). Thus, given the large amount of carbon (C) stored asSOM, it is imperative to understand how microbialEHEs will respond to global change (and warming in particular) to better predict the links betweenSOMand the globalCcycle. Here, we measured theMichaelis–Menten kinetics [maximal rate of velocity (Vmax) and half‐saturation constant (Km)] of five hydrolytic enzymes involved inSOMdegradation (cellobiohydrolase, β‐glucosidase, β‐xylosidase, α‐glucosidase, andN‐acetyl‐β‐d‐glucosaminidase) in five sites spanning a boreal forest to a tropical rainforest. We tested the specific hypothesis that enzymes from higher latitudes would show greater temperature sensitivities than those from lower latitudes. We then used our data to parameterize a mathematical model to test the relative roles ofVmaxandKmtemperature sensitivities inSOMdecomposition. We found that bothVmaxandKmwere temperature sensitive, withQ10values ranging from 1.53 to 2.27 forVmaxand 0.90 to 1.57 forKm. TheQ10values for theKmof the cellulose‐degrading enzyme β‐glucosidase showed a significant (P = 0.004) negative relationship with mean annual temperature, indicating that enzymes from cooler climates can indeed be more sensitive to temperature. Our model showed thatKmtemperature sensitivity can offsetSOMlosses due toVmaxtemperature sensitivity, but the offset depends on the size of theSOMpool and the magnitude ofVmax. Overall, our results suggest that there is a local adaptation of microbialEHEkinetics to temperature and that this should be taken into account when making predictions about the responses of C cycling to global change.

Dynamics of extracellular enzyme activities in seawater under changed atmospheric pCO2: a mesocosm investigation

As part of the PeECE II mesocosm project, we investigated the effects of pCO2 levels on the initial step of heterotrophic carbon cycling in the surface ocean. The activities of microbial extracellular enzymes hydrolyzing 4 polysaccharides were measured during the development of a natural phytoplankton bloom under pCO2 conditions representing glacial (190 µatm) and future (750 µatm) atmospheric pCO2. We observed that (1) chondroitin hydrolysis was variable throughout the pre-, early- and late-bloom phases, (2) fucoidanase activity was measurable only in the glacial mesocosm as the bloom developed, (3) laminarinase activity was low and constant, and (4) xylanase activity declined as the bloom progressed. Concurrent measurements of microbial community composition, using denaturing-gradient gel electrophoresis (DGGE), showed that the 2 mesocosms diverged temporally, and from one another, especially in the late-bloom phase. Enzyme activities correlated with bloom phase and pCO2, suggesting functional as well as compositional changes in microbial communities in the different pCO2 environments. These changes, however, may be a response to temporal changes in the development of phytoplankton communities that differed with the pCO2 environment. We hypothesize that the phytoplankton communities produced dissolved organic carbon (DOC) differing in composition, a hypothesis supported by changing amino acid composition of the DOC, and that enzyme activities responded to changes in substrates. Enzyme activities observed under different pCO2 conditions likely reflect both genetic and population-level responses to changes occurring among multiple components of the microbial loop.

The response of heterotrophic activity and carbon cycling to nitrogen additions and warming in two tropical soils

AbstractNitrogen (N) deposition is projected to increase significantly in tropical regions in the coming decades, where changes in climate are also expected. Additional N and warming each have the potential to alter soil carbon (C) storage via changes in microbial activity and decomposition, but little is known about the combined effects of these global change factors in tropical ecosystems. In this study, we used controlled laboratory incubations of soils from a long‐term N fertilization experiment to explore the sensitivity of soil C to increased N in two N‐rich tropical forests. We found that fertilization corresponded to significant increases in bulk soil C concentrations, and decreases in C loss via heterotrophic respiration (P< 0.05). The increase in soil C was not uniform among C pools, however. The active soil C pool decomposed faster with fertilization, while slowly cycling C pools had longer turnover times. These changes in soil C cycling with N additions corresponded to the responses of two groups of microbial extracellular enzymes. Smaller active C pools corresponded to increased hydrolytic enzyme activities; longer turnover times of the slowly cycling C pool corresponded to reduced activity of oxidative enzymes, which degrade more complex C compounds, in fertilized soils. Warming increased soil respiration overall, and N fertilization significantly increased the temperature sensitivity of slowly cycling C pools in both forests. In the lower elevation forest, respired CO2 from fertilized cores had significantly higher Δ14C values than control soils, indicating losses of relatively older soil C. These results indicate that soil C storage is sensitive to both N deposition and warming in N‐rich tropical soils, with interacting effects of these two global change factors. N deposition has the potential to increase total soil C stocks in tropical forests, but the long‐term stability of this added C will likely depend on future changes in temperature.

Variation in ecosystem function in Appalachian streams along an acidity gradient

Acidification is a widespread phenomenon that damages aquatic systems, and it has been the focus of intensive management efforts. While most management has focused on community structure as an endpoint, ecosystem function is also sensitive to acidification and important in stream health. We examined how a key ecosystem function in streams, leaf breakdown, varied along a gradient of pH resulting from acid deposition, natural conditions, and liming. We also measured how invertebrate and microbial assemblage structure and microbial function were related to altered leaf breakdown rates. Leaf breakdown rates declined more than threefold along a gradient of stream acidity from pH 6.8 to 4.9. The diversity of leaf-shredding invertebrates, bacteria, and fungi showed little response to variation in pH. The abundance of one acid-sensitive caddisfly, Lepidostoma, declined with acidification, and Lepidostoma abundance explained 37% of the variation in leaf breakdown rates among sites. Microbial respiration was suppressed along the acidity gradient, although the pattern was weaker than that for breakdown rate. In short-term laboratory incubations, microbes at acidic and circumneutral sites demonstrated adaptation to ambient pH. The activity of microbial extracellular enzymes was strongly influenced by pH. In particular, the pattern of activity of phosphatase indicated increasing P limitation of microbes with increasing acidification. Our results show that leaf breakdown is a sensitive tool for examining the response of stream function to acidification and also for defining the mechanisms that drive functional response. Future management efforts should focus on key taxa that are particularly sensitive and effective at shredding leaves and also the role of shifting acidity in mediating the availability of phosphorus to microbial films that are important for stream function.

Stimulation of microbial extracellular enzyme activities by elevated CO2 depends on soil aggregate size

AbstractIncreased belowground carbon (C) transfer by plant roots at elevated CO2 may change properties of the microbial community in the rhizosphere. Previous investigations that focused on total soil organic C or total microbial C showed contrasting results: small increase, small decrease or no changes. We evaluated the effect of 5 years of elevated CO2 (550 ppm) on four extracellular enzymes: β‐glucosidase, chitinase, phosphatase, and sulfatase. We expected microorganisms to be differently localized in aggregates of various sizes and, therefore analyzed microbial biomass (Cmic by SIR) and enzyme activities in three aggregate‐size classes: large macro‐ (> 2 mm), small macro‐ (0.25–2 mm), and microaggregates (< 0.25 mm). To estimate the potential enzyme production, we activated microorganisms by substrate (glucose and nutrients) amendment. Although Ctotal and Cmic as well as the activities of β‐glucosidase, phosphatase, and sulfatase were unaffected in bulk soil and in aggregate‐size classes by elevated CO2, significant changes were observed in potential enzyme production after substrate amendment. After adding glucose, enzyme activities under elevated CO2 were 1.2–1.9‐fold higher than under ambient CO2. This indicates the increased activity of microorganisms, which leads to accelerated C turnover in soil under elevated CO2. Significantly higher chitinase activity in bulk soil and in large macroaggregates under elevated CO2 revealed an increased contribution of fungi to turnover processes. At the same time, less chitinase activity in microaggregates underlined microaggregate stability and the difficulties for fungal hyphae penetrating them. We conclude that quantitative and qualitative changes of C input by plants into the soil at elevated CO2 affect microbial community functioning, but not its total content. Future studies should therefore focus more on the changes of functions and activities, but less on the pools.

Photoacceleration of plant litter decomposition in an arid environment

In arid ecosystems, abiotic processes facilitate the physical and chemical degradation of plant litter to the extent that decomposition models that use climatic and litter composition variables as surrogates for microbial activity are not predictive. The purpose of this study was to estimate the potential contribution of photodegradation to the decomposition of plant litters that varies in architecture and chemical composition. Litter of Pinus edulis, Juniperus monosperma and Populus deltoides were exposed to ambient and attenuated sunlight, with and without supplemental water additions, at a riparian forest site along the Middle Rio Grande (New Mexico, USA). Mass loss, elemental composition, and microbial extracellular enzyme activities (EEA) were measured over 639 days. The composition of the fungal communities associated with the decomposing litters was compared by analyses of fungal ITS nrDNA sequences. Litter exposed to ambient sunlight had greater mass loss rates than shaded litter, independent of the water treatment: Populus increased by 100%, Pinus by 86% and Juniperus by 46%. The increases were proportional to exposed litter surface area per g dry mass. EEA potentials, particularly oxidative activities, were low in comparison to those measured in mesic ecosystems. For Populus litter, the principal driver of photoacceleration appeared to be photodegradation of cellulose; for Pinus, it was photodegradation of polyphenols; for Juniperus accelerated mass loss was associated with photodegradation of both polysaccharides and polyphenols. Fungal community composition varied by litter type, but the dominant colonizers were yeasts and dark-septate hyphal taxa; a finding consistent with the low enzymatic oxidation potential. This study shows that photochemical oxidation can supplement enzymatic oxidation and increase decomposition rates. As a result, organic matter decomposition in arid ecosystems is not restricted to periods of high moisture availability as is plant production. This decoupling may partly account for the low soil organic matter content of these ecosystems.

Fine Scale Patterns in Microbial Extracellular Enzyme Activity during Leaf Litter Decomposition in a Stream and its Floodplain

Microorganisms mediate the decomposition of leaf-litter through the release of extracellular enzymes. The surfaces of decomposing leaves are both chemically and physically heterogeneous, and spatial patterns in microbial enzyme activity on the litter surface should provide insights into fine-scale patterns of leaf-litter decomposition. Platanus occidentalis leaves were collected from the floodplain of a third-order stream in northern Mississippi, enclosed in individual litter bags, and placed in the stream channel and in the floodplain. Replicate leaves were collected approximately monthly over a 9-month period and assayed for spatial variation in microbial extracellular enzyme activity and rates of organic matter (OM) decomposition. Spatial variation in enzyme activity was measured by sampling 96 small discs (5-mm diameter) cut from each leaf. Discs were assayed for the activity of enzymes involved in lignin (oxidative enzymes) and cellulose (beta-glucosidase, cellobiohydrolase) degradation. Rates of OM loss were greater in the stream than the floodplain. Activities of all enzymes displayed high variability in both environments, with severalfold differences across individual leaves, and replicate leaves varied greatly in their distribution of activities. Geostatistical analysis revealed no clear patterns in spatial distribution of activity over time or among replicates, and replicate leaves were highly variable. These results show that fine-scale spatial heterogeneity occurs on decomposing leaves, but the level of spatial variability varies among individual leaves at the measured spatial scales. This study is the first to use geostatistical analyses to analyze landscape patterns of microbial activity on decomposing leaf litter and in conjunction with studies of the microbial community composition and/or substrate characteristics, should provide key insights into the function of these processes.

Genetic mosaics of ecosystem functioning across aspen-dominated landscapes

Genetic diversity is the foundation of all biodiversity, and the genetic variation within species is increasingly recognized as being important to ecosystem level processes. Recent research demonstrates that plant genotype influences above- and belowground communities as well as basic ecosystem functions. However, the extent to which plant genotypes create spatial mosaics of genetically mediated ecosystem processes in natural forests is uncertain. We use Populus tremuloides as a model system to demonstrate the importance of plant genotype on carbon and nitrogen cycling in natural systems. We identified 24 distinct P. tremuloides clones with multiple ramets across 25 km(2) in southern Wisconsin, United States, using microsatellite makers. We then sampled clone leaf chemistry and belowground nutrient content and microbial extracellular enzyme activity. Aspen-induced variation in belowground carbon and nitrogen content, and microbial activity, varied widely among clones. Variation in green leaf chemistry and belowground microbial activity were correlated with genetic distance among clones, such that more genetically distant clones created more divergent patches of ecosystem processes. These data suggest that aspen genotypes create spatial mosaics of genetically mediated ecosystem functioning across natural landscapes and can therefore have evolutionary consequences for co-occurring species.

Characterization and Wash Performance Analysis of Microbial Extracellular Enzymes from East Calcutta Wetland in India

Extracellular protease from a novel bacterial isolate showing maximum similarity of 98.22% with Microbacterium luteolum was obtained from East Calcutta Wetland, India. It showed compatibility with commercial detergents. The enzyme retains more than 60% of its activity between 6.0 to 10.5 pH. The maximum activity is at pH 7.5 with 71% activity at pH 10.0 and 10.5. The protease retained its activity between 4 to 60°C with maximum activity at 30°C and a residual activity of 74.4% at 60°C after overnight incubation. It was completely inhibited by 5mM PMSF pointing towards the presence of serine group of protease. Its inhibition by EDTA indicates the involvement of metal cations in its catalytic activity. It is not effected by Cu +2 , partially inhibited by Pb +2 and Ni +2 , while completely inhibited by Co +1 , Cr +6 , Zn +1 , Al +3 , Ag +3 and Hg +2 . Strong reducing agents like β- merceptoethanol and oxidants like bleach and hydrogen peroxide inactivate the enzyme. The enzyme retains 88% of its activity on being mixed with commercially available detergents while it is inactivated by non-ionic Triton X 100. Its efficiency as an additive with detergent in terms of cleaning stains like grease, burnt mobil, vegetable curry and blood was found to be satisfactory. It could enhance the quality of washing as additive in case of all the ten detergents that were tried. The protease alone was also capable of cleaning but the detergent additive mixture could work better. The enzyme was found to work efficiently on different colors as well as on fabric. On mixing with detergent it was found to retain activity up to 2 months and there after, there was a drop in efficiency of washing. The bacterial cells were immobilized in calcium alginate and the released enzyme was found to be equally effective. Market surveys were carried out and the satisfactory result prompted the use of another additive (extracellular lipase) obtained from yet another bacterial strain from East Calcutta Wetland. The lipase activity was confirmed through degradation of coconut oil analyzed by Gas Chromatography. Thus the combination was observed to be more successful as indicated through the market survey. These observations suggest the suitability of the protease and lipase combination as additive to commercially available detergents.

Fluorescence anisotropy as a means to determine extracellular polysaccharide hydrolase activity in environmental samples

Current approaches to measure the activities of microbial extracellular enzymes in aquatic environments are hampered by slow throughput or by differences between the structure of simple substrate proxies and macromolecules. Here we show that measurements of fluorescence anisotropy can be used to determine the hydrolysis rate of two fluorescently labeled polysaccharides, laminarin and xylan, in environmental samples. A simple analysis shows that the anisotropy of these fluorescently labeled polysaccharides can be approximated using a modification of the Perrin equation.

PLANT AND MICROBE CONTRIBUTION TO COMMUNITY RESILIENCE IN A DIRECTIONALLY CHANGING ENVIRONMENT

To understand the role biota play in resilience or vulnerability to environmental change, we investigated soil, plant, and microbial responses to a widespread environmental change, increased nitrogen (N). Our aim was to test the plant–soil threshold hypothesis: that changed biotic structure influences resilience to accumulated changes in N. For six years, we removed one of two codominant species, Geum rossii and Deschampsia caespitosa, in moist-meadow alpine tundra in Colorado, USA. We also manipulated nutrient availability by adding carbon (C) or N, separately and in combination with the species removals. Consistent with our hypothesis, Geum was associated with soil feedbacks that slowed rates of N cycling and Deschampsia with feedbacks that increased rates of N cycling. After a four-year initial resilience period, Geum dramatically declined (by almost 70%) due to increasing N availability. In contrast, Deschampsia abundance did not respond to changes in N supply; it only responded to the removal of Geum. Forbs and graminoids responded more positively to Deschampsia removal than to Geum removal, indicating stronger competitive effects by Deschampsia. The changed biotic interactions appear to have community-level consequences: after six years of Geum (but not Deschampsia) removal, evenness of the community declined by over 35%. Increased N affected the soil–microbial feedbacks, particularly in association with Geum. Microbial biomass N declined at higher N, as did the activities of two C-acquiring and one N-acquiring extracellular microbial enzymes. In the presence of Geum, N fertilization slowed the activity of phenol oxidase, a tannin-degrading enzyme, suggesting that microbes shift from degrading Geum-derived compounds. In the absence of Geum, acid phosphatase activity increased, suggesting increased phosphorus limitation in association with Deschampsia. With continued N deposition forecast for this system, these results suggest that initial resilience of Geum to increased N will be overwhelmed through elimination of microbial feedbacks. Once Geum declines, the loss will indirectly facilitate Deschampsia via competitive release. Because Deschampsia exerts strong competitive effects on subordinate species, increased Deschampsia abundance may be accompanied by a community-wide drop in diversity. We conclude that plant–soil feedbacks through the microbial community can influence vulnerability to exogenous changes in N and contribute to threshold dynamics.

Structural and Functional Changes with Depth in Microbial Communities in a Tropical Malaysian Peat Swamp Forest

Tropical peat swamp forests are important and endangered ecosystems, although little is known of their microbial diversity and ecology. We used molecular and enzymatic techniques to examine patterns in prokaryotic community structure and overall microbial activity at 0-, 10-, 20-, and 50-cm depths in sediments in a peat swamp forest in Malaysia. Denaturing gradient gel electrophoresis profiles of amplified 16S ribosomal ribonucleic acid (rRNA) gene fragments showed that different depths harbored different bacterial assemblages and that Archaea appeared to be limited to the deeper samples. Cloning and sequencing of longer 16S rRNA gene fragments suggested reduced microbial diversity in the deeper samples compared to the surface. Bacterial clone libraries were largely dominated by ribotypes affiliated with the Acidobacteria, which accounted for at least 27-54% of the sequences obtained. All of the sequenced representatives from the archaeal clone libraries were Crenarchaeota. Activities of microbial extracellular enzymes involved in carbon, nitrogen, and phosphorus cycling declined appreciably with depth, the only exception being peroxidase. These results show that tropical peat swamp forests are unusual systems with microbial assemblages dominated by members of the Acidobacteria and Crenarchaeota. Microbial communities show clear changes with depth, and most microbial activity is likely confined to populations in the upper few centimeters, the site of new leaf litter fall, rather than the deeper, older, peat layers.

Microbial activity and decomposition of fine particulate organic matter in a Louisiana cypress swamp

AbstractFine particulate organic matter (FPOM) is an important source of C and energy in aquatic systems, but the decomposition of FPOM has rarely been studied. Litterbags were used to study the decomposition of particles in 2 size fractions of FPOM in surface sediments of a cypress swamp in southeastern Louisiana for slightly over 1 y. Particles in both size fractions followed linear decay models, but fine particles (0.25–1 mm) derived from the remains of coarser material decomposed more slowly than very fine particles (0.063–0.25 mm) that probably were derived from a number of sources. The activities of 6 microbial extracellular enzymes involved in the degradation of lignocellulose also were analyzed, and enzymatic decomposition models were developed to relate the decomposition of particles in each size fraction of FPOM to microbial activity. Very fine particles decomposed more rapidly than fine particles, although enzyme activities were lower, suggesting that this material was more efficiently degraded...

Degradation of dietary fibre from ‘Gari' by faecal bacteria and bacteria extracellular polysaccharidases

Dietary fibre (soluble and insoluble fibre) was extracted from ‘gari' (a fermented cassava product). The ‘gari' fibre was subjected to degradation by faecal microflora and the microbial extracellular enzymes obtained from six clinically healthy adults (S1-S6). Other common components of dietary fibre namely starch, xylan, carboxymethlcellulose (CMC) and polygalacturonic acid (PGA) were also treated with the extracellular enzymes. Degradation of the fibre was monitored by measuring the reducing sugar groups in the reaction mixture. Enzyme activity was expressed as units/mg protein. The results obtained demonstrated that the human faecal microflora were able to degrade the gari fibre considerably within 24 hr of incubation. The values obtained for the reducing sugars ranged from 1.5-4.5 mg/ml. Degradation rate varied considerably between the six individuals. Effect of the faecal extracellular enzyme on the fibre indicated a high concentration of the starch hydrolyzing enzyme, amylase. For all the six subjects the activities were (U/mg protein): amylase 2.5-5.4; xylanase 0.8-3.6 and pectinase 0.088- 2.1. Cellulases activity detected in only one of the subjects was 0.76 U/mg protein. The results of this study suggested that the fibre from gari may be rich in starch component resistant to the action of amylase and amyloglucosidase and this component were readily degraded by enzyme from the faecal microflora. Keywords: Dietary fibre, gari, faecal bacteria, extracellular polysacharidases. Nigerian Food Journal Vol. 25 (1) 2007: pp. 46-55