Extracellular Enzyme Activity Associated with Degradation of Beech Wood in a Central European Stream

The degradation of beech wood (Fagus sylvatica L.) was followed over 16 months in a central European upland stream, the Breitenbach. 1 cm³ cubes of beech wood were placed on the stream bed and sampled at monthly intervals. Besides mass loss, fungal biomass (ergosterol content) and lignin content, the activity of two extracellular enzymes was measured: β‐D‐glucosidase, an enzyme involved in the degradation of cellulose, and phenoloxidase, a ligninolytic enzyme. The suitability of the fluorigenic model substrate methylumbelliferyl‐β‐D‐glucoside for measuring β‐D‐glucosidase activity in wood from aquatic environments was tested. This technique is much more sensitive than the conventional photometric method. The beech wood was degraded at a constant rate of k = 0.00272 d^–1 across the entire 16‐month incubation period. There was a rapid onset of microbial colonisation, as witnessed by the initial detection of enzyme activity, after only 7 days of exposure. Lignin and ergosterol content as well as β‐glucosidase activity reached their highest values at the end of the 16‐month incubation period. Phenoloxidase activity increased rapidly to a maximum after 6 weeks, and then decreased to almost zero by the end of the experiment. The combination of biochemical techniques for measuring extracellular enzyme activities with measurements of mass loss, chemical composition and microbial colonisation provided valuable insights into the decomposition of wood in aquatic environments.     

Comparison of Methods for Inhibiting Bacterial Activity in Sediment

Dilute formaldehyde was the most suitable treatment to inhibit sediment bacteria, since bacterial activity remained low during long-term incubations and the chemical changes in the sediment were minimal. The inhibiting effects of HgCl₂, autoclaving, and gamma radiation were diminished during longer incubations; these treatments also caused increases in dissolved nutrients.     

Bactericidal Activity of Curcumin I Is Associated with Damaging of Bacterial Membrane

Curcumin, an important constituent of turmeric, is known for various biological activities, primarily due to its antioxidant mechanism. The present study focused on the antibacterial activity of curcumin I, a significant component of commercial curcumin, against four genera of bacteria, including those that are Gram-positive (Staphylococcus aureus and Enterococcus faecalis) and Gram-negative (Escherichia coli and Pseudomonas aeruginosa). These represent prominent human pathogens, particularly in hospital settings. Our study shows the strong antibacterial potential of curcumin I against all the tested bacteria from Gram-positive as well as Gram-negative groups. The integrity of the bacterial membrane was checked using two differential permeabilization indicating fluorescent probes, namely, propidium iodide and calcein. Both the membrane permeabilization assays confirmed membrane leakage in Gram-negative and Gram-positive bacteria on exposure to curcumin I. In addition, scanning electron microscopy and fluorescence microscopy were employed to confirm the membrane damages in bacterial cells on exposure to curcumin I. The present study confirms the broad-spectrum antibacterial nature of curcumin I, and its membrane damaging property. Findings from this study could provide impetus for further research on curcumin I regarding its antibiotic potential against rapidly emerging bacterial pathogens.     

Leaf Decomposition in a Mountain Stream in the Sultanate of Oman

Decomposition of Juglans regia leaves was studied in fine and coarse mesh bags in a permanent mountain stream in Oman. A rapid initial mass loss, attributed to leaching, was followed by a more gradual decline. Daily exponential decay rates (k) calculated over 32 days were 0.011 (fine mesh litter bags) and 0.014 (coarse mesh litter bags). The difference between bag types was not significant, suggesting limited impact of leaf‐shredding invertebrates. Ergosterol levels on leaves from fine mesh bags peaked at 0.3 mg g^–1 AFDM after 16 days of stream exposure. During the experimental period, which followed the annual leaf fall, the concentration of aquatic hyphomycete conidia in the stream varied between 82 and 1362 l^–1. Based on the morphology of conidia found in the water column or released from leaves, we identified 14 species of aquatic hyphomycetes. Tetracladium apiense was the most common taxon (62.2% of conidia in water column during the field experiment). Three other Tetracladium species contributed another 8%. Plating out leaf particles yielded common epiphytic taxa such as Alternaria sp., Aureobasidium pullulans and Phoma sp. The measured metrics of leaf decay in this desert stream fall within the range of values observed in temperate and tropical streams, with clear evidence for an early leaching phase, and no evidence of a strong impact of leaf shredders. The community of aquatic hyphomycetes appears impoverished. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Variations in Diversity and Richness of Gut Bacterial Communities of Termites (Reticulitermes flavipes) Fed with Grassy and Woody Plant Substrates

Diets shape the animal gut microbiota, although the relationships between diets and the structure of the gut microbial community are not yet well understood. The gut bacterial communities of Reticulitermes flavipes termites fed on four individual plant biomasses with different degrees of recalcitrance to biodegradation were investigated by 16S rRNA pyrosequencing analysis. The termite gut bacterial communities could be differentiated between grassy and woody diets, and among grassy diets (corn stover vs. sorghum). The majority of bacterial taxa were shared across all diets, but each diet significantly enriched some taxa. Interestingly, the diet of corn stover reduced gut bacterial richness and diversity compared to other diets, and this may be related to the lower recalcitrance of this biomass to degradation.     

Environmental Factors Correlated with Size of Bacterial Populations in a Polluted Stream

Samples of water were taken from a polluted zone of the Gallinas River and analyzed as to numbers of total bacteria, coliforms, and fecal streptococci. Environmental factors measured were temperature, pH and concentrations of detergent, nitrate plus nitrite nitrogen, sulfate, chloride, bicarbonate, and phosphate. Thirty-two observations were made from 12 March through 22 July 1971. Stepwise multiple linear regression analyses of the data were carried out by computer to determine which of the environmental factors were significantly correlated with numbers of bacteria present. A multiple linear regression equation was constructed for each bacteriological parameter as a function of significant variables only. Log total bacteria was correlated positively with bicarbonate, phosphate, and detergent concentrations. Log coliforms was correlated positively with phosphate and sulfate concentrations and negatively with chloride concentration. Log fecal streptococci was correlated positively with bicarbonate and chloride concentrations.     

Microorganisms Associated with Uranium Bioremediation in a High-Salinity Subsurface Sediment

Although stimulation of dissimilatory metal reduction to promote the reductive precipitation of uranium has been shown to successfully remove uranium from some aquifer sediments, the organisms in the family Geobacteraceae that have been found to be associated with metal reduction in previous studies are not known to grow at the high salinities found in some uranium-contaminated groundwaters. Studies with a highly saline uranium-contaminated aquifer sediment demonstrated that the addition of acetate could stimulate the removal of U(VI) from the groundwater. This removal was associated with an enrichment in microorganisms most closely related to Pseudomonas and Desulfosporosinus species.     

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 (β-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.     

Metagenome of a Microbial Community Inhabiting a Metal-Rich Tropical Stream Sediment

Here, we describe the metagenome and functional composition of a microbial community in a historically metal-contaminated tropical freshwater stream sediment. The sediment was collected from the Mina Stream located in the Iron Quadrangle (Brazil), one of the world’s largest mining regions. Environmental DNA was extracted and was sequenced using SOLiD technology, and a total of 7.9 Gbp was produced. A taxonomic profile that was obtained by comparison to the Greengenes database revealed a complex microbial community with a dominance of Proteobacteria and Parvarcheota. Contigs were recruited by bacterial and archaeal genomes, especially Candidatus Nitrospira defluvii and Nitrosopumilus maritimus, and their presence implicated them in the process of N cycling in the Mina Stream sediment (MSS). Functional reconstruction revealed a large, diverse set of genes for ammonium assimilation and ammonification. These processes have been implicated in the maintenance of the N cycle and the health of the sediment. SEED subsystems functional annotation unveiled a high degree of diversity of metal resistance genes, suggesting that the prokaryotic community is adapted to metal contamination. Furthermore, a high metabolic diversity was detected in the MSS, suggesting that the historical arsenic contamination is no longer affecting the prokaryotic community. These results expand the current knowledge of the microbial taxonomic and functional composition of tropical metal-contaminated freshwater sediments.     

Increased Bacterial Uptake of Macromolecular Substrates with Fluid Shear

To investigate the effect of fluid shear on uptake rates of low-diffusivity macromolecular substrates by suspended cultures, we measured the uptake of two compounds as models of macromolecules, a protein (bovine serum albumin [BSA]) and a polysaccharide (dextran), using pure cultures of Zoogloea ramigera and Escherichia coli, respectively. Oxygen utilization rates of stirred samples grown on BSA and dextran were 2.3 and 2.9 times higher, respectively, than those of undisturbed (still) samples. Uptake rates of ³H-BSA and [³H]dextran by stirred samples were 12.6 and 6.2 times higher, respectively, than those by still samples. These experimentally obtained increases are larger than those predicted with a mass transfer model. Model results indicated that stirring would increase uptake by factors of 1.6 and 1.8 for BSA and dextran. As predicted by the model, we also found that uptake rates of low-molecular-weight substrates with high diffusivities, such as leucine and glucose, were only slightly affected by fluid shear. Since macromolecules can make up a major portion of bacterial substrate in natural, laboratory, and engineered systems, the demonstrated effect of fluid shear has wide implications for kinetic studies performed in basic metabolic research as well as in the evaluation of engineered bioreactors used for wastewater treatment.     

Decomposition of Fire Exposed Eucalyptus Leaves in a Portuguese Lowland Stream

We compared fire exposed with normal abscised eucalyptus leaves incubated in a stream running through eucalyptus plantations in central Portugal, in terms of breakdown rates, microbial activity, diversity and macroinvertebrate abundance. Although leaves exposed to fire had lower nutritional value, mass loss was similar for both leaf types (k = 0.0089–0.0095 d^–1 for fire and k = 0.0084–0.00103 d^–1 for normal leaves). Fungal biomass was similar among treatments, whereas sporulation and microbial respiration were lower in fire exposed leaves. Both leaf types had similar aquatic hyphomycetes communities. Physical fragmentation was important in fire exposed leaves breakdown. Invertebrates colonized leaves in low numbers in both treatments. Alteration of leaf litter quality determined by fires in streams does not seem to determine changes in ecosystem functioning in a short term. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

The Response of Three Bacterial Populations to Pollution in a Stream

Abstract Practical methods for biomonitoring of natural systems are still under development. Bacteria are potentially useful indicators of water quality because of their species diversity and ability to rapidly respond to changing environmental conditions. In this study, bacterial populations from unpolluted and polluted stream sites in two watersheds were compared to determine their suitability for use as environmental indicators. Upper Three Runs Creek and Four Mile Creek headwaters have had little anthropogenic disturbance, as opposed to lower Four Mile Creek which received thermal, radioactive, and chemical perturbations. Chemical and physical measurements provided evidence that seepage from holding ponds polluted Four Mile Creek. Polluted sites did not have altered total bacterial numbers but had decreased numbers of colony-forming units. Abundances of three bacterial species, Acinetobacter calcoaceticus, Burkholderia cepacia, and Pseudomonas putida, were determined by colony hybridization with species-specific rDNA probes. Contribution of A. calcoaceticus to the assemblage was higher at polluted sites, which indicated either tolerance of polluted conditions or the ability to utilize compounds existing at these sites to reach larger populations. No differences in B. cepacia populations were detected, and differences in P. putida populations could not be attributed solely to disturbance. The pollution of Four Mile Creek induced differences in bacterial populations that could be monitored using the described approach. Received: 24 September 1996; Accepted: 20 December 1996     

Identification of Methanogenic archaea in the Hyporheic Sediment of Sitka Stream

Methanogenic archaea produce methane as a metabolic product under anoxic conditions and they play a crucial role in the global methane cycle. In this study molecular diversity of methanogenic archaea in the hyporheic sediment of the lowland stream Sitka (Olomouc, Czech Republic) was analyzed by PCR amplification, cloning and sequencing analysis of the methyl coenzyme M reductase alpha subunit (mcrA) gene. Sequencing analysis of 60 clones revealed 24 different mcrA phylotypes from hyporheic sedimentary layers to a depth of 50 cm. Phylotypes were affiliated with Methanomicrobiales, Methanosarcinales and Methanobacteriales orders. Only one phylotype remains unclassified. The majority of the phylotypes showed higher affiliation with uncultured methanogens than with known methanogenic species. The presence of relatively rich assemblage of methanogenic archaea confirmed that methanogens may be an important component of hyporheic microbial communities and may affect CH₄ cycling in rivers.     

Coarse Woody Debris Stimulates Soil Enzymatic Activity and Litter Decomposition in an Old-Growth Temperate Forest of Patagonia, Argentina

In most temperate forest ecosystems, tree mortality over time generates downed logs that accumulate as coarse woody debris (CWD) on the forest floor. These downed logs and trunks have important recognized ecosystem functions including habitat for different organisms and long-term organic C storage. Due to its recalcitrant chemical composition and slow decomposition, CWD can also have direct effects on ecosystem carbon and nutrient turnover. CWD could also cause changes indirectly through the physical and chemical alterations that it generates, although it is not well-understood how important these indirect effects could be for ecosystem processes and soil biogeochemistry. We hypothesized that in an old-growth mature forest, CWD affects carbon and nutrient cycles through its “proximity effects”, meaning that the forest floor near CWD would have altered soil biotic activity due to the environmental and biogeochemical effects of the presence of CWD. We conducted our study in an old-growth southern beech temperate forest in Patagonia, Argentina, where we estimated and classified the distribution and mass, nutrient pools and decay stage of CWD on the forest floor, and evaluated its impact on litter decomposition, soil mites and soil enzymatic activity of carbon and phosphorus-degrading enzymes. We demonstrate here that CWD in this ecosystem represents an important organic carbon reservoir (85 Mg ha^?1) and nitrogen pool (0.42 Mg ha^?1), similar in magnitude to other old-growth forests of the Northern Hemisphere. In addition, we found significant proximity effects of CWD, with increased C-degrading soil enzyme activity, decreased mite abundance, and more rapid litter decomposition beneath highly decayed CWD. Considered at the ecosystem scale in this forest, the removal of CWD could cause a decrease of 6% in soil enzyme activity, particularly in the summer dry season, and nearly 15% in annual litter decomposition. We conclude that beyond the established importance of CWD as a long-term carbon reservoir and habitat, CWD contributes functionally to the forest floor by influencing the spatial heterogeneity of microbial activity and carbon and nutrient turnover. These proximity effects demonstrate the importance of maintenance of this ecosystem component and should be taken into consideration for management decisions pertaining to carbon sequestration and functional diversity in natural forest ecosystems.     

Bacterial Community Composition and Extracellular Enzyme Activity in Temperate Streambed Sediment during Drying and Rewetting

Droughts are among the most important disturbance events for stream ecosystems; they not only affect stream hydrology but also the stream biota. Although desiccation of streams is common in Mediterranean regions, phases of dryness in headwaters have been observed more often and for longer periods in extended temperate regions, including Central Europe, reflecting global climate change and enhanced water withdrawal. The effects of desiccation and rewetting on the bacterial community composition and extracellular enzyme activity, a key process in the carbon flow of streams and rivers, were investigated in a typical Central European stream, the Breitenbach (Hesse, Germany). Wet streambed sediment is an important habitat in streams. It was sampled and exposed in the laboratory to different drying scenarios (fast, intermediate, slow) for 13 weeks, followed by rewetting of the sediment from the fast drying scenario via a sediment core perfusion technique for 2 weeks. Bacterial community structure was analyzed using CARD-FISH and TGGE, and extracellular enzyme activity was assessed using fluorogenic model substrates. During desiccation the bacterial community composition shifted toward composition in soil, exhibiting increasing proportions of Actinobacteria and Alphaproteobacteria and decreasing proportions of Bacteroidetes and Betaproteobacteria. Simultaneously the activities of extracellular enzymes decreased, most pronounced with aminopeptidases and less pronounced with enzymes involved in the degradation of polymeric carbohydrates. After rewetting, the general ecosystem functioning, with respect to extracellular enzyme activity, recovered after 10 to 14 days. However, the bacterial community composition had not yet achieved its original composition as in unaffected sediments within this time. Thus, whether the bacterial community eventually recovers completely after these events remains unknown. Perhaps this community undergoes permanent changes, especially after harsh desiccation, followed by loss of the specialized functions of specific groups of bacteria.     

Response of Stream Metabolism to Coarse Woody Debris Additions Along a Catchment Disturbance Gradient

Ecosystems - We evaluated the ecological effectiveness of an in-stream restoration project involving coarse woody debris (CWD) additions to streams along an upland soil and vegetation disturbance...     

Transisomaltosylation Activity of a Bacterial Isomalto-dextranase

A bacterial isomalto-dextranase, described previously as a new type of dextranase different from the known 1,6-α-d-glucan 6-glucanohydrolase [EC 3.2.1.11], was found to be a configuration-retaining exo-glucanase so far as judged from the downward mutarotation shown by products in a dextran digest, and from the lower activity of the enzyme on lesspolymerized isomaltodextrins according to one of the criteria proposed by Reese et al. The dextranase was observed to cause not only transisomaltosylation (isomaltotetraose formation in dextran digests, isomaltotriose formation in dextran digests containing glucose and transisomaltosylation among isomaltodextrins) but also isomaltose condensation to isomaltotetraose in concentrated solutions. These activities shown by the isomalto-dextranase are in keeping with the novel concept that carbohydrases are catalysts of glycosylation (glycosylhydrogen interchange), proposed by Hehre and his coworkers. The relative ease of isomaltose condensation catalyzed by the enzyme appears due to the exergonic nature of the reaction. A free energy change value of ca. ?1200 cal/mole was obtained for the condensation.