New insights into enzymes in the environment

This article introduces the thematic special issue “Enzymes in the Environment: Incorporating Enzymes and Microbial Physiology into Biogeochemical Models”. This collection of review articles, original studies, and models stemmed from a workshop organized by the Enzymes in the Environment Research Coordination Network, which was held at Colorado State University in Fort Collins, CO, USA in May 2012. The meeting, themed “Incorporating Enzymes and Microbial Physiology into Biogeochemical Models” featured talks from both modelers and experimentalists with experience ranging across terrestrial, aquatic, and marine ecosystems. This special issue represents a series of integrative discussions that occurred among experimentalists and modelers at the meeting. This issue highlights that a better understanding of carbon cycling pathways and subsequent carbon availability dynamics among ecosystems may be achieved by simultaneously integrating aspects of terrestrial and aquatic carbon cycling and microbial physiology into biogeochemical cycling models.     

Elevated carbon dioxide accelerates the spatial turnover of soil microbial communities

Although elevated CO₂ (eCO₂) significantly affects the α‐diversity, composition, function, interaction and dynamics of soil microbial communities at the local scale, little is known about eCO₂ impacts on the geographic distribution of micro‐organisms regionally or globally. Here, we examined the β‐diversity of 110 soil microbial communities across six free air CO₂ enrichment (FACE) experimental sites using a high‐throughput functional gene array. The β‐diversity of soil microbial communities was significantly (P < 0.05) correlated with geographic distance under both CO₂ conditions, but declined significantly (P < 0.05) faster at eCO₂ with a slope of ?0.0250 than at ambient CO₂ (aCO₂) with a slope of ?0.0231 although it varied within each individual site, indicating that the spatial turnover rate of soil microbial communities was accelerated under eCO₂ at a larger geographic scale (e.g. regionally). Both distance and soil properties significantly (P < 0.05) contributed to the observed microbial β‐diversity. This study provides new hypotheses for further understanding their assembly mechanisms that may be especially important as global CO₂ continues to increase.     

Cytotoxicity induced by grape seed proanthocyanidins: Role of nitric oxide

Grape seed proanthocyanidin extract (GPSE) at high doses has been shown to exhibit cytotoxicity that is associated with increased apoptotic cell death. Nitric oxide (NO), being a regulator of apoptosis, can be increased in production by the administration of GSPE. In a chick cardiomyocyte study, we demonstrated that high-dose (500 μg/ml) GSPE produces a significantly high level of NO that contributes to increased apoptotic cell death detected by propidium iodide and terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL) staining. It is also associated with the depletion of intracellular glutathione (GSH), probably due to increased consumption by NO with the formation of S-nitrosoglutathione. Co-treatment with L-NAME, a NO synthase inhibitor, results in reduction of NO and apoptotic cell death. The decline in reduced GSH/oxidized GSH (GSSG) ratio is also reversed. N-Acetylcysteine, a thiol compound that reacts directly with NO, can reduce the increased NO generation and reverse the decreased GSH/GSSG ratio, thereby attenuating the cytotoxicity induced by high-dose GSPE. Taken together, these results suggest that endogenous NO synthase (NOS) activation and excessive NO production play a key role in the pathogenesis of high-dose GSPE-induced cytotoxicity.     

The mutation rates of di-, tri- and tetranucleotide repeats in Drosophila melanogaster

In a recent study, we reported that the combined average mutation rate of 10 di-, 6 tri-, and 8 tetranucleotide repeats in Drosophila melanogaster was 6.3 x 10(-6) mutations per locus per generation, a rate substantially below that of microsatellite repeat units in mammals studied to date (range = 10(-2)-10(-5) per locus per generation). To obtain a more precise estimate of mutation rate for dinucleotide repeat motifs alone, we assayed 39 new dinucleotide repeat microsatellite loci in the mutation accumulation lines from our earlier study. Our estimate of mutation rate for a total of 49 dinucleotide repeats is 9.3 x 10(-6) per locus per generation, only slightly higher than the estimate from our earlier study. We also estimated the relative difference in microsatellite mutation rate among di-, tri-, and tetranucleotide repeats in the genome of D. melanogaster using a method based on population variation, and we found that tri- and tetranucleotide repeats mutate at rates 6.4 and 8.4 times slower than that of dinucleotide repeats, respectively. The slower mutation rates of tri- and tetranucleotide repeats appear to be associated with a relatively short repeat unit length of these repeat motifs in the genome of D. melanogaster. A positive correlation between repeat unit length and allelic variation suggests that mutation rate increases as the repeat unit lengths of microsatellites increase.      

Morphology of the endometrial microvasculature during early placentation in the rat

Summary The morphology of the uterine microvasculature during early placentation was investigated by light microscopy, scanning electron microscopy of microvascular corrosion casts and transmission electron microscopy in rats 26 and 50 h after initiation of implantation. Increased vascular permeability at implantation sites was observed as a positive blue-dye test, spacing of vessels, and as localized extravasations of resin from postcapillary venules in the center of the endometrium. The subepithelial capillary plexus in the primary decidual zone adjacent to the blastocyst was shut down 50 h after initiation of implantation, most probably due to swelling of the metabolically activated endothelium and volume expansion of the decidual cells. This phenomenon coincided with the mesometrial orientation of the inner cell mass of the blastocyst; it may be a uterine mechanism to direct the ectoplacental cone toward the patent vessels in the mesometrial portion of the uterus. The remaining vessels at implantation sites were generally fewer, larger in diameter, more irregular in caliber, and more uniformly oriented along the implantation axis than their counterparts at inter-implantation sites. No vascular sprouts were observed during the interval studied.     

Proffered papers 14.00–15.00 Tuesday 16 September 2003

Background  ERCP-directed brush cytology is used to sample lesions of the pancreatic and biliary ducts and the ampulla of Vater. With conventional preparations, the sensitivity and specificity range from 44% to 63% and 80% to 98%, respectively, and increased N : C ratio, nuclear molding and loss of honeycombing are reliable features of malignancy. The performance and morphology of specimens prepared by ThinPrep, a liquid-based cytology technique is mostly unknown.
Methods  The laboratory information system was searched for all cases prepared by ThinPrep. Patient disease classification of benign or malignant was determined by linkage with the provincial cancer registry and was the gold standard against which sensitivity, specificity, positive (PPV) and negative predictive values (NPV) were calculated. True positives and negatives were reviewed to identify predictive cytomorphologic features.
Results  Between 1996 and 2001, there were 149 ThinPrep specimens; 55 (37%) were reported as positive for malignancy and 94 (63%) as negative. Disease was classified as malignant in 86 (58%) patients and benign in 63 (42%). There were 42 false negative, 11 false positive, 52 true negative, and 44 true positive cytology results. Sensitivity was 51.2% (CI; 40.2 : 62.0), specificity 82.5% (CI; 70.5 : 90.6), and PPV and NPV 80.0% (CI; 66.6 : 89) and 55.3% (CI; 44.7 : 65.5), respectively. Cell groups with crowded, enlarged, irregular nuclei and nuclear features of vesicular chromatin and large, multiple irregular nucleoli correlated with malignant disease, while monolayered sheets of uniform columnar cells, regular nuclei and a finely granular chromatin correlated with benign disease.
Conclusions  The performance of ThinPrep brushings from this anatomic site equals conventional preparations. Cytomorphologic features of malignancy are more frequent and pronounced with ThinPrep.     

Biofloc Technology: Emerging Microbial Biotechnology for the Improvement of Aquaculture Productivity

With the significant increases in the human population, global aquaculture has undergone a great increase during the last decade. The management of optimum conditions for fish production, which are entirely based on the physicochemical and biological qualities of water, plays a vital role in the prompt aquaculture growth. Therefore, focusing on research that highlights the understanding of water quality and breeding systems’ stability is very important. The biofloc technology (BFT) is a system that maximizes aquaculture productivity by using microbial biotechnology to increase the efficacy and utilization of fish feeds, where toxic materials such as nitrogen components are treated and converted to a useful product, like a protein for using as supplementary feeds to the fish and crustaceans. Thus, biofloc is an excellent technology used to develop the aquaculture system under limited or zero water exchange with high fish stocking density, strong aeration, and biota. This review is highlighted on biofloc composition and mechanism of system work, especially the optimization of water quality and treatment of ammonium wastes. In addition, the advantages and disadvantages of the BFT system have been explained. Finally, the importance of contemporary research on biofloc systems as a figure of microbial biotechnology has been emphasized with arguments for developing this system for better production of aquaculture with limited natural resources of water.Key words: biofloc, BFT, aquaculture, microbes, water quality, wastes     

Molecular characterization of Pseudomonas aeruginosa 2NR degrading naphthalene

Three naphthalene-degrading strains were isolated from compost, characterized by morphological and physiological properties and differentiated by 16S rDNA RFLP. During growth on naphthalene, Pseudomonas aeruginosa 2NR produced ortho catechol pathway intermediates and gentisic acid. The ability to accumulate and degrade gentisic acid shows that Ps. aeruginosa 2NR has a different salicylate pathway to that of the intensely studied Ps. putida NCIB 9816. Molecular analysis showed the presence both of genes of the upper naphthalene pathway and genes of the ortho and meta catechol pathways. The insertion of nagH and nagG, coding for salicylate 5-hydroxylase in Pseudomonas sp. U2, was absent in Ps. aeruginosa 2NR, as in Ps. putida NCIMB 9816.     

Fungal Taxa Target Different Carbon Sources in Forest Soil

Soil microbes are among the most abundant and diverse organisms on Earth. Although microbial decomposers, particularly fungi, are important mediators of global carbon and nutrient cycling, the functional roles of specific taxa within natural environments remain unclear. We used a nucleotide-analog technique in soils from the Harvard Forest to characterize the fungal taxa that responded to the addition of five different carbon substrates—glycine, sucrose, cellulose, lignin, and tannin-protein. We show that fungal community structure and richness shift in response to different carbon sources, and we demonstrate that particular fungal taxa target different organic compounds within soil microcosms. Specifically, we identified eleven taxa that exhibited changes in relative abundances across substrate treatments. These results imply that niche partitioning through specialized resource use may be an important mechanism by which soil microbial diversity is maintained in ecosystems. Consequently, high microbial diversity may be necessary to sustain ecosystem processes and stability under global change. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. K. K. T., M. A. B., and M. D. W. conceived the project. C. A. H. performed the molecular work and sequence alignments. M. A. B. performed the substrate-induced respiration experiment. S. D. A. and K. K. T. analyzed the data. C. A. H. wrote the article with input from the other authors.