De novo assembly of a fruit transcriptome set identifies AmMYB10 as a key regulator of anthocyanin biosynthesis in Aronia melanocarpa.

Aronia is a group of deciduous fruiting shrubs, of the Rosaceae family, native to eastern North America. Interest in Aronia has increased because of the high levels of dietary antioxidants in Aronia fruits. Using Illumina RNA-seq transcriptome analysis, this study investigates the molecular mechanisms of polyphenol biosynthesis during Aronia fruit development. Six A. melanocarpa (diploid) accessions were collected at four fruit developmental stages. De novo assembly was performed with 341 million clean reads from 24 samples and assembled into 90,008 transcripts with an average length of 801 bp. The transcriptome had 96.1% complete according to Benchmarking Universal Single-Copy Orthologs (BUSCOs). The differentially expressed genes (DEGs) were identified in flavonoid biosynthetic and metabolic processes, pigment biosynthesis, carbohydrate metabolic processes, and polysaccharide metabolic processes based on significant Gene Ontology (GO) biological terms. The expression of ten anthocyanin biosynthetic genes showed significant up-regulation during fruit development according to the transcriptomic data, which was further confirmed using qRT-PCR expression analyses. Additionally, transcription factor genes were identified among the DEGs. Using a transient expression assay, we confirmed that AmMYB10 induces anthocyanin biosynthesis. The de novo transcriptome data provides a valuable resource for the understanding the molecular mechanisms of fruit anthocyanin biosynthesis in Aronia and species of the Rosaceae family.

Agreement of primary outcomes in chiropractic-related clinical trials registered in clinicaltrials.gov with corresponding publication.

INTRODUCTION: Previous analysis of registered clinical trials has found a number of protocols result in changes in the registered primary outcome measures. This investigation determined if reported primary outcomes in chiropractic-related clinical trials registered in clinicaltrials.gov match their published results. Additionally, we assessed secondary outcomes, publication status and whether raw data were posted to the registry. METHODS: Clinicaltrials.gov was searched for chiropractic-related trials and having a completed status. If the study was published, outcome measures were compared between the clinicaltrials.gov entry and the published paper to assess for consistency. RESULTS: Within clinicaltrials.gov 171 chiropracticrelated protocols were identified with 102 of those published (59.6% publication rate). Ninety-two of the published papers (90.2%) had agreement between their primary outcome and the entry on clinicaltrials.gov and 82 (80.4%) agreed with the secondary outcomes. CONCLUSION: A modest rate of agreement between clinicaltrials.gov entries and the published papers was found. While chiropractic-related clinical trials are fewer compared to medical trials, chiropractic-related research has a substantially better rate of primary and secondary outcome concordance with registered protocols.

INTRODUCTION: En examinant des essais cliniques enregistrés, on s'est rendu compte qu'un certain nombre de protocoles faisaient varier les résultats principaux. On a mené une étude pour savoir si les résultats primaires d'essais cliniques sur la chiropratique enregistrés sur clinicaltrials.gov correspondaient à ceux publiés. On a aussi examiné les résultats secondaires, l'état de publication et cherché à savoir si les données brutes étaient publiées dans le registre. MÉTHODOLOGIE: Dans la base de données Clinicaltrials.gov, on a repéré des essais cliniques sur la chiropratique qui étaient terminés. Lorsque l'essai clinique avait été publié, on a comparé les résultats au moment de son enregistrement sur clinicaltrials.gov à ceux parus dans des publications pour savoir s'ils concordaient. RÉSULTATS: Sur le site clinicaltrials.gov, on a trouvé 171 études sur la chiropratique, dont 102 avaient été publiés (taux de publication:59,6 %). Pour quatrevingt-douze publications (90,2 %), on a observé une concordance entre les résultats primaires au moment de l'enregistrement sur clinicaltrials.gov et 82 (80,4 %) et les résultats secondaires. CONCLUSION: On a observé un taux modeste de concordance entre les données à l'enregistrement sur clinicaltrails.gov et les données publiées. Les essais cliniques sur la chiropratique sont moins nombreux que des essais cliniques de médicaments. Mais le taux de concordance entre les résultats primaires et les résultats secondaires était considérablement plus élevé lorsque les protocoles de recherches sur la chiropratique sont enregistrés.

Aronia berry polyphenols have matrix-dependent effects on the gut microbiota.

The objective of this study was to determine the extent that the aronia berry matrix affects gut microbiota composition, fecal short chain fatty acids (SCFAs), and colonic anthocyanins in healthy mice. C57BL/6J mice were fed AIN-93 M control diet (C) or C with whole aronia berry (AB), aronia extract (AE), or polyphenol-depleted AB (D) at the expense of cornstarch. After one week of feeding, AB and D increased fecal anthocyanins more than AE. Diets differentially affected SCFA and microbiota. AB fecal SCFA was associated with increased metabolism of succinate and pyruvate to butyrate. D increased acetic acid production, was associated with increased abundance of predicted genes for fermentation of carbohydrates to acetyl-coA. AB and D also increased predicted abundance of microbial catechol metabolism pathway I relative to C, which was attributed to enrichment of Lachnospiraceae. Therefore, the berry matrix impacts how aronia polyphenols interact with the gut microbiota in healthy mice.

Aronia Berry Supplementation Mitigates Inflammation in T Cell Transfer-Induced Colitis by Decreasing Oxidative Stress.

Oxidative stress is involved in the pathogenesis and progression of inflammatory bowel disease. Consumption of aronia berry inhibits T cell transfer colitis, but the antioxidant mechanisms pertinent to immune function are unclear. We hypothesized that aronia berry consumption could inhibit inflammation by modulating the antioxidant function of immunocytes and gastrointestinal tissues. Colitis was induced in recombinase activating gene-1 deficient (Rag1-/-) mice injected with syngeneic CD4+CD62L+ naïve T cells. Concurrent with transfer, mice consumed either 4.5% w/w aronia berry-supplemented or a control diet for five weeks. Aronia berry inhibited intestinal inflammation evidenced by lower colon weight/length ratios, 2-deoxy-2-[18F]fluoro-d-glucose (FDG) uptake, mRNA expressions of tumor necrosis factor alpha (TNF-α), and interferon gamma (IFN-γ) in the colon. Aronia berry also suppressed systemic inflammation evidenced by lower FDG uptake in the spleen, liver, and lung. Colitis induced increased colon malondialdehyde (MDA), decreased colon glutathione peroxidase (GPx) activity, reduced glutathione (rGSH) level, and suppressed expression of antioxidant enzymes in the colon and mesenteric lymph node (MLN). Aronia berry upregulated expression of antioxidant enzymes, prevented colitis-associated depletion of rGSH, and maintained GPx activity. Moreover, aronia berry modulated mitochondria-specific antioxidant activity and decreased splenic mitochondrial H2O2 production in colitic mice. Thus, aronia berry consumption inhibits oxidative stress in the colon during T cell transfer colitis because of its multifaceted antioxidant function in both the cytosol and mitochondria of immunocytes.

Use of high-throughput screening results to prioritize chemicals for potential adverse biological effects within a West Virginia watershed.

Organic chemicals from industrial, agricultural, and residential activities can enter surface waters through regulated and unregulated discharges, combined sewer overflows, stormwater runoff, accidental spills, and leaking septic-conveyance systems on a daily basis. The impact of point and nonpoint contaminant sources can result in adverse biological effects for organisms living in or near surface waters. Assessing the adverse or toxic effects that may result when exposure occurs is complicated by the fact that many commonly used chemicals lack toxicity information or water quality standards. To address these challenges, an exposure-activity ratio (EAR) screening approach was used to prioritize environmental chemistry data in a West Virginia watershed (Wolf Creek). Wolf Creek is a drinking water source and recreation resource with documented water quality impacts from point and nonpoint sources. The EAR screening approach uses high-throughput screening (HTS) data from ToxCast as a method of integrating environmental chemical occurrence and biological effects data. Using water quality schedule 4433, which targets 69 organic waste compounds typically found in domestic and industrial wastewater, chemicals were screened for potential adverse biological affects at multiple sites in the Wolf Creek watershed. Cumulative EAR mixture values were greatest at Sites 2 and 3, where bisphenol A (BPA) and pentachlorophenol exhibited maximum EAR values of 0.05 and 0.002, respectively. Site 2 is downstream of an unconventional oil and gas (UOG) wastewater disposal facility with documented water quality impacts. Low-level organic contaminants were found at all sample sites in Wolf Creek, except Site 10, where Wolf Creek enters the New River. The application of an EAR screening approach allowed our study to extend beyond traditional environmental monitoring methods to identify multiple sites and chemicals that warrant further investigation.

Dietary Prevention of Colitis by Aronia Berry is Mediated Through Increased Th17 and Treg.

SCOPE: Increased fruit consumption is associated with reduced risk of colitis. It has been investigated whether the anti-colitic effects of the polyphenol-rich aronia berry (Aronia mitschurinii 'Viking') are mediated through Th17 and Treg. METHODS AND RESULTS: Colitis is induced in recombinase activating gene-1 deficient mice injected with syngeneic CD4+ CD62L+ naïve T cells. Mice consume either 4.5% w/w aronia-berry-supplemented or a control diet concurrent with T cell transfer. The extent of colitis and immunocyte populations are evaluated at weeks 3 to 7 after transfer. Aronia consumption prevents colitic wasting and reduces colon weight/length ratios relative to the control diet at weeks 5 and 7. Compared to the control diet, aronia feeding increases Treg in mesenteric lymph node at all colitis stages. Treg and regulatory Th17 subpopulations (IL-17A+ IL-10+ and IL-17A+ IL-22+ ) are increased in lamina propria and spleen at week 5 in aronia-fed mice. Aronia feeding also decreases total CD4+ cells but increases colonic Tregs. The ability of aronia to modulate colonic cytokines is associated with functional T cell IL-10 and increased diversity of microbiota. CONCLUSIONS: Aronia berry consumption inhibits adoptive transfer colitis by increasing Treg and regulatory Th17 cells. Dietary modulation of T cells is dynamic and precedes colitic wasting.

A common antimicrobial additive increases colonic inflammation and colitis-associated colon tumorigenesis in mice.

Triclosan (TCS) is a high-volume chemical used as an antimicrobial ingredient in more than 2000 consumer products, such as toothpaste, cosmetics, kitchenware, and toys. We report that brief exposure to TCS, at relatively low doses, causes low-grade colonic inflammation, increases colitis, and exacerbates colitis-associated colon cancer in mice. Exposure to TCS alters gut microbiota in mice, and its proinflammatory effect is attenuated in germ-free mice. In addition, TCS treatment increases activation of Toll-like receptor 4 (TLR4) signaling in vivo and fails to promote colitis in Tlr4-/- mice. Together, our results demonstrate that this widely used antimicrobial ingredient could have adverse effects on colonic inflammation and associated colon tumorigenesis through modulation of the gut microbiota and TLR4 signaling. Together, these results highlight the need to reassess the effects of TCS on human health and potentially update policies regulating the use of this widely used antimicrobial.

Premeal Low-Fat Yogurt Consumption Reduces Postprandial Inflammation and Markers of Endotoxin Exposure in Healthy Premenopausal Women in a Randomized Controlled Trial.

Background: Metabolic endotoxemia is associated with obesity and contributes to postprandial inflammation. Objective: We aimed to determine if low-fat yogurt consumption prevents postprandial inflammation and dysmetabolism in healthy women by inhibiting biomarkers of metabolic endotoxemia. Methods: Premenopausal women defined as obese and nonobese [body mass index (BMI, in kg/m2) 30-40 and 18.5-27, respectively, n = 120] were randomly assigned to consume 339 g of low-fat yogurt (YN, yogurt nonobese; YO, yogurt obese) or 324 g of soy pudding (CN, control nonobese; CO, control obese) for 9 wk (n = 30/group). The intervention foods each supplied 330 kcal with 3 g fat, 66 g carbohydrate, and 4-6 g protein. At weeks 0 and 9, participants ingested 226 g of yogurt or 216 g of soy pudding before a meal providing 56-60 g fat, 82 g carbohydrate, and 28-30 g protein. Plasma soluble CD14 (sCD14), lipopolysaccharide-binding protein (LBP), LPS activity, interleukin-6 (IL-6), glucose, triglyceride, and insulin were measured hourly for 4 h to assess differences in postprandial responses between groups by 2-factor ANOVA. Results: Premeal yogurt consumption prevented the postprandial decrease in sCD14 net incremental area under the curve (net iAUC) by 72% in obese individuals at week 0 (P = 0.0323). YN and YO had ≥40% lower net iAUC of LBP-to-sCD14 ratio and plasma IL-6 concentration than CN and CO, respectively (P < 0.05). CO had postprandial hyperglycemia which was not evident in YO; in contrast YN had 57% less postprandial hypoglycemia than did CN (P-interaction = 0.0013). After 9 wk of yogurt consumption, ΔAUC of LBP-to-sCD14 ratios of YO and YN were less than half of those of the control groups (P = 0.0093). Conclusion: Yogurt consumption improved postprandial metabolism and biomarkers of metabolic endotoxemia in healthy premenopausal women. Premeal yogurt consumption is a feasible strategy to inhibit postprandial dysmetabolism and thus may reduce cardiometabolic risk. This trial was registered at clinicaltrials.gov as NCT01686204.

Displacement of a landslide retaining wall and application of an enhanced failure forecasting approach.

The 10-mile Slide is contained within an ancient earthflow located in British Columbia, Canada. The landslide has been moving slowly for over 40 years, requiring regular maintenance work along where a highway and a railway track cross the sliding mass. Since 2013, the landslide has shown signs of retrogression. Monitoring prisms were installed on a retaining wall immediately downslope from the railway alignment to monitor the evolution of the retrogression. As of September 2016, cumulative displacements in the horizontal direction approached 4.5 m in the central section of the railway retaining wall. After an initial phase of acceleration, horizontal velocities showed a steadier trend between 3 and 9 mm/day, which was then followed by a second acceleration phase. This paper presents an analysis of the characteristics of the surface displacement vectors measured at the monitoring prisms. Critical insight on the behavior and kinematics of the 10-mile Slide retrogression was gained. An advanced analysis of the trends of inverse velocity plots was also performed to assess the potential for a slope collapse at the 10-mile Slide and to obtain further knowledge on the nature of the sliding surface.

Low-fat yogurt consumption reduces biomarkers of chronic inflammation and inhibits markers of endotoxin exposure in healthy premenopausal women: a randomised controlled trial.

The anti-inflammatory mechanisms of low-fat dairy product consumption are largely unknown. The objective of this study was to determine whether low-fat yogurt reduces biomarkers of chronic inflammation and endotoxin exposure in women. Premenopausal women (BMI 18·5-27 and 30-40 kg/m2) were randomised to consume 339 g of low-fat yogurt (yogurt non-obese (YN); yogurt obese (YO)) or 324 g of soya pudding (control non-obese; control obese (CO)) daily for 9 weeks (n 30/group). Fasting blood samples were analysed for IL-6, TNF-α/soluble TNF II (sTNF-RII), high-sensitivity C-reactive protein, 2-arachidonoyl glycerol, anandamide, monocyte gene expression, soluble CD14 (sCD14), lipopolysaccharide (LPS), LPS binding protein (LBP), IgM endotoxin-core antibody (IgM EndoCAb), and zonulin. BMI, waist circumference and blood pressure were also determined. After 9-week yogurt consumption, YO and YN had decreased TNF-α/sTNFR-RII. Yogurt consumption increased plasma IgM EndoCAb regardless of obesity status. sCD14 was not affected by diet, but LBP/sCD14 was lowered by yogurt consumption in both YN and YO. Yogurt intervention increased plasma 2-arachidonoylglycerol in YO but not YN. YO peripheral blood mononuclear cells expression of NF-κB inhibitor α and transforming growth factor ß1 increased relative to CO at 9 weeks. Other biomarkers were unchanged by diet. CO and YO gained approximately 0·9 kg in body weight. YO had 3·6 % lower diastolic blood pressure at week 3. Low-fat yogurt for 9 weeks reduced biomarkers of chronic inflammation and endotoxin exposure in premenopausal women compared with a non-dairy control food. This trial was registered as NCT01686204.

Evidence for the effects of yogurt on gut health and obesity.

Obesity is associated with increased risk for chronic diseases, and affects both developed and developing nations. Yogurt is a nutrient-dense food that may benefit individuals with lactose intolerance, constipation and diarrheal diseases, hypertension, cardiovascular diseases, diabetes, and certain types of cancer. Emerging evidence suggests that yogurt consumption might also improve the health of obese individuals. Obesity is often accompanied by chronic, low-grade inflammation perpetuated by adipose tissue and the gut. In the gut, obesity-associated dysregulation of microbiota and impaired gut barrier function may increase endotoxin exposure. Intestinal barrier function can be compromised by pathogens, inflammatory cytokines, endocannabinoids, diet, exercise, and gastrointestinal peptides. Yogurt consumption may improve gut health and reduce chronic inflammation by enhancing innate and adaptive immune responses, intestinal barrier function, lipid profiles, and by regulating appetite. While this evidence suggests that yogurt consumption is beneficial for obese individuals, randomized-controlled trials are needed to further support this hypothesis.

A review of the efficacy of dietary polyphenols in experimental models of inflammatory bowel diseases.

Crohn's disease and ulcerative colitis presently have no cure and are treated with anti-inflammatory drugs or monoclonal antibodies targeting pro-inflammatory cytokines. A variety of rodent models have been used to model chronic and acute colitis. Dietary polyphenols in foods and botanicals are of considerable interest for prevention and treatment of colitis. Many dietary polyphenols have been utilized for prevention of colitis in rodent models. Berries, green tea polyphenols, curcumin, and stilbenes have been the most extensively tested polyphenols in rodent models of colitis. The majority of polyphenols tested have inhibited colitis in rodents, but increasing doses of EGCG and green tea, isoflavones, flaxseed, and α-mangostin have exacerbated colitis. Few studies have examined combination of polyphenols or other bioactives for inhibition of colitis. Translating polyphenol doses used in rodent models of colitis to human equivalent doses reveals that supplemental doses are most likely required to inhibit colitis from a single polyphenol treatment. The ability to translate polyphenol treatments in rodent models is likely to be limited by species differences in xenobiotic metabolism and microbiota. Given these limitations, data from polyphenols in rodent models suggests merit for pursuing additional clinical studies for prevention of colitis.

PELS (Planetary Environmental Liquid Simulator): a new type of simulation facility to study extraterrestrial aqueous environments.

Investigations of other planetary bodies, including Mars and icy moons such as Enceladus and Europa, show that they may have hosted aqueous environments in the past and may do so even today. Therefore, a major challenge in astrobiology is to build facilities that will allow us to study the geochemistry and habitability of these extraterrestrial environments. Here, we describe a simulation facility (PELS: Planetary Environmental Liquid Simulator) with the capability for liquid input and output that allows for the study of such environments. The facility, containing six separate sample vessels, allows for statistical replication of samples. Control of pressure, gas composition, UV irradiation conditions, and temperature allows for the precise replication of aqueous conditions, including subzero brines under martian atmospheric conditions. A sample acquisition system allows for the collection of both liquid and solid samples from within the chamber without breaking the atmospheric conditions, enabling detailed studies of the geochemical evolution and habitability of past and present extraterrestrial environments. The facility we describe represents a new frontier in planetary simulation-continuous flow-through simulation of extraterrestrial aqueous environments.

Fish functional traits correlated with environmental variables in a temperate biodiversity hotspot.

The global biodiversity crisis has invigorated the search for generalized patterns in most disciplines within the natural sciences. Studies based on organismal functional traits attempt to broaden implications of results by identifying the response of functional traits, instead of taxonomic units, to environmental variables. Determining the functional trait responses enables more direct comparisons with, or predictions for, communities of different taxonomic composition. The North American freshwater fish fauna is both diverse and increasingly imperiled through human mediated disturbances, including climate change. The Tennessee River, USA, contains one of the most diverse assemblages of freshwater fish in North America and has more imperiled species than other rivers, but there has been no trait-based study of community structure in the system. We identified 211 localities in the upper Tennessee River that were sampled by the Tennessee Valley Authority between 2009 and 2011 and compiled fish functional traits for the observed species and environmental variables for each locality. Using fourth corner analysis, we identified significant correlations between many fish functional traits and environmental variables. Functional traits associated with an opportunistic life history strategy were correlated with localities subject to greater land use disturbance and less flow regulation, while functional traits associated with a periodic life history strategy were correlated with localities subject to regular disturbance and regulated flow. These are patterns observed at the continental scale, highlighting the generalizability of trait-based methods. Contrary to studies that found no community structure differences when considering riparian buffer zones, we found that fish functional traits were correlated with different environmental variables between analyses with buffer zones vs. entire catchment area land cover proportions. Using existing databases and fourth corner analysis, our results support the broad application potential for trait-based methods and indicate trait-based methods can detect environmental filtering by riparian zone land cover.

Carbonate precipitation under pressure for bioengineering in the anaerobic subsurface via denitrification.

A number of bioengineering techniques are being developed using microbially catalyzed hydrolysis of urea to precipitate calcium carbonate for soil and sand strengthening in the subsurface. In this study, we evaluate denitrification as an alternative microbial metabolism to induce carbonate precipitation for bioengineering under anaerobic conditions and at high pressure. In anaerobic batch culture, the halophile Halomonas halodenitrificans is shown to be able to precipitate calcium carbonate at high salinity and at a pressure of 8 MPa, with results comparable to those observed when grown at ambient pressure. A larger scale proof-of-concept experiment shows that, as well as sand, coarse gravel can also be cemented with calcium carbonate using this technique. Possible practical applications in the subsurface are discussed, including sealing of improperly abandoned wells and remediation of hydraulic fracturing during shale gas extraction.

Aronia melanocarpa (chokeberry) polyphenol-rich extract improves antioxidant function and reduces total plasma cholesterol in apolipoprotein E knockout mice.

We hypothesized that a polyphenol-rich chokeberry extract (CBE) would modulate hepatic lipid metabolism and improve antioxidant function in apolipoprotein E knockout (apoE(-/-)) mice. ApoE(-/-) mice were fed diets containing 15% fat with 0.2% cholesterol alone or supplemented with 0.005% or 0.05% CBE for 4 weeks. CBE polyphenol content was determined by the total phenols, 4-dimethylaminocinnamaldehyde, and ultra high-performance liquid chromatography-mass spectrometry methods. The 0.05% CBE diet provided mice with mean daily doses of 1.2 mg gallic acid equivalents of total phenols, 0.19 mg anthocyanins, 0.17 mg phenolic acids, 0.06 mg proanthocyanidins (as catechin-equivalents), and 0.02 mg flavonols. The 0.05% CBE group had 12% less plasma total cholesterol concentrations than the control. Despite the hypocholesterolemic effect of CBE, hepatic mRNA levels of low-density lipoprotein receptor, hydroxyl-3-methylglutaryl coenzyme A reductase and cholesterol 7α-hydroxylase in CBE-fed mice were not significantly different from controls. Dietary CBE did not alter hepatic lipid content or the hepatic expression of genes involved in lipogenesis and fatty acid ß-oxidation such as fatty acid synthase, carnitine palmitoyltransferase 1 and acyl-CoA oxidase. Plasma paraoxonase and catalase activities were significantly increased in mice fed 0.05% CBE. Both CBE diets increased hepatic glutathione peroxidase (GPx) activity but the 0.05% CBE group had 24% less proximal intestine GPx activity relative to controls. Thus, dietary CBE lowered total cholesterol and improved plasma and hepatic antioxidant function at nutritionally-relevant doses in apoE(-/-) mice. Furthermore, the CBE cholesterol-lowering mechanism in apoE(-/-) mice was independent of hepatic expression of genes involved in cholesterol metabolism.

Reliable and robust molecular sexing of the hen harrier (Circus cyaneus) using PCR-RFLP analysis of the CHD 1 gene.

The hen harrier (Circus cyaneus) is a bird of prey that is persecuted in the United Kingdom, and there is a need for a DNA-based individual identification and sexing system for the use in forensic investigations. This study reports a new set of PCR primers for the chromo-helicase-DNA-binding protein 1 gene, which allows sexing using PCR-RFLP. Instead of exonic primers that amplify across a large intron, this set consists of a primer within the intron, enabling reduction in amplicon sizes from 356 to 212 bp and 565 to 219 bp in W and Z chromosomes. DNA degradation and dilution experiments demonstrate that this set is significantly more robust than one that amplifies across the intron, and sequencing of the intronic primer-binding region across several individuals shows that it is highly conserved. While our objective is to incorporate this primer set into an STR-based individualization kit, it may in the meantime prove useful in forensic or conservation studies.

Inhibition of Sporosarcina pasteurii under anoxic conditions: implications for subsurface carbonate precipitation and remediation via ureolysis.

The use of Sporosarcina pasteurii to precipitate calcium carbonate in the anoxic subsurface via ureolysis has been proposed for reducing porosity and sealing fractures in rocks. Here we show that S. pasteurii is unable to grow anaerobically and that the ureolytic activity previously shown under anoxic conditions is a consequence of the urease enzyme already present in the cells of the aerobically grown inoculum. The implications are discussed, suggesting that de novo synthesis of urease under anoxic conditions is not possible and that ureolysis may decline over time without repeated injection of S. pasteurii as the urease enzyme degrades and/or becomes inhibited. Augmentation with a different ureolytic species that is able to grow anaerobically or stimulation of natural communities may be preferable for carbonate precipitation over the long term.

Culturable prokaryotic diversity of deep, gas hydrate sediments: first use of a continuous high-pressure, anaerobic, enrichment and isolation system for subseafloor sediments (DeepIsoBUG).

Deep subseafloor sediments may contain depressurization-sensitive, anaerobic, piezophilic prokaryotes. To test this we developed the DeepIsoBUG system, which when coupled with the HYACINTH pressure-retaining drilling and core storage system and the PRESS core cutting and processing system, enables deep sediments to be handled without depressurization (up to 25 MPa) and anaerobic prokaryotic enrichments and isolation to be conducted up to 100 MPa. Here, we describe the system and its first use with subsurface gas hydrate sediments from the Indian Continental Shelf, Cascadia Margin and Gulf of Mexico. Generally, highest cell concentrations in enrichments occurred close to in situ pressures (14 MPa) in a variety of media, although growth continued up to at least 80 MPa. Predominant sequences in enrichments were Carnobacterium, Clostridium, Marinilactibacillus and Pseudomonas, plus Acetobacterium and Bacteroidetes in Indian samples, largely independent of media and pressures. Related 16S rRNA gene sequences for all of these Bacteria have been detected in deep, subsurface environments, although isolated strains were piezotolerant, being able to grow at atmospheric pressure. Only the Clostridium and Acetobacterium were obligate anaerobes. No Archaea were enriched. It may be that these sediment samples were not deep enough (total depth 1126-1527 m) to obtain obligate piezophiles.

Acetate and ethanol as potential enhancers of low temperature denitrification in soil contaminated by fur farms: a pilot-scale study.

Ethanol and acetate were examined as potential candidates to enhance denitrification at low temperature in soils contaminated by fur farms. Five pilot-scale sand and gravel columns with a top layer of soil from a fur farm were set up and fed with nitrate-containing water (influent concentration of 100 and 200 mg L(-1)) for 459 days at 6+/-2 degrees C. Two of the columns also received acetate and two other ethanol while one received no additional C-substrate. During the experiment, various C:N-ratios were tested to find the most optimal concentration of the added C-substrates, and effluent concentrations of nitrate, nitrite, and TOC were monitored. At the end of the experiments, soils in the columns were unpacked and the soils were used to measure a pattern of enzyme activities and the rates of denitrification in microcosms. The fur farm contaminated soil appeared to harbour a good intrinsic potential for denitrification, which could be greatly enhanced by the introduction of ethanol or acetate. Consequently, in the C-substrate-fed columns, 95-100% of the influent nitrate was removed after an acclimatization period of some weeks. Ethanol with C:N-ratio of ca. 6 at the nitrate level 200 mg L(-1) proved to be the most promising candidate to be used in field trials.