Emergent quality of service - a bacterial approach

A possible model for future network quality of service control is proposed. This is based on a community of bacterial strains, each organism handling network requests in the same way as bacteria metabolise energy sources. This model makes use of the unique methods that bacteria use to transfer and share genetic material, to create a more robust solution to the service provision problems associated with future data networks

Evaluation of Effects of Wastewater Treatment Discharge on Estuarine Water Quality

This report marks the completion of a two-year project focused on observed and estimated effects of wastewater treatment facilities (WWTFs) on estuarine water quality within the New Hampshire (NH) Seacoast region. This study was designed and carried out in an effort to help the NH Department of Environmental Services (NHDES) and NH Estuaries Project (NHEP) evaluate the effects of WWTF effluent quality on bacterial and nutrient concentrations in New Hampshire’s estuarine waters, as well as to help NHDES/NHEP identify related WWTF infrastructure problems. An extensive database of bacterial and nutrient concentrations in effluent collected post-disinfection from 9 NH WWTFs and 2 Maine WWTFs that discharge into the Great Bay and Hampton/Seabrook estuaries was developed. The data were used to determine ratios between different bacterial indicators in WWTF effluent, estimates of in-stream bacterial concentrations following effluent discharge to receiving waters and estimates of nutrient loading from selected WWTFs

Evaluating the Stormwater Treatment Performance of AbTech Industries Smart Sponge® Plus, Landry, N

The ability of AbTech’s Smart Sponge® Plus to remove fecal-borne bacteria from stormwater was evaluated in a storm drainage system located in Seabrook, New Hampshire. The Smart Sponge ® Plus was installed into a water quality inlet and samples were collected from influent (pre-treatment) and effluent (post-treatment) for analysis of bacterial concentrations and loadings during 15 storm events from September 3, 2003 to May 24, 2004, excluding winter months. The 15 storms included events with a range of rainfall intensities and amounts, as well as accompanying runoff volumes. Flow weighted composite samples were analyzed for fecal coliforms, Escherichia coli and enterococci to determine if concentrations were lowered as stormwater passed through the Smart Sponge® Plus material. In most cases, bacterial concentrations were reduced within the treatment system, but to varying degrees. The efficiency ratio based on reduction in event mean concentration for each bacterial indicator in the flow was calculated for each storm event. The values ranged most widely for fecal coliforms, whereas the range of ratios was narrower and the values were more consistent for enterococci. The overall load reductions for the bacterial indicators were 50.3% for fecal coliforms, 51.3% for Escherichia coli and 43.2% for enterococci. Relatively consistent pH values were observed in influent and effluent samples. The overall range of pH values was large, ranging from 5.21 units in influent from storm event #11 to 7.64 units in influent from storm event #1. Conductivity values were gr eater in the effluent in 14 of the 15 storm events, especially in storm events #12 and #13 when effluent conductivities were \u3e50% higher than influent values. Quality assurance/quality control procedures supported the methods and results of the study. Overall, the observed reductions in bacterial concentrations in post-treatment stormwater would still result in discharge of elevated bacterial levels that would continue to limit uses in receiving waters

Responses of a bacterial pathogen to phosphorus limitation of its aquatic invertebrate host

Host nutrition is thought to affect the establishment, persistence, and severity of pathogenic infections. Nutrient-deficient foods possibly benefit pathogens by constraining host immune function or benefit hosts by limiting parasite growth and reproduction. However, the effects of poor elemental food quality on a host's susceptibility to infection and disease have received little study. Here we show that the bacterial microparasite Pasteuria ramosa is affected by the elemental nutrition of its aquatic invertebrate host, Daphnia magna. We found that high food carbon : phosphorus (C: P) ratios significantly reduced infection rates of Pasteuria in Daphnia and led to lower within-host pathogen multiplication. In addition, greater virulent effects of bacterial infection on host reproduction were found in Daphnia-consuming P-deficient food. Poor Daphnia elemental nutrition thus reduced the growth and reproduction of its bacterial parasite, Pasteuria. The effects of poor host nutrition on the pathogen were further evidenced by Pasteuria's greater inhibition of reproduction in P-limited Daphnia. Our results provide strong evidence that elemental food quality can significantly influence the incidence and intensity of infectious disease in invertebrate hosts

Salivary bacterial leakage into implant-abutment connections: preliminary results of an in vitro study

OBJECTIVE: The occurrence of bacterial leakage in the internal surface of implants, through implant-abutment interface (IAI), is one of the parameters for analyzing the fabrication quality of the connections. The aim of this in vitro study is to evaluate two different types of implant-abutment connections: the screwed connection (Group 1) and the cemented connection (Group 2), analyzing the permeability of the IAI to bacterial colonization, using human saliva as culture medium. PATIENTS AND METHODS: A total of twelve implants were tested, six in each experimental group. Five healthy patients were enrolled in this study. Two milliliters of non-stimulated saliva were collected from each subject and mixed in a test tube. After 14 days of incubation of the bacteria sample in the implant fixtures, a PCR-Real Time analysis was performed. Fisher's exact test was used to compare the proportions of implant-abutment assembled structures detected with bacterial leakage. Differences in the bacterial counts of the two groups were compared using the Mann-Whitney U test. A p value < 0.05 was considered significant. RESULTS: The results showed a decreased stability with the screwed implant-abutment connections compared to the cemented implant-abutment connections. A mean total bacterial count of 1.2E+07 (± 0.25E+07) for Group 1 and of 7.2E+04 (± 14.4E+04) for Group 2 was found, with a high level of significance, p = .0001. CONCLUSIONS: Within the limitations of this study it can be concluded that bacterial species from human saliva may penetrate along the implant-abutment interface in both connections, however the cemented connection implants showed the lowest amount of bacterial colonization

Acidification increases abundances of Vibrionales and Planctomycetia associated to a seaweed-grazer system: potential consequences for disease and prey digestion efficiency

Ocean acidification significantly affects marine organisms in several ways, with complex interactions. Seaweeds might benefit from rising CO2 through increased photosynthesis and carbon acquisition, with subsequent higher growth rates. However, changes in seaweed chemistry due to increased CO2 may change the nutritional quality of tissue for grazers. In addition, organisms live in close association with a diverse microbiota, which can also be influenced by environmental changes, with feedback effects. As gut microbiomes are often linked to diet, changes in seaweed characteristics and associated microbiome can affect the gut microbiome of the grazer, with possible fitness consequences. In this study, we experimentally investigated the effects of acidification on the microbiome of the invasive brown seaweed Sargassum muticum and a native isopod consumer Synisoma nadejda. Both were exposed to ambient CO2 conditions (380 ppm, pH 8.16) and an acidification treatment (1,000 ppm, pH 7.86) for three weeks. Microbiome diversity and composition were determined using high-throughput sequencing of the variable regions V5-7 of 16S rRNA. We anticipated that as a result of acidification, the seaweed-associated bacterial community would change, leading to further changes in the gut microbiome of grazers. However, no significant effects of elevated CO2 on the overall bacterial community structure and composition were revealed in the seaweed. In contrast, significant changes were observed in the bacterial community of the grazer gut. Although the bacterial community of S. muticum as whole did not change, Oceanospirillales and Vibrionales (mainly Pseudoalteromonas) significantly increased their abundance in acidified conditions. The former, which uses organic matter compounds as its main source, may have opportunistically taken advantage of the possible increase of the C/N ratio in the seaweed under acidified conditions. Pseudoalteromonas, commonly associated to diseased seaweeds, suggesting that acidification may facilitate opportunistic/pathogenic bacteria. In the gut of S. nadejda, the bacterial genus Planctomycetia increased abundance under elevated CO2. This shift might be associated to changes in food (S. muticum) quality under acidification. Planctomycetia are slow-acting decomposers of algal polymers that could be providing the isopod with an elevated algal digestion and availability of inorganic compounds to compensate the shifted C/N ratio under acidification in their food. In conclusion, our results indicate that even after only three weeks of acidified conditions, bacterial communities associated to ungrazed seaweed and to an isopod grazer show specific, differential shifts in associated bacterial community. These have potential consequences for seaweed health (as shown in corals) and isopod food digestion. The observed changes in the gut microbiome of the grazer seem to reflect changes in the seaweed chemistry rather than its microbial composition.Erasmus Mundus Doctoral Programme MARES on Marine Ecosystem Health Conservation [MARES_13_08]; FCT (Foundation for Science and Technology, Portugal) [SFRH/BPD/63703/2009, SFRH/BPD/107878/2015, SFRH/BPD/116774/2016]; EU SEAS-ERA project INVASIVES [SEAS-ERA/0001/2012]; [CCMAR/Multi/04326/2013

Evaluation of rice–legume–rice cropping system on grain yield, nutrient uptake, nitrogen fixation, and chemical, physical, and biological properties of soil

To achieve higher yields and better soil quality under rice–legume–rice (RLR) rotation in a rainfed production system, we formulated integrated nutrient management (INM) comprised of Azospirillum (Azo), Rhizobium (Rh), and phosphate-solubilizing bacteria (PSB) with phosphate rock (PR), compost, and muriate of potash (MOP). Performance of bacterial bioinoculants was evaluated by determining grain yield, nitrogenase activity, uptake and balance of N, P, and Zn, changes in water stability and distribution of soil aggregates, soil organic C and pH, fungal/bacterial biomass C ratio, casting activities of earthworms, and bacterial community composition using denaturing gradient gel electrophoresis (DGGE) fingerprinting. The performance comparison was made against the prevailing farmers’ nutrient management practices [N/P2O5/K2O at 40:20:20 kg ha−1 for rice and 20:30:20 kg ha−1 for legume as urea/single super-phosphate/MOP (urea/SSP/MOP)]. Cumulative grain yields of crops increased by 7–16% per RLR rotation and removal of N and P by six crops of 2 years rotation increased significantly (P < 0.05) in bacterial bioinoculants-based INM plots over that in compost alone or urea/SSP/MOP plots. Apparent loss of soil total N and P at 0–15 cm soil depth was minimum and apparent N gain at 15–30 cm depth was maximum in Azo/Rh plus PSB dual INM plots. Zinc uptake by rice crop and diethylenetriaminepentaacetate-extractable Zn content in soil increased significantly (P < 0.05) in bacterial bioinoculants-based INM plots compared to other nutrient management plots. Total organic C content in soil declined at 0–15 cm depth and increased at 15–30 cm depth in all nutrient management plots after a 2-year crop cycle; however, bacterial bioinoculants-based INM plots showed minimum loss and maximum gain of total organic C content in the corresponding soil depths. Water-stable aggregation and distribution of soil aggregates in 53–250- and 250–2,000 μm classes increased significantly (P < 0.05) in bacterial bioinoculants-based INM plots compared to other nutrient management plots. Fungal/bacterial biomass C ratio seems to be a more reliable indicator of C and N dynamics in acidic soils than total microbial biomass C. Compost alone or Azo/Rh plus PSB dual INM plots showed significantly (P < 0.05) higher numbers of earthworms’ casts compared to urea/SSP/MOP alone and bacterial bioinoculants with urea or SSP-applied plots. Hierarchical cluster analysis based on similarity matrix of DGGE profiles revealed changes in bacterial community composition in soils due to differences in nutrient management, and these changes were seen to occur according to the states of C and N dynamics in acidic soil under RLR rotation

Cerulean: A hybrid assembly using high throughput short and long reads

Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking regions. The emergence of third generation sequencing (Pacific Biosciences) with long reads enables the opportunity to resolve complicated repeats that could not be resolved by the short read data. However, these long reads have high error rate and it is an uphill task to assemble the genome without using additional high quality short reads. Recently, Koren et al. 2012 proposed an approach to use high quality short reads data to correct these long reads and, thus, make the assembly from long reads possible. However, due to the large size of both dataset (short and long reads), error-correction of these long reads requires excessively high computational resources, even on small bacterial genomes. In this work, instead of error correction of long reads, we first assemble the short reads and later map these long reads on the assembly graph to resolve repeats. Contribution: We present a hybrid assembly approach that is both computationally effective and produces high quality assemblies. Our algorithm first operates with a simplified version of the assembly graph consisting only of long contigs and gradually improves the assembly by adding smaller contigs in each iteration. In contrast to the state-of-the-art long reads error correction technique, which requires high computational resources and long running time on a supercomputer even for bacterial genome datasets, our software can produce comparable assembly using only a standard desktop in a short running time.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

The Prevalence and Control of Bacillus and Related Spore-Forming Bacteria in the Dairy Industry

peer-reviewedMilk produced in udder cells is sterile but due to its high nutrient content, it can be a good growth substrate for contaminating bacteria. The quality of milk is monitored via somatic cell counts and total bacterial counts, with prescribed regulatory limits to ensure quality and safety. Bacterial contaminants can cause disease, or spoilage of milk and its secondary products. Aerobic spore-forming bacteria, such as those from the genera Sporosarcina, Paenisporosarcina, Brevibacillus, Paenibacillus, Geobacillus and Bacillus, are a particular concern in this regard as they are able to survive industrial pasteurization and form biofilms within pipes and stainless steel equipment. These single or multiple-species biofilms become a reservoir of spoilage microorganisms and a cycle of contamination can be initiated. Indeed, previous studies have highlighted that these microorganisms are highly prevalent in dead ends, corners, cracks, crevices, gaskets, valves and the joints of stainless steel equipment used in the dairy manufacturing plants. Hence, adequate monitoring and control measures are essential to prevent spoilage and ensure consumer safety. Common controlling approaches include specific cleaning-in-place processes, chemical and biological biocides and other novel methods. In this review, we highlight the problems caused by these microorganisms, and discuss issues relating to their prevalence, monitoring thereof and control with respect to the dairy industry.NG is funded by the Teagasc Walsh Fellowship Scheme and through the Irish Dairy Levy funded project ‘Thermodur-Out.