Cations and microbial indicators: strong relationships in waters of urban/mixed land use watersheds of Southwest, VA

NASA Astrophysics Data System (ADS)

Steele, M.; Badgley, B.

2016-12-01

Background The salinity and composition of salts in freshwater streams, rivers, and waterbodies varies substantially, often impacted by human urban, agricultural, and mining land uses. While extreme fluctuations in salinity have been shown to influence both microbial communities and biogeochemical cycles, the differential effects of specific ion species at low salinity levels is poorly understood. The objective of this study was to examine the relationship between water chemistry and microbial water quality indicators. We collected weekly grab samples from nine sub-watersheds in Southwest Virginia. Samples were measured for standard physical and chemical properties: dissolved oxygen, temperature, specific conductance, pH, calcium, magnesium, potassium, chloride, fluoride, sulfate, nitrogen species, phosphorus, and dissolved organic carbon. In addition, three types of microbial fecal indicators were measured: total coliforms, E. coli, and HF183 (a human specific genomic marker). Results The relationships within and between water chemistry and water quality indicators are complex and frequently co-correlated. Concentrations of traditional biogeochemical elements (N, P, C) were less strongly related to water quality indicators than were Ca, Mg, Na in watersheds. Ca and Mg were strongly correlated with total coliforms, r2 = 0.88 and r2 = 0.86 respectively. While potassium is very strongly related to E. coli (r2 = 0.96). Currently, we cannot reasonably explain these relationships by the land use composition or common sources within the landscape. The human specific fecal indicator was not well correlated with other microbial water quality indicators, and yet found ubiquitously across the developed watersheds and most strongly correlated with sodium concentrations (r2 = 0.84). The results suggest that 1) wastewater via subsurface flowpaths may more broadly impact surface water chemistry and quality than expected, and 2) that cation chemistry may influence the microbial community and serve as a mediator of watershed biogeochemical cycling.

Metaproteogenomics reveals the soil microbial communities active in nutrient cycling processes under different tree species

NASA Astrophysics Data System (ADS)

Keiblinger, Katharina Maria; Masse, Jacynthe; Zühlke, Daniela; Riedel, Katharina; Zechmeister-Boltenstern, Sophie; Prescott, Cindy E.; Grayston, Sue

2016-04-01

Tree species exert strong effects on microbial communities in litter and soil and may alter rates of soil processes fundamental to nutrient cycling and carbon fluxes (Prescott and Grayston 2013). However, the influence of tree species on decomposition processes are still contradictory and poorly understood. An understanding of the mechanisms underlying plant influences on soil processes is important for our ability to predict ecosystem response to altered global/environmental conditions. In order to link microbial community structure and function to forest-floor nutrient cycling processes, we sampled forest floors under western redcedar (Thuja plicata), Douglas-fir (Pseudotsuga menziesii) and Sitka spruce (Picea sitchensis) grown in nutrient-poor sites in common garden experiments on Vancouver island (Canada). We measured forest-floor total N, total C, initial NH4+ and NO3- concentrations, DOC, Cmic and Nmic. Gross rates of ammonification and NH4+ consumption were measured using the 15N pool-dilution method. Organic carbon quality was assessed through FTIR analyses. Microbial community structure was analysed by a metaproteogenomic approach using 16S and ITS amplification and sequencing with MiSeq platform. Proteins were extracted and peptides characterized via LC-MS/MS on a Velos Orbitrap to assess the active microbial community. Different microbial communities were active under the three tree species and variation in process rates were observed and will be discussed. This research provides new insights on microbial processes during organic matter decomposition. The metaproteogenomic approach enables us to investigate these changes with respect to possible effects on soil C-storage at even finer taxonomic resolution.

Hydrogeological controls of variable microbial water quality in a complex subtropical karst system in Northern Vietnam

NASA Astrophysics Data System (ADS)

Ender, Anna; Goeppert, Nadine; Goldscheider, Nico

2018-05-01

Karst aquifers are particularly vulnerable to bacterial contamination. Especially in developing countries, poor microbial water quality poses a threat to human health. In order to develop effective groundwater protection strategies, a profound understanding of the hydrogeological setting is crucial. The goal of this study was to elucidate the relationships between high spatio-temporal variability in microbial contamination and the hydrogeological conditions. Based on extensive field studies, including mapping, tracer tests and hydrochemical analyses, a conceptual hydrogeological model was developed for a remote and geologically complex karst area in Northern Vietnam called Dong Van. Four different physicochemical water types were identified; the most important ones correspond to the karstified Bac Son and the fractured Na Quan aquifer. Alongside comprehensive investigation of the local hydrogeology, water quality was evaluated by analysis for three types of fecal indicator bacteria (FIB): Escherichia coli, enterococci and thermotolerant coliforms. The major findings are: (1) Springs from the Bac Son formation displayed the highest microbial contamination, while (2) springs that are involved in a polje series with connections to sinking streams were distinctly more contaminated than springs with a catchment area characterized by a more diffuse infiltration. (3) FIB concentrations are dependent on the season, with higher values under wet season conditions. Furthermore, (4) the type of spring capture also affects the water quality. Nevertheless, all studied springs were faecally impacted, along with several shallow wells within the confined karst aquifer. Based on these findings, effective protection strategies can be developed to improve groundwater quality.

The Impact of Human Activities on Microbial Quality of Rivers in the Vhembe District, South Africa.

PubMed

Traoré, Afsatou N; Mulaudzi, Khodani; Chari, Gamuchirai J E; Foord, Stefan H; Mudau, Lutendo S; Barnard, Tobias G; Potgieter, Natasha

2016-08-12

Water quality testing is dictated by microbial agents found at the time of sampling in reference to their acceptable risk levels. Human activities might contaminate valuable water resources and add to the microbial load present in water bodies. Therefore, the effects of human activities on the microbial quality of rivers collected from twelve catchments in the Vhembe District in South Africa were investigated, with samples analyzed for total coliform (TC) and Eschericha coli (E. coli) contents. Physical parameters and various human activities were recorded for each sampling site. The Quanti-Tray(®) method was adopted for the assessment of TC and E. coli contents in the rivers over a two-year period. A multiplex polymerase chain (PCR) method was used to characterize the strains of E. coli found. The microbial quality of the rivers was poor with both TC and E. coli contents found to be over acceptable limits set by the South African Department of Water and Sanitation (DWS). No significant difference (p > 0.05) was detected between TC and E. coli risks in dry and wet seasons. All six pathogenic E. coli strains were identified and Enteroaggregative E. coli (EAEC), atypical Enteropathogenic E. coli (a-EPEC) and Enterotoxigenic E. coli (ETEC) were the most prevalent E. coli strains detected (respectively, 87%, 86% and 83%). The study indicated that contamination in the majority of sampling sites, due to human activities such as car wash, animal grazing and farming, poses health risks to communities using the rivers for various domestic chores. It is therefore recommended that more education by the respective departments is done to avert pollution of rivers and prevent health risks to the communities in the Vhembe District.

The Impact of Human Activities on Microbial Quality of Rivers in the Vhembe District, South Africa

PubMed Central

Traoré, Afsatou N.; Mulaudzi, Khodani; Chari, Gamuchirai J.E.; Foord, Stefan H.; Mudau, Lutendo S.; Barnard, Tobias G.; Potgieter, Natasha

2016-01-01

Background: Water quality testing is dictated by microbial agents found at the time of sampling in reference to their acceptable risk levels. Human activities might contaminate valuable water resources and add to the microbial load present in water bodies. Therefore, the effects of human activities on the microbial quality of rivers collected from twelve catchments in the Vhembe District in South Africa were investigated, with samples analyzed for total coliform (TC) and Eschericha coli (E. coli) contents. Methods: Physical parameters and various human activities were recorded for each sampling site. The Quanti-Tray® method was adopted for the assessment of TC and E. coli contents in the rivers over a two-year period. A multiplex polymerase chain (PCR) method was used to characterize the strains of E. coli found. Results: The microbial quality of the rivers was poor with both TC and E. coli contents found to be over acceptable limits set by the South African Department of Water and Sanitation (DWS). No significant difference (p > 0.05) was detected between TC and E. coli risks in dry and wet seasons. All six pathogenic E. coli strains were identified and Enteroaggregative E. coli (EAEC), atypical Enteropathogenic E. coli (a-EPEC) and Enterotoxigenic E. coli (ETEC) were the most prevalent E. coli strains detected (respectively, 87%, 86% and 83%). Conclusions: The study indicated that contamination in the majority of sampling sites, due to human activities such as car wash, animal grazing and farming, poses health risks to communities using the rivers for various domestic chores. It is therefore recommended that more education by the respective departments is done to avert pollution of rivers and prevent health risks to the communities in the Vhembe District. PMID:27529265

Environmental Stress-mediated EPS Production Shape Microbial Activity on Various Hydrated Rough Surfaces

NASA Astrophysics Data System (ADS)

Wang, G.; Liu, L.; Chen, G.

2016-12-01

The complex environmental physical and chemical processes and interplay with the associating biological responses are keys to understanding the environmental microbiology ensconced in environmental remediation, water quality control, food safety, nutrient cycling, and etc., yet remain poorly understood. Using experimental micromodels, we study how environmental conditions (e.g., hydration fluctuation, nutrient limitation, pH variation, etc.) affect microbial extracellular polymeric substances (EPS) production and their configuration within various hydrated surfaces, and impacts on microbial motility, surface attachment, aggregation, and other bioremediation activities. To elucidate the potential mechanisms underlying the complex bio-physicochemical processes, we developed an individual-based and spatio-temporally resolved modeling platform that explicitly considers microscale aqueous-phase configuration and nutrient transport/diffusion and associated biophysical processes affecting individual microbial cell life history. We quantitatively explore the effects of the above microscale environmental processes on bio-physicochemical interactions affecting microbial growth, motility, surface attachment and aggregation, and shaping population interactions and functions. Simulation scenarios of microbial induced pollutant (e.g., roxarsone) biotransformation on various hydrated rough surfaces will also be present.

Dynamics of microbial communities during decomposition of litter from pioneering plants in initial soil ecosystems

NASA Astrophysics Data System (ADS)

Esperschütz, J.; Zimmermann, C.; Dümig, A.; Welzl, G.; Buegger, F.; Elmer, M.; Munch, J. C.; Schloter, M.

2013-07-01

In initial ecosystems, concentrations of all macro- and micronutrients can be considered as extremely low. Plant litter therefore strongly influences the development of a degrader's food web and is an important source for C and N input into soil in such ecosystems. In the present study, a 13C litter decomposition field experiment was performed for 30 weeks in initial soils from a post-mining area near the city of Cottbus (Germany). Two of this region's dominant but contrasting pioneering plant species (Lotus corniculatus L. and Calamagrostis epigejos L.) were chosen to investigate the effects of litter quality on the litter decomposing microbial food web in initially nutrient-poor substrates. The results clearly indicate the importance of litter quality, as indicated by its N content, its bioavailability for the degradation process and the development of microbial communities in the detritusphere and soil. The degradation of the L. corniculatus litter, which had a low C / N ratio, was fast and showed pronounced changes in the microbial community structure 1-4 weeks after litter addition. The degradation of the C. epigejos litter material was slow and microbial community changes mainly occurred between 4 and 30 weeks after litter addition to the soil. However, for both litter materials a clear indication of the importance of fungi for the degradation process was observed both in terms of fungal abundance and activity (13C incorporation activity)

The effect of lactic acid bacterial starter culture and chemical additives on wilted rice straw silage.

PubMed

Wang, Yan-Su; Shi, Wei; Huang, Lin-Ting; Ding, Cheng-Long; Dai, Chuan-Chao

2016-04-01

Lactic acid bacteria (LAB) are suitable for rice straw silage fermentation, but have been studied rarely, and rice straw as raw material for ensiling is difficult because of its disadvantages, such as low nutrition for microbial activities and low abundances of natural populations of LAB. So we investigated the effect of application of LAB and chemical additives on the fermentation quality and microbial community of wilted rice straw silage. Treatment with chemical additives increased the concentrations of crude protein (CP), water soluble carbohydrate (WSC), acetic acid and lactic acid, reduced the concentrations of acid detergent fiber (ADF) and neutral detergent fiber (NDF), but did not effectively inhibit the growth of spoilage organisms. Inoculation with LABs did not improve the nutritional value of the silage because of poor growth of LABs in wilted rice straw. Inoculation with LAB and addition of chemical materials improved the quality of silage similar to the effects of addition of chemical materials alone. Growth of aerobic and facultatively anaerobic bacteria was inhibited by this mixed treatment and the LAB gradually dominated the microbial community. In summary, the fermentation quality of wilted rice straw silage had improved by addition of LAB and chemical materials. © 2015 Japanese Society of Animal Science.

Life cycle of soil sggregates: from root residue to microbial and physical hotspots

NASA Astrophysics Data System (ADS)

Ghezzehei, T. A.; Or, D.

2017-12-01

Soil aggregation is a physical state of soil in which clumps of primary soil particles are held together by biological and/or chemical cementing agents. Aggregations plays important role in storage and movement of water and essential gases, nutrient cycling, and ultimately supporting microbial and plant life. It is also one of the most dynamic and sensitive soil qualities, which readily responds to disturbances such as cultivation, fire, drought, flooding, and changes in vegetation. Soil aggregation that is primarily controlled by organic matter generally exhibits hierarchical organization of soil constituents into stable units that range in size from a few microns to centimeters. However, this conceptual model of soil aggregation as the key unifying mechanism remains poorly quantified and is rarely included in predictive soil models. Here we provide a biophysical framework for quantitative and predictive modeling of soil aggregation and its attendant soil characteristics. The framework treats aggregates as hotspots of biological, chemical and physical processes centered around roots and root residue. We keep track of the life cycle of an individual aggregate from it genesis in the rhizosphere, fueled by rhizodeposition and mediated by vigorous microbial activity, until its disappearance when the root-derived resources are depleted. The framework synthesizes current understanding of microbial life in porous media; water holding and soil binding capacity of biopolymers; and environmental controls on soil organic matter dynamics. The framework paves a way for integration of processes that are presently modeled as disparate or poorly coupled processes, including storage and protection of carbon, microbial activity, greenhouse gas fluxes, movement and storage of water, resistance of soils against erosion.

Wildlife, urban inputs, and landscape configuration are responsible for degraded swimming water quality at an embayed beach

USGS Publications Warehouse

Byappanahalli, Muruleedhara N.; Nevers, Meredith; Whitman, Richard L.; Ge, Zhongfu; Shively, Dawn A.; Spoljaric, Ashley; Przybyla-Kelly, Katarzyna

2015-01-01

Jeorse Park Beach, on southern Lake Michigan, experiences frequent closures due to high Escherichia coli (E. coli) levels since regular monitoring was implemented in 2005. During the summer of 2010, contaminant source tracking techniques, such as the conventional microbial and physical surveys and hydrodynamic models, were used to determine the reasons for poor water quality at Jeorse Park. Fecal indicator bacteria (E. coli, enterococci) were high throughout the season, with densities ranging from 12–2419 (culturable E. coli) and 1–2550 and < 1–5831 (culturable and qPCR enterococci, respectively). Genetic markers for human (Bacteroides HF183) and gull (Catellicoccus marimammalium) fecal contamination were found in 15% and 37% of the samples indicating multiple sources contributing to poor water quality. Nesting colonies of double-crested cormorants (Phalacrocorax auritus) have steadily increased since 2005, coinciding with high E. colilevels. A hydrodynamic model indicated that limited circulation allows bacteria entering the embayed area to be retained in nearshore areas; and bacterial resuspension from sand and stranded beach wrack during storm events compounds the problem. The integration of hydrodynamics, expanded use of chemical and biological markers, as well as more complex statistical multivariate techniques can improve microbial source tracking, informing management actions to improve recreational water quality. Alterations to embayed structures to improve circulation and reduce nuisance algae as well as growing native plants to retain sand to improve beach morphometry are among some of the restoration strategies under consideration in ongoing multi-agency collaborations.

Microbial and geochemical quality of shallow well water in high-density areas in Mzuzu City in Malawi

NASA Astrophysics Data System (ADS)

Msilimba, Golden; Wanda, Elijah M. M.

In Malawi, shallow wells constitute the most important water sources for domestic purposes. However, increasing human population coupled with poor sanitation and infrastructure is undermining the quality of shallow well water. An assessment of microbial and geochemical quality of shallow well water in high-density areas of Zolozolo, Ching’ambo and Chiputula in Mzuzu City, Northern Malawi, has been carried out. The study aimed at characterising domestic water sources, identifying possible sources of water contamination and determining levels of microbial and chemical contamination. Arc-view GIS was used to map the water sources. A questionnaire survey was carried out to elicit information on characteristics of drinking water sources. Water samples were collected from quasi-randomly selected shallow wells and analysed for microbial and chemical parameters using standard methods. HCA, performed using R-programme, was used to group sampled sites according to their bio-physicochemical characteristics. Compliance of the water with MBS/WHO water quality guidelines was determined. The WQI was computed to turn multifaceted data obtained from laboratory analyses into simple information that is comprehensible and useable by the public to assess overall quality of water at a specific water points. The GW-chart was used to show hydrogeochemical water types from each sampled site. Microbial analysis revealed that water from 96.3% of shallow wells recorded faecal coliforms ranging from 129 to 920 cfu per 100 ml which were significantly higher than the Malawi Standards and WHO thresholds. In general, shallow well water is of low mineralisation (EC range 80-500 μS cm-1), with hydrogeochemical facies dominated by Ca-HCO3, which evolves to Ca-Cl water type. The shallow well water registered a WQI range of 50.16-66.04%, with a medium WQ rating. This suggested that the water obtained from the shallow wells is unsuitable for direct human consumption. It was observed that 100% of the shallow wells were at risk of pollution from onsite sanitation because of their proximity to sanitary facilities. It was strongly recommended that onsite treatment interventions have to be mobilised and initiated to protect the households from further possible consequences of using the water.

Quality and Labelling Information Moringa Oleifera Products Marketed for HIV-infected People in Zimbabwe

PubMed Central

Jani, Zvinji Tella; Maponga, Charles Chiedza; Mudzengi, Josephine; Morse, Gene D.; Nhachi, Charles Fungai Brian

2016-01-01

Labeling information and quality of marketed Moringa oleifera products were assessed. Personnel in 60 pharmacies and 11 herbal shops were interviewed about the sources, dosages, indications and counseling information of Moringa oleifera products. Content analysis of written information provided on Moringa oleifera products was also done. Three samples of Moringa from popular sources were acquired to determine heavy metal content and microbial contamination. The results were compared to specified limits in the European and Chinese pharmacopeia, World Health Organization guidelines and Bureau of Indian Standards. Moringa was available as capsules or powder in 73% of the premises. Moringa was recommended for seven different disease conditions. Four different dosage regimens were prescribed. The main references cited for the counseling information were unscientific literature (62%). The selected Moringa samples were contaminated with bacteria and fungi above the European Pharmacopeia specified limits. Escherichia coli and Salmonella species were present in all three samples. All three samples contained arsenic, nickel and cadmium above the permissible limits. Moringa oleifera with variable labeling information and poor microbial and heavy metal quality is widely available in Zimbabwe. PMID:28239441

Quality and labeling information of Moringa oleifera products marketed for HIV-infected people in Zimbabwe.

PubMed

Monera-Penduka, Tsitsi Grace; Jani, Zvinji Tella; Maponga, Charles Chiedza; Mudzengi, Josephine; Morse, Gene D; Nhachi, Charles Fungai Brian

2016-12-31

Labeling information and quality of marketed Moringa oleifera products were assessed. Personnel in 60 pharmacies and 11 herbal shops were interviewed about the sources, dosages, indications and counseling information of Moringa oleifera products. Content analysis of written information provided on Moringa oleifera products was also done. Three samples of Moringa from popular sources were acquired to determine heavy metal content and microbial contamination. The results were compared to specified limits in the European and Chinese pharmacopeia, World Health Organization guidelines and Bureau of Indian Standards. Moringa was available as capsules or powder in 73% of the premises. Moringa was recommended for seven different disease conditions. Four different dosage regimens were prescribed. The main references cited for the counseling information were unscientific literature (62%). The selected Moringa samples were contaminated with bacteria and fungi above the European Pharmacopeia specified limits. Escherichia coli and Salmonella species were present in all three samples. All three samples contained arsenic, nickel and cadmium above the permissible limits. Moringa oleifera with variable labeling information and poor microbial and heavy metal quality is widely available in Zimbabwe.

The influence of processing on the microbial risk associated with Rooibos (Aspalathus linearis) tea.

PubMed

Gouws, Pieter; Hartel, Toni; van Wyk, Rudean

2014-12-01

This review discusses the influence of processing on the microbial risk associated with Salmonella in Rooibos tea, the identification of Salmonella and preventative and control measures to control microbial contamination. Rooibos tea, like other plant products, naturally contains a high microbial load. Downstream processing steps of these products usually help in reducing any contaminants present. Due to the delicate flavour properties and nature of Rooibos, gentle processing techniques are necessary for the production of good quality tea. However, this has a major influence on the microbiological status of the product. The presence of Salmonella in Rooibos is poorly understood. The ubiquitous distribution of Salmonella in the natural environment and its prevalence in the global food chain, the physiological adaptability, virulence of the bacterial pathogen and its serious economic impact on the food industry, emphasises the need for continued awareness and stringent controls at all levels of food production. With the advances of technology and information at hand, the processing of Rooibos needs to be re-evaluated. Since the delicate nature of Rooibos prohibits the use of harsh methods to control Salmonella, alternative methods for the steam pasteurisation of Rooibos show great potential to control Salmonella in a fast, efficient and cost-effective manner. These alternative methods will significantly improve the microbiological quality of Rooibos and provide a product that is safe to consumers. © 2014 Society of Chemical Industry.

A probabilistic model of gastroenteritis risks associated with consumption of street food salads in Kumasi, Ghana: evaluation of methods to estimate pathogen dose from water, produce or food quality.

PubMed

Barker, S Fiona; Amoah, Philip; Drechsel, Pay

2014-07-15

With a rapidly growing urban population in Kumasi, Ghana, the consumption of street food is increasing. Raw salads, which often accompany street food dishes, are typically composed of perishable vegetables that are grown in close proximity to the city using poor quality water for irrigation. This study assessed the risk of gastroenteritis illness (caused by rotavirus, norovirus and Ascaris lumbricoides) associated with the consumption of street food salads using Quantitative Microbial Risk Assessment (QMRA). Three different risk assessment models were constructed, based on availability of microbial concentrations: 1) Water - starting from irrigation water quality, 2) Produce - starting from the quality of produce at market, and 3) Street - using microbial quality of street food salad. In the absence of viral concentrations, published ratios between faecal coliforms and viruses were used to estimate the quality of water, produce and salad, and annual disease burdens were determined. Rotavirus dominated the estimates of annual disease burden (~10(-3)Disability Adjusted Life Years per person per year (DALYs pppy)), although norovirus also exceeded the 10(-4)DALY threshold for both Produce and Street models. The Water model ignored other on-farm and post-harvest sources of contamination and consistently produced lower estimates of risk; it likely underestimates disease burden and therefore is not recommended. Required log reductions of up to 5.3 (95th percentile) for rotavirus were estimated for the Street model, demonstrating that significant interventions are required to protect the health and safety of street food consumers in Kumasi. Estimates of virus concentrations were a significant source of model uncertainty and more data on pathogen concentrations is needed to refine QMRA estimates of disease burden. Copyright © 2014 Elsevier B.V. All rights reserved.

Changes in dissolved organic matter quality in a peatland and forest headwater stream as a function of seasonality and hydrologic conditions

NASA Astrophysics Data System (ADS)

Broder, Tanja; Knorr, Klaus-Holger; Biester, Harald

2017-04-01

Peatlands and peaty riparian zones are major sources of dissolved organic matter (DOM), but are poorly understood in terms of export dynamics and controls thereof. Thereby quality of DOM affects function and behavior of DOM in aquatic ecosystems, but DOM quality can also help to track DOM sources and their export dynamics under specific hydrologic preconditions. The objective of this study was to elucidate controls on temporal variability in DOM concentration and quality in stream water draining a bog and a forested peaty riparian zone, particularly considering drought and storm flow events. DOM quality was monitored using spectrofluorometric indices for aromaticity (SUVA254), apparent molecular size (SR) and precursor organic material (FI), as well as PARAFAC modeling of excitation emission matrices (EEMs). Indices for DOM quality exhibited major changes due to different hydrologic conditions, but patterns were also dependent on season. Stream water at the forested site with mineral, peaty soils generally exhibited higher variability in DOM concentrations and quality compared to the outflow of an ombrotrophic bog, where DOM was less susceptible to changes in hydrologic conditions. During snowmelt and spring events, near-surface protein-like DOM pools were exported. A microbial DOM fraction originating from groundwater and deep peat layers was increasing during drought, while a strongly microbially altered DOM fraction was also exported by discharge events with dry preconditions at the forested site. This might be due to accelerated microbial activity in the peaty riparian zone of the forested site under these preconditions. Our study demonstrated that DOM export dynamics are not only a passive mixing of different hydrological sources, but monitoring studies have to consider that DOM quality depends on hydrologic preconditions and season. Moreover, the forested peaty riparian zone generated the most variability in headwater DOM quantity and quality, as could be tracked by the used spectrofluorometric indices.

Decreases in Soil Moisture and Organic Matter Quality Suppress Microbial Decomposition Following a Boreal Forest Fire

DOE Office of Scientific and Technical Information (OSTI.GOV)

Holden, Sandra R.; Berhe, Asmeret A.; Treseder, Kathleen K.

Climate warming is projected to increase the frequency and severity of wildfires in boreal forests, and increased wildfire activity may alter the large soil carbon (C) stocks in boreal forests. Changes in boreal soil C stocks that result from increased wildfire activity will be regulated in part by the response of microbial decomposition to fire, but post-fire changes in microbial decomposition are poorly understood. Here, we investigate the response of microbial decomposition to a boreal forest fire in interior Alaska and test the mechanisms that control post-fire changes in microbial decomposition. We used a reciprocal transplant between a recently burnedmore » boreal forest stand and a late successional boreal forest stand to test how post-fire changes in abiotic conditions, soil organic matter (SOM) composition, and soil microbial communities influence microbial decomposition. We found that SOM decomposing at the burned site lost 30.9% less mass over two years than SOM decomposing at the unburned site, indicating that post-fire changes in abiotic conditions suppress microbial decomposition. Our results suggest that moisture availability is one abiotic factor that constrains microbial decomposition in recently burned forests. In addition, we observed that burned SOM decomposed more slowly than unburned SOM, but the exact nature of SOM changes in the recently burned stand are unclear. Finally, we found no evidence that post-fire changes in soil microbial community composition significantly affect decomposition. Taken together, our study has demonstrated that boreal forest fires can suppress microbial decomposition due to post-fire changes in abiotic factors and the composition of SOM. Models that predict the consequences of increased wildfires for C storage in boreal forests may increase their predictive power by incorporating the observed negative response of microbial decomposition to boreal wildfires.« less

Microbial quality and associated health risks of raw milk marketed in the Tanga region of Tanzania.

PubMed

Swai, E S; Schoonman, L

2011-06-01

To evaluate microbial quality and associated health risks of raw milk marketed in the Tanga region of Tanzania. A microbial quality assessment of marketed raw milk was undertaken by evaluating 59 samples of milk from selling points (collecting centres =15), bicycle boys (12) and kiosks/restaurants (32) in Tanga city during April-May 2005. Quality and milk-borne hazards were assessed using a combination of tests in order to quantify the occurrence of Brucellosis (milk ring test), Escherichia coli (E. coli) O157:H7 (culture), the coliform bacteria as well as standard plate count (SPC). Specific gravity (SG) determination was used as an indicator of adulteration. The mean coliform plate count (c.f.u/mL) of milk handled by bicycle boys (4.2×10(6)) was significantly higher than that handled by collecting centres (3.0×10(6)) and kiosk/ restaurants (1.4×10(6)), respectively (P < 0.05). Of the 59 milk samples collected, 33 (56%) were Brucella milk ring test (MRT)-positive and 78% and 17% of the samples graded satisfactorily based on SG and coliform plate counts as prescribed by East African Community standards for raw milk. There was no verocytotoxigenic E. coli (VTEC) O157: H7 in any of the milk samples collected and analysed during the present study. It can be concluded that raw market milk in the study area is of poor bacteriological quality and hazardous for human consumption. This highlights the need to implement good hygiene practices and effective monitoring from production through the delivery chain to the consumer. Further studies are needed for detection of toxins that are produced by E. coli, other pathogenic spore forming bacteria (Bacillus spp. and Clostridium spp.) and other harmful microorganisms.

Biochar affects soil organic matter cycling and microbial functions but does not alter microbial community structure in a paddy soil.

PubMed

Tian, Jing; Wang, Jingyuan; Dippold, Michaela; Gao, Yang; Blagodatskaya, Evgenia; Kuzyakov, Yakov

2016-06-15

The application of biochar (BC) in conjunction with mineral fertilizers is one of the most promising management practices recommended to improve soil quality. However, the interactive mechanisms of BC and mineral fertilizer addition affecting microbial communities and functions associated with soil organic matter (SOM) cycling are poorly understood. We investigated the SOM in physical and chemical fractions, microbial community structure (using phospholipid fatty acid analysis, PLFA) and functions (by analyzing enzymes involved in C and N cycling and Biolog) in a 6-year field experiment with BC and NPK amendment. BC application increased total soil C and particulate organic C for 47.4-50.4% and 63.7-74.6%, respectively. The effects of BC on the microbial community and C-cycling enzymes were dependent on fertilization. Addition of BC alone did not change the microbial community compared with the control, but altered the microbial community structure in conjunction with NPK fertilization. SOM fractions accounted for 55% of the variance in the PLFA-related microbial community structure. The particulate organic N explained the largest variation in the microbial community structure. Microbial metabolic activity strongly increased after BC addition, particularly the utilization of amino acids and amines due to an increase in the activity of proteolytic (l-leucine aminopeptidase) enzymes. These results indicate that microorganisms start to mine N from the SOM to compensate for high C:N ratios after BC application, which consequently accelerate cycling of stable N. Concluding, BC in combination with NPK fertilizer application strongly affected microbial community composition and functions, which consequently influenced SOM cycling. Copyright © 2016 Elsevier B.V. All rights reserved.

Anoxia stimulates microbially catalyzed metal release from Animas River sediments.

PubMed

Saup, Casey M; Williams, Kenneth H; Rodríguez-Freire, Lucía; Cerrato, José M; Johnston, Michael D; Wilkins, Michael J

2017-04-19

The Gold King Mine spill in August 2015 released 11 million liters of metal-rich mine waste to the Animas River watershed, an area that has been previously exposed to historical mining activity spanning more than a century. Although adsorption onto fluvial sediments was responsible for rapid immobilization of a significant fraction of the spill-associated metals, patterns of longer-term mobility are poorly constrained. Metals associated with river sediments collected downstream of the Gold King Mine in August 2015 exhibited distinct presence and abundance patterns linked to location and mineralogy. Simulating riverbed burial and development of anoxic conditions, sediment microcosm experiments amended with Animas River dissolved organic carbon revealed the release of specific metal pools coupled to microbial Fe- and SO 4 2- -reduction. Results suggest that future sedimentation and burial of riverbed materials may drive longer-term changes in patterns of metal remobilization linked to anaerobic microbial metabolism, potentially driving decreases in downstream water quality. Such patterns emphasize the need for long-term water monitoring efforts in metal-impacted watersheds.

Impact of land-use change and soil organic carbon quality on microbial diversity in soils across Europe.

PubMed

Szoboszlay, Márton; Dohrmann, Anja B; Poeplau, Christopher; Don, Axel; Tebbe, Christoph C

2017-12-01

Land-use and their change have dramatic consequences for above-ground biodiversity, but their impact on soil microbial communities is poorly understood. In this study, soils from 19 European sites representing conversion of croplands to grasslands or forests and of grasslands to croplands or forests were characterized for microbial abundance and bacterial diversity. The abundance of Bacteria and Fungi but not Archaea responded to land-use change. Site was the major determinant of the soil bacterial community structure, explaining 32% of the variation in 16S rRNA gene diversity. While the quantity of soil organic carbon (SOC) only explained 5% of the variation, SOC when differentiated by its quality could explain 22%. This was similar to the impact of soil pH (21%) and higher than that of land-use type (15%). Croplands had the highest bacterial diversity. Converting croplands to grassland caused an increase of Verrucomicrobia; croplands to forest increased Rhizobiales but decreased Bacteroidetes and Nitrospirae; and grasslands to cropland increased Gemmatimonadetes but decreased Verrucomicrobia and Planctomycetes. Network analysis identified associations between particular SOC fractions and specific bacterial taxa. We conclude that land-use-related effects on soil microorganisms can be consistently observed across a continental scale. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Microbial quality of some vegetables sold in ED DueimTwon, Sudan.

PubMed

Goja, Arafat Mohammed; Mahmoud, Mohamed Salih Osman

2013-06-15

This study was probably the first research carried out to investigate the microbiological quality of some vegetables sold in ED DueimTwon, Sudan. Four species of vegetables were used, Arugula (Eruca sativa), Mloukhia (Corchorus olitorius), Tomato (Lycopersicon esculentum) and Green pepper (Capsicum annuum). The samples were collected and examined according to standardized methods for total viable bacteria, coliforms and fecal coliform count. The average of total viable count ranged from 1.2 x 105-5.6 x 105 CFU mL(-1) for Arugula; 2.1 x 105-2.8 x 107 CFU mL(-1) for Mloukhia; 3.4 x 105-4.8 x 105 for Tomato and 2.3 x 105-8.0 x 106 CFU mL(-1) for Green pepper. However, the maximum level of total and fecal coliform were (93, 21); (28, 11); (75, 15) and (150, 20) MPN 100 mL(-1), respectively. Twelve bacteria belonging to five genera were isolated. Staphylococcus (33%) was the most predominant isolated followed by Enterobacteriaceae (25%), Bacillus (17%) and Streptococcus (17%). Micrococcus (8%) was the least dominant isolated. The results of microbial counts of these vegetable samples in this study indicate that, the agricultural practices, harvesting, hygiene, transporting and selling points are poor and therefore, the higher microbial load could be risked for public health.

Differences in the sensitivity of fungi and bacteria to season and invertebrates affect leaf litter decomposition in a Mediterranean stream.

PubMed

Mora-Gómez, Juanita; Elosegi, Arturo; Duarte, Sofia; Cássio, Fernanda; Pascoal, Cláudia; Romaní, Anna M

2016-08-01

Microorganisms are key drivers of leaf litter decomposition; however, the mechanisms underlying the dynamics of different microbial groups are poorly understood. We investigated the effects of seasonal variation and invertebrates on fungal and bacterial dynamics, and on leaf litter decomposition. We followed the decomposition of Populus nigra litter in a Mediterranean stream through an annual cycle, using fine and coarse mesh bags. Irrespective of the season, microbial decomposition followed two stages. Initially, bacterial contribution to total microbial biomass was higher compared to later stages, and it was related to disaccharide and lignin degradation; in a later stage, bacteria were less important and were associated with hemicellulose and cellulose degradation, while fungi were related to lignin decomposition. The relevance of microbial groups in decomposition differed among seasons: fungi were more important in spring, whereas in summer, water quality changes seemed to favour bacteria and slowed down lignin and hemicellulose degradation. Invertebrates influenced litter-associated microbial assemblages (especially bacteria), stimulated enzyme efficiencies and reduced fungal biomass. We conclude that bacterial and fungal assemblages play distinctive roles in microbial decomposition and differ in their sensitivity to environmental changes, ultimately affecting litter decomposition, which might be particularly relevant in highly seasonal ecosystems, such as intermittent streams. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Bacteriological quality of drinking water from source to household in Ibadan, Nigeria.

PubMed

Oloruntoba, E O; Sridhar, M K C

2007-06-01

The bacteriological quality of drinking water from well, spring, borehole, and tap sources and that stored in containers by urban households in Ibadan was assessed during wet and dry seasons. The MPN technique was used to detect and enumerate the number of coliforms in water samples. Results showed that majority of households relied on wells, which were found to be the most contaminated of all the sources. At the household level, water quality significantly deteriorated after collection and storage as a result of poor handling. Furthermore, there was significant seasonal variation in E. coli count at source (P=0.013) and household (P=0.001). The study concludes that there is a need to improve the microbial quality of drinking water at source and the household level through hygiene education, and provision of simple, acceptable, low-cost treatment methods.

Microbial Source Tracking: Current and Future Molecular Tools in Microbial Water Quality Forensics

EPA Science Inventory

Current regulations in the United States stipulate that the microbial quality of waters used for consumption and recreational activities should be determined regularly by measuring microbial indicators of fecal pollution. Hence, the microbial risk associated with these waters is...

Decoding the Secrets of Carbon Preservation and GHG Flux in Lower-Latitude Peatlands

NASA Astrophysics Data System (ADS)

Richardson, C. J.; Flanagan, N. E.; Wang, H.; Ho, M.; Hodgkins, S. B.; Cooper, W. T.; Chanton, J.; Winton, S.

2017-12-01

The mechanisms regulating peat decomposition and C carbon storage in peatlands are poorly understood, particularly with regard to the importance of the biochemical compounds produced by different plant species and in turn peat quality controls on C storage and GHG flux. To examine the role of carbon quality in C accretion in northern compared to tropical peatlands we completed field and lab studies on bog peats collected in Minnesota, North Carolina, Florida and Peru to answer three fundamental questions; 1) is tropical peat more recalcitrant than northern peat 2) does the addition of aromatic and phenolic C compounds increase towards the tropics 3) do differences in the chemical structure of organic matter explain variances in carbon storage and GHG flux in tropical versus northern peatlands? Our main hypothesize is that high concentrations of phenolics and aromatic C compounds produced in shrub and tree plant communities in peatlands coupled with the fire production of biochar aromatics in peatlands may provide a dual biogeochemical latch mechanism controlling microbial decomposition of peat even under higher temperatures and seasonal drought. By comparing the peat bog soil cores collected from the MN peat bogs, NC Pocosins, FL Everglades and Peru palm swamps we find that the soils in the shrub-dominant Pocosin contain the highest phenolics, which microbial studies indicate have the strongest resistance to microbial decomposition. A chemical comparison of plant driven peat carbon quality along a north to south latitudinal gradient indicates that tropical peatlands have higher aromatic compounds, and enhanced phenolics, especially after light fires, which enhances C storage and affect GHG flux across the latitudinal gradient.

Monitoring and modeling of microbial and biological water quality

USDA-ARS?s Scientific Manuscript database

Microbial and biological water quality informs on the health of water systems and their suitability for uses in irrigation, recreation, aquaculture, and other activities. Indicators of microbial and biological water quality demonstrate high spatial and temporal variability. Therefore, monitoring str...

Anoxia stimulates microbially catalyzed metal release from Animas River sediments

DOE PAGES

Saup, Casey M.; Williams, Kenneth H.; Rodríguez-Freire, Lucía; ...

2017-03-06

The Gold King Mine spill in August 2015 released 11 million liters of metal-rich mine waste to the Animas River watershed, an area that has been previously exposed to historical mining activity spanning more than a century. Although adsorption onto fluvial sediments was responsible for rapid immobilization of a significant fraction of the spill-associated metals, patterns of longer-term mobility are poorly constrained. Metals associated with river sediments collected downstream of the Gold King Mine in August 2015 exhibited distinct presence and abundance patterns linked to location and mineralogy. Simulating riverbed burial and development of anoxic conditions, sediment microcosm experiments amendedmore » with Animas River dissolved organic carbon revealed the release of specific metal pools coupled to microbial Fe- and SO 4 2-reduction. Results suggest that future sedimentation and burial of riverbed materials may drive longer-term changes in patterns of metal remobilization linked to anaerobic microbial metabolism, potentially driving decreases in downstream water quality. Such patterns emphasize the need for long-term water monitoring efforts in metal-impacted watersheds.« less

Anoxia stimulates microbially catalyzed metal release from Animas River sediments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saup, Casey M.; Williams, Kenneth H.; Rodríguez-Freire, Lucía

The Gold King Mine spill in August 2015 released 11 million liters of metal-rich mine waste to the Animas River watershed, an area that has been previously exposed to historical mining activity spanning more than a century. Although adsorption onto fluvial sediments was responsible for rapid immobilization of a significant fraction of the spill-associated metals, patterns of longer-term mobility are poorly constrained. Metals associated with river sediments collected downstream of the Gold King Mine in August 2015 exhibited distinct presence and abundance patterns linked to location and mineralogy. Simulating riverbed burial and development of anoxic conditions, sediment microcosm experiments amendedmore » with Animas River dissolved organic carbon revealed the release of specific metal pools coupled to microbial Fe- and SO 4 2-reduction. Results suggest that future sedimentation and burial of riverbed materials may drive longer-term changes in patterns of metal remobilization linked to anaerobic microbial metabolism, potentially driving decreases in downstream water quality. Such patterns emphasize the need for long-term water monitoring efforts in metal-impacted watersheds.« less

Assessing market-sold remedies in lomé (togo) for hygienic quality.

PubMed

de Souza, Comlan; Ameyapoh, Yaovi; Karou, Simplice D; Anani, Kokou T; Kpodar, Madje L; Gbeassor, Mensavi

2011-01-01

Traditional concoctions sold in marketplaces are always assumed to be safe and efficient; however, they can be potentially toxic because of poor hygienic practices in plant processing or storage. The present study aimed to assess for the microbial quality of market-sold vegetable drugs in Lomé. Thus, a total of 209 plant remedies were collected in marketplaces and analysed for the presence of total aerobic bacteria, total coliforms, thermotolerant coliforms, Staphylococcus aureus, sulphite reducing bacteria, and yeast and moulds according to the French Association of Normalisation (AFNOR) guidelines. The results revealed that all formulations were contaminated by several microorganisms, excepted alcohol-based mixtures. According to AFNOR limits nonconform drugs were according to total aerobic bacteria (86.96% powders, 81.82% capsules, 66.67% tisanes, and 42.11% decoctions); to total coliforms (9.10% capsules, 8.70% powders and 1.75% decoction); to yeasts and moulds (77.78% ointments, 40% calcined powders, 36.36% capsules, and 23.91% powders). The microbiological analysis revealed that the majority of contaminating bacteria were gram positive catalase positive and oxidase positive bacilli. Quality control studies on market-sold remedies are currently needed to evaluate the microbial risk in consuming these products and they may allow the standardisation of plant processing and storage.

Assessing Market-Sold Remedies in Lomé (Togo) for Hygienic Quality

PubMed Central

de Souza, Comlan; Ameyapoh, Yaovi; Karou, Simplice D.; Anani, Kokou T.; Kpodar, Madje L.; Gbeassor, Mensavi

2011-01-01

Traditional concoctions sold in marketplaces are always assumed to be safe and efficient; however, they can be potentially toxic because of poor hygienic practices in plant processing or storage. The present study aimed to assess for the microbial quality of market-sold vegetable drugs in Lomé. Thus, a total of 209 plant remedies were collected in marketplaces and analysed for the presence of total aerobic bacteria, total coliforms, thermotolerant coliforms, Staphylococcus aureus, sulphite reducing bacteria, and yeast and moulds according to the French Association of Normalisation (AFNOR) guidelines. The results revealed that all formulations were contaminated by several microorganisms, excepted alcohol-based mixtures. According to AFNOR limits nonconform drugs were according to total aerobic bacteria (86.96% powders, 81.82% capsules, 66.67% tisanes, and 42.11% decoctions); to total coliforms (9.10% capsules, 8.70% powders and 1.75% decoction); to yeasts and moulds (77.78% ointments, 40% calcined powders, 36.36% capsules, and 23.91% powders). The microbiological analysis revealed that the majority of contaminating bacteria were gram positive catalase positive and oxidase positive bacilli. Quality control studies on market-sold remedies are currently needed to evaluate the microbial risk in consuming these products and they may allow the standardisation of plant processing and storage. PMID:21350662

Microbial keratitis secondary to unintended poor compliance with scleral gas-permeable contact lenses.

PubMed

Zimmerman, Aaron B; Marks, Amanda

2014-01-01

To report a case of neurotrophic keratitis in which scleral contact lenses improved vision from 20/100 to 20/20, however, due to poor lens care, an incident of microbial keratitis developed. A 64-year-old man with an ocular history of neurotrophic keratitis secondary to herpes simplex in each eye was successfully fit with scleral lenses. He subsequently developed microbial keratitis due to a number of risk factors. The lesion was culture negative, yet was very responsive to treatment with moxifloxacin. The lesion fully healed, and the patient did not suffer additional vision loss. This case demonstrates the ability of scleral lenses to correct visual impairments secondary to poor epithelial integrity and illustrates the importance of the practitioner providing detailed lens care instruction.

Improving chocolate flavor in poor-quality cocoa almonds by enzymatic treatment.

PubMed

Oliveira, Hilana Salete Silva; Mamede, Maria Eugênia Oliveira; Góes-Neto, Aristóteles; Koblitz, Maria Gabriela Bello

2011-01-01

This paper proposes a method to enzymatically treat poor-quality cocoa almonds (known as "slate") to ensure the formation of chocolate flavor precursors. The production of flavor precursors improves the quality of these almonds, which are usually responsible for the low quality of the liquor produced. Proteases and carboxypeptidases from different sources were tested under various conditions. The different treatments were evaluated by chemical analysis (hydrolysis efficiency) and sensory analysis of the treated material compared to good-quality cocoa almonds. The results show that it is possible, through the use of microbial enzymes, to generate the mixture of compounds that will release, after roasting, the characteristic chocolate flavor in poor-quality almonds. However, it is necessary to optimize the conditions of enzymatic treatment to obtain better results and thus establish a process that can be used for industrial purposes for manufacturing cocoa and chocolate. The basidiomycete Moniliophtora perniciosa is the causative agent of witches' broom disease (WBD) of the cocoa tree, whose seeds are the source of chocolate. It is the most important phytopathological problem of cocoa-producing areas of the American continent, and has decimated the Brazilian cocoa industry. In Bahia (Brazil), M. perniciosa was identified in 1989 and, as a consequence of its spreading, the annual production of cocoa almonds dropped from 450,000 to 90,000 tons within 12 y, reducing export values from an all-time high of about US$ 1 billion to 110 million. The high incidence of WBD incapacitates Brazil to produce enough cocoa almonds even for the internal market, leading the country to import low-quality cocoa almonds mainly from African countries. Our work proposes an enzymatic treatment to increase the quality of that cocoa almonds and, consequently, to improve the quality of the chocolate produced and consumed in the country. © 2011 Institute of Food Technologists®

Assessing the microbial quality of improved drinking water sources: results from the Dominican Republic.

PubMed

Baum, Rachel; Kayser, Georgia; Stauber, Christine; Sobsey, Mark

2014-01-01

Millennium Development Goal Target 7c (to halve between 1990 and 2015 the proportion of the global population without sustainable access to safe drinking water), was celebrated as achieved in 2012. However, new studies show that we may be prematurely celebrating. Access to safe drinking water may be overestimated if microbial water quality is considered. The objective of this study was to examine the relationship between microbial drinking water quality and drinking water source in the Puerto Plata region of the Dominican Republic. This study analyzed microbial drinking water quality data from 409 households in 33 communities. Results showed that 47% of improved drinking water sources were of high to very-high risk water quality, and therefore unsafe for drinking. This study provides evidence that the current estimate of safe water access may be overly optimistic, and microbial water quality data are needed to reliably assess the safety of drinking water.

Assessing the Microbial Quality of Improved Drinking Water Sources: Results from the Dominican Republic

PubMed Central

Baum, Rachel; Kayser, Georgia; Stauber, Christine; Sobsey, Mark

2014-01-01

Millennium Development Goal Target 7c (to halve between 1990 and 2015 the proportion of the global population without sustainable access to safe drinking water), was celebrated as achieved in 2012. However, new studies show that we may be prematurely celebrating. Access to safe drinking water may be overestimated if microbial water quality is considered. The objective of this study was to examine the relationship between microbial drinking water quality and drinking water source in the Puerto Plata region of the Dominican Republic. This study analyzed microbial drinking water quality data from 409 households in 33 communities. Results showed that 47% of improved drinking water sources were of high to very-high risk water quality, and therefore unsafe for drinking. This study provides evidence that the current estimate of safe water access may be overly optimistic, and microbial water quality data are needed to reliably assess the safety of drinking water. PMID:24218411

Water pollution in Pakistan and its impact on public health--a review.

PubMed

Azizullah, Azizullah; Khattak, Muhammad Nasir Khan; Richter, Peter; Häder, Donat-Peter

2011-02-01

Water pollution is one of the major threats to public health in Pakistan. Drinking water quality is poorly managed and monitored. Pakistan ranks at number 80 among 122 nations regarding drinking water quality. Drinking water sources, both surface and groundwater are contaminated with coliforms, toxic metals and pesticides throughout the country. Various drinking water quality parameters set by WHO are frequently violated. Human activities like improper disposal of municipal and industrial effluents and indiscriminate applications of agrochemicals in agriculture are the main factors contributing to the deterioration of water quality. Microbial and chemical pollutants are the main factors responsible exclusively or in combination for various public health problems. This review discusses a detailed layout of drinking water quality in Pakistan with special emphasis on major pollutants, sources of pollution and the consequent health problems. The data presented in this review are extracted from various studies published in national and international journals. Also reports released by the government and non-governmental organizations are included. Copyright © 2010 Elsevier Ltd. All rights reserved.

Modeling the interannual variability of microbial quality metrics of irrigation water in a Pennsylvania stream.

PubMed

Hong, Eun-Mi; Shelton, Daniel; Pachepsky, Yakov A; Nam, Won-Ho; Coppock, Cary; Muirhead, Richard

2017-02-01

Knowledge of the microbial quality of irrigation waters is extremely limited. For this reason, the US FDA has promulgated the Produce Rule, mandating the testing of irrigation water sources for many farms. The rule requires the collection and analysis of at least 20 water samples over two to four years to adequately evaluate the quality of water intended for produce irrigation. The objective of this work was to evaluate the effect of interannual weather variability on surface water microbial quality. We used the Soil and Water Assessment Tool model to simulate E. coli concentrations in the Little Cove Creek; this is a perennial creek located in an agricultural watershed in south-eastern Pennsylvania. The model performance was evaluated using the US FDA regulatory microbial water quality metrics of geometric mean (GM) and the statistical threshold value (STV). Using the 90-year time series of weather observations, we simulated and randomly sampled the time series of E. coli concentrations. We found that weather conditions of a specific year may strongly affect the evaluation of microbial quality and that the long-term assessment of microbial water quality may be quite different from the evaluation based on short-term observations. The variations in microbial concentrations and water quality metrics were affected by location, wetness of the hydrological years, and seasonality, with 15.7-70.1% of samples exceeding the regulatory threshold. The results of this work demonstrate the value of using modeling to design and evaluate monitoring protocols to assess the microbial quality of water used for produce irrigation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Leaf and root C-to-N ratios are poor predictors of soil microbial biomass C and respiration across 32 tree species.

PubMed

Ferlian, Olga; Wirth, Christian; Eisenhauer, Nico

2017-11-01

Soil microorganisms are the main primary decomposers of plant material and drive biogeochemical processes like carbon and nitrogen cycles. Hence, knowledge of their nutritional demands and limitations for activity and growth is of particular importance. However, potential effects of the stoichiometry of soil and plant species on soil microbial activity and carbon use efficiency are poorly understood. Soil properties and plant traits are assumed to drive microbial carbon and community structure. We investigated the associations between C and N concentrations of leaf, root, and soil as well as their ratios and soil microbial biomass C and activity (microbial basal respiration and specific respiratory quotient) across 32 young native angiosperm tree species at two locations in Central Germany. Correlations between C:N ratios of leaves, roots, and soil were positive but overall weak. Only regressions between root and leaf C:N ratios as well as between root and soil C:N ratios were significant at one site. Soil microbial properties differed significantly between the two sites and were significantly correlated with soil C:N ratio across sites. Soil C concentrations rather than N concentrations drove significant effects of soil C:N ratio on soil microbial properties. No significant correlations between soil microbial properties and leaf as well as root C:N ratios were found. We found weak correlations of C:N ratios between plant aboveground and belowground tissues. Furthermore, microorganisms were not affected by the stoichiometry of plant tissues in the investigated young trees. The results suggest that soil stoichiometry represents a consistent determinant of soil microbial biomass and respiration. Our study indicates that stoichiometric relationships among tree organs can be weak and poor predictors of soil microbial properties in young tree stands. Further research in controlled experimental settings with a wide range of tree species is needed to study the role of plant chemical traits like the composition and stoichiometry of root exudates in determining interactions between above- and belowground compartments.

Development and application of the microbial fate and transport module for the Agricultural Policy/Environmental eXtender (APEX) model

NASA Astrophysics Data System (ADS)

Hong, E.; Park, Y.; Muirhead, R.; Jeong, J.; Pachepsky, Y. A.

2017-12-01

Pathogenic microorganisms in recreational and irrigation waters remain the subject of concern. Water quality models are used to estimate microbial quality of water sources, to evaluate microbial contamination-related risks, to guide the microbial water quality monitoring, and to evaluate the effect of agricultural management on the microbial water quality. The Agricultural Policy/Environmental eXtender (APEX) is the watershed-scale water quality model that includes highly detailed representation of agricultural management. The APEX currently does not have microbial fate and transport simulation capabilities. The objective of this work was to develop the first APEX microbial fate and transport module that could use the APEX conceptual model of manure removal together with recently introduced conceptualizations of the in-stream microbial fate and transport. The module utilizes manure erosion rates found in the APEX. Bacteria survival in soil-manure mixing layer was simulated with the two-stage survival model. Individual survival patterns were simulated for each manure application date. Simulated in-stream microbial fate and transport processes included the reach-scale passive release of bacteria with resuspended bottom sediment during high flow events, the transport of bacteria from bottom sediment due to the hyporheic exchange during low flow periods, the deposition with settling sediment, and the two-stage survival. Default parameter values were available from recently published databases. The APEX model with the newly developed microbial fate and transport module was applied to simulate seven years of monitoring data for the Toenepi watershed in New Zealand. Based on calibration and testing results, the APEX with the microbe module reproduced well the monitored pattern of E. coli concentrations at the watershed outlet. The APEX with the microbial fate and transport module will be utilized for predicting microbial quality of water under various agricultural practices, evaluating monitoring protocols, and supporting the selection of management practices based on regulations that rely on fecal indicator bacteria concentrations.

Land-use history has a stronger impact on soil microbial community composition than aboveground vegetation and soil properties

USDA-ARS?s Scientific Manuscript database

The response of soil microbial communities following soil disturbances is poorly understood. The development of soil microbial communities in two restoration gradients was studied to investigate the impact of land-management regime at the W. K. Kellogg Biological Station, Michigan. The first restora...

A low-cost procedure for production of fresh autochthonous wine yeast.

PubMed

Maqueda, Matilde; Pérez-Nevado, Francisco; Regodón, José A; Zamora, Emiliano; Alvarez, María L; Rebollo, José E; Ramírez, Manuel

2011-03-01

A low-cost procedure was designed for easy and rapid response-on-demand production of fresh wine yeast for local wine-making. The pilot plant produced fresh yeast culture concentrate with good microbial quality and excellent oenological properties from four selected wine yeasts. The best production yields were obtained using 2% sugar beet molasses and a working culture volume of less than 60% of the fermenter capacity. The yeast yield using 2% sugar grape juice was low and had poor cell viability after freeze storage, although the resulting yeast would be directly available for use in the winery. The performance of these yeasts in commercial wineries was excellent; they dominated must fermentation and improved its kinetics, as well as improving the physicochemical parameters and the organoleptic quality of red and white wines.

MICROBIAL BIOFILMS AS INTEGRATIVE SENSORS OF ENVIRONMENTAL QUALITY

EPA Science Inventory

Snyder, Richard A., Michael A. Lewis, Andreas Nocker and Joe E. Lepo. In press. Microbial Biofilms as Integrative Sensors of Environmental Quality. In: Estuarine Indicators Workshop Proceedings. CRC Press, Boca Raton, FL. 34 p. (ERL,GB 1198).

Microbial biofilms are comple...

Strain-specific probiotic (microbial cell preparation) and omega-3 fatty acid in modulating quality of life and inflammatory markers in colorectal cancer patients: a randomized controlled trial.

PubMed

Golkhalkhali, Babak; Rajandram, Retnagowri; Paliany, Audra Shaleena; Ho, Gwo Fuang; Wan Ishak, Wan Zamaniah; Johari, Che Shafini; Chin, Kin Fah

2018-06-01

Colorectal cancer patients on chemotherapy usually have elevated levels of inflammatory markers and experience numerous side effects from chemotherapy thereby leading to poor quality of life. Omega-3 fatty acid and microbial cell preparation (MCP) have been known to provide significant benefits in patients on chemotherapy. The aim of this study was to determine the effect of supplementation of omega-3 fatty acid and MCP in quality of life, chemotherapy side effects and inflammatory markers in colorectal cancer patients on chemotherapy. A double-blind randomized study was carried out with 140 colorectal cancer patients on chemotherapy. Subjects were separated into two groups to receive either placebo or MCP [30 billion colony-forming unit (CFUs) per sachet] at a dose of two sachets daily for 4 weeks, and omega-3 fatty acid at a dose of 2 g daily for 8 weeks. Outcomes measured were quality of life, side effects of chemotherapy and levels of inflammatory markers such as interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α) and C-reactive protein. The supplementation with MCP and omega-3 fatty acid improved the overall quality of life and alleviated certain side effects of chemotherapy. The supplementation with MCP and omega-3 fatty acid also managed to reduce the level of IL-6 (P = 0.002). There was a significant rise in the placebo group's serum TNF-α (P = 0.048) and IL-6 (P = 0.004). The combined supplementation with MCP and omega-3 fatty acid may improve quality of life, reduce certain inflammatory biomarkers and relieve certain side effects of chemotherapy in colorectal patients on chemotherapy. © 2017 John Wiley & Sons Australia, Ltd.

Assessment of the impact of traditional septic tank soakaway systems on water quality in Ireland.

PubMed

Keegan, Mary; Kilroy, Kate; Nolan, Daniel; Dubber, Donata; Johnston, Paul M; Misstear, Bruce D R; O'Flaherty, Vincent; Barrett, Maria; Gill, Laurence W

2014-01-01

One of the key threats to groundwater and surface water quality in Ireland is the impact of poorly designed, constructed or maintained on-site wastewater treatment systems. An extensive study was carried out to quantify the impact of existing sites on water quality. Six existing sites, consisting of a traditional septic tank and soakaway system, located in various ranges of subsoil permeabilities were identified and monitored to determine how well they function under varying subsoil and weather conditions. The preliminary results of the chemical and microbiological pollutant attenuation in the subsoil of the systems have been assessed and treatment performance evaluated, as well as impact on local surface water and groundwater quality. The source of any faecal contamination detected in groundwater, nearby surface water and effluent samples was confirmed by microbial source tracking. From this, it can be seen that the transport and treatment of percolate vary greatly depending on the permeability and composition of the subsoil.

A QRM Discussion of Microbial Contamination of Non-sterile Drug Products, Using FDA and EMA Warning Letters Recorded between 2008 and 2016.

PubMed

Santos, Ana M C; Doria, Mara S; Meirinhos-Soares, Luís; Almeida, António J; Menezes, José C

2018-01-01

Microbial quality control of non-sterile drug products has been a concern to regulatory agencies and the pharmaceutical industry since the 1960s. Despite being an old challenge to companies, microbial contamination still affects a high number of manufacturers of non-sterile products. Consequences go well beyond the obvious direct costs related to batch rejections or product recalls, as human lives and a company's reputation are significantly impacted if such events occur. To better manage risk and establish effective mitigation strategies, it is necessary to understand the microbial hazards involved in non-sterile drug products manufacturing, be able to evaluate their potential impact on final product quality, and apply mitigation actions. Herein we discuss the most likely root causes involved in microbial contaminations referenced in warning letters issued by US health authorities and non-compliance reports issued by European health authorities over a period of several years. The quality risk management tools proposed were applied to the data gathered from those databases, and a generic risk ranking was provided based on a panel of non-sterile drug product manufacturers that was assembled and given the opportunity to perform the risk assessments. That panel identified gaps and defined potential mitigation actions, based on their own experience of potential risks expected for their processes. Major findings clearly indicate that the manufacturers affected by the warning letters should focus their attention on process improvements and microbial control strategies, especially those related to microbial analysis and raw material quality control. Additionally, the WLs considered frequently referred to failures in quality-related issues, which indicates that the quality commitment should be reinforced at most companies to avoid microbiological contaminations. LAY ABSTRACT: Microbial contamination of drug products affects the quality of non-sterile drug products produced by numerous manufacturers, representing a major risk to patients. It is necessary to understand the microbial hazards involved in the manufacturing process and evaluate their impact on final product quality so that effective prevention strategies can be implemented. A risk-based classification of most likely root causes for microbial contamination found in the warning letters issued by the US Food and Drug Administration and the European Medicines Agency is proposed. To validate the likely root causes extracted from the warning letters, a subject matter expert panel made of several manufacturers was formed and consulted. A quality risk management approach to assess microbiological contamination of non-sterile drug products is proposed for the identification of microbial hazards involved in the manufacturing process. To enable ranking of microbial contamination risks, quality risk management metrics related to criticality and overall risk were applied. The results showed that manufacturers of non-sterile drug products should improve their microbial control strategy, with special attention to quality controls of raw materials, primary containers, and closures. Besides that, they should invest in a more robust quality system and culture. As a start, manufacturers may consider investigating their specific microbiological risks, adressing their sites' own microbial ecology, type of manufacturing processes, and dosage form characteristics, as these may lead to increased contamination risks. Authorities should allow and enforce innovative, more comprehensive, and more effective approaches to in-process contamination monitoring and controls. © PDA, Inc. 2018.

Soil biodiversity in artificial black pine stands one year after selective silvicultural treatments

NASA Astrophysics Data System (ADS)

Mocali, Stefano; Fabiani, Arturo; Landi, Silvia; Bianchetto, Elisa; Montini, Piergiuseppe; Samaden, Stefano; Cantiani, Paolo

2017-04-01

The decay of forest cover and soil erosion is a consequence of continual intensive forest exploitation, such as grazing and wild fires over the centuries. From the end of the eighteenth century up to the mid-1900s, black pine plantations were established throughout the Apennines' range in Italy, to improve forest soil quality. The main aim of this silvicultural treatment was to re-establish the pine as a first cover and pioneer species. A series of thinning activities were therefore planned by foresters when these plantations were designed. The project Selpibiolife (LIFE13 BIO/IT/000282) has the main objective to demonstrate the potential of an innovative silvicultural treatment to enhance soil and flora biodiversity and under black pine stands. The monitoring will be carried out by comparing selective and traditional thinning methods (selecting trees from below leaving well-spaced, highest-quality trees) to areas without any silvicultural treatments (e.g. weeding, cleaning, liberation cutting). The monitoring survey was carried out in Pratomagno and Amiata Val D'Orcia areas on the Appennines (Italy) and involved different biotic levels: microorganisms, mesofauna, nematodes and macrofauna (Coleoptera) and flora. The microbial (bacteria and fungi) diversity was assessed by both biochemical (microbial biomass, microbial respiration, metabolic quotient) and molecular (microbiota) approaches whereas QBS (Soil Biological Quality) index and diversity indexes were determined for mesofauna and other organisms, respectively, including flora. The overall results highlighted different a composition and activity of microbial communities within the two areas before thinning, and revealed a significant difference between the overall biodiversity of the two areas. Even though silvicultural treatments provided no significant differences at floristic level, microbial and mesofaunal parameters revealed to be differently affected by treatments. In particular, little but significant differences were observed for mesofauna and nematode community diversity which displayed a higher diversity after thinning in both Amiata and Pratomagno. Nevertheless, Coleoptera showed higher richness values in Pratomagno, where the wood degrader Nebria tibialis subcontracta specie dominated, compared to Amiata. In conclusion, a general increase of soil biodiversity occurred in the plots after thinning compared to untreated control within the two areas, but such results are still heterogeneous and poorly statistically significant. As expected, one year is not enough time to appreciate significant enhance of the overall biodiversity after such silvicultural treatments. Thus, more evident and significant results are expected on the next two years.

FACTORS INFLUENCING LIGHT-INDUCED MORTALITY OF ENTEROCOCCI IN SEDIMENT SUSPENSIONS

EPA Science Inventory

Contamination of recreational waters by pathogenic microorganisms occurs through complex, poorly understood interactions involving variable microbial sources, hydrodynamic transport, arid microbial fate processes. Fecal indicator bacteria such as enterococci have been used to ass...

Modelling the impact of future socio-economic and climate change scenarios on river microbial water quality.

PubMed

Islam, M M Majedul; Iqbal, Muhammad Shahid; Leemans, Rik; Hofstra, Nynke

2018-03-01

Microbial surface water quality is important, as it is related to health risk when the population is exposed through drinking, recreation or consumption of irrigated vegetables. The microbial surface water quality is expected to change with socio-economic development and climate change. This study explores the combined impacts of future socio-economic and climate change scenarios on microbial water quality using a coupled hydrodynamic and water quality model (MIKE21FM-ECOLab). The model was applied to simulate the baseline (2014-2015) and future (2040s and 2090s) faecal indicator bacteria (FIB: E. coli and enterococci) concentrations in the Betna river in Bangladesh. The scenarios comprise changes in socio-economic variables (e.g. population, urbanization, land use, sanitation and sewage treatment) and climate variables (temperature, precipitation and sea-level rise). Scenarios have been developed building on the most recent Shared Socio-economic Pathways: SSP1 and SSP3 and Representative Concentration Pathways: RCP4.5 and RCP8.5 in a matrix. An uncontrolled future results in a deterioration of the microbial water quality (+75% by the 2090s) due to socio-economic changes, such as higher population growth, and changes in rainfall patterns. However, microbial water quality improves under a sustainable scenario with improved sewage treatment (-98% by the 2090s). Contaminant loads were more influenced by changes in socio-economic factors than by climatic change. To our knowledge, this is the first study that combines climate change and socio-economic development scenarios to simulate the future microbial water quality of a river. This approach can also be used to assess future consequences for health risks. Copyright © 2017 The Authors. Published by Elsevier GmbH.. All rights reserved.

Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities

PubMed Central

Tan, BoonFei; Ng, Charmaine; Nshimyimana, Jean Pierre; Loh, Lay Leng; Gin, Karina Y.-H.; Thompson, Janelle R.

2015-01-01

Water quality is an emergent property of a complex system comprised of interacting microbial populations and introduced microbial and chemical contaminants. Studies leveraging next-generation sequencing (NGS) technologies are providing new insights into the ecology of microbially mediated processes that influence fresh water quality such as algal blooms, contaminant biodegradation, and pathogen dissemination. In addition, sequencing methods targeting small subunit (SSU) rRNA hypervariable regions have allowed identification of signature microbial species that serve as bioindicators for sewage contamination in these environments. Beyond amplicon sequencing, metagenomic and metatranscriptomic analyses of microbial communities in fresh water environments reveal the genetic capabilities and interplay of waterborne microorganisms, shedding light on the mechanisms for production and biodegradation of toxins and other contaminants. This review discusses the challenges and benefits of applying NGS-based methods to water quality research and assessment. We will consider the suitability and biases inherent in the application of NGS as a screening tool for assessment of biological risks and discuss the potential and limitations for direct quantitative interpretation of NGS data. Secondly, we will examine case studies from recent literature where NGS based methods have been applied to topics in water quality assessment, including development of bioindicators for sewage pollution and microbial source tracking, characterizing the distribution of toxin and antibiotic resistance genes in water samples, and investigating mechanisms of biodegradation of harmful pollutants that threaten water quality. Finally, we provide a short review of emerging NGS platforms and their potential applications to the next generation of water quality assessment tools. PMID:26441948

Lateral gene transfer in a heavy metal-contaminated-groundwater microbial community

DOE PAGES

Hemme, Christopher L.; Green, Stefan J.; Rishishwar, Lavanya; ...

2016-04-05

Here, unraveling the drivers controlling the response and adaptation of biological communities to environmental change, especially anthropogenic activities, is a central but poorly understood issue in ecology and evolution. Comparative genomics studies suggest that lateral gene transfer (LGT) is a major force driving microbial genome evolution, but its role in the evolution of microbial communities remains elusive.

Mechanisms of Soil Aggregation: a biophysical modeling framework

NASA Astrophysics Data System (ADS)

Ghezzehei, T. A.; Or, D.

2016-12-01

Soil aggregation is one of the main crosscutting concepts in all sub-disciplines and applications of soil science from agriculture to climate regulation. The concept generally refers to adhesion of primary soil particles into distinct units that remain stable when subjected to disruptive forces. It is one of the most sensitive soil qualities that readily respond to disturbances such as cultivation, fire, drought, flooding, and changes in vegetation. These changes are commonly quantified and incorporated in soil models indirectly as alterations in carbon content and type, bulk density, aeration, permeability, as well as water retention characteristics. Soil aggregation that is primarily controlled by organic matter generally exhibits hierarchical organization of soil constituents into stable units that range in size from a few microns to centimeters. However, this conceptual model of soil aggregation as the key unifying mechanism remains poorly quantified and is rarely included in predictive soil models. Here we provide a biophysical framework for quantitative and predictive modeling of soil aggregation and its attendant soil characteristics. The framework treats aggregates as hotspots of biological, chemical and physical processes centered around roots and root residue. We keep track of the life cycle of an individual aggregate from it genesis in the rhizosphere, fueled by rhizodeposition and mediated by vigorous microbial activity, until its disappearance when the root-derived resources are depleted. The framework synthesizes current understanding of microbial life in porous media; water holding and soil binding capacity of biopolymers; and environmental controls on soil organic matter dynamics. The framework paves a way for integration of processes that are presently modeled as disparate or poorly coupled processes, including storage and protection of carbon, microbial activity, greenhouse gas fluxes, movement and storage of water, resistance of soils against erosion.

The indoor air we breathe.

PubMed Central

Oliver, L C; Shackleton, B W

1998-01-01

Increasingly recognized as a potential public health problem since the outbreak of Legionnaire's disease in Philadelphia in 1976, polluted indoor air has been associated with health problems that include asthma, sick building syndrome, multiple chemical sensitivity, and hypersensitivity pneumonitis. Symptoms are often nonspecific and include headache, eye and throat irritation, chest tightness and shortness of breath, and fatigue. Air-borne contaminants include commonly used chemicals, vehicular exhaust, microbial organisms, fibrous glass particles, and dust. Identified causes include defective building design and construction, aging of buildings and their ventilation systems, poor climate control, inattention to building maintenance. A major contributory factor is the explosion in the use of chemicals in building construction and furnishing materials over the past four decades. Organizational issues and psychological variables often contribute to the problem and hinder its resolution. This article describes the health problems related to poor indoor air quality and offers solutions. Images p398-a p399-a PMID:9769764

Impacts of Human Activity on the Microbial Communities of Devon Island, Canadian High Arctic

NASA Astrophysics Data System (ADS)

Bywaters, K. B.; Burton, A. S.; Wallace, S. L.; Glass, B. J.

2016-09-01

The impacts of human activities on microbial communities in arctic environments are poorly understood. This project compares the distribution of microbes at the HMP Mars analog site prior to and after human settlement.

Neurotoxicity of fungal volatile organic compounds in Drosophila melanogaster.

PubMed

Inamdar, Arati A; Masurekar, Prakash; Bennett, Joan Wennstrom

2010-10-01

Many volatile organic compounds (VOCs) are found in indoor environment as products of microbial metabolism. In damp indoor environments, fungi are associated with poor air quality. Some epidemiological studies have suggested that microbial VOCs have a negative impact on human health. Our study was designed to provide a reductionist approach toward studying fungal VOC-mediated toxicity using the inexpensive model organism, Drosophila melanogaster, and pure chemical standards of several important fungal VOCs. Low concentrations of the following known fungal VOCs, 0.1% of 1-octen-3-ol and 0.5% of 2-octanone; 2,5 dimethylfuran; 3-octanol; and trans-2-octenal, caused locomotory defects and changes in green fluorescent protein (GFP)- and antigen-labeled dopaminergic neurons in adult D. melanogaster. Locomotory defects could be partially rescued with L-DOPA. Ingestion of the antioxidant, vitamin E, improved the survival span and delayed the VOC-mediated changes in dopaminergic neurons, indicating that the VOC-mediated toxicity was due, in part, to generation of reactive oxygen species.

High adherence is necessary to realize health gains from water quality interventions.

PubMed

Brown, Joe; Clasen, Thomas

2012-01-01

Safe drinking water is critical for health. Household water treatment (HWT) has been recommended for improving access to potable water where existing sources are unsafe. Reports of low adherence to HWT may limit the usefulness of this approach, however. We constructed a quantitative microbial risk model to predict gains in health attributable to water quality interventions based on a range of assumptions about pre-treatment water quality; treatment effectiveness in reducing bacteria, viruses, and protozoan parasites; adherence to treatment interventions; volume of water consumed per person per day; and other variables. According to mean estimates, greater than 500 DALYs may be averted per 100,000 person-years with increased access to safe water, assuming moderately poor pre-treatment water quality that is a source of risk and high treatment adherence (>90% of water consumed is treated). A decline in adherence from 100% to 90% reduces predicted health gains by up to 96%, with sharpest declines when pre-treatment water quality is of higher risk. Results suggest that high adherence is essential in order to realize potential health gains from HWT.

High Adherence Is Necessary to Realize Health Gains from Water Quality Interventions

PubMed Central

Brown, Joe; Clasen, Thomas

2012-01-01

Background Safe drinking water is critical for health. Household water treatment (HWT) has been recommended for improving access to potable water where existing sources are unsafe. Reports of low adherence to HWT may limit the usefulness of this approach, however. Methods and Findings We constructed a quantitative microbial risk model to predict gains in health attributable to water quality interventions based on a range of assumptions about pre-treatment water quality; treatment effectiveness in reducing bacteria, viruses, and protozoan parasites; adherence to treatment interventions; volume of water consumed per person per day; and other variables. According to mean estimates, greater than 500 DALYs may be averted per 100,000 person-years with increased access to safe water, assuming moderately poor pre-treatment water quality that is a source of risk and high treatment adherence (>90% of water consumed is treated). A decline in adherence from 100% to 90% reduces predicted health gains by up to 96%, with sharpest declines when pre-treatment water quality is of higher risk. Conclusions Results suggest that high adherence is essential in order to realize potential health gains from HWT. PMID:22586491

Replicating the microbial community and water quality performance of full-scale slow sand filters in laboratory-scale filters.

PubMed

Haig, Sarah-Jane; Quince, Christopher; Davies, Robert L; Dorea, Caetano C; Collins, Gavin

2014-09-15

Previous laboratory-scale studies to characterise the functional microbial ecology of slow sand filters have suffered from methodological limitations that could compromise their relevance to full-scale systems. Therefore, to ascertain if laboratory-scale slow sand filters (L-SSFs) can replicate the microbial community and water quality production of industrially operated full-scale slow sand filters (I-SSFs), eight cylindrical L-SSFs were constructed and were used to treat water from the same source as the I-SSFs. Half of the L-SSFs sand beds were composed of sterilized sand (sterile) from the industrial filters and the other half with sand taken directly from the same industrial filter (non-sterile). All filters were operated for 10 weeks, with the microbial community and water quality parameters sampled and analysed weekly. To characterize the microbial community phyla-specific qPCR assays and 454 pyrosequencing of the 16S rRNA gene were used in conjunction with an array of statistical techniques. The results demonstrate that it is possible to mimic both the water quality production and the structure of the microbial community of full-scale filters in the laboratory - at all levels of taxonomic classification except OTU - thus allowing comparison of LSSF experiments with full-scale units. Further, it was found that the sand type composing the filter bed (non-sterile or sterile), the water quality produced, the age of the filters and the depth of sand samples were all significant factors in explaining observed differences in the structure of the microbial consortia. This study is the first to the authors' knowledge that demonstrates that scaled-down slow sand filters can accurately reproduce the water quality and microbial consortia of full-scale slow sand filters. Copyright © 2014 Elsevier Ltd. All rights reserved.

Development and evaluation of the microbial fate and transport module for the Agricultural Policy/Environmental eXtender (APEX) model

NASA Astrophysics Data System (ADS)

Hong, Eun-Mi; Park, Yongeun; Muirhead, Richard; Pachepsky, Yakov

2017-04-01

Pathogenic microorganisms in recreational and irrigation waters remain the subject of concern. Water quality models are used to estimate microbial quality of water sources, to evaluate microbial contamination-related risks, to guide the microbial water quality monitoring, and to evaluate the effect of agricultural management on the microbial water quality. The Agricultural Policy/Environmental eXtender (APEX) is the watershed-scale water quality model that includes highly detailed representation of agricultural management. The APEX currently does not have microbial fate and transport simulation capabilities. The objective of this work was to develop the first APEX microbial fate and transport module that could use the APEX conceptual model of manure removal together with recently introduced conceptualizations of the in-stream microbial fate and transport. The module utilizes manure erosion rates found in the APEX. The total number of removed bacteria was set to the concentrations of bacteria in soil-manure mixing layer and eroded manure amount. Bacteria survival in soil-manure mixing layer was simulated with the two-stage survival model. Individual survival patterns were simulated for each manure application date. Simulated in-stream microbial fate and transport processes included the reach-scale passive release of bacteria with resuspended bottom sediment during high flow events, the transport of bacteria from bottom sediment due to the hyporheic exchange during low flow periods, the deposition with settling sediment, and the two-stage survival. Default parameter values were available from recently published databases. The APEX model with the newly developed microbial fate and transport module was applied to simulate seven years of monitoring data for the Toenepi watershed in New Zealand. The stream network of the watershed ran through grazing lands with the daily bovine waste deposition. Based on calibration and testing results, the APEX with the microbe module reproduced well the monitored pattern of E. coli concentrations at the watershed outlet. The APEX with the microbial fate and transport module will be utilized for predicting microbial quality of water under various agricultural practices (grazing, cropping, and manure application), evaluating monitoring protocols, and supporting the selection of management practices based on regulations that rely on fecal indicator bacteria concentrations. Future development should include modeling contributions of wildlife, manure weathering, and weather effects on manure-borne microorganism survival and release.

Microbial (Pathogen)/Recreational Water Quality Criteria

EPA Pesticide Factsheets

Documents pertaining to Recreational Human Health Ambient Water Quality Criteria for Microbial Organisms (Pathogens). These documents include safe levels for cyanotoxins microcystin and cylindrospermopsin, and Coliphage to protect human health.

HYGIENE PRACTICES IN URBAN RESTAURANTS AND CHALLENGES TO IMPLEMENTING FOOD SAFETY AND HAZARD ANALYSIS CRITICAL CONTROL POINTS (HACCP) PROGRAMMES IN THIKA TOWN, KENYA.

PubMed

Muinde, R K; Kiinyukia, C; Rombo, G O; Muoki, M A

2012-12-01

To determine the microbial load in food, examination of safety measures and possibility of implementing an Hazard Analysis Critical Control Points (HACCP) system. The target population for this study consisted of restaurants owners in Thika. Municipality (n = 30). Simple randomsamples of restaurantswere selected on a systematic sampling method of microbial analysis in cooked, non-cooked, raw food and water sanitation in the selected restaurants. Two hundred and ninety eight restaurants within Thika Municipality were selected. Of these, 30 were sampled for microbiological testing. From the study, 221 (74%) of the restaurants were ready to eat establishments where food was prepared early enough to hold and only 77(26%) of the total restaurants, customers made an order of food they wanted. 118(63%) of the restaurant operators/staff had knowledge on quality control on food safety measures, 24 (8%) of the restaurants applied these knowledge while 256 (86%) of the restaurants staff showed that food contains ingredients that were hazard if poorly handled. 238 (80%) of the resultants used weighing and sorting of food materials, 45 (15%) used preservation methods and the rest used dry foods as critical control points on food safety measures. The study showed that there was need for implementation of Hazard Analysis Critical Control Points (HACCP) system to enhance food safety. Knowledge of HACCP was very low with 89 (30%) of the restaurants applying some of quality measures to the food production process systems. There was contamination with Coliforms, Escherichia coli and Staphylococcus aureus microbial though at very low level. The means of Coliforms, Escherichia coli and Staphylococcus aureas microbial in sampled food were 9.7 x 103CFU/gm, 8.2 x 103 CFU/gm and 5.4 x 103 CFU/gm respectively with Coliforms taking the highest mean.

The importance of plant-soil interactions for N mineralisation in different soil types

NASA Astrophysics Data System (ADS)

Murphy, Conor; Paterson, Eric; Baggs, Elizabeth; Morley, Nicholas; Wall, David; Schulte, Rogier

2013-04-01

The last hundred years has seen major advancements in our knowledge of nitrogen mineralisation in soil, but key drivers and controls remain poorly understood. Due to an increase in the global population there is a higher demand on food production. To accommodate this demand agriculture has increased its use of N based fertilizers, but these pose risks for water quality and GHG emissions as N can be lost through nitrate leaching, ammonia volatilization, and denitrification processes (Velthof, et al., 2009). Therefore, understanding the underlying processes that determine the soils ability to supply N to the plant is vital for effective optimisation of N-fertilisation with crop demand. Carbon rich compounds exuded from plant roots to the rhizosphere, which are utilized by the microbial biomass and support activities including nutrient transformations, may be a key unaccounted for driver of N mineralisation. The main aim of this study was to study the impact of root exudates on turnover of C and N in soil, as mediated by the microbial community. Two soil types, known to contrast in N-mineralisation capacity, were used to determine relationships between C inputs, organic matter mineralisation (priming effects) and N fluxes. 15N and 13C stable isotope approaches were used to quantify the importance of rhizosphere processes on C and N mineralisation. Gross nitrogen mineralisation was measured using 15N pool dilution. Total soil CO2 efflux was measured and 13C isotope partitioning was applied to quantify SOM turnover and microbial biomass respiration. Also, 13C was traced through the microbial biomass (chloroform fumigation) to separate pool-substitution effects (apparent priming) from altered microbial utilisation of soil organic matter (real priming effects). Addition of labile carbon resulted in an increase in N-mineralisation from soil organic matter in both soils. Concurrent with this there was an increase in microbial biomass size, indicating that labile C elicited real priming effects that mobilised N from organic matter. The results from this experiment indicate that rhizosphere processes play an important role in mediating rates of C and N mineralisation and should be accounted for in estimating soil N-supply capacities. Velthof, G.L., Oudendag, D., Witzke, H.P., Asman, W.A.H., Klimont, Z., Oenema, O., 2009. Integrated assessment of nitrogen losses from agriculture in EU-27 using MITERRA-EUROPE. Journal of Environmental Quality 38, 402-417.

The microbial temperature sensitivity to warming is controlled by thermal adaptation and is independent of C-quality across a pan-continental survey

NASA Astrophysics Data System (ADS)

Berglund, Eva; Rousk, Johannes

2017-04-01

Climate models predict that warming will result in an increased loss of soil organic matter (SOM). However, field experiments suggest that although warming results in an immediate increase in SOM turnover, the effect diminishes over time. Although the use and subsequent turnover of SOM is dominated by the soil microbial community, the underlying physiology underpinning warming responses are not considered in current climate models. It has been suggested that a reduction in the perceived quality of SOM to the microbial community, and changes in the microbial thermal adaptation, could be important feed-backs to soil warming. Thus, studies distinguishing between temperature relationships and how substrate quality influences microbial decomposition are a priority. We examined microbial communities and temperature sensitivities along a natural climate gradient including 56 independent samples from across Europe. The gradient included mean annual temperatures (MAT) from ca -4 to 18 ˚ C, along with wide spans of environmental factors known to influence microbial communities, such as pH (4.0 to 8.8), nutrients (C/N from 7 to 50), SOM (from 4 to 94%), and plant communities, etc. The extensive ranges of environmental conditions resulted in wide ranges of substrate quality, indexed as microbial respiration per unit SOM, from 5-150 μg CO2g-1 SOM g-1 h-1. We hypothesised microbial communities to (1) be adapted to the temperature of their climate, leading to warm adapted bacterial communities that were more temperature sensitive (higher Q10s) at higher MAT; (2) have temperature sensitivities affected by the quality of SOM, with higher Q10s for lower quality SOM. To determine the microbial use of SOM and its dependence on temperature, we characterized microbial temperature dependences of bacterial growth (leu inc), fungal growth (ac-in-erg) and soil respiration in all 56 sites. Temperature dependences were determined using brief (ca. 1-2 h at 25˚ C) laboratory incubation experiments including temperatures from 0 to 35˚ C. Temperature relationships were modelled using the Ratkowsky model, and cardinal points including minimum temperature (Tmin) for growth and respiration along with temperature sensitivity (Q10) values were used as indices to compare sites. Microbial communities were cold-adapted in cold sites and warm-adapted in warm sites, as shown by Tmin values ranging from ca. -20 ˚ C to 0 ˚ C. For every 1˚ C rise in MAT, Tmin increased by 0.22˚ C and 0.28˚ C for bacteria and fungi, respectively. Soil respiration was less dependent on MAT, increasing 0.16 ˚ C per 1˚ C. Temperature dependence analyses grew stronger when regressed against summer temperatures, and weaker when regressed against winter temperatures. Hence, microbial communities adjusted their temperature dependence for growth more than for respiration, and higher temperatures had more impact than low temperatures did. The correlation between Tmin and MAT resulted in Q10s increasing with MAT, showing that microorganisms from cold regions were less temperature sensitive than those from warmer regions. For every 1˚ C increase in MAT, Q10 increased with 0.04 and 0.03 units for bacterial and fungal growth respectively, and 0.08 units for soil respiration. In contrast to previous studies, we found no relationship between temperature sensitivity and substrate quality. We demonstrate that the strongest driver of variation in microbial temperatures sensitivities (Q10s) is the microbial adaptation to its thermal environment. Surprisingly, the quality of SOM had no influence on the temperature sensitivity. This calls for a revision of the understanding for how microbial decomposers feed-back to climate warming. Specifically, the thermal adaptation of microbial communities need to be incorporated into climate models to capture responses to warming, while the quality of SOM can be ignored.

Exploring the under-investigated “microbial dark matter” of drinking water treatment plants

PubMed Central

Bruno, Antonia; Sandionigi, Anna; Rizzi, Ermanno; Bernasconi, Marzia; Vicario, Saverio; Galimberti, Andrea; Cocuzza, Clementina; Labra, Massimo; Casiraghi, Maurizio

2017-01-01

Scientists recently reported the unexpected detection of unknown or poorly studied bacterial diversity in groundwater. The ability to uncover this neglected biodiversity mainly derives from technical improvements, and the term “microbial dark matter” was used to group taxa poorly investigated and not necessarily monophyletic. We focused on such under-investigated microbial dark matter of drinking water treatment plant from groundwater, across carbon filters, to post-chlorination. We tackled this topic using an integrated approach where the efficacy of stringent water filtration (10000 MWCO) in recovering even the smallest environmental microorganisms was coupled with high-throughput DNA sequencing to depict an informative spectrum of the neglected microbial diversity. Our results revealed that the composition of bacterial communities varies across the plant system: Parcubacteria (OD1) superphylum is found mainly in treated water, while groundwater has the highest heterogeneity, encompassing non-OD1 candidate phyla (Microgenomates, Saccharibacteria, Dependentiae, OP3, OP1, BRC1, WS3). Carbon filters probably act as substrate for microorganism growth and contribute to seeding water downstream, since chlorination does not modify the incoming bacterial community. New questions arise about the role of microbial dark matter in drinking water. Indeed, our results suggest that these bacteria might play a central role in the microbial dynamics of drinking water. PMID:28290543

Exploring the under-investigated "microbial dark matter" of drinking water treatment plants.

PubMed

Bruno, Antonia; Sandionigi, Anna; Rizzi, Ermanno; Bernasconi, Marzia; Vicario, Saverio; Galimberti, Andrea; Cocuzza, Clementina; Labra, Massimo; Casiraghi, Maurizio

2017-03-14

Scientists recently reported the unexpected detection of unknown or poorly studied bacterial diversity in groundwater. The ability to uncover this neglected biodiversity mainly derives from technical improvements, and the term "microbial dark matter" was used to group taxa poorly investigated and not necessarily monophyletic. We focused on such under-investigated microbial dark matter of drinking water treatment plant from groundwater, across carbon filters, to post-chlorination. We tackled this topic using an integrated approach where the efficacy of stringent water filtration (10000 MWCO) in recovering even the smallest environmental microorganisms was coupled with high-throughput DNA sequencing to depict an informative spectrum of the neglected microbial diversity. Our results revealed that the composition of bacterial communities varies across the plant system: Parcubacteria (OD1) superphylum is found mainly in treated water, while groundwater has the highest heterogeneity, encompassing non-OD1 candidate phyla (Microgenomates, Saccharibacteria, Dependentiae, OP3, OP1, BRC1, WS3). Carbon filters probably act as substrate for microorganism growth and contribute to seeding water downstream, since chlorination does not modify the incoming bacterial community. New questions arise about the role of microbial dark matter in drinking water. Indeed, our results suggest that these bacteria might play a central role in the microbial dynamics of drinking water.

Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales

DOE Office of Scientific and Technical Information (OSTI.GOV)

Daly, Rebecca A.; Borton, Mikayla A.; Wilkins, Michael J.

Hydraulic fracturing is the industry standard for extracting hydrocarbons from shale formations. Attention has been paid to the economic benefits and environmental impacts of this process, yet the biogeochemical changes induced in the deep subsurface are poorly understood. Recent single-gene investigations revealed that halotolerant microbial communities were enriched after hydraulic fracturing. Here the reconstruction of 31 unique genomes coupled to metabolite data from the Marcellus and Utica shales revealed that methylamine cycling supports methanogenesis in the deep biosphere. Fermentation of injected chemical additives also sustains long-term microbial persistence, while sulfide generation from thiosulfate represents a poorly recognized corrosion mechanism inmore » shales. Extensive links between viruses and microbial hosts demonstrate active viral predation, which may contribute to the release of labile cellular constituents into the extracellular environment. Our analyses show that hydraulic fracturing provides the organismal and chemical inputs for colonization and persistence in the deep terrestrial subsurface.« less

Changes in microbial community characteristics and soil organic matter with nitrogen additions in two tropical forests.

PubMed

Cusack, Daniela F; Silver, Whendee L; Torn, Margaret S; Burton, Sarah D; Firestone, Mary K

2011-03-01

Microbial communities and their associated enzyme activities affect the amount and chemical quality of carbon (C) in soils. Increasing nitrogen (N) deposition, particularly in N-rich tropical forests, is likely to change the composition and behavior of microbial communities and feed back on ecosystem structure and function. This study presents a novel assessment of mechanistic links between microbial responses to N deposition and shifts in soil organic matter (SOM) quality and quantity. We used phospholipid fatty acid (PLFA) analysis and microbial enzyme assays in soils to assess microbial community responses to long-term N additions in two distinct tropical rain forests. We used soil density fractionation and 13C nuclear magnetic resonance (NMR) spectroscopy to measure related changes in SOM pool sizes and chemical quality. Microbial biomass increased in response to N fertilization in both tropical forests and corresponded to declines in pools of low-density SOM. The chemical quality of this soil C pool reflected ecosystem-specific changes in microbial community composition. In the lower-elevation forest, there was an increase in gram-negative bacteria PLFA biomass, and there were significant losses of labile C chemical groups (O-alkyls). In contrast, the upper-elevation tropical forest had an increase in fungal PLFAs with N additions and declines in C groups associated with increased soil C storage (alkyls). The dynamics of microbial enzymatic activities with N addition provided a functional link between changes in microbial community structure and SOM chemistry. Ecosystem-specific changes in microbial community composition are likely to have far-reaching effects on soil carbon storage and cycling. This study indicates that microbial communities in N-rich tropical forests can be sensitive to added N, but we can expect significant variability in how ecosystem structure and function respond to N deposition among tropical forest types.

Source tracking swine fecal waste in surface water proximal to swine concentrated animal feeding operations

PubMed Central

Heaney, Christopher D.; Myers, Kevin; Wing, Steve; Hall, Devon; Baron, Dothula; Stewart, Jill R.

2015-01-01

Swine farming has gone through many changes in the last few decades, resulting in operations with a high animal density known as confined animal feeding operations (CAFOs). These operations produce a large quantity of fecal waste whose environmental impacts are not well understood. The purpose of this study was to investigate microbial water quality in surface waters proximal to swine CAFOs including microbial source tracking of fecal microbes specific to swine. For one year, surface water samples at up- and downstream sites proximal to swine CAFO lagoon waste land application sites were tested for fecal indicator bacteria (fecal coliforms, Escherichia coli and Enterococcus) and candidate swine-specific microbial source-tracking (MST) markers (Bacteroidales Pig-1-Bac, Pig-2-Bac, and Pig-Bac-2, and methanogen P23-2). Testing of 187 samples showed high fecal indicator bacteria concentrations at both up- and downstream sites. Overall, 40%, 23%, and 61% of samples exceeded state and federal recreational water quality guidelines for fecal coliforms, E. coli, and Enterococcus, respectively. Pig-1-Bac and Pig-2-Bac showed the highest specificity to swine fecal wastes and were 2.47 (95% confidence interval [CI] = 1.03, 5.94) and 2.30 times (95% CI = 0.90, 5.88) as prevalent proximal down- than proximal upstream of swine CAFOs, respectively. Pig-1-Bac and Pig-2-Bac were also 2.87 (95% CI = 1.21, 6.80) and 3.36 (95% CI = 1.34, 8.41) times as prevalent when 48 hour antecedent rainfall was greater than versus less than the mean, respectively. Results suggest diffuse and overall poor sanitary quality of surface waters where swine CAFO density is high. Pig-1-Bac and Pig-2-Bac are useful for tracking off-site conveyance of swine fecal wastes into surface waters proximal to and downstream of swine CAFOs and during rain events. PMID:25600418

Source tracking swine fecal waste in surface water proximal to swine concentrated animal feeding operations.

PubMed

Heaney, Christopher D; Myers, Kevin; Wing, Steve; Hall, Devon; Baron, Dothula; Stewart, Jill R

2015-04-01

Swine farming has gone through many changes in the last few decades, resulting in operations with a high animal density known as confined animal feeding operations (CAFOs). These operations produce a large quantity of fecal waste whose environmental impacts are not well understood. The purpose of this study was to investigate microbial water quality in surface waters proximal to swine CAFOs including microbial source tracking of fecal microbes specific to swine. For one year, surface water samples at up- and downstream sites proximal to swine CAFO lagoon waste land application sites were tested for fecal indicator bacteria (fecal coliforms, Escherichia coli and Enterococcus) and candidate swine-specific microbial source-tracking (MST) markers (Bacteroidales Pig-1-Bac, Pig-2-Bac, and Pig-Bac-2, and methanogen P23-2). Testing of 187 samples showed high fecal indicator bacteria concentrations at both up- and downstream sites. Overall, 40%, 23%, and 61% of samples exceeded state and federal recreational water quality guidelines for fecal coliforms, E. coli, and Enterococcus, respectively. Pig-1-Bac and Pig-2-Bac showed the highest specificity to swine fecal wastes and were 2.47 (95% confidence interval [CI]=1.03, 5.94) and 2.30 times (95% CI=0.90, 5.88) as prevalent proximal down- than proximal upstream of swine CAFOs, respectively. Pig-1-Bac and Pig-2-Bac were also 2.87 (95% CI=1.21, 6.80) and 3.36 (95% CI=1.34, 8.41) times as prevalent when 48 hour antecedent rainfall was greater than versus less than the mean, respectively. Results suggest diffuse and overall poor sanitary quality of surface waters where swine CAFO density is high. Pig-1-Bac and Pig-2-Bac are useful for tracking off-site conveyance of swine fecal wastes into surface waters proximal to and downstream of swine CAFOs and during rain events. Copyright © 2014 Elsevier B.V. All rights reserved.

Physicochemical and biological quality of soil in hexavalent chromium-contaminated soils as affected by chemical and microbial remediation.

PubMed

Liao, Yingping; Min, Xiaobo; Yang, Zhihui; Chai, Liyuan; Zhang, Shujuan; Wang, Yangyang

2014-01-01

Chemical and microbial methods are the main remediation technologies for chromium-contaminated soil. These technologies have progressed rapidly in recent years; however, there is still a lack of methods for evaluating the chemical and biological quality of soil after different remediation technologies have been applied. In this paper, microbial remediation with indigenous bacteria and chemical remediation with ferrous sulphate were used for the remediation of soils contaminated with Cr(VI) at two levels (80 and 1,276 mg kg(-1)) through a column leaching experiment. After microbial remediation with indigenous bacteria, the average concentration of water-soluble Cr(VI) in the soils was reduced to less than 5.0 mg kg(-1). Soil quality was evaluated based on 11 soil properties and the fuzzy comprehensive assessment method, including fuzzy mathematics and correlative analysis. The chemical fertility quality index was improved by one grade using microbial remediation with indigenous bacteria, and the biological fertility quality index increased by at least a factor of 6. Chemical remediation with ferrous sulphate, however, resulted in lower levels of available phosphorus, dehydrogenase, catalase and polyphenol oxidase. The result showed that microbial remediation with indigenous bacteria was more effective for remedying Cr(VI)-contaminated soils with high pH value than chemical remediation with ferrous sulphate. In addition, the fuzzy comprehensive evaluation method was proven to be a useful tool for monitoring the quality change in chromium-contaminated soils.

Geochemical control of microbial Fe(III) reduction potential in wetlands: Comparison of the rhizosphere to non-rhizosphere soil

USGS Publications Warehouse

Weiss, J.V.; Emerson, D.; Megonigal, J.P.

2004-01-01

We compared the reactivity and microbial reduction potential of Fe(III) minerals in the rhizosphere and non-rhizosphere soil to test the hypothesis that rapid Fe(III) reduction rates in wetland soils are explained by rhizosphere processes. The rhizosphere was defined as the area immediately adjacent to a root encrusted with Fe(III)-oxides or Fe plaque, and non-rhizosphere soil was 0.5 cm from the root surface. The rhizosphere had a significantly higher percentage of poorly crystalline Fe (66??7%) than non-rhizosphere soil (23??7%); conversely, non-rhizosphere soil had a significantly higher proportion of crystalline Fe (50??7%) than the rhizosphere (18??7%, P<0.05 in all cases). The percentage of poorly crystalline Fe(III) was significantly correlated with the percentage of FeRB (r=0.76), reflecting the fact that poorly crystalline Fe(III) minerals are labile with respect to microbial reduction. Abiotic reductive dissolution consumed about 75% of the rhizosphere Fe(III)-oxide pool in 4 h compared to 23% of the soil Fe(III)-oxide pool. Similarly, microbial reduction consumed 75-80% of the rhizosphere pool in 10 days compared to 30-40% of the non-rhizosphere soil pool. Differences between the two pools persisted when samples were amended with an electron-shuttling compound (AQDS), an Fe(III)-reducing bacterium (Geobacter metallireducens), and organic carbon. Thus, Fe(III)-oxide mineralogy contributed strongly to differences in the Fe(III) reduction potential of the two pools. Higher amounts of poorly crystalline Fe(III) and possibly humic substances, and a higher Fe(III) reduction potential in the rhizosphere compared to the non-rhizosphere soil, suggested the rhizosphere is a site of unusually active microbial Fe cycling. The results were consistent with previous speculation that rapid Fe cycling in wetlands is due to the activity of wetland plant roots. ?? 2004 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.

Quality assessment of commercially supplied drinking jar water in Chittagong City, Bangladesh

NASA Astrophysics Data System (ADS)

Mina, Sohana Akter; Marzan, Lolo Wal; Sultana, Tasrin; Akter, Yasmin

2018-03-01

Chittagong is the second most populated city in Bangladesh where drinking water is supplied using small jar. Water quality is an important concern for the consumers and, therefore, the present study was done by collecting 38 drinking jar water samples from Chittagong City, Bangladesh to determine the microbial contamination and physiochemical properties. Molecular study was done by the PCR amplification of 16SrDNA, LacZ and uidA gene for the identification of bacteria, coliform and fecal coliform. TVC, MPN and different biochemical test were done for enumeration and identification. TDS, pH, and metals (Fe, As, Pb and Cr) concentration were also measured. No heavy metal (As, Pb and Cr) was found in any of the water samples but Fe was detected in low concentrations (0.02-0.05 mg/l). TDS and pH level were normal in all samples. But microbial contaminations were (60.53 and 50%) recorded in molecular and biochemical test, respectively. The range of total bacterial count was (1.5 × 102-1.6 × 104) cfu/ml. The total coliform count (TCCm) was recorded (14-40) in 100 ml of water samples. The presence of total coliform and fecal coliform was 26.32 and 18.42%, respectively, in PCR analysis but in biochemical test those were 18.42 and 15.78%, respectively. A total of 11 bacterial species: Enterobacter aerogenes, Escherrichia coli, Aeromonas, Bacillus sp., Cardiobacterium, Corynebacterium, Clostridium, Klebsiella sp., Lactobacillus, Micrococcus sp., Pseudomonas sp. were found. This study indicates that some of the drinking jar water samples were of poor quality which may increase the risk of water-borne disease. Hence, the producer of drinking jar water has to implement necessary quality control steps.

Eutrophication triggers contrasting multilevel feedbacks on litter accumulation and decomposition in fens.

PubMed

Emsens, W-J; Aggenbach, C J S; Grootjans, A P; Nfor, E E; Schoelynck, J; Struyf, E; van Diggelen, R

2016-10-01

Eutrophication is a major threat for the persistence of nutrient-poor fens, as multilevel feedbacks on decomposition rates could trigger carbon loss and increase nutrient cycling. Here, we experimentally investigate the effects of macronutrient (NPK) enrichment on litter quality of six species of sedge (Carex sp.), which we relate to litter decomposition rates in a nutrient-poor and nutrient-rich environment. Our research focused on four levels: we examined how eutrophication alters (1) fresh litter production ("productivity shift"), (2) litter stoichiometry within the same species ("intraspecific shift"), (3) overall litter stoichiometry of the vegetation under the prediction that low-competitive species are outcompeted by fast-growing competitors ("interspecific shift"), and (4) litter decomposition rates due to an altered external environment (e.g., shifts in microbial activity; "exogenous shift"). Eutrophication triggered a strong increase in fresh litter production. Moreover, individuals of the same species produced litter with lower C:N and C:P ratios, higher K contents, and lower lignin, Ca and Mg contents (intraspecific shift), which increased litter decomposability. In addition, species typical for eutrophic conditions produced more easily degradable litter than did species typical for nutrient-poor conditions (interspecific shift). However, the effects of nutrient loading of the external environment (exogenous shift) were contradictory. Here, interactions between litter type and ambient nutrient level indicate that the (exogenous) effects of eutrophication on litter decomposition rates are strongly dependent of litter quality. Moreover, parameters of litter quality only correlated with decomposition rates for litter incubated in nutrient-poor environments, but not in eutrophic environments. This suggests that rates of litter decomposition can be uncoupled from litter stoichiometry under eutrophic conditions. In conclusion, our results show that eutrophication affects litter accumulation and -decomposition at multiple levels, in which stimulatory and inhibitory effects interact. The cumulative effect of these interactions ultimately determine whether peatlands remain sinks or become sources of carbon under eutrophic conditions. © 2016 by the Ecological Society of America.

Microbial Indicators of Soil Quality under Different Land Use Systems in Subtropical Soils

NASA Astrophysics Data System (ADS)

Maharjan, M.

2016-12-01

Land-use change from native forest to intensive agricultural systems can negatively impact numerous soil parameters. Understanding the effects of forest ecosystem transformations on markers of long-term soil health is particularly important in rapidly developing regions such as Nepal, where unprecedented levels of agriculturally-driven deforestation have occurred in recent decades. However, the effects of widespread land use changes on soil quality in this region have yet to be properly characterized. Microbial indicators (soil microbial biomass, metabolic quotient and enzymes activities) are particularly suited to assessing the consequences of such ecosystem disturbances, as microbial communities are especially sensitive to environmental change. Thus, the aim of this study was to assess the effect of land use system; i.e. forest, organic and conventional farming, on soil quality in Chitwan, Nepal using markers of microbial community size and activity. Total organic C and N contents were higher in organic farming compared with conventional farming and forest, suggesting higher nutrient retention and soil preservation with organic farming practices compared to conventional. These differences in soil composition were reflected in the health of the soil microbial communities: Organic farm soil exhibited higher microbial biomass C, elevated β-glucosidase and chitinase activities, and a lower metabolic quotient relative to other soils, indicating a larger, more active, and less stressed microbial community, respectively. These results collectively demonstrate that application of organic fertilizers and organic residues positively influence nutrient availability, with subsequent improvements in soil quality and productivity. Furthermore, the sensitivity of microbial indicators to different management practices demonstrated in this study supports their use as effective markers of ecosystem disturbance in subtropical soils.

Microbial translocation and microbiome dsybiosis in HIV-associated immune activation

PubMed Central

Zevin, Alexander S.; McKinnon, Lyle; Burgener, Adam; Klatt, Nichole R.

2016-01-01

Purpose of Review To describe the mechanisms and consequences of both microbial translocation and microbial dysbiosis in HIV infection. Recent Findings Microbes in HIV are likely playing a large role in contributing to HIV pathogenesis, morbidities and mortality. Two major disruptions to microbial systems in HIV infection include microbial translocation and microbiome dysbiosis. Microbial translocation occurs when the bacteria (or bacterial products) that should be in the lumen of the intestine translocate across the tight epithelial barrier into systemic circulation, where they contribute to inflammation and pathogenesis. This is associated with poorer health outcomes in HIV infected individuals. In addition, microbial populations in the GI tract are also altered after HIV infection, resulting in microbiome dysbiosis, which further exacerbates microbial translocation, epithelial barrier disruption, inflammation, and mucosal immune functioning. Summary Altered microbial regulation in HIV infection can lead to poor health outcomes, and understanding the mechanisms underlying microbial dysbiosis and translocation may result in novel pathways for therapeutic interventions. PMID:26679414

Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate

PubMed Central

Bokulich, Nicholas A.; Thorngate, John H.; Richardson, Paul M.; Mills, David A.

2014-01-01

Wine grapes present a unique biogeography model, wherein microbial biodiversity patterns across viticultural zones not only answer questions of dispersal and community maintenance, they are also an inherent component of the quality, consumer acceptance, and economic appreciation of a culturally important food product. On their journey from the vineyard to the wine bottle, grapes are transformed to wine through microbial activity, with indisputable consequences for wine quality parameters. Wine grapes harbor a wide range of microbes originating from the surrounding environment, many of which are recognized for their role in grapevine health and wine quality. However, determinants of regional wine characteristics have not been identified, but are frequently assumed to stem from viticultural or geological factors alone. This study used a high-throughput, short-amplicon sequencing approach to demonstrate that regional, site-specific, and grape-variety factors shape the fungal and bacterial consortia inhabiting wine-grape surfaces. Furthermore, these microbial assemblages are correlated to specific climatic features, suggesting a link between vineyard environmental conditions and microbial inhabitation patterns. Taken together, these factors shape the unique microbial inputs to regional wine fermentations, posing the existence of nonrandom “microbial terroir” as a determining factor in regional variation among wine grapes. PMID:24277822

Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate.

PubMed

Bokulich, Nicholas A; Thorngate, John H; Richardson, Paul M; Mills, David A

2014-01-07

Wine grapes present a unique biogeography model, wherein microbial biodiversity patterns across viticultural zones not only answer questions of dispersal and community maintenance, they are also an inherent component of the quality, consumer acceptance, and economic appreciation of a culturally important food product. On their journey from the vineyard to the wine bottle, grapes are transformed to wine through microbial activity, with indisputable consequences for wine quality parameters. Wine grapes harbor a wide range of microbes originating from the surrounding environment, many of which are recognized for their role in grapevine health and wine quality. However, determinants of regional wine characteristics have not been identified, but are frequently assumed to stem from viticultural or geological factors alone. This study used a high-throughput, short-amplicon sequencing approach to demonstrate that regional, site-specific, and grape-variety factors shape the fungal and bacterial consortia inhabiting wine-grape surfaces. Furthermore, these microbial assemblages are correlated to specific climatic features, suggesting a link between vineyard environmental conditions and microbial inhabitation patterns. Taken together, these factors shape the unique microbial inputs to regional wine fermentations, posing the existence of nonrandom "microbial terroir" as a determining factor in regional variation among wine grapes.

Precipitation Effects on Microbial Pollution in a River: Lag Structures and Seasonal Effect Modification

PubMed Central

Tornevi, Andreas; Bergstedt, Olof; Forsberg, Bertil

2014-01-01

Background The river Göta Älv is a source of freshwater for 0.7 million swedes. The river is subject to contamination from sewer systems discharge and runoff from agricultural lands. Climate models projects an increase in precipitation and heavy rainfall in this region. This study aimed to determine how daily rainfall causes variation in indicators of pathogen loads, to increase knowledge of variations in river water quality and discuss implications for risk management. Methods Data covering 7 years of daily monitoring of river water turbidity and concentrations of E. coli, Clostridium and coliforms were obtained, and their short-term variations in relation with precipitation were analyzed with time series regression and non-linear distributed lag models. We studied how precipitation effects varied with season and compared different weather stations for predictive ability. Results Generally, the lowest raw water quality occurs 2 days after rainfall, with poor raw water quality continuing for several more days. A rainfall event of >15 mm/24-h (local 95 percentile) was associated with a three-fold higher concentration of E. coli and 30% higher turbidity levels (lag 2). Rainfall was associated with exponential increases in concentrations of indicator bacteria while the effect on turbidity attenuated with very heavy rainfall. Clear associations were also observed between consecutive days of wet weather and decreased water quality. The precipitation effect on increased levels of indicator bacteria was significant in all seasons. Conclusions Rainfall elevates microbial risks year-round in this river and freshwater source and acts as the main driver of varying water quality. Heavy rainfall appears to be a better predictor of fecal pollution than water turbidity. An increase of wet weather and extreme events with climate change will lower river water quality even more, indicating greater challenges for drinking water producers, and suggesting better control of sources of pollution. PMID:24874010

Advanced nutrient removal from surface water by a consortium of attached microalgae and bacteria: A review.

PubMed

Liu, Junzhuo; Wu, Yonghong; Wu, Chenxi; Muylaert, Koenraad; Vyverman, Wim; Yu, Han-Qing; Muñoz, Raúl; Rittmann, Bruce

2017-10-01

Innovative and cost-effective technologies for advanced nutrient removal from surface water are urgently needed for improving water quality. Conventional biotechnologies, such as ecological floating beds, or constructed wetlands, are not effective in removing nutrients present at low-concentration. However, microalgae-bacteria consortium is promising for advanced nutrient removal from wastewater. Suspended algal-bacterial systems can easily wash out unless the hydraulic retention time is long, attached microalgae-bacteria consortium is more realistic. This critical review summarizes the fundamentals and status of attached microalgae-bacteria consortium for advanced nutrient removal from surface water. Key advantages are the various nutrient removal pathways, reduction of nutrients to very low concentration, and diversified photobioreactor configurations. Challenges include poor identification of functional species, poor control of the community composition, and long start-up times. Future research should focus on the selection and engineering of robust microbial species, mathematical modelling of the composition and functionality of the consortium, and novel photobioreactor configurations. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evaluation of Shiraz wastewater treatment plant effluent quality for agricultural irrigation by Canadian Water Quality Index (CWQI)

PubMed Central

2013-01-01

Background Using treated wastewater in agriculture irrigation could be a realistic solution for the shortage of fresh water in Iran, however, it is associated with environmental and health threats; therefore, effluent quality assessment is quite necessary before use. The present study aimed to evaluate the physicochemical and microbial quality of Shiraz wastewater treatment plant effluent for being used in agricultural irrigation. In this study, 20 physicochemical and 3 microbial parameters were measured during warm (April to September) and cold months (October to march). Using the measured parameters and the Canadian Water Quality Index, the quality of the effluent was determined in both warm and cold seasons and in all the seasons together. Results The calculated index for the physicochemical parameters in the effluent was equal (87) in warm and cold months and it was obtained as 85 for the seasons all together. When the microbial parameters were used in order to calculate the index, it declined to 67 in warm and cold seasons and 64 in all the seasons together. Also, it was found that three physicochemical parameters (TDS, EC, and NO3) and three microbial parameters (Fecal coliform, Helminthes egg, and Total coliform) had the most contribution to the reduction of the index value. Conclusions The results showed that the physicochemical quality of Shiraz Wastewater Treatment Plant Effluent was good for irrigation in the warm, cold, and total of the two kinds of seasons. However, by applying the microbial parameter, the index value declined dramatically and the quality of the effluent was marginal. PMID:23566673

Plant–microbial competition for nitrogen increases microbial activities and carbon loss in invaded soils

Treesearch

Matthew E. Craig; Jennifer M. Fraterrigo

2017-01-01

Many invasive plant species show high rates of nutrient acquisition relative to their competitors. Yet the mechanisms underlying this phenomenon, and its implications for ecosystem functioning, are poorly understood, particularly in nutrient-limited systems. Here, we test the hypothesis that an invasive plant species (Microstegium vimineum...

Using blue mussels (Mytilus spp.) as biosentinels of Cryptosporidium spp. and Toxoplasma gondii contamination in marine aquatic environments

USDA-ARS?s Scientific Manuscript database

Methods to monitor microbial contamination typically involve collecting discrete samples at specific time-points and analyzing for a single contaminant. While informative, many of these methods suffer from poor recovery rates and only provide a snapshot of the microbial load at the time of collectio...

Microbial characterization of probiotics–Advisory report of the Working Group “8651 Probiotics” of the Belgian Superior Health Council (SHC)

PubMed Central

Huys, Geert; Botteldoorn, Nadine; Delvigne, Frank; Vuyst, Luc De; Heyndrickx, Marc; Pot, Bruno; Dubois, Jean-Jacques; Daube, Georges

2013-01-01

When ingested in sufficient numbers, probiotics are expected to confer one or more proven health benefits on the consumer. Theoretically, the effectiveness of a probiotic food product is the sum of its microbial quality and its functional potential. Whereas the latter may vary much with the body (target) site, delivery mode, human target population, and health benefit envisaged microbial assessment of the probiotic product quality is more straightforward. The range of stakeholders that need to be informed on probiotic quality assessments is extremely broad, including academics, food and biotherapeutic industries, healthcare professionals, competent authorities, consumers, and professional press. In view of the rapidly expanding knowledge on this subject, the Belgian Superior Health Council installed Working Group “8651 Probiotics” to review the state of knowledge regarding the methodologies that make it possible to characterize strains and products with purported probiotic activity. This advisory report covers three main steps in the microbial quality assessment process, i.e. (i) correct species identification and strain-specific typing of bacterial and yeast strains used in probiotic applications, (ii) safety assessment of probiotic strains used for human consumption, and (iii) quality of the final probiotic product in terms of its microbial composition, concentration, stability, authenticity, and labeling. PMID:23801655

The relationships between microbiological attributes and soil and litter quality in pure and mixed stands of native tree species in southeastern Bahia, Brazil.

PubMed

Gama-Rodrigues, Emanuela F; Gama-Rodrigues, Antonio Carlos; Barros, Nairam F; Moço, Maria Kellen S

2011-11-01

This study was conducted to link soil and litter microbial biomass and activity with soil and litter quality in the surface layer for different pure and mixed stands of native tree species in southeastern Bahia, Brazil. The purpose of the study was to see how strongly the differences among species and stands affect the microbiological attributes of the soil and to identify how microbial processes can be influenced by soil and litter quality. Soil and litter samples were collected from six pure and mixed stands of six hardwood species (Peltogyne angustifolia, Centrolobium robustum, Arapatiella psilophylla, Sclerolobium chrysophyllum, Cordia trichotoma, Macrolobium latifolium) native to the southeastern region of Bahia, Brazil. In plantations of native tree species in humid tropical regions, the immobilization efficiency of C and N by soil microbial biomass was strongly related to the chemical quality of the litter and to the organic matter quality of the soil. According to the variables analyzed, the mixed stand was similar to the natural forest and dissimilar to the pure stands. Litter microbial biomass represented a greater sink of C and N than soil microbial biomass and is an important contributor of resources to tropical soils having low C and N availability.

Good Manufacturing Practices and Microbial Contamination Sources in Orange Fleshed Sweet Potato Puree Processing Plant in Kenya

PubMed Central

Abong', George Ooko

2018-01-01

Limited information exists on the status of hygiene and probable sources of microbial contamination in Orange Fleshed Sweet Potato (OFSP) puree processing. The current study is aimed at determining the level of compliance to Good Manufacturing Practices (GMPs), hygiene, and microbial quality in OFSP puree processing plant in Kenya. Intensive observation and interviews using a structured GMPs checklist, environmental sampling, and microbial analysis by standard microbiological methods were used in data collection. The results indicated low level of compliance to GMPs with an overall compliance score of 58%. Microbial counts on food equipment surfaces, installations, and personnel hands and in packaged OFSP puree were above the recommended microbial safety and quality legal limits. Steaming significantly (P < 0.05) reduced microbial load in OFSP cooked roots but the counts significantly (P < 0.05) increased in the puree due to postprocessing contamination. Total counts, yeasts and molds, Enterobacteriaceae, total coliforms, and E. coli and S. aureus counts in OFSP puree were 8.0, 4.0, 6.6, 5.8, 4.8, and 5.9 log10 cfu/g, respectively. In conclusion, equipment surfaces, personnel hands, and processing water were major sources of contamination in OFSP puree processing and handling. Plant hygiene inspection, environmental monitoring, and food safety trainings are recommended to improve hygiene, microbial quality, and safety of OFSP puree. PMID:29808161

Good Manufacturing Practices and Microbial Contamination Sources in Orange Fleshed Sweet Potato Puree Processing Plant in Kenya.

PubMed

Malavi, Derick Nyabera; Muzhingi, Tawanda; Abong', George Ooko

2018-01-01

Limited information exists on the status of hygiene and probable sources of microbial contamination in Orange Fleshed Sweet Potato (OFSP) puree processing. The current study is aimed at determining the level of compliance to Good Manufacturing Practices (GMPs), hygiene, and microbial quality in OFSP puree processing plant in Kenya. Intensive observation and interviews using a structured GMPs checklist, environmental sampling, and microbial analysis by standard microbiological methods were used in data collection. The results indicated low level of compliance to GMPs with an overall compliance score of 58%. Microbial counts on food equipment surfaces, installations, and personnel hands and in packaged OFSP puree were above the recommended microbial safety and quality legal limits. Steaming significantly ( P < 0.05) reduced microbial load in OFSP cooked roots but the counts significantly ( P < 0.05) increased in the puree due to postprocessing contamination. Total counts, yeasts and molds, Enterobacteriaceae, total coliforms, and E. coli and S. aureus counts in OFSP puree were 8.0, 4.0, 6.6, 5.8, 4.8, and 5.9 log 10 cfu/g, respectively. In conclusion, equipment surfaces, personnel hands, and processing water were major sources of contamination in OFSP puree processing and handling. Plant hygiene inspection, environmental monitoring, and food safety trainings are recommended to improve hygiene, microbial quality, and safety of OFSP puree.

Strong linkage between active microbial communities and microbial carbon usage in a deglaciated terrain of the High Arctic

NASA Astrophysics Data System (ADS)

Kim, M.; Gyeong, H. R.; Lee, Y. K.

2017-12-01

Soil microorganisms play pivotal roles in ecosystem development and carbon cycling in newly exposed glacier forelands. However, little is known about carbon utilization pattern by metabolically active microbes over the course of ecosystem succession in these nutrient-poor environments. We investigated RNA-based microbial community dynamics and its relation to microbial carbon usage along the chronosequence of a High Arctic glacier foreland. Among microbial taxa surveyed (bacteria, archaea and fungi), bacteria are among the most metabolically active taxa with a dominance of Cyanobacteria and Actinobacteria. There was a strong association between microbial carbon usage and active Actinobacterial communities, suggesting that member of Actinobacteria are actively involved in organic carbon degradation in glacier forelands. Both bacterial community and microbial carbon usage are converged towards later stage of succession, indicating that the composition of soil organic carbon plays important roles in structuring bacterial decomposer communities during ecosystem development.

Effects of inorganic and organic amendment on soil chemical properties, enzyme activities, microbial community and soil quality in yellow clayey soil.

PubMed

Liu, Zhanjun; Rong, Qinlei; Zhou, Wei; Liang, Guoqing

2017-01-01

Understanding the effects of external organic and inorganic components on soil fertility and quality is essential for improving low-yielding soils. We conducted a field study over two consecutive rice growing seasons to investigate the effect of applying chemical fertilizer (NPK), NPK plus green manure (NPKG), NPK plus pig manure (NPKM), and NPK plus straw (NPKS) on the soil nutrient status, enzyme activities involved in C, N, P, and S cycling, microbial community and rice yields of yellow clayey soil. Results showed that the fertilized treatments significantly improved rice yields over the first three experimental seasons. Compared with the NPK treatment, organic amendments produced more favorable effects on soil productivity. Notably, the NPKM treatment exhibited the highest levels of nutrient availability, microbial biomass carbon (MBC), activities of most enzymes and the microbial community. This resulted in the highest soil quality index (SQI) and rice yield, indicating better soil fertility and quality. Significant differences in enzyme activities and the microbial community were observed among the treatments, and redundancy analysis showed that MBC and available N were the key determinants affecting the soil enzyme activities and microbial community. The SQI score of the non-fertilized control (0.72) was comparable to that of the NPK (0.77), NPKG (0.81) and NPKS (0.79) treatments but significantly lower compared with NPKM (0.85). The significant correlation between rice yield and SQI suggests that SQI can be a useful to quantify soil quality changes caused by different agricultural management practices. The results indicate that application of NPK plus pig manure is the preferred option to enhance SOC accumulation, improve soil fertility and quality, and increase rice yield in yellow clayey soil.

Effects of inorganic and organic amendment on soil chemical properties, enzyme activities, microbial community and soil quality in yellow clayey soil

PubMed Central

Liu, Zhanjun; Rong, Qinlei; Zhou, Wei; Liang, Guoqing

2017-01-01

Understanding the effects of external organic and inorganic components on soil fertility and quality is essential for improving low-yielding soils. We conducted a field study over two consecutive rice growing seasons to investigate the effect of applying chemical fertilizer (NPK), NPK plus green manure (NPKG), NPK plus pig manure (NPKM), and NPK plus straw (NPKS) on the soil nutrient status, enzyme activities involved in C, N, P, and S cycling, microbial community and rice yields of yellow clayey soil. Results showed that the fertilized treatments significantly improved rice yields over the first three experimental seasons. Compared with the NPK treatment, organic amendments produced more favorable effects on soil productivity. Notably, the NPKM treatment exhibited the highest levels of nutrient availability, microbial biomass carbon (MBC), activities of most enzymes and the microbial community. This resulted in the highest soil quality index (SQI) and rice yield, indicating better soil fertility and quality. Significant differences in enzyme activities and the microbial community were observed among the treatments, and redundancy analysis showed that MBC and available N were the key determinants affecting the soil enzyme activities and microbial community. The SQI score of the non-fertilized control (0.72) was comparable to that of the NPK (0.77), NPKG (0.81) and NPKS (0.79) treatments but significantly lower compared with NPKM (0.85). The significant correlation between rice yield and SQI suggests that SQI can be a useful to quantify soil quality changes caused by different agricultural management practices. The results indicate that application of NPK plus pig manure is the preferred option to enhance SOC accumulation, improve soil fertility and quality, and increase rice yield in yellow clayey soil. PMID:28263999

Effects of gamma irradiation on microbial safety and quality of stir fry chicken dices with hot chili during storage

NASA Astrophysics Data System (ADS)

Chen, Qian; Cao, Mei; Chen, Hao; Gao, Peng; Fu, Yi; Liu, Mianxue; Wang, Yan; Huang, Min

2016-10-01

The purpose of this study was to investigate effects of irradiation with different doses on microbial safety, sensory quality and protein content of ready-to-eat stir fry chicken dices with hot chili (FCC) during one year storage. Fresh chicken meat was cut into small dices and fried at approximately 180 °C for 10 min for preparation of FCC samples. The samples were vacuum-packaged and gamma irradiated at 10, 20, 30 and 40 kGy. The results suggest that irradiation with the doses of 10 and 20 kGy could ensure microbiological safety of the samples without deterioration of sensory quality. Microbial counts, sensory qualities and protein contents of the samples were investigated during one year storage. No viable cells were observed and the samples were completely sterilized. Sensory qualities showed no significant difference after irradiated at the doses of 10 and 20 kGy during the storage period. Protein contents were also not affected by irradiation at the same doses. Our results indicate that gamma irradiation of 10 and 20 kGy are effective to maintain shelf stability of ready-to-eat FCC products with microbial safety, sensory quality and nutritional value.

Microbial mineral illization of montmorillonite in low-permeability oil reservoirs for microbial enhanced oil recovery.

PubMed

Cui, Kai; Sun, Shanshan; Xiao, Meng; Liu, Tongjing; Xu, Quanshu; Dong, Honghong; Wang, Di; Gong, Yejing; Sha, Te; Hou, Jirui; Zhang, Zhongzhi; Fu, Pengcheng

2018-05-11

Microbial mineral illization has been investigated for its role in the extraction and recovery of metals from ores. Here we report our application of mineral bioillization for the microbial enhanced oil recovery in low-permeability oil reservoirs. It aimed to reveal the etching mechanism of the four Fe (III)-reducing microbial strains under anaerobic growth conditions on the Ca-montmorillonite. The mineralogical characterization of the Ca-montmorillonite was performed by Fourier transform infrared spectroscopy, X-ray powder diffraction, scanning electron microscopy and energy dispersive spectrometer. Results showed that the microbial strains could efficiently reduce Fe (III) at an optimal rate of 71 %, and alter the crystal lattice structure of the lamella to promote the interlayer cation exchange, and to efficiently inhibit the Ca-montmorillonite swelling at an inhibitory rate of 48.9 %. Importance Microbial mineral illization is ubiquitous in the natural environment. Microbes in low-permeability reservoirs are able to enable the alteration of the structure and phase of the Fe-poor minerals by reducing Fe (III) and inhibiting clay swelling which is still poorly studied. This study aimed to reveal the interaction mechanism between Fe (III)-reducing bacterial strains and Ca-montmorillonite under anaerobic atmosphere, and to investigate the extent and rates of Fe (III) reduction and phase changes with their activities. Application of Fe (III)-reducing bacteria will provide a new way to inhibit clay swelling, to elevate reservoir permeability, and to reduce pore throat resistance after water flooding for enhanced oil recovery in low-permeability reservoirs. Copyright © 2018 American Society for Microbiology.

Evaluation of Microbial Contamination and Chemical Qualities of Cream-filled Pastries in Confectioneries of Chaharmahal Va Bakhtiari Province (Southwestern Iran).

PubMed

Sharifzadeh, Ali; Hajsharifi-Shahreza, Mohammad; Ghasemi-Dehkordi, Payam

2016-12-01

High consumption of bakery products such as cream-filled pastries may cause serious health risks and food poisoning to humans. Therefore, investigation of the microbial and chemical qualities of bakery products containing cream is necessary. The purpose of the present study was to investigate the chemical qualities and microbial contaminations of cream-filled pastries collected from confectioneries located in six cities in Chaharmahal Va Bakhtiari province (Southwestern Iran). Microbial tests and chemical characteristics (fat and acidity level) were done on 228 cream-filled pastries samples that were collected randomly from various confectioneries. After microbial tests, it was found that 33.33% of all samples were contaminated by microbial agents. The microbial tests showed that Shahrekord (10.09%) and Broujen (9.21%) cities had high levels of contamination and in Koohrang (1.31%) it was low compared with the other four cities. High contamination of coliforms (61.84%), staphylococci (48.68%), and yeast (27.63%) were observed in almost all samples. The chemical analysis showed maximum amounts of fat content and titratable acidity in cream-filled pastry samples obtained from Lordegan and Shahrekord cities, respectively. The findings of the present work demonstrated that the microbial contamination and chemical quality of cream-filled pastries produced in confectionaries of Chaharmahal Va Bakhtiari province were not in acceptable ranges. These problems may be related to fecal contamination of cream samples or lack of hygiene by handlers and it is necessary to observe the standards of hygiene and to develop safe food handling techniques and aseptic pastry manufacturing systems in some confectioneries of Chaharmahal Va Bakhtiari province.

Innovative biological approaches for monitoring and improving water quality

PubMed Central

Aracic, Sanja; Manna, Sam; Petrovski, Steve; Wiltshire, Jennifer L.; Mann, Gülay; Franks, Ashley E.

2015-01-01

Water quality is largely influenced by the abundance and diversity of indigenous microbes present within an aquatic environment. Physical, chemical and biological contaminants from anthropogenic activities can accumulate in aquatic systems causing detrimental ecological consequences. Approaches exploiting microbial processes are now being utilized for the detection, and removal or reduction of contaminants. Contaminants can be identified and quantified in situ using microbial whole-cell biosensors, negating the need for water samples to be tested off-site. Similarly, the innate biodegradative processes can be enhanced through manipulation of the composition and/or function of the indigenous microbial communities present within the contaminated environments. Biological contaminants, such as detrimental/pathogenic bacteria, can be specifically targeted and reduced in number using bacteriophages. This mini-review discusses the potential application of whole-cell microbial biosensors for the detection of contaminants, the exploitation of microbial biodegradative processes for environmental restoration and the manipulation of microbial communities using phages. PMID:26322034

Predicting microbial water quality with models: over-arching questions for managing risk in agricultural catchments

USDA-ARS?s Scientific Manuscript database

Determining the microbial quality of recreational, irrigation and shellfish-harvesting waters is important to ensure compliance with health-related standards and associated legislation. Animal faeces represent a significant human health risk, and concentrations of fecal indicator organisms (FIOs) pr...

WATERBORNE DISEASES AND MICROBIAL QUALITY MONITORING FOR RECREATIONAL WATER BODIES USING REGULATORY METHODS

EPA Science Inventory

This chapter will provide the reader with a historical perspective of microbial water quality and monitoring of recreational waters, with special attention to marine environments. It will review the regulations that are currently in effect in the United States and discuss critic...

Rapid determination of soil quality and earthworm impacts on soil microbial communities using fluorescence-based respirometry

NASA Astrophysics Data System (ADS)

Prendergast-Miller, Miranda T.; Thurston, Josh; Taylor, Joe; Helgason, Thorunn; Ashauer, Roman; Hodson, Mark E.

2017-04-01

We applied a fluorescence-based respirometry method currently devised for aquatic ecotoxicology studies to rapidly measure soil microbial oxygen consumption as a function of soil quality. In this study, soil was collected from an arable wheat field and the field margin. These two soil habitats are known to differ in their soil quality due to differences in their use and management as well as plant, microbial and earthworm community. The earthworm Lumbricus terrestris was incubated in arable or margin soil for three weeks. After this initial phase, a transfer experiment was then conducted to test the hypothesis that earthworm 'migration' alters soil microbial community function and diversity. In this transfer experiment, earthworms incubated in margin soil were transferred to arable soil. The converse transfer (i.e. earthworms incubated in arable soil) was also conducted. Soils of each type with no earthworms were also incubated as controls. After a further four week incubation, the impact of earthworm migration on the soil microbial community was tested by measuring oxygen consumption. Replicated soil slurry subsamples were aliquoted into individual respirometer wells (600 μl volume) on a glass 24-well microplate (Loligo Systems, Denmark) fitted with non-invasive, reusable oxygen sensor spots. The sealed microplate was then attached to an oxygen fluorescence sensor (SDR SensorDish Reader, PreSens, Germany). Oxygen consumption was measured in real-time over a 2 hr period following standard operating procedures. Soil microbial activity was measured with and without an added carbon source (glucose or cellulose, 50 mg C L-1). Using this system, we were able to differentiate between soil type, earthworm treatment and C source. Earthworm-driven impacts on soil microbial oxygen consumption were also supported by changes in soil microbial community structure and diversity revealed using DNA-based sequencing techniques. This method provides a simple and rapid system for measuring soil quality and has the potential for use in a variety of scenarios investigating impacts on soil microbial function.

Microbial characterization of probiotics--advisory report of the Working Group "8651 Probiotics" of the Belgian Superior Health Council (SHC).

PubMed

Huys, Geert; Botteldoorn, Nadine; Delvigne, Frank; De Vuyst, Luc; Heyndrickx, Marc; Pot, Bruno; Dubois, Jean-Jacques; Daube, Georges

2013-08-01

When ingested in sufficient numbers, probiotics are expected to confer one or more proven health benefits on the consumer. Theoretically, the effectiveness of a probiotic food product is the sum of its microbial quality and its functional potential. Whereas the latter may vary much with the body (target) site, delivery mode, human target population, and health benefit envisaged microbial assessment of the probiotic product quality is more straightforward. The range of stakeholders that need to be informed on probiotic quality assessments is extremely broad, including academics, food and biotherapeutic industries, healthcare professionals, competent authorities, consumers, and professional press. In view of the rapidly expanding knowledge on this subject, the Belgian Superior Health Council installed Working Group "8651 Probiotics" to review the state of knowledge regarding the methodologies that make it possible to characterize strains and products with purported probiotic activity. This advisory report covers three main steps in the microbial quality assessment process, i.e. (i) correct species identification and strain-specific typing of bacterial and yeast strains used in probiotic applications, (ii) safety assessment of probiotic strains used for human consumption, and (iii) quality of the final probiotic product in terms of its microbial composition, concentration, stability, authenticity, and labeling. © 2013 The Authors. Molecular Nutrition & Food Research published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Substrate and environmental controls on microbial assimilation of soil organic carbon: a framework for Earth System Models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Xiaofeng; Schimel, Joshua; Thornton, Peter E

2014-01-01

Microbial assimilation of soil organic carbon is one of the fundamental processes of global carbon cycling and it determines the magnitude of microbial biomass in soils. Mechanistic understanding of microbial assimilation of soil organic carbon and its controls is important for to improve Earth system models ability to simulate carbon-climate feedbacks. Although microbial assimilation of soil organic carbon is broadly considered to be an important parameter, it really comprises two separate physiological processes: one-time assimilation efficiency and time-dependent microbial maintenance energy. Representing of these two mechanisms is crucial to more accurately simulate carbon cycling in soils. In this study, amore » simple modeling framework was developed to evaluate the substrate and environmental controls on microbial assimilation of soil organic carbon using a new term: microbial annual active period (the length of microbes remaining active in one year). Substrate quality has a positive effect on microbial assimilation of soil organic carbon: higher substrate quality (lower C:N ratio) leads to higher ratio of microbial carbon to soil organic carbon and vice versa. Increases in microbial annual active period from zero stimulate microbial assimilation of soil organic carbon; however, when microbial annual active period is longer than an optimal threshold, increasing this period decreases microbial biomass. The simulated ratios of soil microbial biomass to soil organic carbon are reasonably consistent with a recently compiled global dataset at the biome-level. The modeling framework of microbial assimilation of soil organic carbon and its controls developed in this study offers an applicable ways to incorporate microbial contributions to the carbon cycling into Earth system models for simulating carbon-climate feedbacks and to explain global patterns of microbial biomass.« less

Influence of Household Water Filters on Bacteria Growth and Trace Metals in Tap Water of Doha, Qatar.

PubMed

Nriagu, Jerome; Xi, Chuanwu; Siddique, Azhar; Vincent, Annette; Shomar, Basem

2018-05-29

Deteriorating water quality from aging infrastructure, growing threat of pollution from industrialization and urbanization, and increasing awareness about waterborne diseases are among the factors driving the surge in worldwide use of point-of-entry (POE) and point-of-use (POU) filters. Any adverse influence of such consumer point-of-use systems on quality of water at the tap remains poorly understood, however. We determined the chemical and microbiological changes in municipal water from the point of entry into the household plumbing system until it leaves from the tap in houses equipped with filters. We show that POE/POU devices can induce significant deterioration of the quality of tap water by functioning as traps and reservoirs for sludge, scale, rust, algae or slime deposits which promote microbial growth and biofilm formation in the household water distribution system. With changes in water pressure and physical or chemical disturbance of the plumbing system, the microorganisms and contaminants may be flushed into the tap water. Such changes in quality of household water carry a potential health risk which calls for some introspection in widespread deployment of POE/POU filters in water distribution systems.

THE FUTURE OF MICROBIAL SOURCE TRACKING STUDIES

EPA Science Inventory

Microbial source tracking (MST) is differentiated from traditional microbial water quality efforts by the need to identify the host species from which the bacteria originate, rather than necessarily identifying an individual point source. Despite recent advances in the developmen...

Spatial and temporal variation of fecal indicator organisms in two creeks in Beltsville, Maryland

USDA-ARS?s Scientific Manuscript database

Evaluation of microbial water quality is commonly achieved by monitoring populations of indicator bacteria such as E. coli and enterococci. Monitoring data are utilized by water managers to predict potential fecal contaminations as well as a decision tool to improve microbial water quality. Both te...

Biofilm-induced changes in microbial quality of irrigation water: Indicator bacteria and antibiotic-resistance

USDA-ARS?s Scientific Manuscript database

Irrigation waters are implicated in the transmission of pathogens to fresh produce, and microbial release and retention from biofilms that form on inner surfaces of irrigation lines may impact the quality of delivered water. Biofilms in water distribution systems have been suggested as a reservoir ...

Artificial groundwater treatment: biofilm activity and organic carbon removal performance.

PubMed

Långmark, Jonas; Storey, Michael V; Ashbolt, Nicholas J; Stenström, Thor Axel

2004-02-01

The artificial recharge of sand aquifers with raw source waters is a means both explored and utilised by many water utilities to meet the future potable water demands for increasing urban populations. The microbial ecology within these systems is however, poorly understood, as is the role that microbial biofilms play in the quality of finished water. Knowledge of the ability of biofilm bacteria to metabolise natural organic matter (NOM) is limited, particularly in respect to the degradation of normally recalcitrant hydrophilic and hydrophobic humic acid fractions by sessile and planktonic microbial consortia within sand aquifer systems. To simulate the artificial recharge of sand aquifers that were proposed for the Greater Stockholm Area, four separate 4 m deep sand columns were fed raw lake water and examined over a 45-week study period. The simulated aquifer system (hydraulic retention time 9-16 h) demonstrated the removal of total organic carbon (TOC) (10+/-5%), direct total counts (DTC) of bacteria (74+/-11%), heterotrophic plate count (HPC) bacteria (87+/-5%) and assimilable organic carbon (AOC) (87+/-5%), thereby fulfilling an important barrier function, except for the removal of TOC. Hydrophilic humic acid fractions were more readily metabolised by microbiota (HPC and EUB338-positive cells) harvested from the raw source water (SSM-W), whilst hydrophobic humic acid fractions promoted higher activity by microbiota harvested from the sand matrix (SSM-S). The apparent low activity demonstrated by biofilm microbiota (approximately 40% and 25% of DTC were positive to EUB338 probing for sand matrix and slide biofilms, respectively) could be attributed to the highly recalcitrant nature of the organic loads, whilst at the same time explain the poor removal of TOC. Following nutrient activation (by the PAC assay) nonetheless, a 3-fold increase in the percentage of EUB-positive bacteria was observed on glass slides. Furthermore, the incubation of SSM-S with R2A increased probe-active cells from 57+/-8% to 75+/-7% of DTC and at the same time increased SSM-W from 38+/-8% to 50+/-10%. Whilst these results may imply a good potential for the biological treatment of water by shallow sand aquifers, further work should address the poor removal of TOC observed in this study.

Physico-chemical parameters, bioactive compounds and microbial quality of thermo-sonicated carrot juice during storage.

PubMed

Martínez-Flores, Héctor E; Garnica-Romo, Ma Guadalupe; Bermúdez-Aguirre, Daniela; Pokhrel, Prashant Raj; Barbosa-Cánovas, Gustavo V

2015-04-01

Thermosonication has been successfully tested in food for microbial inactivation; however, changes in bioactive compounds and shelf-life of treated products have not been thoroughly investigated. Carrot juice was thermo-sonicated (24 kHz, 120 μm amplitude) at 50 °C, 54 °C and 58 °C for 10 min (acoustic power 2204.40, 2155.72, 2181.68 mW/mL, respectively). Quality parameters and microbial growth were evaluated after processing and during storage at 4 °C. Control and sonicated treatments at 50 °C and 54 °C had 10, 12 and 14 d of shelf-life, respectively. Samples sonicated at 58 °C had the best quality; microbial growth remained low at around 3-log for mesophiles, 4.5-log for yeasts and molds and 2-log for enterobacteria after 20 d of storage. Furthermore, thermo-sonicated juice at 58 °C retained >98% of carotenoids and 100% of ascorbic acid. Phenolic compounds increased in all stored, treated juices. Thermo-sonication is therefore a promising technology for preserving the quality of carrot juice by minimising the physicochemical changes during storage, retarding microbial growth and retaining the bioactive compounds. Copyright © 2014 Elsevier Ltd. All rights reserved.

Biofilm-induced bioclogging produces sharp interfaces in hyporheic flow, redox conditions, and microbial community structure

NASA Astrophysics Data System (ADS)

Caruso, Alice; Boano, Fulvio; Ridolfi, Luca; Chopp, David L.; Packman, Aaron

2017-05-01

Riverbed sediments host important biogeochemical processes that play a key role in nutrient dynamics. Sedimentary nutrient transformations are mediated by bacteria in the form of attached biofilms. The influence of microbial metabolic activity on the hydrochemical conditions within the hyporheic zone is poorly understood. We present a hydrobiogeochemical model to assess how the growth of heterotrophic and autotrophic biomass affects the transport and transformation of dissolved nitrogen compounds in bed form-induced hyporheic zones. Coupling between hyporheic exchange, nitrogen metabolism, and biomass growth leads to an equilibrium between permeability reduction and microbial metabolism that yields shallow hyporheic flows in a region with low permeability and high rates of microbial metabolism near the stream-sediment interface. The results show that the bioclogging caused by microbial growth can constrain rates and patterns of hyporheic fluxes and microbial transformation rate in many streams.

[Responses of soil microbial carbon metabolism to the leaf litter composition in Liaohe River Nature Reserve of northern Hebei Province, China].

PubMed

Li, Tian-yu; Kang, Feng-feng; Han, Hai-rong; Gao, Jing; Song, Xiao-shuai; Yu, Shu; Zhao, Jin-long; Yu, Xiao-wen

2015-03-01

Using litter bag method, we studied the effects of single and mixed litters from Betula platyphlla, Populus davidiana and Quercus mongolica on soil microbial biomass carbon (MBC), microbial respiration (MR) and microbial metabolic quotient (qCO2) in 0-5, 5-10 and 10-20 cm soil layers. The results showed that the average contents of MBC in 0-20 cm soil layer were 124.84, 325.29, 349.79 and 319.02 mg . kg-1 in the leaf litter removal treatment, Betula platyphlla treatment, Populus davidiana treatment and Quercus mongolica treatment, and the corresponding average rates of MR were 0.66, 1.12, 1.16 and 1.10 µg . g-1 . h-1, respectively. Meanwhile, in 0-20 cm soil layer, the average contents of MBC in the treatments with single leaf litter, mixed litter of two plant species and mixed litter of three plant species were 331. 37, 418. 52 and 529. 34 mg . kg-1, and the corresponding average rates of MR were 1.13, 1.30 and 1.46 µg . g-1 . h-1, respectively. In contrast to the MBC and MR, qCO2 in soil showed a reverse pattern. Our study suggested that characteristics of microbial carbolic metabolism were influenced by litter quality. Namely, the treatment with high litter quality had higher MBC, MR and utilization efficiency of soil carbon, compared with the treatment with low litter quality. Moreover, mixture of different species of leaf litter improved soil microbial activities, increased utilization efficiency on soil carbon and promoted diversity of microbial metabolic pathways, which could then contribute to maintaining and enhancing soil quality of forestland.

The resistance of the active microbiome as a fundamental compartment of soil quality in the face of climate change

NASA Astrophysics Data System (ADS)

Bastida, Felipe; Andrés, Manuela; Torres, Irene; García, Carlos; Ruiz Navarro, Antonio; Moreno, Francisco R.; López Serrano, Francisco R.

2017-04-01

Arid and semiarid ecosystems will be severely affected by drought derived from climate change. Forest management can promote the adaptations of plant and microbial communities to drought. For instance, thinning reduces competition for resources through a decrease in tree density and the promotion of plant survival. The resistance of soil microbial communities must be strongly related to the soil quality. However, in order to evaluate these properties, the active (and not only the total) microbial community should be carefully assessed. Here, we studied the functional and phylogenetic responses of the microbial community to six years of drought induced by rainfall exclusion and how thinning shapes its resistance to drought, in a semiarid ecosystem dominated by Pinus halepensis Mill. A multiOMIC approach was applied to reveal novel strategies against drought. The diversity and the composition of the total and active soil microbial communities were evaluated by 16S rRNA gene (bacteria) and ITS (fungal) sequencing, and by metaproteomics. The microbial biomass was analyzed by phospholipid fatty acids (PLFAs), and the microbially-mediated ecosystem multifunctionality was studied by the evaluation of enzyme activities related to C, N, and P dynamics. The microbial biomass and ecosystem multifunctionality decreased in plots subjected to drought, but this decrease was greater in unthinned plots. The diversity of the total bacterial and fungal communities were resistant to drought but were shaped by seasonal dynamics. However, the active community was more sensitive to drought and related to multifunctionality. Thinning in plots without drought increased the active diversity while the total diversity was not affected. Thinning promoted the resistance of multifunctionality to drought by changes in the active microbiome. Protein-based phylogeny was a better predictor of the impacts of drought and the adaptations of microbial communities. We highlight that the resistance of the microbial community and the active microbial community are ecological concepts strongly related to the concept of soil quality in the face of climate change.

Sewage contamination of a densely populated coral 'atoll' (Bermuda).

PubMed

Jones, Ross; Parsons, Rachel; Watkinson, Elaine; Kendell, David

2011-08-01

Bermuda is a densely populated coral 'atoll' located on a seamount in the mid-Atlantic (Sargasso Sea). There is no national sewerage system and the ∼20 × 10(6) L of sewage generated daily is disposed of via marine outfalls, cess pits/septic tanks underneath houses and through waste disposal (injection) wells. Gastrointestinal (GI) enterococci concentrations were measured in surface seawater samples collected monthly at multiple locations across the island over a 5-year period. According to the EU Bathing Water Directive microbial classification categories, 18 of the sites were in the 'excellent' category, four sites in the 'good', five sites were in the 'sufficient' and three sites in the 'poor' categories. One of the sites in the 'poor' category is beside a popular swimming beach. Between 20-30% of 58 sub tidal sediment samples collected from creeks, coves, bays, harbours and marinas in the Great Sound complex on the western side of Bermuda tested positive for the presence of the human specific bacterial biomarker Bacteroides (using culture-independent PCR-based methods) and for the faecal biomarker coprostanol (5β-cholestan-3-β-ol, which ranged in concentration from <0.05-0.77 mg kg( - 1). There was a significant statistical correlation between these two independent techniques for faecal contamination identification. Overall the microbial water quality and sedimentary biomarker surveys suggest sewage contamination in Bermuda was quite low compared with other published studies; nevertheless, several sewage contamination hotpots exist, and these could be attributed to discharge of raw sewage from house boats, from nearby sewage outfalls and leakage from septic tanks/cess pits.

Soil microbial diversity and activity linked to crop yield and quality in a dryland organic wheat production system

USDA-ARS?s Scientific Manuscript database

One of the primary goals of organic agriculture is increasing soil quality through the enhancement of soil biological diversity and activity. Greater soil microbial activity and diversity increase soil organic matter turnover and contribute to soil fertility, one of the main challenges associated wi...

Minimally processed vegetable salads: microbial quality evaluation.

PubMed

Fröder, Hans; Martins, Cecília Geraldes; De Souza, Katia Leani Oliveira; Landgraf, Mariza; Franco, Bernadette D G M; Destro, Maria Teresa

2007-05-01

The increasing demand for fresh fruits and vegetables and for convenience foods is causing an expansion of the market share for minimally processed vegetables. Among the more common pathogenic microorganisms that can be transmitted to humans by these products are Listeria monocytogenes, Escherichia coli O157:H7, and Salmonella. The aim of this study was to evaluate the microbial quality of a selection of minimally processed vegetables. A total of 181 samples of minimally processed leafy salads were collected from retailers in the city of Sao Paulo, Brazil. Counts of total coliforms, fecal coliforms, Enterobacteriaceae, psychrotrophic microorganisms, and Salmonella were conducted for 133 samples. L. monocytogenes was assessed in 181 samples using the BAX System and by plating the enrichment broth onto Palcam and Oxford agars. Suspected Listeria colonies were submitted to classical biochemical tests. Populations of psychrotrophic microorganisms >10(6) CFU/g were found in 51% of the 133 samples, and Enterobacteriaceae populations between 10(5) and 106 CFU/g were found in 42% of the samples. Fecal coliform concentrations higher than 10(2) CFU/g (Brazilian standard) were found in 97 (73%) of the samples, and Salmonella was detected in 4 (3%) of the samples. Two of the Salmonella-positive samples had <10(2) CFU/g concentrations of fecal coliforms. L. monocytogenes was detected in only 1 (0.6%) of the 181 samples examined. This positive sample was simultaneously detected by both methods. The other Listeria species identified by plating were L. welshimeri (one sample of curly lettuce) and L. innocua (2 samples of watercress). The results indicate that minimally processed vegetables had poor microbiological quality, and these products could be a vehicle for pathogens such as Salmonella and L. monocytogenes.

Water quality status of dugouts from five districts in Northern Ghana: implications for sustainable water resources management in a water stressed tropical savannah environment.

PubMed

Cobbina, Samuel J; Anyidoho, Louis Y; Nyame, Frank; Hodgson, I O A

2010-08-01

This study was primarily aimed at investigating the physicochemical and microbial quality of water in 14 such dugouts from five districts in the northern region of Ghana. Results obtained suggest that except for colour, turbidity, total iron and manganese, many physicochemical parameters were either within or close to the World Health Organisation's acceptable limits for drinking water. Generally, colour ranged from 5 to 750 Hz (mean 175 Hz), turbidity from 0.65 to 568 nephelometric turbidity units (NTU; mean 87.9 NTU), total iron from 0.07 to 7.85 mg/L (mean 1.0 mg/L) and manganese from 0.03 to 1.59 mg/L (mean 0.50 mg/L). Coliform counts in water from all the dugouts in both wet and dry seasons were, however, above the recommended limits for drinking water. Total and faecal coliforms ranged from 125 to 68,000 colony forming units (cfu)/100 mL (mean 10,623 cfu/100 mL) and <1 to 19,000 cfu/100 mL (mean 1,310 cfu /100 mL), respectively. The poor microbial quality, as indicated by the analytically significant presence of coliform bacteria in all samples of dugout water, strongly suggests susceptibility and exposure to waterborne diseases of, and consequent health implications on, the many people who continuously patronise these vital water resources throughout the year. In particular, more proactive sustainable water management options, such as introduction to communities of simple but cost-effective purification techniques for water drawn from dugouts for drinking purposes, education and information dissemination to the water users to ensure environmentally hygienic practices around dugouts, may be needed.

Semiquantitative analysis of gaps in microbiological performance of fish processing sector implementing current food safety management systems: a case study.

PubMed

Onjong, Hillary Adawo; Wangoh, John; Njage, Patrick Murigu Kamau

2014-08-01

Fish processing plants still face microbial food safety-related product rejections and the associated economic losses, although they implement legislation, with well-established quality assurance guidelines and standards. We assessed the microbial performance of core control and assurance activities of fish exporting processors to offer suggestions for improvement using a case study. A microbiological assessment scheme was used to systematically analyze microbial counts in six selected critical sampling locations (CSLs). Nine small-, medium- and large-sized companies implementing current food safety management systems (FSMS) were studied. Samples were collected three times on each occasion (n = 324). Microbial indicators representing food safety, plant and personnel hygiene, and overall microbiological performance were analyzed. Microbiological distribution and safety profile levels for the CSLs were calculated. Performance of core control and assurance activities of the FSMS was also diagnosed using an FSMS diagnostic instrument. Final fish products from 67% of the companies were within the legally accepted microbiological limits. Salmonella was absent in all CSLs. Hands or gloves of workers from the majority of companies were highly contaminated with Staphylococcus aureus at levels above the recommended limits. Large-sized companies performed better in Enterobacteriaceae, Escherichia coli, and S. aureus than medium- and small-sized ones in a majority of the CSLs, including receipt of raw fish material, heading and gutting, and the condition of the fish processing tables and facilities before cleaning and sanitation. Fish products of 33% (3 of 9) of the companies and handling surfaces of 22% (2 of 9) of the companies showed high variability in Enterobacteriaceae counts. High variability in total viable counts and Enterobacteriaceae was noted on fish products and handling surfaces. Specific recommendations were made in core control and assurance activities associated with sampling locations showing poor performance.

Interconnection of Key Microbial Functional Genes for Enhanced Benzo[a]pyrene Biodegradation in Sediments by Microbial Electrochemistry.

PubMed

Yan, Zaisheng; He, Yuhong; Cai, Haiyuan; Van Nostrand, Joy D; He, Zhili; Zhou, Jizhong; Krumholz, Lee R; Jiang, He-Long

2017-08-01

Sediment microbial fuel cells (SMFCs) can stimulate the degradation of polycyclic aromatic hydrocarbons in sediments, but the mechanism of this process is poorly understood at the microbial functional gene level. Here, the use of SMFC resulted in 92% benzo[a]pyrene (BaP) removal over 970 days relative to 54% in the controls. Sediment functions, microbial community structure, and network interactions were dramatically altered by the SMFC employment. Functional gene analysis showed that c-type cytochrome genes for electron transfer, aromatic degradation genes, and extracellular ligninolytic enzymes involved in lignin degradation were significantly enriched in bulk sediments during SMFC operation. Correspondingly, chemical analysis of the system showed that these genetic changes resulted in increases in the levels of easily oxidizable organic carbon and humic acids which may have resulted in increased BaP bioavailability and increased degradation rates. Tracking microbial functional genes and corresponding organic matter responses should aid mechanistic understanding of BaP enhanced biodegradation by microbial electrochemistry and development of sustainable bioremediation strategies.

Significance of microbial asynchronous anabolism to soil carbon dynamics driven by litter inputs

PubMed Central

Fan, Zhaosheng; Liang, Chao

2015-01-01

Soil organic carbon (SOC) plays an important role in the global carbon cycle. However, it remains largely unknown how plant litter inputs impact magnitude, composition and source configuration of the SOC stocks over long term through microbial catabolism and anabolism, mostly due to uncoupled research on litter decomposition and SOC formation. This limits our ability to predict soil system responses to changes in land-use and climate. Here, we examine how microbes act as a valve controlling carbon sequestrated from plant litters versus released to the atmosphere in natural ecosystems amended with plant litters varying in quantity and quality. We find that litter quality – not quantity – regulates long-term SOC dynamics under different plausible scenarios. Long-term changes in bulk SOC stock occur only when the quality of carbon inputs causes asynchronous change in a microbial physiological trait, defined as “microbial biosynthesis acceleration” (MBA). This is the first theoretical demonstration that the response of the SOC stocks to litter inputs is critically determined by the microbial physiology. Our work suggests that total SOC at an equilibrium state may be an intrinsic property of a given ecosystem, which ultimately is controlled by the asynchronous MBA between microbial functional groups. PMID:25849864

Significance of microbial asynchronous anabolism to soil carbon dynamics driven by litter inputs

DOE PAGES

Fan, Zhaosheng; Liang, Chao

2015-04-02

Soil organic carbon (SOC) plays an important role in the global carbon cycle. However, it remains largely unknown how plant litter inputs impact magnitude, composition and source configuration of the SOC stocks over long term through microbial catabolism and anabolism, mostly due to uncoupled research on litter decomposition and SOC formation. This limits our ability to predict soil system responses to changes in land-use and climate. Here, we examine how microbes act as a valve controlling carbon sequestrated from plant litters versus released to the atmosphere in natural ecosystems amended with plant litters varying in quantity and quality. We findmore » that litter quality – not quantity – regulates long-term SOC dynamics under different plausible scenarios. Long-term changes in bulk SOC stock occur only when the quality of carbon inputs causes asynchronous change in a microbial physiological trait, defined as ‘‘microbial biosynthesis acceleration’’ (MBA). This is the first theoretical demonstration that the response of the SOC stocks to litter inputs is critically determined by the microbial physiology. Our work suggests that total SOC at an equilibrium state may be an intrinsic property of a given ecosystem, which ultimately is controlled by the asynchronous MBA between microbial functional groups.« less

Subsurface metabolic potential on the Costa Rican Margin

NASA Astrophysics Data System (ADS)

Biddle, J.; Leon, Z. R.; Martino, A. J.; Bousses, K.; House, C. H.

2017-12-01

The distribution of archaea and bacteria and their associated metabolic abilities in the deep subseafloor are poorly understood. In order to explore this, we focused on samples from the Costa Rica margin IODP Expedition 334. The microbial community was analyzed via metagenomics in two different sites at multiple depths. At Site 1378, samples are from 2 meters below the sea floor (mbsf), 33 mbsf and 93 mbsf, and at Site 1379 from 22 mbsf to 45 mbsf. Whole community analysis of conserved gene markers in the metagenome show that the microbial community varies with depth, and drastically differs between the two geographically close sites. Thirty-two genomes were recovered from the metagenomic data with more than 30% completion. Archaea make 49% of all genomes recovered and over 90% of these recovered genomes belong to recently discovered and poorly characterized groups of Archaea. This study explored the relative dynamics of microbial communities in the deep biosphere and presents the metabolic potential of distinct subsurface biosphere archaeal groups.

Microbial ecology of corals, sponges, and algae in mesophotic coral environments

USGS Publications Warehouse

Olson, Julie B.; Kellogg, Christina A.

2010-01-01

Mesophotic coral ecosystems that occur at depths from 30 to 200 m have historically been understudied and yet appear to support a diverse biological community. The microbiology of these systems is particularly poorly understood, especially with regard to the communities associated with corals, sponges, and algae. This lack of information is partly due to the problems associated with gaining access to these environments and poor reproducibility across sampling methods. To summarize what is known about the microbiology of these ecosystems and to highlight areas where research is urgently needed, an overview of the current state of knowledge is presented. Emphasis is placed on the characterization of microbial populations, both prokaryotic and eukaryotic, associated with corals, sponges, and algae and the factors that influence microbial community structure. In topic areas where virtually nothing is known from mesophotic environments, the knowledge pertaining to shallow-water ecosystems is summarized to provide a starting point for a discussion on what might be expected in the mesophotic zone.

Season mediates herbivore effects on litter and soil microbial abundance and activity in a semi-arid woodland

DOE Office of Scientific and Technical Information (OSTI.GOV)

Classen, Aimee T; Overby, Stephen; Hart, Stephen C

2007-01-01

Herbivores can directly impact ecosystem function by altering litter quality entering an ecosystem or indirectly by affecting a shift in the microbial community that mediate nutrient processes. We examine herbivore susceptibility and resistance effects on litter microarthropod and soil microbial communities to test the general hypothesis that herbivore driven changes in litter inputs will feedback to the microbial community. Our study population consisted of individual trees that are susceptible or resistant to the stem-boring moth (Dioryctria albovittella) and trees that herbivores have been manually removed since 1982. Moth herbivory increased pi on litter nitrogen concentrations (16%) and canopy precipitation infiltrationmore » (28%), both significant factors influencing litter and soil microbial populations. Our research resulted in three major conclusions: 1) In spite of an increase in litter quality, herbivory does not change litter microarthropod abundance or species richness. 2) Herbivore susceptibility alters bulk soil microbial communities, but not soil properties. 3) Season has a strong influence on microbial communities, and their response to herbivore inputs, in this semi-arid ecosystem.« less

Using Microbial Source Tracking Markers to Predict Occurrence of Waterborne Pathogens in Urban and Agricultural Watershed

EPA Science Inventory

Runoff from agricultural fields and urban landscapes may carry a variety of microbial contaminants that compromises water quality and increases the possibility of human exposure to pathogenic microorganisms. Establishing the relationship between microbial source tracking (MST) ma...

The Microbial Fecal Indicator Paradigm: Tools in the Toolbox Applications in Recreational Waters

EPA Science Inventory

Summary of ORD’s recent research to develop tools for assessing microbial water quality in recreational waters. Methods discussed include the development of health associations between microbial fecal indicators and the development of culture, and molecular methods for fec...

Short-term incorporation of organic manures and biofertilizers influences biochemical and microbial characteristics of soils under an annual crop [Turmeric (Curcuma longa L.)].

PubMed

Dinesh, R; Srinivasan, V; Hamza, S; Manjusha, A

2010-06-01

The study was conducted to determine whether short-term incorporation of organic manures and biofertilizers influence biochemical and microbial variables reflecting soil quality. For the study, soils were collected from a field experiment conducted on turmeric (Curcuma longa L.) involving organic nutrient management (ONM), chemical nutrient management (CNM) and integrated nutrient management (INM). The findings revealed that application of organic manures and biofertilizers (ONM and INM) positively influenced microbial biomass C, N mineralization, soil respiration and enzymes activities. Contrarily, greater metabolic quotient levels in CNM indicated a stressed soil microbial community. Principal component analysis indicated the strong relationship between microbial activity and the availability of labile and easily mineralizable organic matter. The findings imply that even short-term incorporation of organic manures and biofertilizers promoted soil microbial and enzyme activities and these parameters are sensitive enough to detect changes in soil quality due to short-term incorporation of biological fertilizers. (c) 2010 Elsevier Ltd. All rights reserved.

Single sample resolution of rare microbial dark matter in a marine invertebrate metagenome

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miller, Ian J.; Weyna, Theodore R.; Fong, Stephen S.

Direct, untargeted sequencing of environmental samples (metagenomics) and de novo genome assembly enable the study of uncultured and phylogenetically divergent organisms. However, separating individual genomes from a mixed community has often relied on the differential-coverage analysis of multiple, deeply sequenced samples. In the metagenomic investigation of the marine bryozoan Bugula neritina, we uncovered seven bacterial genomes associated with a single B. neritina individual that appeared to be transient associates, two of which were unique to one individual and undetectable using certain “universal” 16S rRNA primers and probes. We recovered high quality genome assemblies for several rare instances of “microbial darkmore » matter,” or phylogenetically divergent bacteria lacking genomes in reference databases, from a single tissue sample that was not subjected to any physical or chemical pre-treatment. One of these rare, divergent organisms has a small (593 kbp), poorly annotated genome with low GC content (20.9%) and a 16S rRNA gene with just 65% sequence similarity to the closest reference sequence. Lastly, our findings illustrate the importance of sampling strategy and de novo assembly of metagenomic reads to understand the extent and function of bacterial biodiversity.« less

Single sample resolution of rare microbial dark matter in a marine invertebrate metagenome

DOE PAGES

Miller, Ian J.; Weyna, Theodore R.; Fong, Stephen S.; ...

2016-09-29

Direct, untargeted sequencing of environmental samples (metagenomics) and de novo genome assembly enable the study of uncultured and phylogenetically divergent organisms. However, separating individual genomes from a mixed community has often relied on the differential-coverage analysis of multiple, deeply sequenced samples. In the metagenomic investigation of the marine bryozoan Bugula neritina, we uncovered seven bacterial genomes associated with a single B. neritina individual that appeared to be transient associates, two of which were unique to one individual and undetectable using certain “universal” 16S rRNA primers and probes. We recovered high quality genome assemblies for several rare instances of “microbial darkmore » matter,” or phylogenetically divergent bacteria lacking genomes in reference databases, from a single tissue sample that was not subjected to any physical or chemical pre-treatment. One of these rare, divergent organisms has a small (593 kbp), poorly annotated genome with low GC content (20.9%) and a 16S rRNA gene with just 65% sequence similarity to the closest reference sequence. Lastly, our findings illustrate the importance of sampling strategy and de novo assembly of metagenomic reads to understand the extent and function of bacterial biodiversity.« less

Survey of safety practices among hospital laboratories in Oromia Regional State, Ethiopia.

PubMed

Sewunet, Tsegaye; Kebede, Wakjira; Wondafrash, Beyene; Workalemau, Bereket; Abebe, Gemeda

2014-10-01

Unsafe working practices, working environments, disposable waste products, and chemicals in clinical laboratories contribute to infectious and non-infectious hazards. Staffs, the community, and patients are less safe. Furthermore, such practices compromise the quality of laboratory services. We conducted a study to describe safety practices in public hospital laboratories of Oromia Regional State, Ethiopia. Randomly selected ten public hospital laboratories in Oromia Regional State were studied from Oct 2011- Feb 2012. Self-administered structured questionnaire and observation checklists were used for data collection. The respondents were heads of the laboratories, senior technicians, and safety officers. The questionnaire addressed biosafety label, microbial hazards, chemical hazards, physical/mechanical hazards, personal protective equipment, first aid kits and waste disposal system. The data was analyzed using descriptive analysis with SPSS version16 statistical software. All of the respondents reported none of the hospital laboratories were labeled with the appropriate safety label and safety symbols. These respondents also reported they may contain organisms grouped under risk group IV in the absence of microbiological safety cabinets. Overall, the respondents reported that there were poor safety regulations or standards in their laboratories. There were higher risks of microbial, chemical and physical/mechanical hazards. Laboratory safety in public hospitals of Oromia Regional State is below the standard. The laboratory workers are at high risk of combined physical, chemical and microbial hazards. Prompt recognition of the problem and immediate action is mandatory to ensure safe working environment in health laboratories.

Effect of high hydrostatic pressure processing on the background microbial loads and quality of cantaloupe puree

USDA-ARS?s Scientific Manuscript database

The objective of this study was to investigate and evaluate the effects of high hydrostatic pressure (HHP) applied to cantaloupe puree (CP) on microbial loads and product quality during storage for 10 days at 4 degrees C. Freshly prepared, double sealed and double bagged CP (ca. 5 g) was pressure tr...

Modeling the interannual variability of microbial quality metrics of irrigation water in a Pennsylvanian stream

USDA-ARS?s Scientific Manuscript database

Knowledge of the microbial quality of irrigation waters is extremely limited. For this reason, the US FDA has promulgated the Produce Rule, mandating the testing of irrigation water sources for many farms. The rule requires the collection and analysis of at least 20 water samples over two to four ye...

Automated DNA extraction platforms offer solutions to challenges of assessing microbial biofouling in oil production facilities.

PubMed

Oldham, Athenia L; Drilling, Heather S; Stamps, Blake W; Stevenson, Bradley S; Duncan, Kathleen E

2012-11-20

The analysis of microbial assemblages in industrial, marine, and medical systems can inform decisions regarding quality control or mitigation. Modern molecular approaches to detect, characterize, and quantify microorganisms provide rapid and thorough measures unbiased by the need for cultivation. The requirement of timely extraction of high quality nucleic acids for molecular analysis is faced with specific challenges when used to study the influence of microorganisms on oil production. Production facilities are often ill equipped for nucleic acid extraction techniques, making the preservation and transportation of samples off-site a priority. As a potential solution, the possibility of extracting nucleic acids on-site using automated platforms was tested. The performance of two such platforms, the Fujifilm QuickGene-Mini80™ and Promega Maxwell®16 was compared to a widely used manual extraction kit, MOBIO PowerBiofilm™ DNA Isolation Kit, in terms of ease of operation, DNA quality, and microbial community composition. Three pipeline biofilm samples were chosen for these comparisons; two contained crude oil and corrosion products and the third transported seawater. Overall, the two more automated extraction platforms produced higher DNA yields than the manual approach. DNA quality was evaluated for amplification by quantitative PCR (qPCR) and end-point PCR to generate 454 pyrosequencing libraries for 16S rRNA microbial community analysis. Microbial community structure, as assessed by DGGE analysis and pyrosequencing, was comparable among the three extraction methods. Therefore, the use of automated extraction platforms should enhance the feasibility of rapidly evaluating microbial biofouling at remote locations or those with limited resources.

Automated DNA extraction platforms offer solutions to challenges of assessing microbial biofouling in oil production facilities

PubMed Central

2012-01-01

The analysis of microbial assemblages in industrial, marine, and medical systems can inform decisions regarding quality control or mitigation. Modern molecular approaches to detect, characterize, and quantify microorganisms provide rapid and thorough measures unbiased by the need for cultivation. The requirement of timely extraction of high quality nucleic acids for molecular analysis is faced with specific challenges when used to study the influence of microorganisms on oil production. Production facilities are often ill equipped for nucleic acid extraction techniques, making the preservation and transportation of samples off-site a priority. As a potential solution, the possibility of extracting nucleic acids on-site using automated platforms was tested. The performance of two such platforms, the Fujifilm QuickGene-Mini80™ and Promega Maxwell®16 was compared to a widely used manual extraction kit, MOBIO PowerBiofilm™ DNA Isolation Kit, in terms of ease of operation, DNA quality, and microbial community composition. Three pipeline biofilm samples were chosen for these comparisons; two contained crude oil and corrosion products and the third transported seawater. Overall, the two more automated extraction platforms produced higher DNA yields than the manual approach. DNA quality was evaluated for amplification by quantitative PCR (qPCR) and end-point PCR to generate 454 pyrosequencing libraries for 16S rRNA microbial community analysis. Microbial community structure, as assessed by DGGE analysis and pyrosequencing, was comparable among the three extraction methods. Therefore, the use of automated extraction platforms should enhance the feasibility of rapidly evaluating microbial biofouling at remote locations or those with limited resources. PMID:23168231

Land-use legacies regulate decomposition dynamics following bioenergy crop conversion

DOE PAGES

Kallenbach, Cynthia M.; Stuart Grandy, A.

2014-07-14

Land-use conversion into bioenergy crop production can alter litter decomposition processes tightly coupled to soil carbon and nutrient dynamics. Yet, litter decomposition has been poorly described in bioenergy production systems, especially following land-use conversion. Predicting decomposition dynamics in postconversion bioenergy production systems is challenging because of the combined influence of land-use legacies with current management and litter quality. To evaluate how land-use legacies interact with current bioenergy crop management to influence litter decomposition in different litter types, we conducted a landscape-scale litterbag decomposition experiment. We proposed land-use legacies regulate decomposition, but their effects are weakened under higher quality litter andmore » when current land use intensifies ecosystem disturbance relative to prior land use. We compared sites left in historical land uses of either agriculture (AG) or Conservation Reserve Program grassland (CRP) to those that were converted to corn or switchgrass bioenergy crop production. Enzyme activities, mass loss, microbial biomass, and changes in litter chemistry were monitored in corn stover and switchgrass litter over 485 days, accompanied by similar soil measurements. Across all measured variables, legacy had the strongest effect (P < 0.05) relative to litter type and current management, where CRP sites maintained higher soil and litter enzyme activities and microbial biomass relative to AG sites. Decomposition responses to conversion depended on legacy but also current management and litter type. Within the CRP sites, conversion into corn increased litter enzymes, microbial biomass, and litter protein and lipid abundances, especially on decomposing corn litter, relative to nonconverted CRP. However, conversion into switchgrass from CRP, a moderate disturbance, often had no effect on switchgrass litter decomposition parameters. Thus, legacies shape the direction and magnitude of decomposition responses to bioenergy crop conversion and therefore should be considered a key influence on litter and soil C cycling under bioenergy crop management.« less

Spatial and Temporal Microbial Patterns in a Tropical Macrotidal Estuary Subject to Urbanization

PubMed Central

Kaestli, Mirjam; Skillington, Anna; Kennedy, Karen; Majid, Matthew; Williams, David; McGuinness, Keith; Munksgaard, Niels; Gibb, Karen

2017-01-01

Darwin Harbour in northern Australia is an estuary in the wet-dry tropics subject to increasing urbanization with localized water quality degradation due to increased nutrient loads from urban runoff and treated sewage effluent. Tropical estuaries are poorly studied compared to temperate systems and little is known about the microbial community-level response to nutrients. We aimed to examine the spatial and temporal patterns of the bacterial community and its association with abiotic factors. Since Darwin Harbour is macrotidal with strong seasonal patterns and mixing, we sought to determine if a human impact signal was discernible in the microbiota despite the strong hydrodynamic forces. Adopting a single impact–double reference design, we investigated the bacterial community using next-generation sequencing of the 16S rRNA gene from water and sediment from reference creeks and creeks affected by effluent and urban runoff. Samples were collected over two years during neap and spring tides, in the dry and wet seasons. Temporal drivers, namely seasons and tides had the strongest relationship to the water microbiota, reflecting the macrotidal nature of the estuary and its location in the wet-dry tropics. The neap-tide water microbiota provided the clearest spatial resolution while the sediment microbiota reflected current and past water conditions. Differences in patterns of the microbiota between different parts of the harbor reflected the harbor's complex hydrodynamics and bathymetry. Despite these variations, a microbial signature was discernible relating to specific effluent sources and urban runoff, and the composite of nutrient levels accounted for the major part of the explained variation in the microbiota followed by salinity. Our results confirm an overall good water quality but they also reflect the extent of some hypereutrophic areas. Our results show that the microbiota is a sensitive indicator to assess ecosystem health even in this dynamic and complex ecosystem. PMID:28751882

Soil microbial community structure and diversity are largely influenced by soil pH and nutrient quality in 78-year-old tree plantations

NASA Astrophysics Data System (ADS)

Zhou, Xiaoqi; Guo, Zhiying; Chen, Chengrong; Jia, Zhongjun

2017-04-01

Forest plantations have been recognised as a key strategy management tool for stocking carbon (C) in soils, thereby contributing to climate warming mitigation. However, long-term ecological consequences of anthropogenic forest plantations on the community structure and diversity of soil microorganisms and the underlying mechanisms in determining these patterns are poorly understood. In this study, we selected 78-year-old tree plantations that included three coniferous tree species (i.e. slash pine, hoop pine and kauri pine) and a eucalypt species in subtropical Australia. We investigated the patterns of community structure, and the diversity of soil bacteria and eukaryotes by using high-throughput sequencing of 16S rRNA and 18S rRNA genes. We also measured the potential methane oxidation capacity under different tree species. The results showed that slash pine and Eucalyptus significantly increased the dominant taxa of bacterial Acidobacteria and the dominant taxa of eukaryotic Ascomycota, and formed clusters of soil bacterial and eukaryotic communities, which were clearly different from the clusters under hoop pine and kauri pine. Soil pH and nutrient quality indicators such as C : nitrogen (N) and extractable organic C : extractable organic N were key factors in determining the patterns of soil bacterial and eukaryotic communities between the different tree species treatments. Slash pine and Eucalyptus had significantly lower soil bacterial and eukaryotic operational taxonomical unit numbers and lower diversity indices than kauri pine and hoop pine. A key factor limitation hypothesis was introduced, which gives a reasonable explanation for lower diversity indices under slash pine and Eucalyptus. In addition, slash pine and Eucalyptus had a higher soil methane oxidation capacity than the other tree species. These results suggest that significant changes in soil microbial communities may occur in response to chronic disturbance by tree plantations, and highlight the importance of soil pH and physiochemical characteristics in microbially mediated ecological processes in forested soils.

Predicting diffuse microbial pollution risk across catchments: The performance of SCIMAP and recommendations for future development.

PubMed

Porter, Kenneth D H; Reaney, Sim M; Quilliam, Richard S; Burgess, Chris; Oliver, David M

2017-12-31

Microbial pollution of surface waters in agricultural catchments can be a consequence of poor farm management practices, such as excessive stocking of livestock on vulnerable land or inappropriate handling of manures and slurries. Catchment interventions such as fencing of watercourses, streamside buffer strips and constructed wetlands have the potential to reduce faecal pollution of watercourses. However these interventions are expensive and occupy valuable productive land. There is, therefore, a requirement for tools to assist in the spatial targeting of such interventions to areas where they will have the biggest impact on water quality improvements whist occupying the minimal amount of productive land. SCIMAP is a risk-based model that has been developed for this purpose but with a focus on diffuse sediment and nutrient pollution. In this study we investigated the performance of SCIMAP in predicting microbial pollution of watercourses and assessed modelled outputs of E. coli, a common faecal indicator organism (FIO), against observed water quality information. SCIMAP was applied to two river catchments in the UK. SCIMAP uses land cover risk weightings, which are routed through the landscape based on hydrological connectivity to generate catchment scale maps of relative in-stream pollution risk. Assessment of the model's performance and derivation of optimum land cover risk weightings was achieved using a Monte-Carlo sampling approach. Performance of the SCIMAP framework for informing on FIO risk was variable with better performance in the Yealm catchment (r s =0.88; p<0.01) than the Wyre (r s =-0.36; p>0.05). Across both catchments much uncertainty was associated with the application of optimum risk weightings attributed to different land use classes. Overall, SCIMAP showed potential as a useful tool in the spatial targeting of FIO diffuse pollution management strategies; however, improvements are required to transition the existing SCIMAP framework to a robust FIO risk-mapping tool. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Multiparametric monitoring of microbial faecal pollution reveals the dominance of human contamination along the whole Danube River

PubMed Central

Kirschner, A.K.T.; Reischer, G.H.; Jakwerth, S.; Savio, D.; Ixenmaier, S.; Toth, E.; Sommer, R.; Mach, R.L.; Linke, R.; Eiler, A.; Kolarevic, S.; Farnleitner, A.H.

2017-01-01

The microbial faecal pollution of rivers has wide-ranging impacts on a variety of human activities that rely on appropriate river water quality. Thus, detailed knowledge of the extent and origin of microbial faecal pollution is crucial for watershed management activities to maintain safe water use. In this study, the microbial faecal pollution levels were monitored by standard faecal indicator bacteria (SFIB) along a 2580 km stretch of the Danube, the world's most international river, as well as the Danube's most important tributaries. To track the origin of faecal pollution, host-associated Bacteroidetes genetic faecal marker qPCR assays for different host groups were applied in concert with SFIB. The spatial resolution analysis was followed by a time resolution analysis of faecal pollution patterns over 1 year at three selected sites. In this way, a comprehensive faecal pollution map of the total length of the Danube was created, combining substantiated information on both the extent and origin of microbial faecal pollution. Within the environmental data matrix for the river, microbial faecal pollution constituted an independent component and did not cluster with any other measured environmental parameters. Generally, midstream samples representatively depicted the microbial pollution levels at the respective river sites. However, at a few, somewhat unexpected sites, high pollution levels occurred in the lateral zones of the river while the midstream zone had good water quality. Human faecal pollution was demonstrated as the primary pollution source along the whole river, while animal faecal pollution was of minor importance. This study demonstrates that the application of host-associated genetic microbial source tracking markers in concert with the traditional concept of microbial faecal pollution monitoring based on SFIB significantly enhances the knowledge of the extent and origin of microbial faecal pollution patterns in large rivers. It constitutes a powerful tool to guide target-oriented water quality management in large river basins. PMID:28806705

Multiparametric monitoring of microbial faecal pollution reveals the dominance of human contamination along the whole Danube River.

PubMed

Kirschner, A K T; Reischer, G H; Jakwerth, S; Savio, D; Ixenmaier, S; Toth, E; Sommer, R; Mach, R L; Linke, R; Eiler, A; Kolarevic, S; Farnleitner, A H

2017-11-01

The microbial faecal pollution of rivers has wide-ranging impacts on a variety of human activities that rely on appropriate river water quality. Thus, detailed knowledge of the extent and origin of microbial faecal pollution is crucial for watershed management activities to maintain safe water use. In this study, the microbial faecal pollution levels were monitored by standard faecal indicator bacteria (SFIB) along a 2580 km stretch of the Danube, the world's most international river, as well as the Danube's most important tributaries. To track the origin of faecal pollution, host-associated Bacteroidetes genetic faecal marker qPCR assays for different host groups were applied in concert with SFIB. The spatial resolution analysis was followed by a time resolution analysis of faecal pollution patterns over 1 year at three selected sites. In this way, a comprehensive faecal pollution map of the total length of the Danube was created, combining substantiated information on both the extent and origin of microbial faecal pollution. Within the environmental data matrix for the river, microbial faecal pollution constituted an independent component and did not cluster with any other measured environmental parameters. Generally, midstream samples representatively depicted the microbial pollution levels at the respective river sites. However, at a few, somewhat unexpected sites, high pollution levels occurred in the lateral zones of the river while the midstream zone had good water quality. Human faecal pollution was demonstrated as the primary pollution source along the whole river, while animal faecal pollution was of minor importance. This study demonstrates that the application of host-associated genetic microbial source tracking markers in concert with the traditional concept of microbial faecal pollution monitoring based on SFIB significantly enhances the knowledge of the extent and origin of microbial faecal pollution patterns in large rivers. It constitutes a powerful tool to guide target-oriented water quality management in large river basins. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Antimicrobial Materials for Advanced Microbial Control in Spacecraft Water Systems

NASA Technical Reports Server (NTRS)

Birmele, Michele; Caro, Janicce; Newsham, Gerard; Roberts, Michael; Morford, Megan; Wheeler, Ray

2012-01-01

Microbial detection, identification, and control are essential for the maintenance and preservation of spacecraft water systems. Requirements set by NASA put limitations on the energy, mass, materials, noise, cost, and crew time that can be devoted to microbial control. Efforts are being made to attain real-time detection and identification of microbial contamination in microgravity environments. Research for evaluating technologies for capability enhancement on-orbit is currently focused on the use of adenosine triphosphate (ATP) analysis for detection purposes and polymerase chain reaction (peR) for microbial identification. Additional research is being conducted on how to control for microbial contamination on a continual basis. Existing microbial control methods in spacecraft utilize iodine or ionic silver biocides, physical disinfection, and point-of-use sterilization filters. Although these methods are effective, they require re-dosing due to loss of efficacy, have low human toxicity thresholds, produce poor taste, and consume valuable mass and crew time. Thus, alternative methods for microbial control are needed. This project also explores ultraviolet light-emitting diodes (UV-LEDs), surface passivation methods for maintaining residual biocide levels, and several antimicrobial materials aimed at improving current microbial control techniques, as well as addressing other materials presently under analysis and future directions to be pursued.

Quality of fresh organic matter affects priming of soil organic matter and substrate utilization patterns of microbes

PubMed Central

Wang, Hui; Boutton, Thomas W.; Xu, Wenhua; Hu, Guoqing; Jiang, Ping; Bai, Edith

2015-01-01

Changes in biogeochemical cycles and the climate system due to human activities are expected to change the quantity and quality of plant litter inputs to soils. How changing quality of fresh organic matter (FOM) might influence the priming effect (PE) on soil organic matter (SOM) mineralization is still under debate. Here we determined the PE induced by two 13C-labeled FOMs with contrasting nutritional quality (leaf vs. stalk of Zea mays L.). Soils from two different forest types yielded consistent results: soils amended with leaf tissue switched faster from negative PE to positive PE due to greater microbial growth compared to soils amended with stalks. However, after 16 d of incubation, soils amended with stalks had a higher PE than those amended with leaf. Phospholipid fatty acid (PLFA) results suggested that microbial demand for carbon and other nutrients was one of the major determinants of the PE observed. Therefore, consideration of both microbial demands for nutrients and FOM supply simultaneously is essential to understand the underlying mechanisms of PE. Our study provided evidence that changes in FOM quality could affect microbial utilization of substrate and PE on SOM mineralization, which may exacerbate global warming problems under future climate change. PMID:25960162

Quality of fresh organic matter affects priming of soil organic matter and substrate utilization patterns of microbes.

PubMed

Wang, Hui; Boutton, Thomas W; Xu, Wenhua; Hu, Guoqing; Jiang, Ping; Bai, Edith

2015-05-11

Changes in biogeochemical cycles and the climate system due to human activities are expected to change the quantity and quality of plant litter inputs to soils. How changing quality of fresh organic matter (FOM) might influence the priming effect (PE) on soil organic matter (SOM) mineralization is still under debate. Here we determined the PE induced by two (13)C-labeled FOMs with contrasting nutritional quality (leaf vs. stalk of Zea mays L.). Soils from two different forest types yielded consistent results: soils amended with leaf tissue switched faster from negative PE to positive PE due to greater microbial growth compared to soils amended with stalks. However, after 16 d of incubation, soils amended with stalks had a higher PE than those amended with leaf. Phospholipid fatty acid (PLFA) results suggested that microbial demand for carbon and other nutrients was one of the major determinants of the PE observed. Therefore, consideration of both microbial demands for nutrients and FOM supply simultaneously is essential to understand the underlying mechanisms of PE. Our study provided evidence that changes in FOM quality could affect microbial utilization of substrate and PE on SOM mineralization, which may exacerbate global warming problems under future climate change.

Quality of fresh organic matter affects priming of soil organic matter and substrate utilization patterns of microbes

NASA Astrophysics Data System (ADS)

Wang, Hui; Boutton, Thomas W.; Xu, Wenhua; Hu, Guoqing; Jiang, Ping; Bai, Edith

2015-05-01

Changes in biogeochemical cycles and the climate system due to human activities are expected to change the quantity and quality of plant litter inputs to soils. How changing quality of fresh organic matter (FOM) might influence the priming effect (PE) on soil organic matter (SOM) mineralization is still under debate. Here we determined the PE induced by two 13C-labeled FOMs with contrasting nutritional quality (leaf vs. stalk of Zea mays L.). Soils from two different forest types yielded consistent results: soils amended with leaf tissue switched faster from negative PE to positive PE due to greater microbial growth compared to soils amended with stalks. However, after 16 d of incubation, soils amended with stalks had a higher PE than those amended with leaf. Phospholipid fatty acid (PLFA) results suggested that microbial demand for carbon and other nutrients was one of the major determinants of the PE observed. Therefore, consideration of both microbial demands for nutrients and FOM supply simultaneously is essential to understand the underlying mechanisms of PE. Our study provided evidence that changes in FOM quality could affect microbial utilization of substrate and PE on SOM mineralization, which may exacerbate global warming problems under future climate change.

Microbial Life Under Extreme Energy Limitation

NASA Technical Reports Server (NTRS)

Hoehler, Tori M.; Jorgensen, Bo Barker

2013-01-01

A great number of the bacteria and archaea on Earth are found in subsurface environments in a physiological state that is poorly represented or explained by laboratory cultures. Microbial cells in these very stable and oligotrophic settings catabolize 104- to 106-fold more slowly than model organisms in nutrient-rich cultures, turn over biomass on timescales of centuries to millennia rather than hours to days, and subsist with energy fluxes that are 1,000-fold lower than the typical culture-based estimates of maintenance requirements. To reconcile this disparate state of being with our knowledge of microbial physiology will require a revised understanding of microbial energy requirements, including identifying the factors that comprise true basal maintenance and the adaptations that might serve to minimize these factors.

Poorly known microbial taxa dominate the microbiome of permafrost thaw ponds.

PubMed

Wurzbacher, Christian; Nilsson, R Henrik; Rautio, Milla; Peura, Sari

2017-08-01

In the transition zone of the shifting permafrost border, thaw ponds emerge as hotspots of microbial activity, processing the ancient carbon freed from the permafrost. We analyzed the microbial succession across a gradient of recently emerged to older ponds using three molecular markers: one universal, one bacterial and one fungal. Age was a major modulator of the microbial community of the thaw ponds. Surprisingly, typical freshwater taxa comprised only a small fraction of the community. Instead, thaw ponds of all age classes were dominated by enigmatic bacterial and fungal phyla. Our results on permafrost thaw ponds lead to a revised perception of the thaw pond ecosystem and their microbes, with potential implications for carbon and nutrient cycling in this increasingly important class of freshwaters.

Assessing the microbial quality of a tropical watershed with an urbanization gradient using traditional and alternate fecal indicators.

PubMed

Santiago-Rodriguez, Tasha M; Toranzos, Gary A; Arce-Nazario, Javier A

2016-10-01

Urbanization affects the microbial loading into tropical streams, but its impact on water quality varies across watersheds. Rainfall in tropical environments also complicates microbial dynamics due to high seasonal and annual variations. Understanding the dynamics of fecal contamination in tropical surface waters may be further hindered by limitations from the utilization of traditional microbial indicators. We measured traditional (Enterococcus spp. and Escherichia coli), as well as alternate (enterophages and coliphages) indicators of fecal contamination in a tropical watershed in Puerto Rico during a 1-year period, and examined their relationship with rainfall events across an urbanization gradient. Enterococcus spp. and E. coli concentrations were 4 to 5 logs higher in non-urbanized or pristine sites when compared to enterophages and coliphages, suggesting that traditional fecal indicator bacteria may be natural inhabitants of pristine tropical waters. All of the tested indicators were positively correlated with rainfall and urbanization, except in the most urbanized sites, where rainfall may have had a dilution effect. The present study indicates that utilizing novel indicators of microbial water quality may improve the assessment of fecal contamination and pathogen risk for tropical watersheds.

Influence of air quality on the composition of microbial pathogens in fresh rainwater.

PubMed

Kaushik, Rajni; Balasubramanian, Rajasekhar; de la Cruz, Armah A

2012-04-01

In this study, the microbiological quality of fresh rainwater was assessed from 50 rain events under tropical weather conditions for a year. The levels of four major opportunistic waterborne pathogens, namely, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Aeromonas hydrophila, in rainwater samples were quantified by using a robust and sensitive quantitative PCR (qPCR) method. Of the 50 rainwater samples, 25 were found to be positive for at least one pathogen: 21 for E. coli, 16 for P. aeruginosa, 6 for K. pneumoniae, and 1 for A. hydrophila. In addition to the microbiological assessment of rainwater samples, we also studied the influence of prevailing air quality on the microbial quality of rainwater over the sampling period. A significant change in the diversity and relative abundance of the basic microbial indicator organisms in rainwater was observed during a major regional air pollution episode in Southeast Asia due to biomass-burning emissions.

Active microbial biofilms in deep poor porous continental subsurface rocks.

PubMed

Escudero, Cristina; Vera, Mario; Oggerin, Monike; Amils, Ricardo

2018-01-24

Deep continental subsurface is defined as oligotrophic environments where microorganisms present a very low metabolic rate. To date, due to the energetic cost of production and maintenance of biofilms, their existence has not been considered in poor porous subsurface rocks. We applied fluorescence in situ hybridization techniques and confocal laser scanning microscopy in samples from a continental deep drilling project to analyze the prokaryotic diversity and distribution and the possible existence of biofilms. Our results show the existence of natural microbial biofilms at all checked depths of the Iberian Pyrite Belt (IPB) subsurface and the co-occurrence of bacteria and archaea in this environment. This observation suggests that multi-species biofilms may be a common and widespread lifestyle in subsurface environments.

A meta-analysis of soil microbial biomass responses to forest disturbances

PubMed Central

Holden, Sandra R.; Treseder, Kathleen K.

2013-01-01

Climate warming is likely to increase the frequency and severity of forest disturbances, with uncertain consequences for soil microbial communities and their contribution to ecosystem C dynamics. To address this uncertainty, we conducted a meta-analysis of 139 published soil microbial responses to forest disturbances. These disturbances included abiotic (fire, harvesting, storm) and biotic (insect, pathogen) disturbances. We hypothesized that soil microbial biomass would decline following forest disturbances, but that abiotic disturbances would elicit greater reductions in microbial biomass than biotic disturbances. In support of this hypothesis, across all published studies, disturbances reduced soil microbial biomass by an average of 29.4%. However, microbial responses differed between abiotic and biotic disturbances. Microbial responses were significantly negative following fires, harvest, and storms (48.7, 19.1, and 41.7% reductions in microbial biomass, respectively). In contrast, changes in soil microbial biomass following insect infestation and pathogen-induced tree mortality were non-significant, although biotic disturbances were poorly represented in the literature. When measured separately, fungal and bacterial responses to disturbances mirrored the response of the microbial community as a whole. Changes in microbial abundance following disturbance were significantly positively correlated with changes in microbial respiration. We propose that the differential effect of abiotic and biotic disturbances on microbial biomass may be attributable to differences in soil disruption and organic C removal from forests among disturbance types. Altogether, these results suggest that abiotic forest disturbances may significantly decrease soil microbial abundance, with corresponding consequences for microbial respiration. Further studies are needed on the effect of biotic disturbances on forest soil microbial communities and soil C dynamics. PMID:23801985

Soil mineral assemblage influences on microbial communities and carbon cycling under fresh organic matter input

NASA Astrophysics Data System (ADS)

Finley, B. K.; Schwartz, E.; Koch, B.; Dijkstra, P.; Hungate, B. A.

2017-12-01

The interactions between soil mineral assemblages and microbial communities are important drivers of soil organic carbon (SOC) cycling and storage, although the mechanisms driving these interactions remain unclear. There is increasing evidence supporting the importance of associations with poorly crystalline, short-range order (SRO) minerals in protection of SOC from microbial utilization. However, how the microbial processing of SRO-associated SOC may be influenced by fresh organic matter inputs (priming) remains poorly understood. The influence on SRO minerals on soil microbial community dynamics is uncertain as well. Therefore, we conducted a priming incubation by adding either a simulated root exudate mixture or conifer needle litter to three soils from a mixed-conifer ecosystem. The parent material of the soils were andesite, basalt, and granite and decreased in SRO mineral content, respectively. We also conducted a parallel quantitative stable isotope probing incubation by adding 18O-labelled water to the soils to isotopically label microbial DNA in situ. This allowed us to characterize and identify the active bacterial and archaeal community and taxon-specific growth under fresh organic matter input. While the granite soil (lowest SRO content), had the largest total mineralization, the least priming occurred. The andesite and basalt soils (greater SRO content) had lower total respiration, but greater priming. Across all treatments, the granite soil, while having the lowest species richness of the entire community (249 taxa, both active and inactive), had a larger active community (90%) in response to new SOC input. The andesite and basalt soils, while having greater total species richness of the entire community at 333 and 325 taxa, respectively, had fewer active taxa in response to new C compared to the granite soil (30% and 49% taxa, respectively). These findings suggest that the soil mineral assemblage is an important driver on SOC cycling under fresh organic matter inputs, as well as on the activity and diversity of the microbial community. Often, microbial diversity is associated with function. Our results suggest that the soil environment, in this case SRO mineral content, may be more important on SOC cycling and storage than microbial diversity alone.

Effects of Actinomycete Secondary Metabolites on Sediment Microbial Communities.

PubMed

Patin, Nastassia V; Schorn, Michelle; Aguinaldo, Kristen; Lincecum, Tommie; Moore, Bradley S; Jensen, Paul R

2017-02-15

Marine sediments harbor complex microbial communities that remain poorly studied relative to other biomes such as seawater. Moreover, bacteria in these communities produce antibiotics and other bioactive secondary metabolites, yet little is known about how these compounds affect microbial community structure. In this study, we used next-generation amplicon sequencing to assess native microbial community composition in shallow tropical marine sediments. The results revealed complex communities comprised of largely uncultured taxa, with considerable spatial heterogeneity and known antibiotic producers comprising only a small fraction of the total diversity. Organic extracts from cultured strains of the sediment-dwelling actinomycete genus Salinispora were then used in mesocosm studies to address how secondary metabolites shape sediment community composition. We identified predatory bacteria and other taxa that were consistently reduced in the extract-treated mesocosms, suggesting that they may be the targets of allelopathic interactions. We tested related taxa for extract sensitivity and found general agreement with the culture-independent results. Conversely, several taxa were enriched in the extract-treated mesocosms, suggesting that some bacteria benefited from the interactions. The results provide evidence that bacterial secondary metabolites can have complex and significant effects on sediment microbial communities. Ocean sediments represent one of Earth's largest and most poorly studied biomes. These habitats are characterized by complex microbial communities where competition for space and nutrients can be intense. This study addressed the hypothesis that secondary metabolites produced by the sediment-inhabiting actinomycete Salinispora arenicola affect community composition and thus mediate interactions among competing microbes. Next-generation amplicon sequencing of mesocosm experiments revealed complex communities that shifted following exposure to S. arenicola extracts. The results reveal that certain predatory bacteria were consistently less abundant following exposure to extracts, suggesting that microbial metabolites mediate competitive interactions. Other taxa increased in relative abundance, suggesting a benefit from the extracts themselves or the resulting changes in the community. This study takes a first step toward assessing the impacts of bacterial metabolites on sediment microbial communities. The results provide insight into how low-abundance organisms may help structure microbial communities in ocean sediments. Copyright © 2017 American Society for Microbiology.

Impact of Roadway Stormwater Runoff on Microbial Contamination in the Receiving Stream.

PubMed

Wyckoff, Kristen N; Chen, Si; Steinman, Andrew J; He, Qiang

2017-09-01

Stormwater runoff from roadways has increasingly become a regulatory concern for water pollution control. Recent work has suggested roadway stormwater runoff as a potential source of microbial pollutants. The objective of this study was to determine the impact of roadway runoff on the microbiological quality of receiving streams. Microbiological quality of roadway stormwater runoff and the receiving stream was monitored during storm events with both cultivation-dependent fecal bacteria enumeration and cultivation-independent high-throughput sequencing techniques. Enumeration of total coliforms as a measure of fecal microbial pollution found consistently lower total coliform counts in roadway runoff than those in the stream water, suggesting that roadway runoff was not a major contributor of microbial pollutants to the receiving stream. Further characterization of the microbial community in the stormwater samples by 16S ribosomal RNA gene-based high-throughput amplicon sequencing revealed significant differences in the microbial composition of stormwater runoff from the roadways and the receiving stream. The differences in microbial composition between the roadway runoff and stream water demonstrate that roadway runoff did not appear to have a major influence on the stream in terms of microbiological quality. Thus, results from both fecal bacteria enumeration and high-throughput amplicon sequencing techniques were consistent that roadway stormwater runoff was not the primary contributor of microbial loading to the stream. Further studies of additional watersheds with distinct characteristics are needed to validate these findings. Understanding gained in this study could support the development of more effective strategies for stormwater management in sensitive watersheds. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Alteration of soil microbial communities and water quality in restored wetlands

USGS Publications Warehouse

Bossio, D.A.; Fleck, J.A.; Scow, K.M.; Fujii, R.

2006-01-01

Land usage is a strong determinant of soil microbial community composition and activity, which in turn determine organic matter decomposition rates and decomposition products in soils. Microbial communities in permanently flooded wetlands, such as those created by wetland restoration on Sacramento-San Joaquin Delta islands in California, function under restricted aeration conditions that result in increasing anaerobiosis with depth. It was hypothesized that the change from agricultural management to permanently flooded wetland would alter microbial community composition, increase the amount and reactivity of dissolved organic carbon (DOC) compounds in Delta waters; and have a predominant impact on microbial communities as compared with the effects of other environmental factors including soil type and agricultural management. Based on phospholipid fatty acid (PLFA) analysis, active microbial communities of the restored wetlands were changed significantly from those of the agricultural fields, and wetland microbial communities varied widely with soil depth. The relative abundance of monounsaturated fatty acids decreased with increasing soil depth in both wetland and agricultural profiles, whereas branched fatty acids were relatively more abundant at all soil depths in wetlands as compared to agricultural fields. Decomposition conditions were linked to DOC quantity and quality using fatty acid functional groups to conclude that restricted aeration conditions found in the wetlands were strongly related to production of reactive carbon compounds. But current vegetation may have had an equally important role in determining DOC quality in restored wetlands. In a larger scale analysis, that included data from wetland and agricultural sites on Delta islands and data from two previous studies from the Sacramento Valley, an aeration gradient was defined as the predominant determinant of active microbial communities across soil types and land usage. ?? 2005 Elsevier Ltd. All rights reserved.

Manipulation of the rhizosphere microbial community through application of a new bio-organic fertilizer improves watermelon quality and health

PubMed Central

Huang, Jing; Chen, Zhe; Nie, Yuanjun; Wang, Changbiao

2018-01-01

Bio-organic fertilizers (BOFs) combine functional microbes with a suitable substrate and have been shown to effectively suppress soil-borne diseases and promote plant growth. Here, we developed a novel bio-organic fertilizer (BOF) by fermentation of a cow plus chicken manure (M) compost using Fen-liquor Daqu (FLD) as a fermentation starter and compared the compositions of bacterial and fungal communities in the rhizosphere soil of watermelon plants after treatment with different fertilizers. Further, we aimed to explore the mechanisms underlying plant-promoting and disease (Fusarium wilt)-suppressing activities of each rhizosphere microbial community. The microbial communities of soil amended with cow plus chicken manure compost (S+M), soil amended with the BOF (S+BOF), and untreated control soil (S) without plants were analyzed through sequence analysis using the Illumina MiSeq platform. The results showed that a new microbial community was formed in the manure compost after fermentation by the Daqu. Application of the BOF to the soil induced remarkable changes in the rhizosphere microbial communities, with increased bacterial diversity and decreased fungal diversity. Most importantly, S+BOF showed the lowest abundance of Fusarium. Moreover, watermelon quality was higher (P < 0.05) in the S+BOF than in the S+M treatment. Thus, application of the BOF favorably altered the composition of the rhizosphere microbial community, suppressing Fusarium wilt disease and promoting plant quality. PMID:29451918

Manipulation of the rhizosphere microbial community through application of a new bio-organic fertilizer improves watermelon quality and health.

PubMed

Zhao, Jia; Liu, Jiang; Liang, Hong; Huang, Jing; Chen, Zhe; Nie, Yuanjun; Wang, Changbiao; Wang, Yuguo

2018-01-01

Bio-organic fertilizers (BOFs) combine functional microbes with a suitable substrate and have been shown to effectively suppress soil-borne diseases and promote plant growth. Here, we developed a novel bio-organic fertilizer (BOF) by fermentation of a cow plus chicken manure (M) compost using Fen-liquor Daqu (FLD) as a fermentation starter and compared the compositions of bacterial and fungal communities in the rhizosphere soil of watermelon plants after treatment with different fertilizers. Further, we aimed to explore the mechanisms underlying plant-promoting and disease (Fusarium wilt)-suppressing activities of each rhizosphere microbial community. The microbial communities of soil amended with cow plus chicken manure compost (S+M), soil amended with the BOF (S+BOF), and untreated control soil (S) without plants were analyzed through sequence analysis using the Illumina MiSeq platform. The results showed that a new microbial community was formed in the manure compost after fermentation by the Daqu. Application of the BOF to the soil induced remarkable changes in the rhizosphere microbial communities, with increased bacterial diversity and decreased fungal diversity. Most importantly, S+BOF showed the lowest abundance of Fusarium. Moreover, watermelon quality was higher (P < 0.05) in the S+BOF than in the S+M treatment. Thus, application of the BOF favorably altered the composition of the rhizosphere microbial community, suppressing Fusarium wilt disease and promoting plant quality.

Microbial diversity and their roles in the vinegar fermentation process.

PubMed

Li, Sha; Li, Pan; Feng, Feng; Luo, Li-Xin

2015-06-01

Vinegar is one of the oldest acetic acid-diluted solution products in the world. It is produced from any fermentable sugary substrate by various fermentation methods. The final vinegar products possess unique functions, which are endowed with many kinds of compounds formed in the fermentation process. The quality of vinegar is determined by many factors, especially by the raw materials and microbial diversity involved in vinegar fermentation. Given that metabolic products from the fermenting strains are directly related to the quality of the final products of vinegar, the microbial diversity and features of the dominant strains involved in different fermentation stages should be analyzed to improve the strains and stabilize fermentation. Moreover, although numerous microbiological studies have been conducted to examine the process of vinegar fermentation, knowledge about microbial diversity and their roles involved in fermentation is still fragmentary and not systematic enough. Therefore, in this review, the dominant microorganism species involved in the stages of alcoholic fermentation and acetic acid fermentation of dissimilar vinegars were summarized. We also summarized various physicochemical properties and crucial compounds in disparate types of vinegar. Furthermore, the merits and drawbacks of vital fermentation methods were generalized. Finally, we described in detail the relationships among microbial diversity, raw materials, fermentation methods, physicochemical properties, compounds, functionality, and final quality of vinegar. The integration of this information can provide us a detailed map about the microbial diversity and function involved in vinegar fermentation.

Effect of UV-C treatment on inactivation of Escherichia coli O157:H7, microbial loads, and quality of button mushrooms

USDA-ARS?s Scientific Manuscript database

This study investigated the effects of ultraviolet-C (UV-C) light applied to both sides of mushrooms on microbial loads and product quality during storage for 21 days at 4 C. Microflora populations, color, antioxidant activity, total phenolics, and ascorbic acid were measured at 1, 7, 14 and 21 days...

[Soil quality assessment of forest stand in different plantation esosystems].

PubMed

Huang, Yu; Wang, Silong; Feng, Zongwei; Gao, Hong; Wang, Qingkui; Hu, Yalin; Yan, Shaokui

2004-12-01

After a clear-cutting of the first generation Cunninghamia lanceolata plantation in 1982, three plantation ecosystems, pure Michelia macclurei stand (PMS), pure Chinese-fir stand (PCS) and their mixed stand, were established in spring 1983, and their effects on soil characteristics were evaluated by measuring some soil physical, chemical, microbiological and biochemical parameters. After 20 years' plantation, all test indices showed differences among different forest management models. Both PMS and MCM had a favorable effect on soil fertility maintenance. Soil quality assessment showed that some soil functions, e.g., water availability, nutrient availability, root suitability and soil quality index were all in a moderate level under the mixed and pure PMS stands, whereas in a relatively lower level under successive PCS stand. The results also showed that there existed close correlations between soil total organic C (TOC), cation exchange capacity (CEC), microbial biomass-C (Cmic) and other soil physical, chemical and biological indices. Therefore, TOC, CEC and Cmic could be used as the indicators in assessing soil quality in this study area. In addition, there were also positive correlations between soil microbial biomass-C and TOC, soil microbial biomass-N and total N, and soil microbial biomass-P and total P in the present study.

Direct and indirect influence of parental bedrock on streambed microbial community structure in forested streams.

PubMed

Mosher, Jennifer J; Findlay, Robert H

2011-11-01

A correlative study was performed to determine if variation in streambed microbial community structure in low-order forested streams can be directly or indirectly linked to the chemical nature of the parental bedrock of the environments through which the streams flow. Total microbial and photosynthetic biomass (phospholipid phosphate [PLP] and chlorophyll a), community structure (phospholipid fatty acid analysis), and physical and chemical parameters were measured in six streams, three located in sandstone and three in limestone regions of the Bankhead National Forest in northern Alabama. Although stream water flowing through the two different bedrock types differed significantly in chemical composition, there were no significant differences in total microbial and photosynthetic biomass in the sediments. In contrast, sedimentary microbial community structure differed between the bedrock types and was significantly correlated with stream water ion concentrations. A pattern of seasonal variation in microbial community structure was also observed. Further statistical analysis indicated dissolved organic matter (DOM) quality, which was previously shown to be influenced by geological variation, correlated with variation in bacterial community structure. These results indicate that the geology of underlying bedrock influences benthic microbial communities directly via changes in water chemistry and also indirectly via stream water DOM quality.

Organic Matter Quality and its Influence on Carbon Turnover and Stabilization in Northern Peatlands

NASA Astrophysics Data System (ADS)

Turetsky, M. R.; Wieder, R. K.

2002-12-01

Peatlands cover 3-5 % of the world's ice-free land area, but store about 33 % of global terrestrial soil carbon. Peat accumulation in northern regions generally is controlled by slow decomposition, which may be limited by cold temperatures and water-logging. Poor organic matter quality also may limit decay, and microbial activity in peatlands likely is regulated by the availability of labile carbon and/or nutrients. Conversely, carbon in recalcitrant soil structures may be chemically protected from microbial decay, particularly in peatlands where carbon can be buried in anaerobic soils. Soil organic matter quality is controlled by plant litter chemical composition and the susceptibility of organic compounds to decomposition through time. There are a number of techniques available for characterizing organic quality, ranging from chemical proximate or elemental analysis to more qualitative methods such as nuclear magenetic resonance, pyrolysis/mass spectroscopy, and Fourier transform infrared spectroscopy. We generally have relied on proximate analysis for quantitative determination of several organic fractions (i.e., water-soluble carbohydrates, soluble nonpolars, water-soluble phenolics, holocellulose, and acid insoluble material). Our approaches to studying organic matter quality in relation to C turnover in peatlands include 1) 14C labelling of peatland vegetation along a latitudinal gradient in North America, allowing us to follow the fate of 14C tracer in belowground organic fractions under varying climates, 2) litter bag studies focusing on the role of individual moss species in litter quality and organic matter decomposition, and 3) laboratory incubations of peat to explore relationships between organic matter quality and decay. These studies suggest that proximate organic fractions vary in lability, but that turnover of organic matter is influenced both by plant species and climate. Across boreal peatlands, measures of soil recalcitrance such as acid insoluble material (AIM) and AIM/N were significant predictors of decomposition. However, when limited to individual peatland features or bryophyte species, soluble proximate fractions were better predictors of organic matter decay. This suggests that decomposition within single litter or peat types is controlled by the size of relatively small, labile carbon pools. As peatlands store the majority of soil carbon in the boreal forest, the influences of peat quality on carbon storage and turnover should be considered in understanding the fate of carbon in northern ecosystems.

Microbial factories for recombinant pharmaceuticals

PubMed Central

Ferrer-Miralles, Neus; Domingo-Espín, Joan; Corchero, José Luis; Vázquez, Esther; Villaverde, Antonio

2009-01-01

Most of the hosts used to produce the 151 recombinant pharmaceuticals so far approved for human use by the Food and Drug Administration (FDA) and/or by the European Medicines Agency (EMEA) are microbial cells, either bacteria or yeast. This fact indicates that despite the diverse bottlenecks and obstacles that microbial systems pose to the efficient production of functional mammalian proteins, namely lack or unconventional post-translational modifications, proteolytic instability, poor solubility and activation of cell stress responses, among others, they represent convenient and powerful tools for recombinant protein production. The entering into the market of a progressively increasing number of protein drugs produced in non-microbial systems has not impaired the development of products obtained in microbial cells, proving the robustness of the microbial set of cellular systems (so far Escherichia coli and Saccharomyces cerevisae) developed for protein drug production. We summarize here the nature, properties and applications of all those pharmaceuticals and the relevant features of the current and potential producing hosts, in a comparative way. PMID:19317892

Relating belowground microbial composition to the taxonomic, phylogenetic, and functional trait distributions of trees in a tropical forest.

PubMed

Barberán, Albert; McGuire, Krista L; Wolf, Jeffrey A; Jones, F Andrew; Wright, Stuart Joseph; Turner, Benjamin L; Essene, Adam; Hubbell, Stephen P; Faircloth, Brant C; Fierer, Noah

2015-12-01

The complexities of the relationships between plant and soil microbial communities remain unresolved. We determined the associations between plant aboveground and belowground (root) distributions and the communities of soil fungi and bacteria found across a diverse tropical forest plot. Soil microbial community composition was correlated with the taxonomic and phylogenetic structure of the aboveground plant assemblages even after controlling for differences in soil characteristics, but these relationships were stronger for fungi than for bacteria. In contrast to expectations, the species composition of roots in our soil core samples was a poor predictor of microbial community composition perhaps due to the patchy, ephemeral, and highly overlapping nature of fine root distributions. Our ability to predict soil microbial composition was not improved by incorporating information on plant functional traits suggesting that the most commonly measured plant traits are not particularly useful for predicting the plot-level variability in belowground microbial communities. © 2015 John Wiley & Sons Ltd/CNRS.

Stochastic Community Assembly: Does It Matter in Microbial Ecology?

PubMed

Zhou, Jizhong; Ning, Daliang

2017-12-01

Understanding the mechanisms controlling community diversity, functions, succession, and biogeography is a central, but poorly understood, topic in ecology, particularly in microbial ecology. Although stochastic processes are believed to play nonnegligible roles in shaping community structure, their importance relative to deterministic processes is hotly debated. The importance of ecological stochasticity in shaping microbial community structure is far less appreciated. Some of the main reasons for such heavy debates are the difficulty in defining stochasticity and the diverse methods used for delineating stochasticity. Here, we provide a critical review and synthesis of data from the most recent studies on stochastic community assembly in microbial ecology. We then describe both stochastic and deterministic components embedded in various ecological processes, including selection, dispersal, diversification, and drift. We also describe different approaches for inferring stochasticity from observational diversity patterns and highlight experimental approaches for delineating ecological stochasticity in microbial communities. In addition, we highlight research challenges, gaps, and future directions for microbial community assembly research. Copyright © 2017 American Society for Microbiology.

Microbiota of little penguins and short-tailed shearwaters during development

PubMed Central

Arnould, John P. Y.; Allnutt, Theo R.; Crowley, Tamsyn; Krause, Lutz; Reynolds, John; Dann, Peter; Smith, Stuart C.

2017-01-01

The establishment and early colonisation of the gastrointestinal (GI) tract has been recognised as a crucial stage in chick development, with pioneering microbial species responsible for influencing the development of the GI tract and influencing host health, fitness and disease status throughout life. Development of the microbiota in long lived seabirds is poorly understood. This study characterised the microbial composition of little penguin and short-tailed shearwater chicks throughout development, using Quantitative Real Time PCR (qPCR) and 16S rRNA sequencing. The results indicated that microbial development differed between the two seabird species with the short-tailed shearwater microbiota being relatively stable throughout development whilst significant fluctuations in the microbial composition and an upward trend in the abundance of Firmicutes and Bacteroidetes were observed in the little penguin. When the microbial composition of adults and chicks was compared, both species showed low similarity in microbial composition, indicating that the adult microbiota may have a negligible influence over the chick’s microbiota. PMID:28806408

Microbial and physical properties as indicators of sandy soil quality under cropland and grassland

NASA Astrophysics Data System (ADS)

Frac, Magdalena; Lipiec, Jerzy; Usowicz, Boguslaw; Oszust, Karolina; Brzezinska, Malgorzata

2017-04-01

Land use is one of the key factor driving changes in soil properties influencing on soil health and quality. Microbial diversity and physical properties are sensitive indicators for assessing soil health and quality. The alterations of microbial diversity and physical properties following land use changes have not been sufficiently elucidated, especially for sandy soils. We investigated microbial diversity indicators including fungal communities composition and physical properties of sandy acid soil under cropland and more than 20-yr-old grassland (after cropland) in Trzebieszów, Podlasie Region, Poland (N 51° 59' 24", E 22° 33' 37"). The study included four depths within 0-60 cm. Microbial genetic diversity was assessed by terminal restriction fragment length polymorphism (t-RFLP) analysis, fungal community composition was evaluated by next generation sequencing (NGS) analysis and functional diversity was determined by Biolog EcoPlate method. Overall microbial activity was assessed by soil enzymes (dehydrogenases, β-glucosidase) and respiration test. At the same places soil texture, organic carbon content, pH, bulk density, water holding capacity were determined. Our results showed that grassland soil was characterized by higher activity of soil enzymes than cropland. The average well color development of soil microorganisms, the microbial functional diversity and the number of carbon source utilization were significantly affected by land use type and were differentiated among soil depths. In grassland compared to cropland soil a significant increase of carboxylic acids and decrease of amino acids utilization was observed. The quantitative and qualitative differences were found in community of ammonia oxidizing archaea in cropland and grassland soil. The results of fungal community composition help to explain the soil health of grassland and cropland based on the appearance of phytopathogenic and antagonistic fungi. In general bulk density and field water capacity were greater and saturated hydraulic conductivity was lower under grassland than cropland soil. The study was funded by HORIZON 2020, European Commission, Programme: H2020-SFS-4-2014: Soil quality and function, project No. 635750, Interactive Soil Quality Assessment in Europe and China for Agricultural Productivity and Environmental Resilience (iSQAPER, 2015-2020).

DEEP BIOSPHERE. Exploring deep microbial life in coal-bearing sediment down to ~2.5 km below the ocean floor.

PubMed

Inagaki, F; Hinrichs, K-U; Kubo, Y; Bowles, M W; Heuer, V B; Hong, W-L; Hoshino, T; Ijiri, A; Imachi, H; Ito, M; Kaneko, M; Lever, M A; Lin, Y-S; Methé, B A; Morita, S; Morono, Y; Tanikawa, W; Bihan, M; Bowden, S A; Elvert, M; Glombitza, C; Gross, D; Harrington, G J; Hori, T; Li, K; Limmer, D; Liu, C-H; Murayama, M; Ohkouchi, N; Ono, S; Park, Y-S; Phillips, S C; Prieto-Mollar, X; Purkey, M; Riedinger, N; Sanada, Y; Sauvage, J; Snyder, G; Susilawati, R; Takano, Y; Tasumi, E; Terada, T; Tomaru, H; Trembath-Reichert, E; Wang, D T; Yamada, Y

2015-07-24

Microbial life inhabits deeply buried marine sediments, but the extent of this vast ecosystem remains poorly constrained. Here we provide evidence for the existence of microbial communities in ~40° to 60°C sediment associated with lignite coal beds at ~1.5 to 2.5 km below the seafloor in the Pacific Ocean off Japan. Microbial methanogenesis was indicated by the isotopic compositions of methane and carbon dioxide, biomarkers, cultivation data, and gas compositions. Concentrations of indigenous microbial cells below 1.5 km ranged from <10 to ~10(4) cells cm(-3). Peak concentrations occurred in lignite layers, where communities differed markedly from shallower subseafloor communities and instead resembled organotrophic communities in forest soils. This suggests that terrigenous sediments retain indigenous community members tens of millions of years after burial in the seabed. Copyright © 2015, American Association for the Advancement of Science.

Biofilm community succession: a neutral perspective.

PubMed

Woodcock, Stephen; Sloan, William T

2017-05-22

Although biofilms represent one of the dominant forms of life in aqueous environments, our understanding of the assembly and development of their microbial communities remains relatively poor. In recent years, several studies have addressed this and have extended the concepts of succession theory in classical ecology into microbial systems. From these datasets, niche-based conceptual models have been developed explaining observed biodiversity patterns and their dynamics. These models have not, however, been formulated mathematically and so remain untested. Here, we further develop spatially resolved neutral community models and demonstrate that these can also explain these patterns and offer alternative explanations of microbial succession. The success of neutral models suggests that stochastic effects alone may have a much greater influence on microbial community succession than previously acknowledged. Furthermore, such models are much more readily parameterised and can be used as the foundation of more complex and realistic models of microbial community succession.

Mangrove succession enriches the sediment microbial community in South China

PubMed Central

Chen, Quan; Zhao, Qian; Li, Jing; Jian, Shuguang; Ren, Hai

2016-01-01

Sediment microorganisms help create and maintain mangrove ecosystems. Although the changes in vegetation during mangrove forest succession have been well studied, the changes in the sediment microbial community during mangrove succession are poorly understood. To investigate the changes in the sediment microbial community during succession of mangroves at Zhanjiang, South China, we used phospholipid fatty acid (PLFA) analysis and the following chronosequence from primary to climax community: unvegetated shoal; Avicennia marina community; Aegiceras corniculatum community; and Bruguiera gymnorrhiza + Rhizophora stylosa community. The PLFA concentrations of all sediment microbial groups (total microorganisms, fungi, gram-positive bacteria, gram-negative bacteria, and actinomycetes) increased significantly with each stage of mangrove succession. Microbial PLFA concentrations in the sediment were significantly lower in the wet season than in the dry season. Regression and ordination analyses indicated that the changes in the microbial community with mangrove succession were mainly associated with properties of the aboveground vegetation (mainly plant height) and the sediment (mainly sediment organic matter and total nitrogen). The changes in the sediment microbial community can probably be explained by increases in nutrients and microhabitat heterogeneity during mangrove succession. PMID:27265262

Mangrove succession enriches the sediment microbial community in South China.

PubMed

Chen, Quan; Zhao, Qian; Li, Jing; Jian, Shuguang; Ren, Hai

2016-06-06

Sediment microorganisms help create and maintain mangrove ecosystems. Although the changes in vegetation during mangrove forest succession have been well studied, the changes in the sediment microbial community during mangrove succession are poorly understood. To investigate the changes in the sediment microbial community during succession of mangroves at Zhanjiang, South China, we used phospholipid fatty acid (PLFA) analysis and the following chronosequence from primary to climax community: unvegetated shoal; Avicennia marina community; Aegiceras corniculatum community; and Bruguiera gymnorrhiza + Rhizophora stylosa community. The PLFA concentrations of all sediment microbial groups (total microorganisms, fungi, gram-positive bacteria, gram-negative bacteria, and actinomycetes) increased significantly with each stage of mangrove succession. Microbial PLFA concentrations in the sediment were significantly lower in the wet season than in the dry season. Regression and ordination analyses indicated that the changes in the microbial community with mangrove succession were mainly associated with properties of the aboveground vegetation (mainly plant height) and the sediment (mainly sediment organic matter and total nitrogen). The changes in the sediment microbial community can probably be explained by increases in nutrients and microhabitat heterogeneity during mangrove succession.

NIOSH testimony on indoor air quality before the Subcommittee on Natural Resources, Agriculture Research and Environment Committee on Science, Space, and Technology, US House of Representatives by P. J. Bierbaum, September 27, 1989

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1989-09-27

Testimony considered the activities of the National Institute for Occupational Safety and Health (NIOSH) in the area of indoor air quality. Energy conservation concerns in the 1970s forced the construction of buildings with the key element being preventing infiltration of untempered outside air. Many buildings were effectively sealed against air entry. Requests for health-hazard evaluations due to a suspected poor quality of indoor air have increased dramatically in recent years. Indoor-air-quality problems may arise from a variety of sources including human metabolic activity, smoking, structural components of the building and contents, biological contamination, office and mechanical equipment, and outside airmore » pollutants that enter the building. Many times the symptoms and health complaints reported by workers were diverse and not specific enough to readily identify the causative agent. The results from the health hazard evaluations have enabled NIOSH to classify the findings by primary type of problem: contamination from the building materials, 4%; microbial contamination, 5%; other contamination from inside the building, 15%; contamination from outside the building, 10%; inadequate ventilation, 53%; and unknown, 13%. Ergonomic and psychosocial issues often complicated the findings.« less

Microbial communities may modify how litter quality affects potential decomposition rates as tree species migrate

Treesearch

Ashley D. Keiser; Jennifer D. Knoepp; Mark A. Bradford

2013-01-01

Background and aims Climate change alters regional plant species distributions, creating new combinations of litter species and soil communities. Biogeographic patterns in microbial communities relate to dissimilarity in microbial community function, meaning novel litters to communities may decompose differently than predicted from their chemical composition. Therefore...

Development and evaluation of the microbial fate and transport module for the Agricultural Policy/Environmental eXtender (APEX) model

USDA-ARS?s Scientific Manuscript database

Microbial contamination of waters in agricultural watershed is the critical public health issue. The watershed-scale model has been proven to be one of the candidate tools for predicting microbial water quality and evaluating management practices. The Agricultural Policy/Environmental eXtender (APEX...

The need for high-quality whole-genome sequence databases in microbial forensics.

PubMed

Sjödin, Andreas; Broman, Tina; Melefors, Öjar; Andersson, Gunnar; Rasmusson, Birgitta; Knutsson, Rickard; Forsman, Mats

2013-09-01

Microbial forensics is an important part of a strengthened capability to respond to biocrime and bioterrorism incidents to aid in the complex task of distinguishing between natural outbreaks and deliberate acts. The goal of a microbial forensic investigation is to identify and criminally prosecute those responsible for a biological attack, and it involves a detailed analysis of the weapon--that is, the pathogen. The recent development of next-generation sequencing (NGS) technologies has greatly increased the resolution that can be achieved in microbial forensic analyses. It is now possible to identify, quickly and in an unbiased manner, previously undetectable genome differences between closely related isolates. This development is particularly relevant for the most deadly bacterial diseases that are caused by bacterial lineages with extremely low levels of genetic diversity. Whole-genome analysis of pathogens is envisaged to be increasingly essential for this purpose. In a microbial forensic context, whole-genome sequence analysis is the ultimate method for strain comparisons as it is informative during identification, characterization, and attribution--all 3 major stages of the investigation--and at all levels of microbial strain identity resolution (ie, it resolves the full spectrum from family to isolate). Given these capabilities, one bottleneck in microbial forensics investigations is the availability of high-quality reference databases of bacterial whole-genome sequences. To be of high quality, databases need to be curated and accurate in terms of sequences, metadata, and genetic diversity coverage. The development of whole-genome sequence databases will be instrumental in successfully tracing pathogens in the future.

The Importance of Diet and Gut Health to the Treatment and Prevention of Mental Disorders.

PubMed

Dawson, S L; Dash, S R; Jacka, F N

2016-01-01

The departure from traditional lifestyles and the rising disease burden of mental disorders are increasing global health concerns. Changes in diet around the world mean that populations are now increasingly reliant on highly processed, poor quality foods, which have been linked to increased risk for mental disorder. Conversely, a nutrient-rich diet is understood to be protective of mental health, and researchers are now aiming to understand the biological underpinnings of this relationship. The gut microbiota has been proposed as a key mediator of this link, given its association with both diet and mental health. Importantly, several critical "windows of opportunity" for prevention and intervention have been identified, particularly early life and adolescence; these are periods of rapid development and transition that provide a foundation for future health. Strategies that promote overall diet quality, high in fiber and nutrients, have been linked to increased microbial diversity and gut health. Improving diet quality and subsequent gut health may have benefits for individuals' mental health, as well as the mental health of future generations. Here we discuss specific, targeted dietary and gut focused strategies for the prevention and treatment of mental disorder. © 2016 Elsevier Inc. All rights reserved.

Quality of wastewater reuse in agricultural irrigation and its impact on public health.

PubMed

Al-Hammad, Bushra Ahmed; Abd El-Salam, Magda Magdy; Ibrahim, Sahar Yassin

2014-11-01

This study is planned to perform a sanitary survey of the largest sewage treatment plant in Riyadh, KSA, fortnightly for 6 months to examine its effluent quality as an example for the growing dependence on reuse of treated municipal wastewater in agricultural irrigation purposes to cope with increasing water shortage. The biological and physico-chemical parameters of 12 wastewater samples from the plant were examined using standard methods. The physico-chemical analysis indicated that the surveyed municipal wastewater treatment plant contained some of the studied parameters, such as turbidity, total suspended solids, biochemical oxygen demand, chemical oxygen demand and residual chlorine above the maximum permissible wastewater limits set by the Saudi Standards. However, heavy metal concentrations in all samples were lower than the recommended standards. Total and faecal coliform counts were above the permissible limits indicating poor sanitation level. Fifty percent of all wastewater samples were contaminated with faecal coliforms but, surprisingly, Escherichia coli were only detected in 8.3 % of the samples. Regular monitoring and enhancement of microbial and physico-chemical parameters of the wastewater quality served by different wastewater treatment plants for reuse in agricultural irrigation is recommended to preserve the environment and public health.

On the Rocks: Microbiological Quality and Microbial Diversity of Packaged Ice in Southern California.

PubMed

Lee, Kun Ho; Ab Samad, Liana S; Lwin, Phillip M; Riedel, Stefan F; Magin, Ashley; Bashir, Mina; Vaishampayan, Parag A; Lin, Wei-Jen

2017-06-01

Ice is defined as a food and is frequently used in direct contact with food and beverages. Packaged ice is commercially produced and can be easily found in grocery and convenience stores. However, the quality and safety of packaged ice products is not consistent. The Packaged Ice Quality Control Standards manual (PIQCS) published by the International Packaged Ice Association provides the quality and processing standards for packaged ice produced by its members. Packaged ice produced on the premise of stores (on-site packaged ice) is not required to be in compliance with these standards. In this study, packaged ice produced by manufacturing plants or by in-store bagger (ISB) machines and on-site packaged ice were compared for their microbiological quality and microbial diversity. Our results revealed that 19% of the 120 on-site packaged ice samples did not meet the PIQCS microbial limit of 500 CFU/mL (or g) and also the absence of coliforms and Escherichia coli . Staphylococci were found in 34% of the on-site packaged ice samples, most likely through contamination from the packaging workers. None of the ISB and manufactured packaged ice samples had unacceptable microbial levels, and all were devoid of staphylococci. Salmonella was absent in all samples analyzed in this study. Microbial community analysis of ice based on 16S/18S rRNA targeted sequencing revealed a much higher microbial diversity and abundance in the on-site packaged ice than in the ISB ice. Proteobacteria, especially Alphaproteobacteria and Betaproteobacteria, were the dominant bacterial groups in all samples tested. Most of these bacteria were oligotrophic; however, a few opportunistic or potential pathogens were found at low levels in the on-site packaged ice but not in the ISB packaged ice. The types of microbes identified may provide information needed to investigate potential sources of contamination. Our data also suggest a need for enforcement of processing standards during the on-site packaging of ice.

Development of autochthonous microbial consortia for enhanced phytoremediation of salt-marsh sediments contaminated with cadmium.

PubMed

Teixeira, Catarina; Almeida, C Marisa R; Nunes da Silva, Marta; Bordalo, Adriano A; Mucha, Ana P

2014-09-15

Microbial assisted phytoremediation is a promising, though yet poorly explored, new remediation technique. The aim of this study was to develop autochthonous microbial consortia resistant to cadmium that could enhance phytoremediation of salt-marsh sediments contaminated with this metal. The microbial consortia were selectively enriched from rhizosediments colonized by Juncus maritimus and Phragmites australis. The obtained consortia presented similar microbial abundance but a fairly different community structure, showing that the microbial community was a function of the sediment from which the consortia were enriched. The effect of the bioaugmentation with the developed consortia on cadmium uptake, and the microbial community structure associated to the different sediments were assessed using a microcosm experiment. Our results showed that the addition of the cadmium resistant microbial consortia increased J. maritimus metal phytostabilization capacity. On the other hand, in P. australis, microbial consortia amendment promoted metal phytoextraction. The addition of the consortia did not alter the bacterial structure present in the sediments at the end of the experiments. This study provides new evidences that the development of autochthonous microbial consortia for enhanced phytoremediation of salt-marsh sediments contaminated with cadmium might be a simple, efficient, and environmental friendly remediation procedure. Development of autochthonous microbial consortia resistant to cadmium that enhanced phytoremediation by salt-marsh plants, without a long term effect on sediment bacterial diversity. Copyright © 2014 Elsevier B.V. All rights reserved.

Seasonal dynamics alter taxonomical and functional microbial profiles in Pampa biome soils under natural grasslands

PubMed Central

Barboza, Anthony Diego Muller; Pylro, Victor Satler; Jacques, Rodrigo Josemar Seminot; Gubiani, Paulo Ivonir; de Quadros, Fernando Luiz Ferreira; da Trindade, Júlio Kuhn; Triplett, Eric W.

2018-01-01

Soil microbial communities’ assembly is strongly tied to changes in temperature and moisture. Although microbial functional redundancy seems to overcome taxonomical composition changes, the sensitivity and resilience of soil microbial communities from subtropical regions in response to seasonal variations are still poorly understood. Thus, the development of new strategies for biodiversity conservation and sustainable management require a complete understanding of the soil abiotic process involved in the selection of microbial taxa and functions. In this work, we used state of the art molecular methodologies (Next Generation Sequencing) to compare the taxonomic (metataxonomics) and functional (metatranscriptomics) profiles among soil samples from two subtropical natural grasslands located in the Pampa biome, Brazil, in response to short-term seasonal variations. Our data suggest that grasslands maintained a stable microbial community membership along the year with oscillation in abundance. Apparently soil microbial taxa are more susceptible to natural climatic disturbances while functions are more stable and change with less intensity along the year. Finally, our data allow us to conclude that the most abundant microbial groups and functions were shared between seasons and locations reflecting the existence of a stable taxonomical and functional core microbiota.

Microbial Community Response to Warming and Correlations to Organic Carbon Degradation in an Arctic Tundra Soil

NASA Astrophysics Data System (ADS)

Yang, Z.; Yang, S.; Zhou, J.; Wullschleger, S. D.; Graham, D. E.; Yang, Y.; Gu, B.

2016-12-01

Climate warming increases microbial activity and thus decomposition of soil organic carbon (SOC) stored in Arctic tundra, but changes in microbial community and its correlations to SOC decomposition are poorly understood. Using a microbial functional gene array (GeoChip 5.0), we examined the microbial functional community structure changes with temperature (-2 and +8 °C) in an anoxic incubation experiment with a high-centered polygon trough soil from Barrow, Alaska. Through a 122-day incubation, we show that functional community structure was significantly altered (P < 0.05) by 8 °C warming, with functional diversity decreasing in response to warming and rapid degradation of the labile soil organic substrates. In contrast, microbial community structure was largely unchanged by -2 °C incubation. In the organic layer soil, gene abundances associated with fermentation, methanogenesis, and iron reduction all decreased significantly (P < 0.05) following the incubation at 8 °C. These observations corroborate strongly with decreased methane and reducing sugar production rates and iron reduction during the incubation. These results demonstrate a rapid and sensitive microbial response to increasing soil temperature, and suggest important roles of microbial communities in moderating SOC degradation and iron cycling in warming Arctic tundra.

Impacts of forest harvest on active carbon and microbial properties of a volcanic ash cap soil in northern Idaho

Treesearch

Deborah S. Page-Dumroese; Matt D. Busse; Steven T. Overby; Brian D. Gardner; Joanne M. Tirocke

2015-01-01

Soil quality assessments are essential for determining impacts on belowground microbial community structure and function. We evaluated the suitability of active carbon (C), a rapid field test, as an indicator of soil biological quality in five paired forest stands (clear cut harvested 40 years prior and unharvested) growing on volcanic ash-cap soils in northern Idaho....

Soil microbial diversity and activity as terroir elements of Sangiovese vineyards in the Chianti Classico region (Italy)

NASA Astrophysics Data System (ADS)

Fabiani, Arturo; Mocali, Stefano; Priori, Simone; Valboa, Giuseppe; Vignozzi, Nadia; Pellegrini, Sergio; Storchi, Paolo; Perria, Rita; Costantini, Edoardo

2016-04-01

Linking the uniqueness and quality of grapes and wine to the environment they are produced, based on the terroir concept, have recently become popular in many parts of world. The natural components of terroir are actually a set of processes, which together create a delicate equilibrium and regulation of its effect on products in both space and time. Climate, geology, geomorphology and soil are therefore the main environmental factors which make up the terroir effect on different scales. However, information on the impact of soil microbial communities on soil functions, grapevine plants and wine quality is still lacking. Thus, four of the most suitable areas (so called "cru") for the production of Sangiovese wine were chosen within the Barone Ricasoli farm of Brolio, the largest winery in the Chianti Classico area in central Italy: Fattoio, Miniera, Ceni and Colli-Agresto. Based on previous pedological and sensing technologies surveys, each area was further divided into two distinct homogeneous areas of about 1.5 ha called Basic Terroir Unit (UTB), which were monitored over 3 years (2012-2014) for the soil the chemical-physical variability (moisture, organic matter, nitrogen, potassium), the vineyard physiological status (water stress, grape production, characteristics of the grapes and wine) and the structure and activity of soil microbial communities (determined through DGGE, soil respiration and microbial biomass, respectively). The aim of the work was to assess the relationships among soil parameters and vine quality at intra- and inter- UTB level and, in particular, the potential impact of microbial composition and/or function on the terroir concept. The overall results highlighted a microbial community structure specific for each cru area and, in particular, associated to each UTB. Furthermore, microbial activity in Miniera and Ceni appeared to be positively related to Sangiovese quality, as determined through the Sangiovese Performance Index. However, except for Fattoio area which showed a higher stability over time, all the other cru displayed a remarkably higher variability in terms of both microbial community structure and functions, suggesting a predominant role of annual climatic variations.

Efficacy of different washing solutions and contact times on the microbial quality and safety of fresh-cut paprika.

PubMed

Das, B Kumar; Kim, Ji Gang; Choi, Ji Weon

2011-10-01

The role of different washing solutions and contact times was investigated to determine their use as potential sanitizers for maintaining the microbial quality and food safety of fresh-cut paprika. Samples were cut into small pieces, washed for both 90 and 180 s by different washing solutions: tap water, chlorinated water (100 mg/L and pH 6.5-7), electrolyzed water (pH 7.2) and ozonized water (4 mg/L). Then, samples were packaged in 50 µm polypropylene bags and stored at 5 °C for 12 days, followed by an evaluation of the antimicrobial efficacy of the treatments. Various quality and safety parameters, such as gas composition, color, off-odor, electrical conductivity and microbial numbers, were evaluated during storage. Results revealed insignificant differences in gas composition, and no off-odor was observed in any of the samples during the storage period. However, longer contact time resulted in slightly lower hue angle value than a short one for all washing solutions. Moreover, samples washed with ozone washings showed lower electrolyte leakage than other washing solutions. Samples washed for longer contact time except those washed in ozonized water showed increased microbial numbers during storage. Hence, it has been concluded that longer contact time with ozone has positive effects, whereas the other washing solutions adversely affect the microbial quality and safety aspects of fresh-cut paprika.

Microbial community assembly and metabolic function during mammalian corpse decomposition

USGS Publications Warehouse

Metcalf, Jessica L; Xu, Zhenjiang Zech; Weiss, Sophie; Lax, Simon; Van Treuren, Will; Hyde, Embriette R.; Song, Se Jin; Amir, Amnon; Larsen, Peter; Sangwan, Naseer; Haarmann, Daniel; Humphrey, Greg C; Ackermann, Gail; Thompson, Luke R; Lauber, Christian; Bibat, Alexander; Nicholas, Catherine; Gebert, Matthew J; Petrosino, Joseph F; Reed, Sasha C.; Gilbert, Jack A; Lynne, Aaron M; Bucheli, Sibyl R; Carter, David O; Knight, Rob

2016-01-01

Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations.

Microbial community assembly and metabolic function during mammalian corpse decomposition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Metcalf, J. L.; Xu, Z. Z.; Weiss, S.

2015-12-10

Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in lowmore » abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations.« less

Microbial communities and natural fermentation of corn silages prepared with farm bunker-silo in Southwest China.

PubMed

Guan, Hao; Yan, Yanhong; Li, Xiaoling; Li, Xiaomei; Shuai, Yang; Feng, Guangyan; Ran, Qifan; Cai, Yimin; Li, Ying; Zhang, Xinquan

2018-06-08

This study analyzed the variation of microbial communities, their achieved fermentation quality, and the association between microbial diversity and environmental factors after ensiling of 96 samples prepared with bunker-silo in Southwest China. Most of natural corn silages achieved good fermentation, e.g., low pH value (<4.2) and high levels of lactic acid (36.26-79.83 mg/g DM). Weissella species were the dominant epiphytic bacteria in raw material, while Lactobacillus and Acetobacter species were prevalent in silages. Natural Lactobacillus and Pediococcus species produced more lactic acid during ensiling, while the production of acetic acid was highly positively correlated with both Acetobacter and Bradyrhizobium species. Rainfall and humidity affected community of epiphytic bacteria on the corn material, and the temperature affected richness of bacterial species during ensiling. The results confirmed that microbial community of silages in hot and humid area is unique and climatic factors ultimately affect the fermentation quality through influencing microbial community. Copyright © 2018 Elsevier Ltd. All rights reserved.

Changes in Microbial Plankton Assemblages Induced by Mesoscale Oceanographic Features in the Northern Gulf of Mexico.

PubMed

Williams, Alicia K; McInnes, Allison S; Rooker, Jay R; Quigg, Antonietta

2015-01-01

Mesoscale circulation generated by the Loop Current in the Northern Gulf of Mexico (NGOM) delivers growth-limiting nutrients to the microbial plankton of the euphotic zone. Consequences of physicochemically driven community shifts on higher order consumers and subsequent impacts on the biological carbon pump remain poorly understood. This study evaluates microbial plankton <10 μm abundance and community structure across both cyclonic and anti-cyclonic circulation features in the NGOM using flow cytometry (SYBR Green I and autofluorescence parameters). Non-parametric multivariate hierarchical cluster analyses indicated that significant spatial variability in community structure exists such that stations that clustered together were defined as having a specific 'microbial signature' (i.e. statistically homogeneous community structure profiles based on relative abundance of microbial groups). Salinity and a combination of sea surface height anomaly and sea surface temperature were determined by distance based linear modeling to be abiotic predictor variables significantly correlated to changes in microbial signatures. Correlations between increased microbial abundance and availability of nitrogen suggest nitrogen-limitation of microbial plankton in this open ocean area. Regions of combined coastal water entrainment and mesoscale convergence corresponded to increased heterotrophic prokaryote abundance relative to autotrophic plankton. The results provide an initial assessment of how mesoscale circulation potentially influences microbial plankton abundance and community structure in the NGOM.

Forest Soil Phosphorus Resources and Fertilization Affect Ectomycorrhizal Community Composition, Beech P Uptake Efficiency, and Photosynthesis

PubMed Central

Zavišić, Aljosa; Yang, Nan; Marhan, Sven; Kandeler, Ellen; Polle, Andrea

2018-01-01

Phosphorus (P) is an important nutrient, whose plant-available form phosphate is often low in natural forest ecosystems. Mycorrhizal fungi mine the soil for P and supply their host with this resource. It is unknown how ectomycorrhizal communities respond to changes in P availability. Here, we used young beech (Fagus sylvatica L.) trees in natural forest soil from a P-rich and P-poor site to investigate the impact of P amendment on soil microbes, mycorrhizas, beech P nutrition, and photosynthesis. We hypothesized that addition of P to forest soil increased P availability, thereby, leading to enhanced microbial biomass and mycorrhizal diversity in P-poor but not in P-rich soil. We expected that P amendment resulted in increased plant P uptake and enhanced photosynthesis in both soil types. Young beech trees with intact soil cores from a P-rich and a P-poor forest were kept in a common garden experiment and supplied once in fall with triple superphosphate. In the following summer, labile P in the organic layer, but not in the mineral top soil, was significantly increased in response to fertilizer treatment. P-rich soil contained higher microbial biomass than P-poor soil. P treatment had no effect on microbial biomass but influenced the mycorrhizal communities in P-poor soil and shifted their composition toward higher similarities to those in P-rich soil. Plant uptake efficiency was negatively correlated with the diversity of mycorrhizal communities and highest for trees in P-poor soil and lowest for fertilized trees. In both soil types, radioactive P tracing (H333PO4) revealed preferential aboveground allocation of new P in fertilized trees, resulting in increased bound P in xylem tissue and enhanced soluble P in bark, indicating increased storage and transport. Fertilized beeches from P-poor soil showed a strong increase in leaf P concentrations from deficient to luxurious conditions along with increased photosynthesis. Based on the divergent behavior of beech in P-poor and P-rich forest soil, we conclude that acclimation of beech to low P stocks involves dedicated mycorrhizal community structures, low P reserves in storage tissues and photosynthetic inhibition, while storage and aboveground allocation of additional P occurs regardless of the P nutritional status. PMID:29706979

The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation.

PubMed

Mavromatis, Konstantinos; Land, Miriam L; Brettin, Thomas S; Quest, Daniel J; Copeland, Alex; Clum, Alicia; Goodwin, Lynne; Woyke, Tanja; Lapidus, Alla; Klenk, Hans Peter; Cottingham, Robert W; Kyrpides, Nikos C

2012-01-01

The emergence of next generation sequencing (NGS) has provided the means for rapid and high throughput sequencing and data generation at low cost, while concomitantly creating a new set of challenges. The number of available assembled microbial genomes continues to grow rapidly and their quality reflects the quality of the sequencing technology used, but also of the analysis software employed for assembly and annotation. In this work, we have explored the quality of the microbial draft genomes across various sequencing technologies. We have compared the draft and finished assemblies of 133 microbial genomes sequenced at the Department of Energy-Joint Genome Institute and finished at the Los Alamos National Laboratory using a variety of combinations of sequencing technologies, reflecting the transition of the institute from Sanger-based sequencing platforms to NGS platforms. The quality of the public assemblies and of the associated gene annotations was evaluated using various metrics. Results obtained with the different sequencing technologies, as well as their effects on downstream processes, were analyzed. Our results demonstrate that the Illumina HiSeq 2000 sequencing system, the primary sequencing technology currently used for de novo genome sequencing and assembly at JGI, has various advantages in terms of total sequence throughput and cost, but it also introduces challenges for the downstream analyses. In all cases assembly results although on average are of high quality, need to be viewed critically and consider sources of errors in them prior to analysis. These data follow the evolution of microbial sequencing and downstream processing at the JGI from draft genome sequences with large gaps corresponding to missing genes of significant biological role to assemblies with multiple small gaps (Illumina) and finally to assemblies that generate almost complete genomes (Illumina+PacBio).

Microbial and nutritional aspects on the production of live feeds in a fish farming industry.

PubMed

De Donno, A; Lugoli, F; Bagordo, F; Vilella, S; Campa, A; Grassi, T; Guido, M

2010-03-01

Aquaculture is an enterprise in constant development, in particular relating to its effect on the environment and also the quality of its products. It represents a valid alternative to traditional fishing, facing the increasing demand for fish products. To guarantee to the consumer a product of high nutritional, organoleptic and hygienic quality, it is fundamental to monitor every phase of the fish farming industry, isolating the potential risk points. For this reason there has been a rapid evolution of productive technique, particularly in the technology, artificial reproduction and feed sectors. The aim of this research has been the monitoring of the evolution of certain microbial and nutritional quality indexes (total microbial counts and lipid analysis on suspensions of Rotifers and Artemia, used as live feed) in the larval phase of the productive cycle of the farm raised fish, in an intensive system. The study has shown an increment in the total microbial counts in the fish farming industry within the production of Rotifers and Artemia, more evident in the suspensions of Rotifers. In addition the study has demonstrated that the maintenance phase, in the enrichment protocol, can reduce the EPA and DHA content. The results confirm the importance of microbial and nutritional control of the live feeds before they get supplied to fish larvae.

Impact of the reusing of food manufacturing wastewater for irrigation in a closed system on the microbiological quality of the food crops.

PubMed

Beneduce, Luciano; Gatta, Giuseppe; Bevilacqua, Antonio; Libutti, Angela; Tarantino, Emanuele; Bellucci, Micol; Troiano, Eleonora; Spano, Giuseppe

2017-11-02

In order to evaluate if the reuse of food industry treated wastewater is compatible for irrigation of food crops, without increased health risk, in the present study a cropping system, in which ground water and treated wastewater were used for irrigation of tomato and broccoli, during consecutive crop seasons was monitored. Water, crop environment and final products were monitored for microbial indicators and pathogenic bacteria, by conventional and molecular methods. The microbial quality of the irrigation waters influenced sporadically the presence of microbial indicators in soil. No water sample was found positive for pathogenic bacteria, independently from the source. Salmonella spp. and Listeria monocytogenes were detected in soil samples, independently from the irrigation water source. No pathogen was found to contaminate tomato plants, while Listeria monocytogenes and E. coli O157:H7 were detected on broccoli plant, but when final produce were harvested, no pathogen was detected on edible part. The level of microbial indicators and detection of pathogenic bacteria in field and plant was not dependent upon wastewater used. Our results, suggest that reuse of food industry wastewater for irrigation of agricultural crop can be applied without significant increase of potential health risk related to microbial quality. Copyright © 2017 Elsevier B.V. All rights reserved.

Effect of sodium alginate coating incorporated with nisin, Cinnamomum zeylanicum, and rosemary essential oils on microbial quality of chicken meat and fate of Listeria monocytogenes during refrigeration.

PubMed

Raeisi, Mojtaba; Tabaraei, Alijan; Hashemi, Mohammad; Behnampour, Nasser

2016-12-05

The present study was conducted to preserve the microbial quality of chicken meat fillets during storage time by using sodium alginate active coating solutions incorporated with different natural antimicrobials including nisin, Cinnamomum zeylanicum (cinnamon), and rosemary essential oils (EOs) which were added individually and in combination. The samples were stored in refrigeration condition for 15days and were analyzed for total viable count, Enterobacteriaceae count, lactic acid bacteria count, Pseudomonas spp. count, psychrotrophic count, and yeast and mold count, as well as fate of inoculated Listeria monocytogenes at 3-day intervals. Results indicated that values of tested microbial indicators in all samples increased during storage. Antimicrobial agents, when used in combination, had stronger effect in preserving the microbial quality of chicken meat samples rather than their individual use and the strongest effect was observed in samples coated with alginate solution containing both cinnamon and rosemary EOs (CEO+REO). However, all treatments significantly inhibited microbial growth when compared to the control (P<0.05). Therefore, based on the results of this study, application of alginate coating solutions containing nisin, cinnamon, and rosemary EOs as natural preservatives is recommended in meat products especially in chicken meats. Copyright © 2016. Published by Elsevier B.V.

A Pilot Study of Microbial Contamination of Subtropical Recreational Waters

PubMed Central

Fleming, Lora E; Solo, Gabriele H.; Elmir, Samir; Shibata, Tomoyuki; Squicciarini, Dominick; Quirino, Wendy; Arguello, Margia; Van de Bogart, Gayl

2009-01-01

Microbial water quality indicators are used to determine whether a water body is safe for recreational purposes. There have been concerns raised about the appropriate use of microbial indicators to regulate recreational uses of water bodies, in particular those located in tropical and sub-tropical environments. This prospective cohort pilot study evaluated the relationship between microbial water quality indicators and public health within two public beaches without known sewage discharge, but with historically high microbial levels for one beach, in subtropical Miami-Dade County (Florida). Monitoring was conducted in three phases: daily water monitoring, beach sand sampling, and spatially intense water sampling. An epidemiological questionnaire from a Los Angeles recreational beach-goer study was used to assess the self-reported swimming-related symptoms and exposures. There was no significant association between the number nor the type of reported symptoms and the different sampling months or beach sites, although persons who returned repeatedly to the beach were more likely to report symptoms. The number of indicator organisms correlated negatively with the frequency of symptoms reported by recreational beach goers. Results of the daily monitoring indicated that different indicators provided conflicting results concerning beach water quality. Larger epidemiologic studies with individual exposure monitoring are recommended to further evaluate these potentially important associations in subtropical recreational waters. PMID:20151031

High-Throughput Sequencing of Microbial Community Diversity and Dynamics during Douchi Fermentation.

PubMed

Yang, Lin; Yang, Hui-Lin; Tu, Zong-Cai; Wang, Xiao-Lan

2016-01-01

Douchi is a type of Chinese traditional fermented food that is an important source of protein and is used in flavouring ingredients. The end product is affected by the microbial community present during fermentation, but exactly how microbes influence the fermentation process remains poorly understood. We used an Illumina MiSeq approach to investigate bacterial and fungal community diversity during both douchi-koji making and fermentation. A total of 181,443 high quality bacterial 16S rRNA sequences and 221,059 high quality fungal internal transcribed spacer reads were used for taxonomic classification, revealing eight bacterial and three fungal phyla. Firmicutes, Actinobacteria and Proteobacteria were the dominant bacterial phyla, while Ascomycota and Zygomycota were the dominant fungal phyla. At the genus level, Staphylococcus and Weissella were the dominant bacteria, while Aspergillus and Lichtheimia were the dominant fungi. Principal coordinate analysis showed structural separation between the composition of bacteria in koji making and fermentation. However, multivariate analysis of variance based on unweighted UniFrac distances did identify distinct differences (p <0.05), and redundancy analysis identified two key genera that are largely responsible for the differences in bacterial composition between the two steps. Staphylococcus was enriched in koji making, while Corynebacterium was enriched in fermentation. This is the first investigation to integrate douchi fermentation and koji making and fermentation processes through this technological approach. The results provide insight into the microbiome of the douchi fermentation process, and reveal a structural separation that may be stratified by the environment during the production of this traditional fermented food.

High-Throughput Sequencing of Microbial Community Diversity and Dynamics during Douchi Fermentation

PubMed Central

Tu, Zong-cai; Wang, Xiao-lan

2016-01-01

Douchi is a type of Chinese traditional fermented food that is an important source of protein and is used in flavouring ingredients. The end product is affected by the microbial community present during fermentation, but exactly how microbes influence the fermentation process remains poorly understood. We used an Illumina MiSeq approach to investigate bacterial and fungal community diversity during both douchi-koji making and fermentation. A total of 181,443 high quality bacterial 16S rRNA sequences and 221,059 high quality fungal internal transcribed spacer reads were used for taxonomic classification, revealing eight bacterial and three fungal phyla. Firmicutes, Actinobacteria and Proteobacteria were the dominant bacterial phyla, while Ascomycota and Zygomycota were the dominant fungal phyla. At the genus level, Staphylococcus and Weissella were the dominant bacteria, while Aspergillus and Lichtheimia were the dominant fungi. Principal coordinate analysis showed structural separation between the composition of bacteria in koji making and fermentation. However, multivariate analysis of variance based on unweighted UniFrac distances did identify distinct differences (p <0.05), and redundancy analysis identified two key genera that are largely responsible for the differences in bacterial composition between the two steps. Staphylococcus was enriched in koji making, while Corynebacterium was enriched in fermentation. This is the first investigation to integrate douchi fermentation and koji making and fermentation processes through this technological approach. The results provide insight into the microbiome of the douchi fermentation process, and reveal a structural separation that may be stratified by the environment during the production of this traditional fermented food. PMID:27992473

Microbes as engines of ecosystem function: When does community structure enhance predictions of ecosystem processes?

DOE PAGES

Graham, Emily B.; Knelman, Joseph E.; Schindlbacher, Andreas; ...

2016-02-24

In this study, microorganisms are vital in mediating the earth’s biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: ‘When do we need to understand microbial community structure to accurately predict function?’ We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of processmore » rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.« less

Microbes as engines of ecosystem function: When does community structure enhance predictions of ecosystem processes?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Graham, Emily B.; Knelman, Joseph E.; Schindlbacher, Andreas

In this study, microorganisms are vital in mediating the earth’s biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: ‘When do we need to understand microbial community structure to accurately predict function?’ We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of processmore » rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.« less

Microbial community succession in alkaline, saline bauxite residue: a cross-refinery study

NASA Astrophysics Data System (ADS)

Santini, T.; Malcolm, L. I.; Tyson, G. W.; Warren, L. A.

2015-12-01

Bauxite residue, a byproduct of the Bayer process for alumina refining, is an alkaline, saline tailings material that is generally considered to be inhospitable to microbial life. In situ remediation strategies promote soil formation in bauxite residue by enhancing leaching of saline, alkaline pore water, and through incorporation of amendments to boost organic matter content, decrease pH, and improve physical structure. The amelioration of chemical and physical conditions in bauxite residue is assumed to support diversification of microbial communities from narrow, poorly functioning microbial communities towards diverse, well-functioning communities. This study aimed to characterise microbial communities in fresh and remediated bauxite residues from refineries worldwide, to identify (a) whether initial microbial communities differed between refineries; (b) major environmental controls on microbial community composition; and (c) whether remediation successfully shifts the composition of microbial communities in bauxite residue towards those found in reference (desired endpoint) soils. Samples were collected from 16 refineries and characterised using 16S amplicon sequencing to examine microbial community composition and structure, in conjunction with physicochemical analyses. Initial microbial community composition was similar across refineries but partitioned into two major groups. Microbial community composition changes slowly over time and indicates that alkalinity and salinity inhibit diversification. Microbially-based strategies for in situ remediation should consider the initial microbial community composition and whether the pre-treatment of chemical properties would optimise subsequent bioremediation outcomes. During in situ remediation, microbial communities become more diverse and develop wider functional capacity, indicating progression towards communities more commonly observed in natural grassland and forest soils.

Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?

PubMed Central

Graham, Emily B.; Knelman, Joseph E.; Schindlbacher, Andreas; Siciliano, Steven; Breulmann, Marc; Yannarell, Anthony; Beman, J. M.; Abell, Guy; Philippot, Laurent; Prosser, James; Foulquier, Arnaud; Yuste, Jorge C.; Glanville, Helen C.; Jones, Davey L.; Angel, Roey; Salminen, Janne; Newton, Ryan J.; Bürgmann, Helmut; Ingram, Lachlan J.; Hamer, Ute; Siljanen, Henri M. P.; Peltoniemi, Krista; Potthast, Karin; Bañeras, Lluís; Hartmann, Martin; Banerjee, Samiran; Yu, Ri-Qing; Nogaro, Geraldine; Richter, Andreas; Koranda, Marianne; Castle, Sarah C.; Goberna, Marta; Song, Bongkeun; Chatterjee, Amitava; Nunes, Olga C.; Lopes, Ana R.; Cao, Yiping; Kaisermann, Aurore; Hallin, Sara; Strickland, Michael S.; Garcia-Pausas, Jordi; Barba, Josep; Kang, Hojeong; Isobe, Kazuo; Papaspyrou, Sokratis; Pastorelli, Roberta; Lagomarsino, Alessandra; Lindström, Eva S.; Basiliko, Nathan; Nemergut, Diana R.

2016-01-01

Microorganisms are vital in mediating the earth’s biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: ‘When do we need to understand microbial community structure to accurately predict function?’ We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology. PMID:26941732

Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?

PubMed

Graham, Emily B; Knelman, Joseph E; Schindlbacher, Andreas; Siciliano, Steven; Breulmann, Marc; Yannarell, Anthony; Beman, J M; Abell, Guy; Philippot, Laurent; Prosser, James; Foulquier, Arnaud; Yuste, Jorge C; Glanville, Helen C; Jones, Davey L; Angel, Roey; Salminen, Janne; Newton, Ryan J; Bürgmann, Helmut; Ingram, Lachlan J; Hamer, Ute; Siljanen, Henri M P; Peltoniemi, Krista; Potthast, Karin; Bañeras, Lluís; Hartmann, Martin; Banerjee, Samiran; Yu, Ri-Qing; Nogaro, Geraldine; Richter, Andreas; Koranda, Marianne; Castle, Sarah C; Goberna, Marta; Song, Bongkeun; Chatterjee, Amitava; Nunes, Olga C; Lopes, Ana R; Cao, Yiping; Kaisermann, Aurore; Hallin, Sara; Strickland, Michael S; Garcia-Pausas, Jordi; Barba, Josep; Kang, Hojeong; Isobe, Kazuo; Papaspyrou, Sokratis; Pastorelli, Roberta; Lagomarsino, Alessandra; Lindström, Eva S; Basiliko, Nathan; Nemergut, Diana R

2016-01-01

Microorganisms are vital in mediating the earth's biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: 'When do we need to understand microbial community structure to accurately predict function?' We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.

Performance of two quantitative PCR methods for microbial source tracking of human sewage and implications for microbial risk assessment in recreational waters

EPA Science Inventory

Before new, rapid quantitative PCR (qPCR) methods for recreational water quality assessment and microbial source tracking (MST) can be useful in a regulatory context, an understanding of the ability of the method to detect a DNA target (marker) when the contaminant soure has been...

A new method for long-term storage of titred microbial standard solutions suitable for microbiologic quality control activities of pharmaceutical companies.

PubMed

Chiellini, Carolina; Mocali, Stefano; Fani, Renato; Ferro, Iolanda; Bruschi, Serenella; Pinzani, Alessandro

2016-08-01

Commercially available lyophilized microbial standards are expensive and subject to reduction in cell viability due to freeze-drying stress. Here we introduce an inexpensive and straightforward method for in-house microbial standard preparation and cryoconservation that preserves constant cell titre and cell viability over 14 months.

Combination of sodium chlorite and calcium propionate reduces enzymatic browning and microbial population of fresh-cut ‘Granny Smith’ apples

USDA-ARS?s Scientific Manuscript database

Tissue browning and microbial growth are the main concerns associated with fresh-cut apples. In this study, effects of sodium chlorite (SC) and calcium propionate (CP), individually and combined, on quality and microbial population of apple slices were investigated. ‘Granny Smith’ apple slices, dipp...

Microbial Source Tracking

EPA Science Inventory

Bacterial indicators of fecal contamination provide the basis for assessing the microbial quality of environmental waters. While the indicator concept has overall helped reduce waterborne outbreaks in recreational waters, the public health value of currently used indicator bacter...

Genetic and functional diversity of soil microbial communities associated to grapevine plants and wine quality

NASA Astrophysics Data System (ADS)

Mocali, Stefano; Fabiani, Arturo; Kuramae, Eiko; de Hollander, Mattias; Kowalchuk, George A.; Vignozzi, Nadia; Valboa, Giuseppe; Costantini, Edoardo

2013-04-01

Despite the economic importance of vineyards in Italy, the wine sector is facing severe challenges from increased global competition and climate changes. The quality of the grape at harvest has a strong direct impact on wine final quality and the strong relationship between wine composition, aroma, taste, and soil properties has been outlined in the "Terroir concept". However, information on the impact of soil microbial communities on soil functions, grapevine plants, and wine quality is generally lacking. In the current study, soils from two close sites in Central Tuscany (BRO11 and BRO12) cultivated with the same grapevine cultivar Sangiovese, but with contrasting wine quality, were examined. Although the BRO12 site provided a better wine quality than the BRO11, the two soils showed similar physical, chemical, and hydrological properties. Also soil humidity, as determined by FDR (Frequency Domain Reflectometry) sensors, indicated a similar water availability in the first 75 cm during a three years trial (2000-2010). Interestingly, the mean three years value of the ratio between the two stable carbon isotopes 13C/12C, measured in the alcohol of the wines, was significantly higher in BRO12 than in BRO11 (-28,3‰ and -24,4‰, respectively), indicating the presence of a relatively higher water stress in the BRO11 soil. Functional GeoChip microarray analyses revealed higher presence of Actinobacteria in the BRO12 than in the BRO11 soil, where the alfa-Proteobacteria were more abundant. Furthermore, a consistent difference in genes involved in S cycling, with a significant overrepresentation of sulphur-oxidation genes in BRO11 and increased levels of sulphate reduction genes BRO12 was detected. These results are consistent with the high content of sulphates and the abundance of Firmicutes such as Sulfobacillus thermosulfidooxidans in the BRO11 soil. Therefore, the different microbiology of the two soils could be related to the different redox conditions of the two soils. The structure of soil microbial communities was assessed using 16S and 18S rRNA genes pyrosequencing and the determination of some soil microbial properties such as microbial respiration, microbial C-biomass were also determined. The role of both genetic and functional diversity of soil bacterial community on grape physiology and wine quality will be discussed.

Metagenomic Taxonomy-Guided Database-Searching Strategy for Improving Metaproteomic Analysis.

PubMed

Xiao, Jinqiu; Tanca, Alessandro; Jia, Ben; Yang, Runqing; Wang, Bo; Zhang, Yu; Li, Jing

2018-04-06

Metaproteomics provides a direct measure of the functional information by investigating all proteins expressed by a microbiota. However, due to the complexity and heterogeneity of microbial communities, it is very hard to construct a sequence database suitable for a metaproteomic study. Using a public database, researchers might not be able to identify proteins from poorly characterized microbial species, while a sequencing-based metagenomic database may not provide adequate coverage for all potentially expressed protein sequences. To address this challenge, we propose a metagenomic taxonomy-guided database-search strategy (MT), in which a merged database is employed, consisting of both taxonomy-guided reference protein sequences from public databases and proteins from metagenome assembly. By applying our MT strategy to a mock microbial mixture, about two times as many peptides were detected as with the metagenomic database only. According to the evaluation of the reliability of taxonomic attribution, the rate of misassignments was comparable to that obtained using an a priori matched database. We also evaluated the MT strategy with a human gut microbial sample, and we found 1.7 times as many peptides as using a standard metagenomic database. In conclusion, our MT strategy allows the construction of databases able to provide high sensitivity and precision in peptide identification in metaproteomic studies, enabling the detection of proteins from poorly characterized species within the microbiota.

Quality of tomato slices disinfected with ozonated water.

PubMed

Aguayo, Encarna; Escalona, Víctor; Silveira, Ana Cecilia; Artés, Francisco

2014-04-01

Fresh-cut industry needs novel disinfectant to replace the use of chlorine. Ozone is one of the most powerful oxidizing agents and is applied in gaseous or aqueous form for sanitation purposes. However, the strong oxidative effect could affect the nutritional and sensorial quality, in particular, when time of washing is extended. For that reason, the overall impact of ozonated water (0.4 mg/L) dipping applied during 1, 3 and 5 min compared to control washed in water during 5 min was studied in tomato slices stored during 14 days at 5 . According to the results, ozonated water treatment of 3 min achieved the best firmness retention, microbial quality (mesophilic, psychrotrophic and yeas load) and reduced the consumption of fructose and glucose. The use of ozonated water did not affect the total acidity, pH, total solid soluble, organic acid as ascorbic, fumaric or succinic acid and the sensorial parameters, which were only affected by storage time. However, the poor appearance, aroma and overall quality obtained in all treatments prevented shelf life of 14 days and the quality at acceptable levels was established in 10 days at 5 . It is recommended to wash tomato slices with 0.4 mg/L ozonated water for 3 min only. Extending treatment duration did not improve the microbiological quality, possibly due to the extra time permitting the ozone to react with other components of the fruit tissue, undermining the antimicrobial benefits.

Assessment of microbiological quality of sachet-packaged drinking water in Western Nigeria and its public health significance.

PubMed

Olaoye, O A; Onilude, A A

2009-11-01

To assess the microbiological quality of sachet-packaged drinking water in Western Nigeria and its impact on public health. Cross-sectional microbiological testing. Ninety-two sachet-packaged water samples were analysed for microbiological and metal qualities. Total bacterial and coliform counts were determined, and the presence of Escherichia coli, an important water quality indicator, was tested. The level of conformity of the water processors with the guidelines of Nigeria's quality regulatory agency was also determined. Varying levels of microbial contamination were recorded in samples from the different sampling locations. The total bacteria count ranged between 2.86 and 3.45log colony-forming units (cfu)/ml. The highest coliform count recorded was 1.62log cfu/ml. Faecal coliform E. coli was detected in one sample from Oke-Iho and one sample from Okaka, representing 2.2% of total samples. Lead and manganese were not found in any of the samples. However, iron was detected and the highest iron concentration (0.10mg/l) was detected in samples from Ikorodu. The bacteria that were identified from the water samples included E. coli, Pseudomonas aeruginosa, Enterobacter aerogenes, Klebsiella sp., Proteus vulgaris, Alcaligenes faecalis, Bacillus cereus, Staphylococcus aureus, Streptococcus lactis, Aeromonas sp. and Micrococcus luteum. Many of the water processors did not comply with the guidelines of the quality regulatory agency. Some of the sachet-packaged samples of drinking water were of poor quality. The results indicate a need for Nigeria's quality regulatory agency to take appropriate measures in safeguarding public health.

Changes in microbial community characteristics and soil organic matter with nitrogen additions in two tropical forests

Treesearch

Daniela F. Cusack; Whendee L. Silver; Margaret S. Torn; Sarah D. Burton; Mary K. Firestone

2011-01-01

Microbial communities and their associated enzyme activities affect the amount and chemical quality of carbon (C) in soils. Increasing nitrogen (N) deposition, particularly in N-rich tropical forests, is likely to change the composition and behavior of microbial communities and feed back on ecosystem structure and function. This study presents a novel assessment of...

Season mediates herbivore effects on litter and soil microbial abundance and activity in a semi-arid woodland

Treesearch

Aimee T. Classen; Steven T. Overby; Stephen C. Hart; George W. Koch; Thomas G. Whitham

2007-01-01

Herbivores can directly impact ecosystem function by altering litter quality of an ecosystem or indirectly by shifting the composition of microbial communities that mediate nutrient processes. We examined the effects of tree susceptibility and resistance to herbivory on litter microarthropod and soil microbial communities to test the general hypothesis that herbivore...

Relationship between dissolved organic matter quality and microbial community composition across polar glacial environments.

PubMed

Smith, H J; Dieser, M; McKnight, D M; SanClements, M D; Foreman, C M

2018-05-14

Vast expanses of Earth's surface are covered by ice, with microorganisms in these systems affecting local and global biogeochemical cycles. We examined microbial assemblages from habitats fed by glacial meltwater within the McMurdo Dry Valleys, Antarctica, and on the west Greenland Ice Sheet, (GrIS) evaluating potential physicochemical factors explaining trends in community structure. Microbial assemblages present in the different Antarctic dry valley habitats were dominated by Sphingobacteria and Flavobacteria, while Gammaproteobacteria and Sphingobacteria prevailed in west GrIS supraglacial environments. Microbial assemblages clustered by location (Canada Glacier, Cotton Glacier, west GrIS) and were separated by habitat type (i.e. ice, cryoconite holes, supraglacial lakes, sediment, and stream water). Community dissimilarities were strongly correlated with dissolved organic matter (DOM) quality. Microbial meltwater assemblages were most closely associated with different protein-like components of the DOM pool. Microbes in environments with mineral particles (i.e. stream sediments, cryoconite holes) were linked to DOM containing more humic-like fluorescence. Our results demonstrate the establishment of distinct microbial communities within ephemeral glacial meltwater habitats, with DOM-microbe interactions playing an integral role in shaping communities on local and polar spatial scales.

Microbial taxonomy in the post-genomic era: Rebuilding from scratch?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thompson, Cristiane C.; Amaral, Gilda R.; Campeão, Mariana

2014-12-23

Microbial taxonomy should provide adequate descriptions of bacterial, archaeal, and eukaryotic microbial diversity in ecological, clinical, and industrial environments. We re-evaluated the prokaryote species twice. It is time to revisit polyphasic taxonomy, its principles, and its practice, including its underlying pragmatic species concept. We will be able to realize an old dream of our predecessor taxonomists and build a genomic-based microbial taxonomy, using standardized and automated curation of high-quality complete genome sequences as the new gold standard.

Polythiophene biosensor for rapid detection of microbial particles in water.

PubMed

Plante, Marie-Pier; Bérubé, Eve; Bissonnette, Luc; Bergeron, Michel G; Leclerc, Mario

2013-06-12

Most microbial particles have a negatively charged surface and in this work, we describe a water quality monitoring application of a cationic polythiophene derivative (AH-35) for the rapid assessment of microbial contamination of water. Using E. coli as a prototype microbial particle, we demonstrate that the AH-35 polymer can provide a qualitative assessment of water if exposed to more than 500 CFU/mL, thereby paving the way to a new family of biosensors potentially useful for monitoring drinking water distribution systems.

Sustainable microbial water quality monitoring programme design using phage-lysis and multivariate techniques.

PubMed

Nnane, Daniel Ekane

2011-11-15

Contamination of surface waters is a pervasive threat to human health, hence, the need to better understand the sources and spatio-temporal variations of contaminants within river catchments. River catchment managers are required to sustainably monitor and manage the quality of surface waters. Catchment managers therefore need cost-effective low-cost long-term sustainable water quality monitoring and management designs to proactively protect public health and aquatic ecosystems. Multivariate and phage-lysis techniques were used to investigate spatio-temporal variations of water quality, main polluting chemophysical and microbial parameters, faecal micro-organisms sources, and to establish 'sentry' sampling sites in the Ouse River catchment, southeast England, UK. 350 river water samples were analysed for fourteen chemophysical and microbial water quality parameters in conjunction with the novel human-specific phages of Bacteroides GB-124 (Bacteroides GB-124). Annual, autumn, spring, summer, and winter principal components (PCs) explained approximately 54%, 75%, 62%, 48%, and 60%, respectively, of the total variance present in the datasets. Significant loadings of Escherichia coli, intestinal enterococci, turbidity, and human-specific Bacteroides GB-124 were observed in all datasets. Cluster analysis successfully grouped sampling sites into five clusters. Importantly, multivariate and phage-lysis techniques were useful in determining the sources and spatial extent of water contamination in the catchment. Though human faecal contamination was significant during dry periods, the main source of contamination was non-human. Bacteroides GB-124 could potentially be used for catchment routine microbial water quality monitoring. For a cost-effective low-cost long-term sustainable water quality monitoring design, E. coli or intestinal enterococci, turbidity, and Bacteroides GB-124 should be monitored all-year round in this river catchment. Copyright © 2011 Elsevier B.V. All rights reserved.

Fluorescence spectroscopy as a tool for determining microbial quality in potable water applications.

PubMed

Cumberland, Susan; Bridgeman, John; Baker, Andy; Sterling, Mark; Ward, David

2012-01-01

Building on previous work where fluorescence spectroscopy has been used to detect sewage in rivers, a portable LED spectrophotometer was used for the first time to establish bacterial numbers in a range of water samples. A mixed-method approach was used with standard bacteria enumeration techniques on diluted river water and sewage works final effluent using a number of diluents (Ringer's solution, tap water and potable spring water). Fluorescence from uncultured dilutions was detected at a 280 nm excitation/360 nm emission wavelength (corresponding to the region of tryptophan and indole fluorescence) and compared with bacteria numbers on the same cultured sample. Good correlations were obtained for total coliforms, E. coli and heterotrophic bacteria with the portable LED spectrophotometer (R2 = 0.78, 0.72 and 0.81 respectively). The results indicate that the portable spectrophotometer could be applied to establish the quality of drinking water in areas of poor sanitation that are subject to faecal contamination, where infrastructure failure has occurred in the supply of clean drinking water. This would be particularly useful where laboratory facilities are not at hand.

Effects of management practices on yield and quality of milk from smallholder dairy units in urban and peri-urban Morogoro, Tanzania.

PubMed

Gillah, Kejeri A; Kifaro, George C; Madsen, Jorgen

2014-10-01

A longitudinal study design was used to assess the management, chemical composition of cows' milk and quantify the microbial load of raw milk produced at farm level. Data were collected between December 2010 and September 2011 in Morogoro municipality. Milk samples were collected once every month and analysed for butter fat (BF), crude protein (CP), total solids (TS) and solids non-fat (SNF). Total bacterial count (TBC) and coliform counts (CC) were normalized by log transformation. The average milk yield was 7.0 l/day and was not influenced by feeding systems and breeds. Dairy cows owned by people who had no regular income produced more milk than government employees and retired officers. Means of BF, TS, SNF and CP were similar in different feeding systems. Wet season had significantly higher TBC (5.9 log10 cfu/ml) and CC (2.4 log10 cfu/ml) but feeding systems had no effect. Stocking density influenced TBC but not CC. It can be concluded that dairy cows produced low milk yield and its quality was poor.

The Mineralosphere Concept: Mineralogical Control of the Distribution and Function of Mineral-associated Bacterial Communities.

PubMed

Uroz, Stephane; Kelly, Laura Catherine; Turpault, Marie-Pierre; Lepleux, Cendrella; Frey-Klett, Pascale

2015-12-01

Soil is composed of a mosaic of different rocks and minerals, usually considered as an inert substrata for microbial colonization. However, recent findings suggest that minerals, in soils and elsewhere, favour the development of specific microbial communities according to their mineralogy, nutritive content, and weatherability. Based upon recent studies, we highlight how bacterial communities are distributed on the surface of, and in close proximity to, minerals. We also consider the potential role of the mineral-associated bacterial communities in mineral weathering and nutrient cycling in soils, with a specific focus on nutrient-poor and acidic forest ecosystems. We propose to define this microbial habitat as the mineralosphere, where key drivers of the microbial communities are the physicochemical properties of the minerals. Copyright © 2015 Elsevier Ltd. All rights reserved.

Microbial community assembly and metabolic function during mammalian corpse decomposition.

PubMed

Metcalf, Jessica L; Xu, Zhenjiang Zech; Weiss, Sophie; Lax, Simon; Van Treuren, Will; Hyde, Embriette R; Song, Se Jin; Amir, Amnon; Larsen, Peter; Sangwan, Naseer; Haarmann, Daniel; Humphrey, Greg C; Ackermann, Gail; Thompson, Luke R; Lauber, Christian; Bibat, Alexander; Nicholas, Catherine; Gebert, Matthew J; Petrosino, Joseph F; Reed, Sasha C; Gilbert, Jack A; Lynne, Aaron M; Bucheli, Sibyl R; Carter, David O; Knight, Rob

2016-01-08

Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations. Copyright © 2016, American Association for the Advancement of Science.

Effects of Resource Chemistry on the Composition and Function of Stream Hyporheic Biofilms

PubMed Central

Hall, E. K.; Besemer, K.; Kohl, L.; Preiler, C.; Riedel, K.; Schneider, T.; Wanek, W.; Battin, T. J.

2012-01-01

Fluvial ecosystems process large quantities of dissolved organic matter as it moves from the headwater streams to the sea. In particular, hyporheic sediments are centers of high biogeochemical reactivity due to their elevated residence time and high microbial biomass and activity. However, the interaction between organic matter and microbial dynamics in the hyporheic zone remains poorly understood. We evaluated how variance in resource chemistry affected the microbial community and its associated activity in experimentally grown hyporheic biofilms. To do this we fed beech leaf leachates that differed in chemical composition to a series of bioreactors filled with sediment from a sub-alpine stream. Differences in resource chemistry resulted in differences in diversity and phylogenetic origin of microbial proteins, enzyme activity, and microbial biomass stoichiometry. Specifically, increased lignin, phenolics, and manganese in a single leachate resulted in increased phenoloxidase and peroxidase activity, elevated microbial biomass carbon:nitrogen ratio, and a greater proportion of proteins of Betaproteobacteria origin. We used this model system to attempt to link microbial form (community composition and metaproteome) with function (enzyme activity) in order to better understand the mechanisms that link resource heterogeneity to ecosystem function in stream ecosystems. PMID:22347877

Microbial diversity in restored wetlands of San Francisco Bay

DOE Office of Scientific and Technical Information (OSTI.GOV)

Theroux, Susanna; Hartman, Wyatt; He, Shaomei

Wetland ecosystems may serve as either a source or a sink for atmospheric carbon and greenhouse gases. This delicate carbon balance is influenced by the activity of belowground microbial communities that return carbon dioxide and methane to the atmosphere. Wetland restoration efforts in the San Francisco Bay-Delta region may help to reverse land subsidence and possibly increase carbon storage in soils. However, the effects of wetland restoration on microbial communities, which mediate soil metabolic activity and carbon cycling, are poorly studied. In an effort to better understand the underlying factors which shape the balance of carbon flux in wetland soils,more » we targeted the microbial communities in a suite of restored and historic wetlands in the San Francisco Bay-Delta region. Using DNA and RNA sequencing, coupled with greenhouse gas monitoring, we profiled the diversity and metabolic potential of the wetland soil microbial communities along biogeochemical and wetland age gradients. Our results show relationships among geochemical gradients, availability of electron acceptors, and microbial community composition. Our study provides the first genomic glimpse into microbial populations in natural and restored wetlands of the San Francisco Bay-Delta region and provides a valuable benchmark for future studies.« less

Effects of resource chemistry on the composition and function of stream hyporheic biofilms.

USGS Publications Warehouse

Hall, E.K.; Besemer, K.; Kohl, L.; Preiler, C.; Reidel, K.; Schneider, T.; Wanek, W.; Battin, T.J.

2012-01-01

Fluvial ecosystems process large quantities of dissolved organic matter as it moves from the headwater streams to the sea. In particular, hyporheic sediments are centers of high biogeochemical reactivity due to their elevated residence time and high microbial biomass and activity. However, the interaction between organic matter and microbial dynamics in the hyporheic zone remains poorly understood. We evaluated how variance in resource chemistry affected the microbial community and its associated activity in experimentally grown hyporheic biofilms. To do this we fed beech leaf leachates that differed in chemical composition to a series of bioreactors filled with sediment from a sub-alpine stream. Differences in resource chemistry resulted in differences in diversity and phylogenetic origin of microbial proteins, enzyme activity, and microbial biomass stoichiometry. Specifically, increased lignin, phenolics, and manganese in a single leachate resulted in increased phenoloxidase and peroxidase activity, elevated microbial biomass carbon:nitrogen ratio, and a greater proportion of proteins of Betaproteobacteria origin. We used this model system to attempt to link microbial form (community composition and metaproteome) with function (enzyme activity) in order to better understand the mechanisms that link resource heterogeneity to ecosystem function in stream ecosystems.

Effects of Different Regeneration Scenarios and Fertilizer Treatments on Soil Microbial Ecology in Reclaimed Opencast Mining Areas on the Loess Plateau, China

PubMed Central

Li, Junjian; Zheng, Yuanming; Yan, Junxia; Li, Hongjian; Wang, Xiang; He, Jizheng; Ding, Guangwei

2013-01-01

The soil microbial community in reclaimed mining areas is fundamental to vegetative establishment. However, how this community responds to different regeneration scenarios and fertilizer treatments is poorly understood. This research evaluated plant and soil microbial communities from different regeneration scenarios and different fertilizer treatments. Regeneration scenarios significantly influenced soil bacterial, archaeal, and fungal rDNA abundance. The ratios of fungi to bacteria or archaea were increased with fertilizer application. The diversity of both plants and microbes was lowest in Lotus corniculatus grasslands. Regeneration scenario, fertilizer treatment, and their interaction influenced soil microbial richness, diversity and evenness indices. Labile carbon pool 2 was a significant factor affected plant and microbe communities in July, suggesting that plants and microbes may be competing for nutrients. The higher ratios of positive to negative association were found in soil bacteria and total microbe than in archaea and fungi. Stronger clustering of microbial communities from the same regeneration scenario indicated that the vegetative composition of regeneration site may have a greater influence on soil microbial communities than fertilizer treatment. PMID:23658819

Metabolic interactions and dynamics in microbial communities

NASA Astrophysics Data System (ADS)

Segre', Daniel

Metabolism, in addition to being the engine of every living cell, plays a major role in the cell-cell and cell-environment relations that shape the dynamics and evolution of microbial communities, e.g. by mediating competition and cross-feeding interactions between different species. Despite the increasing availability of metagenomic sequencing data for numerous microbial ecosystems, fundamental aspects of these communities, such as the unculturability of many isolates, and the conditions necessary for taxonomic or functional stability, are still poorly understood. We are developing mechanistic computational approaches for studying the interactions between different organisms based on the knowledge of their entire metabolic networks. In particular, we have recently built an open source platform for the Computation of Microbial Ecosystems in Time and Space (COMETS), which combines metabolic models with convection-diffusion equations to simulate the spatio-temporal dynamics of metabolism in microbial communities. COMETS has been experimentally tested on small artificial communities, and is scalable to hundreds of species in complex environments. I will discuss recent developments and challenges towards the implementation of models for microbiomes and synthetic microbial communities.

Oral Health in a Sample of Pregnant Women from Northern Appalachia (2011–2015)

PubMed Central

Neiswanger, Katherine; McNeil, Daniel W.; Foxman, Betsy; Govil, Manika; Cooper, Margaret E.; Weyant, Robert J.; Shaffer, John R.; Crout, Richard J.; Simhan, Hyagriv N.; Beach, Scott R.; Chapman, Stella; Zovko, Jayme G.; Brown, Linda J.; Strotmeyer, Stephen J.; Maurer, Jennifer L.; Marazita, Mary L.

2015-01-01

Background. Chronic poor oral health has a high prevalence in Appalachia, a large region in the eastern USA. The Center for Oral Health Research in Appalachia (COHRA) has been enrolling pregnant women and their babies since 2011 in the COHRA2 study of genetic, microbial, and environmental factors involved in oral health in Northern Appalachia. Methods. The COHRA2 protocol is presented in detail, including inclusion criteria (healthy, adult, pregnant, US Caucasian, English speaking, and nonimmunocompromised women), recruiting (two sites: Pittsburgh, Pennsylvania, and West Virginia, USA), assessments (demographic, medical, dental, psychosocial/behavioral, and oral microbial samples and DNA), timelines (longitudinal from pregnancy to young childhood), quality control, and retention rates. Results. Preliminary oral health and demographic data are presented in 727 pregnant women, half from the greater Pittsburgh region and half from West Virginia. Despite similar tooth brushing and flossing habits, COHRA2 women in West Virginia have significantly worse oral health than the Pittsburgh sample. Women from Pittsburgh are older and more educated and have less unemployment than the West Virginia sample. Conclusions. We observed different prevalence of oral health and demographic variables between pregnant women from West Virginia (primarily rural) and Pittsburgh (primarily urban). These observations suggest site-specific differences within Northern Appalachia that warrant future studies. PMID:26089906

Tracing C Fluxes From Leaf Litter To Microbial Respired CO2 And Specific Soil Compounds

NASA Astrophysics Data System (ADS)

Rubino, M.; Lubritto, C.; D'Onofrio, A.; Gleixner, G.; Terrasi, F.; Cotrufo, F. M.

2004-12-01

Despite litter decomposition is one of the major process controlling soil C stores and nutrient cycling, yet C dynamics during litter decay are poorly understood and quantified. Here we report the results of a laboratory experiment where 13C depleted leaf litter was incubated on a 13C enriched soil with the aims to: i) partition the C loss during litter decay into microbial respired-CO2 and C input into the soil; ii) identify the soil compounds where litter derived C is retained; iii) assess whether litter quality is a determinant of both the above processes. Three 13C-depleted leaf litter(delta13C ca. -43), differing in their degradability, were incubated on C4 soil (delta13C ca. -18) under laboratory controlled conditions for 8 months, with litter respiration and delta13C-CO2 being measured at regular intervals. At harvest, Compound Specific Isotope Analyses was performed on soil and litter samples in order to follow the fate of litter-derived C compounds in the various pools of SOMƒn The delta13C of soils carbohydrates, alkanes and Phospho Lipids Fatty Acids (PLFA) were measured, and the mixing model approach used to quantify the contribution of litter derived C to the specific compounds.

Impact of Hydraulic Well Restoration on Native Bacterial Communities in Drinking Water Wells

PubMed Central

Karwautz, Clemens; Lueders, Tillmann

2014-01-01

The microbial monitoring of drinking water production systems is essential to assure water quality and minimize possible risks. However, the comparative impact of microbes from the surrounding aquifer and of those established within drinking water wells on water parameters remains poorly understood. High pressure jetting is a routine method to impede well clogging by fine sediments and also biofilms. In the present study, bacterial communities were investigated in a drinking water production system before, during, and after hydraulic purging. Variations were observed in bacterial communities between different wells of the same production system before maintenance, despite them having practically identical water chemistries. This may have reflected the distinct usage practices of the different wells, and also local aquifer heterogeneity. Hydraulic jetting of one well preferentially purged a subset of the dominating taxa, including lineages related to Diaphorobacter, Nitrospira, Sphingobium, Ralstonia, Alkanindiges, Janthinobacterium, and Pseudomonas spp, suggesting their tendency for growth in well-associated biofilms. Lineages of potential drinking water concern (i.e. Legionellaceae, Pseudomonadaceae, and Acinetobacter spp.) reacted distinctly to hydraulic jetting. Bacterial diversity was markedly reduced in drinking water 2 weeks after the cleaning procedure. The results of the present study provide a better understanding of drinking water wells as a microbial habitat, as well as their role in the microbiology of drinking water systems. PMID:25273229

Impact of hydraulic well restoration on native bacterial communities in drinking water wells.

PubMed

Karwautz, Clemens; Lueders, Tillmann

2014-01-01

The microbial monitoring of drinking water production systems is essential to assure water quality and minimize possible risks. However, the comparative impact of microbes from the surrounding aquifer and of those established within drinking water wells on water parameters remains poorly understood. High pressure jetting is a routine method to impede well clogging by fine sediments and also biofilms. In the present study, bacterial communities were investigated in a drinking water production system before, during, and after hydraulic purging. Variations were observed in bacterial communities between different wells of the same production system before maintenance, despite them having practically identical water chemistries. This may have reflected the distinct usage practices of the different wells, and also local aquifer heterogeneity. Hydraulic jetting of one well preferentially purged a subset of the dominating taxa, including lineages related to Diaphorobacter, Nitrospira, Sphingobium, Ralstonia, Alkanindiges, Janthinobacterium, and Pseudomonas spp, suggesting their tendency for growth in well-associated biofilms. Lineages of potential drinking water concern (i.e. Legionellaceae, Pseudomonadaceae, and Acinetobacter spp.) reacted distinctly to hydraulic jetting. Bacterial diversity was markedly reduced in drinking water 2 weeks after the cleaning procedure. The results of the present study provide a better understanding of drinking water wells as a microbial habitat, as well as their role in the microbiology of drinking water systems.

Molecular Ecology of Drinking Water

EPA Science Inventory

The presentation consists of examples of molecular research: –Detection and control (removal and/or inactivation) of microbes in drinking source waters –Changing microbial quality of water during distribution and storage –Detection and identification of microbial agents, incl...

Microbial eukaryotic distributions and diversity patterns in a deep-sea methane seep ecosystem.

PubMed

Pasulka, Alexis L; Levin, Lisa A; Steele, Josh A; Case, David H; Landry, Michael R; Orphan, Victoria J

2016-09-01

Although chemosynthetic ecosystems are known to support diverse assemblages of microorganisms, the ecological and environmental factors that structure microbial eukaryotes (heterotrophic protists and fungi) are poorly characterized. In this study, we examined the geographic, geochemical and ecological factors that influence microbial eukaryotic composition and distribution patterns within Hydrate Ridge, a methane seep ecosystem off the coast of Oregon using a combination of high-throughput 18S rRNA tag sequencing, terminal restriction fragment length polymorphism fingerprinting, and cloning and sequencing of full-length 18S rRNA genes. Microbial eukaryotic composition and diversity varied as a function of substrate (carbonate versus sediment), activity (low activity versus active seep sites), sulfide concentration, and region (North versus South Hydrate Ridge). Sulfide concentration was correlated with changes in microbial eukaryotic composition and richness. This work also revealed the influence of oxygen content in the overlying water column and water depth on microbial eukaryotic composition and diversity, and identified distinct patterns from those previously observed for bacteria, archaea and macrofauna in methane seep ecosystems. Characterizing the structure of microbial eukaryotic communities in response to environmental variability is a key step towards understanding if and how microbial eukaryotes influence seep ecosystem structure and function. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Harmonisation of microbial sampling and testing methods for distillate fuels

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hill, G.C.; Hill, E.C.

1995-05-01

Increased incidence of microbial infection in distillate fuels has led to a demand for organisations such as the Institute of Petroleum to propose standards for microbiological quality, based on numbers of viable microbial colony forming units. Variations in quality requirements, and in the spoilage significance of contaminating microbes plus a tendency for temporal and spatial changes in the distribution of microbes, makes such standards difficult to implement. The problem is compounded by a diversity in the procedures employed for sampling and testing for microbial contamination and in the interpretation of the data obtained. The following paper reviews these problems andmore » describes the efforts of The Institute of Petroleum Microbiology Fuels Group to address these issues and in particular to bring about harmonisation of sampling and testing methods. The benefits and drawbacks of available test methods, both laboratory based and on-site, are discussed.« less

MetaSort untangles metagenome assembly by reducing microbial community complexity

PubMed Central

Ji, Peifeng; Zhang, Yanming; Wang, Jinfeng; Zhao, Fangqing

2017-01-01

Most current approaches to analyse metagenomic data rely on reference genomes. Novel microbial communities extend far beyond the coverage of reference databases and de novo metagenome assembly from complex microbial communities remains a great challenge. Here we present a novel experimental and bioinformatic framework, metaSort, for effective construction of bacterial genomes from metagenomic samples. MetaSort provides a sorted mini-metagenome approach based on flow cytometry and single-cell sequencing methodologies, and employs new computational algorithms to efficiently recover high-quality genomes from the sorted mini-metagenome by the complementary of the original metagenome. Through extensive evaluations, we demonstrated that metaSort has an excellent and unbiased performance on genome recovery and assembly. Furthermore, we applied metaSort to an unexplored microflora colonized on the surface of marine kelp and successfully recovered 75 high-quality genomes at one time. This approach will greatly improve access to microbial genomes from complex or novel communities. PMID:28112173

Modeling central metabolism and energy biosynthesis across microbial life

DOE PAGES

Edirisinghe, Janaka N.; Weisenhorn, Pamela; Conrad, Neal; ...

2016-08-08

Here, automatically generated bacterial metabolic models, and even some curated models, lack accuracy in predicting energy yields due to poor representation of key pathways in energy biosynthesis and the electron transport chain (ETC). Further compounding the problem, complex interlinking pathways in genome-scale metabolic models, and the need for extensive gapfilling to support complex biomass reactions, often results in predicting unrealistic yields or unrealistic physiological flux profiles. As a result, to overcome this challenge, we developed methods and tools to build high quality core metabolic models (CMM) representing accurate energy biosynthesis based on a well studied, phylogenetically diverse set of modelmore » organisms. We compare these models to explore the variability of core pathways across all microbial life, and by analyzing the ability of our core models to synthesize ATP and essential biomass precursors, we evaluate the extent to which the core metabolic pathways and functional ETCs are known for all microbes. 6,600 (80 %) of our models were found to have some type of aerobic ETC, whereas 5,100 (62 %) have an anaerobic ETC, and 1,279 (15 %) do not have any ETC. Using our manually curated ETC and energy biosynthesis pathways with no gapfilling at all, we predict accurate ATP yields for nearly 5586 (70 %) of the models under aerobic and anaerobic growth conditions. This study revealed gaps in our knowledge of the central pathways that result in 2,495 (30 %) CMMs being unable to produce ATP under any of the tested conditions. We then established a methodology for the systematic identification and correction of inconsistent annotations using core metabolic models coupled with phylogenetic analysis. In conclusion, we predict accurate energy yields based on our improved annotations in energy biosynthesis pathways and the implementation of diverse ETC reactions across the microbial tree of life. We highlighted missing annotations that were essential to energy biosynthesis in our models. We examine the diversity of these pathways across all microbial life and enable the scientific community to explore the analyses generated from this large-scale analysis of over 8000 microbial genomes.« less

Modeling central metabolism and energy biosynthesis across microbial life

DOE Office of Scientific and Technical Information (OSTI.GOV)

Edirisinghe, Janaka N.; Weisenhorn, Pamela; Conrad, Neal

Here, automatically generated bacterial metabolic models, and even some curated models, lack accuracy in predicting energy yields due to poor representation of key pathways in energy biosynthesis and the electron transport chain (ETC). Further compounding the problem, complex interlinking pathways in genome-scale metabolic models, and the need for extensive gapfilling to support complex biomass reactions, often results in predicting unrealistic yields or unrealistic physiological flux profiles. As a result, to overcome this challenge, we developed methods and tools to build high quality core metabolic models (CMM) representing accurate energy biosynthesis based on a well studied, phylogenetically diverse set of modelmore » organisms. We compare these models to explore the variability of core pathways across all microbial life, and by analyzing the ability of our core models to synthesize ATP and essential biomass precursors, we evaluate the extent to which the core metabolic pathways and functional ETCs are known for all microbes. 6,600 (80 %) of our models were found to have some type of aerobic ETC, whereas 5,100 (62 %) have an anaerobic ETC, and 1,279 (15 %) do not have any ETC. Using our manually curated ETC and energy biosynthesis pathways with no gapfilling at all, we predict accurate ATP yields for nearly 5586 (70 %) of the models under aerobic and anaerobic growth conditions. This study revealed gaps in our knowledge of the central pathways that result in 2,495 (30 %) CMMs being unable to produce ATP under any of the tested conditions. We then established a methodology for the systematic identification and correction of inconsistent annotations using core metabolic models coupled with phylogenetic analysis. In conclusion, we predict accurate energy yields based on our improved annotations in energy biosynthesis pathways and the implementation of diverse ETC reactions across the microbial tree of life. We highlighted missing annotations that were essential to energy biosynthesis in our models. We examine the diversity of these pathways across all microbial life and enable the scientific community to explore the analyses generated from this large-scale analysis of over 8000 microbial genomes.« less

Coupling of Belowground Carbon Cycling and Stoichiometry from Organisms to Ecosystems along a Soil C Gradient Under Rice Cultivation

NASA Astrophysics Data System (ADS)

Hartman, W.; Ye, R.; Horwath, W. R.; Tringe, S. G.

2015-12-01

Ecological stoichiometry is a framework linking biogeochemical cycles to organism functional traits that has been widely applied in aquatic ecosystems, animals and plants, but is poorly explored in soil microbes. We evaluated relationships among soil stoichiometry, carbon (C) cycling, and microbial community structure and function along a soil gradient spanning ~5-25% C in cultivated rice fields with experimental nitrogen (N) amendments. We found rates of soil C turnover were associated with nutrient stoichiometry and phosphorus (P) availability at ecosystem, community, and organism scales. At the ecosystem scale, soil C turnover was highest in mineral soils with lower C content and N:P ratios, and was positively correlated with soil inorganic P. Effects of N fertilization on soil C cycling also appeared to be mediated by soil P availability, while microbial community composition (by 16S rRNA sequencing) was not altered by N addition. Microbial communities varied along the soil C gradient, corresponding with highly covariant soil %C, N:P ratios, C quality, and carbon turnover. In contrast, we observed unambiguous shifts in microbial community function, imputed from taxonomy and directly assessed by shotgun sequenced metagenomes. The abundance of genes for carbohydrate utilization decreased with increasing soil C (and declining C turnover), while genes for aromatic C uptake, N fixation and P scavenging increased along with potential incorporation of C into biomass pools. Ecosystem and community-scale associations between C and nutrient substrate availability were also reflected in patterns of resource allocation among individual genomes (imputed and assembled). Microbes associated with higher rates of soil C turnover harbored more genes for carbohydrate utilization, fewer genes for obtaining energetically costly forms of C, N and P, more ribosomal RNA gene copies, and potentially lower C use efficiency. We suggest genome clustering by functional gene suites might yield simplified guilds related to biogeochemical cycling, even when function is imputed directly from taxonomy. Our findings in a controlled model wetland ecosystem bolster evidence for the role of P in influencing soil C cycling, and our approach could be leveraged to reduce complex microbial data for trait-based modeling of soil C cycling.

Modeling central metabolism and energy biosynthesis across microbial life.

PubMed

Edirisinghe, Janaka N; Weisenhorn, Pamela; Conrad, Neal; Xia, Fangfang; Overbeek, Ross; Stevens, Rick L; Henry, Christopher S

2016-08-08

Automatically generated bacterial metabolic models, and even some curated models, lack accuracy in predicting energy yields due to poor representation of key pathways in energy biosynthesis and the electron transport chain (ETC). Further compounding the problem, complex interlinking pathways in genome-scale metabolic models, and the need for extensive gapfilling to support complex biomass reactions, often results in predicting unrealistic yields or unrealistic physiological flux profiles. To overcome this challenge, we developed methods and tools ( http://coremodels.mcs.anl.gov ) to build high quality core metabolic models (CMM) representing accurate energy biosynthesis based on a well studied, phylogenetically diverse set of model organisms. We compare these models to explore the variability of core pathways across all microbial life, and by analyzing the ability of our core models to synthesize ATP and essential biomass precursors, we evaluate the extent to which the core metabolic pathways and functional ETCs are known for all microbes. 6,600 (80 %) of our models were found to have some type of aerobic ETC, whereas 5,100 (62 %) have an anaerobic ETC, and 1,279 (15 %) do not have any ETC. Using our manually curated ETC and energy biosynthesis pathways with no gapfilling at all, we predict accurate ATP yields for nearly 5586 (70 %) of the models under aerobic and anaerobic growth conditions. This study revealed gaps in our knowledge of the central pathways that result in 2,495 (30 %) CMMs being unable to produce ATP under any of the tested conditions. We then established a methodology for the systematic identification and correction of inconsistent annotations using core metabolic models coupled with phylogenetic analysis. We predict accurate energy yields based on our improved annotations in energy biosynthesis pathways and the implementation of diverse ETC reactions across the microbial tree of life. We highlighted missing annotations that were essential to energy biosynthesis in our models. We examine the diversity of these pathways across all microbial life and enable the scientific community to explore the analyses generated from this large-scale analysis of over 8000 microbial genomes.

Phenazines and Other Redox-Active Antibiotics Promote Microbial Mineral Reduction

PubMed Central

Hernandez, Maria E.; Kappler, Andreas; Newman, Dianne K.

2004-01-01

Natural products with important therapeutic properties are known to be produced by a variety of soil bacteria, yet the ecological function of these compounds is not well understood. Here we show that phenazines and other redox-active antibiotics can promote microbial mineral reduction. Pseudomonas chlororaphis PCL1391, a root isolate that produces phenazine-1-carboxamide (PCN), is able to reductively dissolve poorly crystalline iron and manganese oxides, whereas a strain carrying a mutation in one of the phenazine-biosynthetic genes (phzB) is not; the addition of purified PCN restores this ability to the mutant strain. The small amount of PCN produced relative to the large amount of ferric iron reduced in cultures of P. chlororaphis implies that PCN is recycled multiple times; moreover, poorly crystalline iron (hydr)oxide can be reduced abiotically by reduced PCN. This ability suggests that PCN functions as an electron shuttle rather than an iron chelator, a finding that is consistent with the observation that dissolved ferric iron is undetectable in culture fluids. Multiple phenazines and the glycopeptidic antibiotic bleomycin can also stimulate mineral reduction by the dissimilatory iron-reducing bacterium Shewanella oneidensis MR1. Because diverse bacterial strains that cannot grow on iron can reduce phenazines, and because thermodynamic calculations suggest that phenazines have lower redox potentials than those of poorly crystalline iron (hydr)oxides in a range of relevant environmental pH (5 to 9), we suggest that natural products like phenazines may promote microbial mineral reduction in the environment. PMID:14766572

Physicochemical Drivers of Microbial Community Structure in Sediments of Lake Hazen, Nunavut, Canada.

PubMed

Ruuskanen, Matti O; St Pierre, Kyra A; St Louis, Vincent L; Aris-Brosou, Stéphane; Poulain, Alexandre J

2018-01-01

The Arctic is undergoing rapid environmental change, potentially affecting the physicochemical constraints of microbial communities that play a large role in both carbon and nutrient cycling in lacustrine environments. However, the microbial communities in such Arctic environments have seldom been studied, and the drivers of their composition are poorly characterized. To address these gaps, we surveyed the biologically active surface sediments in Lake Hazen, the largest lake by volume north of the Arctic Circle, and a small lake and shoreline pond in its watershed. High-throughput amplicon sequencing of the 16S rRNA gene uncovered a community dominated by Proteobacteria, Bacteroidetes, and Chloroflexi, similar to those found in other cold and oligotrophic lake sediments. We also show that the microbial community structure in this Arctic polar desert is shaped by pH and redox gradients. This study lays the groundwork for predicting how sediment microbial communities in the Arctic could respond as climate change proceeds to alter their physicochemical constraints.

Effect of methionine supplementation in chicken feed on the quality and shelf life of fresh poultry meat.

PubMed

Albrecht, Antonia; Herbert, Ulrike; Miskel, Dennis; Heinemann, Celine; Braun, Carina; Dohlen, Sophia; Zeitz, Johanna O; Eder, Klaus; Saremi, Behnam; Kreyenschmidt, Judith

2017-08-01

The aim of this study was to investigate the influence of different methionine sources and concentrations on the quality and spoilage process of broiler meat. The trial was comprised of 7 treatment groups: one basal group (suboptimal in Methionine+Cysteine; i.e., 0.89, 0.74, 0.69% in DM SID Met+Cys in starter, grower, and finisher diets, respectively) and 3 doses (0.10, 0.25, and 0.40%) of either DL-Methionine (DLM) or DL-2-hydroxy-4-methylthio butanoic acid (DL-HMTBA) on an equimolar basis of the DLM-supplemented groups. The broilers were fed the diets for 35 d, then slaughtered and processed. The filets were aerobically packed and stored under temperature controlled conditions at 4°C. Meat quality investigations were comprised of microbial investigations (total viable count and Pseudomonas spp.), pH and drip loss measurements of the filets. The shelf life of the meat samples was determined based on sensory parameters. After slaughtering, all supplemented meat samples showed a high quality, whereby no differences between the 2 methionine sources could be detected for the microbial load, pH, and drip loss. In comparison to the control group, the supplemented samples showed a higher sensory quality, characterized by a fresh smell and fresh red color. Methionine supplementation had a significant influence on meat quality parameters during storage. The microbial load, pH and drip loss of the chicken filets were positively correlated to the methionine concentration. Additionally, the microbial load at the end of storage was positively correlated to pH and drip loss values. Nevertheless, the microbial parameters were in a normal range and the positive correlation to methionine concentration did not affect the sensory shelf life. The mean sensory shelf life of the broiler filets varied between 7 to 9 d. During storage, no difference in the development of sensory parameters was observed between the supplemented groups, while the spoilage process of the basal group occurred slightly faster. In conclusion, methionine concentration, but not methionine source, effected meat quality parameters in breast muscles of broilers. © 2017 Poultry Science Association Inc.

Changes in Microbial Plankton Assemblages Induced by Mesoscale Oceanographic Features in the Northern Gulf of Mexico

PubMed Central

Williams, Alicia K.; McInnes, Allison S.; Rooker, Jay R.; Quigg, Antonietta

2015-01-01

Mesoscale circulation generated by the Loop Current in the Northern Gulf of Mexico (NGOM) delivers growth-limiting nutrients to the microbial plankton of the euphotic zone. Consequences of physicochemically driven community shifts on higher order consumers and subsequent impacts on the biological carbon pump remain poorly understood. This study evaluates microbial plankton <10 μm abundance and community structure across both cyclonic and anti-cyclonic circulation features in the NGOM using flow cytometry (SYBR Green I and autofluorescence parameters). Non-parametric multivariate hierarchical cluster analyses indicated that significant spatial variability in community structure exists such that stations that clustered together were defined as having a specific ‘microbial signature’ (i.e. statistically homogeneous community structure profiles based on relative abundance of microbial groups). Salinity and a combination of sea surface height anomaly and sea surface temperature were determined by distance based linear modeling to be abiotic predictor variables significantly correlated to changes in microbial signatures. Correlations between increased microbial abundance and availability of nitrogen suggest nitrogen-limitation of microbial plankton in this open ocean area. Regions of combined coastal water entrainment and mesoscale convergence corresponded to increased heterotrophic prokaryote abundance relative to autotrophic plankton. The results provide an initial assessment of how mesoscale circulation potentially influences microbial plankton abundance and community structure in the NGOM. PMID:26375709

To what extent do food preferences explain the trophic position of heterotrophic and mixotrophic microbial consumers in a Sphagnum peatland?

PubMed

Jassey, Vincent E J; Meyer, Caroline; Dupuy, Christine; Bernard, Nadine; Mitchell, Edward A D; Toussaint, Marie-Laure; Metian, Marc; Chatelain, Auriel P; Gilbert, Daniel

2013-10-01

Although microorganisms are the primary drivers of biogeochemical cycles, the structure and functioning of microbial food webs are poorly studied. This is the case in Sphagnum peatlands, where microbial communities play a key role in the global carbon cycle. Here, we explored the structure of the microbial food web from a Sphagnum peatland by analyzing (1) the density and biomass of different microbial functional groups, (2) the natural stable isotope (δ(13)C and δ(15)N) signatures of key microbial consumers (testate amoebae), and (3) the digestive vacuole contents of Hyalosphenia papilio, the dominant testate amoeba species in our system. Our results showed that the feeding type of testate amoeba species (bacterivory, algivory, or both) translates into their trophic position as assessed by isotopic signatures. Our study further demonstrates, for H. papilio, the energetic benefits of mixotrophy when the density of its preferential prey is low. Overall, our results show that testate amoebae occupy different trophic levels within the microbial food web, depending on their feeding behavior, the density of their food resources, and their metabolism (i.e., mixotrophy vs. heterotrophy). Combined analyses of predation, community structure, and stable isotopes now allow the structure of microbial food webs to be more completely described, which should lead to improved models of microbial community function.

Microbial quality of yellow seasoned “pindang” fish treated with turmeric and tamarind

NASA Astrophysics Data System (ADS)

Handayani, B. R.; Dipokusumo, B.; Werdiningsih, W.; Rahayu, T. I.; Sugita, D. L.

2018-01-01

The objective of this study was to determine the microbial quality of yellow seasoned pindang fish. The fish was treated using combination of turmeric and tamarind at different ratio. This research used Randomized Block Design with 2 (two) factors ie concentration of turmeric (0%, 2%, and 6%) and concentration of tamarind (0%, 3%, and 6%). Each treatment was replicated 3 times to obtain 27 experimental units. The parameters observed were total microbe, total fungi and some pathogenic bacteria. Some microbial data were analyzed using descriptive method, however, the number of S. aureus was analyzed at 5% significance level by using software co-Stat and if there was a real difference then tested further by test Honestly Significant Difference (HSD). The results showed that increasing the use of curcumin and tamarind tended to decrease the total number of microbial from treatment control 5.1 x 105 CFU/gram to <1.0 x 103 CFU/gram. All the treatment produced yellow seasoned pindang fish with fungi <1.0 x 102 CFU/gram. The products contain pathogenic bacteria E. coli < 3 MPN/gram; S. aureus <1.0 x 103 CFU/gram; Salmonella and V. cholerae were negative in 25 gram of sample. Based on microbial quality, it is recommended that the use of 3-6% of turmeric and 2-4% of tamarind are the best spices combination to produce safe consumption of yellow seasoned pindang fish.

Microbial quality of water in dental unit waterlines.

PubMed

Nikaeen, Mahnaz; Hatamzadeh, Maryam; Sabzevari, Zohre; Zareh, Omolbanin

2009-09-01

Dental unit waterlines (DUWLs) are ideal environment for development of microbial biofilms. Microbial contamination of water in DUWLs is thought to be the result of biofilm formation as it could serves as a haven for pathogens. The aim of this study was to assess microbial quality of water in dental unit waterlines of dental units located at the dental school of Isfahan University of Medical Sciences. Water samples were collected from air/water syringe and high-speed handpiece. Generally, 100-200 ml water samples were collected aseptically in sterile containers with sodium thiosulfate at the beginning of the day after a 2 minute purge. Samples were transferred to the laboratory in insulated box with cooling packs and examined for total viable heterotrophic bacteria and fungi. The heterotrophic plate count levels were significantly exceeded the American Dental Association recommendations for DUWL water quality (< 200 CFU/ml), in both air/water syringe (84%, CFU/ml: 500-20000) and high-speed handpiece (96%, CFU/ml: 710-36800) samples. However, there was no significant difference between the level of contamination in the air/water syringe and high-speed handpiece. Fungi were found in 28% and 36% of air/water syringe and high-speed handpiece samples, respectively; and filamentous fungi were the most frequently isolated fungi. DUWLs should be subjected to routine microbial monitoring and to a decontamination protocol in order to minimize the risk of exposure to potential pathogens from dental units.

Marine microbial communities of the Great Barrier Reef lagoon are influenced by riverine floodwaters and seasonal weather events.

PubMed

Angly, Florent E; Heath, Candice; Morgan, Thomas C; Tonin, Hemerson; Rich, Virginia; Schaffelke, Britta; Bourne, David G; Tyson, Gene W

2016-01-01

The role of microorganisms in maintaining coral reef health is increasingly recognized. Riverine floodwater containing herbicides and excess nutrients from fertilizers compromises water quality in the inshore Great Barrier Reef (GBR), with unknown consequences for planktonic marine microbial communities and thus coral reefs. In this baseline study, inshore GBR microbial communities were monitored along a 124 km long transect between 2011 and 2013 using 16S rRNA gene amplicon sequencing. Members of the bacterial orders Rickettsiales (e.g., Pelagibacteraceae) and Synechococcales (e.g., Prochlorococcus), and of the archaeal class Marine Group II were prevalent in all samples, exhibiting a clear seasonal dynamics. Microbial communities near the Tully river mouth included a mixture of taxa from offshore marine sites and from the river system. The environmental parameters collected could be summarized into four groups, represented by salinity, rainfall, temperature and water quality, that drove the composition of microbial communities. During the wet season, lower salinity and a lower water quality index resulting from higher river discharge corresponded to increases in riverine taxa at sites near the river mouth. Particularly large, transient changes in microbial community structure were seen during the extreme wet season 2010-11, and may be partially attributed to the effects of wind and waves, which resuspend sediments and homogenize the water column in shallow near-shore regions. This work shows that anthropogenic floodwaters and other environmental parameters work in conjunction to drive the spatial distribution of microorganisms in the GBR lagoon, as well as their seasonal and daily dynamics.

Marine microbial communities of the Great Barrier Reef lagoon are influenced by riverine floodwaters and seasonal weather events

PubMed Central

Heath, Candice; Morgan, Thomas C.; Tonin, Hemerson; Rich, Virginia; Schaffelke, Britta; Bourne, David G.; Tyson, Gene W.

2016-01-01

The role of microorganisms in maintaining coral reef health is increasingly recognized. Riverine floodwater containing herbicides and excess nutrients from fertilizers compromises water quality in the inshore Great Barrier Reef (GBR), with unknown consequences for planktonic marine microbial communities and thus coral reefs. In this baseline study, inshore GBR microbial communities were monitored along a 124 km long transect between 2011 and 2013 using 16S rRNA gene amplicon sequencing. Members of the bacterial orders Rickettsiales (e.g., Pelagibacteraceae) and Synechococcales (e.g., Prochlorococcus), and of the archaeal class Marine Group II were prevalent in all samples, exhibiting a clear seasonal dynamics. Microbial communities near the Tully river mouth included a mixture of taxa from offshore marine sites and from the river system. The environmental parameters collected could be summarized into four groups, represented by salinity, rainfall, temperature and water quality, that drove the composition of microbial communities. During the wet season, lower salinity and a lower water quality index resulting from higher river discharge corresponded to increases in riverine taxa at sites near the river mouth. Particularly large, transient changes in microbial community structure were seen during the extreme wet season 2010–11, and may be partially attributed to the effects of wind and waves, which resuspend sediments and homogenize the water column in shallow near-shore regions. This work shows that anthropogenic floodwaters and other environmental parameters work in conjunction to drive the spatial distribution of microorganisms in the GBR lagoon, as well as their seasonal and daily dynamics. PMID:26839738

Microbial Safety Improvement of Sea Buckthorn by Electron Beam Irradiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nemtanu, Monica R.; Minea, R.; Mazilu, Elena

2007-04-23

The commercialization of medicinal plants and/or their products is highly increased in Romania lately. One of the most used herbs is sea buckthorn being well known for its quality with a large potential for curing some diseases. Sea buckthorn can be contaminated with undesirable microorganisms which may affect negatively its quality. The paper presents the results regarding the action of a non-conventional technology meaning electron beam technique on sea buckthorn in order to improve its microbiological quality. Our study revealed that the sea buckthorn microbial load has been improved after 3 kGy irradiation keeping its active principles.

Microbial Safety Improvement of Sea Buckthorn by Electron Beam Irradiation

NASA Astrophysics Data System (ADS)

Nemţanu, Monica R.; Minea, R.; Mazilu, Elena; Rǎdulescu, Nora

2007-04-01

The commercialization of medicinal plants and/or their products is highly increased in Romania lately. One of the most used herbs is sea buckthorn being well known for its quality with a large potential for curing some diseases. Sea buckthorn can be contaminated with undesirable microorganisms which may affect negatively its quality. The paper presents the results regarding the action of a non-conventional technology meaning electron beam technique on sea buckthorn in order to improve its microbiological quality. Our study revealed that the sea buckthorn microbial load has been improved after 3 kGy irradiation keeping its active principles.

Actinorhizal Alder Phytostabilization Alters Microbial Community Dynamics in Gold Mine Waste Rock from Northern Quebec: A Greenhouse Study

PubMed Central

Callender, Katrina L.; Roy, Sébastien; Khasa, Damase P.; Whyte, Lyle G.; Greer, Charles W.

2016-01-01

Phytotechnologies are rapidly replacing conventional ex-situ remediation techniques as they have the added benefit of restoring aesthetic value, important in the reclamation of mine sites. Alders are pioneer species that can tolerate and proliferate in nutrient-poor, contaminated environments, largely due to symbiotic root associations with the N2-fixing bacteria, Frankia and ectomycorrhizal (ECM) fungi. In this study, we investigated the growth of two Frankia-inoculated (actinorhizal) alder species, A. crispa and A. glutinosa, in gold mine waste rock from northern Quebec. Alder species had similar survival rates and positively impacted soil quality and physico-chemical properties in similar ways, restoring soil pH to neutrality and reducing extractable metals up to two-fold, while not hyperaccumulating them into above-ground plant biomass. A. glutinosa outperformed A. crispa in terms of growth, as estimated by the seedling volume index (SVI), and root length. Pyrosequencing of the bacterial 16S rRNA gene for bacteria and the ribosomal internal transcribed spacer (ITS) region for fungi provided a comprehensive, direct characterization of microbial communities in gold mine waste rock and fine tailings. Plant- and treatment-specific shifts in soil microbial community compositions were observed in planted mine residues. Shannon diversity and the abundance of microbes involved in key ecosystem processes such as contaminant degradation (Sphingomonas, Sphingobium and Pseudomonas), metal sequestration (Brevundimonas and Caulobacter) and N2-fixation (Azotobacter, Mesorhizobium, Rhizobium and Pseudomonas) increased over time, i.e., as plants established in mine waste rock. Acetate mineralization and most probable number (MPN) assays showed that revegetation positively stimulated both bulk and rhizosphere communities, increasing microbial density (biomass increase of 2 orders of magnitude) and mineralization (five-fold). Genomic techniques proved useful in investigating tripartite (plant-bacteria-fungi) interactions during phytostabilization, contributing to our knowledge in this field of study. PMID:26928913

Microbial Risk Assessment of Air Conditioning Condensate Reuse

EPA Science Inventory

Air conditioning condensate can provide a substantial water source for building-scale collection and non-potable use. Although produced water is anticipated to be of generally high quality, the potential for microbial contamination by biofilm-associated opportunistic pathogens t...

Electron beam irradiation of Matricaria chamomilla L. for microbial decontamination

NASA Astrophysics Data System (ADS)

Nemţanu, Monica R.; Kikuchi, Irene Satiko; de Jesus Andreoli Pinto, Terezinha; Mazilu, Elena; Setnic, Silvia; Bucur, Marcela; Duliu, Octavian G.; Meltzer, Viorica; Pincu, Elena

2008-05-01

Wild chamomile (Matricaria chamomilla L.) is one of the most popular herbal materials with both internal and external use to cure different health disturbances. As a consequence of its origin, chamomile could carry various microbial contaminants which offer different hazards to the final consumer. Reduction of the microbial load to the in force regulation limits represents an important phase in the technological process of vegetal materials, and the electron beam treatment might be an efficient alternative to the classical methods of hygienic quality assurance. The purpose of the study was to analyze the potential application of the electron beam treatment in order to assure the microbial safety of the wild chamomile. Samples of chamomile dry inflorescences were treated in electron beam (e-beam) of 6 MeV mean energy, at room temperature and ambient pressure. Some loss of the chemical compounds with bioactive role could be noticed, but the number of microorganisms decreased as a function on the absorbed dose. Consequently, the microbial quality of studied vegetal material inflorescences was improved by e-beam irradiation.

No tillage combined with crop rotation improves soil microbial community composition and metabolic activity.

PubMed

Sun, Bingjie; Jia, Shuxia; Zhang, Shixiu; McLaughlin, Neil B; Liang, Aizhen; Chen, Xuewen; Liu, Siyi; Zhang, Xiaoping

2016-04-01

Soil microbial community can vary with different agricultural managements, which in turn can affect soil quality. The objective of this work was to evaluate the effects of long-term tillage practice (no tillage (NT) and conventional tillage (CT)) and crop rotation (maize-soybean (MS) rotation and monoculture maize (MM)) on soil microbial community composition and metabolic capacity in different soil layers. Long-term NT increased the soil organic carbon (SOC) and total nitrogen (TN) mainly at the 0-5 cm depth which was accompanied with a greater microbial abundance. The greater fungi-to-bacteria (F/B) ratio was found in NTMS at the 0-5 cm depth. Both tillage and crop rotation had a significant effect on the metabolic activity, with the greatest average well color development (AWCD) value in NTMS soil at all three soil depths. Redundancy analysis (RDA) showed that the shift in microbial community composition was accompanied with the changes in capacity of utilizing different carbon substrates. Therefore, no tillage combined with crop rotation could improve soil biological quality and make agricultural systems more sustainable.

Recovery of microbial community structure and functioning after wildfire in semi-arid environments: optimising methods for monitoring and assessment

NASA Astrophysics Data System (ADS)

Muñoz-Rojas, Miriam; Martini, Dylan; Erickson, Todd; Merritt, David; Dixon, Kingsley

2015-04-01

Introduction In semi-arid areas such as northern Western Australia, wildfires are a natural part of the environment and many ecosystems in these landscapes have evolved and developed a strong relationship with fire. Soil microbial communities play a crucial role in ecosystem processes by regulating the cycling of nutrients via decomposition, mineralization, and immobilization processes. Thus, the structure (e.g. soil microbial biomass) and functioning (e.g. soil microbial activity) of microbial communities, as well as their changes after ecosystem disturbance, can be useful indicators of soil quality and health recovery. In this research, we assess the impacts of fire on soil microbial communities and their recovery in a biodiverse semi-arid environment of Western Australia (Pilbara region). New methods for determining soil microbial respiration as an indicator of microbial activity and soil health are also tested. Methodology Soil samples were collected from 10 similar ecosystems in the Pilbara with analogous native vegetation, but differing levels of post-fire disturbance (i.e. 3 months, 1 year, 5, 7 and 14 years after wildfire). Soil microbial activity was measured with the Solvita test which determines soil microbial respiration rate based on the measurement of the CO2 burst of a dry soil after it is moistened. Soils were dried and re-wetted and a CO2 probe was inserted before incubation at constant conditions of 25°C during 24 h. Measurements were taken with a digital mini spectrometer. Microbial (bacteria and fungi) biomass and community composition were measured by phospholipid fatty acid analysis (PLFA). Results Immediately after the fire (i.e. 3 months), soil microbial activity and microbial biomass are similar to 14 years 'undisturbed' levels (53.18±3.68 ppm CO2-CO and 14.07±0.65 mg kg-1, respectively). However, after the first year post-fire, with larger plant productivity, microbial biomass and microbial activity increase rapidly, peaking after 5-7 years post fire (70.70±8.94 ppm CO2-CO and 21.67±2.62 mg kg-1, respectively). Microbial activity measured with the Solvita test was significantly correlated (R Pearson > 0.7; P < 0.001) with microbial parameters analysed with PLFA such as microbial biomass, bacteria biomass or mycorrhizhal fungi. This method has proven to be reliable, fast and easy to interpret for assessment of soil microbial activity in the recovery of soil quality during the recovery after fire. Keywords Pilbara region, biodiverse ecosystems, microbial biomass, microbial respiration, Solvita test, CO2 burst.

Combined effects of sleep quality and depression on quality of life in patients with type 2 diabetes.

PubMed

Zhang, Pan; Lou, Peian; Chang, Guiqiu; Chen, Peipei; Zhang, Lei; Li, Ting; Qiao, Cheng

2016-04-05

Poor sleep quality and depression negatively impact the health-related quality of life of patients with type 2 diabetes, but the combined effect of the two factors is unknown. This study aimed to assess the interactive effects of poor sleep quality and depression on the quality of life in patients with type 2 diabetes. Patients with type 2 diabetes (n = 944) completed the Diabetes Specificity Quality of Life scale (DSQL) and questionnaires on sleep quality and depression. The products of poor sleep quality and depression were added to the logistic regression model to evaluate their multiplicative interactions, which were expressed as the relative excess risk of interaction (RERI), the attributable proportion (AP) of interaction, and the synergy index (S). Poor sleep quality and depressive symptoms both increased DSQL scores. The co-presence of poor sleep quality and depressive symptoms significantly reduced DSQL scores by a factor of 3.96 on biological interaction measures. The relative excess risk of interaction was 1.08. The combined effect of poor sleep quality and depressive symptoms was observed only in women. Patients with both depressive symptoms and poor sleep quality are at an increased risk of reduction in diabetes-related quality of life, and this risk is particularly high for women due to the interaction effect. Clinicians should screen for and treat sleep difficulties and depressive symptoms in patients with type 2 diabetes.

Impact of sleep quality on the quality of life of patients with Parkinson's disease: a questionnaire based study.

PubMed

Pandey, Shweta; Bajaj, Bhupender Kumar; Wadhwa, Ankur; Anand, Kuljeet Singh

2016-09-01

Poor sleep quality contributes to the inferior quality of life of patients with Parkinson's disease (PD) despite appropriate treatment of motor symptoms. The literature about the impact of sleep quality on quality of life of patients with PD is as yet sparse. One hundred patients of PD diagnosed as per UK Brain Bank criteria were assessed for severity and stage of PD using UPDRS and modified Hoehn &Yahr scales. The quality of sleep was assessed by Pittsburgh Sleep Quality Index and excessive daytime somnolence (EDS) was evaluated using Epworth Sleepiness Scale. Parkinson's Disease Questionnaire -39 (PDQ-39) was used to determine quality of life of the patients. Comorbid depression and anxiety were assessed using Inventory of Depressive Symptoms-Self Rated and Hamilton Anxiety Rating Scale. Pearson's correlation and multiple linear regressions were used to analyze relation of sleep quality with quality of life of patients. Fifty patients had poor sleep quality. EDS was present in only 9 patients. Co-morbid depression and anxiety were present in 52 and 34 patients respectively. While the motor severity assessed by UPDRS-III was observed to adversely affect quality of life, it did not negatively impact quality of sleep. Higher score on UPDRS-total and UPDRS IV suggesting advanced disease correlated with poor sleep quality. Depression and anxiety were significantly more frequent in patients with poor sleep quality (p<0.01). Patients with poor sleep quality had worse quality of life (r=0.338, p<0.05). Depression and anxiety were also observed to have significant negative impact on quality of life of PD patients (p<0.01). Poor sleep quality was not found to be an independent predictor of quality of life using multiple linear regression analysis. Poor sleep quality along with comorbid depression, anxiety and advanced stage of disease is associated with poor quality of life. Copyright © 2016 Elsevier B.V. All rights reserved.

Shift in soil microbial communities with shrub encroachment in Inner Mongolia grasslands, China

NASA Astrophysics Data System (ADS)

Shen, H.; Li, H.; Zhang, J.; Hu, H.; Chen, L.; Zhu, Y.; Fang, J.

2017-12-01

The ongoing expansion of shrub encroachment into grasslands represents a unique form of land cover change. How this process affects soil microbial communities is poorly understood. In this study, we aim to assess the effects of shrub encroachment on soil microbial biomass, abundance and composition by comparing data between shrub patches and neighboring herb patches in shrub-encroached grasslands (SEGs) in Inner Mongolia, China. Fourteen SEG sites from two ecosystem types (typical and desert grasslands) were investigated. The phospholipid fatty acid (PLFA) method was used to analyze the composition and biomass of the soil microbial community. Our results showed that the top-soil microbial biomass and abundances of gram-negative bacteria, arbuscular mycorrhizal fungi, and actinomycetes were significantly higher in shrub patches than in herb patches in both typical and desert grasslands (P < 0.05). The fungi to bacteria ratio was significantly higher in shrub patches than in herb patches in desert grassland (P < 0.05). The microbial biomass was positively associated with mean annual precipitation, total nitrogen and available phosphorus, and negatively associated with mean annual temperature. Our results also indicated that the variation in microbial composition was largely explained by edaphic factors, followed by climate factors. In conclusion, shrub encroachment in Inner Mongolia grasslands has significantly influenced the structure and abundance of soil microbial communities, which makes the microbial communities toward a fresh organic carbon-based structure. This study highlights the importance of edaphic and climate factors in microbial community shifts in SEGs.

Quantitative microbial faecal source tracking with sampling guided by hydrological catchment dynamics.

PubMed

Reischer, G H; Haider, J M; Sommer, R; Stadler, H; Keiblinger, K M; Hornek, R; Zerobin, W; Mach, R L; Farnleitner, A H

2008-10-01

The impairment of water quality by faecal pollution is a global public health concern. Microbial source tracking methods help to identify faecal sources but the few recent quantitative microbial source tracking applications disregarded catchment hydrology and pollution dynamics. This quantitative microbial source tracking study, conducted in a large karstic spring catchment potentially influenced by humans and ruminant animals, was based on a tiered sampling approach: a 31-month water quality monitoring (Monitoring) covering seasonal hydrological dynamics and an investigation of flood events (Events) as periods of the strongest pollution. The detection of a ruminant-specific and a human-specific faecal Bacteroidetes marker by quantitative real-time PCR was complemented by standard microbiological and on-line hydrological parameters. Both quantitative microbial source tracking markers were detected in spring water during Monitoring and Events, with preponderance of the ruminant-specific marker. Applying multiparametric analysis of all data allowed linking the ruminant-specific marker to general faecal pollution indicators, especially during Events. Up to 80% of the variation of faecal indicator levels during Events could be explained by ruminant-specific marker levels proving the dominance of ruminant faecal sources in the catchment. Furthermore, soil was ruled out as a source of quantitative microbial source tracking markers. This study demonstrates the applicability of quantitative microbial source tracking methods and highlights the prerequisite of considering hydrological catchment dynamics in source tracking study design.

Studying Microbial Mat Functioning Amidst "Unexpected Diversity": Methodological Approaches and Initial Results from Metatranscriptomes of Mats Over Diel cycles, iTags from Long Term Manipulations, and Biogeochemical Cycling in Simplified Microbial Mats Constructed from Cultures

NASA Astrophysics Data System (ADS)

Bebout, B.; Bebout, L. E.; Detweiler, A. M.; Everroad, R. C.; Lee, J.; Pett-Ridge, J.; Weber, P. K.

2014-12-01

Microbial mats are famously amongst the most diverse microbial ecosystems on Earth, inhabiting some of the most inclement environments known, including hypersaline, dry, hot, cold, nutrient poor, and high UV environments. The high microbial diversity of microbial mats makes studies of microbial ecology notably difficult. To address this challenge, we have been using a combination of metagenomics, metatranscriptomics, iTags and culture-based simplified microbial mats to study biogeochemical cycling (H2 production, N2 fixation, and fermentation) in microbial mats collected from Elkhorn Slough, Monterey Bay, California. Metatranscriptomes of microbial mats incubated over a diel cycle have revealed that a number of gene systems activate only during the day in Cyanobacteria, while the remaining appear to be constitutive. The dominant cyanobacterium in the mat (Microcoleus chthonoplastes) expresses several pathways for nitrogen scavenging undocumented in cultured strains, as well as the expression of two starch storage and utilization cycles. Community composition shifts in response to long term manipulations of mats were assessed using iTags. Changes in community diversity were observed as hydrogen fluxes increased in response to a lowering of sulfate concentrations. To produce simplified microbial mats, we have isolated members of 13 of the 15 top taxa from our iTag libraries into culture. Simplified microbial mats and simple co-cultures and consortia constructed from these isolates reproduce many of the natural patterns of biogeochemical cycling in the parent natural microbial mats, but against a background of far lower overall diversity, simplifying studies of changes in gene expression (over the short term), interactions between community members, and community composition changes (over the longer term), in response to environmental forcing.

Molecular characterization of organic matter mobilized from Bangladeshi aquifer sediment: tracking carbon compositional change during microbial utilization

NASA Astrophysics Data System (ADS)

Pracht, Lara E.; Tfaily, Malak M.; Ardissono, Robert J.; Neumann, Rebecca B.

2018-03-01

Bioavailable organic carbon in aquifer recharge waters and sediments can fuel microbial reactions with implications for groundwater quality. A previous incubation experiment showed that sedimentary organic carbon (SOC) mobilized off sandy sediment collected from an arsenic-contaminated and methanogenic aquifer in Bangladesh was bioavailable; it was transformed into methane. We used high-resolution mass spectrometry to molecularly characterize this mobilized SOC, reference its composition against dissolved organic carbon (DOC) in surface recharge water, track compositional changes during incubation, and advance understanding of microbial processing of organic carbon in anaerobic environments. Organic carbon mobilized off aquifer sediment was more diverse, proportionately larger, more aromatic, and more oxidized than DOC in surface recharge. Mobilized SOC was predominately composed of terrestrially derived organic matter and had characteristics signifying that it evaded microbial processing within the aquifer. Approximately 50 % of identified compounds in mobilized SOC and in DOC from surface recharge water contained sulfur. During incubation, after mobilized SOC was converted into methane, new organosulfur compounds with high S-to-C ratios and a high nominal oxidation state of carbon (NOSC) were detected. We reason that these detected compounds formed abiotically following microbial reduction of sulfate to sulfide, which could have occurred during incubation but was not directly measured or that they were microbially synthesized. Most notably, microbes transformed all carbon types during incubation, including those currently considered thermodynamically unviable for microbes to degrade in anaerobic conditions (i.e., those with a low NOSC). In anaerobic environments, energy yields from redox reactions are small and the amount of energy required to remove electrons from highly reduced carbon substrates during oxidation decreases the thermodynamic favorability of degrading compounds with a low NOSC. While all compound types were eventually degraded during incubation, NOSC and compound size controlled the rates of carbon transformation. Large, more thermodynamically favorable compounds (e.g., aromatics with a high NOSC) were targeted first, while small, less thermodynamically favorable compounds (e.g., alkanes and olefinics with a low NOSC) were used last. These results indicate that in anaerobic conditions, microbial communities are capable of degrading and mineralizing all forms of organic matter, converting larger energy-rich compounds into smaller energy-poor compounds. However, in an open system, where fresh carbon is continually supplied, the slower degradation rate of reduced carbon compounds would enable this portion of the organic carbon pool to build up, explaining the apparent persistence of compounds with a low NOSC in anaerobic environments.

Retardation of quality changes in camel meat sausages by phenolic compounds and phenolic extracts.

PubMed

Maqsood, Sajid; Manheem, Kusaimah; Abushelaibi, Aisha; Kadim, Isam Tawfik

2016-11-01

Impact of tannic acid (TA), date seed extract (DSE), catechin (CT) and green tea extract (GTE) on lipid oxidation, microbial load and textural properties of camel meat sausages during 12 days of refrigerated storage was investigated. TA and CT showed higher activities in all antioxidative assays compared to DSE and GTE. Lipid oxidation and microbial growth was higher for control sausages when compared to other samples. TA and CT at a level of 200 mg/kg were more effective in retarding lipid oxidation and lowering microbial count (P < 0.05). Sausages treated with TA and DSE were found to have higher hardness, gumminess and chewiness values compared to other treatments (P < 0.05). Addition of different phenolic compounds or extract did not influence the sensory color of sausages. Furthermore, sensory quality was also found to be superior in TA and CT treated sausages. Therefore, pure phenolic compounds (TA and CT) proved to be more effective in retaining microbial and sensorial qualities of camel meat sausages compared to phenolic extracts (GTE and DSE) over 12 days of storage at 4°C. © 2016 Japanese Society of Animal Science.

Use of ion chromatography for monitoring microbial spoilage in the fruit juice industry.

PubMed

Trifirò, A; Saccani, G; Gherardi, S; Vicini, E; Spotti, E; Previdi, M P; Ndagijimana, M; Cavalli, S; Reschiotto, C

1997-05-16

Fruit juices and purees are defined as fermentable, but unfermented, products obtained by mechanical processing of fresh fruits. The presence of undesired metabolites derived from microbial growth can arise from the use of unsuitable fruit or from defects in the production line or subsequent contamination. This involves a loss in the overall quality that cannot be resolved by thermal treatment following the start of fermentation. With these considerations, together with microbiological control, the analysis of different metabolites, which can be considered as microbial growth markers, such as alcohols (i.e. ethanol, etc.), acids (i.e. acetic, fumaric, lactic, etc.) is fundamental in order to achieve a better evaluation of product quality. Enzymatic determination and other single-component analytical techniques are often used for the determination of these metabolites. When the microbial spoilage is not well known, this results in a long and cumbersome procedure. A versatile technique that is capable of determining many metabolites in one analysis could be helpful in improving routine quality control. For this purpose, an ion chromatographic technique, such as ion exclusion, for separation, and diode array spectrophotometry and conductivity, for detection, were evaluated. Both different industrial samples and inoculated samples were analyzed.

Effect of long term chilled (up to 5weeks) then frozen (up to 12months) storage at two different sub-zero holding temperatures on beef: 1. Meat quality and microbial loads.

PubMed

Holman, Benjamin W B; Coombs, Cassius E O; Morris, Stephen; Kerr, Matthew J; Hopkins, David L

2017-11-01

Beef loins (LL) stored under different chilled-then-frozen storage combinations (up to 5 and 52weeks, respectively) and two frozen holding temperatures were evaluated for microbial load and meat quality parameters. We found holding temperature effects to be negligible, which suggest -12°C could deliver comparable quality LL to -18°C across these same storage periods. Meat quality parameters varied significantly, but when compared to existing consumer thresholds these may not be perceptible, colour being the exception which proved unacceptable, earlier into retail display when either chilled and subsequent frozen storage periods were increased. There was insufficient detection of key spoilage microbes to allow for statistical analysis, potentially due to the hygienic and commercially representative LL source, although variation in water activity, glycogen content, pH and other moisture parameters conducive to microbial proliferation were influenced by chilled-then-frozen storage. These outcomes could be applied to defining storage thresholds that assure beef quality within export networks, leveraging market access, and improving product management. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

The influence of nitrogen fertilization on the magnitude of rhizosphere effects

NASA Astrophysics Data System (ADS)

Zhu, B.; Panke-Buisse, K.; Kao-Kniffin, J.

2012-12-01

The labile carbon released from roots to the rhizosphere enhances soil microbial activity and nutrient availability, but factors that regulate such "rhizosphere effects" are poorly understood. Nitrogen fertilization may suppress rhizosphere effects by reducing plant carbon allocation belowground. Here we investigated the impact of nitrogen fertilization (+100 mg NH4NO3-N kg soil-1) on the magnitude of rhizosphere effects of two grass species (Bermuda grass Cynodon dactylon and smooth crabgrass Digitaria ischaemum) grown in a nutrient-poor soil for 80-100 days inside a growth chamber. Rhizosphere effects were estimated by the percentage difference between the planted soil (rhizosphere soil) and the unplanted soil (bulk soil) for several assays. We found that the rhizosphere soil of both plants had higher pH (+ 0.5~0.7 units), similar microbial biomass carbon, but lower microbial biomass nitrogen (- 27~37%) compared to the bulk soil. The rate of net N mineralization and the activity of three soil enzymes that degrade chitin (NAG), protein (LAP) and lignin (peroxidase) and produce mineral nitrogen were generally enhanced by the rhizosphere effects (up to 80%). Although nitrogen fertilization significantly increased plant biomass, it generally affected microbial biomass, activity and net N mineralization rate to a similar extent between rhizosphere soil and bulk soil, and thus did not significantly impact the magnitude of rhizosphere effects. Moreover, the community structure of soil bacteria (indicated by T-RFLP) showed remarkable divergence between the planted and unplanted soils, but not between the control and fertilized soils. Collectively, these results suggest that grass roots affects soil microbial activity and community structure, but short-term nitrogen fertilization may not significantly influence these rhizosphere effects.

Fluid mixing and the deep biosphere of a fossil Lost City-type hydrothermal system at the Iberia Margin.

PubMed

Klein, Frieder; Humphris, Susan E; Guo, Weifu; Schubotz, Florence; Schwarzenbach, Esther M; Orsi, William D

2015-09-29

Subseafloor mixing of reduced hydrothermal fluids with seawater is believed to provide the energy and substrates needed to support deep chemolithoautotrophic life in the hydrated oceanic mantle (i.e., serpentinite). However, geosphere-biosphere interactions in serpentinite-hosted subseafloor mixing zones remain poorly constrained. Here we examine fossil microbial communities and fluid mixing processes in the subseafloor of a Cretaceous Lost City-type hydrothermal system at the magma-poor passive Iberia Margin (Ocean Drilling Program Leg 149, Hole 897D). Brucite-calcite mineral assemblages precipitated from mixed fluids ca. 65 m below the Cretaceous paleo-seafloor at temperatures of 31.7 ± 4.3 °C within steep chemical gradients between weathered, carbonate-rich serpentinite breccia and serpentinite. Mixing of oxidized seawater and strongly reducing hydrothermal fluid at moderate temperatures created conditions capable of supporting microbial activity. Dense microbial colonies are fossilized in brucite-calcite veins that are strongly enriched in organic carbon (up to 0.5 wt.% of the total carbon) but depleted in (13)C (δ(13)C(TOC) = -19.4‰). We detected a combination of bacterial diether lipid biomarkers, archaeol, and archaeal tetraethers analogous to those found in carbonate chimneys at the active Lost City hydrothermal field. The exposure of mantle rocks to seawater during the breakup of Pangaea fueled chemolithoautotrophic microbial communities at the Iberia Margin, possibly before the onset of seafloor spreading. Lost City-type serpentinization systems have been discovered at midocean ridges, in forearc settings of subduction zones, and at continental margins. It appears that, wherever they occur, they can support microbial life, even in deep subseafloor environments.

Fluid mixing and the deep biosphere of a fossil Lost City-type hydrothermal system at the Iberia Margin

PubMed Central

Klein, Frieder; Humphris, Susan E.; Guo, Weifu; Schubotz, Florence; Schwarzenbach, Esther M.; Orsi, William D.

2015-01-01

Subseafloor mixing of reduced hydrothermal fluids with seawater is believed to provide the energy and substrates needed to support deep chemolithoautotrophic life in the hydrated oceanic mantle (i.e., serpentinite). However, geosphere-biosphere interactions in serpentinite-hosted subseafloor mixing zones remain poorly constrained. Here we examine fossil microbial communities and fluid mixing processes in the subseafloor of a Cretaceous Lost City-type hydrothermal system at the magma-poor passive Iberia Margin (Ocean Drilling Program Leg 149, Hole 897D). Brucite−calcite mineral assemblages precipitated from mixed fluids ca. 65 m below the Cretaceous paleo-seafloor at temperatures of 31.7 ± 4.3 °C within steep chemical gradients between weathered, carbonate-rich serpentinite breccia and serpentinite. Mixing of oxidized seawater and strongly reducing hydrothermal fluid at moderate temperatures created conditions capable of supporting microbial activity. Dense microbial colonies are fossilized in brucite−calcite veins that are strongly enriched in organic carbon (up to 0.5 wt.% of the total carbon) but depleted in 13C (δ13CTOC = −19.4‰). We detected a combination of bacterial diether lipid biomarkers, archaeol, and archaeal tetraethers analogous to those found in carbonate chimneys at the active Lost City hydrothermal field. The exposure of mantle rocks to seawater during the breakup of Pangaea fueled chemolithoautotrophic microbial communities at the Iberia Margin, possibly before the onset of seafloor spreading. Lost City-type serpentinization systems have been discovered at midocean ridges, in forearc settings of subduction zones, and at continental margins. It appears that, wherever they occur, they can support microbial life, even in deep subseafloor environments. PMID:26324888

Microbial Community Analysis in Water Storage Tank Sediment Exposed to Monochloramine - Portland

EPA Science Inventory

Sediment accumulation in water storage facilities causes water quality degradation, including enhanced biological growth and more rapid disinfectant decay. The current research evaluated the microbial community composition after a drinking water storage facility’s sediment was e...

Metagenomic Analysis of Water Distribution System Bacterial Communities

EPA Science Inventory

The microbial quality of drinking water is assessed using culture-based methods that are highly selective and that tend to underestimate the densities and diversity of microbial populations inhabiting distribution systems. In order to better understand the effect of different dis...

Microbial Community Analysis in Water Storage Tank Sediment Exposed to Monochloramine

EPA Science Inventory

Sediment accumulation in water storage facilities causes water quality degradation, including enhanced biological growth and more rapid disinfectant decay. The current research evaluated the microbial community composition after a drinking water storage facility’s sediment was e...

New perspectives on dandruff and seborrheic dermatitis: lessons we learned from bacterial and fungal skin microbiota.

PubMed

Paulino, Luciana Campos

2017-06-01

The human body is inhabited by complex microbial communities, which positively impact different aspects of our health, and might also be related to the development of diseases. Progress in technologies, particularly sequencing methods and bioinformatics tools, has been crucial for the advances in this field. Microbial communities from skin can modulate immune response and protect the host against pathogens, and there are also data supporting their association with several skin conditions; including dandruff and seborrheic dermatitis. For decades, they have been thought to be related to Malassezia yeasts; however, the microbial role has not been elucidated, and their etiology remains poorly understood. This review discusses the recent findings in dandruff and seborrheic dermatitis and their relation to the skin microbiota. Data provided new perceptions to aid in the understanding of these skin disorders, broadening our view of their etiology and the possible roles of microbial communities in symptom development.

Landscape topography structures the soil microbiome in arctic polygonal tundra.

PubMed

Taş, Neslihan; Prestat, Emmanuel; Wang, Shi; Wu, Yuxin; Ulrich, Craig; Kneafsey, Timothy; Tringe, Susannah G; Torn, Margaret S; Hubbard, Susan S; Jansson, Janet K

2018-02-22

In the Arctic, environmental factors governing microbial degradation of soil carbon (C) in active layer and permafrost are poorly understood. Here we determined the functional potential of soil microbiomes horizontally and vertically across a cryoperturbed polygonal landscape in Alaska. With comparative metagenomics, genome binning of novel microbes, and gas flux measurements we show that microbial greenhouse gas (GHG) production is strongly correlated to landscape topography. Active layer and permafrost harbor contrasting microbiomes, with increasing amounts of Actinobacteria correlating with decreasing soil C in permafrost. While microbial functions such as fermentation and methanogenesis were dominant in wetter polygons, in drier polygons genes for C mineralization and CH 4 oxidation were abundant. The active layer microbiome was poised to assimilate N and not to release N 2 O, reflecting low N 2 O flux measurements. These results provide mechanistic links of microbial metabolism to GHG fluxes that are needed for the refinement of model predictions.

Population density controls on microbial pollution across the Ganga catchment.

PubMed

Milledge, D G; Gurjar, S K; Bunce, J T; Tare, V; Sinha, R; Carbonneau, P E

2018-01-01

For millions of people worldwide, sewage-polluted surface waters threaten water security, food security and human health. Yet the extent of the problem and its causes are poorly understood. Given rapid widespread global urbanisation, the impact of urban versus rural populations is particularly important but unknown. Exploiting previously unpublished archival data for the Ganga (Ganges) catchment, we find a strong non-linear relationship between upstream population density and microbial pollution, and predict that these river systems would fail faecal coliform standards for irrigation waters available to 79% of the catchment's 500 million inhabitants. Overall, this work shows that microbial pollution is conditioned by the continental-scale network structure of rivers, compounded by the location of cities whose growing populations contribute c. 100 times more microbial pollutants per capita than their rural counterparts. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Origin of microbial biomineralization and magnetotaxis during the Archean.

PubMed

Lin, Wei; Paterson, Greig A; Zhu, Qiyun; Wang, Yinzhao; Kopylova, Evguenia; Li, Ying; Knight, Rob; Bazylinski, Dennis A; Zhu, Rixiang; Kirschvink, Joseph L; Pan, Yongxin

2017-02-28

Microbes that synthesize minerals, a process known as microbial biomineralization, contributed substantially to the evolution of current planetary environments through numerous important geochemical processes. Despite its geological significance, the origin and evolution of microbial biomineralization remain poorly understood. Through combined metagenomic and phylogenetic analyses of deep-branching magnetotactic bacteria from the Nitrospirae phylum, and using a Bayesian molecular clock-dating method, we show here that the gene cluster responsible for biomineralization of magnetosomes, and the arrangement of magnetosome chain(s) within cells, both originated before or near the Archean divergence between the Nitrospirae and Proteobacteria This phylogenetic divergence occurred well before the Great Oxygenation Event. Magnetotaxis likely evolved due to environmental pressures conferring an evolutionary advantage to navigation via the geomagnetic field. Earth's dynamo must therefore have been sufficiently strong to sustain microbial magnetotaxis in the Archean, suggesting that magnetotaxis coevolved with the geodynamo over geological time.

Native soil organic matter conditions the response of microbial communities to organic inputs with different stability

NASA Astrophysics Data System (ADS)

Yanardaǧ, Ibrahim H.; Zornoza, Raúl; Bastida, Felipe; Büyükkiliç-Yanardaǧ, Asuman; Acosta, Jose A.; García, Carlos; Faz, Ángel; Mermut, Ahmet R.

2017-04-01

The response of soil microbial communities from soils with different soil organic matter (SOM) content to organic inputs with different stability is still poorly understood. Thus, an incubation experiment was designed to study how the addition of pig slurry (PS), its manure (M) and its biochar (BC) affect soil microbial community and activity in three soils differing in SOM content (Regosol, Luvisol and Kastanozem). The evolution of different C and N fractions, microbial biomass C and N, enzyme activities and microbial community structure by the use of phospholipid fatty acid (PLFA) analysis was assessed for 60 days. Results showed that the different amendments had different effect on microbial properties depending on the soil type. The addition of M caused the highest increase in all microbial properties in the three soils, followed by PS. These changes were more intense in the soil with the lowest SOM (Regosol). The addition of M and PS caused changes in the microbial community structure in all soils, which were more related to the presence of available sources of N than to the labile fractions of C. The addition of BC was followed by increases in the proportions of fungi and Gram positive bacteria in the Regosol, while enhanced the proportion of actinobacteria in all soil types, related to increments in pH and soil C recalcitrance. Thus, native SOM determined the response of microbial communities to external inputs with different stability, soils with low SOM being more prone to increase microbial biomass and activity and change microbial community structure.

The effects of the mineral phase on C stabilization mechanisms and the microbial community along an eroding slope transect

NASA Astrophysics Data System (ADS)

Doetterl, S.; Opfergelt, S.; Cornelis, J.; Boeckx, P. F.; van oost, K.; Six, J.

2013-12-01

An increasing number of studies show the importance of including soil redistribution processes in understanding carbon (C) dynamics in eroding landscapes. The quality and quantity of soil organic carbon in sloping cropland differs with topographic position. These differences are commonly more visible in the subsoil, while the size and composition of topsoil C pools are similar along the hillslope. The type (plant- or microbial-derived) and quality (level of degradation) of C found in a specific soil fraction depends on the interplay between the temporal dynamic of the specific mechanism and it's strength to protect C from decomposition. Here, we present an analysis that aims to clarify the bio/geo-chemical and mineralogical components involved in stabilizing C at various depths and slope positions and how they affect the microbial community and the degradation of C. For this we analyzed soil samples from different soil depths along a slope transect applying (i) a sequential extraction of the reactive soil phase using pyrophosphate, oxalate and dithionite-citrate-bicarbonate, (ii) a semi-quantitative and qualitative analysis of the clay mineralogy, (iii) an analysis of the microbial community using amino sugars and (iv) an analysis of the level of degradation of C in different soil fractions focusing on the soil Lignin signature. The results show that the pattern of minerals and their relative importance in stabilizing C varies greatly along the transect. In the investigated soils, pyrophosphate extractable Manganese, and not Iron or Aluminum as often observed, is strongly correlated to C in the bulk soil and in the non-aggregated silt and clay fractions. This suggests a certain role of Manganese for C stabilization where physical protection is absent. In contrast, pyrophosphate extractable Iron and Aluminum components are largely abundant in water-stable soil aggregates but not correlated to C, suggesting importance of these extracts to stabilize aggregates and, hence, providing physical protection of C. Oxalate extractable amorphous and poorly crystalline minerals are correlated to C, especially for the more recalcitrant C fractions, but only at the depositional site. However, decreasing contents of oxalate extractable elements with depth indicate a temporal limitation of this stabilization mechanism and this is also supported by the results of our lignin extraction. Non-expandable clay minerals experience a relative enrichment at the depositional site while expandable clay minerals experience the same at the eroding site. These changes in clay mineralogy along the slope are partly responsible for the abundance of silt and clay associated C. The changes in soil mineralogy and micro-scale environmental conditions led to an adaptation of the microbial community in comparison to sites not affected by soil redistribution.

Integrating microbial physiology and enzyme traits in the quality model

NASA Astrophysics Data System (ADS)

Sainte-Marie, Julien; Barrandon, Matthieu; Martin, Francis; Saint-André, Laurent; Derrien, Delphine

2017-04-01

Microbe activity plays an undisputable role in soil carbon storage and there have been many calls to integrate microbial ecology in soil carbon (C) models. With regard to this challenge, a few trait-based microbial models of C dynamics have emerged during the past decade. They parameterize specific traits related to decomposer physiology (substrate use efficiency, growth and mortality rates...) and enzyme properties (enzyme production rate, catalytic properties of enzymes…). But these models are built on the premise that organic matter (OM) can be represented as one single entity or are divided into a few pools, while organic matter exists as a continuum of many different compounds spanning from intact plant molecules to highly oxidised microbial metabolites. In addition, a given molecule may also exist in different forms, depending on its stage of polymerization or on its interactions with other organic compounds or mineral phases of the soil. Here we develop a general theoretical model relating the evolution of soil organic matter, as a continuum of progressively decomposing compounds, with decomposer activity and enzyme traits. The model is based on the notion of quality developed by Agren and Bosatta (1998), which is a measure of molecule accessibility to degradation. The model integrates three major processes: OM depolymerisation by enzyme action, OM assimilation and OM biotransformation. For any enzyme, the model reports the quality range where this enzyme selectively operates and how the initial quality distribution of the OM subset evolves into another distribution of qualities under the enzyme action. The model also defines the quality range where the OM can be uptaken and assimilated by microbes. It finally describes how the quality of the assimilated molecules is transformed into another quality distribution, corresponding to the decomposer metabolites signature. Upon decomposer death, these metabolites return to the substrate. We explore here the how microbial physiology and enzyme traits can be incorporated in a model based on a continuous representation of the organic matter and evaluate how it can improve our ability to predict soil C cycling. To do so, we analyse the properties of the model by implementing different scenarii and test the sensitivity of its parameters. Agren, G. I., & Bosatta, E. (1998). Theoretical ecosystem ecology: understanding element cycles. Cambridge University Press.

Online fluorescence spectroscopy for the real-time evaluation of the microbial quality of drinking water.

PubMed

Sorensen, J P R; Vivanco, A; Ascott, M J; Gooddy, D C; Lapworth, D J; Read, D S; Rushworth, C M; Bucknall, J; Herbert, K; Karapanos, I; Gumm, L P; Taylor, R G

2018-06-15

We assessed the utility of online fluorescence spectroscopy for the real-time evaluation of the microbial quality of untreated drinking water. Online fluorimeters were installed on the raw water intake at four groundwater-derived UK public water supplies alongside existing turbidity sensors that are used to forewarn of the presence of microbial contamination in the water industry. The fluorimeters targeted fluorescent dissolved organic matter (DOM) peaks at excitation/emission wavelengths of 280/365 nm (tryptophan-like fluorescence, TLF) and 280/450 nm (humic-like fluorescence, HLF). Discrete samples were collected for Escherichia coli, total bacterial cell counts by flow cytometry, and laboratory-based fluorescence and absorbance. Both TLF and HLF were strongly correlated with E. coli (ρ = 0.71-0.77) and total bacterial cell concentrations (ρ = 0.73-0.76), whereas the correlations between turbidity and E. coli (ρ = 0.48) and total bacterial cell counts (ρ = 0.40) were much weaker. No clear TLF peak was observed at the sites and all apparent TLF was considered to be optical bleed-through from the neighbouring HLF peak. Therefore, a HLF fluorimeter alone would be sufficient to evaluate the microbial water quality at these sources. Fluorescent DOM was also influenced by site operations such as pump start-up and the precipitation of cations on the sensor windows. Online fluorescent DOM sensors are a better indicator of the microbial quality of untreated drinking water than turbidity and they have wide-ranging potential applications within the water industry. Copyright © 2018 British Geological Survey, a component institute of NERC - 'BGS © NERC 2018'. Published by Elsevier Ltd.. All rights reserved.

Microbiological performance of dairy processing plants is influenced by scale of production and the implemented food safety management system: a case study.

PubMed

Opiyo, Beatrice Atieno; Wangoh, John; Njage, Patrick Murigu Kamau

2013-06-01

The effects of existing food safety management systems and size of the production facility on microbiological quality in the dairy industry in Kenya were studied. A microbial assessment scheme was used to evaluate 14 dairies in Nairobi and its environs, and their performance was compared based on their size and on whether they were implementing hazard analysis critical control point (HACCP) systems and International Organization for Standardization (ISO) 22000 recommendations. Environmental samples from critical sampling locations, i.e., workers' hands and food contact surfaces, and from end products were analyzed for microbial quality, including hygiene indicators and pathogens. Microbial safety level profiles (MSLPs) were constructed from the microbiological data to obtain an overview of contamination. The maximum MSLP score for environmental samples was 18 (six microbiological parameters, each with a maximum MSLP score of 3) and that for end products was 15 (five microbiological parameters). Three dairies (two large scale and one medium scale; 21% of total) achieved the maximum MSLP scores of 18 for environmental samples and 15 for the end product. Escherichia coli was detected on food contact surfaces in three dairies, all of which were small scale dairies, and the microorganism was also present in end product samples from two of these dairies, an indication of cross-contamination. Microbial quality was poorest in small scale dairies. Most operations in these dairies were manual, with minimal system documentation. Noncompliance with hygienic practices such as hand washing and cleaning and disinfection procedures, which is common in small dairies, directly affects the microbial quality of the end products. Dairies implementing HACCP systems or ISO 22000 recommendations achieved maximum MSLP scores and hence produced safer products.

Fungal–bacterial dynamics and their contribution to terrigenous carbon turnover in relation to organic matter quality

PubMed Central

Fabian, Jenny; Zlatanovic, Sanja; Mutz, Michael; Premke, Katrin

2017-01-01

Ecological functions of fungal and bacterial decomposers vary with environmental conditions. However, the response of these decomposers to particulate organic matter (POM) quality, which varies widely in aquatic ecosystems, remains poorly understood. Here we investigated how POM pools of substrates of different qualities determine the relative contributions of aquatic fungi and bacteria to terrigenous carbon (C) turnover. To this end, surface sediments were incubated with different POM pools of algae and/or leaf litter. 13C stable-isotope measurements of C mineralization were combined with phospholipid analysis to link the metabolic activities and substrate preferences of fungal and bacterial heterotrophs to dynamics in their abundance. We found that the presence of labile POM greatly affected the dominance of bacteria over fungi within the degrader communities and stimulated the decomposition of beech litter primarily through an increase in metabolic activity. Our data indicated that fungi primarily contribute to terrigenous C turnover by providing litter C for the microbial loop, whereas bacteria determine whether the supplied C substrate is assimilated into biomass or recycled back into the atmosphere in relation to phosphate availability. Thus, this study provides a better understanding of the role of fungi and bacteria in terrestrial–aquatic C cycling in relation to environmental conditions. PMID:27983721

A Molecular MST Approach to Investigate Fecal Indicator Bacteria in Bioaerosols, Bathing Water, Seaweed Wrack, and Sand at Recreational Beaches

NASA Astrophysics Data System (ADS)

Thoren, K. M.; Sinigalliano, C. D.

2016-02-01

Despite numerous cases of beach bacteria affecting millions of people worldwide, the persistence of the bacteria populations in coastal areas is still not well understood. The purpose of this study was to test the levels of persistence of Fecal Indicating Bacteria (FIB) of enterococci, Escherichia coli, and Human-source Bacteroidales, within the intertidal "swash zone" and the deeper waist zone in which people commonly bathe and play. In addition, the study sought to determine if these bacterial contaminants may also be found in aerosols at the beach. Measuring solar insolation in relation to bacterial persistence in seaweed wrack was used to determine if sunlight plays a role in modifying concentrations of FIB at the beach. Light intensity measured by a solar photometer and air quality measured by aerosol plate counts and qPCR Microbial Source Tracking (MST) was compared to varying locations where the beach samples were collected. Results from water samples demonstrate that bacteria measured using plate counts and qPCR were indeed higher within the swash zone than in the waist zone. This is in contrast with the way that the EPA currently measures and determines the public safety of beach waters. They commonly measure the waist zone, but disregard the swash zone. Results from beach bio-aerosol samples showed a wide variety of fungi and bacteria in the beach air, and qPCR MST analysis of these bio-aerosols showed the presence of FIBs such as enterococci on several of the aerosol collection plates. This emphasizes the need to collect samples from the entire beach instead of just measuring at an isolated area, and that exposure to microbial contaminants may include bathing water, beach sand, seaweed wrack, and bio-aerosols. Thus, the data reveals a potential way to identify harmful levels of bacteria and dangerous levels of poor air quality at recreational beaches. These results expound the need for broader assessment of potential beach contamination, not only the swimming water, but also the beach air, shoreline, and also varying depths of water, which can be extremely beneficial to reduce people's risk from microbial contamination exposure.

Microbial production of isoquinoline alkaloids as plant secondary metabolites based on metabolic engineering research.

PubMed

Sato, Fumihiko; Kumagai, Hidehiko

2013-01-01

Plants produce a variety of secondary metabolites that possess strong physiological activities. Unfortunately, however, their production can suffer from a variety of serious problems, including low levels of productivity and heterogeneous quality, as well as difficulty in raw material supply. In contrast, microorganisms can be used to produce their primary and some of their secondary metabolites in a controlled environment, thus assuring high levels of efficiency and uniform quality. In an attempt to overcome the problems associated with secondary metabolite production in plants, we developed a microbial platform for the production of plant isoquinoline alkaloids involving the unification of the microbial and plant metabolic pathways into a single system. The potential applications of this system have also been discussed.

Microbial production of isoquinoline alkaloids as plant secondary metabolites based on metabolic engineering research

PubMed Central

SATO, Fumihiko; KUMAGAI, Hidehiko

2013-01-01

Plants produce a variety of secondary metabolites that possess strong physiological activities. Unfortunately, however, their production can suffer from a variety of serious problems, including low levels of productivity and heterogeneous quality, as well as difficulty in raw material supply. In contrast, microorganisms can be used to produce their primary and some of their secondary metabolites in a controlled environment, thus assuring high levels of efficiency and uniform quality. In an attempt to overcome the problems associated with secondary metabolite production in plants, we developed a microbial platform for the production of plant isoquinoline alkaloids involving the unification of the microbial and plant metabolic pathways into a single system. The potential applications of this system have also been discussed. PMID:23666088

Impact of diverse soil microbial communities on crop residues decomposition

NASA Astrophysics Data System (ADS)

Mrad, Fida; Bennegadi-Laurent, Nadia; Ailhas, Jérôme; Leblanc, Nathalie; Trinsoutrot-Gattin, Isabelle; Laval, Karine; Gattin, Richard

2017-04-01

Soils provide many basic ecosystem services for our society and most of these services are carried out by the soil communities, thus influencing soils quality. Soil organic matter (SOM) can be considered as one of the most important soil quality indices for it plays a determinant role in many physical, chemical and biological processes, such as soil structure and erosion resistance, cation exchange capacity, nutrient cycling and biological activity (Andrews et al., 2004). Since a long time, exogenous organic inputs are largely used for improving agricultural soils, affecting highly soil fertility and productivity. The use of organic amendments such as crop residues influences the soil microbial populations' diversity and abundance. In the meantime, soil microbial communities play a major role in the organic matter degradation, and the effect of different microbial communities on the decomposition of crop residues is not well documented. In this context, studying the impact of crop residues on soil microbial ecology and the processes controlling the fate of plant residues in different management practices is essential for understanding the long-term environmental and agronomic effects on soil and organic matters. Our purpose in the present work was to investigate the decomposition by two contrasting microbial communities of three crop residues, and compare the effect of different residues amendments on the abundance and function of each soil microbial communities. Among the main crops which produce large amounts of residues, we focused on three different plants: wheat (Triticum aestivum L.), rape (Brassica napus) and sunflower (Helianthus annuus). The residues degradation in two soils of different management practices and the microbial activity were evaluated by: microbial abundance (microbial carbon, culturable bacteria, total DNA, qPCR), in combination with functional indicators (enzymatic assays and Biolog substrate utilization), kinetics of C and N mineralization, and chemical measures. Physicochemical composition of crop residues was assessed by Fourier transform infrared spectroscopy FTIR technique at 0 and 83 days. The experiment was conducted in microcosms over 83 days for the biological measurements and 175 days for the C mineralization. The first results showed variations in the C & N rates, and the microbial abundances and functions over time, with a peak at 5 days and a decrease at 83 days for most of the measurements. The soil microbial communities' composition (different management practices) highly impacted the crop residues decomposition. The biochemical composition of crop residues influenced less the microbial communities of each soil. Further studies on the valorization of these residues into agro materials will be carried out. References: Andrews SS., Karlen DL., and Cambardella CA. (2004) The soil management assessment framework: a quantitative soil quality evaluation method. Soil Science Society of America, 68: 1945-1962

Microbial host interactions and impaired wound healing in mice and humans: defining a role for BD14 and NOD2.

PubMed

Williams, Helen; Campbell, Laura; Crompton, Rachel A; Singh, Gurdeep; McHugh, Brian J; Davidson, Donald J; McBain, Andrew J; Cruickshank, Sheena M; Hardman, Matthew J

2018-04-30

Chronic wounds cause significant patient morbidity and mortality. A key factor in their etiology is microbial infection, yet skin host-microbiota interactions during wound repair remain poorly understood. Microbiome profiles of non-infected human chronic wounds are associated with subsequent healing outcome. Furthermore, poor clinical healing outcome was associated with increased local expression of the pattern recognition receptor NOD2. To investigate NOD2 function in the context of cutaneous healing, we treated mice with the NOD2 ligand muramyl dipeptide (MDP) and analyzed wound repair parameters and expression of anti-microbial peptides. MDP treatment of littermate controls significantly delayed wound repair associated with reduced re-epithelialization, heightened inflammation and upregulation of murine β-Defensins (mBD) 1, 3 and particularly 14. We postulated that although BD14 might impact on local skin microbial communities it may further impact other healing parameters. Indeed, exogenously administered mBD14 directly delayed mouse primary keratinocyte scratch wound closure in vitro. To further explore the role of mBD14 in wound repair, we employed Defb14 -/- mice, and showed they had a global delay in healing in vivo, associated with alterations in wound microbiota. Taken together these studies suggest a key role for NOD2-mediated regulation of local skin microbiota which in turn impacts on chronic wound etiology. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

The Role of Soil Organic Matter, Nutrients, and Microbial Community Structure on the Performance of Microbial Fuel Cells

NASA Astrophysics Data System (ADS)

Rooney-Varga, J. N.; Dunaj, S. J.; Vallino, J. J.; Hines, M. E.; Gay, M.; Kobyljanec, C.

2011-12-01

Microbial fuel cells (MFCs) offer the potential for generating electricity, mitigating greenhouse gas emissions, and bioremediating pollutants through utilization of a plentiful, natural, and renewable resource: soil organic carbon. In the current study, we analyzed microbial community structure, MFC performance, and soil characteristics in different microhabitats (bulk soil, anode, and cathode) within MFCs constructed from agricultural or forest soils in order to determine how soil type and microbial dynamics influence MFC performance. MFCs were constructed with soils from agricultural and hardwood forest sites at Harvard Forest (Petersham, MA). The bulk soil characteristics were analyzed, including polyphenols, short chain fatty acids, total organic C and N, abiotic macronutrients, N and P mineralization rates, CO2 respiration rates, and MFC power output. Microbial community structure of the anodes, cathodes, and bulk soils was determined with molecular fingerprinting methods, which included terminal restriction length polymorphism (T-RFLP) analysis and 16S rRNA gene sequencing analysis. Our results indicated that MFCs constructed from agricultural soil had power output about 17 times that of forest soil-based MFCs and respiration rates about 10 times higher than forest soil MFCs. Agricultural soil MFCs had lower C:N ratios, polyphenol content, and acetate concentrations than forest soil MFCs, suggesting that active agricultural MFC microbial communities were supported by higher quality organic carbon. Microbial community profile data indicate that the microbial communities at the anode of the high power MFCs were less diverse than in low power MFCs and were dominated by Deltaproteobacteria, Geobacter, and, to a lesser extent, Clostridia, while low-power MFC anode communities were dominated by Clostridia. These data suggest that the presence of organic carbon substrate (acetate) was not the major limiting factor in selecting for highly electrogenic microbial communities, while the quality of available organic matter may have played a significant role in supporting high performing microbial communities.

Effects of silage additives on ruminal and intestinal microbiology

USDA-ARS?s Scientific Manuscript database

Ensiling is the preservation of forage for livestock through microbial fermentation. Although ensiling of plant material by its associated surface microbial community alone is possible, the cost of an uncontrolled fermentation can include dry matter loss, decreased quality, and spoilage. While prope...

MOLECULAR DIVERSITY OF DRINKING WATER MICROBIAL COMMUNITIES: A PHYLOGENETIC APPROACH

EPA Science Inventory

The microbiological quality of drinking water is assessed using culture-based methods that are highly selective and that tend to underestimate the densities and diversity of microbial populations inhabiting distribution systems. In order to better understand the effect of differe...

INFLUENCE OF SURFACTANTS ON MICROBIAL DEGRADATION OF ORGANIC COMPOUNDS

EPA Science Inventory

Surfactants have the ability to increase aqueous concentrations of poorly soluble compounds and interfacial areas between immiscible fluids, thus potentially improving the accessibility of these substrates to microorganisms. However, both enhancements and inhibitions of biodegrad...

TREATMENT OF CHRONIC HERPESVIRAL DERMATITIS IN A CAPTIVE CHEETAH (ACINONYX JUBATUS) IN NAMIBIA.

PubMed

Flacke, Gabriella L; Schmidt-Küntzel, Anne; Marker, Laurie

2015-09-01

A 9-yr-old male cheetah (Acinonyx jubatus) housed at the Cheetah Conservation Fund in Namibia developed cutaneous lesions consisting of alopecia, erythema, ulceration, and crusting on the left fore and hind limbs. Histopathology of skin biopsies in conjunction with indirect fluorescent antibody and polymerase chain reaction testing confirmed a diagnosis of feline herpesvirus-1 dermatitis; microbial culture indicated secondary bacterial infection. Therapy included targeted systemic antimicrobial and antiviral treatment, topical medications, and repeated cryotherapy. Lesions exhibited varying degrees of clinical improvement but, overall, progressed in extent, size, and severity during the subsequent 2.5 yr of intense treatment. The cheetah was ultimately euthanized due to a guarded prognosis and concerns about poor quality of life. Potential factors initiating or contributing (or both) to the severity and nonhealing nature of the cutaneous lesions include chronic unidentified stress, altered immune system function, and other environmental influences.

Engineering microbial cell factories for the production of plant natural products: from design principles to industrial-scale production.

PubMed

Liu, Xiaonan; Ding, Wentao; Jiang, Huifeng

2017-07-19

Plant natural products (PNPs) are widely used as pharmaceuticals, nutraceuticals, seasonings, pigments, etc., with a huge commercial value on the global market. However, most of these PNPs are still being extracted from plants. A resource-conserving and environment-friendly synthesis route for PNPs that utilizes microbial cell factories has attracted increasing attention since the 1940s. However, at the present only a handful of PNPs are being produced by microbial cell factories at an industrial scale, and there are still many challenges in their large-scale application. One of the challenges is that most biosynthetic pathways of PNPs are still unknown, which largely limits the number of candidate PNPs for heterologous microbial production. Another challenge is that the metabolic fluxes toward the target products in microbial hosts are often hindered by poor precursor supply, low catalytic activity of enzymes and obstructed product transport. Consequently, despite intensive studies on the metabolic engineering of microbial hosts, the fermentation costs of most heterologously produced PNPs are still too high for industrial-scale production. In this paper, we review several aspects of PNP production in microbial cell factories, including important design principles and recent progress in pathway mining and metabolic engineering. In addition, implemented cases of industrial-scale production of PNPs in microbial cell factories are also highlighted.

Microbially mediated alteration of crystalline basalts as identified from analogical reactive percolation experiments

NASA Astrophysics Data System (ADS)

Moore, Rachael; Ménez, Bénédicte; Stéphant, Sylvian; Dupraz, Sébastien; Ranchou-Peyruse, Magali; Ranchou-Peyruse, Anthony; Gérard, Emmanuelle

2017-04-01

Alteration in the ocean crust through fluid circulation is an ongoing process affecting the first kilometers and at low temperatures some alteration may be microbially mediated. Hydrothermal activity through the hard rock basement supports diverse microbial communities within the rock by providing nutrient and energy sources. Currently, the impact of basement hosted microbial communities on alteration is poorly understood. In order to identify and quantify the nature of microbially mediated alteration two reactive percolation experiments mimicking circulation of CO2 enriched ground water were performed at 35 °C and 30 bar for 21 days each. The experiments were performed using a crystalline basalt substrate from an earlier drilled deep Icelandic aquifer. One experiment was conducted on sterile rock while the other was conducted with the addition of a microbial inoculate derived from groundwater enrichment cultures obtained from the same aquifer. µCT on the experimental basaltic substrate before and after the reactive percolation experiment along with synchrotron radiation x-ray tomographic microscopy and the mineralogical characterization of resulting material allows for the comparative volumetric quantification of dissolution and precipitation. The unique design of this experiment allows for the identification of alteration which occurs solely abiotically and of microbially mediated alteration. Experimental results are compared to natural basaltic cores from Iceland retrieved following a large field CO2 injection experiment that stimulated microbial activity at depth.

Microbial contamination of dental unit waterlines and effect on quality of indoor air.

PubMed

Kadaifciler, Duygu Göksay; Cotuk, Aysin

2014-06-01

The microbiological quality in dental unit waterlines (DUWLs) is considered to be important because patients and dental staff with suppressed immune systems are regularly exposed to water and aerosols generated from dental units (DUs). Opportunistic pathogens like Pseudomonas, Legionella, Candida, and Aspergillus can be present in DUWLs, while during consultations, bioaerosols can be dispersed in the air, thus resulting in effects on microbiological quality of indoor air. This present study represents microbiological air and water quality in dental offices (DOs) and also concerns the relationship between the quality of DO air and dental unit water. This study aimed to assess both the microbial quality of dental unit water and the indoor air in 20 DOs and to survey the effect on the quality of the indoor air with the existing microorganisms in dental unit water. Fourteen out of 20 (70 %) DUWLs were found to be contaminated with a high number of aerobic mesophilic heterotrophic bacteria. In terms of bacterial air contamination levels, in 90 % of DOs, a medium level (<500 colony-forming units (CFU)/m(3)) of contamination was determined, while in terms of microfungal air contamination, in all DOs, a low level (<100 CFU/m(3)) of contamination was determined. Potential infection or allergen agents, such as Pseudomonas, Micrococcus, Staphylococcus, Alternaria, Cladosporium, Penicillium, Aspergillus, and Paecilomyces were isolated from water and air samples. This study's determination of contamination sources and evaluation of microbial load in DOs could contribute to the development of quality control methods in the future.

Estimated Under-Five Deaths Associated with Poor-Quality Antimalarials in Sub-Saharan Africa

PubMed Central

Renschler, John P.; Walters, Kelsey M.; Newton, Paul N.; Laxminarayan, Ramanan

2015-01-01

Many antimalarials sold in sub-Saharan Africa are poor-quality (falsified, substandard, or degraded), and the burden of disease caused by this problem is inadequately quantified. In this article, we estimate the number of under-five deaths caused by ineffective treatment of malaria associated with consumption of poor-quality antimalarials in 39 sub-Saharan countries. Using Latin hypercube sampling our estimates were calculated as the product of the number of private sector antimalarials consumed by malaria-positive children in 2013; the proportion of private sector antimalarials consumed that were of poor-quality; and the case fatality rate (CFR) of under-five malaria-positive children who did not receive appropriate treatment. An estimated 122,350 (interquartile range [IQR]: 91,577–154,736) under-five malaria deaths were associated with consumption of poor-quality antimalarials, representing 3.75% (IQR: 2.81–4.75%) of all under-five deaths in our sample of 39 countries. There is considerable uncertainty surrounding our results because of gaps in data on case fatality rates and prevalence of poor-quality antimalarials. Our analysis highlights the need for further investigation into the distribution of poor-quality antimalarials and the need for stronger surveillance and regulatory efforts to prevent the sale of poor-quality antimalarials. PMID:25897068

Whey protein isolate/cellulose nanofibre/TiO2 nanoparticle/rosemary essential oil nanocomposite film: Its effect on microbial and sensory quality of lamb meat and growth of common foodborne pathogenic bacteria during refrigeration.

PubMed

Alizadeh Sani, Mahmood; Ehsani, Ali; Hashemi, Mohammad

2017-06-19

The use of biodegradable nanocomposite films in active packaging is of great importance since they can have a controlled release of antimicrobial compounds. This study was conducted to evaluate the efficacy of whey protein isolate (WPI)/cellulose nanofibre (CNF) nanocomposite films containing 1.0% (w/w) titanium dioxide (TiO 2 ) and 2.0% (w/v) rosemary essential oil (REO) in preserving the microbial and sensory quality of lamb meat during the storage at 4±1°C. Initially, the best concentration of each compound to be added to the film was determined by micro-dilution and disc diffusion methods. The microbial and sensory properties of lamb meat were controlled in two groups (control and treatment) over 15days of storage. Then, the samples were analysed for total viable count (TVC), Pseudomonas spp. count, Enterobacteriaceae count, Lactic acid bacteria (LAB) count, inoculated Staphylococcus aureus count, Listeria monocytogenes count, and Escherichia coli O 157 :H 7 count. Microbial analysis and nine-point hedonic scale was applied for the sensory analysis. Results indicated that the use of nanocomposite films significantly reduced the bacterial counts of treatment group. Higher inhibition effect was observed on Gram-positive bacteria than on Gram-negative bacteria (P<0.05). The microbial and sensory evaluations also showed that the use of nanocomposite films significantly increased the shelf life of treated meat (15days) compared to the control meat (6days). Based on the results of this study, the edible nanocomposite films were effective in preserving the microbial and sensory qualities of lamb meat; therefore, this application is recommended in meat especially red meat. Copyright © 2017 Elsevier B.V. All rights reserved.

The prevalence of poor sleep quality and its association with depression and anxiety scores in patients admitted for cardiovascular disease: A cross-sectional designed study.

PubMed

Matsuda, Risa; Kohno, Takashi; Kohsaka, Shun; Fukuoka, Ryoma; Maekawa, Yuichiro; Sano, Motoaki; Takatsuki, Seiji; Fukuda, Keiichi

2017-02-01

Poor sleep quality contributes to the development of various cardiovascular conditions. However, its real-world prevalence among cardiovascular inpatients and association with psychological disturbance is unknown. This study aimed to assess the prevalence of poor sleep quality and its association with depression and anxiety in cardiovascular patients, and explored whether sex and cardiovascular comorbidities modified these associations. A total of 1071 patients hospitalized for a broad spectrum of cardiovascular diseases at a single university hospital were assessed (790 men, mean age 64±14years). We assessed sleep quality during their index hospitalization period using the Pittsburgh Sleep Quality Index (PSQI); poor sleep quality was defined as PSQI>5. Depression and anxiety were assessed with the Hospital Anxiety and Depression Scale (HADS). The median PSQI score was 5.0 [3.0-7.0], and 461 inpatients (43%) had poor sleep quality. Multivariate regression analysis adjusting for patient background, medical risk factors, and laboratory data revealed that poor sleep quality was associated with higher HADS subscores for depression (HADS-depression; odds ratio [OR]: 1.09, 95% confidence interval [CI]: 1.03-1.15) and anxiety (HADS-anxiety; OR: 1.17, 95% CI: 1.11-1.24). Poor sleep quality was associated with markedly higher HADS-depression among women than men (p value for interaction: 0.008). The association between poor sleep quality and HADS-anxiety was more significant among patients without coronary artery diseases (p value for interaction: 0.017). Poor sleep quality was highly prevalent and associated with depression and anxiety in cardiovascular patients. These associations may be modified by sex and the presence of coronary artery diseases. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Microbial colonization and lung function in adolescents with cystic fibrosis.

PubMed

Hector, Andreas; Kirn, Tobias; Ralhan, Anjali; Graepler-Mainka, Ute; Berenbrinker, Sina; Riethmueller, Joachim; Hogardt, Michael; Wagner, Marlies; Pfleger, Andreas; Autenrieth, Ingo; Kappler, Matthias; Griese, Matthias; Eber, Ernst; Martus, Peter; Hartl, Dominik

2016-05-01

With intensified antibiotic therapy and longer survival, patients with cystic fibrosis (CF) are colonized with a more complex pattern of bacteria and fungi. However, the clinical relevance of these emerging pathogens for lung function remains poorly defined. The aim of this study was to assess the association of bacterial and fungal colonization patterns with lung function in adolescent patients with CF. Microbial colonization patterns and lung function parameters were assessed in 770 adolescent European (German/Austrian) CF patients in a retrospective study (median follow-up time: 10years). Colonization with Pseudomonas aeruginosa and MRSA were most strongly associated with loss of lung function, while mainly colonization with Haemophilus influenzae was associated with preserved lung function. Aspergillus fumigatus was the only species that was associated with an increased risk for infection with P. aeruginosa. Microbial interaction analysis revealed three distinct microbial clusters within the longitudinal course of CF lung disease. Collectively, this study identified potentially protective and harmful microbial colonization patterns in adolescent CF patients. Further studies in different patient cohorts are required to evaluate these microbial patterns and to assess their clinical relevance. Copyright © 2016 European Cystic Fibrosis Society. Published by Elsevier B.V. All rights reserved.

Microbial colonization of biopolymeric thin films containing natural compounds and antibiotics fabricated by MAPLE

NASA Astrophysics Data System (ADS)

Cristescu, R.; Surdu, A. V.; Grumezescu, A. M.; Oprea, A. E.; Trusca, R.; Vasile, O.; Dorcioman, G.; Visan, A.; Socol, G.; Mihailescu, I. N.; Mihaiescu, D.; Enculescu, M.; Chifiriuc, M. C.; Boehm, R. D.; Narayan, R. J.; Chrisey, D. B.

2015-05-01

Although a great number of antibiotics are currently available, they are often rendered ineffective by the ability of microbial strains to develop genetic resistance and to grow in biofilms. Since many antimicrobial agents poorly penetrate biofilms, biofilm-associated infections often require high concentrations of antimicrobial agents for effective treatment. Among the various strategies that may be used to inhibit microbial biofilms, one strategy that has generated significant interest involves the use of bioactive surfaces that are resistant to microbial colonization. In this respect, we used matrix assisted pulsed laser evaporation (MAPLE) involving a pulsed KrF* excimer laser source (λ = 248 nm, τ = 25 ns, ν = 10 Hz) to obtain thin composite biopolymeric films containing natural (flavonoid) or synthetic (antibiotic) compounds as bioactive substances. Chemical composition and film structures were investigated by Fourier transform infrared spectroscopy and X-ray diffraction. Films morphology was studied by scanning electron microscopy and transmission electron microscopy. The antimicrobial assay of the microbial biofilms formed on these films was assessed by the viable cell counts method. The flavonoid-containing thin films showed increased resistance to microbial colonization, highlighting their potential to be used for the design of anti-biofilm surfaces.

The Denitrification Characteristics of Pseudomonas stutzeri SC221-M and Its Application to Water Quality Control in Grass Carp Aquaculture

PubMed Central

Zhang, Xiaoping; Zheng, Jiajia; Peng, Lisha; Sun, Jiandong; Zhu, Haiyan; Wang, Yibing; Li, Weifen; Wu, Xuexiang; Wu, Di

2014-01-01

To reduce ammonium and nitrite in aquaculture water, an isolate of the denitrifying bacterium Pseudomonas stutzeri, SC221-M, was obtained. The effects of various nitrogen and carbon sources, the ratio of carbon to nitrogen and temperature on bacterial growth, denitrification rates and the expression levels of nirS and nosZ in SC221-M were studied. The following conditions were determined to be optimal for growth and denitrification in SC221-M: NaNO2 as the nitrogen source, sodium citrate as the carbon source, a carbon to nitrogen ratio range of 4–8, and a temperature range of 20–35°C. Subsequently, SC221-M and the Bacillus cereus BSC24 strain were selected to generate microbial preparations. The results showed that addition of the microbial preparations decreased various hydrochemical parameters, including total dissolved solids, ammonium, nitrite, total nitrogen and the chemical oxygen demand. Nitrogen removal rates were highest on day 9; the removal rates of BSC24, SC221-M, a mixed preparation and a 3× mixed preparation were 24.5%, 26.6%, 53.9% and 53.4%, respectively. The mixed preparation (SC221-M+BSC24) was more effective at removing nitrogen than either the SC221-M or BSC24 preparation. Roche 454 pyrosequencing and subsequent analysis indicated that the control and other groups formed separate clusters, and the microbial community structure in the water changed significantly after the addition of microbial preparations. These results indicate that the addition of microbial preparations can improve both the water quality and microbial community structure in an experimental aquaculture system. P. stutzeri strain SC221-M and its related microbial preparations are potential candidates for the regulation of water quality in commercial aquaculture systems. PMID:25489740

Generation of soluble microbial products by bio-activated carbon filter during drinking water advanced treatment and its influence on spectral characteristics.

PubMed

Shen, Hong; Chen, Xin; Zhang, Dong; Chen, Hong-Bin

2016-11-01

In order to improve our understanding of bio-activated carbon (BAC) filter, the water quality of influent and effluent treated with BAC in a drinking water treatment plant (DWTP) of Shanghai during 2015 was valued. Combining the results from UV254, SUVA254, dissolved organic carbon (DOC) and scanning electron microscopic (SEM), it is found that performance of BAC treatment will be affected by characteristics of activated carbon (AC), which is relevant to the type of activated carbon (including shape and operating time) in this study. Fluorescence excitation-emission matrix (FEEM) shows that the humification index (HIX) and index of recent autochthonous contribution (BIX) is a reliable indicator to descript the variation of dissolved organic matter (DOM) during BAC process. The pattern of variation in BIX and HIX implies that soluble microbial products (SMPs) are formed and humic-like substances are removed during BAC treatment, which is also confirmed by the change of peaks of FEEM in BAC effluent. Large, positive correlations between SUVA254 and disinfection by-products formation potential yield (DBPFP yield) demonstrate that UV-absorbing DOM is directly related to the generation of DBPs. Poor correlations of HIX with DBPFP suggest that non-humic substances with UV-absorbing properties play an important role in the generation of DBPs in water with low SUVA254. Finally, strong but negative correlations between BIX and DBPFP suggest that vigorous microbial metabolism of BAC results in a decrease in DBPFP. However, the DBPFP yield will be enhanced for the generation of SMPs by BAC, especially in summer. Copyright © 2016 Elsevier B.V. All rights reserved.

Rainfall-induced fecal indicator organisms transport from manured fields: Model sensitivity analysis

EPA Science Inventory

Microbial quality of surface waters attracts attention due to food- and waterborne disease outbreaks. Fecal indicator organisms (FIOs) are commonly used for the microbial pollution level evaluation. Models predicting the fate and transport of FIOs are required to design and evalu...

TEMPORAL VARIABILITY OF MICROBIAL INDICATORS OF FECAL CONTAMINATION OF MARINE AND FRESHWATER BEACHES

EPA Science Inventory

Monitoring methods for microbial indicators of fecal contamination are an integral component for protecting the health of swimmers exposed to potentially contaminated bathing beach waters. The design of monitoring systems which will accurately characterize the quality of water is...

Systems Reliability Framework for Surface Water Sustainability and Risk Management

NASA Astrophysics Data System (ADS)

Myers, J. R.; Yeghiazarian, L.

2016-12-01

With microbial contamination posing a serious threat to the availability of clean water across the world, it is necessary to develop a framework that evaluates the safety and sustainability of water systems in respect to non-point source fecal microbial contamination. The concept of water safety is closely related to the concept of failure in reliability theory. In water quality problems, the event of failure can be defined as the concentration of microbial contamination exceeding a certain standard for usability of water. It is pertinent in watershed management to know the likelihood of such an event of failure occurring at a particular point in space and time. Microbial fate and transport are driven by environmental processes taking place in complex, multi-component, interdependent environmental systems that are dynamic and spatially heterogeneous, which means these processes and therefore their influences upon microbial transport must be considered stochastic and variable through space and time. A physics-based stochastic model of microbial dynamics is presented that propagates uncertainty using a unique sampling method based on artificial neural networks to produce a correlation between watershed characteristics and spatial-temporal probabilistic patterns of microbial contamination. These results are used to address the question of water safety through several sustainability metrics: reliability, vulnerability, resilience and a composite sustainability index. System reliability is described uniquely though the temporal evolution of risk along watershed points or pathways. Probabilistic resilience describes how long the system is above a certain probability of failure, and the vulnerability metric describes how the temporal evolution of risk changes throughout a hierarchy of failure levels. Additionally our approach allows for the identification of contributions in microbial contamination and uncertainty from specific pathways and sources. We expect that this framework will significantly improve the efficiency and precision of sustainable watershed management strategies through providing a better understanding of how watershed characteristics and environmental parameters affect surface water quality and sustainability. With microbial contamination posing a serious threat to the availability of clean water across the world, it is necessary to develop a framework that evaluates the safety and sustainability of water systems in respect to non-point source fecal microbial contamination. The concept of water safety is closely related to the concept of failure in reliability theory. In water quality problems, the event of failure can be defined as the concentration of microbial contamination exceeding a certain standard for usability of water. It is pertinent in watershed management to know the likelihood of such an event of failure occurring at a particular point in space and time. Microbial fate and transport are driven by environmental processes taking place in complex, multi-component, interdependent environmental systems that are dynamic and spatially heterogeneous, which means these processes and therefore their influences upon microbial transport must be considered stochastic and variable through space and time. A physics-based stochastic model of microbial dynamics is presented that propagates uncertainty using a unique sampling method based on artificial neural networks to produce a correlation between watershed characteristics and spatial-temporal probabilistic patterns of microbial contamination. These results are used to address the question of water safety through several sustainability metrics: reliability, vulnerability, resilience and a composite sustainability index. System reliability is described uniquely though the temporal evolution of risk along watershed points or pathways. Probabilistic resilience describes how long the system is above a certain probability of failure, and the vulnerability metric describes how the temporal evolution of risk changes throughout a hierarchy of failure levels. Additionally our approach allows for the identification of contributions in microbial contamination and uncertainty from specific pathways and sources. We expect that this framework will significantly improve the efficiency and precision of sustainable watershed management strategies through providing a better understanding of how watershed characteristics and environmental parameters affect surface water quality and sustainability.

Microbial Resources and Enological Significance: Opportunities and Benefits

PubMed Central

Petruzzi, Leonardo; Capozzi, Vittorio; Berbegal, Carmen; Corbo, Maria R.; Bevilacqua, Antonio; Spano, Giuseppe; Sinigaglia, Milena

2017-01-01

Among the innovative trends in the wine sector, the continuous exploration of enological properties associated with wine microbial resources represents a cornerstone driver of quality improvement. Since the advent of starter cultures technology, the attention has been focused on intraspecific biodiversity within the primary species responsible for alcoholic fermentation (Saccharomyces cerevisiae) and, subsequently, for the so-called ‘malolactic fermentation’ (Oenococcus oeni). However, in the last decade, a relevant number of studies proposed the enological exploitation of an increasing number of species (e.g., non-Saccharomyces yeasts) associated with spontaneous fermentation in wine. These new species/strains may provide technological solutions to specific problems and/or improve sensory characteristics, such as complexity, mouth-feel and flavors. This review offers an overview of the available information on the enological/protechnological significance of microbial resources associated with winemaking, summarizing the opportunities and the benefits associated with the enological exploitation of this microbial potential. We discuss proposed solutions to improve quality and safety of wines (e.g., alternative starter cultures, multistrains starter cultures) and future perspectives. PMID:28642742

Co-composting of organic fraction of municipal solid waste mixed with different bulking waste: characterization of physicochemical parameters and microbial enzymatic dynamic.

PubMed

Awasthi, Mukesh Kumar; Pandey, Akhilesh Kumar; Bundela, Pushpendra Singh; Khan, Jamaluddin

2015-04-01

The effect of various bulking waste such as wood shaving, agricultural and yard trimming waste combined with organic fraction of municipal solid waste (OFMSW) composting was investigated through assessing their influence on microbial enzymatic activities and quality of finished compost. All three piles of OFMSW with different bulking waste were inoculated with microbial consortium. The results revealed that OFMSW combined with wood shaving and microbial consortium (Phanerochaete chrysosporium, Trichoderma viride and Pseudomonas aeruginosa) were helpful tool to facilitate the enzymatic activity and shortened composting period within 4 weeks. Maximum enzymatic activity were observed in pile 1 and 3 during the first 3 weeks, while in pile 2 relatively very low. But phosphatase activity was relatively higher in all piles until the end of the process. Maturity parameters of compost quality also favored the pile 1 as the best formulation for OFMSW composting. Copyright © 2015 Elsevier Ltd. All rights reserved.

Effects of Jet Fuel Spills on the Microbial Community of Soil †

PubMed Central

Song, Hong-Gyu; Bartha, Richard

1990-01-01

Hydrocarbon residues, microbial numbers, and microbial activity were measured and correlated in loam soil contaminated by jet fuel spills resulting in 50 and 135 mg of hydrocarbon g of soil−1. Contaminated soil was incubated at 27°C either as well-aerated surface soil or as poorly aerated subsurface soil. In the former case, the effects of bioremediation treatment on residues, microbial numbers, and microbial activity were also assessed. Hydrocarbon residues were measured by quantitative gas chromatography. Enumerations included direct counts of metabolically active bacteria, measurement of mycelial length, plate counts of aerobic heterotrophs, and most probable numbers of hydrocarbon degraders. Activity was assessed by fluorescein diacetate (FDA) hydrolysis. Jet fuel disappeared much more rapidly from surface soil than it did from subsurface soil. In surface soil, microbial numbers and mycelial length were increased by 2 to 2.5 orders of magnitude as a result of jet fuel contamination alone and by 3 to 4 orders of magnitude as a result of the combination of jet fuel contamination and bioremediation. FDA hydrolysis was stimulated by jet fuel and bioremediation, but was inhibited by jet fuel alone. The latter was traced to an inhibition of the FDA assay by jet fuel biodegradation products. In subsurface soil, oxygen limitation strongly attenuated microbial responses to jet fuel. An increase in the most probable numbers of hydrocarbon degraders was accompanied by a decline in other aerobic heterotrophs, so that total plate counts changed little. The correlations between hydrocarbon residues, microbial numbers, and microbial activity help in elucidating microbial contributions to jet fuel elimination from soil. PMID:16348138

Influences of space, soil, nematodes and plants on microbial community composition of chalk grassland soils.

PubMed

Yergeau, Etienne; Bezemer, T Martijn; Hedlund, Katarina; Mortimer, Simon R; Kowalchuk, George A; Van Der Putten, Wim H

2010-08-01

Microbial communities respond to a variety of environmental factors related to resources (e.g. plant and soil organic matter), habitat (e.g. soil characteristics) and predation (e.g. nematodes, protozoa and viruses). However, the relative contribution of these factors on microbial community composition is poorly understood. Here, we sampled soils from 30 chalk grassland fields located in three different chalk hill ridges of Southern England, using a spatially explicit sampling scheme. We assessed microbial communities via phospholipid fatty acid (PLFA) analyses and PCR-denaturing gradient gel electrophoresis (DGGE) and measured soil characteristics, as well as nematode and plant community composition. The relative influences of space, soil, vegetation and nematodes on soil microorganisms were contrasted using variation partitioning and path analysis. Results indicate that soil characteristics and plant community composition, representing habitat and resources, shape soil microbial community composition, whereas the influence of nematodes, a potential predation factor, appears to be relatively small. Spatial variation in microbial community structure was detected at broad (between fields) and fine (within fields) scales, suggesting that microbial communities exhibit biogeographic patterns at different scales. Although our analysis included several relevant explanatory data sets, a large part of the variation in microbial communities remained unexplained (up to 92% in some analyses). However, in several analyses, significant parts of the variation in microbial community structure could be explained. The results of this study contribute to our understanding of the relative importance of different environmental and spatial factors in driving the composition of soil-borne microbial communities. © 2009 Society for Applied Microbiology and Blackwell Publishing Ltd.

Soil organic matter quantity and quality shape microbial community compositions of subtropical broadleaved forests.

PubMed

Ding, Junjun; Zhang, Yuguang; Wang, Mengmeng; Sun, Xin; Cong, Jing; Deng, Ye; Lu, Hui; Yuan, Tong; Van Nostrand, Joy D; Li, Diqiang; Zhou, Jizhong; Yang, Yunfeng

2015-10-01

As two major forest types in the subtropics, broadleaved evergreen and broadleaved deciduous forests have long interested ecologists. However, little is known about their belowground ecosystems despite their ecological importance in driving biogeochemical cycling. Here, we used Illumina MiSeq sequencing targeting 16S rRNA gene and a microarray named GeoChip targeting functional genes to analyse microbial communities in broadleaved evergreen and deciduous forest soils of Shennongjia Mountain of Central China, a region known as 'The Oriental Botanic Garden' for its extraordinarily rich biodiversity. We observed higher plant diversity and relatively richer nutrients in the broadleaved evergreen forest than the deciduous forest. In odds to our expectation that plant communities shaped soil microbial communities, we found that soil organic matter quantity and quality, but not plant community parameters, were the best predictors of microbial communities. Actinobacteria, a copiotrophic phylum, was more abundant in the broadleaved evergreen forest, while Verrucomicrobia, an oligotrophic phylum, was more abundant in the broadleaved deciduous forest. The density of the correlation network of microbial OTUs was higher in the broadleaved deciduous forest but its modularity was smaller, reflecting lower resistance to environment changes. In addition, keystone OTUs of the broadleaved deciduous forest were mainly oligotrophic. Microbial functional genes associated with recalcitrant carbon degradation were also more abundant in the broadleaved deciduous forests, resulting in low accumulation of organic matters. Collectively, these findings revealed the important role of soil organic matter in shaping microbial taxonomic and functional traits. © 2015 John Wiley & Sons Ltd.

Optimization of whole-transcriptome amplification from low cell density deep-sea microbial samples for metatranscriptomic analysis.

PubMed

Wu, Jieying; Gao, Weimin; Zhang, Weiwen; Meldrum, Deirdre R

2011-01-01

Limitation in sample quality and quantity is one of the big obstacles for applying metatranscriptomic technologies to explore gene expression and functionality of microbial communities in natural environments. In this study, several amplification methods were evaluated for whole-transcriptome amplification of deep-sea microbial samples, which are of low cell density and high impurity. The best amplification method was identified and incorporated into a complete protocol to isolate and amplify deep-sea microbial samples. In the protocol, total RNA was first isolated by a modified method combining Trizol (Invitrogen, CA) and RNeasy (QIAGEN, CA) method, amplified with a WT-Ovation™ Pico RNA Amplification System (NuGEN, CA), and then converted to double-strand DNA from single-strand cDNA with a WT-Ovation™ Exon Module (NuGEN, CA). The products from the whole-transcriptome amplification of deep-sea microbial samples were assessed first through random clone library sequencing. The BLAST search results showed that marine-based sequences are dominant in the libraries, consistent with the ecological source of the samples. The products were then used for next-generation Roche GS FLX Titanium sequencing to obtain metatranscriptome data. Preliminary analysis of the metatranscriptomic data showed good sequencing quality. Although the protocol was designed and demonstrated to be effective for deep-sea microbial samples, it should be applicable to similar samples from other extreme environments in exploring community structure and functionality of microbial communities. Copyright © 2010 Elsevier B.V. All rights reserved.

Effect of high hydrostatic pressure on seed germination, microbial quality, anatomy-morphology and physiological characteristics of garden cress (Lepidium sativum) seedlings

NASA Astrophysics Data System (ADS)

İşlek, Cemil; Murat Altuner, Ergin; Çeter, Talip; Alpas, Hami

2013-06-01

High hydrostatic pressure is a non-thermal food processing technology that is found to increase the percentage of germination, decrease the germination time and improve the microbial quality of seeds. In this study, pressures of 100-400 MPa for 10 min at 30°C are used to compare the percentage of germination, the microbial quality of seeds, chlorophyll a and b, and total phenolic compounds concentrations in seedlings, and the anatomy-morphology characteristics of garden cress. Enhanced reductions of total aerobic mesophilic bacteria, total and fecal coliforms, and yeast and mould populations in seeds were observed, especially at 300 MPa. In addition, the percentage of germination, chlorophyll content and phenolic compounds concentrations, fresh and dry weights, and hypocotyl lengths of the seedlings are higher than those of all samples, where the percentage of germination is equal to controls but higher than other samples, and radicula length is lower than controls but higher than others.

Validation Study of Rapid Assays of Bioburden, Endotoxins and Other Contamination.

PubMed

Shintani, Hideharu

2016-01-01

Microbial testing performed in support of pharmaceutical and biopharmaceutical production falls into three main categories: detection (qualitative), enumeration (quantitative), and characterization/identification. Traditional microbiological methods are listed in the compendia and discussed by using the conventional growth-based techniques, which are labor intensive and time consuming. In general, such tests require several days of incubation for microbial contamination (bioburden) to be detected, and therefore management seldom is able to take proactive corrective measures. In addition, microbial growth is limited by the growth medium used and incubation conditions, thus impacting testing sensitivity, accuracy, and reproducibility. 　For more than 20 years various technology platforms for rapid microbiological methods (RMM) have been developed, and many have been readily adopted by the food industry and clinical microbiology laboratories. Their use would certainly offer drug companies faster test turnaround times to accommodate the aggressive deadlines for manufacturing processes and product release. Some rapid methods also offer the possibility for real-time microbial analyses, enabling management to respond to microbial contamination events in a more timely fashion, and can provide cost savings and higher efficiencies in quality control testing laboratories. Despite the many proven business and quality benefits and the fact that the FDA's initiative to promote the use of process analytical technology (PAT) includes rapid microbial methods, pharmaceutical and biopharmaceutical industries have been somewhat slow to embrace alternative microbial methodologies for several reasons. The major reason is that the bioburden counts detected by the incubation method and rapid assay are greatly divergent. 　The use of rapid methods is a dynamic field in applied microbiology and one that has gained increased attention nationally and internationally over time. This topic has been extensively addressed at conferences and in published documents around the world. More recently, the use of alternative methods for control of the microbiological quality of pharmaceutical products and materials used in pharmaceutical production has been addressed by the compendia in an attempt to facilitate implementation of these technologies by pharmaceutical companies. The author presents some of the rapid method technologies under evaluation or in use by pharmaceutical microbiologists and the current status of the implementation of alternative microbial methods.

Effects of dissolved CO2 on Shallow Freshwater Microbial Communities simulating a CO2 Leakage Scenario

NASA Astrophysics Data System (ADS)

Gulliver, D. M.; Lowry, G. V.; Gregory, K.

2013-12-01

Geological carbon sequestration is likely to be part of a comprehensive strategy to minimize the atmospheric release of greenhouse gasses, establishing a concern of sequestered CO2 leakage into overlying potable aquifers. Leaking CO2 may affect existing biogeochemical processes and therefore water quality. There is a critical need to understand the evolution of CO2 exposed microbial communities that influence the biogeochemistry in these freshwater aquifers. The evolution of microbial ecology for different CO2 exposure concentrations was investigated using fluid-slurry samples obtained from a shallow freshwater aquifer (55 m depth, 0.5 MPa, 22 °C, Escatawpa, MS). The microbial community of well samples upstream and downstream of CO2 injection was characterized. In addition, batch vessel experiments were conducted with the upstream aquifer samples exposed to varying pCO2 from 0% to 100% under reservoir temperature and pressure for up to 56 days. The microbial community of the in situ experiment and the batch reactor experiment were analyzed with 16S rRNA clone libraries and qPCR. In both the in situ experiment and the batch reactor experiment, DNA concentration did not correlate with CO2 exposure. Both the in situ experiment and the batch reactors displayed a changing microbial community with increased CO2 exposure. The well water isolate, Curvibacter, appeared to be the most tolerant genus to high CO2 concentrations in the in situ experiments and to mid-CO2 concentrations in the batch reactors. In batch reactors with pCO2 concentrations higher than experienced in situ (pCO2 = 0.5 MPa), Pseudomonas appeared to be the most tolerant genus. Findings provide insight into a dynamic biogeochemical system that will alter with CO2 exposure. Adapted microbial populations will eventually give rise to the community that will impact the metal mobility and water quality. Knowledge of the surviving microbial populations will enable improved models for predicting the fate of CO2 following leakage and lead to better strategies for ensuring the quality of potable aquifer water.

Sleep quality moderates the association between physical activity frequency and feelings of energy and fatigue in adolescents.

PubMed

Herring, Matthew P; Monroe, Derek C; Kline, Christopher E; O'Connor, Patrick J; MacDonncha, Ciaran

2018-03-05

Physical activity (PA) can improve sleep quality, low energy, and fatigue. Though poor sleep quality may induce feelings of low energy and fatigue, the potential moderating effect of sleep quality on associations between PA and feelings of energy and fatigue among adolescents is unknown. Thus, this study examined the moderating effect of sleep quality on associations between PA frequency and feelings of energy and fatigue among adolescents in Ireland. Adolescents (N = 481; 281 males, 200 females) aged 15.1 ± 1.7 years self-reported PA frequency, feelings of energy and fatigue, and sleep quality (September to December 2015). Two-way ANCOVAs examined variation in feelings of energy and fatigue according to the interaction of PA and sleep quality. Standardized mean difference (d) quantified the magnitude of differences. Poor sleepers with low PA reported greater feelings of fatigue compared to normal sleepers with low PA (d = 1.02; 95% CI 0.60, 1.44), and poor sleepers with moderate PA reported greater feelings of fatigue compared to normal sleepers with moderate PA (d = 0.50; 0.17, 0.82). Poor sleepers with low PA reported greater feelings of fatigue compared to both poor sleepers with moderate PA (d = 0.44; 0.05, 0.83) and poor sleepers with high PA (d = 0.87; 0.46, 1.28). Poor sleepers with moderate PA reported greater feelings of fatigue compared to poor sleepers with high PA (d = 0.52; 0.14, 0.91). Poor sleep did not moderate the association between PA and feelings of energy. Sleep quality moderates the association between PA frequency and feelings of fatigue. Fatigue symptoms improve as PA frequency increases among adolescents with poor sleep quality.

Water quality program elements for Space Station Freedom

NASA Technical Reports Server (NTRS)

Sauer, Richard L.; Ramanathan, Raghupathy; Straub, John E.; Schultz, John R.

1991-01-01

A strategy is outlined for the development of water-quality criteria and standards relevant to recycling and monitoring the in-flight water for the Space Station Freedom (SSF). The water-reclamation subsystem of the SSF's ECLSS is described, and the objectives of the water-quality are set forth with attention to contaminants. Quality parameters are listed for potable and hygiene-related water including physical and organic parameters, inorganic constituents, bactericides, and microbial content. Comparisons are made to the quality parameters established for the Shuttle's potable water and to the EPA's current standards. Specific research is required to develop in-flight monitoring techniques for unique SSF contaminants, ECLSS microbial control, and on- and off-line monitoring. After discussing some of the in-flight water-monitoring hardware it is concluded that water reclamation and recycling are necessary and feasible for the SSF.

Examples of, reasons for, and consequences of the poor quality of wind data from ships for the marine boundary layer: Implications for remote sensing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pierson, W.J. Jr.

1990-08-15

Wind reports by data buoys are used to demonstrate that these reports have in the past provided useful values for the synoptic scale winds and that at present these reports provide very reliable values for the synoptic scale winds. Past studies of wind reports by ships have revealed that the data are of poor quality, but the causes for this poor quality are not identified. Examples of the poor quality of wind data from ships are obtained by comparing ship reports with buoy reports and comparing reports of different kinds of ships with each other. These comparisons identify many differentmore » reasons for the poor quality of wind data from ships. Suggestions are made for improving the quality of ship data. The consequences of the poor quality of ship winds are described in terms of the effects on weather and wave forecasts. The implications for remotely sensed winds are discussed.« less

Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale

PubMed Central

Schmidt, Thomas S. B.; Matias Rodrigues, João F.; von Mering, Christian

2014-01-01

Operational Taxonomic Units (OTUs), usually defined as clusters of similar 16S/18S rRNA sequences, are the most widely used basic diversity units in large-scale characterizations of microbial communities. However, it remains unclear how well the various proposed OTU clustering algorithms approximate ‘true’ microbial taxa. Here, we explore the ecological consistency of OTUs – based on the assumption that, like true microbial taxa, they should show measurable habitat preferences (niche conservatism). In a global and comprehensive survey of available microbial sequence data, we systematically parse sequence annotations to obtain broad ecological descriptions of sampling sites. Based on these, we observe that sequence-based microbial OTUs generally show high levels of ecological consistency. However, different OTU clustering methods result in marked differences in the strength of this signal. Assuming that ecological consistency can serve as an objective external benchmark for cluster quality, we conclude that hierarchical complete linkage clustering, which provided the most ecologically consistent partitions, should be the default choice for OTU clustering. To our knowledge, this is the first approach to assess cluster quality using an external, biologically meaningful parameter as a benchmark, on a global scale. PMID:24763141

Reducing assembly complexity of microbial genomes with single-molecule sequencing.

PubMed

Koren, Sergey; Harhay, Gregory P; Smith, Timothy P L; Bono, James L; Harhay, Dayna M; Mcvey, Scott D; Radune, Diana; Bergman, Nicholas H; Phillippy, Adam M

2013-01-01

The short reads output by first- and second-generation DNA sequencing instruments cannot completely reconstruct microbial chromosomes. Therefore, most genomes have been left unfinished due to the significant resources required to manually close gaps in draft assemblies. Third-generation, single-molecule sequencing addresses this problem by greatly increasing sequencing read length, which simplifies the assembly problem. To measure the benefit of single-molecule sequencing on microbial genome assembly, we sequenced and assembled the genomes of six bacteria and analyzed the repeat complexity of 2,267 complete bacteria and archaea. Our results indicate that the majority of known bacterial and archaeal genomes can be assembled without gaps, at finished-grade quality, using a single PacBio RS sequencing library. These single-library assemblies are also more accurate than typical short-read assemblies and hybrid assemblies of short and long reads. Automated assembly of long, single-molecule sequencing data reduces the cost of microbial finishing to $1,000 for most genomes, and future advances in this technology are expected to drive the cost lower. This is expected to increase the number of completed genomes, improve the quality of microbial genome databases, and enable high-fidelity, population-scale studies of pan-genomes and chromosomal organization.

Evaluation of instant cup noodle, irradiated for immuno-compromised patients

NASA Astrophysics Data System (ADS)

Lee, Ji-Hye; Kim, Jae-Kyung; Park, Jae-Nam; Yoon, Young-Min; Sung, Nak-Yun; Kim, Jae-Hun; Song, Beom-Seok; Yook, Hong-Sun; Kim, Byeong-Keun; Lee, Ju-Woon

2012-08-01

In the present study, initial microbial load of instant cup noodle (ICN) was investigated and gamma irradiation applied to develop immuno-compromised patients food for their safe consumption. The initial microbial population of dried vegetable and meat, and noodle was below the detection limit (1 log CFU/g); however, that of seasoning powder was just above 4 log CFU/g. Moreover, rehydrated-ICN with water at 100 °C still show above 3 log CFU/g of microbial load, which indicates the need for an additional process to control microbial safety of the seasoning powder. The total aerobic bacteria in seasoning powder and rehydrated-ICN could be controlled with 17 kGy gamma irradiation. This result referred 17 kGy gamma irradiation could reach 'practical sterility' of ICN. The overall difference in sensory properties between the non-irradiated and irradiated ICN was insignificant. Thus, gamma irradiation could improve the microbial quality of ICN, and reduce the risk of infection posed by the seasoning powder, without any adverse effects on their sensory quality. These results suggest that gamma-irradiated ICN can be used as a snack food for immuno-compromised patients.

Microbial Biotreatment of Actual Textile Wastewater in a Continuous Sequential Rice Husk Biofilter and the Microbial Community Involved

PubMed Central

Lindh, Markus V.; Pinhassi, Jarone; Welander, Ulrika

2017-01-01

Textile dying processes often pollute wastewater with recalcitrant azo and anthraquinone dyes. Yet, there is little development of effective and affordable degradation systems for textile wastewater applicable in countries where water technologies remain poor. We determined biodegradation of actual textile wastewater in biofilters containing rice husks by spectrophotometry and liquid chromatography mass spectrometry. The indigenous microflora from the rice husks consistently performed >90% decolorization at a hydraulic retention time of 67 h. Analysis of microbial community composition of bacterial 16S rRNA genes and fungal internal transcribed spacer (ITS) gene fragments in the biofilters revealed a bacterial consortium known to carry azoreductase genes, such as Dysgonomonas, and Pseudomonas and the presence of fungal phylotypes such as Gibberella and Fusarium. Our findings emphasize that rice husk biofilters support a microbial community of both bacteria and fungi with key features for biodegradation of actual textile wastewater. These results suggest that microbial processes can substantially contribute to efficient and reliable degradation of actual textile wastewater. Thus, development of biodegradation systems holds promise for application of affordable wastewater treatment in polluted environments. PMID:28114377

Microbial Transformation of Esters of Chlorinated Carboxylic Acids

PubMed Central

Paris, D. F.; Wolfe, N. L.; Steen, W. C.

1984-01-01

Two groups of compounds were selected for microbial transformation studies. In the first group were carboxylic acid esters having a fixed aromatic moiety and an increasing length of the alkyl component. Ethyl esters of chlorine-substituted carboxylic acids were in the second group. Microorganisms from environmental waters and a pure culture of Pseudomonas putida U were used. The bacterial populations were monitored by plate counts, and disappearance of the parent compound was followed by gas-liquid chromatography as a function of time. The products of microbial hydrolysis were the respective carboxylic acids. Octanol-water partition coefficients (Kow) for the compounds were measured. These values spanned three orders of magnitude, whereas microbial transformation rate constants (kb) varied only 50-fold. The microbial rate constants of the carboxylic acid esters with a fixed aromatic moiety increased with an increasing length of alkyl substituents. The regression coefficient for the linear relationships between log kb and log Kow was high for group 1 compounds, indicating that these parameters correlated well. The regression coefficient for the linear relationships for group 2 compounds, however, was low, indicating that these parameters correlated poorly. PMID:16346459

Attached biofilms and suspended aggregates are distinct microbial lifestyles emanating from differing hydraulics.

PubMed

Niederdorfer, Robert; Peter, Hannes; Battin, Tom J

2016-10-03

Small-scale hydraulics affects microbial behaviour at the cell level 1 , trophic interactions in marine aggregates 2 and the physical structure and function of stream biofilms 3,4 . However, it remains unclear how hydraulics, predictably changing from small streams to large rivers, impacts the structure and biodiversity of complex microbial communities in these ecosystems. Here, we present experimental evidence unveiling hydraulics as a hitherto poorly recognized control of microbial lifestyle differentiation in fluvial ecosystems. Exposing planktonic source communities from stream and floodplain ecosystems to different hydraulic environments revealed strong selective hydraulic pressures but only minor founder effects on the differentiation of attached biofilms and suspended aggregates and their biodiversity dynamics. Key taxa with a coherent phylogenetic underpinning drove this differentiation. Only a few resident and phylogenetically related taxa formed the backbone of biofilm communities, whereas numerous resident taxa characterized aggregate communities. Our findings unveil fundamental differences between biofilms and aggregates and build the basis for a mechanistic understanding of how hydraulics drives the distribution of microbial diversity along the fluvial continuum 5-7 .

Assessment of Drinking Water Quality from Bottled Water Coolers

PubMed Central

FARHADKHANI, Marzieh; NIKAEEN, Mahnaz; AKBARI ADERGANI, Behrouz; HATAMZADEH, Maryam; NABAVI, Bibi Fatemeh; HASSANZADEH, Akbar

2014-01-01

Abstract Background Drinking water quality can be deteriorated by microbial and toxic chemicals during transport, storage and handling before using by the consumer. This study was conducted to evaluate the microbial and physicochemical quality of drinking water from bottled water coolers. Methods A total of 64 water samples, over a 5-month period in 2012-2013, were collected from free standing bottled water coolers and water taps in Isfahan. Water samples were analyzed for heterotrophic plate count (HPC), temperature, pH, residual chlorine, turbidity, electrical conductivity (EC) and total organic carbon (TOC). Identification of predominant bacteria was also performed by sequence analysis of 16S rDNA. Results The mean HPC of water coolers was determined at 38864 CFU/ml which exceeded the acceptable level for drinking water in 62% of analyzed samples. The HPC from the water coolers was also found to be significantly (P < 0.05) higher than that of the tap waters. The statistical analysis showed no significant difference between the values of pH, EC, turbidity and TOC in water coolers and tap waters. According to sequence analysis eleven species of bacteria were identified. Conclusion A high HPC is indicative of microbial water quality deterioration in water coolers. The presence of some opportunistic pathogens in water coolers, furthermore, is a concern from a public health point of view. The results highlight the importance of a periodic disinfection procedure and monitoring system for water coolers in order to keep the level of microbial contamination under control. PMID:26060769

Enhancing antioxidant activity, microbial and sensory quality of mango (Mangifera indica L.) juice by γ-irradiation and its in vitro radioprotective potential.

PubMed

Naresh, Kondapalli; Varakumar, Sadineni; Variyar, Prasad Shekhar; Sharma, Arun; Reddy, Obulam Vijaya Sarathi

2015-07-01

Gamma irradiation is an effective method currently being used for microbial decontamination and insect disinfestations of foods. In the present study, mango (Mangifera indica L.) juice was irradiated at doses of 0, 1.0, 3.0 and 5.0 kGy and microbial load, total polyphenols, flavonoids, ascorbic acid content, antioxidant activities, colour and sensory properties were evaluated immediately after irradiation and also during storage. Microbiological assay of the fresh and stored mango juice showed better quality after γ-irradiation. The total polyphenols and flavonoids were significantly (p < 0.05) increased while the ascorbic acid content decreased with the irradiation doses applied. As a result of γ-irradiation, a significant increment in gallic, syringic and chlorogenic acids and a significant reduction in ferulic and synapic acids were noted when analyzed by HPLC. In vitro antioxidant potentials were measured using DPPH, FRAP and NO scavenging assays; the results showed significant enhancement in the activities after irradiation, that correlated well with the increase in phenolic and flavonoid content. γ-irradiation improved the colour of mango juice without any adverse changes in the sensory qualities. Significant in vitro plasmid DNA protection was observed in the presence of mango juice against radiation induced damage, even at the dose of 5 kGy. This study confirmed the potential of γ-irradiation as a method for microbial decontamination and improving the quality of the mango juice without compromising on the sensory attributes.

Monitoring bacterial indicators of water quality in a tidally influenced delta: A Sisyphean pursuit.

PubMed

Partyka, Melissa L; Bond, Ronald F; Chase, Jennifer A; Atwill, Edward R

2017-02-01

The Sacramento-San Joaquin Delta Estuary (Delta) is the confluence of two major watersheds draining the Western Sierra Nevada mountains into the Central Valley of California, ultimately terminating into San Francisco Bay. We sampled 88 sites once a month for two years (2006-2008) over 87 separate sampling events for a total of 1740 samples. Water samples were analyzed for fecal indicator bacteria (Escherichia coli, enterococci and fecal coliforms), and 53 other physiochemical, land use, and environmental characteristics. The purpose of the study was to create a baseline of microbial water quality in the Delta and to identify various factors (climatic, land use, tidal, etc.) that were associated with elevated concentrations of indicator bacteria. Fecal indicator bacteria generally had weak to modest relationships to environmental conditions; the strength and direction of which varied for each microbial indicator, drainage region, and across seasons. Measured and unmeasured, site-specific effects accounted for large portions of variance in model predictions (ρ=0.086 to 0.255), indicating that spatial autocorrelation was a major component of water quality outcomes. The effects of tidal cycling and lack of connectivity between waterways and surrounding landscapes likely contributed to the lack of association between local land uses and microbial outcomes, though weak associations may also be indicative of mismatched spatiotemporal scales. The complex nature of this system necessitates continued monitoring and regular updates to statistical models designed to predict microbial water quality. Copyright © 2016 Elsevier B.V. All rights reserved.

The responses of microbial temperature relationships to seasonal change and winter warming in a temperate grassland.

PubMed

Birgander, Johanna; Olsson, Pål Axel; Rousk, Johannes

2018-01-18

Microorganisms dominate the decomposition of organic matter and their activities are strongly influenced by temperature. As the carbon (C) flux from soil to the atmosphere due to microbial activity is substantial, understanding temperature relationships of microbial processes is critical. It has been shown that microbial temperature relationships in soil correlate with the climate, and microorganisms in field experiments become more warm-tolerant in response to chronic warming. It is also known that microbial temperature relationships reflect the seasons in aquatic ecosystems, but to date this has not been investigated in soil. Although climate change predictions suggest that temperatures will be mostly affected during winter in temperate ecosystems, no assessments exist of the responses of microbial temperature relationships to winter warming. We investigated the responses of the temperature relationships of bacterial growth, fungal growth, and respiration in a temperate grassland to seasonal change, and to 2 years' winter warming. The warming treatments increased winter soil temperatures by 5-6°C, corresponding to 3°C warming of the mean annual temperature. Microbial temperature relationships and temperature sensitivities (Q 10 ) could be accurately established, but did not respond to winter warming or to seasonal temperature change, despite significant shifts in the microbial community structure. The lack of response to winter warming that we demonstrate, and the strong response to chronic warming treatments previously shown, together suggest that it is the peak annual soil temperature that influences the microbial temperature relationships, and that temperatures during colder seasons will have little impact. Thus, mean annual temperatures are poor predictors for microbial temperature relationships. Instead, the intensity of summer heat-spells in temperate systems is likely to shape the microbial temperature relationships that govern the soil-atmosphere C exchange. © 2018 John Wiley & Sons Ltd.

Effect of muscle type and frozen storage on the quality parameters of Iberian restructured meat preparations.

PubMed

Antequera, Teresa; Pérez-Palacios, Trinidad; Rodas, Elena; Rodríguez, Mar; Córdoba, Juan J

2014-10-01

The main objective of this study was to evaluate the effect of muscle type and frozen storage on the quality of restructured meat preparations from undervalued Iberian muscle to make use of meat from a high-quality and natural pig production system. The effect of two muscle types (i.e. white-glycolytic (W) and red-oxidative (R)) and frozen storage (lasting 0, 30, 60 and 90 days) on quality characteristics were assessed. Significant differences were found between the W and R Iberian restructured preparations in most physicochemical and some colour, texture and sensory traits, and in the fatty acid profile and oxidative measurements, suggesting that the R muscles are more suitable; however, the microbial contamination should be reduced. Frozen storage reduced but did not eliminate the initial microbial contamination, and it enhanced some quality traits in the Iberian restructured preparations, i.e. increased a* values, cohesiveness and juiciness and decreased adhesiveness and pastiness, without negatively affecting any parameter. Thus, frozen Iberian restructured preparations are recommended to be commercialized. In addition, the implementation or revision of Hazard Analysis and Critical Control Point is recommended to reduce microbial contamination. © The Author(s) 2013 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

Immature pea seeds: effect of storage under modified atmosphere packaging and sanitation with acidified sodium chlorite.

PubMed

Collado, Elena; Venzke Klug, Tâmmila; Martínez-Sánchez, Ascensión; Artés-Hernandez, Francisco; Aguayo, Encarna; Artés, Francisco; Fernández, Juan A; Gómez, Perla A

2017-10-01

Appropriate sanitation is a priority for extending the shelf life and promoting the consumption of immature pea seeds, as processing accelerates quality deterioration and microbial growth. The combined effect of disinfection with acidified sodium chlorite (ASC) or sodium hypochlorite (SH) and packaging under a passive modified atmosphere (MAP) at 1 or 4 °C on quality was analysed. After 14 days, greenness and vitamin C had decreased, especially in the SH-disinfected samples. Total phenols and antioxidant capacity were not affected by disinfection. Proteins levels fell by around 27%, regardless of the sanitizer and storage temperature. Compared with the initial microbial load, samples stored at 1 °C showed an increase of 1 log CFU g -1 in psychrophiles when treated with SH, whereas no increase of note occurred with ASC. In general, microbial counts were always below 3 log CFU g -1 for all the treatments. Immature pea seeds could be stored for 14 days at 1-4 °C under MAP with only minor quality changes. Disinfection with ASC resulted in better sensory quality, higher content of vitamin C and lower psychrophile counts. More research is needed to analyse the effect of these treatments on other quality parameters. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Bacteria that Travel: The Quality of Aircraft Water

PubMed Central

Handschuh, Harald; Dwyer, Jean O’; Adley, Catherine C.

2015-01-01

The travelling population is increasing globally year on year. International tourist arrival figures reached 1087 million in 2013 and 1133 million in 2014; of which 53% and 54% respectively accounted for air transport. The water on board aircraft is sourced from surface or ground water; piped to a central filling point and distributed to each aircraft by water service vehicles at the home base or at the destination airport. The purpose of this study was to ascertain the microbial, chemical (pH; Total and Free chlorine) and physical (temperature) quality of water from two aircraft, long- and short-haul, as well as from the original water source and the water service vehicle. A total of 154 water samples were collected and analysed. Long-haul flights were found to be significantly poorer in terms of microbial quality than short haul flights (p = 0.015). Furthermore, correlation and regression analysis showed that the water service vehicle was a significant source of increased microbial load in aircraft. Microbial diversity was also demonstrated, with 37 bacterial species identified belonging to eight classes: γ-Proteobacteria; β-Proteobacteria; α-Proteobacteria; Bacilli; Actinobacteria; Flavobacteria; Sphingobacteria and Cytophaga; using phenotypic and 16S rDNA sequence-based analysis. We present a novel quantified study of aircraft-related potable water supplies. PMID:26529000

Bacteria that Travel: The Quality of Aircraft Water.

PubMed

Handschuh, Harald; O'Dwyer, Jean; Adley, Catherine C

2015-10-30

The travelling population is increasing globally year on year. International tourist arrival figures reached 1087 million in 2013 and 1133 million in 2014; of which 53% and 54% respectively accounted for air transport. The water on board aircraft is sourced from surface or ground water; piped to a central filling point and distributed to each aircraft by water service vehicles at the home base or at the destination airport. The purpose of this study was to ascertain the microbial, chemical (pH; Total and Free chlorine) and physical (temperature) quality of water from two aircraft, long- and short-haul, as well as from the original water source and the water service vehicle. A total of 154 water samples were collected and analysed. Long-haul flights were found to be significantly poorer in terms of microbial quality than short haul flights (p = 0.015). Furthermore, correlation and regression analysis showed that the water service vehicle was a significant source of increased microbial load in aircraft. Microbial diversity was also demonstrated, with 37 bacterial species identified belonging to eight classes: γ-Proteobacteria; β-Proteobacteria; α-Proteobacteria; Bacilli; Actinobacteria; Flavobacteria; Sphingobacteria and Cytophaga; using phenotypic and 16S rDNA sequence-based analysis. We present a novel quantified study of aircraft-related potable water supplies.

Physico-Chemical and Microbial Analysis of Selected Borehole Water in Mahikeng, South Africa.

PubMed

Palamuleni, Lobina; Akoth, Mercy

2015-07-23

Groundwater is generally considered a "safe source" of drinking water because it is abstracted with low microbial load with little need for treatment before drinking. However, groundwater resources are commonly vulnerable to pollution, which may degrade their quality. An assessment of microbial and physicochemical qualities of borehole water in the rural environs of Mahikeng town, South Africa, was carried out. The study aimed at determining levels of physicochemical (temperature, pH, turbidity and nitrate) and bacteriological (both faecal and total coliform bacteria) contaminants in drinking water using standard microbiology methods. Furthermore, identities of isolates were determined using the API 20E assay. Results were compared with World Health Organisation (WHO) and Department of Water Affairs (DWAF-SA) water quality drinking standards. All analyses for physicochemical parameters were within acceptable limits except for turbidity while microbial loads during spring were higher than the WHO and DWAF thresholds. The detection of Escherichia coli, Salmonella and Klebsiella species in borehole water that was intended for human consumption suggests that water from these sources may pose severe health risks to consumers and is unsuitable for direct human consumption without treatment. The study recommends mobilisation of onsite treatment interventions to protect the households from further possible consequences of using the water.

Recent advances in electronic nose techniques for monitoring of fermentation process.

PubMed

Jiang, Hui; Zhang, Hang; Chen, Quansheng; Mei, Congli; Liu, Guohai

2015-12-01

Microbial fermentation process is often sensitive to even slight changes of conditions that may result in unacceptable end-product quality. Thus, the monitoring of the process is critical for discovering unfavorable deviations as early as possible and taking the appropriate measures. However, the use of traditional analytical techniques is often time-consuming and labor-intensive. In this sense, the most effective way of developing rapid, accurate and relatively economical method for quality assurance in microbial fermentation process is the use of novel chemical sensor systems. Electronic nose techniques have particular advantages in non-invasive monitoring of microbial fermentation process. Therefore, in this review, we present an overview of the most important contributions dealing with the quality control in microbial fermentation process using the electronic nose techniques. After a brief description of the fundamentals of the sensor techniques, some examples of potential applications of electronic nose techniques monitoring are provided, including the implementation of control strategies and the combination with other monitoring tools (i.e. sensor fusion). Finally, on the basis of the review, the electronic nose techniques are critically commented, and its strengths and weaknesses being highlighted. In addition, on the basis of the observed trends, we also propose the technical challenges and future outlook for the electronic nose techniques.

Inequalities in microbial contamination of drinking water supplies in urban areas: the case of Lilongwe, Malawi.

PubMed

Boakye-Ansah, Akosua Sarpong; Ferrero, Giuliana; Rusca, Maria; van der Zaag, Pieter

2016-10-01

Over past decades strategies for improving access to drinking water in cities of the Global South have mainly focused on increasing coverage, while water quality has often been overlooked. This paper focuses on drinking water quality in the centralized water supply network of Lilongwe, the capital of Malawi. It shows how microbial contamination of drinking water is unequally distributed to consumers in low-income (unplanned areas) and higher-income neighbourhoods (planned areas). Microbial contamination and residual disinfectant concentration were measured in 170 water samples collected from in-house taps in high-income areas and from kiosks and water storage facilities in low-income areas between November 2014 and January 2015. Faecal contamination (Escherichia coli) was detected in 10% of the 40 samples collected from planned areas, in 59% of the 64 samples collected from kiosks in the unplanned areas and in 75% of the 32 samples of water stored at household level. Differences in water quality in planned and unplanned areas were found to be statistically significant at p < 0.05. Finally, the paper shows how the inequalities in microbial contamination of drinking water are produced by decisions both on the development of the water supply infrastructure and on how this is operated and maintained.

Microbial Monitoring of Surface Water in South Africa: An Overview

PubMed Central

Luyt, Catherine D.; Tandlich, Roman; Muller, Wilhelmine J.; Wilhelmi, Brendan S.

2012-01-01

Infrastructural problems force South African households to supplement their drinking water consumption from water resources of inadequate microbial quality. Microbial water quality monitoring is currently based on the Colilert®18 system which leads to rapidly available results. Using Escherichia coli as the indicator microorganism limits the influence of environmental sources on the reported results. The current system allows for understanding of long-term trends of microbial surface water quality and the related public health risks. However, rates of false positive for the Colilert®18-derived concentrations have been reported to range from 7.4% to 36.4%. At the same time, rates of false negative results vary from 3.5% to 12.5%; and the Colilert medium has been reported to provide for cultivation of only 56.8% of relevant strains. Identification of unknown sources of faecal contamination is not currently feasible. Based on literature review, calibration of the antibiotic-resistance spectra of Escherichia coli or the bifidobacterial tracking ratio should be investigated locally for potential implementation into the existing monitoring system. The current system could be too costly to implement in certain areas of South Africa where the modified H2S strip test might be used as a surrogate for the Colilert®18. PMID:23066390

Physico-Chemical and Microbial Analysis of Selected Borehole Water in Mahikeng, South Africa

PubMed Central

Palamuleni, Lobina; Akoth, Mercy

2015-01-01

Groundwater is generally considered a “safe source” of drinking water because it is abstracted with low microbial load with little need for treatment before drinking. However, groundwater resources are commonly vulnerable to pollution, which may degrade their quality. An assessment of microbial and physicochemical qualities of borehole water in the rural environs of Mahikeng town, South Africa, was carried out. The study aimed at determining levels of physicochemical (temperature, pH, turbidity and nitrate) and bacteriological (both faecal and total coliform bacteria) contaminants in drinking water using standard microbiology methods. Furthermore, identities of isolates were determined using the API 20E assay. Results were compared with World Health Organisation (WHO) and Department of Water Affairs (DWAF-SA) water quality drinking standards. All analyses for physicochemical parameters were within acceptable limits except for turbidity while microbial loads during spring were higher than the WHO and DWAF thresholds. The detection of Escherichia coli, Salmonella and Klebsiella species in borehole water that was intended for human consumption suggests that water from these sources may pose severe health risks to consumers and is unsuitable for direct human consumption without treatment. The study recommends mobilisation of onsite treatment interventions to protect the households from further possible consequences of using the water. PMID:26213950

Advanced Oxidation Process sanitation of hatching eggs reduces Salmonella in broiler chicks

USDA-ARS?s Scientific Manuscript database

Reduction of Salmonella contamination of eggs is important in improving the microbial food safety of poultry and poultry products. Developing interventions to reduce Salmonella contamination of eggs is important to improving the microbial quality of eggs entering the hatchery. Previously, the hydr...

Characterization of microbial growth on processing equipment by electrochemical impedance spectroscopy

USDA-ARS?s Scientific Manuscript database

Microbial activity that leads to the formation of biofilms on process equipment can accelerate corrosion, reduce heat transfer rates, and generally decrease process efficiencies. Additional concerns arise in the food and pharma industries where product quality and safety are a high priority. Followi...

Using Omics to Study Microbial Water Quality

EPA Science Inventory

Water is one of the most important resources of all natural ecosystems. Not only is water important to life, but it is also a habitat for a large diversity of microbial forms, in many cases carrying critical geochemical functions. In other instances, water is implicated in outbre...

Management of microbial food safety in the Arab countries

USDA-ARS?s Scientific Manuscript database

Microbial food safety remains a major economical and public health concern in the Arab countries. Over the several past years, many of these countries have attempted to revise and upgrade food quality control and surveillance programs. However, these systems vary in scope and effectiveness. This rev...

Use of Quantitative Microbial Risk Assessment to Improve Interpretation of a Recreational Water Epidemiological Study

EPA Science Inventory

We conducted a supplemental water quality monitoring study and quantitative microbial risk assessment (QMRA) to complement the United States Environmental Protection Agency’s (U.S. EPA) National Epidemiological and Environmental Assessment of Recreational Water study at Boquerón ...

Using Omics to Study Microbial Water Quality - abstract

EPA Science Inventory

Water is one of the most important resources of all natural ecosystems. Not only is water important to life, but it is also a habitat for a large diversity of microbial forms, in many cases carrying critical geochemical functions. In other instances, water is implicated in outbre...

Tools and perspectives for a unified approach to understanding microbial ecology in the critical zone

NASA Astrophysics Data System (ADS)

Gallery, R. E.; Aronson, E. L.; Fairbanks, D.; Murphy, M. A.; Rich, V. I.; Hart, S. C.

2015-12-01

Microbial communities that control nutrient transformation and storage in ecosystems are themselves influenced by landscape topography and vegetative cover. Globally, disturbances such as fires and insect outbreaks are increasing in frequency and severity with enormous impacts on global carbon cycling. The resiliency of soil microbial communities to these heterogeneous disturbances determines rates of nutrient transformations as well as ecosystem structure and recovery. Natural and anthropogenic disturbances are a common thread throughout Critical Zone Observatories and ecosystems in general. Using the 2013 Thompson Ridge Fire in the Jemez River Basin CZO as a case study, we examine the effect of a wildfire disturbance regime on successional changes in soil microbiota and ecosystem fluxes across a landscape with high topographic variation. We find that, layered over the topographic controls of hotspots of biogeochemical activity, fire alters organic substrate quality, microbial biomass, community structure, and activity. For example, fire increases soil pH, which is commonly found as an explanatory variable describing bacterial community structure. Soil microbes excrete exoenzymes to decompose polymers and acquire nutrients, and these activities can indicate changing microbial function or soil quality. In these mixed conifer forests, we find shifts from carbon to nitrogen-dominated exoenzyme activities in burned forests with alkaline soils, suggesting shifts of microbial taxa and function that correspond with recovering soil microbial biomass. More generally we ask - what combination of tools and perspectives is needed to fully understand soil microbial ecology and biogeochemistry of the critical zone? Results from an NSF Science Across Virtual Institutes (SAVI) CZO Network Biogeochemistry Workshop highlight the importance of incorporating a standard suite of microbial activity and community assays along with soil biogeochemical and flux measurements to enable comparisons across the broader CZO network. These characterizations would provide regional microbial function and biodiversity data in a standardized framework that can be used to enable more effective management and valuation of critical zone services and inform projections under global change scenarios.

Effect of DNA Extraction Methods and Sampling Techniques on the Apparent Structure of Cow and Sheep Rumen Microbial Communities

PubMed Central

Henderson, Gemma; Cox, Faith; Kittelmann, Sandra; Miri, Vahideh Heidarian; Zethof, Michael; Noel, Samantha J.; Waghorn, Garry C.; Janssen, Peter H.

2013-01-01

Molecular microbial ecology techniques are widely used to study the composition of the rumen microbiota and to increase understanding of the roles they play. Therefore, sampling and DNA extraction methods that result in adequate yields of microbial DNA that also accurately represents the microbial community are crucial. Fifteen different methods were used to extract DNA from cow and sheep rumen samples. The DNA yield and quality, and its suitability for downstream PCR amplifications varied considerably, depending on the DNA extraction method used. DNA extracts from nine extraction methods that passed these first quality criteria were evaluated further by quantitative PCR enumeration of microbial marker loci. Absolute microbial numbers, determined on the same rumen samples, differed by more than 100-fold, depending on the DNA extraction method used. The apparent compositions of the archaeal, bacterial, ciliate protozoal, and fungal communities in identical rumen samples were assessed using 454 Titanium pyrosequencing. Significant differences in microbial community composition were observed between extraction methods, for example in the relative abundances of members of the phyla Bacteroidetes and Firmicutes. Microbial communities in parallel samples collected from cows by oral stomach-tubing or through a rumen fistula, and in liquid and solid rumen digesta fractions, were compared using one of the DNA extraction methods. Community representations were generally similar, regardless of the rumen sampling technique used, but significant differences in the abundances of some microbial taxa such as the Clostridiales and the Methanobrevibacter ruminantium clade were observed. The apparent microbial community composition differed between rumen sample fractions, and Prevotellaceae were most abundant in the liquid fraction. DNA extraction methods that involved phenol-chloroform extraction and mechanical lysis steps tended to be more comparable. However, comparison of data from studies in which different sampling techniques, different rumen sample fractions or different DNA extraction methods were used should be avoided. PMID:24040342

Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities.

PubMed

Henderson, Gemma; Cox, Faith; Kittelmann, Sandra; Miri, Vahideh Heidarian; Zethof, Michael; Noel, Samantha J; Waghorn, Garry C; Janssen, Peter H

2013-01-01

Molecular microbial ecology techniques are widely used to study the composition of the rumen microbiota and to increase understanding of the roles they play. Therefore, sampling and DNA extraction methods that result in adequate yields of microbial DNA that also accurately represents the microbial community are crucial. Fifteen different methods were used to extract DNA from cow and sheep rumen samples. The DNA yield and quality, and its suitability for downstream PCR amplifications varied considerably, depending on the DNA extraction method used. DNA extracts from nine extraction methods that passed these first quality criteria were evaluated further by quantitative PCR enumeration of microbial marker loci. Absolute microbial numbers, determined on the same rumen samples, differed by more than 100-fold, depending on the DNA extraction method used. The apparent compositions of the archaeal, bacterial, ciliate protozoal, and fungal communities in identical rumen samples were assessed using 454 Titanium pyrosequencing. Significant differences in microbial community composition were observed between extraction methods, for example in the relative abundances of members of the phyla Bacteroidetes and Firmicutes. Microbial communities in parallel samples collected from cows by oral stomach-tubing or through a rumen fistula, and in liquid and solid rumen digesta fractions, were compared using one of the DNA extraction methods. Community representations were generally similar, regardless of the rumen sampling technique used, but significant differences in the abundances of some microbial taxa such as the Clostridiales and the Methanobrevibacter ruminantium clade were observed. The apparent microbial community composition differed between rumen sample fractions, and Prevotellaceae were most abundant in the liquid fraction. DNA extraction methods that involved phenol-chloroform extraction and mechanical lysis steps tended to be more comparable. However, comparison of data from studies in which different sampling techniques, different rumen sample fractions or different DNA extraction methods were used should be avoided.

Exploring Gender Difference in Sleep Quality of Young Adults: Findings from a Large Population Study

PubMed Central

Fatima, Yaqoot; Doi, Suhail A.R.; Najman, Jake M.; Mamun, Abdullah Al

2016-01-01

Objectives To explore if gender difference in sleep quality is due to higher prevalence of depression in females, and whether socio-demographic and lifestyle factors have a differential effect on sleep quality in males and females. Methods Youth self-reports and the Pittsburgh Sleep Quality Index were used to assess sleep quality and associated risk factors. Logistic regression analyses were used to analyze the association between various risk factors and poor sleep quality. Results Reports from 3,778 young adults (20.6±0.86 years) indicate a higher prevalence of poor sleep quality in females than males (65.1% vs. 49.8%). It seems that gender difference in poor sleep is independent of depression, socio-demographics, and lifestyle factors, since the higher odds of poor sleep quality in females was robust to adjust for depression, socio-demographics, and lifestyle factors (OR: 1.53, 95% CI: 1.23–1.90). Lifestyle factors (eg, smoking) (OR 1.91; 95% CI 1.05–3.46) were associated with sleep quality in only males. Conclusion Our findings indicate that female vulnerability to poor sleep quality should be explored beyond psycho-social disparities. Perhaps, exploring if the female predisposition to poor sleep quality originates at the biological level could lead to the answer. PMID:28188139

Poor sleep quality is associated with increased arterial stiffness in Japanese patients with type 2 diabetes mellitus.

PubMed

Osonoi, Yusuke; Mita, Tomoya; Osonoi, Takeshi; Saito, Miyoko; Tamasawa, Atsuko; Nakayama, Shiho; Someya, Yuki; Ishida, Hidenori; Kanazawa, Akio; Gosho, Masahiko; Fujitani, Yoshio; Watada, Hirotaka

2015-06-18

While poor sleep quality can worsen cardiovascular risk factors such as glucose and lipid profiles in patients with type 2 diabetes mellitus (T2DM), the relationship between sleep quality and atherosclerosis remains largely unknown. The aim of this study was to examine this relationship. The study participants comprised 724 Japanese T2DM outpatients free of history of cardiovascular diseases. The relationships between sleep quality (assessed by the Pittsburgh Sleep Quality Index (PSQI)) and various clinical and laboratory parameters were investigated. The mean PSQI was 5.1 ± 3.0 (±SD). Patients were divided into three groups based on the total PSQI score; subjects with good sleep quality (n = 462), average sleep quality (n = 185), and poor sleep quality (n = 77). In the age/gender-adjusted model, patients with poor sleep quality tended to be obese, evening type and depressed. However, other lifestyles showed no significant trends. Alanine aminotransferase, fasting blood glucose, HbA1c, systolic blood pressure, urinary albumin excretion, and brachial-ankle pulse wave velocity (baPWV) tended to be higher in patients with poor sleep quality. High baPWV was the only parameter that correlated with poor sleep in a model adjusted for several other lifestyle factors. Our study indicates that poor sleep quality in T2DM patients correlates with increased arterial wall stiffness, a marker of atherosclerosis and a risk factor for cardiovascular diseases.

ADSA Foundation Scholar Award: Trends in culture-independent methods for assessing dairy food quality and safety: emerging metagenomic tools.

PubMed

Yeung, Marie

2012-12-01

Enhancing the quality and safety of dairy food is critical to maintaining the competitiveness of dairy products in the food and beverage market and in reinforcing consumer confidence in the dairy industry. Raw milk quality has a significant effect on finished product quality. Several microbial groups found in raw milk have been shown to adversely affect the shelf life of pasteurized milk. Current microbiological criteria used to define milk quality are based primarily on culture-dependent methods, some of which are perceived to lack the desired sensitivity and specificity. To supplement traditional methods, culture-independent methods are increasingly being used to identify specific species or microbial groups, and to detect indicator genes or proteins in raw milk or dairy products. Some molecular subtyping techniques have been developed to track the transmission of microbes in dairy environments. The burgeoning "-omics" technologies offer new and exciting opportunities to enhance our understanding of food quality and safety in relation to microbes. Metagenomics has the potential to characterize microbial diversity, detect nonculturable microbes, and identify unique sequences or other factors associated with dairy product quality and safety. In this review, fluid milk will be used as the primary example to examine the adequacy and validity of conventional methods, the current trend of culture-independent methods, and the potential applications of metagenomics in dairy food research. Copyright © 2012 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

An investigation of the relationship between subjective sleep quality, loneliness and mood in an Australian sample: can daily routine explain the links?

PubMed

Smith, Simon Squire; Kozak, Nahum; Sullivan, Karen Anne

2012-03-01

Loneliness and low mood are associated with significant negative health outcomes including poor sleep, but the strength of the evidence underlying these associations varies. There is strong evidence that poor sleep quality and low mood are linked, but only emerging evidence that loneliness and poor sleep are associated. To independently replicate the finding that loneliness and poor subjective sleep quality are associated and to extend past research by investigating lifestyle regularity as a possible mediator of relationships, since lifestyle regularity has been linked to loneliness and poor sleep. Using a cross-sectional design, 97 adults completed standardized measures of loneliness, lifestyle regularity, subjective sleep quality and mood. Loneliness was a significant predictor of sleep quality. Lifestyle regularity was not a predictor of, nor associated with, mood, sleep quality or loneliness. This study provides an important independent replication of the association between poor sleep and loneliness. However, the mechanism underlying this link remains unclear. A theoretically plausible mechanism for this link, lifestyle regularity, does not explain the relationship between loneliness and poor sleep. The nexus between loneliness and poor sleep is unlikely to be broken by altering the social rhythm of patients who present with poor sleep and loneliness.

Leveraging knowledge engineering and machine learning for microbial bio-manufacturing.

PubMed

Oyetunde, Tolutola; Bao, Forrest Sheng; Chen, Jiung-Wen; Martin, Hector Garcia; Tang, Yinjie J

2018-05-03

Genome scale modeling (GSM) predicts the performance of microbial workhorses and helps identify beneficial gene targets. GSM integrated with intracellular flux dynamics, omics, and thermodynamics have shown remarkable progress in both elucidating complex cellular phenomena and computational strain design (CSD). Nonetheless, these models still show high uncertainty due to a poor understanding of innate pathway regulations, metabolic burdens, and other factors (such as stress tolerance and metabolite channeling). Besides, the engineered hosts may have genetic mutations or non-genetic variations in bioreactor conditions and thus CSD rarely foresees fermentation rate and titer. Metabolic models play important role in design-build-test-learn cycles for strain improvement, and machine learning (ML) may provide a viable complementary approach for driving strain design and deciphering cellular processes. In order to develop quality ML models, knowledge engineering leverages and standardizes the wealth of information in literature (e.g., genomic/phenomic data, synthetic biology strategies, and bioprocess variables). Data driven frameworks can offer new constraints for mechanistic models to describe cellular regulations, to design pathways, to search gene targets, and to estimate fermentation titer/rate/yield under specified growth conditions (e.g., mixing, nutrients, and O 2 ). This review highlights the scope of information collections, database constructions, and machine learning techniques (such as deep learning and transfer learning), which may facilitate "Learn and Design" for strain development. Copyright © 2018. Published by Elsevier Inc.

Biofilm formation - What we can learn from recent developments.

PubMed

Bjarnsholt, Thomas; Buhlin, Kåre; Dufrêne, Yves F; Gomelsky, Mark; Moroni, Anna; Ramstedt, Madeleine; Rumbaugh, Kendra P; Schulte, Tim; Sun, Lei; Åkerlund, Börje; Römling, Ute

2018-06-01

Although biofilms have been observed early in the history of microbial research, their impact has only recently been fully recognized. Biofilm infections, which contribute to up to 80% of human microbial infections, are associated with common human disorders, such as diabetes mellitus and poor dental hygiene, but also with medical implants. The associated chronic infections such as wound infections, dental caries and periodontitis significantly enhance morbidity, affect quality of life and can result in contraction of follow-up diseases such as cancer. Biofilm infections remain challenging to treat and antibiotic monotherapy is often insufficient, although some rediscovered traditional compounds have shown surprising efficiency. Innovative anti-biofilm strategies include application of anti-biofilm small molecules, intrinsic or external stimulation of production of reactive molecules, utilization of materials with antimicrobial properties and dispersion of biofilms by digestion of the extracellular matrix, also in combination with physical biofilm breakdown. Although basic principles of biofilm formation have been deciphered, the molecular understanding of the formation and structural organization of various types of biofilms has just begun to emerge. Basic studies of biofilm physiology have also resulted in an unexpected discovery of cyclic dinucleotide second messengers that are involved in interkingdom crosstalk via specific mammalian receptors. These findings even open up new venues for exploring novel anti-biofilm strategies. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Total Protein Extraction for Metaproteomics Analysis of Methane Producing Biofilm: The Effects of Detergents

PubMed Central

Huang, Hung-Jen; Chen, Wei-Yu; Wu, Jer-Horng

2014-01-01

Protein recovery is crucial for shotgun metaproteomics to study the in situ functionality of microbial populations from complex biofilms but still poorly addressed by far. To fill this knowledge gap, we systematically evaluated the sample preparation with extraction buffers comprising four detergents for the metaproteomics analysis of a terephthalate-degrading methanogenic biofilm using an on-line two-dimensional liquid chromatography tandem mass spectrometry (2D-LC-MS/MS) system. Totally, 1018 non-repeated proteins were identified with the four treatments. On the whole, each treatment could recover the biofilm proteins with specific distributions of molecular weight, hydrophobicity, and isoelectric point. The extraction buffers containing zwitterionic and anionic detergents were found to harvest the proteins with better efficiency and quality, allowing identification up to 76.2% of total identified proteins with the LC-MS/MS analysis. According to the annotation with a relevant metagenomic database, we further observed different taxonomic profiles of bacterial and archaeal members and discriminable patterns of the functional expression among the extraction buffers used. Overall, the finding of the present study provides first insight to the effect of the detergents on the characteristics of extractable proteins from biofilm and the developed protocol combined with nano 2D-LC/MS/MS analysis can improve the metaproteomics studies on microbial functionality of biofilms in the wastewater treatment systems. PMID:24914765

Metagenomic Assessment of a Dynamic Microbial Population from Subseafloor Aquifer Fluids in the Cold, Oxygenated Crust

NASA Astrophysics Data System (ADS)

Tully, B. J.; Heidelberg, J. F.; Kraft, B.; Girguis, P. R.; Huber, J. A.

2016-12-01

The oceanic crust contains the largest aquifer on Earth with a volume approximately 2% of the global ocean. Ongoing research at the North Pond (NP) site, west of the Mid-Atlantic Ridge, provides an environment representative of oxygenated crustal aquifers beneath oligotrophic surface waters. Using subseafloor CORK observatories for multiple sampling depths beneath the seafloor, crustal fluids were sampled along the predicted aquifer fluid flow path over a two-year period. DNA was extracted and sequenced for metagenomic analysis from 22 crustal fluid samples, along with the overlying bottom. At broad taxonomic groupings, the aquifer system is highly dynamic over time and space, with shifts in dominant taxa and "blooms" of transient groups that appear at discreet time points and sample depths. We were able to reconstruct 194 high-quality, low-contamination bacterial and archaeal metagenomic-assembled genomes (MAGs) with estimated completeness >50% (429 MAGs >20% complete). Environmental genomes were assigned to phylogenies from the major bacterial phyla, putative novel groups, and poorly sampled phylogenetic groups, including the Marinimicrobia, Candidate Phyla Radiation, and Planctomycetes. Biogeochemically relevant processes were assigned to MAGs, including denitrification, dissimilatory sulfur and hydrogen cycling, and carbon fixation. Collectively, the oxic NP aquifer system represents a diverse, dynamic microbial habitat with the metabolic potential to impact multiple globally relevant biogeochemical cycles, including nitrogen, sulfur, and carbon.

New perspectives on microbial community distortion after whole-genome amplification

EPA Science Inventory

Whole-genome amplification (WGA) has become an important tool to explore the genomic information of microorganisms in an environmental sample with limited biomass, however potential selective biases during the amplification processes are poorly understood. Here, we describe the e...

Water quality and microbial diversity in cisterns from semiarid areas in Brazil.

PubMed

Alves, Fellipe; Köchling, Thorsten; Luz, Julio; Santos, Sylvana Melo; Gavazza, Savia

2014-09-01

Harvesting rainwater is a common practice worldwide, particularly in areas with no access to a public water supply or insufficient groundwater reserves. More than two million people living in semiarid regions of Brazil consume rainwater stored in cisterns, and little information is available regarding the water quality. Despite the initial good quality of the rainwater, its harvest and storage can introduce contaminants that must be eliminated before consumption. To evaluate the influence of handling, cistern age and precipitation on the quality of harvested rainwater, we monitored seven cisterns in the semiarid Brazilian Northeast over 4 years. Microbial and physicochemical parameters were monitored once a month, and denaturant gradient gel electrophoresis (DGGE) was performed at the end of the monitoring period. Coliform bacteria were detected in 100% of samples, while Escherichia coli were observed in 73.8%. The alkalinity and conductivity were the highest for the recently built cisterns due to the dissolution of construction materials. The DGGE of the 16S r DNA did not reveal the presence of E. coli. Instead, DGGE bands sequencing indicated that species primarily affiliated with Alphaproteobacteria were present in all cisterns, indicating the presence of microbial ecosystems capable of purifying and stabilizing the stored rainwater.

Chronic Rhinosinusitis and the Evolving Understanding of Microbial Ecology in Chronic Inflammatory Mucosal Disease.

PubMed

Hoggard, Michael; Wagner Mackenzie, Brett; Jain, Ravi; Taylor, Michael W; Biswas, Kristi; Douglas, Richard G

2017-01-01

Chronic rhinosinusitis (CRS) encompasses a heterogeneous group of debilitating chronic inflammatory sinonasal diseases. Despite considerable research, the etiology of CRS remains poorly understood, and debate on potential roles of microbial communities is unresolved. Modern culture-independent (molecular) techniques have vastly improved our understanding of the microbiology of the human body. Recent studies that better capture the full complexity of the microbial communities associated with CRS reintroduce the possible importance of the microbiota either as a direct driver of disease or as being potentially involved in its exacerbation. This review presents a comprehensive discussion of the current understanding of bacterial, fungal, and viral associations with CRS, with a specific focus on the transition to the new perspective offered in recent years by modern technology in microbiological research. Clinical implications of this new perspective, including the role of antimicrobials, are discussed in depth. While principally framed within the context of CRS, this discussion also provides an analogue for reframing our understanding of many similarly complex and poorly understood chronic inflammatory diseases for which roles of microbes have been suggested but specific mechanisms of disease remain unclear. Finally, further technological advancements on the horizon, and current pressing questions for CRS microbiological research, are considered. Copyright © 2016 American Society for Microbiology.

Impact of a wastewater treatment plant on microbial community composition and function in a hyporheic zone of a eutrophic river

NASA Astrophysics Data System (ADS)

Atashgahi, Siavash; Aydin, Rozelin; Dimitrov, Mauricio R.; Sipkema, Detmer; Hamonts, Kelly; Lahti, Leo; Maphosa, Farai; Kruse, Thomas; Saccenti, Edoardo; Springael, Dirk; Dejonghe, Winnie; Smidt, Hauke

2015-11-01

The impact of the installation of a technologically advanced wastewater treatment plant (WWTP) on the benthic microbial community of a vinyl chloride (VC) impacted eutrophic river was examined two years before, and three and four years after installation of the WWTP. Reduced dissolved organic carbon and increased dissolved oxygen concentrations in surface water and reduced total organic carbon and total nitrogen content in the sediment were recorded in the post-WWTP samples. Pyrosequencing of bacterial 16S rRNA gene fragments in sediment cores showed reduced relative abundance of heterotrophs and fermenters such as Chloroflexi and Firmicutes in more oxic and nutrient poor post-WWTP sediments. Similarly, quantitative PCR analysis showed 1-3 orders of magnitude reduction in phylogenetic and functional genes of sulphate reducers, denitrifiers, ammonium oxidizers, methanogens and VC-respiring Dehalococcoides mccartyi. In contrast, members of Proteobacteria adapted to nutrient-poor conditions were enriched in post-WWTP samples. This transition in the trophic state of the hyporheic sediments reduced but did not abolish the VC respiration potential in the post-WWTP sediments as an important hyporheic sediment function. Our results highlight effective nutrient load reduction and parallel microbial ecological state restoration of a human-stressed urban river as a result of installation of a WWTP.

The Quality of In Vivo Upconversion Fluorescence Signals Inside Different Anatomic Structures.

PubMed

Wang, Lijiang; Draz, Mohamed Shehata; Wang, Wei; Liao, Guodong; Xu, Yuhong

2015-02-01

Fluorescence imaging is a broadly interesting and rapidly growing strategy for non-invasive clinical applications. However, because of interference from light scattering, absorbance, and tissue autofluorescence, the images can exhibit low sensitivity and poor quality. Upconversion fluorescence imaging, which is based on the use of near-infrared (NIR) light for excitation, has recently been introduced as an improved approach to minimize the effects of light scattering and tissue autofluorescence. This strategy is promising for ultrasensitive and deep tissue imaging applications. However, the emitted upconversion fluorescence signals are primarily in the visible range and are likely to be absorbed and scattered by tissues. Therefore, different anatomic structures could impose various effects on the quality of the images. In this study, we used upconversion-core/silica-shell nanoprobes to evaluate the quality of upconversion fluorescence at different anatomic locations in athymic nude mice. The nanoprobe contained an upconversion core, which was green (β-NaYF4:Yb3+/Ho3+) or red (β-NaYF4:Yb3+/Er3+), and a nonporous silica shell to allow for multicolor imaging. High-quality upconversion fluorescence signals were detected with signal-to-noise ratios of up to 170 at tissue depths of up to - 1.0 cm when a 980 nm laser excitation source and a bandpass emission filter were used. The presence of dense tissue structures along the imaging path reduced the signal intensity and imaging quality, and nanoprobes with longer-wavelength emission spectra were therefore preferable. This study offers a detailed analysis of the quality of upconversion signals in vivo inside different anatomic structures. Such information could be essential for the analysis of upconversion fluorescence images in any in vivo biodiagnostic and microbial tracking applications.

Modeling the unmeasurable: scaling soil physiology from microns to meters and seconds to centuries (Invited)

NASA Astrophysics Data System (ADS)

Schimel, J.; Xu, X.; Lawrence, C. R.

2013-12-01

Models are essential tools for linking microbial dynamics to their manifestations at large scales. Yet, developing mechanistically accurate models requires data that we often don't have and may not be able to get, such as the functional life-span of an extracellular enzyme. Yet there are approaches to condense complex microbial dynamics into 'workable' models. One example is in describing soil responses to moisture pulses. We developed a family of five separate models to capture microbial dynamics through dry/wet cycles. The simplest was a straight multi-pool, 1st-order decomposition model, with versions adding levels of microbial mechanism, culminating in one that included exoenzyme-breakdown of detritus. However, this identified the critical mechanism, not as exoenzymes, but as the production of a bioavailable C pool that accumulates in dry soil and is rapidly metabolized on rewetting. A final version of the model therefore stripped out explicit enzymes but retained separate polymer breakdown and substrate use; this model was the most robust. A second pervasive question in soil biology has been what controls the size of the microbial biomass across biomes? We approached this through a physiological model that regulated microbial C assimilation into biomass by two processes: initial assimilation followed by ongoing maintenance. Assimilation is a function of substrate quality, while maintenance is regulated by climate--notably the period of the year during which microbes are active. This model was tested against a global dataset of microbial biomass. It explains why, for example, deserts and tundra have relatively high proportions of their organic matter in microbial biomass, while the low substrate quality and long active periods common in temperate conifer forests lead to low biomass levels.

Evaluation of ATP measurements to detect microbial ingress by wastewater and surface water in drinking water.

PubMed

Vang, Óluva K; Corfitzen, Charlotte B; Smith, Christian; Albrechtsen, Hans-Jørgen

2014-11-01

Fast and reliable methods are required for monitoring of microbial drinking water quality in order to protect public health. Adenosine triphosphate (ATP) was investigated as a potential real-time parameter for detecting microbial ingress in drinking water contaminated with wastewater or surface water. To investigate the ability of the ATP assay in detecting different contamination types, the contaminant was diluted with non-chlorinated drinking water. Wastewater, diluted at 10(4) in drinking water, was detected with the ATP assay, as well as 10(2) to 10(3) times diluted surface water. To improve the performance of the ATP assay in detecting microbial ingress in drinking water, different approaches were investigated, i.e. quantifying microbial ATP or applying reagents of different sensitivities to reduce measurement variations; however, none of these approaches contributed significantly in this respect. Compared to traditional microbiological methods, the ATP assay could detect wastewater and surface water in drinking water to a higher degree than total direct counts (TDCs), while both heterotrophic plate counts (HPC 22 °C and HPC 37 °C) and Colilert-18 (Escherichia coli and coliforms) were more sensitive than the ATP measurements, though with much longer response times. Continuous sampling combined with ATP measurements displays definite monitoring potential for microbial drinking water quality, since microbial ingress in drinking water can be detected in real-time with ATP measurements. The ability of the ATP assay to detect microbial ingress is influenced by both the ATP load from the contaminant itself and the ATP concentration in the specific drinking water. Consequently, a low ATP concentration of the specific drinking water facilitates a better detection of a potential contamination of the water supply with the ATP assay. Copyright © 2014 Elsevier Ltd. All rights reserved.

Comparing dependencies of E. coli, Salmonella, and Enterococci survival on temperature in surface waters

USDA-ARS?s Scientific Manuscript database

Microbial water quality is attracting substantial attention due to the documented role of produce in microbial food contamination, shellfish industry concerns, and recreation disruptions. In particular, irrigated produce accounted for nearly half of all food-borne illnesses in the USA from 1998 to 2...

Development and Evaluation of a Quantitative PCR Assay Targeting Sandhill Crane (Grus canadensis) Fecal Pollution

EPA Science Inventory

While the microbial water quality in the Platte River is seasonally impacted by excreta from migrating cranes, there are no methods available to study crane fecal contamination. Here we characterized microbial populations in crane feces using phylogenetic analysis of 16S rRNA gen...

76 FR 58266 - Agency Information Collection Activities; Proposed Collection; Comment Request; Reporting...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-20

... contents of the docket, and access those documents in the public docket that are available electronically... monitor recreational water quality; assess, manage, and communicate health risks from waterborne microbial... public exposure to microbial pathogens. To qualify for a BEACH Act Grant, a state must submit information...

Soil Searching. Dishing the Dirt on Microbes.

ERIC Educational Resources Information Center

Kennedy, Ann C.; And Others

1995-01-01

This activity attempts to address a lack of emphasis in most science curricula on the microbial activity that determines soil's health. Presents an experiment that involves students in seeing how the enzyme assay is used as an indicator of soil quality and microbial activity. Contains procedures and discussion questions. (LZ)

Low intake of vegetables, high intake of confectionary, and unhealthy eating habits are associated with poor sleep quality among middle-aged female Japanese workers.

PubMed

Katagiri, Ryoko; Asakura, Keiko; Kobayashi, Satomi; Suga, Hitomi; Sasaki, Satoshi

2014-01-01

Although workers with poor sleep quality are reported to have problems with work performance, few studies have assessed the association between dietary factors and sleep quality using validated indexes. Here, we examined this association using information acquired from validated questionnaires. A total of 3,129 female workers aged 34 to 65 years were analyzed. Dietary intake was assessed using a self-administered diet history questionnaire (DHQ), and subjective sleep quality was assessed using the Pittsburgh Sleep Quality Index (PSQI). The relationship between the intake of several food groups and nutrients and sleep quality was examined using multivariable logistic regression models. The effect of eating habits on sleep quality was also examined. Poor sleep quality was associated with low intake of vegetables (p for trend 0.002) and fish (p for trend 0.04) and high intake of confectionary (p for trend 0.004) and noodles (p for trend 0.03) after adjustment for potential confounding factors (age, body mass index, physical activity, depression score, employment status, alcohol intake and smoking status). Poor sleep quality was also significantly and positively associated with consumption of energy drinks and sugar-sweetened beverages, skipping breakfast, and eating irregularly. In addition, poor sleep quality was significantly associated with high carbohydrate intake (p for trend 0.03). A low intake of vegetables and fish, high intake of confectionary and noodles and unhealthy eating habits were independently associated with poor sleep quality. Poor sleep quality was also associated with high carbohydrate intake in free-living Japanese middle-aged female workers.

Are we doing enough to prevent poor-quality antimalarial medicines in the developing world?

PubMed

Walker, Erin J; Peterson, Gregory M; Grech, James; Paragalli, Evie; Thomas, Jackson

2018-05-15

Malaria is a deadly parasitic disease that affects more than 3 billion people worldwide, in predominantly resource-poor countries. Despite malaria being preventable and treatable, a large number of adults and children, mostly in Africa, die from this disease each year. One contributor to needless morbidity and mortality is the production and distribution of poor-quality antimalarial medicines; indeed, it is estimated that over 122,000 deaths of children under 5 years of age in sub-Saharan countries were caused by poor-quality antimalarial medicines, in 2013 alone. Poor-quality medicines include those that are deliberately falsified for monetary gain and may contain incorrect amounts or even no active ingredients at all, as well as products that are inadequate due to poor compliance to conventional quality standards and medicines that have degraded over time. Across a number of studies it has been reported that 4-92% of antimalarials tested are poor quality. This represents a massive risk to the population subjected to the use of these medicines, in the form of more severe and prolonged illness, additional costs to individuals who already have very little money, and lack of confidence in treatments. The continuing circulation of poor-quality medicines results from a number of factors, including insufficient regulatory capacity in susceptible countries, inadequate funding to perform regulatory functions, poor coordination between regulatory authorities, and inefficient import/export control systems. To combat the distribution of poor-quality medicines a number of organisations have developed guidelines for the procurement of antimalarials, and programs to educate consumers about the risks of poor-quality medicines and incentivise retailers to identify and report falsified medicines. The development of new technologies to quickly identify poor-quality medicines in the field is also essential, and some significant advances have been made. There has been considerable improvement in the delivery of high-quality antimalarials to those who need them; however, there is still an urgent need for a collective response by the international community, political leaders, regulatory bodies, and pharmaceutical companies. This should include political commitment for enhanced research and development funding, such as for new innovative track-and-trace field devices, and international efforts to strengthen and harmonise drug regulation practices.

Relationships between the occurrence of Giardia and Cryptosporidium and physicochemical properties of marine waters of the Pacific Coast of Mexico.

PubMed

Magana-Ordorica, Dalia; Mena, Kristina; Valdez-Torres, Jose B; Soto-Beltran, Marcela; Leon-Felix, Josefina; Chaidez, Cristobal

2010-12-01

Untreated sewage has adversely affected the quality of marine recreational waters worldwide. Exposure to marine recreational water with poor microbial quality may pose a threat to bathers. The objectives of this study were to assess the effect of physicochemical parameters on Cryptosporidium and Giardia presence in marine recreational water of Sinaloa, Mexico, by Logistic Regression Analyses. Thirty-two 10-litre water samples were collected from two tourist beaches, Altata and Mazatlan, between November 2006 and May 2007. Water samples were processed by the EPA 1623 method and pH, temperature, salinity and turbidity were also determined. Cryptosporidium and Giardia were present in 71 and 57% of the samples collected from Altata, respectively. In Mazatlan, Cryptosporidium and Giardia were found in 83 and 72% of the samples, respectively. The overall concentration of Cryptosporidium ranged from 150 to 2,050 oocysts/10 L with an average of 581 oocysts/10 L and Giardia ranged from 10 to 300 cysts/10 L with an average of 73 cysts/10 L. The occurrence of both parasites increased in water with decreasing temperatures and increasing turbidity of the water.

Linking microbial and ecosystem ecology using ecological stoichiometry: a synthesis of conceptual and empirical approaches

USGS Publications Warehouse

Hall, E.K.; Maixner, F.; Franklin, O.; Daims, H.; Richter, A.; Battin, T.

2011-01-01

Currently, one of the biggest challenges in microbial and ecosystem ecology is to develop conceptual models that organize the growing body of information on environmental microbiology into a clear mechanistic framework with a direct link to ecosystem processes. Doing so will enable development of testable hypotheses to better direct future research and increase understanding of key constraints on biogeochemical networks. Although the understanding of phenotypic and genotypic diversity of microorganisms in the environment is rapidly accumulating, how controls on microbial physiology ultimately affect biogeochemical fluxes remains poorly understood. We propose that insight into constraints on biogeochemical cycles can be achieved by a more rigorous evaluation of microbial community biomass composition within the context of ecological stoichiometry. Multiple recent studies have pointed to microbial biomass stoichiometry as an important determinant of when microorganisms retain or recycle mineral nutrients. We identify the relevant cellular components that most likely drive changes in microbial biomass stoichiometry by defining a conceptual model rooted in ecological stoichiometry. More importantly, we show how X-ray microanalysis (XRMA), nanoscale secondary ion mass spectroscopy (NanoSIMS), Raman microspectroscopy, and in situ hybridization techniques (for example, FISH) can be applied in concert to allow for direct empirical evaluation of the proposed conceptual framework. This approach links an important piece of the ecological literature, ecological stoichiometry, with the molecular front of the microbial revolution, in an attempt to provide new insight into how microbial physiology could constrain ecosystem processes.

The Role of Microbial Community Composition in Controlling Soil Respiration Responses to Temperature

PubMed Central

Khachane, Amit; Dungait, Jennifer A. J.; Fraser, Fiona; Hopkins, David W.; Wookey, Philip A.; Singh, Brajesh K.; Freitag, Thomas E.; Hartley, Iain P.; Prosser, James I.

2016-01-01

Rising global temperatures may increase the rates of soil organic matter decomposition by heterotrophic microorganisms, potentially accelerating climate change further by releasing additional carbon dioxide (CO2) to the atmosphere. However, the possibility that microbial community responses to prolonged warming may modify the temperature sensitivity of soil respiration creates large uncertainty in the strength of this positive feedback. Both compensatory responses (decreasing temperature sensitivity of soil respiration in the long-term) and enhancing responses (increasing temperature sensitivity) have been reported, but the mechanisms underlying these responses are poorly understood. In this study, microbial biomass, community structure and the activities of dehydrogenase and β-glucosidase enzymes were determined for 18 soils that had previously demonstrated either no response or varying magnitude of enhancing or compensatory responses of temperature sensitivity of heterotrophic microbial respiration to prolonged cooling. The soil cooling approach, in contrast to warming experiments, discriminates between microbial community responses and the consequences of substrate depletion, by minimising changes in substrate availability. The initial microbial community composition, determined by molecular analysis of soils showing contrasting respiration responses to cooling, provided evidence that the magnitude of enhancing responses was partly related to microbial community composition. There was also evidence that higher relative abundance of saprophytic Basidiomycota may explain the compensatory response observed in one soil, but neither microbial biomass nor enzymatic capacity were significantly affected by cooling. Our findings emphasise the key importance of soil microbial community responses for feedbacks to global change, but also highlight important areas where our understanding remains limited. PMID:27798702

Contribution of above- and below-ground plant traits to the structure and function of grassland soil microbial communities

PubMed Central

Legay, N.; Baxendale, C.; Grigulis, K.; Krainer, U.; Kastl, E.; Schloter, M.; Bardgett, R. D.; Arnoldi, C.; Bahn, M.; Dumont, M.; Poly, F.; Pommier, T.; Clément, J. C.; Lavorel, S.

2014-01-01

Background and Aims Abiotic properties of soil are known to be major drivers of the microbial community within it. Our understanding of how soil microbial properties are related to the functional structure and diversity of plant communities, however, is limited and largely restricted to above-ground plant traits, with the role of below-ground traits being poorly understood. This study investigated the relative contributions of soil abiotic properties and plant traits, both above-ground and below-ground, to variations in microbial processes involved in grassland nitrogen turnover. Methods In mountain grasslands distributed across three European sites, a correlative approach was used to examine the role of a large range of plant functional traits and soil abiotic factors on microbial variables, including gene abundance of nitrifiers and denitrifiers and their potential activities. Key Results Direct effects of soil abiotic parameters were found to have the most significant influence on the microbial groups investigated. Indirect pathways via plant functional traits contributed substantially to explaining the relative abundance of fungi and bacteria and gene abundances of the investigated microbial communities, while they explained little of the variance in microbial activities. Gene abundances of nitrifiers and denitrifiers were most strongly related to below-ground plant traits, suggesting that they were the most relevant traits for explaining variation in community structure and abundances of soil microbes involved in nitrification and denitrification. Conclusions The results suggest that consideration of plant traits, and especially below-ground traits, increases our ability to describe variation in the abundances and the functional characteristics of microbial communities in grassland soils. PMID:25122656

The Role of Microbial Community Composition in Controlling Soil Respiration Responses to Temperature.

PubMed

Auffret, Marc D; Karhu, Kristiina; Khachane, Amit; Dungait, Jennifer A J; Fraser, Fiona; Hopkins, David W; Wookey, Philip A; Singh, Brajesh K; Freitag, Thomas E; Hartley, Iain P; Prosser, James I

2016-01-01

Rising global temperatures may increase the rates of soil organic matter decomposition by heterotrophic microorganisms, potentially accelerating climate change further by releasing additional carbon dioxide (CO2) to the atmosphere. However, the possibility that microbial community responses to prolonged warming may modify the temperature sensitivity of soil respiration creates large uncertainty in the strength of this positive feedback. Both compensatory responses (decreasing temperature sensitivity of soil respiration in the long-term) and enhancing responses (increasing temperature sensitivity) have been reported, but the mechanisms underlying these responses are poorly understood. In this study, microbial biomass, community structure and the activities of dehydrogenase and β-glucosidase enzymes were determined for 18 soils that had previously demonstrated either no response or varying magnitude of enhancing or compensatory responses of temperature sensitivity of heterotrophic microbial respiration to prolonged cooling. The soil cooling approach, in contrast to warming experiments, discriminates between microbial community responses and the consequences of substrate depletion, by minimising changes in substrate availability. The initial microbial community composition, determined by molecular analysis of soils showing contrasting respiration responses to cooling, provided evidence that the magnitude of enhancing responses was partly related to microbial community composition. There was also evidence that higher relative abundance of saprophytic Basidiomycota may explain the compensatory response observed in one soil, but neither microbial biomass nor enzymatic capacity were significantly affected by cooling. Our findings emphasise the key importance of soil microbial community responses for feedbacks to global change, but also highlight important areas where our understanding remains limited.

Microbial analysis of in situ biofilm formation in drinking water distribution systems: implications for monitoring and control of drinking water quality.

PubMed

Douterelo, Isabel; Jackson, M; Solomon, C; Boxall, J

2016-04-01

Biofilm formation in drinking water distribution systems (DWDS) is influenced by the source water, the supply infrastructure and the operation of the system. A holistic approach was used to advance knowledge on the development of mixed species biofilms in situ, by using biofilm sampling devices installed in chlorinated networks. Key physico-chemical parameters and conventional microbial indicators for drinking water quality were analysed. Biofilm coverage on pipes was evaluated by scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM). The microbial community structure, bacteria and fungi, of water and biofilms was assessed using pyrosequencing. Conventional wisdom leads to an expectation for less microbial diversity in groundwater supplied systems. However, the analysis of bulk water showed higher microbial diversity in groundwater site samples compared with the surface water site. Conversely, higher diversity and richness were detected in biofilms from the surface water site. The average biofilm coverage was similar among sites. Disinfection residual and other key variables were similar between the two sites, other than nitrates, alkalinity and the hydraulic conditions which were extremely low at the groundwater site. Thus, the unexpected result of an exceptionally low diversity with few dominant genera (Pseudomonas and Basidiobolus) in groundwater biofilm samples, despite the more diverse community in the bulk water, is attributed to the low-flow hydraulic conditions. This finding evidences that the local environmental conditions are shaping biofilm formation, composition and amount, and hence managing these is critical for the best operation of DWDS to safeguard water quality.

Microbial water quality before and after the repair of a failing onsite wastewater treatment system adjacent to coastal waters

USGS Publications Warehouse

Conn, K.E.; Habteselassie, M.Y.; Denene, Blackwood A.; Noble, R.T.

2012-01-01

Aims: The objective was to assess the impacts of repairing a failing onsite wastewater treatment system (OWTS, i.e., septic system) as related to coastal microbial water quality. Methods and Results: Wastewater, groundwater and surface water were monitored for environmental parameters, faecal indicator bacteria (total coliforms, Escherichia coli, enterococci) and the viral tracer MS2 before and after repairing a failing OWTS. MS2 results using plaque enumeration and quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) often agreed, but inhibition limited the qRT-PCR assay sensitivity. Prerepair, MS2 persisted in groundwater and was detected in the nearby creek; postrepair, it was not detected. In groundwater, total coliform concentrations were lower and E.??coli was not detected, while enterococci concentrations were similar to prerepair levels. E.??coli and enterococci surface water concentrations were elevated both before and after the repair. Conclusions: Repairing the failing OWTS improved groundwater microbial water quality, although persistence of bacteria in surface water suggests that the OWTS was not the singular faecal contributor to adjacent coastal waters. A suite of tracers is needed to fully assess OWTS performance in treating microbial contaminants and related impacts on receiving waters. Molecular methods like qRT-PCR have potential but require optimization. Significance and Impact of Study: This is the first before and after study of a failing OWTS and provides guidance on selection of microbial tracers and methods. ?? 2011 The Authors. Journal of Applied Microbiology ?? 2011 The Society for Applied Microbiology.

Towards a paradigm shift in the modeling of soil organic carbon decomposition for earth system models

NASA Astrophysics Data System (ADS)

He, Yujie

Soils are the largest terrestrial carbon pools and contain approximately 2200 Pg of carbon. Thus, the dynamics of soil carbon plays an important role in the global carbon cycle and climate system. Earth System Models are used to project future interactions between terrestrial ecosystem carbon dynamics and climate. However, these models often predict a wide range of soil carbon responses and their formulations have lagged behind recent soil science advances, omitting key biogeochemical mechanisms. In contrast, recent mechanistically-based biogeochemical models that explicitly account for microbial biomass pools and enzyme kinetics that catalyze soil carbon decomposition produce notably different results and provide a closer match to recent observations. However, a systematic evaluation of the advantages and disadvantages of the microbial models and how they differ from empirical, first-order formulations in soil decomposition models for soil organic carbon is still needed. This dissertation consists of a series of model sensitivity and uncertainty analyses and identifies dominant decomposition processes in determining soil organic carbon dynamics. Poorly constrained processes or parameters that require more experimental data integration are also identified. This dissertation also demonstrates the critical role of microbial life-history traits (e.g. microbial dormancy) in the modeling of microbial activity in soil organic matter decomposition models. Finally, this study surveys and synthesizes a number of recently published microbial models and provides suggestions for future microbial model developments.

Demonstrating microbial co-occurrence pattern analyses within and between ecosystems

PubMed Central

Williams, Ryan J.; Howe, Adina; Hofmockel, Kirsten S.

2014-01-01

Co-occurrence patterns are used in ecology to explore interactions between organisms and environmental effects on coexistence within biological communities. Analysis of co-occurrence patterns among microbial communities has ranged from simple pairwise comparisons between all community members to direct hypothesis testing between focal species. However, co-occurrence patterns are rarely studied across multiple ecosystems or multiple scales of biological organization within the same study. Here we outline an approach to produce co-occurrence analyses that are focused at three different scales: co-occurrence patterns between ecosystems at the community scale, modules of co-occurring microorganisms within communities, and co-occurring pairs within modules that are nested within microbial communities. To demonstrate our co-occurrence analysis approach, we gathered publicly available 16S rRNA amplicon datasets to compare and contrast microbial co-occurrence at different taxonomic levels across different ecosystems. We found differences in community composition and co-occurrence that reflect environmental filtering at the community scale and consistent pairwise occurrences that may be used to infer ecological traits about poorly understood microbial taxa. However, we also found that conclusions derived from applying network statistics to microbial relationships can vary depending on the taxonomic level chosen and criteria used to build co-occurrence networks. We present our statistical analysis and code for public use in analysis of co-occurrence patterns across microbial communities. PMID:25101065

Microbial succession and stimulation following a test well injection simulating CO2 leakage into shallow Newark Basin aquifers

NASA Astrophysics Data System (ADS)

Dueker, M.; Clauson, K.; Yang, Q.; Umemoto, K.; Seltzer, A. M.; Zakharova, N. V.; Matter, J. M.; Stute, M.; Takahashi, T.; Goldberg, D.; O'Mullan, G. D.

2012-12-01

Despite growing appreciation for the importance of microbes in altering geochemical reactions in the subsurface, the microbial response to geological carbon sequestration injections and the role of microbes in altering metal mobilization following leakage scenarios in shallow aquifers remain poorly constrained. A Newark Basin test well was utilized in field experiments to investigate patterns of microbial succession following injection of CO2 saturated water into isolated aquifer intervals. Additionally, laboratory mesocosm experiments, including microbially-active and inactive (autoclave sterilized) treatments, were used to constrain the microbial role in mineral dissolution, trace metal release, and gas production (e.g. hydrogen and methane). Hydrogen production was detected in both sterilized and unsterilized laboratory mesocosm treatments, indicating abiotic hydrogen production may occur following CO2 leakage, and methane production was detected in unsterilized, microbially active mesocosms. In field experiments, a decrease in pH following injection of CO2 saturated aquifer water was accompanied by mobilization of trace elements (e.g. Fe and Mn), the production of hydrogen gas, and increased bacterial cell concentrations. 16S ribosomal RNA clone libraries, from samples collected before and after the test well injection, were compared in an attempt to link variability in geochemistry to changes in aquifer microbiology. Significant changes in microbial composition, compared to background conditions, were found following the test well injection, including a decrease in Proteobacteria, and an increased presence of Firmicutes, Verrucomicrobia, Acidobacteria and other microbes associated with iron reducing and syntrophic metabolism. The concurrence of increased microbial cell concentration, and rapid microbial community succession, with increased concentrations of hydrogen gas suggests that abiotically produced hydrogen may serve as an ecologically-relevant energy source stimulating changes in aquifer microbial communities immediately following CO2 leakage.

Insights from intercomparison of microbial and conventional soil models

NASA Astrophysics Data System (ADS)

Allison, S. D.; Li, J.; Luo, Y.; Mayes, M. A.; Wang, G.

2014-12-01

Changing the structure of soil biogeochemical models to represent coupling between microbial biomass and carbon substrate pools could improve predictions of carbon-climate feedbacks. So-called "microbial models" with this structure make very different predictions from conventional models based on first-order decay of carbon substrate pools. Still, the value of microbial models is uncertain because microbial physiological parameters are poorly constrained and model behaviors have not been fully explored. To address these issues, we developed an approach for inter-comparing microbial and conventional models. We initially focused on soil carbon responses to microbial carbon use efficiency (CUE) and temperature. Three scenarios were implemented in all models at a common reference temperature (20°C): constant CUE (held at 0.31), varied CUE (-0.016°C-1), and 50% acclimated CUE (-0.008°C-1). Whereas the conventional model always showed soil carbon losses with increasing temperature, the microbial models each predicted a temperature threshold above which warming led to soil carbon gain. The location of this threshold depended on CUE scenario, with higher temperature thresholds under the acclimated and constant scenarios. This result suggests that the temperature sensitivity of CUE and the structure of the soil carbon model together regulate the long-term soil carbon response to warming. Compared to the conventional model, all microbial models showed oscillatory behavior in response to perturbations and were much less sensitive to changing inputs. Oscillations were weakest in the most complex model with explicit enzyme pools, suggesting that multi-pool coupling might be a more realistic representation of the soil system. This study suggests that model structure and CUE parameterization should be carefully evaluated when scaling up microbial models to ecosystems and the globe.

Deep-biosphere methane production stimulated by geofluids in the Nankai accretionary complex

PubMed Central

Kubo, Yusuke; Hoshino, Tatsuhiko; Sakai, Sanae; Arnold, Gail L.; Case, David H.; Lever, Mark A.; Morita, Sumito; Nakamura, Ko-ichi

2018-01-01

Microbial life inhabiting subseafloor sediments plays an important role in Earth’s carbon cycle. However, the impact of geodynamic processes on the distributions and carbon-cycling activities of subseafloor life remains poorly constrained. We explore a submarine mud volcano of the Nankai accretionary complex by drilling down to 200 m below the summit. Stable isotopic compositions of water and carbon compounds, including clumped methane isotopologues, suggest that ~90% of methane is microbially produced at 16° to 30°C and 300 to 900 m below seafloor, corresponding to the basin bottom, where fluids in the accretionary prism are supplied via megasplay faults. Radiotracer experiments showed that relatively small microbial populations in deep mud volcano sediments (102 to 103 cells cm−3) include highly active hydrogenotrophic methanogens and acetogens. Our findings indicate that subduction-associated fluid migration has stimulated microbial activity in the mud reservoir and that mud volcanoes may contribute more substantially to the methane budget than previously estimated. PMID:29928689

Microbial Photoelectrosynthesis for Self-Sustaining Hydrogen Generation.

PubMed

Lu, Lu; Williams, Nicholas B; Turner, John A; Maness, Pin-Ching; Gu, Jing; Ren, Zhiyong Jason

2017-11-21

Current artificial photosynthesis (APS) systems are promising for the storage of solar energy via transportable and storable fuels, but the anodic half-reaction of water oxidation is an energy intensive process which in many cases poorly couples with the cathodic half-reaction. Here we demonstrate a self-sustaining microbial photoelectrosynthesis (MPES) system that pairs microbial electrochemical oxidation with photoelectrochemical water reduction for energy efficient H 2 generation. MPES reduces the overall energy requirements thereby greatly expanding the range of semiconductors that can be utilized in APS. Due to the recovery of chemical energy from waste organics by the mild microbial process and utilization of cost-effective and stable catalyst/electrode materials, our MPES system produced a stable current of 0.4 mA/cm 2 for 24 h without any external bias and ∼10 mA/cm 2 with a modest bias under one sun illumination. This system also showed other merits, such as creating benefits of wastewater treatment and facile preparation and scalability.

Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales.

PubMed

Daly, Rebecca A; Borton, Mikayla A; Wilkins, Michael J; Hoyt, David W; Kountz, Duncan J; Wolfe, Richard A; Welch, Susan A; Marcus, Daniel N; Trexler, Ryan V; MacRae, Jean D; Krzycki, Joseph A; Cole, David R; Mouser, Paula J; Wrighton, Kelly C

2016-09-05

Hydraulic fracturing is the industry standard for extracting hydrocarbons from shale formations. Attention has been paid to the economic benefits and environmental impacts of this process, yet the biogeochemical changes induced in the deep subsurface are poorly understood. Recent single-gene investigations revealed that halotolerant microbial communities were enriched after hydraulic fracturing. Here, the reconstruction of 31 unique genomes coupled to metabolite data from the Marcellus and Utica shales revealed that many of the persisting organisms play roles in methylamine cycling, ultimately supporting methanogenesis in the deep biosphere. Fermentation of injected chemical additives also sustains long-term microbial persistence, while thiosulfate reduction could produce sulfide, contributing to reservoir souring and infrastructure corrosion. Extensive links between viruses and microbial hosts demonstrate active viral predation, which may contribute to the release of labile cellular constituents into the extracellular environment. Our analyses show that hydraulic fracturing provides the organismal and chemical inputs for colonization and persistence in the deep terrestrial subsurface.

Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide

USGS Publications Warehouse

Prober, Suzanne M.; Leff, Jonathan W.; Bates, Scott T.; Borer, Elizabeth T.; Firn, Jennifer; Harpole, W. Stanley; Lind, Eric M.; Seabloom, Eric W.; Adler, Peter B.; Bakker, Jonathan D.; Cleland, Elsa E.; DeCrappeo, Nicole; DeLorenze, Elizabeth; Hagenah, Nicole; Hautier, Yann; Hofmockel, Kirsten S.; Kirkman, Kevin P.; Knops, Johannes M. H.; La Pierre, Kimberly J.; MacDougall, Andrew S.; McCulley, Rebecca L.; Mitchell, Charles E.; Risch, Anita C.; Schuetz, Martin; Stevens, Carly J.; Williams, Ryan J.; Fierer, Noah

2015-01-01

Aboveground–belowground interactions exert critical controls on the composition and function of terrestrial ecosystems, yet the fundamental relationships between plant diversity and soil microbial diversity remain elusive. Theory predicts predominantly positive associations but tests within single sites have shown variable relationships, and associations between plant and microbial diversity across broad spatial scales remain largely unexplored. We compared the diversity of plant, bacterial, archaeal and fungal communities in one hundred and forty-five 1 m2 plots across 25 temperate grassland sites from four continents. Across sites, the plant alpha diversity patterns were poorly related to those observed for any soil microbial group. However, plant beta diversity (compositional dissimilarity between sites) was significantly correlated with the beta diversity of bacterial and fungal communities, even after controlling for environmental factors. Thus, across a global range of temperate grasslands, plant diversity can predict patterns in the composition of soil microbial communities, but not patterns in alpha diversity.

The distinctive microbial community improves composting efficiency in a full-scale hyperthermophilic composting plant.

PubMed

Yu, Zhen; Tang, Jia; Liao, Hanpeng; Liu, Xiaoming; Zhou, Puxiong; Chen, Zhi; Rensing, Christopher; Zhou, Shungui

2018-06-07

The application of conventional thermophilic composting (TC) is limited by poor efficiency. Newly-developed hyperthermophilic composting (HTC) is expected to overcome this shortcoming. However, the characterization of microbial communities associated with HTC remains unclear. Here, we compared the performance of HTC and TC in a full-scale sludge composting plant, and found that HTC running at the hyperthermophilic and thermophilic phases for 21 days, led to higher composting efficiency and techno-economic advantages over TC. Results of high-throughput sequencing showed drastic changes in the microbial community during HTC. Thermaceae (35.5-41.7%) was the predominant family in the hyperthermophilic phase, while the thermophilic phase was dominated by both Thermaceae (28.0-53.3%) and Thermoactinomycetaceae (29.9-36.1%). The change of microbial community could be the cause of continuous high temperature in HTC, and thus improve composting efficiency by accelerating the maturation process. This work has provided theoretical and practical guidance for managing sewage sludge by HTC. Copyright © 2018 Elsevier Ltd. All rights reserved.

Toward Linking Aboveground Vegetation Properties and Soil Microbial Communities Using Remote Sensing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hamada, Yuki; Gilbert, Jack A.; Larsen, Peter E.

2014-04-01

Despite their vital role in terrestrial ecosystem function, the distributions and dynamics of soil microbial communities (SMCs) are poorly understood. Vegetation and soil properties are the primary factors that influence SMCs. This paper discusses the potential effectiveness of remote sensing science and technologies for mapping SMC biogeography by characterizing surface biophysical properties (e.g., plant traits and community composition) strongly correlated with SMCs. Using remotely sensed biophysical properties to predict SMC distributions is extremely challenging because of the intricate interactions between biotic and abiotic factors and between above- and belowground ecosystems. However, the integration of biophysical and soil remote sensing withmore » geospatial information about the e nvironment holds great promise for mapping SMC biogeography. Additional research needs invol ve microbial taxonomic definition, soil environmental complexity, and scaling strategies. The collaborative effort of experts from diverse disciplines is essential to linking terrestrial surface biosphere observations with subsurface microbial community distributions using remote sensing.« less

Toward Linking Aboveground Vegetation Properties and Soil Microbial Communities Using Remote Sensing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hamada, Yuki; Gilbert, Jack A.; Larsen, Peter E.

2014-04-01

Despite their vital role in terrestrial ecosystem function, the distributions and dynamics of soil microbial communities (SMCs) are poorly understood. Vegetation and soil properties are the primary factors that influence SMCs. This paper discusses the potential effectiveness of remote sensing science and technologies for mapping SMC biogeography by characterizing surface biophysical properties (e.g., plant traits and community composition) strongly correlated with SMCs. Using remotely sensed biophysical properties to predict SMC distributions is extremely challenging because of the intricate interactions between biotic and abiotic factors and between above- and below-ground ecosystems. However, the integration of biophysical and soil remote sensing withmore » geospatial information about the environment holds great promise for mapping SMC biogeography. Additional research needs involve microbial taxonomic definition, soil environmental complexity, and scaling strategies. The collaborative effort of experts from diverse disciplines is essential to linking terrestrial surface biosphere observations with subsurface microbial community distributions using remote sensing.« less

Association of sociodemographic, lifestyle, and health factors with sleep quality and daytime sleepiness in women: findings from the 2007 National Sleep Foundation "Sleep in America Poll".

PubMed

Baker, Fiona C; Wolfson, Amy R; Lee, Kathryn A

2009-06-01

To investigate factors associated with poor sleep quality and daytime sleepiness in women living in the United States. Data are presented from the National Sleep Foundation's 2007 Sleep in America Poll that included 959 women (18-64 years of age) surveyed by telephone about their sleep quality, daytime sleepiness, and sociodemographic, health, and lifestyle factors. Poor sleep quality was reported by 27% and daytime sleepiness was reported by 21% of respondents. Logistic multivariate regression analyses revealed that poor sleep quality and daytime sleepiness were both independently associated with poor health, having a sleep disorder, and psychological distress. Also, multivariate analyses showed that women who consumed more caffeinated beverages and those who had more than one job were more likely to report poor sleep quality but not daytime sleepiness. Daytime sleepiness, on the other hand, was independently associated with being black/African American, younger, disabled, having less education, and daytime napping. Poor sleep quality and daytime sleepiness are common in American women and are associated with health-related, as well as sociodemographic, factors. Addressing sleep-related complaints in women is important to improve their daytime functioning and quality of life.

Influence of Pig Slurry on Microbial and Biochemical Characteristics of Soil in Albacete Region, SE Spain

NASA Astrophysics Data System (ADS)

Halil Yanardaǧ, Ibrahim

2013-04-01

Soil quality is very important in terms of agricultural sustainability, ecosystem and terrestrial carbon (C) cycle. In turn, soil microbial and biochemical characteristics are indicative of nutrient cycling and soil organic matter dynamics. We investigated the effects of the pig slurries (raw pig slurry (RPS) and treated pig slurry (TPS) from liquid and solid feeding diets) on microbial and biochemical characteristics of soil under barley cropping system. Application doses of slurries are identified with legal doses of Castilla La Mancha Region, which is 210 kg N ha-1 year-1. Microbial biomass C, soluble C, black C and three soil enzymes (β-Glucosidase, β-galactosidase and Arylesterase enzymes) are studied to determine effect slurry on soil biochemical characteristics, which are very important in terms of C cycle in soil. Black carbon content and β-Glucosidase enzyme activities are increased with all pig slurry applications from liquid and traditional feeding diet, as well as microbial biomass and organic carbon content and β-galactosidase enzyme activities are increased with slurry from liquid feeding diet doses. However, pig slurry application from liquid feeding diet doses have increased yield, quality, length and total biomass content of barley. Bioavailable metal contents are increased with all slurry application and with using high doses of slurry can be caused soil pollution. Pig slurries from liquid feeding diet had positive impacts on microbial and biochemical characteristics in terms of soil quality in comparison to the different feeding diets. PS addition to soil had a very significant stimulating effect on the enzyme activities, microbial biomass, soluble and black C compared with different kind of PS and control plots on Mediterranean soil in barley monoculture. This effect may originate from the organic C, N, P and S compounds added with PS. The highest enzyme activity and microbial biomass were observed on the soil samples from the RPS treatment, whereas, black and soluble C was decreased with PS addition. There may have been a transient positive effect of the RPS treatments on the soil biochemical parameters. However, the effect could not be detected because of less labile C content during the experiment. The beneficial effects of the PS additions were less pronounced in the 0-30 cm. soil layer. In this monoculture barley production system and under these Mediterranean climate conditions, applications of TPS should be avoided, so they were associated with a decline in microbial counts and a leveling of almost all the enzymatic activities and microbial biomass C. Keywords: Pig slurry, Microbial biomass C, soluble C, black C, β-Glucosidase, β-galactosidase and Arylesterase enzyme activities.

Health-hazard evaluation report HETA 88-369-2141, Raymond W. Bliss Army Community Hospital, Ft. Huachuca, Arizona

DOE Office of Scientific and Technical Information (OSTI.GOV)

Klein, M.; Gunter, B.

1991-09-01

In response to a request from a representative of the Raymond W. Bliss Army Community Hospital concerning indoor air quality at Greely Hall, Fort Huachuca (SIC-9711), Arizona, an environmental and ventilation survey was conducted. Greely Hall was a three story, multipurpose building with approximately 120,000 feet per floor. The building housed primarily offices, but also had a cafeteria, auditorium, computer rooms, conference rooms and electronics maintenance area. Over 2100 persons worked in the building. Average carbon-dioxide (124389) levels were 584 parts per million (ppm) in the morning, increasing to 1040ppm for the last measurements made that day. The levels rangedmore » from 350 to 1000ppm in the morning to 800 to 1800ppm in the afternoon. Inordinate temperature increases during the day were found in some areas of the building. Many of the air handling units had inoperable or closed main outside air dampers. Maintenance was poor. Improperly maintained or poorly draining condesate pans, renovation of the building without upgrading the ventilation systems and insufficient maintenance personnel were some of the problems identified. The authors conclude that the potential for thermal comfort problems and microbial contamination existed. The authors recommend measures to remedy these situations.« less

A minimalistic microbial food web in an excavated deep subsurface clay rock.

PubMed

Bagnoud, Alexandre; de Bruijn, Ino; Andersson, Anders F; Diomidis, Nikitas; Leupin, Olivier X; Schwyn, Bernhard; Bernier-Latmani, Rizlan

2016-01-01

Clay rocks are being considered for radioactive waste disposal, but relatively little is known about the impact of microbes on the long-term safety of geological repositories. Thus, a more complete understanding of microbial community structure and function in these environments would provide further detail for the evaluation of the safety of geological disposal of radioactive waste in clay rocks. It would also provide a unique glimpse into a poorly studied deep subsurface microbial ecosystem. Previous studies concluded that microorganisms were present in pristine Opalinus Clay, but inactive. In this work, we describe the microbial community and assess the metabolic activities taking place within borehole water. Metagenomic sequencing and genome-binning of a porewater sample containing suspended clay particles revealed a remarkably simple heterotrophic microbial community, fueled by sedimentary organic carbon, mainly composed of two organisms: a Pseudomonas sp. fermenting bacterium growing on organic macromolecules and releasing organic acids and H2, and a sulfate-reducing Peptococcaceae able to oxidize organic molecules to CO(2). In Opalinus Clay, this microbial system likely thrives where pore space allows it. In a repository, this may occur where the clay rock has been locally damaged by excavation or in engineered backfills. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Humans differ in their personal microbial cloud

PubMed Central

Altrichter, Adam E.; Bateman, Ashley C.; Stenson, Jason; Brown, GZ; Green, Jessica L.; Bohannan, Brendan J.M.

2015-01-01

Dispersal of microbes between humans and the built environment can occur through direct contact with surfaces or through airborne release; the latter mechanism remains poorly understood. Humans emit upwards of 106 biological particles per hour, and have long been known to transmit pathogens to other individuals and to indoor surfaces. However it has not previously been demonstrated that humans emit a detectible microbial cloud into surrounding indoor air, nor whether such clouds are sufficiently differentiated to allow the identification of individual occupants. We used high-throughput sequencing of 16S rRNA genes to characterize the airborne bacterial contribution of a single person sitting in a sanitized custom experimental climate chamber. We compared that to air sampled in an adjacent, identical, unoccupied chamber, as well as to supply and exhaust air sources. Additionally, we assessed microbial communities in settled particles surrounding each occupant, to investigate the potential long-term fate of airborne microbial emissions. Most occupants could be clearly detected by their airborne bacterial emissions, as well as their contribution to settled particles, within 1.5–4 h. Bacterial clouds from the occupants were statistically distinct, allowing the identification of some individual occupants. Our results confirm that an occupied space is microbially distinct from an unoccupied one, and demonstrate for the first time that individuals release their own personalized microbial cloud. PMID:26417541

Dormancy contributes to the maintenance of microbial diversity.

PubMed

Jones, Stuart E; Lennon, Jay T

2010-03-30

Dormancy is a bet-hedging strategy used by a variety of organisms to overcome unfavorable environmental conditions. By entering a reversible state of low metabolic activity, dormant individuals become members of a seed bank, which can determine community dynamics in future generations. Although microbiologists have documented dormancy in both clinical and natural settings, the importance of seed banks for the diversity and functioning of microbial communities remains untested. Here, we develop a theoretical model demonstrating that microbial communities are structured by environmental cues that trigger dormancy. A molecular survey of lake ecosystems revealed that dormancy plays a more important role in shaping bacterial communities than eukaryotic microbial communities. The proportion of dormant bacteria was relatively low in productive ecosystems but accounted for up to 40% of taxon richness in nutrient-poor systems. Our simulations and empirical data suggest that regional environmental cues and dormancy synchronize the composition of active communities across the landscape while decoupling active microbes from the total community at local scales. Furthermore, we observed that rare bacterial taxa were disproportionately active relative to common bacterial taxa, suggesting that microbial rank-abundance curves are more dynamic than previously considered. We propose that repeated transitions to and from the seed bank may help maintain the high levels of microbial biodiversity that are observed in nearly all ecosystems.

Preservation in microbial mats: mineralization by a talc-like phase of a fish embedded in a microbial sarcophagus

NASA Astrophysics Data System (ADS)

Iniesto, Miguel; Zeyen, Nina; López-Archilla, Ana; Bernard, Sylvain; Buscalioni, Ángela; Guerrero, M. Carmen; Benzerara, Karim

2015-09-01

Microbial mats have been repeatedly suggested to promote early fossilization of macroorganisms. Yet, experimental simulations of this process remain scarce. Here, we report results of 5 year-long experiments performed onfish carcasses to document the influence of microbial mats on mineral precipitation during early fossilization. Carcasses were initially placed on top of microbial mats. After two weeks, fishes became coated by the mats forming a compact sarcophagus, which modified the microenvironment close to the corpses. Our results showed that these conditions favoured the precipitation of a poorly crystalline silicate phase rich in magnesium. This talc-like mineral phase has been detected in three different locations within the carcasses placed in microbial mats for more than 4 years: 1) within inner tissues, colonized by several bacillary cells; 2) at the surface of bones of the upper face of the corpse buried in the mat; and 3) at the surface of several bones such as the dorsal fin which appeared to be gradually replaced by the Mg-silicate phase. This mineral phase has been previously shown to promote bacteria fossilization. Here we provide first experimental evidence that such Mg-rich phase can also be involved in exceptional preservation of animals.

Planting increases the abundance and structure complexity of soil core functional genes relevant to carbon and nitrogen cycling

PubMed Central

Wang, Feng; Liang, Yuting; Jiang, Yuji; Yang, Yunfeng; Xue, Kai; Xiong, Jinbo; Zhou, Jizhong; Sun, Bo

2015-01-01

Plants have an important impact on soil microbial communities and their functions. However, how plants determine the microbial composition and network interactions is still poorly understood. During a four-year field experiment, we investigated the functional gene composition of three types of soils (Phaeozem, Cambisols and Acrisol) under maize planting and bare fallow regimes located in cold temperate, warm temperate and subtropical regions, respectively. The core genes were identified using high-throughput functional gene microarray (GeoChip 3.0), and functional molecular ecological networks (fMENs) were subsequently developed with the random matrix theory (RMT)-based conceptual framework. Our results demonstrated that planting significantly (P < 0.05) increased the gene alpha-diversity in terms of richness and Shannon – Simpson’s indexes for all three types of soils and 83.5% of microbial alpha-diversity can be explained by the plant factor. Moreover, planting had significant impacts on the microbial community structure and the network interactions of the microbial communities. The calculated network complexity was higher under maize planting than under bare fallow regimes. The increase of the functional genes led to an increase in both soil respiration and nitrification potential with maize planting, indicating that changes in the soil microbial communities and network interactions influenced ecological functioning. PMID:26396042

Short-term precipitation exclusion alters microbial responses to soil moisture in a wet tropical forest.

PubMed

Waring, Bonnie G; Hawkes, Christine V

2015-05-01

Many wet tropical forests, which contain a quarter of global terrestrial biomass carbon stocks, will experience changes in precipitation regime over the next century. Soil microbial responses to altered rainfall are likely to be an important feedback on ecosystem carbon cycling, but the ecological mechanisms underpinning these responses are poorly understood. We examined how reduced rainfall affected soil microbial abundance, activity, and community composition using a 6-month precipitation exclusion experiment at La Selva Biological Station, Costa Rica. Thereafter, we addressed the persistent effects of field moisture treatments by exposing soils to a controlled soil moisture gradient in the lab for 4 weeks. In the field, compositional and functional responses to reduced rainfall were dependent on initial conditions, consistent with a large degree of spatial heterogeneity in tropical forests. However, the precipitation manipulation significantly altered microbial functional responses to soil moisture. Communities with prior drought exposure exhibited higher respiration rates per unit microbial biomass under all conditions and respired significantly more CO2 than control soils at low soil moisture. These functional patterns suggest that changes in microbial physiology may drive positive feedbacks to rising atmospheric CO2 concentrations if wet tropical forests experience longer or more intense dry seasons in the future.

Physicochemical and microbial assessment of spring water quality for drinking supply in Piedmont of Béni-Mellal Atlas (Morocco)

NASA Astrophysics Data System (ADS)

Barakat, Ahmed; Meddah, Redouane; Afdali, Mustapha; Touhami, Fatima

2018-04-01

The present study was conducted to examine the water quality of karst springs located along the Piedmont of Béni-Mellal Atlas (Morocco) for drinking purposes. Twenty-five water samples were collected from seven springs in June, July, August and September 2013, and May 2016 have been analyzed for their physicochemical and microbial characteristics. The analytical data of temperature, pH, DO, TAC, TH, oxidizability and NH4+ showed that all sampled springs are suitable as drinking water according to Moroccan and the World Health Organization (WHO) standards. Nevertheless, EC, turbidity, and NO3- were sometimes noted higher than the allowable limits, what would be ascribed to erosion and leaching of soil and karstic rocks. The microbial analysis revealed the presence of fecal contamination (total coliforms, E. coli, and intestinal enterococci) in all springs at various times. The water quality index (WQI) calculated based on physicochemical and microbial data reveled that water quality categorization for all sampling springs was found to be 'medium' to 'good' for drinking uses in the National Sanitation Foundation WQI (NSF-WQI), and ''necessary treatment becoming more extensive'' to ''purification not necessary'' in the Dinius' Second Index (D-WQI). The Aine Asserdoune and Foum el Anceur springs showed the good quality of drinking water. According to Moroccan standards for water used for drinking purposes, the waters belong to category A1 that requires becoming drinkable a simple physical treatment and disinfection. From the type of parameters present in quantities exceeding drinking water limits, it is very obvious that these water resources are under the influence of anthropogenic activities such as sewage, waste disposal, deforestation and agricultural activities, caused land degradation and nonpoint pollution sources. Environmental attention, such as systematic quality control and adequate treatment before being used for drinking use and access to sewage sanitation, are required to guarantee sufficient protection of the studied springs.

Evaluating the U.S. Food Safety Modernization Act Produce Safety Rule Standard for Microbial Quality of Agricultural Water for Growing Produce.

PubMed

Havelaar, Arie H; Vazquez, Kathleen M; Topalcengiz, Zeynal; Muñoz-Carpena, Rafael; Danyluk, Michelle D

2017-10-09

The U.S. Food and Drug Administration (FDA) has defined standards for the microbial quality of agricultural surface water used for irrigation. According to the FDA produce safety rule (PSR), a microbial water quality profile requires analysis of a minimum of 20 samples for Escherichia coli over 2 to 4 years. The geometric mean (GM) level of E. coli should not exceed 126 CFU/100 mL, and the statistical threshold value (STV) should not exceed 410 CFU/100 mL. The water quality profile should be updated by analysis of a minimum of five samples per year. We used an extensive set of data on levels of E. coli and other fecal indicator organisms, the presence or absence of Salmonella, and physicochemical parameters in six agricultural irrigation ponds in West Central Florida to evaluate the empirical and theoretical basis of this PSR. We found highly variable log-transformed E. coli levels, with standard deviations exceeding those assumed in the PSR by up to threefold. Lognormal distributions provided an acceptable fit to the data in most cases but may underestimate extreme levels. Replacing censored data with the detection limit of the microbial tests underestimated the true variability, leading to biased estimates of GM and STV. Maximum likelihood estimation using truncated lognormal distributions is recommended. Twenty samples are not sufficient to characterize the bacteriological quality of irrigation ponds, and a rolling data set of five samples per year used to update GM and STV values results in highly uncertain results and delays in detecting a shift in water quality. In these ponds, E. coli was an adequate predictor of the presence of Salmonella in 150-mL samples, and turbidity was a second significant variable. The variability in levels of E. coli in agricultural water was higher than that anticipated when the PSR was finalized, and more detailed information based on mechanistic modeling is necessary to develop targeted risk management strategies.

Urban groundwater quality in sub-Saharan Africa: current status and implications for water security and public health

NASA Astrophysics Data System (ADS)

Lapworth, D. J.; Nkhuwa, D. C. W.; Okotto-Okotto, J.; Pedley, S.; Stuart, M. E.; Tijani, M. N.; Wright, J.

2017-06-01

Groundwater resources are important sources of drinking water in Africa, and they are hugely important in sustaining urban livelihoods and supporting a diverse range of commercial and agricultural activities. Groundwater has an important role in improving health in sub-Saharan Africa (SSA). An estimated 250 million people (40% of the total) live in urban centres across SSA. SSA has experienced a rapid expansion in urban populations since the 1950s, with increased population densities as well as expanding geographical coverage. Estimates suggest that the urban population in SSA will double between 2000 and 2030. The quality status of shallow urban groundwater resources is often very poor due to inadequate waste management and source protection, and poses a significant health risk to users, while deeper borehole sources often provide an important source of good quality drinking water. Given the growth in future demand from this finite resource, as well as potential changes in future climate in this region, a detailed understanding of both water quantity and quality is required to use this resource sustainably. This paper provides a comprehensive assessment of the water quality status, both microbial and chemical, of urban groundwater in SSA across a range of hydrogeological terrains and different groundwater point types. Lower storage basement terrains, which underlie a significant proportion of urban centres in SSA, are particularly vulnerable to contamination. The relationship between mean nitrate concentration and intrinsic aquifer pollution risk is assessed for urban centres across SSA. Current knowledge gaps are identified and future research needs highlighted.

Microbial load and safety of paper currencies from some food vendors in Jimma Town, Southwest Ethiopia.

PubMed

Girma, Gosa; Ketema, Tsige; Bacha, Ketema

2014-11-25

Paper currency is used for every type of commerce and plays an important role in the life of human beings. However, the combination of its widespread use and constant exchange make paper currency a likely agent for disease transmission. Thus, the aim of this study was to evaluate the microbial load and safety of Ethiopian paper currencies collected from some food vendors in Jimma town. Standard microbiological methods were used for the enumeration of various microbial groups, isolation and characterization of pathogenic bacteria and their growth potential in selected weaning foods. A total of 100 samples of Ethiopian paper currencies, consisting of five denominations, from street food venders, hotels and cafeterias in Jimma town were collected aseptically. Sterile cotton swabs moistened with buffered peptone water solution were used for swabbing and the swabs were separately soaked into 10 ml sterile buffered peptone water solution. Mean microbial counts of Aerobic mesophilic bacteria, Staphylococci, Enterobacteriaceae, coliforms and Aerobic bacterial spores were (log CFU/cm2) 6.32, 4.43, 3.14, 2.98 and 3.78, respectively. However, mean counts of Yeasts and Moulds were below detectable levels. There was statistically significant variation (p<0.05) among the mean counts of microbes isolated from samples of paper currencies. The predominantly isolated microbial groups were Staphylococcus spp. (34.06%) followed by Bacillus spp. (31.88%), Enterobacteraceae (13.39%), Micrococcus spp. (9.55%) and Streptococcus spp. (9.03%). Overall, 25% and 10% of the samples were positive for S. aureus and Salmonella spp, respectively. In challenge study, Salmonella spp. and S. aureus reached the infective dose within 12 to 18 hours of inoculation. Thus, paper currencies could be considered as one of the possible vehicles for transmission of disease causing microorganisms. Poor handling practices and personal hygiene of the food vendors could contribute to the observed microbial counts. Thus, it calls for awareness development on the potential risks associated with poor handling of paper currencies at all level of the food establishments.

The effect of zolpidem on sleep quality, stress status, and nondipping hypertension.

PubMed

Huang, Yuli; Mai, Weiyi; Cai, Xiaoyan; Hu, Yunzhao; Song, Yuanbin; Qiu, Ruofeng; Wu, Yanxian; Kuang, Jian

2012-03-01

Poor sleep quality and stress status have previously been shown to be closely associated with higher activation of the sympathetic nervous system and to be independent predictors of nondipping hypertension. This study aimed to evaluate the effects of the non-hypotensive sedative zolpidem on sleep quality, stress status, and nondipping hypertension. A total of 103 nondippers were defined as poor or good sleepers by the Pittsburgh Sleep Quality Index. They were randomized to receive zolpidem or placebo treatment for 30 days. Stress status was assessed by the Perceived Stress Scale, and levels of epinephrine and norepinephrine were examined to investigate the underlying mechanisms. Poor sleepers treated with zolpidem for 30 days showed significant improvements in sleep quality and stress levels (P<0.01). More nondippers were converted to dippers in the group of poor sleepers treated with zolpidem (11 of 22 patients, 50.0%) than in the placebo (2 of 23, 8.7%) (P<0.01). Epinephrine and norepinephrine levels were significantly reduced in poor sleepers treated with zolpidem (P<0.05). The results of this study suggest that zolpidem can improve sleep quality and stress status, and can convert nondippers with poor sleep quality into dippers. It may be an option for treating nondipping hypertensive patients with poor sleep quality. Copyright © 2011 Elsevier B.V. All rights reserved.

Current issues in determining dietary protein quality and metabolic utilization

USDA-ARS?s Scientific Manuscript database

In resource-limited settings, poor dietary quality has a marked negative impact on health, especially during the sensitive periods of pregnancy and first 2 years of life (the first 1000 days) when stunting, poor development and increased risk of later disease develop. Protein quality is often poor o...

Microbial quality of food available to populations of differing socioeconomic status.

PubMed

Koro, Marlen E; Anandan, Shivanthi; Quinlan, Jennifer J

2010-05-01

Low SES has been shown to be linked to poorer-quality diets, decreased consumption of fresh produce, and an increased reliance on small retail stores. The objective of this research was to determine if there is a difference in the microbial quality and potential safety of food available to low-SES versus high-SES populations at the retail level. Aerobic plate count (APC); yeast and mold counts (Y & M); and total coliforms were determined in ready-to-eat (RTE) greens, pre-cut watermelon, broccoli, strawberries, cucumbers, milk, and orange juice and compared among products purchased in stores in low- versus those purchased in high-SES neighborhoods between June 2005 and September 2006. APC, fecal coliforms, and E. coli in ground beef and the presence of Salmonella and Campylobacter in chicken were also compared. Results showed higher microbial loads on produce from markets in low-SES areas. Significant differences observed included (1) APC and Y&M in RTE greens, (2) APC and Y&M in strawberries, and (3) YMCs in cucumbers. No difference was detected in the level of pathogens in raw meat and poultry; however, the APC in ground beef available in high-SES markets was significantly higher compared with that found in low-SES markets. The results presented here indicate that populations of low SES may be more likely to experience produce of poorer microbial quality, which may have an impact on both the appeal and potential safety of the produce. 2010 American Journal of Preventive Medicine. Published by Elsevier Inc. All rights reserved.

Performance of UV disinfection and the microbial quality of greywater effluent along a reuse system for toilet flushing.

PubMed

Friedler, Eran; Gilboa, Yael

2010-04-01

This paper examines the microbial quality of treated RBC (Rotating Biological Contactor) and MBR (Membrane Bioreactor) light greywater along a continuous pilot-scale reuse system for toilet flushing, quantifies the efficiency of UV disinfection unit, and evaluates the regrowth potential of selected microorganisms along the system. The UV disinfection unit was found to be very efficient in reducing faecal coliforms and Staphylococcus aureus. On the other hand, its efficiency of inactivation of HPC (Heterotrophic Plate Count) and Pseudomonas aeruginosa was lower. Some regrowth occurred in the reuse system as a result of HPC regrowth which included opportunistic pathogens such as P. aeruginosa. Although the membrane (UF) of the MBR system removed all bacteria from the greywater, bacteria were observed in the reuse system due to "hopping phenomenon." The microbial quality of the disinfected greywater was found to be equal or even better than the microbial quality of "clean" water in toilet bowls flushed with potable water (and used for excretion). Thus, the added health risk associated with reusing the UV-disinfected greywater for toilet flushing (regarding P. aeruginosa and S. aureus), was found to be insignificant. The UV disinfection unit totally removed (100%) the viral indicator (F-RNA phage, host: E. coli F(amp)(+)) injected to the treatment systems simulating transient viral contamination. To conclude, this work contributes to better design of UV disinfection reactors and provides an insight into the long-term behavior of selected microorganisms along on-site greywater reuse systems for toilet flushing. (c) 2010 Elsevier B.V. All rights reserved.

Periodic sediment shift in migrating ripples influences benthic microbial activity

NASA Astrophysics Data System (ADS)

Zlatanović, Sanja; Fabian, Jenny; Mendoza-Lera, Clara; Woodward, K. Benjamin; Premke, Katrin; Mutz, Michael

2017-06-01

Migrating bedforms have high levels of particulate organic matter and high rates of pore water exchange, causing them to be proposed as hot spots of carbon turnover in rivers. Yet, the shifting of sediments and associated mechanical disturbance within migrating bedforms, such as ripples, may stress and abrade microbial communities, reducing their activity. In a microcosm experiment, we replicated the mechanical disturbances caused by the periodic sediment shift within ripples under oligotrophic conditions. We assessed the effects on fungal and bacterial biomass ratio (F:B), microbial community respiration (CR), and bacterial production (BCP) and compared with stable undisturbed sediments. Interactions between periodic mechanical disturbance and sediment-associated particulate organic matter (POM) were tested by enriching sediments collected from migrating ripples with different qualities of POM (fish feces, leaf litter fragments and no addition treatments). F:B and BCP were affected by an interaction between mechanical disturbance and POM quality. Fish feces enriched sediments showed increased F:B and BCP compared to sediments with lower POM quality and responded with a decrease of F:B and BCP to sediment disturbance. In the other POM treatments F:B and BCP were not affected by disturbance. Microbial respiration was however reduced by mechanical disturbance to similar low activity levels regardless of POM qualities added, whereas fish feces enriched sediment showed short temporary boost of CR. With the worldwide proliferation of migrating sand ripples due to massive catchment erosion, suppressed mineralization of POM will increasingly affect stream metabolism, downstream transport of POM and carbon cycling from reach to catchment scale.

Subjective Sleep Quality in Women With Divorce Histories: The Role of Intimate Partner Victimization.

PubMed

Newton, Tamara L; Burns, Vicki Ellison; Miller, James J; Fernandez-Botran, G Rafael

2016-05-01

A marital status of divorced or separated, as opposed to married, predicts increased risk of health problems, but not for all persons. Focusing on one established health risk that has been linked with divorce--poor subjective sleep quality--the present cross-sectional study examined whether a history of physical intimate partner victimization (IPV) helps identify divorced women at potentially greater risk of health problems. Community midlife women with divorce histories, all of whom were free of current IPV, reported on their past month sleep quality and lifetime IPV. The predicted odds of poor sleep quality were significantly greater for women with, versus without, IPV histories. This held after adjusting for socioemotional, medical, or sociodemographic risks. A dose-response relationship between IPV chronicity and poor quality sleep was observed. IPV history may help identify divorced women at increased risk of poor quality sleep and, more broadly, poor health. © The Author(s) 2015.

Integrated analysis of water quality parameters for cost-effective faecal pollution management in river catchments.

PubMed

Nnane, Daniel Ekane; Ebdon, James Edward; Taylor, Huw David

2011-03-01

In many parts of the world, microbial contamination of surface waters used for drinking, recreation, and shellfishery remains a pervasive risk to human health, especially in Less Economically Developed Countries (LEDC). However, the capacity to provide effective management strategies to break the waterborne route to human infection is often thwarted by our inability to identify the source of microbial contamination. Microbial Source Tracking (MST) has potential to improve water quality management in complex river catchments that are either routinely, or intermittently contaminated by faecal material from one or more sources, by attributing faecal loads to their human or non-human sources, and thereby supporting more rational approaches to microbial risk assessment. The River Ouse catchment in southeast England (U.K.) was used as a model with which to investigate the integration and application of a novel and simple MST approach to monitor microbial water quality over one calendar year, thereby encompassing a range of meteorological conditions. A key objective of the work was to develop simple low-cost protocols that could be easily replicated. Bacteriophages (viruses) capable of infecting a human specific strain of Bacteroides GB-124, and their correlation with presumptive Escherichia coli, were used to distinguish sources of faecal pollution. The results reported here suggest that in this river catchment the principal source of faecal pollution in most instances was non-human in origin. During storm events, presumptive E. coli and presumptive intestinal enterococci levels were 1.1-1.2 logs higher than during dry weather conditions, and levels of the faecal indicator organisms (FIOs) were closely associated with increased turbidity levels (presumptive E. coli and turbidity, r = 0.43). Spatio-temporal variation in microbial water quality parameters was accounted for by three principal components (67.6%). Cluster Analysis, reduced the fourteen monitoring sites to six representative 'sentinel' sites. The correlation coefficient between presumptive E. coli and phages of Bacteroides GB-124 was very small (r = 0.05) whilst that between turbidity and suspended solids was high (r = 0.62). Variations in climate, animal and anthropogenic interferences were all, either directly or indirectly, related to faecal contamination. The findings show the importance of meteorological conditions, such as storm events, on microbial water quality, and suggest that any future increases in the frequency of storm events (associated with climate change) are likely to result in a greater incidence of FIO/pathogen loads. This low-cost approach could help to predict spatio-temporal 'hotspots' of elevated waterborne disease risk. The work also represents an important step towards integrating novel MST tools into river catchment modelling. Copyright © 2011 Elsevier Ltd. All rights reserved.

Drivers of Microbial Risk for Direct Potable Reuse and de Facto Reuse Treatment Schemes: The Impacts of Source Water Quality and Blending.

PubMed

Chaudhry, Rabia M; Hamilton, Kerry A; Haas, Charles N; Nelson, Kara L

2017-06-13

Although reclaimed water for potable applications has many potential benefits, it poses concerns for chemical and microbial risks to consumers. We present a quantitative microbial risk assessment (QMRA) Monte Carlo framework to compare a de facto water reuse scenario (treated wastewater-impacted surface water) with four hypothetical Direct Potable Reuse (DPR) scenarios for Norovirus, Cryptosporidium , and Salmonella . Consumer microbial risks of surface source water quality (impacted by 0-100% treated wastewater effluent) were assessed. Additionally, we assessed risks for different blending ratios (0-100% surface water blended into advanced-treated DPR water) when source surface water consisted of 50% wastewater effluent. De facto reuse risks exceeded the yearly 10 -4 infections risk benchmark while all modeled DPR risks were significantly lower. Contamination with 1% or more wastewater effluent in the source water, and blending 1% or more wastewater-impacted surface water into the advanced-treated DPR water drove the risk closer to the 10 -4 benchmark. We demonstrate that de facto reuse by itself, or as an input into DPR, drives microbial risks more so than the advanced-treated DPR water. When applied using location-specific inputs, this framework can contribute to project design and public awareness campaigns to build legitimacy for DPR.

Effect of preservatives on microbial safety and quality of smoked blue catfish (Ictalurus furcatus) steaks during room-temperature storage.

PubMed

da Silva, Ligia V Antonia; Prinyawiwatkul, Witoon; King, Joan M; No, Hong Kyoon; Bankston, Joseph D; Ge, Beilei

2008-12-01

The microbial safety and quality of smoked blue catfish (Ictalurus furcatus) steaks treated with antimicrobials and antioxidants were examined during 6-week ambient storage. Five pre-smoking soaking treatments were applied: 25% NaCl and 1% ascorbic acid for 30 min or 1h, 3% sodium lactate with or without 5% rosemary extract for 30 min, and 5% sorbic acid alone for 30 min. After smoking, cooled catfish steaks were packed and analyzed at 0, 2, 4, and 6 weeks of ambient storage. Neither Listeria nor Salmonella was recovered from the smoked catfish steaks. Significant reductions (P<0.05) in total plate counts were observed in all treated samples, with those treated with 3% sodium lactate carrying the lowest microbial load. The rosemary extract-treated samples were the most stable against oxidation. All treated smoked catfish steaks had water activities less than 0.85; however, neither pH nor water activity changed significantly within each treatment group during storage (P> or 0.05). In conclusion, smoking/cooking effectively reduced microbial populations, and the use of antimicrobial agents and antioxidants, particularly 3% sodium lactate, could aid the control of microbial safety during storage, resulting in safe products for up to 6 weeks without refrigeration.

The function of advanced treatment process in a drinking water treatment plant with organic matter-polluted source water.

PubMed

Lin, Huirong; Zhang, Shuting; Zhang, Shenghua; Lin, Wenfang; Yu, Xin

2017-04-01

To understand the relationship between chemical and microbial treatment at each treatment step, as well as the relationship between microbial community structure in biofilms in biofilters and their ecological functions, a drinking water plant with severe organic matter-polluted source water was investigated. The bacterial community dynamics of two drinking water supply systems (traditional and advanced treatment processes) in this plant were studied from the source to the product water. Analysis by 454 pyrosequencing was conducted to characterize the bacterial diversity in each step of the treatment processes. The bacterial communities in these two treatment processes were highly diverse. Proteobacteria, which mainly consisted of beta-proteobacteria, was the dominant phylum. The two treatment processes used in the plant could effectively remove organic pollutants and microbial polution, especially the advanced treatment process. Significant differences in the detection of the major groups were observed in the product water samples in the treatment processes. The treatment processes, particularly the biological pretreatment and O 3 -biological activated carbon in the advanced treatment process, highly influenced the microbial community composition and the water quality. Some opportunistic pathogens were found in the water. Nitrogen-relative microorganisms found in the biofilm of filters may perform an important function on the microbial community composition and water quality improvement.

Microbial ecology of the watery ecosystems of Evros river in North Eastern Greece and its influence upon the cultivated soil ecosystem.

PubMed

Vavias, S; Alexopoulos, A; Plessas, S; Stefanis, C; Voidarou, C; Stavropoulou, E; Bezirtzoglou, E

2011-12-01

The aim of the present study was to evaluate the microbial ecosystem of cultivated soils along the Evros river in NE Greece. Evros river together with its derivative rivers constitute the capital source of life and sustainable development of the area. Along this riverside watery ecosystem systematic agro-cultures were developed such as wheat, corn and vegetable cultures. The evaluation of the ecosystem microbial charge was conducted in both axes which are the watery ecosystem and the riverside cultivated soil area. Considerable discrimination of water quality was observed when considering chemical and microbiological parameters of the Evros river ecosystem. Ardas river possesses a better water quality than Evros and Erythropotamos, which is mainly due to the higher quantities that these two rivers accumulate from industrial, farming and urban residues leading to higher degree of pollution. An increased microbial pollution was recorded in two of the three rivers monitored and a direct relation in microbial and chemical charging between water and cultivated-soil ecosystems was observed. The protection of these ecosystems with appropriate cultivated practices and control of human and animal activities will define the homeostasis of the environmental area. Copyright © 2011 Elsevier Ltd. All rights reserved.

Drivers of Microbial Risk for Direct Potable Reuse and de Facto Reuse Treatment Schemes: The Impacts of Source Water Quality and Blending

PubMed Central

Chaudhry, Rabia M.; Hamilton, Kerry A.; Haas, Charles N.; Nelson, Kara L.

2017-01-01

Although reclaimed water for potable applications has many potential benefits, it poses concerns for chemical and microbial risks to consumers. We present a quantitative microbial risk assessment (QMRA) Monte Carlo framework to compare a de facto water reuse scenario (treated wastewater-impacted surface water) with four hypothetical Direct Potable Reuse (DPR) scenarios for Norovirus, Cryptosporidium, and Salmonella. Consumer microbial risks of surface source water quality (impacted by 0–100% treated wastewater effluent) were assessed. Additionally, we assessed risks for different blending ratios (0–100% surface water blended into advanced-treated DPR water) when source surface water consisted of 50% wastewater effluent. De facto reuse risks exceeded the yearly 10−4 infections risk benchmark while all modeled DPR risks were significantly lower. Contamination with 1% or more wastewater effluent in the source water, and blending 1% or more wastewater-impacted surface water into the advanced-treated DPR water drove the risk closer to the 10−4 benchmark. We demonstrate that de facto reuse by itself, or as an input into DPR, drives microbial risks more so than the advanced-treated DPR water. When applied using location-specific inputs, this framework can contribute to project design and public awareness campaigns to build legitimacy for DPR. PMID:28608808

Microbial counts of mealworm larvae (Tenebrio molitor) and crickets (Acheta domesticus and Gryllodes sigillatus) from different rearing companies and different production batches.

PubMed

Vandeweyer, D; Crauwels, S; Lievens, B; Van Campenhout, L

2017-02-02

The rising interest in insects for human consumption and the changing regulations in Europe require a profound insight into the food safety of insects reared and sold in Western society. The microbial quality of edible insects has only been studied occasionally. This study aimed at generating an overview of intrinsic parameters (pH, water activity and moisture content) and microbial quality of fresh mealworm larvae and crickets for several rearing companies and for several batches per rearer. In total, 21 batches obtained from 7 rearing companies were subjected to analysis of intrinsic parameters, a range of plate counts and presence-absence tests for Salmonella spp. and Listeria monocytogenes. The microbial counts of the fresh insects were generally high. Different rearing batches from a single rearing company showed differences in microbial counts which could not be explained by variations in intrinsic properties. The largest variations were found in numbers of bacterial endospores, psychrotrophs and fungi. Salmonella spp. and L. monocytogenes were not detected in any of the samples. Altogether, our study shows that large variations were found between batches from individual rearers. As a consequence, no overall differences between rearers could be observed. Copyright © 2016 Elsevier B.V. All rights reserved.

Land-use types and soil chemical properties influence soil microbial communities in the semiarid Loess Plateau region in China

PubMed Central

Tian, Qin; Taniguchi, Takeshi; Shi, Wei-Yu; Li, Guoqing; Yamanaka, Norikazu; Du, Sheng

2017-01-01

Similar land-use types usually have similar soil properties, and, most likely, similar microbial communities. Here, we assessed whether land-use types or soil chemical properties are the primary drivers of soil microbial community composition, and how changes in one part of the ecosystem affect another. We applied Ion Torrent sequencing to the bacterial and fungal communities of five different land-use (vegetation) types in the Loess Plateau of China. We found that the overall trend of soil quality was natural forest > plantation > bare land. Dominant bacterial phyla consisted of Proteobacteria (42.35%), Actinobacteria (15.61%), Acidobacteria (13.32%), Bacteroidetes (8.43%), and Gemmatimonadetes (6.0%). The dominant fungi phyla were Ascomycota (40.39%), Basidiomycota (38.01%), and Zygomycota (16.86%). The results of Canonical Correspondence Analysis (CCA) and Redundancy Analysis (RDA) based on land-use types displayed groups according to the land-use types. Furthermore, the bacterial communities were mainly organized by soil organic carbon (SOC). The fungal communities were mainly related to available phosphorus (P). The results suggested that the changes of land use type generated changes in soil chemical properties, controlling the composition of microbial community in the semiarid Loess Plateau region. The microbial community could be an indicator for soil quality with respect to ecological restoration. PMID:28349918

Land-use types and soil chemical properties influence soil microbial communities in the semiarid Loess Plateau region in China

NASA Astrophysics Data System (ADS)

Tian, Qin; Taniguchi, Takeshi; Shi, Wei-Yu; Li, Guoqing; Yamanaka, Norikazu; Du, Sheng

2017-03-01

Similar land-use types usually have similar soil properties, and, most likely, similar microbial communities. Here, we assessed whether land-use types or soil chemical properties are the primary drivers of soil microbial community composition, and how changes in one part of the ecosystem affect another. We applied Ion Torrent sequencing to the bacterial and fungal communities of five different land-use (vegetation) types in the Loess Plateau of China. We found that the overall trend of soil quality was natural forest > plantation > bare land. Dominant bacterial phyla consisted of Proteobacteria (42.35%), Actinobacteria (15.61%), Acidobacteria (13.32%), Bacteroidetes (8.43%), and Gemmatimonadetes (6.0%). The dominant fungi phyla were Ascomycota (40.39%), Basidiomycota (38.01%), and Zygomycota (16.86%). The results of Canonical Correspondence Analysis (CCA) and Redundancy Analysis (RDA) based on land-use types displayed groups according to the land-use types. Furthermore, the bacterial communities were mainly organized by soil organic carbon (SOC). The fungal communities were mainly related to available phosphorus (P). The results suggested that the changes of land use type generated changes in soil chemical properties, controlling the composition of microbial community in the semiarid Loess Plateau region. The microbial community could be an indicator for soil quality with respect to ecological restoration.

Association between Facebook dependence and poor sleep quality: a study in a sample of undergraduate students in Peru.

PubMed

Wolniczak, Isabella; Cáceres-DelAguila, José Alonso; Palma-Ardiles, Gabriela; Arroyo, Karen J; Solís-Visscher, Rodrigo; Paredes-Yauri, Stephania; Mego-Aquije, Karina; Bernabe-Ortiz, Antonio

2013-01-01

Internet can accelerate information exchange. Social networks are the most accessed especially Facebook. This kind of networks might create dependency with several negative consequences in people's life. The aim of this study was to assess potential association between Facebook dependence and poor sleep quality. A cross sectional study was performed enrolling undergraduate students of the Universidad Peruana de Ciencias Aplicadas, Lima, Peru. The Internet Addiction Questionnaire, adapted to the Facebook case, and the Pittsburgh Sleep Quality Index, were used. A global score of 6 or greater was defined as the cutoff to determine poor sleep quality. Generalized linear model were used to determine prevalence ratios (PR) and 95% confidence intervals (95%CI). A total of 418 students were analyzed; of them, 322 (77.0%) were women, with a mean age of 20.1 (SD: 2.5) years. Facebook dependence was found in 8.6% (95% CI: 5.9%-11.3%), whereas poor sleep quality was present in 55.0% (95% CI: 50.2%-59.8%). A significant association between Facebook dependence and poor sleep quality mainly explained by daytime dysfunction was found (PR = 1.31; IC95%: 1.04-1.67) after adjusting for age, sex and years in the faculty. There is a relationship between Facebook dependence and poor quality of sleep. More than half of students reported poor sleep quality. Strategies to moderate the use of this social network and to improve sleep quality in this population are needed.

RELATIONSHIPS BETWEEN CULTURABLE SOIL MICROBIAL POPULATIONS AND GROSS NITROGEN TRANSFORMATION PROCESSES IN A CLAY LOAM SOIL ACROSS ECOSYSTEMS

EPA Science Inventory

The size and quality of soil organic matter (SOM) pool can vary between ecosystems and can affect many soil properties. The objective of this study was to examine the relationship between gross N transformation rates and microbial populations and to investigate the role that SOM...

Runoff delay exerts a strong control on the field-scale removal of manure-borne fecal bacteria with runoff

USDA-ARS?s Scientific Manuscript database

The microbial safety of surface waters is an ongoing issue which is threatened by the transport of manure-borne bacteria to water sources used for irrigation or recreation. Predictive modeling has become an effective tool to forecast the microbial quality of water duringprecipitation events, however...

Microbial community structure is affected by cropping sequences and poultry litter under long-term no-tillage

USDA-ARS?s Scientific Manuscript database

Soil microorganisms play essential roles in soil organic matter dynamics and nutrient cycling in agroecosystems and have been used as soil quality indicators. The response of soil microbial communities to land management is complex and the long-term impacts of cropping systems on soil microbes is l...

Differential Decay of Cattle-associated Fecal Indicator Bacteria and Microbial Source Tracking Markers in Fresh and Marine Water

EPA Science Inventory

Background: Fecal indicator bacteria (FIB) have a long history of use in the assessment of the microbial quality of recreational waters. However, quantification of FIB provides no information about the pollution source(s) and relatively little is known about their fate in the amb...

77 FR 3263 - Agency Information Collection Activities; Submission to OMB for Review and Approval; Comment...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-23

... index listing of the contents of the docket, and to access those documents in the docket that are... recreational water quality; assess, manage, and communicate health risks from waterborne microbial... public exposure to microbial pathogens. To qualify for a BEACH Act Grant, a state must submit information...

Human virus and microbial indicator occurrence in public-supply groundwater systems: meta-analysis of 12 international studies

USDA-ARS?s Scientific Manuscript database

Groundwater quality is often evaluated using microbial indicators. This study examines data from 12 international groundwater studies (conducted 1992–2013). Sites were chosen from 718 public drinking-water systems with a range of hydrogeological conditions. Focus was on testing the value of indicato...

Effects of forest management practices in temperate beech forests on bacterial and fungal communities involved in leaf litter degradation.

PubMed

Purahong, Witoon; Kapturska, Danuta; Pecyna, Marek J; Jariyavidyanont, Katalee; Kaunzner, Jennifer; Juncheed, Kantida; Uengwetwanit, Tanaporn; Rudloff, Renate; Schulz, Elke; Hofrichter, Martin; Schloter, Michael; Krüger, Dirk; Buscot, François

2015-05-01

Forest management practices (FMPs) significantly influence important ecological processes and services in Central European forests, such as leaf litter decomposition and nutrient cycling. Changes in leaf litter diversity, and thus, its quality as well as microbial community structure and function induced by different FMPs were hypothesized to be the main drivers causing shifts in decomposition rates and nutrient release in managed forests. In a litterbag experiment lasting 473 days, we aimed to investigate the effects of FMPs (even-aged timber management, selective logging and unmanaged) on bacterial and fungal communities involved in leaf litter degradation over time. Our results showed that microbial communities in leaf litter were strongly influenced by both FMPs and sampling date. The results from nonmetric multidimensional scaling (NMDS) ordination revealed distinct patterns of bacterial and fungal successions over time in leaf litter. We demonstrated that FMPs and sampling dates can influence a range of factors, including leaf litter quality, microbial macronutrients, and pH, which significantly correlate with microbial community successions.

The mechanisms of granulation of activated sludge in wastewater treatment, its optimization, and impact on effluent quality.

PubMed

Wilén, Britt-Marie; Liébana, Raquel; Persson, Frank; Modin, Oskar; Hermansson, Malte

2018-06-01

Granular activated sludge has gained increasing interest due to its potential in treating wastewater in a compact and efficient way. It is well-established that activated sludge can form granules under certain environmental conditions such as batch-wise operation with feast-famine feeding, high hydrodynamic shear forces, and short settling time which select for dense microbial aggregates. Aerobic granules with stable structure and functionality have been obtained with a range of different wastewaters seeded with different sources of sludge at different operational conditions, but the microbial communities developed differed substantially. In spite of this, granule instability occurs. In this review, the available literature on the mechanisms involved in granulation and how it affects the effluent quality is assessed with special attention given to the microbial interactions involved. To be able to optimize the process further, more knowledge is needed regarding the influence of microbial communities and their metabolism on granule stability and functionality. Studies performed at conditions similar to full-scale such as fluctuation in organic loading rate, hydrodynamic conditions, temperature, incoming particles, and feed water microorganisms need further investigations.

Biotechnological Approach To Preserve Fresh Pasta Quality.

PubMed

Angiolillo, L; Conte, A; Del Nobile, M A

2017-12-01

Fresh pasta is highly susceptible to microbial contamination because of its high water activity and nutrient content. In this study, a new biopreservation system was examined that consists of an active sodium alginate solution containing Lactobacillus reuteri and glycerol, which was added during the production process of pasta. Our aim was to extend the fresh pasta shelf life by the in situ production of reuterin, thereby avoiding the use of thermal treatments that generally compromise food sensory characteristics. Two experimental studies were carried out with the product packaged under either ordinary or modified atmospheric conditions. Microbiological and sensory quality indices were monitored to determine the effectiveness of biopreservation on product quality during storage. The use of the active solution with L. reuteri and glycerol during the production process of pasta improved both microbial and sensory quality, particularly when combined with modified atmosphere.

Connecting Water Quality With Air Quality Through Microbial Aerosols

NASA Astrophysics Data System (ADS)

Dueker, M. Elias

Aerosol production from surface waters results in the transfer of aquatic materials (including nutrients and bacteria) to air. These materials can then be transported by onshore winds to land, representing a biogeochemical connection between aquatic and terrestrial systems not normally considered. In urban waterfront environments, this transfer could result in emissions of pathogenic bacteria from contaminated waters. Despite the potential importance of this link, sources, near-shore deposition, identity and viability of microbial aerosols are largely uncharacterized. This dissertation focuses on the environmental and biological mechanisms that define this water-air connection, as a means to build our understanding of the biogeochemical, biogeographical, and public health implications of the transfer of surface water materials to the near-shore environment in both urban and non-urban environments. The effects of tidal height, wind speed and fog on coastal aerosols and microbial content were first quantified on a non-urban coast of Maine, USA. Culture-based, culture-independent, and molecular methods were used to simultaneously sample microbial aerosols while monitoring meteorological parameters. Aerosols at this site displayed clear marine influence and high concentrations of ecologically-relevant nutrients. Coarse aerosol concentrations significantly increased with tidal height, onshore wind speed, and fog presence. Tidal height and fog presence did not significantly influence total microbial aerosol concentrations, but did have a significant effect on culturable microbial aerosol fallout. Molecular analyses of the microbes settling out of near-shore aerosols provided further evidence of local ocean to terrestrial transport of microbes. Aerosol and surface ocean bacterial communities shared species and in general were dominated by organisms previously sampled in marine environments. Fog presence strengthened the microbial connection between water and land through air by increasing microbial aerosol settling rates and enhancing viability of aerosolized marine microbes. Using methods developed for the non-urban site, the role of local environment and winds in mediating water-air connections was further investigated in the urban environment. The local environment, including water surfaces, was an important source of microbial aerosols at urban sites. Large portions of the urban waterfront microbial aerosol communities were aquatic and, at a highly polluted Superfund waterfront, were closely related to bacteria previously described in environments contaminated with hydrocarbons, heavy metals, sewage and other industrial waste. Culturable urban aerosols and surface waters contained bacterial genera known to include human pathogens and asthma agents. High onshore winds strengthened this water-air connection by playing both a transport and production role. The microbial connection between water and air quality outlined by this dissertation highlights the need for information on the mechanisms that deliver surface water materials to terrestrial systems on a much larger scale. Moving from point measurements to landscape-level analyses will allow for the quantitative assessment of implications for this microbial water-air-land transfer in both urban and non-urban arenas.

Mapping microbial ecosystems and spoilage-gene flow in breweries highlights patterns of contamination and resistance

PubMed Central

Bokulich, Nicholas A; Bergsveinson, Jordyn; Ziola, Barry; Mills, David A

2015-01-01

Distinct microbial ecosystems have evolved to meet the challenges of indoor environments, shaping the microbial communities that interact most with modern human activities. Microbial transmission in food-processing facilities has an enormous impact on the qualities and healthfulness of foods, beneficially or detrimentally interacting with food products. To explore modes of microbial transmission and spoilage-gene frequency in a commercial food-production scenario, we profiled hop-resistance gene frequencies and bacterial and fungal communities in a brewery. We employed a Bayesian approach for predicting routes of contamination, revealing critical control points for microbial management. Physically mapping microbial populations over time illustrates patterns of dispersal and identifies potential contaminant reservoirs within this environment. Habitual exposure to beer is associated with increased abundance of spoilage genes, predicting greater contamination risk. Elucidating the genetic landscapes of indoor environments poses important practical implications for food-production systems and these concepts are translatable to other built environments. DOI: http://dx.doi.org/10.7554/eLife.04634.001 PMID:25756611

Diversity of the human intestinal microbial flora.

PubMed

Eckburg, Paul B; Bik, Elisabeth M; Bernstein, Charles N; Purdom, Elizabeth; Dethlefsen, Les; Sargent, Michael; Gill, Steven R; Nelson, Karen E; Relman, David A

2005-06-10

The human endogenous intestinal microflora is an essential "organ" in providing nourishment, regulating epithelial development, and instructing innate immunity; yet, surprisingly, basic features remain poorly described. We examined 13,355 prokaryotic ribosomal RNA gene sequences from multiple colonic mucosal sites and feces of healthy subjects to improve our understanding of gut microbial diversity. A majority of the bacterial sequences corresponded to uncultivated species and novel microorganisms. We discovered significant intersubject variability and differences between stool and mucosa community composition. Characterization of this immensely diverse ecosystem is the first step in elucidating its role in health and disease.

Quality change of apple slices coated with Aloe vera gel during storage.

PubMed

Song, Hye-Yeon; Jo, Wan-Shin; Song, Nak-Bum; Min, Sea C; Song, Kyung Bin

2013-06-01

Fresh-cut apples are easily susceptible to browning and microbial spoilage. In this study, an edible coating prepared from Aloe vera gel containing antibrowning solution was applied to preserve the quality of fresh-cut apples during storage. Fresh-cut apples were treated with both an Aloe vera gel and an Aloe vera gel containing 0.5% cysteine and then stored at 4 °C for 16 d. The color, firmness, weight loss, soluble solid content, titratable acidity, microbial analysis, and sensory evaluation were analyzed during storage. Fresh-cut apples coated with the Aloe vera gel showed delayed browning and reduced weight loss and softening compared to the control. The Aloe vera gel coating was also effective in reducing the populations of the total aerobic bacteria and yeast and molds. In particular, Aloe vera gel containing 0.5% cysteine was most effective in delaying browning and the reduction of microbial populations among the treatments. These results suggest that an Aloe vera gel coating can be used for maintaining the quality of fresh-cut apples. © 2013 Institute of Food Technologists®

Associations between poor sleep quality and psychosocial stress with obesity in reproductive-age women of lower socioeconomic status.

PubMed

Tom, Sarah E; Berenson, Abbey B

2013-01-01

Prior studies have not examined the role of psychosocial stress in the relationship between poor sleep quality and obesity among women of lower socioeconomic status (SES). We tested the following hypotheses in a sample of reproductive-age women of lower SES: 1) Poor sleep quality is related to increased risk of obesity, and 2) psychosocial stress confounds this association between poor sleep quality and obesity. A total of 927 women age 16 to 40 years attending public health clinics in Southeastern Texas provided information on the Pittsburgh Sleep Quality Index and sociodemographic and health characteristics, including the Perceived Stress Scale. Height, weight, and waist circumference (WC) were measured in clinic. A series of models examined the associations between sleep disturbance, perceived stress, and weight outcomes, accounting for potential confounding factors. Nearly 30% of women were overweight, and 35% were obese. Half of women had a WC of greater than 35 inches. Most women had poor sleep quality and high levels of stress. Sleep quality and perceived stress were not related to body mass index category or WC in models that adjusted for age and race/ethnicity. Adjusting for potential confounding factors did not alter results. Perceived stress did not modify the association between sleep quality and weight outcomes. Poor sleep quality and psychosocial stress were not related to weight in reproductive-aged women of lower SES. However, poor sleep quality, high stress, overweight, and obesity were common in this group. Copyright © 2013 Jacobs Institute of Women's Health. Published by Elsevier Inc. All rights reserved.

Modeling microbial spoilage and quality of gilthead seabream fillets: combined effect of osmotic pretreatment, modified atmosphere packaging, and nisin on shelf life.

PubMed

Tsironi, Theofania N; Taoukis, Petros S

2010-05-01

The objective of the study was the kinetic modeling of the effect of storage temperature on the quality and shelf life of chilled fish, modified atmosphere-packed (MAP), and osmotically pretreated with the addition of nisin as antimicrobial agent. Fresh gilthead seabream (Sparus aurata) fillets were osmotically treated with 50% high dextrose equivalent maltodextrin (DE 47) plus 5% NaCl. Water loss, solid gain, salt content, and water activity were monitored throughout treatment and treatment conditions were selected for the shelf life study. Untreated and osmotically pretreated slices with and without nisin (2 x 10(4) IU/100 g osmotic solution), packed in air or modified atmosphere (50% CO(2)-50% air), and stored at controlled isothermal conditions (0, 5, 10, and 15 degrees C) were studied. Quality assessment and modeling were based on growth of several microbial indices, total volatile nitrogen, trimethylamine nitrogen, lipid oxidation (TBARS), and sensory scoring. Temperature dependence of quality loss rates was modeled by the Arrhenius equation, validated under dynamic conditions. Pretreated samples showed improved quality stability during subsequent refrigerated storage, in terms of microbial growth, chemical changes, and organoleptic degradation. Osmotic pretreatment with the addition of nisin in combination with MAP was the most effective treatment resulting in significant shelf life extension of gilthead seabream fillets (48 days compared to 10 days for the control at 0 degrees C).

Microbial Quality and Shelf Life of Blueberry Purée Developed Using Cavitation Technology.

PubMed

Fan, Lihua; Martynenko, Alex; Doucette, Craig; Hughes, Timothy; Fillmore, Sherry

2018-03-01

Blueberry purée was developed using hydrodynamic cavitation technology. The product was made from entire blueberries without adding any food additives. In this study, microbial reduction following each processing stage (at the industry setting) and after product pasteurization at 86, 88, 90, 92, 94, and 96 °C was investigated. Microbial quality including total plate counts, yeast and molds, and heat-resistant molds counts was determined. Shelf life of pasteurized products stored for up to 24 weeks at room temperature were assessed for microbial quality, soluble solids (°Brix), titratable acidity (citric acid %), pH, viscosity (cP) and flow rate (cm/30 s). Our results indicated that heat-resistant molds, initially present in frozen blueberries with counts at 2.03 log CFU/200g, were totally inactivated at 94 to 96 °C with 1 to 2 min holding time. Shelf life study showed that no product spoilage was caused by bacteria, yeasts and heat-resistant molds along with non-significant changes of textural characteristics. This study provided useful information for the food industry to develop variety of fruit purée products with no wastes of fruit materials. This study provides useful information for the food industry to develop safe liquid food products using cavitation technology without wasting any raw materials. © 2018 Institute of Food Technologists®.

Effect of a residue after evaporation from industrial vitamin C fermentation on chemical and microbial properties of alkali-saline soil.

PubMed

Kong, Tao; Xu, Hui; Wang, Zhenyu; Sun, Hao; Wang, Lihua

2014-07-01

Residue after evaporation (RAE) from industrial vitamin C fermentation is emitted as a waste product at an amount of 60,000 tons per year in China. The disposal of RAE is difficult because of its high chemical oxygen demand (1.17×10(6) mg/l) and low pH (0.27). We hypothesized that RAE could be used as an ameliorant for alkali-saline soils, and tried to verify it by carrying out a pot experiment of pakchoi cultivation and to explore its effect on soil chemical and microbial properties. The results showed that pakchoi yield was increased by 28.13% and pakchoi quality was also enhanced under RAE treatment. The improved chemical and microbial properties of treated soil were also observed: soil pH was decreased from 9.19 to 9.03; total organic carbon, available phosphorus and available potassium were increased by 49.15%, 34.91% and 42.02%, respectively; number of culturable bacteria, actinomycetes and fungi, microbial biomass carbon and enzyme activity number were improved by 52.97%, 104.05%, 79.09%, 57.82% and 31.16%, respectively. These results suggested the residue application led to an improved soil quality and subsequently a higher yield and quality of pakchoi. This study provided a strong evidence for the feasibility of RAE as an ameliorant for alkali-saline soil.

Estimates of microbial quality and concentration of copper in distributed drinking water are highly dependent on sampling strategy.

PubMed

Lehtola, Markku J; Miettinen, Ilkka T; Hirvonen, Arja; Vartiainen, Terttu; Martikainen, Pertti J

2007-12-01

The numbers of bacteria generally increase in distributed water. Often household pipelines or water fittings (e.g., taps) represent the most critical location for microbial growth in water distribution systems. According to the European Union drinking water directive, there should not be abnormal changes in the colony counts in water. We used a pilot distribution system to study the effects of water stagnation on drinking water microbial quality, concentration of copper and formation of biofilms with two commonly used pipeline materials in households; copper and plastic (polyethylene). Water stagnation for more than 4h significantly increased both the copper concentration and the number of bacteria in water. Heterotrophic plate counts were six times higher in PE pipes and ten times higher in copper pipes after 16 h of stagnation than after only 40 min stagnation. The increase in the heterotrophic plate counts was linear with time in both copper and plastic pipelines. In the distribution system, bacteria originated mainly from biofilms, because in laboratory tests with water, there was only minor growth of bacteria after 16 h stagnation. Our study indicates that water stagnation in the distribution system clearly affects microbial numbers and the concentration of copper in water, and should be considered when planning the sampling strategy for drinking water quality control in distribution systems.

Microbial Kinetic Model for the Degradation of Poorly Soluble Organic Materials

EPA Science Inventory

A novel mechanistic model is presented that describes the aerobic biodegradation kinetics of soybean biodiesel and petroleum diesel in batch experiments. The model was built on the assumptions that biodegradation takes place in the aqueous phase according to Monod kinetics, and ...

Microbial Contamination of Drinking Water and Human Health from Community Water Systems.

PubMed

Ashbolt, Nicholas J

2015-03-01

A relatively short list of reference viral, bacterial and protozoan pathogens appears adequate to assess microbial risks and inform a system-based management of drinking waters. Nonetheless, there are data gaps, e.g. human enteric viruses resulting in endemic infection levels if poorly performing disinfection and/or distribution systems are used, and the risks from fungi. Where disinfection is the only treatment and/or filtration is poor, cryptosporidiosis is the most likely enteric disease to be identified during waterborne outbreaks, but generally non-human-infectious genotypes are present in the absence of human or calf fecal contamination. Enteric bacteria may dominate risks during major fecal contamination events that are ineffectively managed. Reliance on culture-based methods exaggerates treatment efficacy and reduces our ability to identify pathogens/indicators; however, next-generation sequencing and polymerase chain reaction approaches are on the cusp of changing that. Overall, water-based Legionella and non-tuberculous mycobacteria probably dominate health burden at exposure points following the various societal uses of drinking water.

The effect of in-stream activities on the Njoro River, Kenya. Part II: Microbial water quality

NASA Astrophysics Data System (ADS)

Yillia, Paul T.; Kreuzinger, Norbert; Mathooko, Jude M.

The influence of periodic in-stream activities of people and livestock on the microbial water quality of the Njoro River in Kenya was monitored at two disturbed pools (Turkana Flats and Njoro Bridge) at the middle reaches. A total of 96 sets of samples were obtained from the two pools in six weeks during dry weather (January-April) in 2006. On each sampling day, two trips were made before and during in-stream activities and on each trip, two sets of samples were collected upstream and downstream of activities. This schedule was repeated four times each for Wednesday, Saturday and Sunday. Samples were processed for heterotrophic plate count bacteria (HPC), total coliform (TC), presumptive Escherichia coli and presumptive Enterococci. Additional samples were analysed for total suspended solids (TSS), turbidity, BOD 5 and ammonium-N. The microbial water quality deteriorated significant ( p < 0.05) downstream during activities at both pools. A similar trend was observed with the chemical indicators (TSS, turbidity, BOD 5 and ammonium-N). The two groups of indicators demonstrated high capacity for site segregation based on pollution levels. Pollution levels for specific days were not significantly different ( p > 0.05). This was incompatible with the variability of in-stream activities with specific days. The pooled data was explained largely by three significant principal components - recent pollution (PC1), metabolic activity (PC2) and residual pollution (PC3). It was concluded that the empirical site parity/disparity in the levels of microbial and non-microbial indicators reflected the diurnal periodicity of in-stream activities and the concomitant pollution they caused. However, microbial source tracking studies are required to distinguish faecal sources. In the meantime, measures should be undertaken to regulate in-stream activities along the stream and minimize the movement of livestock in the catchment.

Effects of nutrient enrichment on the decomposition of wood and associated microbial activity in streams

USGS Publications Warehouse

Gulis, V.; Rosemond, A.D.; Suberkropp, K.; Weyers, H.S.; Benstead, J.P.

2004-01-01

1. We determined the effects of nutrient enrichment on wood decomposition rates and microbial activity during a 3-year study in two headwater streams at Coweeta Hydrologic Laboratory, NC, U.S.A. After a 1-year pretreatment period, one of the streams was continuously enriched with inorganic nutrients (nitrogen and phosphorus) for 2 years while the other stream served as a reference. We determined the effects of enrichment on both wood veneers and sticks, which have similar carbon quality but differ in physical characteristics (e.g. surface area to volume ratios, presence of bark) that potentially affect microbial colonisation and activity. 2. Oak wood veneers (0.5 mm thick) were placed in streams monthly and allowed to decompose for approximately 90 days. Nutrient addition stimulated ash-free dry mass loss and increased mean nitrogen content, fungal biomass and microbial respiration on veneers in the treatment stream compared with the reference. The magnitude of the response to enrichment was great, with mass loss 6.1 times, and per cent N, fungal biomass and microbial respiration approximately four times greater in the treatment versus reference stream. 3. Decomposition rate and nitrogen content of maple sticks (ca. 1-2 cm diameter) also increased; however, the effect was less pronounced than for veneers. Wood response overall was greater than that determined for leaves in a comparable study, supporting the hypothesis that response to enrichment may be greater for lower quality organic matter (high C:N) than for higher quality (low C:N) substrates. 4. Our results show that moderate nutrient enrichment can profoundly affect decomposition rate and microbial activity on wood in streams. Thus, the timing and availability of wood that provides retention, structure, attachment sites and food in stream ecosystems may be affected by nutrient concentrations raised by human activities.

Application of microwaves for microbial load reduction in black pepper (Piper nigrum L.).

PubMed

Jeevitha, G Chengaiyan; Sowbhagya, H Bogegowda; Hebbar, H Umesh

2016-09-01

Black pepper (Piper nigrum L.) is exposed to microbial contamination which could potentially create public health risk and also rejection of consignments in the export market due to non-adherance to microbial safety standards. The present study investigates the use of microwave (MW) radiation for microbial load reduction in black pepper and analyses the effect on quality. Black pepper was exposed to MWs at two different power levels (663 and 800 W) at an intensity of 40 W g(-1) for different time intervals (1-15 min) and moisture content (110 and 260 g kg(-1) on a wet basis). The exposure of black pepper to MWs at 663 W for 12.5 min was found to be sufficient to reduce the microbial load to the permissible level suggested by the International Commission on Microbiological Specifications for Foods and the European Spice Association. The retention of volatile oil, piperine and resin was 91.3 ± 0.03, 87.6 ± 0.02 and 90.7 ± 0.05%, respectively, in MW-treated black pepper. The final moisture content after MW treatment was found to be 100 ± 1 g kg(-1) for black pepper containing initial moisture of 260 ± 3 g kg(-1) . These results suggest that MW heating can be effectively used for microbial load reduction of black pepper without a significant loss in product quality. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Association of suicidal ideation with poor sleep quality among Ethiopian adults.

PubMed

Gelaye, Bizu; Okeiga, Joseph; Ayantoye, Idris; Berhane, Hanna Y; Berhane, Yemane; Williams, Michelle A

2016-12-01

The objective of this study was to examine the extent to which poor sleep quality is associated with suicidal ideation among Ethiopian adults. A cross-sectional study was conducted among 1054 adults attending outpatient clinical facilities in Ethiopia. Standardized questionnaires were utilized to collect data on demographics, sleep quality, lifestyle, and depression status. Depression and suicidal ideation were assessed using the Patient Health Questionnaire-9 (PHQ-9), while the Pittsburgh Sleep Quality Index (PSQI) questionnaire was utilized to assess sleep quality. Multivariate logistic regression models were fit to estimate adjusted odds ratio (AOR) and 95 % confidence intervals (95 % CI). The prevalence of suicidal ideation was 24.3 % while poor sleep quality (PSQI global score of >5 vs. ≤5) was endorsed by 60.2 % of participants. After adjustment for confounders including depression, poor sleep quality was associated with more than 3-fold increased odds of suicidal ideation (AOR = 3.59; 95 % CI 2.34-5.51). When assessed as a continuous variable, each 1-unit increase in the global PSQI score resulted in a 20 % increased odds for suicidal ideation, even after adjusting for depression (AOR = 1.20; 95 % CI 1.14-1.27). Participants with both poor sleep quality and depression had much higher odds (AOR = 23.22, 95 % CI 14.10-38.28) of suicidal ideation as compared with those who had good sleep quality and no depression although inferences from this analysis are limited due to the wide 95 % CI. Suicidal ideation and poor sleep quality are highly prevalent. Individuals with poor sleep quality have higher odds of suicidal ideation. If confirmed, mental health services need to address sleep disturbances seriously to prevent suicidal episodes.

Association of Suicidal Ideation with Poor Sleep Quality among Ethiopian Adults

PubMed Central

Gelaye, Bizu; Okeiga, Joseph; Ayantoye, Idris; Berhane, Hanna Y.; Berhane, Yemane; Williams, Michelle A.

2016-01-01

Objective To examine the extent to which poor sleep quality is associated with suicidal ideation among Ethiopian adults. Methods A cross-sectional study was conducted among 1,054 adults attending outpatient clinical facilities in Ethiopia. Standardized questionnaires were utilized to collect data on demographics, sleep quality, lifestyle, and depression status. Depression and suicidal ideation were assessed using the Patient Health Questionnaire-9 (PHQ-9), while the Pittsburgh Sleep Quality Index (PSQI) questionnaire was utilized to assess sleep quality. Multivariate logistic regression models were fit to estimate adjusted odds ratio (AOR) and 95% confidence intervals (95%CI). Results The prevalence of suicidal ideation was 24.3% while poor sleep quality (PSQI global score of > 5vs. ≤5) was endorsed by 60.2% of participants. After adjustment for confounders including depression, poor sleep quality was associated with more than 3-fold increased odds of suicidal ideation (AOR=3.46; 95%CI 2.27–5.26). When assessed as a continuous variable, each 1-unit increase in the global PSQI score resulted in a 20% increased odds for suicidal ideation, even after adjusting for depression (AOR=1.20; 95%CI 1.14–1.27). Participants with both poor sleep quality and depression had much higher odds (AOR=24.9, 95% CI 15.2–40.8) of suicidal ideation as compared with those who had good sleep quality and no depression although inferences from this analysis are limited due to the wide 95%CI. Conclusion Suicidal ideation and poor sleep quality are highly prevalent. Individuals with poor sleep quality have higher odds of suicidal ideation. If confirmed, mental health services need to address sleep disturbances seriously to prevent suicidal episodes. PMID:27771845

Microbial and diagenetic steps leading to the mineralisation of Great Salt Lake microbialites

NASA Astrophysics Data System (ADS)

Pace, Aurélie; Bourillot, Raphaël; Bouton, Anthony; Vennin, Emmanuelle; Galaup, Serge; Bundeleva, Irina; Patrier, Patricia; Dupraz, Christophe; Thomazo, Christophe; Sansjofre, Pierre; Yokoyama, Yusuke; Franceschi, Michel; Anguy, Yannick; Pigot, Léa; Virgone, Aurélien; Visscher, Pieter T.

2016-08-01

Microbialites are widespread in modern and fossil hypersaline environments, where they provide a unique sedimentary archive. Authigenic mineral precipitation in modern microbialites results from a complex interplay between microbial metabolisms, organic matrices and environmental parameters. Here, we combined mineralogical and microscopic analyses with measurements of metabolic activity in order to characterise the mineralisation of microbial mats forming microbialites in the Great Salt Lake (Utah, USA). Our results show that the mineralisation process takes place in three steps progressing along geochemical gradients produced through microbial activity. First, a poorly crystallized Mg-Si phase precipitates on alveolar extracellular organic matrix due to a rise of the pH in the zone of active oxygenic photosynthesis. Second, aragonite patches nucleate in close proximity to sulfate reduction hotspots, as a result of the degradation of cyanobacteria and extracellular organic matrix mediated by, among others, sulfate reducing bacteria. A final step consists of partial replacement of aragonite by dolomite, possibly in neutral to slightly acidic porewater. This might occur due to dissolution-precipitation reactions when the most recalcitrant part of the organic matrix is degraded. The mineralisation pathways proposed here provide pivotal insight for the interpretation of microbial processes in past hypersaline environments.

Viable cold-tolerant iron-reducing microorganisms in geographically diverse subglacial environments

NASA Astrophysics Data System (ADS)

Nixon, Sophie L.; Telling, Jon P.; Wadham, Jemma L.; Cockell, Charles S.

2017-03-01

Subglacial environments are known to harbour metabolically diverse microbial communities. These microbial communities drive chemical weathering of underlying bedrock and influence the geochemistry of glacial meltwater. Despite its importance in weathering reactions, the microbial cycling of iron in subglacial environments, in particular the role of microbial iron reduction, is poorly understood. In this study we address the prevalence of viable iron-reducing microorganisms in subglacial sediments from five geographically isolated glaciers. Iron-reducing enrichment cultures were established with sediment from beneath Engabreen (Norway), Finsterwalderbreen (Svalbard), Leverett and Russell glaciers (Greenland), and Lower Wright Glacier (Antarctica). Rates of iron reduction were higher at 4 °C compared with 15 °C in all but one duplicated second-generation enrichment culture, indicative of cold-tolerant and perhaps cold-adapted iron reducers. Analysis of bacterial 16S rRNA genes indicates Desulfosporosinus were the dominant iron-reducing microorganisms in low-temperature Engabreen, Finsterwalderbreen and Lower Wright Glacier enrichments, and Geobacter dominated in Russell and Leverett enrichments. Results from this study suggest microbial iron reduction is widespread in subglacial environments and may have important implications for global biogeochemical iron cycling and export to marine ecosystems.

Life in the "plastisphere": microbial communities on plastic marine debris.

PubMed

Zettler, Erik R; Mincer, Tracy J; Amaral-Zettler, Linda A

2013-07-02

Plastics are the most abundant form of marine debris, with global production rising and documented impacts in some marine environments, but the influence of plastic on open ocean ecosystems is poorly understood, particularly for microbial communities. Plastic marine debris (PMD) collected at multiple locations in the North Atlantic was analyzed with scanning electron microscopy (SEM) and next-generation sequencing to characterize the attached microbial communities. We unveiled a diverse microbial community of heterotrophs, autotrophs, predators, and symbionts, a community we refer to as the "Plastisphere". Pits visualized in the PMD surface conformed to bacterial shapes suggesting active hydrolysis of the hydrocarbon polymer. Small-subunit rRNA gene surveys identified several hydrocarbon-degrading bacteria, supporting the possibility that microbes play a role in degrading PMD. Some Plastisphere members may be opportunistic pathogens (the authors, unpublished data) such as specific members of the genus Vibrio that dominated one of our plastic samples. Plastisphere communities are distinct from surrounding surface water, implying that plastic serves as a novel ecological habitat in the open ocean. Plastic has a longer half-life than most natural floating marine substrates, and a hydrophobic surface that promotes microbial colonization and biofilm formation, differing from autochthonous substrates in the upper layers of the ocean.

Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input

PubMed Central

Armstrong, Alacia; Valverde, Angel; Ramond, Jean-Baptiste; Makhalanyane, Thulani P.; Jansson, Janet K.; Hopkins, David W.; Aspray, Thomas J.; Seely, Mary; Trindade, Marla I.; Cowan, Don A.

2016-01-01

The temporal dynamics of desert soil microbial communities are poorly understood. Given the implications for ecosystem functioning under a global change scenario, a better understanding of desert microbial community stability is crucial. Here, we sampled soils in the central Namib Desert on sixteen different occasions over a one-year period. Using Illumina-based amplicon sequencing of the 16S rRNA gene, we found that α-diversity (richness) was more variable at a given sampling date (spatial variability) than over the course of one year (temporal variability). Community composition remained essentially unchanged across the first 10 months, indicating that spatial sampling might be more important than temporal sampling when assessing β-diversity patterns in desert soils. However, a major shift in microbial community composition was found following a single precipitation event. This shift in composition was associated with a rapid increase in CO2 respiration and productivity, supporting the view that desert soil microbial communities respond rapidly to re-wetting and that this response may be the result of both taxon-specific selection and changes in the availability or accessibility of organic substrates. Recovery to quasi pre-disturbance community composition was achieved within one month after rainfall. PMID:27680878

Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input.

PubMed

Armstrong, Alacia; Valverde, Angel; Ramond, Jean-Baptiste; Makhalanyane, Thulani P; Jansson, Janet K; Hopkins, David W; Aspray, Thomas J; Seely, Mary; Trindade, Marla I; Cowan, Don A

2016-09-29

The temporal dynamics of desert soil microbial communities are poorly understood. Given the implications for ecosystem functioning under a global change scenario, a better understanding of desert microbial community stability is crucial. Here, we sampled soils in the central Namib Desert on sixteen different occasions over a one-year period. Using Illumina-based amplicon sequencing of the 16S rRNA gene, we found that α-diversity (richness) was more variable at a given sampling date (spatial variability) than over the course of one year (temporal variability). Community composition remained essentially unchanged across the first 10 months, indicating that spatial sampling might be more important than temporal sampling when assessing β-diversity patterns in desert soils. However, a major shift in microbial community composition was found following a single precipitation event. This shift in composition was associated with a rapid increase in CO 2 respiration and productivity, supporting the view that desert soil microbial communities respond rapidly to re-wetting and that this response may be the result of both taxon-specific selection and changes in the availability or accessibility of organic substrates. Recovery to quasi pre-disturbance community composition was achieved within one month after rainfall.

Study of generic quality of life in patients operated on for post-prostatectomy incontinence.

PubMed

Holm, Henriette Veiby; Fosså, Sophie D; Hedlund, Hans; Dahl, Alv A

2013-09-01

The relationship between urological and psychosocial variables, and generic quality of life in patients operated on for post-prostatectomy incontinence has hardly been studied, and our aim was to investigate this relationship. Patients who had an artificial urinary sphincter AMS800 (n = 100) implanted between January 2002 and June 2010 were invited to complete a mailed questionnaire covering demographic data including work ability, urinary and sexual function, anxiety/depression, and generic quality of life. Poor quality of life was defined as a score <40 on either the physical or the mental Short Form 12 summary scales. Of 85 compliant patients, 30 (35%) reported poor generic quality of life and 55 (65%) reported better quality of life at a median follow-up time of 26 months (range 6-104 months). The poor quality of life group showed significantly more overall urinary and sexual problems, and more men had undergone surgical revisions compared with the better quality of life group. Levels of anxiety and depression were significantly higher, and work ability was lower in the poor quality of life group. In multivariate logistic regression models, increased level of depression and impaired work ability, inability to reach orgasm, and not recommending the operation remained significantly associated with poor quality of life. Poor generic quality of life after surgery for post-prostatectomy incontinence is more strongly associated with reduced work ability and depression rather than urinary and sexual problems. © 2013 The Japanese Urological Association.

Comparison of obese adults with poor versus good sleep quality during a functional neuroimaging delay discounting task: A pilot study.

PubMed

Martin, Laura E; Pollack, Lauren; McCune, Ashley; Schulte, Erica; Savage, Cary R; Lundgren, Jennifer D

2015-10-30

This study aimed to determine if obese adults with poor versus good sleep quality demonstrate reduced self-regulatory capacity and different patterns of neural activation when making impulsive monetary choices. Six obese, good quality sleepers (M age=44.7 years, M BMI=38.1 kg/m(2)) were compared to 13 obese, poor quality sleepers (M age=42.6, M BMI=39.2 kg/m(2)) on sleep and eating behavior and brain activation in prefrontal and insular regions while engaging in a delay discounting task during functional magnetic resonance imaging (fMRI). Poor quality sleepers demonstrated significantly lower brain activation in the right inferior frontal gyrus, right middle frontal gyrus, and bilateral insula when making immediate and smaller (impulsive) monetary choices compared to the baseline condition. Behaviorally, poor compared to good quality sleepers reported higher scores in the night eating questionnaire. Obese adults with poor sleep quality demonstrate decreased brain activation in multiple regions that regulate cognitive control and interceptive awareness, possibly reducing self-regulatory capacity when making immediately gratifying decisions. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Anaerobic Methane Oxidation Driven by Microbial Reduction of Natural Organic Matter in a Tropical Wetland

PubMed Central

Valenzuela, Edgardo I.; Prieto-Davó, Alejandra; López-Lozano, Nguyen E.; Hernández-Eligio, Alberto; Vega-Alvarado, Leticia; Juárez, Katy; García-González, Ana Sarahí; López, Mercedes G.

2017-01-01

ABSTRACT Wetlands constitute the main natural source of methane on Earth due to their high content of natural organic matter (NOM), but key drivers, such as electron acceptors, supporting methanotrophic activities in these habitats are poorly understood. We performed anoxic incubations using freshly collected sediment, along with water samples harvested from a tropical wetland, amended with 13C-methane (0.67 atm) to test the capacity of its microbial community to perform anaerobic oxidation of methane (AOM) linked to the reduction of the humic fraction of its NOM. Collected evidence demonstrates that electron-accepting functional groups (e.g., quinones) present in NOM fueled AOM by serving as a terminal electron acceptor. Indeed, while sulfate reduction was the predominant process, accounting for up to 42.5% of the AOM activities, the microbial reduction of NOM concomitantly occurred. Furthermore, enrichment of wetland sediment with external NOM provided a complementary electron-accepting capacity, of which reduction accounted for ∼100 nmol 13CH4 oxidized · cm−3 · day−1. Spectroscopic evidence showed that quinone moieties were heterogeneously distributed in the wetland sediment, and their reduction occurred during the course of AOM. Moreover, an enrichment derived from wetland sediments performing AOM linked to NOM reduction stoichiometrically oxidized methane coupled to the reduction of the humic analogue anthraquinone-2,6-disulfonate. Microbial populations potentially involved in AOM coupled to microbial reduction of NOM were dominated by divergent biota from putative AOM-associated archaea. We estimate that this microbial process potentially contributes to the suppression of up to 114 teragrams (Tg) of CH4 · year−1 in coastal wetlands and more than 1,300 Tg · year−1, considering the global wetland area. IMPORTANCE The identification of key processes governing methane emissions from natural systems is of major importance considering the global warming effects triggered by this greenhouse gas. Anaerobic oxidation of methane (AOM) coupled to the microbial reduction of distinct electron acceptors plays a pivotal role in mitigating methane emissions from ecosystems. Given their high organic content, wetlands constitute the largest natural source of atmospheric methane. Nevertheless, processes controlling methane emissions in these environments are poorly understood. Here, we provide tracer analysis with 13CH4 and spectroscopic evidence revealing that AOM linked to the microbial reduction of redox functional groups in natural organic matter (NOM) prevails in a tropical wetland. We suggest that microbial reduction of NOM may largely contribute to the suppression of methane emissions from tropical wetlands. This is a novel avenue within the carbon cycle in which slowly decaying NOM (e.g., humic fraction) in organotrophic environments fuels AOM by serving as a terminal electron acceptor. PMID:28341676

Anaerobic Methane Oxidation Driven by Microbial Reduction of Natural Organic Matter in a Tropical Wetland.

PubMed

Valenzuela, Edgardo I; Prieto-Davó, Alejandra; López-Lozano, Nguyen E; Hernández-Eligio, Alberto; Vega-Alvarado, Leticia; Juárez, Katy; García-González, Ana Sarahí; López, Mercedes G; Cervantes, Francisco J

2017-06-01

Wetlands constitute the main natural source of methane on Earth due to their high content of natural organic matter (NOM), but key drivers, such as electron acceptors, supporting methanotrophic activities in these habitats are poorly understood. We performed anoxic incubations using freshly collected sediment, along with water samples harvested from a tropical wetland, amended with 13 C-methane (0.67 atm) to test the capacity of its microbial community to perform anaerobic oxidation of methane (AOM) linked to the reduction of the humic fraction of its NOM. Collected evidence demonstrates that electron-accepting functional groups (e.g., quinones) present in NOM fueled AOM by serving as a terminal electron acceptor. Indeed, while sulfate reduction was the predominant process, accounting for up to 42.5% of the AOM activities, the microbial reduction of NOM concomitantly occurred. Furthermore, enrichment of wetland sediment with external NOM provided a complementary electron-accepting capacity, of which reduction accounted for ∼100 nmol 13 CH 4 oxidized · cm -3 · day -1 Spectroscopic evidence showed that quinone moieties were heterogeneously distributed in the wetland sediment, and their reduction occurred during the course of AOM. Moreover, an enrichment derived from wetland sediments performing AOM linked to NOM reduction stoichiometrically oxidized methane coupled to the reduction of the humic analogue anthraquinone-2,6-disulfonate. Microbial populations potentially involved in AOM coupled to microbial reduction of NOM were dominated by divergent biota from putative AOM-associated archaea. We estimate that this microbial process potentially contributes to the suppression of up to 114 teragrams (Tg) of CH 4 · year -1 in coastal wetlands and more than 1,300 Tg · year -1 , considering the global wetland area. IMPORTANCE The identification of key processes governing methane emissions from natural systems is of major importance considering the global warming effects triggered by this greenhouse gas. Anaerobic oxidation of methane (AOM) coupled to the microbial reduction of distinct electron acceptors plays a pivotal role in mitigating methane emissions from ecosystems. Given their high organic content, wetlands constitute the largest natural source of atmospheric methane. Nevertheless, processes controlling methane emissions in these environments are poorly understood. Here, we provide tracer analysis with 13 CH 4 and spectroscopic evidence revealing that AOM linked to the microbial reduction of redox functional groups in natural organic matter (NOM) prevails in a tropical wetland. We suggest that microbial reduction of NOM may largely contribute to the suppression of methane emissions from tropical wetlands. This is a novel avenue within the carbon cycle in which slowly decaying NOM (e.g., humic fraction) in organotrophic environments fuels AOM by serving as a terminal electron acceptor. Copyright © 2017 American Society for Microbiology.

Organic carbon biolabilty increases with depth in a yedoma permafrost profile in Interior Alaska

NASA Astrophysics Data System (ADS)

Heslop, J. K.; Walter Anthony, K. M.; Spencer, R.; Winkel, M.; Zhang, M.; Liebner, S.; Podgorski, D. C.; Zito, P.; Kholodov, A. L.

2017-12-01

Permafrost organic carbon (OC) biolability is known to be controlled by both the OC molecular composition and redox state and the microbial community structure and its response to permafrost thaw. However, due to their complexity, both these mechanisms remain poorly understood. A substantial portion ( 16%) of global permafrost OC is stored in particularly deep, ice-rich permafrost deposits known as yedoma. We anaerobically incubated sediment from four depths in a 12-m yedoma profile in Interior Alaska with three treatments: control without amendment, inoculated with sediment from an adjacent thermokarst lake, and inoculated with sterilized lake sediment. We quantified CO2 and CH4 as end products of C mineralization, used qPCR to characterize the initial methanogenic communities, and used FT-ICR-MS to characterize the molecular composition of water-extractable organic matter at the beginning and end of the 154-d incubation. Proportions of aliphatics and peptides increased with depth in the permafrost profile, which would be consistent with long-term accumulation of anaerobic fermentation end products in yedoma-type permafrost. Moreover, these compounds positively correlated with anaerobic CO2 and CH4 production and their degradation rates corresponded to high proportions (53.3 ±41.9%) of OC mineralization, suggesting increasing proportions of these compounds with depth correspond to increasing OC quality and increased C mineralization per unit OC. Methanogenic communities were below detection limits in all controls. Following exposure to modern lake sediment microbial communities with detectable methanogens, we observed increases in anaerobic CO2 (65.1% ±75.2%) and CH4 (1,197% ±914%) production. The treatments with sterilized lake sediment did not contain detectable methanogens, and had increased anaerobic CO2 (52.6% ±69.2%) production but decreased CH4 (-74.1% ±33.8%) production. These preliminary results suggest anaerobic CH4 production is limited by ancient microbial communities in yedoma permafrost and might increase if exposed to modern microbial communities during thaw. This finding is important for better understanding how the release of thawed ancient OC from deep yedoma permafrost in thermokarst lake and coastal erosional environments will impact global C cycling.

The use of multiple tracers to evaluate the impact of sewered and non-sewered development on coastal water quality in a rural area of Florida.

PubMed

Meeroff, Daniel E; Bloetscher, Frederick; Long, Sharon C; Bocca, Thais

2014-05-01

When onsite wastewater treatment and disposal systems (OSTDS) are not sited appropriately or installed properly, wastewater constituents can be a source of adverse environmental impacts to soil and groundwater, which can lead to potential public health risks. A paired monitoring design developed to compare water quality in sewered and non-sewered areas is presented here. It is suggested as a possible monitoring scheme for assessing the impact of sewer installation projects. As such, two sets of single-family, rural residential Florida neighborhoods were evaluated over a two-year period to gain insight into the effects of small-community use of OSTDS on coastal water quality. One set of two neighborhoods were connected to the sanitary sewer network and the other set of two were served exclusively by OSTDS. Water quality sampling was conducted at the paired sites during seasonal high water table (SHWT) and seasonal low water table (SLWT) events. Measured surface water quality during the SHWT showed indications of environmental impacts from OSTDS in terms of nutrients, microbial pathogen indicators, and other water quality measures, such as turbidity and conductivity. However, during the SLWT events, no obvious impacts attributable to OSTDS were detected. The water quality results indicate that OSTDS impacts may be measureable in rural areas. Other factors, such as microbial indicator survival and regrowth potential, may confound the understanding of water quality impacts of sewer projects. For example, the microbial indicators Escherichia coli and enterococci were found to persist over time and therefore did not always represent true comparisons of OSTDS and sewered areas between seasons. The timeframe for evaluating the effects of sewer projects may be longer than anticipated because of this survival and regrowth phenomenon.

Water Supplies: Microbiological Analysis

EPA Science Inventory

Producing high-quality drinking water that is free of harmful microorganisms and maintaining its purity through distribution systems are essential for public health. Drinking water quality standards and guidelines for microbial contaminants vary within and among countries but typ...

Perceived Stress and Coffee and Energy Drink Consumption Predict Poor Sleep Quality in Podiatric Medical Students A Cross-sectional Study.

PubMed

Sawah, Mohomad Al; Ruffin, Naeemah; Rimawi, Mohammad; Concerto, Carmen; Aguglia, Eugenio; Chusid, Eileen; Infortuna, Carmenrita; Battaglia, Fortunato

2015-09-01

A cross-sectional survey administered to first- and second-year podiatric medical students aimed to investigate the effect of coffee intake, energy drink consumption, and perceived stress on sleep quality in medical students during their preclinical studies. Ninety-eight of 183 students contacted (53.6%) completed a questionnaire comprising standard instruments measuring sleep quality (Pittsburgh Sleep Quality Index), daytime sleepiness (Epworth Sleepiness scale), and perceived stress (ten-item Perceived Stress Scale). Furthermore, we investigated coffee and energy drink consumption. Logistic regression was conducted to identify factors associated with poor sleep quality and the relation between sleep quality and academic performance (grade point average). High prevalences of poor sleep quality, excessive daytime sleepiness, and perceived stress were reported. In addition, higher odds of developing poor sleep quality were associated with coffee and energy drink intake, perceived stress, and excessive daytime sleepiness. The total Pittsburgh Sleep Quality Index score was inversely correlated with grade point average. First- and second-year podiatric medical students have poor sleep quality. Further research is needed to identify effective strategies to reduce stress and decrease coffee and energy drink intake to minimize their negative effect on sleep quality and academic performance in podiatric medical students.

The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide.

PubMed

He, Zhili; Piceno, Yvette; Deng, Ye; Xu, Meiying; Lu, Zhenmei; Desantis, Todd; Andersen, Gary; Hobbie, Sarah E; Reich, Peter B; Zhou, Jizhong

2012-02-01

One of the major factors associated with global change is the ever-increasing concentration of atmospheric CO(2). Although the stimulating effects of elevated CO(2) (eCO(2)) on plant growth and primary productivity have been established, its impacts on the diversity and function of soil microbial communities are poorly understood. In this study, phylogenetic microarrays (PhyloChip) were used to comprehensively survey the richness, composition and structure of soil microbial communities in a grassland experiment subjected to two CO(2) conditions (ambient, 368 p.p.m., versus elevated, 560 p.p.m.) for 10 years. The richness based on the detected number of operational taxonomic units (OTUs) significantly decreased under eCO(2). PhyloChip detected 2269 OTUs derived from 45 phyla (including two from Archaea), 55 classes, 99 orders, 164 families and 190 subfamilies. Also, the signal intensity of five phyla (Crenarchaeota, Chloroflexi, OP10, OP9/JS1, Verrucomicrobia) significantly decreased at eCO(2), and such significant effects of eCO(2) on microbial composition were also observed at the class or lower taxonomic levels for most abundant phyla, such as Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Acidobacteria, suggesting a shift in microbial community composition at eCO(2). Additionally, statistical analyses showed that the overall taxonomic structure of soil microbial communities was altered at eCO(2). Mantel tests indicated that such changes in species richness, composition and structure of soil microbial communities were closely correlated with soil and plant properties. This study provides insights into our understanding of shifts in the richness, composition and structure of soil microbial communities under eCO(2) and environmental factors shaping the microbial community structure.

Microbial safety and quality of fresh herbs from Los Angeles, Orange County and Seattle farmers' markets.

PubMed

Levy, Donna J; Beck, Nicola K; Kossik, Alexandra L; Patti, Taylor; Meschke, J Scott; Calicchia, Melissa; Hellberg, Rosalee S

2015-10-01

Farmers' markets have been growing in popularity in the United States, but the microbial quality and safety of the food sold at these markets is currently unknown. The purpose of this study was to assess the microbial safety and quality of fresh basil, parsley and cilantro sold at farmers' markets in the Los Angeles, Orange County and greater Seattle areas. A total of 133 samples (52 basil, 41 cilantro and 40 parsley) were collected from 13 different farmers' markets and tested for Salmonella and generic Escherichia coli. One sample (parsley) was confirmed positive for Salmonella and 24.1% of samples were positive for generic E. coli, with a range of 0.70-3.15 log CFU g(-1) . Among the herbs tested, basil showed the highest percentage of samples with generic E. coli (26.9%), followed by cilantro (24.4%) and then parsley (20.0%). For 12% of samples, the levels of generic E. coli exceeded guidelines established by the Public Health Laboratory Service for microbiological quality of ready-to-eat foods. Overall, this study indicates the presence of Salmonella and generic E. coli in fresh herbs sold at farmers' markets; however, additional studies are needed to determine the sources and extent of contamination. © 2014 Society of Chemical Industry.

Effects of Blanching and Natural Convection Solar Drying on Quality Characteristics of Red Pepper (Capsicum annuum L.)

PubMed Central

Kori, Francis K. K.

2017-01-01

The objective of this work was to determine the effects of blanching and two drying methods, open-sun drying and natural convection solar drying, on the quality characteristics of red pepper. A 2 × 3 factorial design with experimental factors as 2 drying methods (open-sun drying and use of solar dryer) and 3 levels of pepper blanching (unblanched, blanched in plain water, and blanched in 2% NaCl) was conducted. Dried pepper samples were analysed for chemical composition, microbial load, and consumer sensory acceptability. Blanching of pepper in 2% NaCl solution followed by drying in a natural convection solar dryer reduced drying time by 15 hours. Similarly, a combination of blanching and drying in the solar dryer improved microbial quality of dried pepper. However, blanching and drying processes resulted in reduction in nutrients such as vitamin C and minerals content of pepper. Blanching followed by drying in natural convection solar dryer had the highest consumer acceptability scores for colour and overall acceptability, while texture and aroma were not significantly (p > 0.05) affected by the different treatments. Therefore, natural convection solar dryer can be used to dry pepper with acceptable microbial and sensory qualities, as an alternative to open-sun drying. PMID:29082236

Microbial quality of drinking water from microfiltered water dispensers.

PubMed

Sacchetti, R; De Luca, G; Dormi, A; Guberti, E; Zanetti, F

2014-03-01

A comparison was made between the microbial quality of drinking water obtained from Microfiltered Water Dispensers (MWDs) and that of municipal tap water. A total of 233 water samples were analyzed. Escherichia coli (EC), enterococci (ENT), total coliforms (TC), Staphylococcus aureus, Pseudomonas aeruginosa and heterotrophic plate count (HPC) at 22 °C and 37 °C were enumerated. In addition, information was collected about the principal structural and functional characteristics of each MWD in order to study the various factors that might influence the microbial quality of the water. EC and ENT were not detected in any of the samples. TC were never detected in the tap water but were found in 5 samples taken from 5 different MWDs. S. aureus was found in a single sample of microfiltered water. P. aeruginosa was found more frequently and at higher concentrations in the samples collected from MWDs. The mean HPCs at 22 °C and 37 °C were significantly higher in microfiltered water samples compared to those of the tap water. In conclusion, the use of MWDs may increase the number of bacteria originally present in tap water. It is therefore important to monitor the quality of the dispensed water over time, especially if it is destined for vulnerable users. Copyright © 2013 Elsevier GmbH. All rights reserved.

Impact of repeated single-metal and multi-metal pollution events on soil quality.

PubMed

Burges, Aritz; Epelde, Lur; Garbisu, Carlos

2015-02-01

Most frequently, soil metal pollution results from the occurrence of repeated single-metal and, above all, multi-metal pollution events, with concomitant adverse consequences for soil quality. Therefore, in this study, we evaluated the impact of repeated single-metal and multi-metal (Cd, Pb, Cu, Zn) pollution events on soil quality, as reflected by the values of a variety of soil microbial parameters with potential as bioindicators of soil functioning. Specifically, parameters of microbial activity (potentially mineralizable nitrogen, β-glucosidase and acid phosphatase activity) and biomass (fungal and bacterial gene abundance by RT-qPCR) were determined, in the artificially metal-polluted soil samples, at regular intervals over a period of 26 weeks. Similarly, we studied the evolution over time of CaCl2-extractable metal fractions, in order to estimate metal bioavailability in soil. Different metals showed different values of bioavailability and relative bioavailability ([metal]bio/[metal]tot) in soil throughout the experiment, under both repeated single-metal and multi-metal pollution events. Both repeated Zn-pollution and multi-metal pollution events led to a significant reduction in the values of acid phosphatase activity, and bacterial and fungal gene abundance, reflecting the negative impact of these repeated events on soil microbial activity and biomass, and, hence, soil quality. Copyright © 2014 Elsevier Ltd. All rights reserved.

[Excessive Daytime Sleepiness, Poor Quality Sleep, and Low Academic Performance in Medical Students].

PubMed

Machado-Duque, Manuel Enrique; Echeverri Chabur, Jorge Enrique; Machado-Alba, Jorge Enrique

2015-01-01

Quality of sleep and excessive daytime sleepiness (EDS) affect cognitive ability and performance of medical students. This study attempts to determine the prevalence of EDS, sleep quality, and assess their association with poor academic performance in this population. A descriptive, observational study was conducted on a random sample of 217 medical students from the Universidad Tecnológica de Pereira, who completed the Pittsburgh Sleep Quality Index (PSQI) questionnaire and the Epworth sleepiness scale. Sociodemographic, clinic and academic variables were also measured. Multivariate analyses for poor academic performance were performed. The included students had a mean age of 21.7±3.3 years, of whom 59.4% were men. Almost half (49.8%) had EDS criteria, and 79.3% were poor sleepers (PSQI ≥ 5), while 43.3% had poor academic performance during the last semester. The bivariate analysis showed that having used tobacco or alcohol until intoxicated, fairly bad subjective sleep quality, sleep efficiency < 65%, and being a poor sleeper were associated with increased risk of low performance. Sleep efficiency < 65% was statistically associated with poor academic performance (P=.024; OR = 4.23; 95% CI, 1.12-15.42) in the multivariate analysis. A poor sleep quality determined by low efficiency was related to poor academic achievement at the end of semester in medical students. Copyright © 2015 Asociación Colombiana de Psiquiatría. Publicado por Elsevier España. All rights reserved.

Hydrodynamics of microbial filter feeding

PubMed Central

Asadzadeh, Seyed Saeed; Dölger, Julia; Walther, Jens H.; Andersen, Anders

2017-01-01

Microbial filter feeders are an important group of grazers, significant to the microbial loop, aquatic food webs, and biogeochemical cycling. Our understanding of microbial filter feeding is poor, and, importantly, it is unknown what force microbial filter feeders must generate to process adequate amounts of water. Also, the trade-off in the filter spacing remains unexplored, despite its simple formulation: A filter too coarse will allow suitably sized prey to pass unintercepted, whereas a filter too fine will cause strong flow resistance. We quantify the feeding flow of the filter-feeding choanoflagellate Diaphanoeca grandis using particle tracking, and demonstrate that the current understanding of microbial filter feeding is inconsistent with computational fluid dynamics (CFD) and analytical estimates. Both approaches underestimate observed filtration rates by more than an order of magnitude; the beating flagellum is simply unable to draw enough water through the fine filter. We find similar discrepancies for other choanoflagellate species, highlighting an apparent paradox. Our observations motivate us to suggest a radically different filtration mechanism that requires a flagellar vane (sheet), something notoriously difficult to visualize but sporadically observed in the related choanocytes (sponges). A CFD model with a flagellar vane correctly predicts the filtration rate of D. grandis, and using a simple model we can account for the filtration rates of other microbial filter feeders. We finally predict how optimum filter mesh size increases with cell size in microbial filter feeders, a prediction that accords very well with observations. We expect our results to be of significance for small-scale biophysics and trait-based ecological modeling. PMID:28808016

Hydrodynamics of microbial filter feeding.

PubMed

Nielsen, Lasse Tor; Asadzadeh, Seyed Saeed; Dölger, Julia; Walther, Jens H; Kiørboe, Thomas; Andersen, Anders

2017-08-29

Microbial filter feeders are an important group of grazers, significant to the microbial loop, aquatic food webs, and biogeochemical cycling. Our understanding of microbial filter feeding is poor, and, importantly, it is unknown what force microbial filter feeders must generate to process adequate amounts of water. Also, the trade-off in the filter spacing remains unexplored, despite its simple formulation: A filter too coarse will allow suitably sized prey to pass unintercepted, whereas a filter too fine will cause strong flow resistance. We quantify the feeding flow of the filter-feeding choanoflagellate Diaphanoeca grandis using particle tracking, and demonstrate that the current understanding of microbial filter feeding is inconsistent with computational fluid dynamics (CFD) and analytical estimates. Both approaches underestimate observed filtration rates by more than an order of magnitude; the beating flagellum is simply unable to draw enough water through the fine filter. We find similar discrepancies for other choanoflagellate species, highlighting an apparent paradox. Our observations motivate us to suggest a radically different filtration mechanism that requires a flagellar vane (sheet), something notoriously difficult to visualize but sporadically observed in the related choanocytes (sponges). A CFD model with a flagellar vane correctly predicts the filtration rate of D. grandis , and using a simple model we can account for the filtration rates of other microbial filter feeders. We finally predict how optimum filter mesh size increases with cell size in microbial filter feeders, a prediction that accords very well with observations. We expect our results to be of significance for small-scale biophysics and trait-based ecological modeling.

Microbial Interactions with Natural Organic Matter Extracted from the Oak Ridge FRC

NASA Astrophysics Data System (ADS)

Wu, X.; Jagadamma, S.; Lancaster, A.; Adams, M. W. W.; Hazen, T.; Justice, N.; Chakraborty, R.

2015-12-01

Natural organic matter (NOM) is central to microbial food webs; however, little is known about the interplay between the physical and chemical characteristics of NOM and its turnover by microbial communities based upon biotic and abiotic parameters (e.g., biogenic precursors, redox state, bioavailability). Microbial activity changes the structures and properties that influence further bioavailability of NOM. To date, our understanding of these interactions is insufficient, and indigenous microbial activities that regulate NOM turnover are poorly resolved. It is critical to identify NOM characteristics to the structure and composition of microbial communities and to the metabolic potential of that community. Towards that end, sediment samples collected from the background area well FW305 (Oak Ridge Field Research Center, Oak Ridge, TN) were tested for NOM extraction methods that used three mild solvents, e.g., phosphate buffered saline (PBS), pyrophosphate, and MilliQ-water. MilliQ-water was finally chosen for extracting sediment samples via shaking and sonication. Groundwater from well FW301 was used as an inoculum to which the extracted NOM was added as carbon sources to feed native microbes. To identify the specific functional groups of extracted NOM that are bioavailable to indigenous microbes, several techniques, including FTIR, LC-MS, EEM, were applied to characterize the extracted NOM as well as the transformed NOM metabolites. 16S rDNA amplicon sequencing was also performed to identify the specific microbial diversity that was enriched and microbial isolates that preferentially grew with these NOM was also cultivated in the lab for future detailed studies.

Microbiology of sugar-rich environments: diversity, ecology and system constraints.

PubMed

Lievens, Bart; Hallsworth, John E; Pozo, Maria I; Belgacem, Zouhaier Ben; Stevenson, Andrew; Willems, Kris A; Jacquemyn, Hans

2015-02-01

Microbial habitats that contain an excess of carbohydrate in the form of sugar are widespread in the microbial biosphere. Depending on the type of sugar, prevailing water activity and other substances present, sugar-rich environments can be highly dynamic or relatively stable, osmotically stressful, and/or destabilizing for macromolecular systems, and can thereby strongly impact the microbial ecology. Here, we review the microbiology of different high-sugar habitats, including their microbial diversity and physicochemical parameters, which act to impact microbial community assembly and constrain the ecosystem. Saturated sugar beet juice and floral nectar are used as case studies to explore the differences between the microbial ecologies of low and higher water-activity habitats respectively. Nectar is a paradigm of an open, dynamic and biodiverse habitat populated by many microbial taxa, often yeasts and bacteria such as, amongst many others, Metschnikowia spp. and Acinetobacter spp., respectively. By contrast, thick juice is a relatively stable, species-poor habitat and is typically dominated by a single, xerotolerant bacterium (Tetragenococcus halophilus). A number of high-sugar habitats contain chaotropic solutes (e.g. ethyl acetate, phenols, ethanol, fructose and glycerol) and hydrophobic stressors (e.g. ethyl octanoate, hexane, octanol and isoamyl acetate), all of which can induce chaotropicity-mediated stresses that inhibit or prevent multiplication of microbes. Additionally, temperature, pH, nutrition, microbial dispersion and habitat history can determine or constrain the microbiology of high-sugar milieux. Findings are discussed in relation to a number of unanswered scientific questions. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Changes in sleep quality with age-a 36-year follow-up study of Finnish working-aged adults.

PubMed

Hublin, Christer; Lehtovirta, Mikko; Partinen, Markku; Koskenvuo, Markku; Kaprio, Jaakko

2017-10-19

Long-term follow-up data on changes in sleep quality among middle-aged adults is scarce. We assessed sleep quality in a population-based cohort (n = 4847) of twins born between 1945 and 1957 during a follow-up of 36 years, with four measurement points in 1975, 1981, 1990 and 2011. Sleep quality was categorized as sleeping well, fairly well, fairly poorly or poorly. The mean age at the beginning of follow-up was 24.0, and at the end was 60.3 years. Of all the adults, 71.1% slept well or fairly well at each time-point throughout the follow-up and 0.5% poorly or fairly poorly. The proportion of those sleeping poorly or fairly poorly increased linearly over time; 3.5% among both sexes at the start, and 15.5% among men and 20.9% among women at the end of the follow-up. The last survey indicated a strong association between self-rated health and sleep quality: sleeping poorly or fairly poorly was reported 15 times more frequently by those rating their health as fairly poor than by those rating their health as very good. There was a strong association between indicators of depression and poor sleep. Although many studies have reported increasing frequencies in sleep problems, our results, based on a long-term cohort study, indicate that the majority of people sleep well or fairly well. Sleep quality declines with age, but only a very small fraction of the adults in this long follow-up consistently slept poorly. © 2017 European Sleep Research Society.

Microbial Diversity of Commercial Makgeolli and Its Influence on the Organoleptic Characteristics of Korean Rice Sourdough, Jeung-Pyun.

PubMed

Park, Jaehyung; Seo, Ji Sun; Kim, Seul-Ah; Shin, So-Yeon; Park, Jong-Hyun; Han, Nam Soo

2017-10-28

Sourdough is made by fermentation of dough by lactic acid bacteria (LAB) and yeast to improve bread properties like volume, flavor, and texture. A Korean traditional sourdough was made by fermenting rice flour with rice wine (makgeolli) and used to make sponge-like bread (jeung-pyun). The aim of this study was to investigate the microbial diversity of makgeolli products and their influence on the organoleptic quality of jeung-pyun. Three commercial makgeolli were tested for jeung-pyun production, with each product exhibiting varied dough swelling rates and organoleptic qualities, and among them, J-product was ranked highest in texture and taste. Microbial analysis of the three makgeolli also showed a big difference in their population and diversity. J-product had the highest LAB and yeast counts, and the predominant species were Lactobacillus casei, Lactobacillus brevis, Leuconostoc pseudomenteroides, and Saccharomyces cerevisiae . Using J-product, sourdough was fermented at 25°C, 30°C, and 35°C, and the microbial growth in and textural properties of jeung-pyun were examined by instrumental and sensory tests. At high temperature (35°C), the rates of dough swelling and acidification were fast due to rapid microbial growth mainly caused by LAB, resulting in a short leavening time and soft and sour jeung-pyun. Sensory tests showed consumer preference for the soft and mild-sour jeung-pyun. This study shows that LAB in makgeolli play key roles in production of jeung-pyun, influencing the textural and sensory properties. For the production of high-quality jeung-pyun, development of LAB starters with high gas productivity and low acidity and establishment of an optimal fermentation procedure for rice dough are necessary.

Metagenomic analysis of soil and freshwater from zoo agricultural area with organic fertilization

PubMed Central

Meneghine, Aylan K.; Nielsen, Shaun; Thomas, Torsten; Carareto Alves, Lucia Maria

2017-01-01

Microbial communities drive biogeochemical cycles in agricultural areas by decomposing organic materials and converting essential nutrients. Organic amendments improve soil quality by increasing the load of essential nutrients and enhancing the productivity. Additionally, fresh water used for irrigation can affect soil quality of agricultural soils, mainly due to the presence of microbial contaminants and pathogens. In this study, we investigated how microbial communities in irrigation water might contribute to the microbial diversity and function of soil. Whole-metagenomic sequencing approaches were used to investigate the taxonomic and the functional profiles of microbial communities present in fresh water used for irrigation, and in soil from a vegetable crop, which received fertilization with organic compost made from animal carcasses. The taxonomic analysis revealed that the most abundant genera were Polynucleobacter (~8% relative abundance) and Bacillus (~10%) in fresh water and soil from the vegetable crop, respectively. Low abundance (0.38%) of cyanobacterial groups were identified. Based on functional gene prediction, denitrification appears to be an important process in the soil community analysed here. Conversely, genes for nitrogen fixation were abundant in freshwater, indicating that the N-fixation plays a crucial role in this particular ecosystem. Moreover, pathogenicity islands, antibiotic resistance and potential virulence related genes were identified in both samples, but no toxigenic genes were detected. This study provides a better understanding of the community structure of an area under strong agricultural activity with regular irrigation and fertilization with an organic compost made from animal carcasses. Additionally, the use of a metagenomic approach to investigate fresh water quality proved to be a relevant method to evaluate its use in an agricultural ecosystem. PMID:29267397

Suitability of different Escherichia coli enumeration techniques to assess the microbial quality of different irrigation water sources.

PubMed

Truchado, P; Lopez-Galvez, F; Gil, M I; Pedrero-Salcedo, F; Alarcón, J J; Allende, A

2016-09-01

The use of fecal indicators such as Escherichia coli has been proposed as a potential tool to characterize microbial contamination of irrigation water. Recently, not only the type of microbial indicator but also the methodologies used for enumeration have been called into question. The goal of this study was to assess the microbial quality of different water sources for irrigation of zucchini plants by using E. coli as an indicator of fecal contamination and the occurrence of foodborne pathogens. Three water sources were evaluated including reclaimed secondary treated water (RW-2), reclaimed tertiary UV-C treated water (RW-3) and surface water (SW). The suitability of two E. coli quantification techniques (plate count and qPCR) was examined for irrigation water and fresh produce. E. coli levels using qPCR assay were significantly higher than that obtained by plate count in all samples of irrigation water and fresh produce. The microbial quality of water samples from RW-2 was well predicted by qPCR, as the presence of foodborne pathogens were positively correlated with high E. coli levels. However, differences in the water characteristics influenced the suitability of qPCR as a tool to predict potential contamination in irrigation water. No significant differences were obtained between the number of cells of E. coli from RW-2 and RW-3, probably due to the fact that qPCR assay cannot distinguish between viable and dead cells. These results indicated that the selection of the most suitable technique for enumeration of indicator microorganisms able to predict potential presence of fecal contamination might be influenced by the water characteristics. Copyright © 2016 Elsevier Ltd. All rights reserved.

Impact of refined petroleum spills on water quality, macro-invertebrate and microbial communities of a tropical aquatic environment.

PubMed

Chukwu, L O; Nwachukwu, S C U

2005-07-01

Water quality characteristics, benthic macro-invertebrates and microbial communities of three first order streams in South West Nigeria were investigated to assess the effects of refined petroleum five months after spillage. All physical and chemical conditions except temperature and pH were significantly different (P<0.01) at the upstream control stations and impacted stations reflecting the perturbational stress. The benthic macro-invertebrate fauna were dominated by arthropods, but the faunal spectrum was dissimilar at all the stations studied. Sampling stations at the epicentre of the spill showed considerable reduction in faunal compositions and relative abundance. Generally, the microbial density and diversity were highest in both soil and water samples from impacted sites than in control sites. There was a significantly higher proportion (P < 0.05) of hydrocarbon utilizers in soil than in water samples in all stations except in samples from stations (P<0.05).

Microbial quality and molecular identification of cultivable microorganisms isolated from an urban drinking water distribution system (Limassol, Cyprus).

PubMed

Botsaris, George; Kanetis, Loukas; Slaný, Michal; Parpouna, Christiana; Makris, Konstantinos C

2015-12-01

Microorganisms can survive and multiply in aged urban drinking water distribution systems, leading to potential health risks. The objective of this work was to investigate the microbial quality of tap water and molecularly identify its predominant cultivable microorganisms. Tap water samples collected from 24 different households scattered in the urban area of Limassol, Cyprus, were microbiologically tested following standard protocols for coliforms, E. coli, Pseudomonas spp., Enterococcus spp., and total viable count at 22 and 37 °C. Molecular identification was performed on isolated predominant single colonies using 16SrRNA sequencing. Approximately 85% of the household water samples were contaminated with one or more microorganisms belonging to the genera of Pseudomonas, Corynebacterium, Agrobacterium, Staphylococcus, Bacillus, Delftia, Acinetobacter, Enterococcus, Enterobacter, and Aeromonas. However, all samples tested were free from E. coli. This is the first report in Cyprus molecularly confirming specific genera of relevant microbial communities in tap water.

Monitoring biodiversity in libraries: a pilot study and perspectives for indoor air quality.

PubMed

Valeriani, F; Cianfanelli, C; Gianfranceschi, G; Santucci, S; Romano Spica, V; Mucci, N

2017-09-01

Indoor Air Quality (IAQ) in libraries is influenced by the presence of specific factors which can impact on both paper storage as well as people health. Microclimatic conditions induce and support a biodiversity pattern involving environmental and anthropic microorganisms. We used a multidisciplinary monitoring model to characterize microflora biodiversity by Next Generation Sequencing (NGS). Biodiversity indexes were adapted to evaluate anthropic vs environmental pollution by combining Shannon mean index (H), species representativeness (E H ), human/environmental pollution ratio (SA) to better characterize the NGS output and acquire synthetic information on Indoor Air Microbial Biodiversity (IAMB). Results indicate a frequently low microbial load (IGCM/m 3 < 1000) characterized by different species (n = 102), including several cellulose metabolizing bacteria. Workers and visitors appeared a relevant source of microbial contamination. Air biodiversity assayed by NGS seems a promising marker for studying IAQ.

Biofilm formation and control in a simulated spacecraft water system - Two-year results

NASA Technical Reports Server (NTRS)

Schultz, John R.; Taylor, Robert D.; Flanagan, David T.; Carr, Sandra E.; Bruce, Rebekah J.; Svoboda, Judy V.; Huls, M. H.; Sauer, Richard L.; Pierson, Duane L.

1991-01-01

The ability of iodine to maintain microbial water quality in a simulated spacecraft water system is being studied. An iodine level of about 2.0 mg/L is maintained by passing ultrapure influent water through an iodinated ion exchange resin. Six liters are withdrawn daily and the chemical and microbial quality of the water is monitored regularly. Stainless steel coupons used to monitor biofilm formation are being analyzed by culture methods, epifluorescence microscopy, and scanning electron microscopy. Results from the first two years of operation show a single episode of high bacterial colony counts in the iodinated system. This growth was apparently controlled by replacing the iodinated ion exchange resin. Scanning electron microscopy indicates that the iodine has limited but not completely eliminated the formation of biofilm during the first two years of operation. Significant microbial contamination has been present continuously in a parallel noniodinated system since the third week of operation.

Product quality and microbial dynamics during vermicomposting and maturation of compost from pig manure.

PubMed

Villar, Iria; Alves, David; Mato, Salustiano

2017-11-01

This research evaluates, through microbial dynamics, the use of earthworms Eisenia andrei for maturation of pre-composted pig manure in comparison with maturation under static conditions and with vermicomposting of fresh pig manure. Therefore, two substrates were used (fresh and pre-composted pig manure) and four treatments were developed: fresh manure vermicomposting, control of fresh manure without earthworms, pre-composting followed by vermicomposting and static maturation of pre-composted manure. In order to determine the microbial dynamics, the enzymatic activities and profiles of phospholipid fatty acids (PLFAs) were evaluated over a 112-days period. Physicochemical and biological parameters of the obtained products were also analyzed. The presence of earthworms significantly reduced (p<0.05) microbial biomass and all the microbial groups (Gram+bacteria, Gram-bacteria, and fungi) in both substrates. The enzymatic activities (cellulase, β-glucosidase and acid phosphatase) behaved in a significantly distinctive manner (p<0.05) depending on the treatment. Microbial communities had significant correlations (p<0.05) with hydrolytic activities during static maturation of pre-composted manure. This indicates a direct effect of microbiota evolution on the degradative processes; however, complex earthworm-microbiota interactions were established in the presence of E. andrei. After earthworms' removal from vermicompost of fresh substrate at 70day, an increase in Gram + (4.4 times), Gram - (3.8 times) and fungi (2.8 times) were observed and, although the vermicompost achieved quality values, it is necessary to optimize the vermicompost aging phase period to improve the stability. Static maturation presented stability on microbial dynamics that indicated a slow degradation of organic compounds so that, maturation of pre-composted manure through vermicomposting is better option. Copyright © 2017 Elsevier Ltd. All rights reserved.

Association between Facebook Dependence and Poor Sleep Quality: A Study in a Sample of Undergraduate Students in Peru

PubMed Central

Wolniczak, Isabella; Cáceres-DelAguila, José Alonso; Palma-Ardiles, Gabriela; Arroyo, Karen J.; Solís-Visscher, Rodrigo; Paredes-Yauri, Stephania; Mego-Aquije, Karina; Bernabe-Ortiz, Antonio

2013-01-01

Objectives Internet can accelerate information exchange. Social networks are the most accessed especially Facebook. This kind of networks might create dependency with several negative consequences in people’s life. The aim of this study was to assess potential association between Facebook dependence and poor sleep quality. Methodology/Principal Findings A cross sectional study was performed enrolling undergraduate students of the Universidad Peruana de Ciencias Aplicadas, Lima, Peru. The Internet Addiction Questionnaire, adapted to the Facebook case, and the Pittsburgh Sleep Quality Index, were used. A global score of 6 or greater was defined as the cutoff to determine poor sleep quality. Generalized linear model were used to determine prevalence ratios (PR) and 95% confidence intervals (95%CI). A total of 418 students were analyzed; of them, 322 (77.0%) were women, with a mean age of 20.1 (SD: 2.5) years. Facebook dependence was found in 8.6% (95% CI: 5.9%–11.3%), whereas poor sleep quality was present in 55.0% (95% CI: 50.2%–59.8%). A significant association between Facebook dependence and poor sleep quality mainly explained by daytime dysfunction was found (PR = 1.31; IC95%: 1.04–1.67) after adjusting for age, sex and years in the faculty. Conclusions There is a relationship between Facebook dependence and poor quality of sleep. More than half of students reported poor sleep quality. Strategies to moderate the use of this social network and to improve sleep quality in this population are needed. PMID:23554978

Accumulation of the antibiotic phenazine-1-carboxylic acid in the rhizosphere of dryland cereals

USDA-ARS?s Scientific Manuscript database

Natural antibiotics are thought to function in microbial defense, fitness, competitiveness, biocontrol, communication and gene regulation. However, the frequency and amount of antibiotics produced in nature are poorly understood. In this study, we assessed the geographic distribution of indigenous p...

Association between fertilizer-mediated changes in microbial communities and Aedes albopictus growth and survival

USDA-ARS?s Scientific Manuscript database

Contamination of aquatic habitats with anthropogenic nutrients has been associated with an increase in mosquito larval populations but the underlying mechanisms remain poorly understood. We examined the individual and combined effects of two synthetic fertilizers (ammonium sulfate and potassium chlo...

Nitrous Oxide Emissions from a Large, Impounded River: The Ohio River

EPA Science Inventory

Models suggest that microbial activity in streams and rivers is a globally significant source of anthropogenic nitrous oxide (N2O), a potent greenhouse gas and the leading cause of stratospheric ozone destruction. However, model estimates of N2O emissions are poorly constrained ...

Influence of different forms of acidities on soil microbiological properties and enzyme activities at an acid mine drainage contaminated site.

PubMed

Sahoo, Prafulla Kumar; Bhattacharyya, Pradip; Tripathy, Subhasish; Equeenuddin, Sk Md; Panigrahi, M K

2010-07-15

Assessment of microbial parameters, viz. microbial biomass, fluorescence diacetate, microbial respiration, acid phosphatase, beta-glucosidase and urease with respect to acidity helps in evaluating the quality of soils. This study was conducted to investigate the effects of different forms of acidities on soil microbial parameters in an acid mine drainage contaminated site around coal deposits in Jainta Hills of India. Total potential and exchangeable acidity, extractable and exchangeable aluminium were significantly higher in contaminated soil compared to the baseline (p<0.01). Different forms of acidity were significantly and positively correlated with each other (p<0.05). Further, all microbial properties were positively and significantly correlated with organic carbon and clay (p<0.05). The ratios of microbial parameters with organic carbon were negatively correlated with different forms of acidity. Principal component analysis and cluster analyses showed that the microbial activities are not directly influenced by the total potential acidity and extractable aluminium. Though acid mine drainage affected soils had higher microbial biomass and activities due to higher organic matter content than those of the baseline soils, the ratios of microbial parameters/organic carbon indicated suppression of microbial growth and activities due to acidity stress. 2010 Elsevier B.V. All rights reserved.

METHODS AND MICROBES FOR MEASURING THE QUALITY OF RECREATIONAL WATERS: PAST, PRESENT AND FUTURE

EPA Science Inventory

The methods and microbes used to measure the quality of recreational waters have changed very little over the last sixty years. The use of microbial indicators used to measure the quality of water under various conditions across the United States, and the serious shortcomings th...

New submodel for watershed-scale simulations of fecal bacteria fate and transport at agricultural and pasture lands

USDA-ARS?s Scientific Manuscript database

Microbial contamination of waters is the critical public health issue. The watershed-scale process-based modeling of bacteria fate and transport (F&T) has been proven to serve as the useful tool for predicting microbial water quality and evaluating management practices. The objective of this work is...

Runoff delay exerts a strong control on the field-scale removal of manure-borne fecal bacteria with runoff

USDA-ARS?s Scientific Manuscript database

The microbial safety of surface waters is an ongoing issue which is threatened by the transport of manure-borne bacteria to water sources used for irrigation or recreation. Predictive modeling has become an effective tool to forecast the microbial quality of water during precipitation events, howeve...

Characterizing relationships among fecal indicator bacteria, microbial source tracking markers, and associated waterborne pathogen occurrence in stream water and sediments in a mixed land use watershed

EPA Science Inventory

Bed sediments of streams and rivers may store high concentrations of fecal indicator bacteria (FIB) and pathogens. Due to resuspension events, these contaminants can be mobilized into the water column and affect overall water quality. Other bacterial indicators such as microbial ...

Differential Decay of Cattle-associated Fecal Indicator Bacteria and Microbial Source Tracking Markers in Fresh and Marine Water (ASM 2017 Presentation)

EPA Science Inventory

Background: Fecal indicator bacteria (FIB) have a long history of use in the assessment of the microbial quality of recreational waters. However, quantification of FIB provides no information about the pollution source(s) and relatively little is known about their fate in the amb...

Vertical distribution of Fe and Fe(III)-reducing bacteria in the sediments of Lake Donghu, China.

PubMed

Tian, Cuicui; Wang, Chunbo; Tian, Yingying; Wu, Xingqiang; Xiao, Bangding

2015-08-01

In lake sediments, iron (Fe) is the most versatile element, and the redox cycling of Fe has a wide influence on the biogeochemical cycling of organic and inorganic substances. The aim of the present study was to analyze the vertical distribution of Fe and Fe(III)-reducing bacteria (FeRB) in the surface sediment (30 cm) of Lake Donghu, China. At the 3 sites we surveyed, FeRB and Fe(II)-oxidizing bacteria (FeOB) coexisted in anoxic sediments. Geobacter-related FeRB accounted for 5%-31% of the total Bacteria, while Gallionella-related FeOB accounted for only 0.1%-1.3%. A significant correlation between the relative abundance of poorly crystalline Fe and Geobacter spp. suggested that poorly crystalline Fe favored microbial Fe(III) reduction. Poorly crystalline Fe and Geobacter spp. were significantly associated with solid-phase Fe(II) and total inorganic phosphorus levels. Pore water Fe(II) concentrations negatively correlated with NO3(-) at all sites. We concluded that Geobacter spp. were abundant in the sediments of Lake Donghu, and the redox of Fe might participate in the cycling of nitrogen and phosphorus in sediments. These observations provided insight into the roles of microbial Fe cycling in lake sediments.

Bullying as a risk for poor sleep quality among high school students in China.

PubMed

Zhou, Ying; Guo, Lan; Lu, Ci-yong; Deng, Jian-xiong; He, Yuan; Huang, Jing-hui; Huang, Guo-liang; Deng, Xue-qing; Gao, Xue

2015-01-01

To determine whether involvement in bullying as a bully, victim, or bully-victim was associated with a higher risk of poor sleep quality among high school students in China. A cross-sectional study was conducted. A total of 23,877 high school students were surveyed in six cities in Guangdong Province. All students were asked to complete the adolescent health status questionnaire, which included the Chinese version of the Pittsburgh Sleep Quality Index (PSQI) and bullying involvement. Descriptive statistics were used to evaluate sleep quality and the prevalence of school bullying. Multi-level logistic regression analyses were conducted to examine the association between being victimized and bullying others with sleep quality. Among the 23,877 students, 6,127 (25.66%) reported having poor sleep quality, and 10.89% reported being involved in bullying behaviors. Of the respondents, 1,410 (5.91%) were pure victims of bullying, 401 (1.68%) were bullies and 784 (3.28%) were bully-victims. Frequently being involved in bullying behaviors (being bullied or bullying others) was related to increased risks of poor sleep quality compared with adolescents who were not involved in bullying behaviors. After adjusting for age, sex, and other confounding factors, the students who were being bullied (OR=2.05, 95%CI=1.81-2.32), bullied others (OR=2.30, 95%CI=1.85-2.86) or both (OR=2.58, 95%CI=2.20-3.03) were at a higher risk for poor sleep quality. Poor sleep quality among high school students is highly prevalent, and school bullying is prevalent among adolescents in China. The present results suggested that being involved in school bullying might be a risk factor for poor sleep quality among adolescents.

Bullying as a Risk for Poor Sleep Quality among High School Students in China

PubMed Central

Lu, Ci-yong; Deng, Jian-xiong; Huang, Jing-hui; Huang, Guo-liang; Deng, Xue-qing; Gao, Xue

2015-01-01

Objective To determine whether involvement in bullying as a bully, victim, or bully-victim was associated with a higher risk of poor sleep quality among high school students in China. Methods A cross-sectional study was conducted. A total of 23,877 high school students were surveyed in six cities in Guangdong Province. All students were asked to complete the adolescent health status questionnaire, which included the Chinese version of the Pittsburgh Sleep Quality Index (PSQI) and bullying involvement. Descriptive statistics were used to evaluate sleep quality and the prevalence of school bullying. Multi-level logistic regression analyses were conducted to examine the association between being victimized and bullying others with sleep quality. Results Among the 23,877 students, 6,127 (25.66%) reported having poor sleep quality, and 10.89% reported being involved in bullying behaviors. Of the respondents, 1,410 (5.91%) were pure victims of bullying, 401 (1.68%) were bullies and 784 (3.28%) were bully-victims. Frequently being involved in bullying behaviors (being bullied or bullying others) was related to increased risks of poor sleep quality compared with adolescents who were not involved in bullying behaviors. After adjusting for age, sex, and other confounding factors, the students who were being bullied (OR=2.05, 95%CI=1.81-2.32), bullied others (OR=2.30, 95%CI=1.85-2.86) or both (OR=2.58, 95%CI=2.20-3.03) were at a higher risk for poor sleep quality. Conclusions Poor sleep quality among high school students is highly prevalent, and school bullying is prevalent among adolescents in China. The present results suggested that being involved in school bullying might be a risk factor for poor sleep quality among adolescents. PMID:25811479

Influence of intermittent stream connectivity on water quality and salmonid survivorship.

NASA Astrophysics Data System (ADS)

Hildebrand, J.; Woelfle-Erskine, C. A.; Larsen, L.

2014-12-01

Anthropogenic stress and climate change are causing an increasing number of California streams to become intermittent and are driving earlier and more severe summertime drying. The extent to which emerging water conservation alternatives impact flows or habitat quality (e.g. temperature, DO) for salmonids remains poorly understood. Here, we investigate the proximal drivers of salmonid mortality over a range of connectivity conditions during summertime intermittency in Salmon Creek watershed, Sonoma County, CA. Through extensive sampling in paired subwatersheds over a period of two years, we tested the hypothesis that accumulation of readily bioavailable DOC in poorly flushed pools drives DO decline associated with loss of salmonids. We then traced the origin and flow pathways of DOC throughout the watershed using Parallel Factor Analysis (PARAFAC). We obtained samples for DOC and stable isotope analyses at monthly intervals from 20 piezometers and surface water in the study reaches and from private wells and springs distributed throughout the watersheds. We also obtained in situ DO, conductivity and pH readings within stream study reaches. We determined DOC quality by SUVA (specific UV absorbance) and fluorescence index. We calculated stream metabolism rates using the single station method. In pools instrumented with DO sensors, we compared changing DOC quality during the summer months to changes in DO concentrations and stream metabolism. Our results show that the duration of complete disconnection of pools during the summer months and stream metabolic rates are positively correlated with salmonid mortality. Furthermore, our results indicate that salmonid mortality is greatest in disconnected pools with low DOC fluorescence indices and high SUVA values, indicative of terrestrially derived DOC and little or no groundwater inflow. Conversely low salmonid mortality was found in disconnected pools with high fluorescence index and low SUVA, indicative of microbially derived DOC. These pools showed clear signs of hyporheic inflow during summertime drying despite complete surficial disconnection. PARAFAC analysis pinpointed groundwater sources of hyporheic flow in the watershed, suggesting that targeted aquifer recharge may contribute to salmonid recovery by augmenting flow in summer refugia.

The Role of Microbial Iron Reduction in the Formation of Proterozoic Molar Tooth Structures

NASA Astrophysics Data System (ADS)

Hodgskiss, M. S. W.; Kunzmann, M.; Halverson, G. P.; Poirier, A.

2016-12-01

Molar tooth structures are poorly understood early diagenetic, microspar-filled voids in clay-rich carbonate sediments. They are a common structure in sedimentary successions dating from 2600-720 Ma, but do not occur in rocks older or younger. Despite being volumetrically significant in carbonate rocks of this age, their formation and disappearance are poorly understood. Here, we present iron isotope data, supported by carbon and oxygen isotopes, major and minor element concentrations, and total organic carbon and pyrite contents for samples from ten regions spanning 1870-635 Ma. The iron isotopic composition of molar tooth structures is almost always lighter (modal depletion of 2‰) than the carbonate or siliciclastic components in the host sediment, whereas carbon isotopes are indistinguishable. We interpret the isotopically light iron in molar tooth structures to have been produced by microbial iron reduction utilising Fe-oxyhydroxides and smectites. The microbial conversion of smectite to illite results in a volume reduction of clay minerals ( 30%), while locally increasing pore water alkalinity. Therefore, this biogeochemical process is a viable mechanism to produce voids and subsequently precipitate carbonate minerals. The disappearance of molar tooth structures is likely linked to a combination of a decrease in smectite abundance, a decline in the marine DIC reservoir, and increase in the concentration of O2 in shallow seawater in the mid-Neoproterozoic.

Assessment of physicochemical parameters and prevalence of virulent and multiple-antibiotic-resistant Escherichia coli in treated effluent of two wastewater treatment plants and receiving aquatic milieu in Durban, South Africa.

PubMed

Pillay, Leanne; Olaniran, Ademola O

2016-05-01

The poor operational status of some wastewater treatment plants often result in the discharge of inadequately treated effluent into receiving surface waters. This is of significant public health concern as there are many informal settlement dwellers (ISDs) that rely on these surface waters for their domestic use. This study investigated the treatment efficiency of two independent wastewater treatment plants (WWTPs) in Durban, South Africa and determined the impact of treated effluent discharge on the physicochemical and microbial quality of the receiving water bodies over a 6-month period. Presumptive Escherichia coli isolates were identified using biochemical tests and detection of the mdh gene via PCR. Six major virulence genes namely eae, hly, fliC, stx1, stx2, and rfbE were also detected via PCR while antibiotic resistance profiles of the isolates were determined using Kirby-Bauer disc diffusion assay. The physicochemical parameters of the wastewater samples ranged variously between 9 and 313.33 mg/L, 1.52 and 76.43 NTUs, and 6.30 and 7.87 for COD, turbidity, and pH respectively, while the E. coli counts ranged between 0 and 31.2 × 10(3) CFU/ml. Of the 200 selected E. coli isolates, the hly gene was found in 28 %, fliC in 20 %, stx2 in 17 %, eae in 14 %, with stx1 and rfbE in only 4 % of the isolates. Notable resistance was observed toward trimethoprim (97 %), tetracycline (56 %), and ampicillin (52.5 %). These results further highlight the poor operational status of these WWTPs and outline the need for improved water quality monitoring and enforcement of stringent guidelines.

Transformations of DOM in forested catchments: the pathways of DOM from litter and soil to river export

NASA Astrophysics Data System (ADS)

Lajtha, K.; Yano, Y.; Crow, S.; Kaushal, S.

2006-12-01

Although the quality and quantity of DOM ultimately derives from plant detritus and soils in watersheds, three is substantial alteration of DOM as it passes from litter through the terrestrial landscape. As DOM is generated from plant and microbial detritus and processing, different fractions may be lost via respiration, form quasi-stable soil organic matter, or be temporarily sorbed to soil minerals. We followed the fate of DOC and DON from forested plots with experimentally altered detritus loads to determine the relative roles of original plant litter chemistry and soil transformations. Our study site was the DIRT (Detrital Input and Removal Treatment) plots at the H.J. Andrews Experimental Forest in Oregon, where treatments include detrital additions (wood vs. needle litter), litter exclusion, and root exclusions. Fractionation of detritus leachate solutions demonstrated significant differences in DOC chemistry from different detrital sources. Root leachates produced high quantities of hydrophilic neutral DOC, a fraction rich in labile sugars and polysaccharides; young wood extracts produced higher quantities of weak hydrophobic acids and hydrophobic neutrals (longer chain hydrocarbons); older wood had lower quantities of most labile constituents but was rich in strong hydrophobic acids. Although laboratory extracts of different litter types showed differences in DOM chemistry, soil solutions collected just below the forest floor from the differing detrital treatments were remarkably uniform and poor in labile constituents, suggesting microbial equalization of DOM leachate in the field. DOM quality and concentrations changed significantly with passage through soil profiles. DOC concentrations decreased through the soil profile in all plots to a greater degree than did dissolved organic nitrogen (DON), most likely due to preferential sorption of high C:N hydrophobic dissolved organic matter (DOM) in upper horizons. Percent hydrophobic DOM decreased significantly with depth, and the remaining hydrophilic DOM had a much lower and narrower C:N ratio than hydrophobic DOM. We also hypothesize that protein-reactive polyphenols, or tannins, may contribute to the decreased lability of N-rich DOM in soil solutions and thus significantly influence the quality of DOM delivered to streams.

Physicochemical and microbiological qualities of steamed and irradiated ground black pepper (Piper nigrum L.).

PubMed

Waje, Catherine K; Kim, Hyun-Ku; Kim, Kyong-Su; Todoriki, Setsuko; Kwon, Joong-Ho

2008-06-25

The effects of steam and irradiation treatments on the physicochemical properties (moisture content, pH, extractable yield, reducing sugar, soluble pigment, antioxidant activity, piperine, Hunter's color, and sensory attributes) and microbiological quality (total aerobic bacteria, coliforms, and yeasts and molds) of ground black pepper stored at refrigerated and room temperatures for 6 months were compared and evaluated. Irradiation resulted in a higher microbial reduction in pepper, with minimal effects on the proximate composition, functional components, color, and sensory attributes of the spice. Steamed peppers appeared darker, and a considerable decrease in the piperine content was observed after treatment and storage. This study illustrates that irradiation is a better decontamination method than steam treatment in eliminating microorganisms without apparently affecting the quality of the powdered spice. Storage at 4 degrees C enhanced the microbial quality and minimized the loss of piperine content in ground black peppers.

Is there a link between hospital profit and quality?

PubMed

Cleverley, W O; Harvey, R K

1992-09-01

In industrial firms, high perceived quality in products or services leads to high return on investment. The link between high quality and high profit is more difficult to document for healthcare products and services. An even more important question for healthcare managers is whether there is a link between poor-quality services and low profitability. A study of a small sample of HCFA high-mortality hospitals shows that poor quality hospitals are less profitable. Although the demand for the products and services of poor-quality hospitals is relatively strong, such hospitals are underinvested in assets and understaffed, the study shows.

Effect of gamma irradiation on the microbial load, nutrient composition and free radical scavenging activity of Nelumbo nucifera rhizome

NASA Astrophysics Data System (ADS)

Khattak, Khanzadi Fatima; Simpson, Thomas James; Ihasnullah

2009-03-01

The assurance of microbial quality is necessary to make plant materials suitable for human consumption and commercialization. The aim of the present study was to evaluate the possibility to apply the gamma radiation treatment on the rhizome samples of Nelumbo nucifera for microbial decontamination. The radiation processing was carried out at dose levels of 1, 2, 4 and 6 kGy. The irradiated and control samples were analyzed for microbial load, organoleptic acceptance, extraction yield, proximate composition, phenolic contents and DPPH scavenging activity. The results indicated that gamma radiation treatment significantly reduced microbial load and increased the storability of the irradiated samples. The treated samples were also acceptable sensorically. The extraction yield and phenolic contents increased with the increase of radiation dose. Gamma radiation also enhanced the DPPH scavenging activity.

Kinetics model development of cocoa bean fermentation

NASA Astrophysics Data System (ADS)

Kresnowati, M. T. A. P.; Gunawan, Agus Yodi; Muliyadini, Winny

2015-12-01

Although Indonesia is one of the biggest cocoa beans producers in the world, Indonesian cocoa beans are oftenly of low quality and thereby frequently priced low in the world market. In order to improve the quality, adequate post-harvest cocoa processing techniques are required. Fermentation is the vital stage in series of cocoa beans post harvest processing which could improve the quality of cocoa beans, in particular taste, aroma, and colours. During the fermentation process, combination of microbes grow producing metabolites that serve as the precursors for cocoa beans flavour. Microbial composition and thereby their activities will affect the fermentation performance and influence the properties of cocoa beans. The correlation could be reviewed using a kinetic model that includes unstructured microbial growth, substrate utilization and metabolic product formation. The developed kinetic model could be further used to design cocoa bean fermentation process to meet the expected quality. Further the development of kinetic model of cocoa bean fermentation also serve as a good case study of mixed culture solid state fermentation, that has rarely been studied. This paper presents the development of a kinetic model for solid-state cocoa beans fermentation using an empirical approach. Series of lab scale cocoa bean fermentations, either natural fermentations without starter addition or fermentations with mixed yeast and lactic acid bacteria starter addition, were used for model parameters estimation. The results showed that cocoa beans fermentation can be modelled mathematically and the best model included substrate utilization, microbial growth, metabolites production and its transport. Although the developed model still can not explain the dynamics in microbial population, this model can sufficiently explained the observed changes in sugar concentration as well as metabolic products in the cocoa bean pulp.

[Evolvement of soil quality in salt marshes and reclaimed farmlands in Yancheng coastal wetland].

PubMed

Mao, Zhi-Gang; Gu, Xiao-Hong; Liu, Jin-E; Ren, Li-Juan; Wang, Guo-Xiang

2010-08-01

Through vegetation investigation and soil analysis, this paper studied the evolvement of soil quality during natural vegetation succession and after farmland reclamation in the Yancheng coastal wetland of Jiangsu Province. Along with the process of vegetation succession, the soil physical, chemical, and biological properties in the wetland improved, which was manifested in the improvement of soil physical properties and the increase of soil nutrient contents, microbial biomass, and enzyme activities. Different vegetation type induced the differences in soil properties. Comparing with those in salt marshes, the soil salt content in reclaimed farmlands decreased to 0.01 - 0.04%, the soil microbial biomass and enzyme activities increased, and the soil quality improved obviously. The soil quality index (SQI) in the wetland was in the order of mudflat (0.194) < Suaeda salsa flat (0.233) < Imperata cylindrica flat (0.278) < Spartina alterniflora flat (0.446) < maize field (0.532) < cotton field (0.674) < soybean field (0.826), suggesting that positive vegetation succession would be an effective approach in improving soil quality.

Secondary mineral formation associated with respiration of nontronite, NAu-1 by iron reducing bacteria

PubMed Central

O'Reilly, S Erin; Watkins, Janet; Furukawa, Yoko

2005-01-01

Experimental batch and miscible-flow cultures were studied in order to determine the mechanistic pathways of microbial Fe(III) respiration in ferruginous smectite clay, NAu-1. The primary purpose was to resolve if alteration of smectite and release of Fe precedes microbial respiration. Alteration of NAu-1, represented by the morphological and mineralogical changes, occurred regardless of the extent of microbial Fe(III) reduction in all of our experimental systems, including those that contained heat-killed bacteria and those in which O2, rather than Fe(III), was the primary terminal electron acceptor. The solid alteration products observed under transmission electron microscopy included poorly crystalline smectite with diffuse electron diffraction signals, discrete grains of Fe-free amorphous aluminosilicate with increased Al/Si ratio, Fe-rich grains, and amorphous Si globules in the immediate vicinity of bacterial cells and extracellular polymeric substances. In reducing systems, Fe was also found as siderite. The small amount of Fe partitioned to the aqueous phase was primarily in the form of dissolved Fe(III) species even in the systems in which Fe(III) was the primary terminal electron acceptor for microbial respiration. From these observations, we conclude that microbial respiration of Fe(III) in our laboratory systems proceeded through the following: (1) alteration of NAu-1 and concurrent release of Fe(III) from the octahedral sheets of NAu-1; and (2) subsequent microbial respiration of Fe(III).